Warning: Permanently added '3.92.209.246' (ED25519) to the list of known hosts. You can reproduce this build on your computer by running: sudo dnf install copr-rpmbuild /usr/bin/copr-rpmbuild --verbose --drop-resultdir --task-url https://copr.fedorainfracloud.org/backend/get-build-task/11213070-fedora-rawhide-x86_64 --chroot fedora-rawhide-x86_64 Version: 1.10 PID: 27914 Logging PID: 27916 Task: {'allow_user_ssh': False, 'appstream': False, 'background': False, 'build_id': 11213070, 'buildroot_pkgs': [], 'chroot': 'fedora-rawhide-x86_64', 'enable_net': False, 'fedora_review': False, 'git_hash': '332fa7a6f988c08af202fe2c499b8a0264b9d1fc', 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/mhough/neurofedora/ucsc-kent-utils', 'isolation': 'default', 'memory_reqs': 2048, 'package_name': 'ucsc-kent-utils', 'package_version': '492-1', 'project_dirname': 'neurofedora', 'project_name': 'neurofedora', 'project_owner': 'mhough', 'repo_priority': None, 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/mhough/neurofedora/fedora-rawhide-x86_64/', 'id': 'copr_base', 'name': 'Copr repository', 'priority': None, 'repo_gpgcheck': False}], 'sandbox': 'mhough/neurofedora--mhough', 'source_json': {}, 'source_type': None, 'ssh_public_keys': None, 'storage': 1, 'submitter': 'mhough', 'tags': [], 'task_id': '11213070-fedora-rawhide-x86_64', 'timeout': 86400, 'uses_devel_repo': False, 'with_opts': [], 'without_opts': []} Running: git clone https://copr-dist-git.fedorainfracloud.org/git/mhough/neurofedora/ucsc-kent-utils /var/lib/copr-rpmbuild/workspace/workdir-xvnu4nu6/ucsc-kent-utils --depth 500 --no-single-branch --recursive cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/mhough/neurofedora/ucsc-kent-utils', '/var/lib/copr-rpmbuild/workspace/workdir-xvnu4nu6/ucsc-kent-utils', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-xvnu4nu6/ucsc-kent-utils'... Running: git checkout 332fa7a6f988c08af202fe2c499b8a0264b9d1fc -- cmd: ['git', 'checkout', '332fa7a6f988c08af202fe2c499b8a0264b9d1fc', '--'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-xvnu4nu6/ucsc-kent-utils rc: 0 stdout: stderr: Note: switching to '332fa7a6f988c08af202fe2c499b8a0264b9d1fc'. You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by switching back to a branch. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -c with the switch command. Example: git switch -c Or undo this operation with: git switch - Turn off this advice by setting config variable advice.detachedHead to false HEAD is now at 332fa7a automatic import of ucsc-kent-utils Running: dist-git-client sources cmd: ['dist-git-client', 'sources'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-xvnu4nu6/ucsc-kent-utils rc: 0 stdout: stderr: INFO: Reading stdout from command: git rev-parse --abbrev-ref HEAD INFO: Reading stdout from command: git rev-parse HEAD INFO: Reading sources specification file: sources INFO: Downloading kent-core-492.tar.gz INFO: Reading stdout from command: curl --help all INFO: Calling: curl -H Pragma: -H 'Accept-Encoding: identity' -o kent-core-492.tar.gz --location --connect-timeout 60 --retry 3 --retry-delay 10 --remote-time --show-error --fail --retry-all-errors https://copr-dist-git.fedorainfracloud.org/repo/pkgs/mhough/neurofedora/ucsc-kent-utils/kent-core-492.tar.gz/md5/0b52885fa27ef4747a74d5a802b1fb8a/kent-core-492.tar.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 24.10M 100 24.10M 0 0 25.92M 0 0 INFO: Reading stdout from command: md5sum kent-core-492.tar.gz tail: /var/lib/copr-rpmbuild/main.log: file truncated Running (timeout=86400): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-xvnu4nu6/ucsc-kent-utils/ucsc-kent-utils.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-xvnu4nu6/ucsc-kent-utils --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1793082781.422399 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 6.9 starting (python version = 3.14.5, NVR = mock-6.9-1.fc44), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-xvnu4nu6/ucsc-kent-utils/ucsc-kent-utils.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-xvnu4nu6/ucsc-kent-utils --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1793082781.422399 -r /var/lib/copr-rpmbuild/results/configs/child.cfg Start(bootstrap): init plugins INFO: tmpfs initialized INFO: selinux enabled INFO: chroot_scan: initialized INFO: compress_logs: initialized Finish(bootstrap): init plugins Start: init plugins INFO: tmpfs initialized INFO: selinux enabled INFO: chroot_scan: initialized INFO: compress_logs: initialized Finish: init plugins INFO: Signal handler active Start: run INFO: Start(/var/lib/copr-rpmbuild/workspace/workdir-xvnu4nu6/ucsc-kent-utils/ucsc-kent-utils.spec) Config(fedora-rawhide-x86_64) Start: clean chroot Finish: clean chroot Mock Version: 6.9 INFO: Mock Version: 6.9 Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1793082781.422399/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata INFO: Guessed host environment type: unknown INFO: Using container image: registry.fedoraproject.org/fedora:rawhide INFO: Pulling image: registry.fedoraproject.org/fedora:rawhide INFO: Tagging container image as mock-bootstrap-ea1ffbc2-9f01-4994-ab70-4f92a37df64b INFO: Checking that 428f565534c378b103a8ec89b338164726967d88fa562966ed69cf5b3af100aa image matches host's architecture INFO: Copy content of container 428f565534c378b103a8ec89b338164726967d88fa562966ed69cf5b3af100aa to /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1793082781.422399/root INFO: mounting 428f565534c378b103a8ec89b338164726967d88fa562966ed69cf5b3af100aa with podman image mount INFO: image 428f565534c378b103a8ec89b338164726967d88fa562966ed69cf5b3af100aa as /var/lib/containers/storage/overlay/f3bc5b33644f09b51b39df99e8ac68c870b366f98319c7db0cebb8708e479ff9/merged INFO: umounting image 428f565534c378b103a8ec89b338164726967d88fa562966ed69cf5b3af100aa (/var/lib/containers/storage/overlay/f3bc5b33644f09b51b39df99e8ac68c870b366f98319c7db0cebb8708e479ff9/merged) with podman image umount INFO: Removing image mock-bootstrap-ea1ffbc2-9f01-4994-ab70-4f92a37df64b INFO: Package manager dnf5 detected and used (fallback) INFO: Not updating bootstrap chroot, bootstrap_image_ready=True Start(bootstrap): creating root cache Finish(bootstrap): creating root cache Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-1793082781.422399/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin INFO: Package manager dnf5 detected and used (direct choice) INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-6.1.0-1.fc46.x86_64 rpm-sequoia-1.10.3-1.fc46.x86_64 dnf5-5.4.6.0-1.fc46.x86_64 dnf5-plugins-5.4.6.0-1.fc46.x86_64 Start: installing minimal buildroot with dnf5 Updating and loading repositories: fedora 100% | 96.3 KiB/s | 22.4 KiB | 00m00s Copr repository 100% | 8.9 KiB/s | 1.5 KiB | 00m00s Repositories loaded. Package Arch Version Repository Size Installing group/module packages: bash x86_64 0:5.3.20-1.fc46 fedora 8.5 MiB bzip2 x86_64 0:1.0.8-24.fc45 fedora 95.0 KiB coreutils x86_64 0:9.12-1.fc46 fedora 6.3 MiB cpio x86_64 0:2.15-10.fc45 fedora 1.1 MiB diffutils x86_64 0:3.12-6.fc45 fedora 1.6 MiB fedora-release-common noarch 0:46-0.1 fedora 4.6 KiB findutils x86_64 1:4.11.0-2.fc45 fedora 1.9 MiB gawk x86_64 0:5.4.1-1.fc45 fedora 2.2 MiB glibc-minimal-langpack x86_64 0:2.44.9000-5.fc46 fedora 0.0 B grep x86_64 0:3.12-4.fc45 fedora 1.0 MiB gzip x86_64 0:1.15-1.fc46 fedora 445.2 KiB info x86_64 0:7.3-3.fc45 fedora 372.4 KiB patch x86_64 0:2.8-6.fc46 fedora 226.6 KiB redhat-rpm-config noarch 0:345-6.fc46 fedora 184.3 KiB rpm-build x86_64 0:6.1.0-1.fc46 fedora 312.1 KiB sed x86_64 0:4.10-2.fc45 fedora 866.5 KiB shadow-utils x86_64 2:4.20.0-2.fc46 fedora 3.9 MiB tar x86_64 2:1.35-9.fc45 fedora 3.0 MiB unzip x86_64 0:6.0-71.fc45 fedora 441.8 KiB util-linux x86_64 0:2.42.4-2.fc46 fedora 3.7 MiB which x86_64 0:2.25-2.fc45 fedora 83.6 KiB xz x86_64 1:5.8.4-1.fc46 fedora 1.4 MiB Installing dependencies: R-srpm-macros noarch 0:1.3.7-3.fc45 fedora 3.5 KiB add-determinism x86_64 0:0.7.3-3.fc45 fedora 2.2 MiB alternatives x86_64 0:1.33-6.fc45 fedora 62.1 KiB ansible-srpm-macros noarch 0:1-22.fc45 fedora 35.7 KiB audit-libs x86_64 0:4.2.1-2.fc45 fedora 390.5 KiB binutils x86_64 0:2.47.50-20.fc46 fedora 24.5 MiB build-reproducibility-srpm-macros noarch 0:0.7.3-3.fc45 fedora 1.2 KiB bzip2-libs x86_64 0:1.0.8-24.fc45 fedora 80.5 KiB ca-certificates noarch 0:2026.2.92_v9.0.319-2.fc46 fedora 2.7 MiB cmake-srpm-macros noarch 0:4.3.0-5.fc45 fedora 524.0 B coreutils-common x86_64 0:9.12-1.fc46 fedora 11.5 MiB crypto-policies noarch 0:20260713-2.gitc42da77.fc45 fedora 134.3 KiB curl x86_64 0:8.23.0-1.fc46 fedora 486.1 KiB cyrus-sasl-lib x86_64 0:2.1.28-37.fc45 fedora 2.3 MiB debugedit x86_64 0:5.3-3.fc45 fedora 220.8 KiB dwz x86_64 0:0.17-3.fc45 fedora 291.1 KiB ed x86_64 0:1.22.6-1.fc46 fedora 150.9 KiB efi-srpm-macros noarch 0:6-9.fc45 fedora 40.3 KiB elfutils x86_64 0:0.197-1.fc46 fedora 3.1 MiB elfutils-debuginfod-client x86_64 0:0.197-1.fc46 fedora 79.9 KiB elfutils-libelf x86_64 0:0.197-1.fc46 fedora 1.6 MiB elfutils-libs x86_64 0:0.197-1.fc46 fedora 719.5 KiB erlang-srpm-macros noarch 0:0.4.1-1.fc46 fedora 2.0 KiB fedora-gpg-keys noarch 0:46-0.3 fedora 130.3 KiB fedora-release noarch 0:46-0.1 fedora 0.0 B fedora-release-identity-basic noarch 0:46-0.1 fedora 664.0 B fedora-repos noarch 0:46-0.3 fedora 4.9 KiB fedora-repos-rawhide noarch 0:46-0.3 fedora 2.2 KiB file x86_64 0:5.48-3.fc46 fedora 101.9 KiB file-libs x86_64 0:5.48-3.fc46 fedora 12.3 MiB filesystem x86_64 0:3.18-59.fc45 fedora 112.0 B filesystem-srpm-macros noarch 0:3.18-59.fc45 fedora 38.2 KiB fips-provider x86_64 0:1.5.3-1.fc46 fedora 4.8 MiB fonts-srpm-macros noarch 1:5.0.0-4.fc45 fedora 55.8 KiB forge-srpm-macros noarch 0:0.4.0-5.fc45 fedora 38.9 KiB fpc-srpm-macros noarch 0:1.3-17.fc45 fedora 144.0 B gap-srpm-macros noarch 0:2-3.fc45 fedora 2.1 KiB gdb-minimal x86_64 0:18.1-1.fc46 fedora 14.4 MiB gdbm-libs x86_64 1:1.26-1.fc46 fedora 134.2 KiB ghc-srpm-macros noarch 0:1.10-2.fc45 fedora 792.0 B glibc x86_64 0:2.44.9000-5.fc46 fedora 7.2 MiB glibc-common x86_64 0:2.44.9000-5.fc46 fedora 1.0 MiB glibc-gconv-extra x86_64 0:2.44.9000-5.fc46 fedora 7.7 MiB gmp x86_64 1:6.3.0-6.fc45 fedora 815.2 KiB gnat-srpm-macros noarch 0:7-3.fc45 fedora 1.0 KiB gnome-srpm-macros noarch 0:1.0-2.fc45 fedora 3.5 KiB gnulib-l10n noarch 0:20241231-4.fc45 fedora 655.0 KiB gnupg2 x86_64 0:2.4.9-18.fc45 fedora 6.5 MiB gnupg2-dirmngr x86_64 0:2.4.9-18.fc45 fedora 630.1 KiB gnupg2-gpg-agent x86_64 0:2.4.9-18.fc45 fedora 678.8 KiB gnupg2-gpgconf x86_64 0:2.4.9-18.fc45 fedora 253.8 KiB gnupg2-keyboxd x86_64 0:2.4.9-18.fc45 fedora 201.3 KiB gnupg2-verify x86_64 0:2.4.9-18.fc45 fedora 356.3 KiB gnutls x86_64 0:3.8.13-5.fc46 fedora 3.8 MiB go-srpm-macros noarch 0:3.8.0-3.fc45 fedora 61.9 KiB gpgverify noarch 0:2.2-5.fc45 fedora 8.7 KiB ima-evm-utils-libs x86_64 0:1.6.2-12.fc45 fedora 56.6 KiB jansson x86_64 0:2.14-5.fc45 fedora 89.0 KiB java-srpm-macros noarch 0:1-9.fc45 fedora 870.0 B json-c x86_64 0:0.18-9.fc45 fedora 82.7 KiB kernel-srpm-macros noarch 0:1.0-30.fc45 fedora 1.9 KiB keyutils-libs x86_64 0:1.6.3-8.fc45 fedora 54.2 KiB krb5-libs x86_64 0:1.22.2-9.fc45 fedora 2.4 MiB libacl x86_64 0:2.4.0-2.fc45 fedora 43.9 KiB libarchive x86_64 0:3.8.9-2.fc46 fedora 1.0 MiB libassuan x86_64 0:2.5.7-6.fc45 fedora 163.9 KiB libattr x86_64 0:2.6.0-2.fc45 fedora 24.3 KiB libblkid x86_64 0:2.42.4-2.fc46 fedora 282.3 KiB libbrotli x86_64 0:1.2.1-1.fc46 fedora 865.0 KiB libcap x86_64 0:2.78-2.fc45 fedora 208.2 KiB libcap-ng x86_64 0:0.9.6-1.fc46 fedora 68.8 KiB libcbor x86_64 0:0.14.0-3.fc45 fedora 83.5 KiB libcom_err x86_64 0:1.47.4-2.fc45 fedora 63.0 KiB libcurl x86_64 0:8.23.0-1.fc46 fedora 1.1 MiB libeconf x86_64 0:0.7.9-4.fc45 fedora 64.8 KiB libevent x86_64 0:2.1.13-1.fc46 fedora 980.7 KiB libfdisk x86_64 0:2.42.4-2.fc46 fedora 392.3 KiB libffi x86_64 0:3.8.0-1.fc46 fedora 95.5 KiB libfido2 x86_64 0:1.17.0-7.fc46 fedora 256.5 KiB libfsverity x86_64 0:1.7-4.fc45 fedora 24.4 KiB libgcc x86_64 0:16.2.1-2.fc46.1 fedora 270.7 KiB libgcrypt x86_64 0:1.12.4-1.fc46 fedora 1.7 MiB libgomp x86_64 0:16.2.1-2.fc46.1 fedora 577.5 KiB libgpg-error x86_64 0:1.61-2.fc45 fedora 953.9 KiB libidn2 x86_64 0:2.3.8-4.fc45 fedora 556.4 KiB libksba x86_64 0:1.8.1-1.fc46 fedora 431.9 KiB liblastlog2 x86_64 0:2.42.4-2.fc46 fedora 37.6 KiB libmount x86_64 0:2.42.4-2.fc46 fedora 408.9 KiB libnghttp2 x86_64 0:1.69.0-6.fc46 fedora 166.1 KiB libnghttp3 x86_64 0:1.18.0-1.fc45 fedora 163.4 KiB libpfm x86_64 0:4.14.1-2.fc46 fedora 2.4 MiB libpkgconf x86_64 0:2.5.1-2.fc45 fedora 90.1 KiB libpsl x86_64 0:0.23.3-1.fc46 fedora 80.4 KiB libselinux x86_64 0:3.11-5.fc46 fedora 205.2 KiB libselinux-utils x86_64 0:3.11-5.fc46 fedora 306.0 KiB libsemanage x86_64 0:3.11-4.fc46 fedora 320.6 KiB libsepol x86_64 0:3.11-2.fc45 fedora 866.1 KiB libsmartcols x86_64 0:2.42.4-2.fc46 fedora 188.5 KiB libssh x86_64 0:0.12.2-1.fc45 fedora 725.7 KiB libssh-config noarch 0:0.12.2-1.fc45 fedora 277.0 B libstdc++ x86_64 0:16.2.1-2.fc46.1 fedora 3.1 MiB libtasn1 x86_64 0:4.21.0-2.fc45 fedora 176.6 KiB libtool-ltdl x86_64 0:2.6.2-1.fc46 fedora 70.0 KiB libunistring x86_64 0:1.1-12.fc45 fedora 1.7 MiB libusb1 x86_64 0:1.0.30-2.fc45 fedora 180.1 KiB libuuid x86_64 0:2.42.4-2.fc46 fedora 37.2 KiB libverto x86_64 0:0.3.2-13.fc45 fedora 25.3 KiB libxcrypt x86_64 0:4.5.2-4.fc45 fedora 293.2 KiB libxml2 x86_64 0:2.15.4-1.fc46 fedora 1.7 MiB libzstd x86_64 0:1.5.7-6.fc45 fedora 956.1 KiB linkdupes x86_64 0:0.7.3-3.fc45 fedora 782.1 KiB lua-libs x86_64 0:5.5.1-2.fc46 fedora 298.0 KiB lua-srpm-macros noarch 0:1-18.fc45 fedora 1.3 KiB lz4-libs x86_64 0:1.10.0-5.fc45 fedora 165.3 KiB meson-srpm-macros noarch 0:1.12.1-2.fc46 fedora 1.7 KiB mpfr x86_64 0:4.2.2-4.fc45 fedora 849.2 KiB ncurses-base noarch 0:6.6-3.fc45 fedora 329.7 KiB ncurses-libs x86_64 0:6.6-3.fc45 fedora 969.1 KiB nettle x86_64 0:4.0-5.fc45 fedora 801.9 KiB ngtcp2 x86_64 0:1.22.1-3.fc45 fedora 334.3 KiB ngtcp2-crypto-ossl x86_64 0:1.22.1-3.fc45 fedora 51.6 KiB npth x86_64 0:1.8-5.fc45 fedora 49.5 KiB ocaml-srpm-macros noarch 0:11-4.fc45 fedora 1.9 KiB openblas-srpm-macros noarch 0:2-23.fc46 fedora 124.0 B openldap x86_64 0:2.6.15-1.fc46 fedora 683.4 KiB openssl-libs x86_64 1:4.0.3-1.fc46 fedora 6.7 MiB p11-kit x86_64 0:0.26.5-1.fc45 fedora 2.6 MiB p11-kit-trust x86_64 0:0.26.5-1.fc45 fedora 478.4 KiB package-notes-srpm-macros noarch 0:0.20-2.fc45 fedora 1.6 KiB pam-libs x86_64 0:1.7.2-4.fc45 fedora 134.5 KiB pcre2 x86_64 0:10.49-1.fc46 fedora 726.5 KiB pcre2-syntax noarch 0:10.49-1.fc46 fedora 292.5 KiB perl-srpm-macros noarch 0:1-65.fc45 fedora 861.0 B pkgconf x86_64 0:2.5.1-2.fc45 fedora 92.7 KiB pkgconf-m4 noarch 0:2.5.1-2.fc45 fedora 14.3 KiB pkgconf-pkg-config x86_64 0:2.5.1-2.fc45 fedora 989.0 B policycoreutils x86_64 0:3.11-2.fc45 fedora 892.9 KiB popt x86_64 0:1.19-11.fc45 fedora 136.7 KiB publicsuffix-list-dafsa noarch 0:20260624-2.fc45 fedora 71.3 KiB pyproject-srpm-macros noarch 0:1.24.0-1.fc46 fedora 3.4 KiB python-srpm-macros noarch 0:3.15-2.fc45 fedora 51.6 KiB qt5-srpm-macros noarch 0:5.15.18-3.fc45 fedora 500.0 B qt6-srpm-macros noarch 0:6.12.0-1.fc46 fedora 472.0 B readline x86_64 0:8.3-7.fc46 fedora 515.6 KiB redhat-systemd-presets noarch 0:102-3.fc45 fedora 1.0 KiB redhat-systemd-presets-common noarch 0:102-3.fc45 fedora 16.9 KiB rpm x86_64 0:6.1.0-1.fc46 fedora 3.1 MiB rpm-build-libs x86_64 0:6.1.0-1.fc46 fedora 288.3 KiB rpm-libs x86_64 0:6.1.0-1.fc46 fedora 1.1 MiB rpm-plugin-selinux x86_64 0:6.1.0-1.fc46 fedora 11.9 KiB rpm-sequoia x86_64 0:1.10.3-1.fc46 fedora 2.4 MiB rpm-sign-libs x86_64 0:6.1.0-1.fc46 fedora 39.6 KiB rust-srpm-macros noarch 0:28.5-2.fc45 fedora 5.5 KiB selinux-policy noarch 0:45.23-1.fc46 fedora 32.1 KiB selinux-policy-targeted noarch 0:45.23-1.fc46 fedora 18.9 MiB setup noarch 0:2.15.1-2.fc45 fedora 725.6 KiB sqlite-libs x86_64 0:3.54.1-1.fc46 fedora 1.6 MiB systemd-libs x86_64 0:262.1-1.fc46 fedora 2.8 MiB systemd-standalone-sysusers x86_64 0:262.1-1.fc46 fedora 981.2 KiB tpm2-tss x86_64 0:4.2.0-1.fc45 fedora 1.7 MiB tree-sitter-srpm-macros noarch 0:0.4.6-2.fc45 fedora 8.6 KiB util-linux-core x86_64 0:2.42.4-2.fc46 fedora 1.5 MiB xxhash-libs x86_64 0:0.8.4-2.fc46 fedora 94.0 KiB xz-libs x86_64 1:5.8.4-1.fc46 fedora 221.7 KiB zig-srpm-macros noarch 0:1-9.fc45 fedora 1.3 KiB zip x86_64 0:3.0-46.fc45 fedora 694.1 KiB zlib-ng-compat x86_64 0:2.3.3-6.fc45 fedora 165.6 KiB zstd x86_64 0:1.5.7-6.fc45 fedora 502.6 KiB Installing groups: Buildsystem building group Transaction Summary: Installing: 190 packages Total size of inbound packages is 72 MiB. Need to download 0 B. After this operation, 231 MiB extra will be used (install 231 MiB, remove 0 B). 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B | 00m00s >>> Already downloaded [170/190] libcurl-0:8.23.0-1.fc46.x86_6 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [171/190] krb5-libs-0:1.22.2-9.fc45.x86 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [172/190] libbrotli-0:1.2.1-1.fc46.x86_ 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [173/190] libnghttp2-0:1.69.0-6.fc46.x8 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [174/190] libnghttp3-0:1.18.0-1.fc45.x8 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [175/190] libpsl-0:0.23.3-1.fc46.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [176/190] libssh-0:0.12.2-1.fc45.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [177/190] ngtcp2-0:1.22.1-3.fc45.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [178/190] ngtcp2-crypto-ossl-0:1.22.1-3 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [179/190] keyutils-libs-0:1.6.3-8.fc45. 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [180/190] libcom_err-0:1.47.4-2.fc45.x8 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [181/190] libverto-0:0.3.2-13.fc45.x86_ 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [182/190] publicsuffix-list-dafsa-0:202 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [183/190] libfido2-0:1.17.0-7.fc46.x86_ 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [184/190] libssh-config-0:0.12.2-1.fc45 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [185/190] libcbor-0:0.14.0-3.fc45.x86_6 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [186/190] selinux-policy-targeted-0:45. 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [187/190] policycoreutils-0:3.11-2.fc45 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [188/190] selinux-policy-0:45.23-1.fc46 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [189/190] libselinux-utils-0:3.11-5.fc4 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [190/190] rpm-plugin-selinux-0:6.1.0-1. 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [190/190] Total 100% | 0.0 B/s | 0.0 B | 00m00s Running transaction Importing OpenPGP key 0x91211FCE: UserID : "Fedora (46) " Fingerprint: D924B10D3E810DABDD8B56B596E7E91491211FCE From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-46-primary The key was successfully imported. Importing OpenPGP key 0x91211FCE: UserID : "Fedora (46) " Fingerprint: D924B10D3E810DABDD8B56B596E7E91491211FCE From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-46-primary The key was successfully imported. Importing OpenPGP key 0xF577861E: UserID : "Fedora (45) " Fingerprint: 4F50A6114CD5C6976A7F1179655A4B02F577861E From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-45-primary The key was successfully imported. Importing OpenPGP key 0x9488FB64: UserID : "Fedora (47) " Fingerprint: B2E766FA50CA6FA2D5ED06FC09D879E09488FB64 From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-47-primary The key was successfully imported. [ 1/192] Verify package files 100% | 745.0 B/s | 190.0 B | 00m00s >>> Running %pretrans scriptlet: filesystem-0:3.18-59.fc45.x86_64 >>> Finished %pretrans scriptlet: filesystem-0:3.18-59.fc45.x86_64 >>> [RPM] failed to open /var/lib/mock/fedora-rawhide-x86_64-1793082781.422399/root/etc/group for id/name lookup: No such file or directory [ 2/192] Prepare transaction 100% | 3.6 KiB/s | 190.0 B | 00m00s [ 3/192] Installing libgcc-0:16.2.1-2. 100% | 266.0 MiB/s | 272.4 KiB | 00m00s [ 4/192] Installing redhat-systemd-pre 100% | 0.0 B/s | 1.5 KiB | 00m00s [ 5/192] Installing redhat-systemd-pre 100% | 0.0 B/s | 18.1 KiB | 00m00s [ 6/192] Installing libssh-config-0:0. 100% | 0.0 B/s | 816.0 B | 00m00s [ 7/192] Installing publicsuffix-list- 100% | 0.0 B/s | 72.0 KiB | 00m00s [ 8/192] Installing fedora-release-ide 100% | 0.0 B/s | 920.0 B | 00m00s [ 9/192] Installing fedora-repos-rawhi 100% | 0.0 B/s | 2.5 KiB | 00m00s [ 10/192] Installing fedora-gpg-keys-0: 100% | 59.2 MiB/s | 181.7 KiB | 00m00s [ 11/192] Installing fedora-repos-0:46- 100% | 0.0 B/s | 5.9 KiB | 00m00s [ 12/192] Installing fedora-release-com 100% | 0.0 B/s | 8.0 KiB | 00m00s [ 13/192] Installing fedora-release-0:4 100% | 20.2 KiB/s | 124.0 B | 00m00s >>> Running sysusers scriptlet: setup-0:2.15.1-2.fc45.noarch >>> Finished sysusers scriptlet: setup-0:2.15.1-2.fc45.noarch >>> Scriptlet output: >>> Creating group 'adm' with GID 4. >>> Creating group 'audio' with GID 63. >>> Creating group 'cdrom' with GID 11. >>> Creating group 'clock' with GID 103. >>> Creating group 'dialout' with GID 18. >>> Creating group 'disk' with GID 6. >>> Creating group 'floppy' with GID 19. >>> Creating group 'ftp' with GID 50. >>> Creating group 'games' with GID 20. >>> Creating group 'input' with GID 104. >>> Creating group 'kmem' with GID 9. >>> Creating group 'kvm' with GID 36. >>> Creating group 'lock' with GID 54. >>> Creating group 'lp' with GID 7. >>> Creating group 'mail' with GID 12. >>> Creating group 'man' with GID 15. >>> Creating group 'mem' with GID 8. >>> Creating group 'nobody' with GID 65534. >>> Creating group 'render' with GID 105. >>> Creating group 'root' with GID 0. >>> Creating group 'sgx' with GID 106. >>> Creating group 'sys' with GID 3. >>> Creating group 'tape' with GID 33. >>> Creating group 'tty' with GID 5. >>> Creating group 'users' with GID 100. >>> Creating group 'utmp' with GID 22. >>> Creating group 'video' with GID 39. >>> Creating group 'wheel' with GID 10. >>> Creating user 'adm' (adm) with UID 3 and GID 4. >>> Creating group 'bin' with GID 1. >>> Creating user 'bin' (bin) with UID 1 and GID 1. >>> Creating group 'daemon' with GID 2. >>> Creating user 'daemon' (daemon) with UID 2 and GID 2. >>> Creating user 'ftp' (FTP User) with UID 14 and GID 50. >>> Creating user 'games' (games) with UID 12 and GID 100. >>> Creating user 'halt' (halt) with UID 7 and GID 0. >>> Creating user 'lp' (lp) with UID 4 and GID 7. >>> Creating user 'mail' (mail) with UID 8 and GID 12. >>> Creating user 'nobody' (Kernel Overflow User) with UID 65534 and GID 65534. >>> Creating user 'operator' (operator) with UID 11 and GID 0. >>> Creating user 'root' (Super User) with UID 0 and GID 0. >>> Creating user 'shutdown' (shutdown) with UID 6 and GID 0. >>> Creating user 'sync' (sync) with UID 5 and GID 0. >>> [ 14/192] Installing setup-0:2.15.1-2.f 100% | 42.0 MiB/s | 731.3 KiB | 00m00s >>> [RPM] /etc/hosts created as /etc/hosts.rpmnew [ 15/192] Installing filesystem-0:3.18- 100% | 2.9 MiB/s | 253.6 KiB | 00m00s [ 16/192] Installing pkgconf-m4-0:2.5.1 100% | 0.0 B/s | 14.7 KiB | 00m00s [ 17/192] Installing pcre2-syntax-0:10. 100% | 288.1 MiB/s | 295.0 KiB | 00m00s [ 18/192] Installing gnulib-l10n-0:2024 100% | 215.5 MiB/s | 661.9 KiB | 00m00s [ 19/192] Installing coreutils-common-0 100% | 412.9 MiB/s | 11.6 MiB | 00m00s [ 20/192] Installing ncurses-base-0:6.6 100% | 86.7 MiB/s | 355.3 KiB | 00m00s [ 21/192] Installing bash-0:5.3.20-1.fc 100% | 256.8 MiB/s | 8.5 MiB | 00m00s [ 22/192] Installing glibc-common-0:2.4 100% | 51.8 MiB/s | 1.0 MiB | 00m00s [ 23/192] Installing glibc-gconv-extra- 100% | 338.6 MiB/s | 7.8 MiB | 00m00s [ 24/192] Installing glibc-0:2.44.9000- 100% | 188.9 MiB/s | 7.2 MiB | 00m00s [ 25/192] Installing ncurses-libs-0:6.6 100% | 317.4 MiB/s | 974.9 KiB | 00m00s [ 26/192] Installing glibc-minimal-lang 100% | 0.0 B/s | 124.0 B | 00m00s [ 27/192] Installing zlib-ng-compat-0:2 100% | 162.5 MiB/s | 166.4 KiB | 00m00s [ 28/192] Installing bzip2-libs-0:1.0.8 100% | 0.0 B/s | 81.6 KiB | 00m00s [ 29/192] Installing libgpg-error-0:1.6 100% | 52.1 MiB/s | 959.7 KiB | 00m00s [ 30/192] Installing readline-0:8.3-7.f 100% | 252.8 MiB/s | 517.7 KiB | 00m00s [ 31/192] Installing libstdc++-0:16.2.1 100% | 440.9 MiB/s | 3.1 MiB | 00m00s [ 32/192] Installing libzstd-0:1.5.7-6. 100% | 467.5 MiB/s | 957.4 KiB | 00m00s [ 33/192] Installing elfutils-libelf-0: 100% | 545.4 MiB/s | 1.6 MiB | 00m00s [ 34/192] Installing libassuan-0:2.5.7- 100% | 161.8 MiB/s | 165.7 KiB | 00m00s [ 35/192] Installing libgcrypt-0:1.12.4 100% | 416.6 MiB/s | 1.7 MiB | 00m00s [ 36/192] Installing libacl-0:2.4.0-2.f 100% | 0.0 B/s | 44.7 KiB | 00m00s [ 37/192] Installing gmp-1:6.3.0-6.fc45 100% | 399.1 MiB/s | 817.4 KiB | 00m00s [ 38/192] Installing systemd-libs-0:262 100% | 395.7 MiB/s | 2.8 MiB | 00m00s [ 39/192] Installing libuuid-0:2.42.4-2 100% | 0.0 B/s | 38.2 KiB | 00m00s [ 40/192] Installing popt-0:1.19-11.fc4 100% | 70.0 MiB/s | 143.3 KiB | 00m00s [ 41/192] Installing xz-libs-1:5.8.4-1. 100% | 217.6 MiB/s | 222.8 KiB | 00m00s [ 42/192] Installing sqlite-libs-0:3.54 100% | 411.7 MiB/s | 1.6 MiB | 00m00s [ 43/192] Installing npth-0:1.8-5.fc45. 100% | 0.0 B/s | 50.6 KiB | 00m00s [ 44/192] Installing elfutils-libs-0:0. 100% | 352.2 MiB/s | 721.4 KiB | 00m00s [ 45/192] Installing libblkid-0:2.42.4- 100% | 276.6 MiB/s | 283.3 KiB | 00m00s [ 46/192] Installing libsepol-0:3.11-2. 100% | 423.4 MiB/s | 867.1 KiB | 00m00s [ 47/192] Installing gnupg2-gpgconf-0:2 100% | 15.6 MiB/s | 255.9 KiB | 00m00s [ 48/192] Installing pcre2-0:10.49-1.fc 100% | 355.5 MiB/s | 728.0 KiB | 00m00s [ 49/192] Installing libselinux-0:3.11- 100% | 201.6 MiB/s | 206.4 KiB | 00m00s [ 50/192] Installing grep-0:3.12-4.fc45 100% | 55.7 MiB/s | 1.0 MiB | 00m00s [ 51/192] Installing sed-0:4.10-2.fc45. 100% | 47.5 MiB/s | 874.9 KiB | 00m00s [ 52/192] Installing findutils-1:4.11.0 100% | 97.9 MiB/s | 2.0 MiB | 00m00s [ 53/192] Installing libxcrypt-0:4.5.2- 100% | 289.0 MiB/s | 295.9 KiB | 00m00s [ 54/192] Installing json-c-0:0.18-9.fc 100% | 0.0 B/s | 83.9 KiB | 00m00s [ 55/192] Installing libtasn1-0:4.21.0- 100% | 174.3 MiB/s | 178.5 KiB | 00m00s [ 56/192] Installing libunistring-0:1.1 100% | 433.6 MiB/s | 1.7 MiB | 00m00s [ 57/192] Installing libidn2-0:2.3.8-4. 100% | 68.7 MiB/s | 562.6 KiB | 00m00s [ 58/192] Installing crypto-policies-0: 100% | 38.9 MiB/s | 159.5 KiB | 00m00s [ 59/192] Installing xz-1:5.8.4-1.fc46. 100% | 67.9 MiB/s | 1.4 MiB | 00m00s [ 60/192] Installing libmount-0:2.42.4- 100% | 400.4 MiB/s | 410.0 KiB | 00m00s [ 61/192] Installing gnupg2-verify-0:2. 100% | 21.8 MiB/s | 357.7 KiB | 00m00s [ 62/192] Installing mpfr-0:4.2.2-4.fc4 100% | 277.0 MiB/s | 850.9 KiB | 00m00s [ 63/192] Installing gawk-0:5.4.1-1.fc4 100% | 106.1 MiB/s | 2.2 MiB | 00m00s [ 64/192] Installing dwz-0:0.17-3.fc45. 100% | 17.9 MiB/s | 292.5 KiB | 00m00s [ 65/192] Installing libksba-0:1.8.1-1. 100% | 424.2 MiB/s | 434.4 KiB | 00m00s [ 66/192] Installing unzip-0:6.0-71.fc4 100% | 27.2 MiB/s | 445.3 KiB | 00m00s [ 67/192] Installing file-libs-0:5.48-3 100% | 726.1 MiB/s | 12.3 MiB | 00m00s [ 68/192] Installing file-0:5.48-3.fc46 100% | 6.7 MiB/s | 103.4 KiB | 00m00s [ 69/192] Installing diffutils-0:3.12-6 100% | 82.4 MiB/s | 1.6 MiB | 00m00s [ 70/192] Installing libattr-0:2.6.0-2. 100% | 0.0 B/s | 25.2 KiB | 00m00s [ 71/192] Installing libeconf-0:0.7.9-4 100% | 0.0 B/s | 66.4 KiB | 00m00s [ 72/192] Installing libcap-ng-0:0.9.6- 100% | 0.0 B/s | 70.6 KiB | 00m00s [ 73/192] Installing audit-libs-0:4.2.1 100% | 383.9 MiB/s | 393.1 KiB | 00m00s [ 74/192] Installing pam-libs-0:1.7.2-4 100% | 133.7 MiB/s | 136.9 KiB | 00m00s [ 75/192] Installing libcap-0:2.78-2.fc 100% | 13.0 MiB/s | 213.3 KiB | 00m00s [ 76/192] Installing libsemanage-0:3.11 100% | 314.8 MiB/s | 322.4 KiB | 00m00s [ 77/192] Installing libsmartcols-0:2.4 100% | 185.2 MiB/s | 189.6 KiB | 00m00s [ 78/192] Installing lua-libs-0:5.5.1-2 100% | 292.4 MiB/s | 299.4 KiB | 00m00s [ 79/192] Installing libffi-0:3.8.0-1.f 100% | 94.6 MiB/s | 96.9 KiB | 00m00s [ 80/192] Installing p11-kit-0:0.26.5-1 100% | 119.8 MiB/s | 2.6 MiB | 00m00s [ 81/192] Installing alternatives-0:1.3 100% | 4.1 MiB/s | 63.6 KiB | 00m00s [ 82/192] Installing p11-kit-trust-0:0. 100% | 20.4 MiB/s | 480.1 KiB | 00m00s [ 83/192] Installing ngtcp2-0:1.22.1-3. 100% | 164.0 MiB/s | 335.8 KiB | 00m00s [ 84/192] Installing util-linux-core-0: 100% | 72.0 MiB/s | 1.5 MiB | 00m00s [ 85/192] Installing liblastlog2-0:2.42 100% | 7.8 MiB/s | 39.8 KiB | 00m00s [ 86/192] Installing zip-0:3.0-46.fc45. 100% | 37.9 MiB/s | 698.0 KiB | 00m00s [ 87/192] Installing gnupg2-keyboxd-0:2 100% | 39.6 MiB/s | 202.5 KiB | 00m00s [ 88/192] Installing libpsl-0:0.23.3-1. 100% | 79.6 MiB/s | 81.5 KiB | 00m00s [ 89/192] Installing tar-2:1.35-9.fc45. 100% | 129.3 MiB/s | 3.0 MiB | 00m00s [ 90/192] Installing linkdupes-0:0.7.3- 100% | 45.0 MiB/s | 783.5 KiB | 00m00s [ 91/192] Installing libselinux-utils-0 100% | 18.4 MiB/s | 320.4 KiB | 00m00s [ 92/192] Installing libfdisk-0:2.42.4- 100% | 384.0 MiB/s | 393.2 KiB | 00m00s [ 93/192] Installing fips-provider-0:1. 100% | 439.0 MiB/s | 4.8 MiB | 00m00s [ 94/192] Installing openssl-libs-1:4.0 100% | 418.7 MiB/s | 6.7 MiB | 00m00s [ 95/192] Installing coreutils-0:9.12-1 100% | 181.5 MiB/s | 6.4 MiB | 00m00s [ 96/192] Installing ca-certificates-0: 100% | 2.5 MiB/s | 2.5 MiB | 00m01s [ 97/192] Installing gzip-0:1.15-1.fc46 100% | 23.2 MiB/s | 450.7 KiB | 00m00s [ 98/192] Installing util-linux-0:2.42. 100% | 101.5 MiB/s | 3.8 MiB | 00m00s [ 99/192] Installing policycoreutils-0: 100% | 34.6 MiB/s | 921.4 KiB | 00m00s [100/192] Installing selinux-policy-0:4 100% | 2.1 MiB/s | 34.5 KiB | 00m00s [101/192] Installing selinux-policy-tar 100% | 232.2 MiB/s | 15.1 MiB | 00m00s [102/192] Installing rpm-sequoia-0:1.10 100% | 407.9 MiB/s | 2.4 MiB | 00m00s [103/192] Installing libfsverity-0:1.7- 100% | 0.0 B/s | 25.4 KiB | 00m00s [104/192] Installing libevent-0:2.1.13- 100% | 320.5 MiB/s | 984.5 KiB | 00m00s [105/192] Installing ngtcp2-crypto-ossl 100% | 0.0 B/s | 52.5 KiB | 00m00s [106/192] Installing libusb1-0:1.0.30-2 100% | 17.7 MiB/s | 181.8 KiB | 00m00s >>> Running sysusers scriptlet: tpm2-tss-0:4.2.0-1.fc45.x86_64 >>> Finished sysusers scriptlet: tpm2-tss-0:4.2.0-1.fc45.x86_64 >>> Scriptlet output: >>> Creating group 'tss' with GID 59. >>> Creating user 'tss' (Account used for TPM access) with UID 59 and GID 59. >>> [107/192] Installing tpm2-tss-0:4.2.0-1 100% | 333.5 MiB/s | 1.7 MiB | 00m00s [108/192] Installing ima-evm-utils-libs 100% | 0.0 B/s | 57.9 KiB | 00m00s [109/192] Installing gnupg2-gpg-agent-0 100% | 29.0 MiB/s | 682.8 KiB | 00m00s [110/192] Installing nettle-0:4.0-5.fc4 100% | 393.1 MiB/s | 805.0 KiB | 00m00s [111/192] Installing gnutls-0:3.8.13-5. 100% | 426.4 MiB/s | 3.8 MiB | 00m00s [112/192] Installing zstd-0:1.5.7-6.fc4 100% | 29.1 MiB/s | 506.1 KiB | 00m00s [113/192] Installing libxml2-0:2.15.4-1 100% | 87.1 MiB/s | 1.7 MiB | 00m00s [114/192] Installing bzip2-0:1.0.8-24.f 100% | 6.1 MiB/s | 99.5 KiB | 00m00s [115/192] Installing add-determinism-0: 100% | 107.9 MiB/s | 2.2 MiB | 00m00s [116/192] Installing build-reproducibil 100% | 0.0 B/s | 1.5 KiB | 00m00s [117/192] Installing cpio-0:2.15-10.fc4 100% | 61.3 MiB/s | 1.1 MiB | 00m00s [118/192] Installing ed-0:1.22.6-1.fc46 100% | 9.3 MiB/s | 153.2 KiB | 00m00s [119/192] Installing patch-0:2.8-6.fc46 100% | 13.9 MiB/s | 228.1 KiB | 00m00s [120/192] Installing libpfm-0:4.14.1-2. 100% | 593.1 MiB/s | 2.4 MiB | 00m00s [121/192] Installing lz4-libs-0:1.10.0- 100% | 162.5 MiB/s | 166.4 KiB | 00m00s [122/192] Installing libarchive-0:3.8.9 100% | 327.4 MiB/s | 1.0 MiB | 00m00s [123/192] Installing libgomp-0:16.2.1-2 100% | 282.7 MiB/s | 578.9 KiB | 00m00s [124/192] Installing libtool-ltdl-0:2.6 100% | 0.0 B/s | 71.1 KiB | 00m00s [125/192] Installing gdbm-libs-1:1.26-1 100% | 132.7 MiB/s | 135.9 KiB | 00m00s [126/192] Installing cyrus-sasl-lib-0:2 100% | 111.4 MiB/s | 2.3 MiB | 00m00s [127/192] Installing openldap-0:2.6.15- 100% | 335.6 MiB/s | 687.2 KiB | 00m00s [128/192] Installing gnupg2-dirmngr-0:2 100% | 28.1 MiB/s | 632.8 KiB | 00m00s [129/192] Installing gnupg2-0:2.4.9-18. 100% | 209.7 MiB/s | 6.5 MiB | 00m00s [130/192] Installing gpgverify-0:2.2-5. 100% | 0.0 B/s | 9.4 KiB | 00m00s [131/192] Installing jansson-0:2.14-5.f 100% | 88.2 MiB/s | 90.3 KiB | 00m00s [132/192] Installing libpkgconf-0:2.5.1 100% | 89.1 MiB/s | 91.3 KiB | 00m00s [133/192] Installing pkgconf-0:2.5.1-2. 100% | 5.8 MiB/s | 95.2 KiB | 00m00s [134/192] Installing pkgconf-pkg-config 100% | 118.2 KiB/s | 1.8 KiB | 00m00s [135/192] Installing systemd-standalone 100% | 56.4 MiB/s | 981.8 KiB | 00m00s [136/192] Installing rpm-libs-0:6.1.0-1 100% | 366.4 MiB/s | 1.1 MiB | 00m00s [137/192] Installing rpm-sign-libs-0:6. 100% | 0.0 B/s | 40.5 KiB | 00m00s [138/192] Installing rpm-build-libs-0:6 100% | 282.4 MiB/s | 289.2 KiB | 00m00s [139/192] Installing xxhash-libs-0:0.8. 100% | 0.0 B/s | 95.4 KiB | 00m00s [140/192] Installing libbrotli-0:1.2.1- 100% | 282.3 MiB/s | 867.3 KiB | 00m00s [141/192] Installing libnghttp2-0:1.69. 100% | 163.3 MiB/s | 167.3 KiB | 00m00s [142/192] Installing libnghttp3-0:1.18. 100% | 161.0 MiB/s | 164.8 KiB | 00m00s [143/192] Installing keyutils-libs-0:1. 100% | 0.0 B/s | 55.6 KiB | 00m00s [144/192] Installing libcom_err-0:1.47. 100% | 0.0 B/s | 64.1 KiB | 00m00s [145/192] Installing libverto-0:0.3.2-1 100% | 0.0 B/s | 27.1 KiB | 00m00s [146/192] Installing krb5-libs-0:1.22.2 100% | 341.0 MiB/s | 2.4 MiB | 00m00s [147/192] Installing libcbor-0:0.14.0-3 100% | 82.9 MiB/s | 84.9 KiB | 00m00s [148/192] Installing libfido2-0:1.17.0- 100% | 252.0 MiB/s | 258.1 KiB | 00m00s [149/192] Installing libssh-0:0.12.2-1. 100% | 355.4 MiB/s | 727.8 KiB | 00m00s [150/192] Installing libcurl-0:8.23.0-1 100% | 361.9 MiB/s | 1.1 MiB | 00m00s [151/192] Installing elfutils-debuginfo 100% | 5.0 MiB/s | 82.2 KiB | 00m00s [152/192] Installing elfutils-0:0.197-1 100% | 133.5 MiB/s | 3.1 MiB | 00m00s [153/192] Installing binutils-0:2.47.50 100% | 331.4 MiB/s | 24.5 MiB | 00m00s [154/192] Installing gdb-minimal-0:18.1 100% | 288.8 MiB/s | 14.4 MiB | 00m00s [155/192] Installing debugedit-0:5.3-3. 100% | 13.7 MiB/s | 224.1 KiB | 00m00s [156/192] Installing curl-0:8.23.0-1.fc 100% | 19.9 MiB/s | 488.7 KiB | 00m00s [157/192] Installing rpm-0:6.1.0-1.fc46 100% | 78.2 MiB/s | 2.5 MiB | 00m00s [158/192] Installing cmake-srpm-macros- 100% | 0.0 B/s | 804.0 B | 00m00s [159/192] Installing efi-srpm-macros-0: 100% | 10.1 MiB/s | 41.3 KiB | 00m00s [160/192] Installing java-srpm-macros-0 100% | 0.0 B/s | 1.1 KiB | 00m00s [161/192] Installing lua-srpm-macros-0: 100% | 0.0 B/s | 1.9 KiB | 00m00s [162/192] Installing tree-sitter-srpm-m 100% | 0.0 B/s | 9.6 KiB | 00m00s [163/192] Installing zig-srpm-macros-0: 100% | 0.0 B/s | 1.9 KiB | 00m00s [164/192] Installing filesystem-srpm-ma 100% | 0.0 B/s | 38.9 KiB | 00m00s [165/192] Installing rust-srpm-macros-0 100% | 0.0 B/s | 6.4 KiB | 00m00s [166/192] Installing qt6-srpm-macros-0: 100% | 0.0 B/s | 748.0 B | 00m00s [167/192] Installing qt5-srpm-macros-0: 100% | 0.0 B/s | 776.0 B | 00m00s [168/192] Installing perl-srpm-macros-0 100% | 0.0 B/s | 1.1 KiB | 00m00s [169/192] Installing package-notes-srpm 100% | 0.0 B/s | 2.1 KiB | 00m00s [170/192] Installing openblas-srpm-macr 100% | 0.0 B/s | 404.0 B | 00m00s [171/192] Installing ocaml-srpm-macros- 100% | 0.0 B/s | 2.1 KiB | 00m00s [172/192] Installing meson-srpm-macros- 100% | 0.0 B/s | 1.9 KiB | 00m00s [173/192] Installing kernel-srpm-macros 100% | 0.0 B/s | 2.3 KiB | 00m00s [174/192] Installing gnome-srpm-macros- 100% | 0.0 B/s | 4.1 KiB | 00m00s [175/192] Installing gnat-srpm-macros-0 100% | 0.0 B/s | 1.3 KiB | 00m00s [176/192] Installing ghc-srpm-macros-0: 100% | 0.0 B/s | 1.0 KiB | 00m00s [177/192] Installing gap-srpm-macros-0: 100% | 0.0 B/s | 2.7 KiB | 00m00s [178/192] Installing fpc-srpm-macros-0: 100% | 0.0 B/s | 420.0 B | 00m00s [179/192] Installing ansible-srpm-macro 100% | 0.0 B/s | 36.2 KiB | 00m00s [180/192] Installing rpm-build-0:6.1.0- 100% | 17.5 MiB/s | 322.1 KiB | 00m00s [181/192] Installing erlang-srpm-macros 100% | 0.0 B/s | 2.6 KiB | 00m00s [182/192] Installing pyproject-srpm-mac 100% | 0.0 B/s | 4.0 KiB | 00m00s [183/192] Installing redhat-rpm-config- 100% | 186.0 MiB/s | 190.5 KiB | 00m00s [184/192] Installing forge-srpm-macros- 100% | 0.0 B/s | 40.3 KiB | 00m00s [185/192] Installing fonts-srpm-macros- 100% | 0.0 B/s | 57.0 KiB | 00m00s [186/192] Installing go-srpm-macros-0:3 100% | 0.0 B/s | 63.0 KiB | 00m00s [187/192] Installing R-srpm-macros-0:1. 100% | 0.0 B/s | 4.4 KiB | 00m00s [188/192] Installing python-srpm-macros 100% | 0.0 B/s | 52.9 KiB | 00m00s [189/192] Installing rpm-plugin-selinux 100% | 0.0 B/s | 12.9 KiB | 00m00s [190/192] Installing which-0:2.25-2.fc4 100% | 5.2 MiB/s | 85.8 KiB | 00m00s [191/192] Installing shadow-utils-2:4.2 100% | 136.1 MiB/s | 3.9 MiB | 00m00s [192/192] Installing info-0:7.3-3.fc45. 100% | 57.4 KiB/s | 372.8 KiB | 00m06s Complete! Finish: installing minimal buildroot with dnf5 Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: R-srpm-macros-1.3.7-3.fc45.noarch add-determinism-0.7.3-3.fc45.x86_64 alternatives-1.33-6.fc45.x86_64 ansible-srpm-macros-1-22.fc45.noarch audit-libs-4.2.1-2.fc45.x86_64 bash-5.3.20-1.fc46.x86_64 binutils-2.47.50-20.fc46.x86_64 build-reproducibility-srpm-macros-0.7.3-3.fc45.noarch bzip2-1.0.8-24.fc45.x86_64 bzip2-libs-1.0.8-24.fc45.x86_64 ca-certificates-2026.2.92_v9.0.319-2.fc46.noarch cmake-srpm-macros-4.3.0-5.fc45.noarch coreutils-9.12-1.fc46.x86_64 coreutils-common-9.12-1.fc46.x86_64 cpio-2.15-10.fc45.x86_64 crypto-policies-20260713-2.gitc42da77.fc45.noarch curl-8.23.0-1.fc46.x86_64 cyrus-sasl-lib-2.1.28-37.fc45.x86_64 debugedit-5.3-3.fc45.x86_64 diffutils-3.12-6.fc45.x86_64 dwz-0.17-3.fc45.x86_64 ed-1.22.6-1.fc46.x86_64 efi-srpm-macros-6-9.fc45.noarch elfutils-0.197-1.fc46.x86_64 elfutils-debuginfod-client-0.197-1.fc46.x86_64 elfutils-libelf-0.197-1.fc46.x86_64 elfutils-libs-0.197-1.fc46.x86_64 erlang-srpm-macros-0.4.1-1.fc46.noarch fedora-gpg-keys-46-0.3.noarch fedora-release-46-0.1.noarch fedora-release-common-46-0.1.noarch fedora-release-identity-basic-46-0.1.noarch fedora-repos-46-0.3.noarch fedora-repos-rawhide-46-0.3.noarch file-5.48-3.fc46.x86_64 file-libs-5.48-3.fc46.x86_64 filesystem-3.18-59.fc45.x86_64 filesystem-srpm-macros-3.18-59.fc45.noarch findutils-4.11.0-2.fc45.x86_64 fips-provider-1.5.3-1.fc46.x86_64 fonts-srpm-macros-5.0.0-4.fc45.noarch forge-srpm-macros-0.4.0-5.fc45.noarch fpc-srpm-macros-1.3-17.fc45.noarch gap-srpm-macros-2-3.fc45.noarch gawk-5.4.1-1.fc45.x86_64 gdb-minimal-18.1-1.fc46.x86_64 gdbm-libs-1.26-1.fc46.x86_64 ghc-srpm-macros-1.10-2.fc45.noarch glibc-2.44.9000-5.fc46.x86_64 glibc-common-2.44.9000-5.fc46.x86_64 glibc-gconv-extra-2.44.9000-5.fc46.x86_64 glibc-minimal-langpack-2.44.9000-5.fc46.x86_64 gmp-6.3.0-6.fc45.x86_64 gnat-srpm-macros-7-3.fc45.noarch gnome-srpm-macros-1.0-2.fc45.noarch gnulib-l10n-20241231-4.fc45.noarch gnupg2-2.4.9-18.fc45.x86_64 gnupg2-dirmngr-2.4.9-18.fc45.x86_64 gnupg2-gpg-agent-2.4.9-18.fc45.x86_64 gnupg2-gpgconf-2.4.9-18.fc45.x86_64 gnupg2-keyboxd-2.4.9-18.fc45.x86_64 gnupg2-verify-2.4.9-18.fc45.x86_64 gnutls-3.8.13-5.fc46.x86_64 go-srpm-macros-3.8.0-3.fc45.noarch gpg-pubkey-4f50a6114cd5c6976a7f1179655a4b02f577861e-6888bc98 gpg-pubkey-b2e766fa50ca6fa2d5ed06fc09d879e09488fb64-6a6b46b4 gpg-pubkey-d924b10d3e810dabdd8b56b596e7e91491211fce-697c9899 gpgverify-2.2-5.fc45.noarch grep-3.12-4.fc45.x86_64 gzip-1.15-1.fc46.x86_64 ima-evm-utils-libs-1.6.2-12.fc45.x86_64 info-7.3-3.fc45.x86_64 jansson-2.14-5.fc45.x86_64 java-srpm-macros-1-9.fc45.noarch json-c-0.18-9.fc45.x86_64 kernel-srpm-macros-1.0-30.fc45.noarch keyutils-libs-1.6.3-8.fc45.x86_64 krb5-libs-1.22.2-9.fc45.x86_64 libacl-2.4.0-2.fc45.x86_64 libarchive-3.8.9-2.fc46.x86_64 libassuan-2.5.7-6.fc45.x86_64 libattr-2.6.0-2.fc45.x86_64 libblkid-2.42.4-2.fc46.x86_64 libbrotli-1.2.1-1.fc46.x86_64 libcap-2.78-2.fc45.x86_64 libcap-ng-0.9.6-1.fc46.x86_64 libcbor-0.14.0-3.fc45.x86_64 libcom_err-1.47.4-2.fc45.x86_64 libcurl-8.23.0-1.fc46.x86_64 libeconf-0.7.9-4.fc45.x86_64 libevent-2.1.13-1.fc46.x86_64 libfdisk-2.42.4-2.fc46.x86_64 libffi-3.8.0-1.fc46.x86_64 libfido2-1.17.0-7.fc46.x86_64 libfsverity-1.7-4.fc45.x86_64 libgcc-16.2.1-2.fc46.1.x86_64 libgcrypt-1.12.4-1.fc46.x86_64 libgomp-16.2.1-2.fc46.1.x86_64 libgpg-error-1.61-2.fc45.x86_64 libidn2-2.3.8-4.fc45.x86_64 libksba-1.8.1-1.fc46.x86_64 liblastlog2-2.42.4-2.fc46.x86_64 libmount-2.42.4-2.fc46.x86_64 libnghttp2-1.69.0-6.fc46.x86_64 libnghttp3-1.18.0-1.fc45.x86_64 libpfm-4.14.1-2.fc46.x86_64 libpkgconf-2.5.1-2.fc45.x86_64 libpsl-0.23.3-1.fc46.x86_64 libselinux-3.11-5.fc46.x86_64 libselinux-utils-3.11-5.fc46.x86_64 libsemanage-3.11-4.fc46.x86_64 libsepol-3.11-2.fc45.x86_64 libsmartcols-2.42.4-2.fc46.x86_64 libssh-0.12.2-1.fc45.x86_64 libssh-config-0.12.2-1.fc45.noarch libstdc++-16.2.1-2.fc46.1.x86_64 libtasn1-4.21.0-2.fc45.x86_64 libtool-ltdl-2.6.2-1.fc46.x86_64 libunistring-1.1-12.fc45.x86_64 libusb1-1.0.30-2.fc45.x86_64 libuuid-2.42.4-2.fc46.x86_64 libverto-0.3.2-13.fc45.x86_64 libxcrypt-4.5.2-4.fc45.x86_64 libxml2-2.15.4-1.fc46.x86_64 libzstd-1.5.7-6.fc45.x86_64 linkdupes-0.7.3-3.fc45.x86_64 lua-libs-5.5.1-2.fc46.x86_64 lua-srpm-macros-1-18.fc45.noarch lz4-libs-1.10.0-5.fc45.x86_64 meson-srpm-macros-1.12.1-2.fc46.noarch mpfr-4.2.2-4.fc45.x86_64 ncurses-base-6.6-3.fc45.noarch ncurses-libs-6.6-3.fc45.x86_64 nettle-4.0-5.fc45.x86_64 ngtcp2-1.22.1-3.fc45.x86_64 ngtcp2-crypto-ossl-1.22.1-3.fc45.x86_64 npth-1.8-5.fc45.x86_64 ocaml-srpm-macros-11-4.fc45.noarch openblas-srpm-macros-2-23.fc46.noarch openldap-2.6.15-1.fc46.x86_64 openssl-libs-4.0.3-1.fc46.x86_64 p11-kit-0.26.5-1.fc45.x86_64 p11-kit-trust-0.26.5-1.fc45.x86_64 package-notes-srpm-macros-0.20-2.fc45.noarch pam-libs-1.7.2-4.fc45.x86_64 patch-2.8-6.fc46.x86_64 pcre2-10.49-1.fc46.x86_64 pcre2-syntax-10.49-1.fc46.noarch perl-srpm-macros-1-65.fc45.noarch pkgconf-2.5.1-2.fc45.x86_64 pkgconf-m4-2.5.1-2.fc45.noarch pkgconf-pkg-config-2.5.1-2.fc45.x86_64 policycoreutils-3.11-2.fc45.x86_64 popt-1.19-11.fc45.x86_64 publicsuffix-list-dafsa-20260624-2.fc45.noarch pyproject-srpm-macros-1.24.0-1.fc46.noarch python-srpm-macros-3.15-2.fc45.noarch qt5-srpm-macros-5.15.18-3.fc45.noarch qt6-srpm-macros-6.12.0-1.fc46.noarch readline-8.3-7.fc46.x86_64 redhat-rpm-config-345-6.fc46.noarch redhat-systemd-presets-102-3.fc45.noarch redhat-systemd-presets-common-102-3.fc45.noarch rpm-6.1.0-1.fc46.x86_64 rpm-build-6.1.0-1.fc46.x86_64 rpm-build-libs-6.1.0-1.fc46.x86_64 rpm-libs-6.1.0-1.fc46.x86_64 rpm-plugin-selinux-6.1.0-1.fc46.x86_64 rpm-sequoia-1.10.3-1.fc46.x86_64 rpm-sign-libs-6.1.0-1.fc46.x86_64 rust-srpm-macros-28.5-2.fc45.noarch sed-4.10-2.fc45.x86_64 selinux-policy-45.23-1.fc46.noarch selinux-policy-targeted-45.23-1.fc46.noarch setup-2.15.1-2.fc45.noarch shadow-utils-4.20.0-2.fc46.x86_64 sqlite-libs-3.54.1-1.fc46.x86_64 systemd-libs-262.1-1.fc46.x86_64 systemd-standalone-sysusers-262.1-1.fc46.x86_64 tar-1.35-9.fc45.x86_64 tpm2-tss-4.2.0-1.fc45.x86_64 tree-sitter-srpm-macros-0.4.6-2.fc45.noarch unzip-6.0-71.fc45.x86_64 util-linux-2.42.4-2.fc46.x86_64 util-linux-core-2.42.4-2.fc46.x86_64 which-2.25-2.fc45.x86_64 xxhash-libs-0.8.4-2.fc46.x86_64 xz-5.8.4-1.fc46.x86_64 xz-libs-5.8.4-1.fc46.x86_64 zig-srpm-macros-1-9.fc45.noarch zip-3.0-46.fc45.x86_64 zlib-ng-compat-2.3.3-6.fc45.x86_64 zstd-1.5.7-6.fc45.x86_64 Start: buildsrpm Start: rpmbuild -bs Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1779148800 Wrote: /builddir/build/SRPMS/ucsc-kent-utils-492-1.fc46.src.rpm Finish: rpmbuild -bs INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-x86_64-1793082781.422399/root/var/log/dnf5.log INFO: chroot_scan: creating tarball /var/lib/copr-rpmbuild/results/chroot_scan.tar.gz /bin/tar: Removing leading `/' from member names Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-xvnu4nu6/ucsc-kent-utils/ucsc-kent-utils.spec) Config(child) 0 minutes 16 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot INFO: Start(/var/lib/copr-rpmbuild/results/ucsc-kent-utils-492-1.fc46.src.rpm) Config(fedora-rawhide-x86_64) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1793082781.422399/root. INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1793082781.422399/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-1793082781.422399/root. INFO: calling preinit hooks INFO: enabled root cache Start: unpacking root cache Finish: unpacking root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-6.1.0-1.fc46.x86_64 rpm-sequoia-1.10.3-1.fc46.x86_64 dnf5-5.4.6.0-1.fc46.x86_64 dnf5-plugins-5.4.6.0-1.fc46.x86_64 Finish: chroot init Start: build phase for ucsc-kent-utils-492-1.fc46.src.rpm Start: build setup for ucsc-kent-utils-492-1.fc46.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1779148800 Wrote: /builddir/build/SRPMS/ucsc-kent-utils-492-1.fc46.src.rpm Updating and loading repositories: fedora 100% | 91.2 KiB/s | 22.4 KiB | 00m00s Copr repository 100% | 9.9 KiB/s | 1.5 KiB | 00m00s Repositories loaded. Package Arch Version Repository Size Installing: bzip2-devel x86_64 0:1.0.8-24.fc45 fedora 309.8 KiB gcc x86_64 0:16.2.1-2.fc46.1 fedora 121.8 MiB gcc-c++ x86_64 0:16.2.1-2.fc46.1 fedora 46.8 MiB libcurl-devel x86_64 0:8.23.0-1.fc46 fedora 1.4 MiB libpng-devel x86_64 2:1.6.58-2.fc45 fedora 906.0 KiB libuuid-devel x86_64 0:2.42.4-2.fc46 fedora 41.0 KiB make x86_64 1:4.4.1-13.fc45 fedora 1.8 MiB mariadb-connector-c-devel x86_64 0:3.4.11-1.fc46 fedora 192.2 KiB openssl-devel x86_64 1:4.0.3-1.fc46 fedora 4.7 MiB python3-devel x86_64 0:3.15.1-1.fc46 fedora 2.5 MiB xz-devel x86_64 1:5.8.4-1.fc46 fedora 258.8 KiB zlib-ng-compat-devel x86_64 0:2.3.3-6.fc45 fedora 107.0 KiB Installing dependencies: annobin-docs noarch 0:13.33-1.fc46 fedora 99.7 KiB annobin-plugin-gcc x86_64 0:13.33-1.fc46 fedora 726.5 KiB brotli x86_64 0:1.2.1-1.fc46 fedora 33.5 KiB brotli-devel x86_64 0:1.2.1-1.fc46 fedora 65.8 KiB cmake-filesystem x86_64 0:4.3.0-5.fc45 fedora 0.0 B cpp x86_64 0:16.2.1-2.fc46.1 fedora 42.6 MiB expat x86_64 0:2.9.0-1.fc46 fedora 349.6 KiB gcc-plugin-annobin x86_64 0:16.2.1-2.fc46.1 fedora 57.1 KiB glibc-devel x86_64 0:2.44.9000-5.fc46 fedora 2.3 MiB kernel-headers x86_64 0:7.3.0-65.fc46 fedora 7.1 MiB keyutils-libs-devel x86_64 0:1.6.3-8.fc45 fedora 48.2 KiB krb5-devel x86_64 0:1.22.2-9.fc45 fedora 709.9 KiB libatomic x86_64 0:16.2.1-2.fc46.1 fedora 45.6 KiB libcom_err-devel x86_64 0:1.47.4-2.fc45 fedora 16.7 KiB libidn2-devel x86_64 0:2.3.8-4.fc45 fedora 152.1 KiB libkadm5 x86_64 0:1.22.2-9.fc45 fedora 217.9 KiB libmpc x86_64 0:1.4.1-2.fc45 fedora 168.8 KiB libnghttp2-devel x86_64 0:1.69.0-6.fc46 fedora 288.0 KiB libnghttp3-devel x86_64 0:1.18.0-1.fc45 fedora 119.4 KiB libpng x86_64 2:1.6.58-2.fc45 fedora 253.7 KiB libpsl-devel x86_64 0:0.23.3-1.fc46 fedora 111.5 KiB libselinux-devel x86_64 0:3.11-5.fc46 fedora 121.9 KiB libsepol-devel x86_64 0:3.11-2.fc45 fedora 120.7 KiB libssh-devel x86_64 0:0.12.2-1.fc45 fedora 204.2 KiB libstdc++-devel x86_64 0:16.2.1-2.fc46.1 fedora 41.2 MiB libverto-devel x86_64 0:0.3.2-13.fc45 fedora 25.7 KiB libxcrypt-devel x86_64 0:4.5.2-4.fc45 fedora 31.0 KiB libzstd-devel x86_64 0:1.5.7-6.fc45 fedora 217.6 KiB mariadb-connector-c x86_64 0:3.4.11-1.fc46 fedora 514.0 KiB mariadb-connector-c-config noarch 0:3.4.11-1.fc46 fedora 26.4 KiB mpdecimal x86_64 0:4.0.1-4.fc45 fedora 221.2 KiB ngtcp2-crypto-ossl-devel x86_64 0:1.22.1-3.fc45 fedora 7.5 KiB ngtcp2-devel x86_64 0:1.22.1-3.fc45 fedora 262.8 KiB pcre2-devel x86_64 0:10.49-1.fc46 fedora 2.1 MiB pcre2-utf16 x86_64 0:10.49-1.fc46 fedora 659.2 KiB pcre2-utf32 x86_64 0:10.49-1.fc46 fedora 627.1 KiB publicsuffix-list noarch 0:20260624-2.fc45 fedora 345.9 KiB pyproject-rpm-macros noarch 0:1.24.0-1.fc46 fedora 169.0 KiB python-pip-wheel noarch 0:26.2.1-1.fc46 fedora 1.3 MiB python-rpm-macros noarch 0:3.15-2.fc45 fedora 28.0 KiB python3 x86_64 0:3.15.1-1.fc46 fedora 28.7 KiB python3-libs x86_64 0:3.15.1-1.fc46 fedora 48.2 MiB python3-packaging noarch 0:26.3-1.fc46 fedora 1.3 MiB python3-rpm-generators noarch 0:14-35.fc46 fedora 81.9 KiB python3-rpm-macros noarch 0:3.15-2.fc45 fedora 6.5 KiB tzdata noarch 0:2026e-1.fc46 fedora 1.3 MiB Transaction Summary: Installing: 58 packages Total size of inbound packages is 107 MiB. Need to download 7 MiB. After this operation, 335 MiB extra will be used (install 335 MiB, remove 0 B). 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Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1779148800 Wrote: /builddir/build/SRPMS/ucsc-kent-utils-492-1.fc46.src.rpm Updating and loading repositories: fedora 100% | 110.0 KiB/s | 22.4 KiB | 00m00s Copr repository 100% | 8.2 KiB/s | 1.5 KiB | 00m00s Repositories loaded. Nothing to do. Package "bzip2-devel-1.0.8-24.fc45.x86_64" is already installed. Package "gcc-16.2.1-2.fc46.1.x86_64" is already installed. Package "gcc-c++-16.2.1-2.fc46.1.x86_64" is already installed. Package "libcurl-devel-8.23.0-1.fc46.x86_64" is already installed. Package "libpng-devel-2:1.6.58-2.fc45.x86_64" is already installed. Package "libuuid-devel-2.42.4-2.fc46.x86_64" is already installed. Package "make-1:4.4.1-13.fc45.x86_64" is already installed. Package "mariadb-connector-c-devel-3.4.11-1.fc46.x86_64" is already installed. Package "openssl-devel-1:4.0.3-1.fc46.x86_64" is already installed. Package "python3-devel-3.15.1-1.fc46.x86_64" is already installed. Package "xz-devel-1:5.8.4-1.fc46.x86_64" is already installed. Package "zlib-ng-compat-devel-2.3.3-6.fc45.x86_64" is already installed. Finish: build setup for ucsc-kent-utils-492-1.fc46.src.rpm Start: rpmbuild ucsc-kent-utils-492-1.fc46.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1779148800 Executing(mkbuilddir): /bin/sh -e /var/tmp/rpm-tmp.WzZl4O Creating(rpmbuild.env): /builddir/build/BUILD/ucsc-kent-utils-492-build/rpmbuild.env RPM_SOURCE_DIR="/builddir/build/SOURCES" RPM_BUILD_DIR="/builddir/build/BUILD/ucsc-kent-utils-492-build" RPM_OPT_FLAGS="-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer" RPM_LD_FLAGS="-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes " RPM_ARCH="x86_64" RPM_OS="linux" RPM_BUILD_NCPUS="4" RPM_SPECPARTS_DIR="/builddir/build/BUILD/ucsc-kent-utils-492-build/SPECPARTS" export RPM_SOURCE_DIR RPM_BUILD_DIR RPM_OPT_FLAGS RPM_ARCH RPM_OS RPM_BUILD_NCPUS RPM_SPECPARTS_DIR RPM_LD_FLAGS RPM_DOC_DIR="/usr/share/doc" export RPM_DOC_DIR RPM_PACKAGE_NAME="ucsc-kent-utils" RPM_PACKAGE_VERSION="492" RPM_PACKAGE_RELEASE="1.fc46" export RPM_PACKAGE_NAME RPM_PACKAGE_VERSION RPM_PACKAGE_RELEASE LANG=C.UTF-8 export LANG unset CDPATH DISPLAY ||: unset DEBUGINFOD_URLS ||: unset RPM_CONFIG_DIR ||: RPM_BUILD_ROOT="/builddir/build/BUILD/ucsc-kent-utils-492-build/BUILDROOT" export RPM_BUILD_ROOT PKG_CONFIG_PATH="${PKG_CONFIG_PATH}:/usr/lib64/pkgconfig:/usr/share/pkgconfig" export PKG_CONFIG_PATH CONFIG_SITE=${CONFIG_SITE:-NONE} export CONFIG_SITE Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.6Z9QBS + umask 022 + cd /builddir/build/BUILD/ucsc-kent-utils-492-build + cd /builddir/build/BUILD/ucsc-kent-utils-492-build + rm -rf kent-core-492 + /usr/bin/rpmuncompress -x /builddir/build/SOURCES/kent-core-492.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + cd kent-core-492 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + /usr/bin/patch -p1 -s --fuzz=0 --no-backup-if-mismatch -f + /usr/bin/rpmuncompress /builddir/build/SOURCES/ucsc-kent-utils-skip-broken-tools.patch + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.UzNZBW + umask 022 + cd /builddir/build/BUILD/ucsc-kent-utils-492-build + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd kent-core-492 ++ uname -m ++ sed 's/-.*//' + export MACHTYPE=x86_64 + MACHTYPE=x86_64 ++ pwd + export BINDIR=/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin + BINDIR=/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin + mkdir -p /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin + export MYSQLINC=/usr/include/mysql + MYSQLINC=/usr/include/mysql + export 'MYSQLLIBS=-lmariadb -lz -lpthread -lm -lssl -lcrypto' + MYSQLLIBS='-lmariadb -lz -lpthread -lm -lssl -lcrypto' + make -j1 BINDIR=/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin MYSQLINC=/usr/include/mysql 'MYSQLLIBS=-lmariadb -lz -lpthread -lm -lssl -lcrypto' mkdir -p bin cd src && make utils USE_HAL=0 USE_FREETYPE=0 USE_HIC=0 BINDIR=/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin make[1]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src' make -C lib make[2]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/lib' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o aliType.o -c aliType.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o annoAssembly.o -c annoAssembly.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o annoFilter.o -c annoFilter.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o annoFormatter.o -c annoFormatter.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o annoFormatTab.o -c annoFormatTab.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o annoGrator.o -c annoGrator.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o annoGrateWig.o -c annoGrateWig.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o annoGratorQuery.o -c annoGratorQuery.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o annoOption.o -c annoOption.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o annoRow.o -c annoRow.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o annoStreamer.o -c annoStreamer.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o annoStreamBigBed.o -c annoStreamBigBed.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o annoStreamBigWig.o -c annoStreamBigWig.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o annoStreamTab.o -c annoStreamTab.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o annoStreamLongTabix.o -c annoStreamLongTabix.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o annoStreamVcf.o -c annoStreamVcf.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o apacheLog.o -c apacheLog.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o asParse.o -c asParse.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o aveStats.o -c aveStats.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o axt.o -c axt.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o axtAffine.o -c axtAffine.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o bamFile.o -c bamFile.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o base64.o -c base64.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o basicBed.o -c basicBed.c basicBed.c: In function ‘bedParseRgb’: basicBed.c:1072:1: warning: ‘strncpy’ specified bound 64 equals destination size [-Wstringop-truncation] 1072 | strncpy(dupe, itemRgb, sizeof(dupe)); | ^ gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o bbiAlias.o -c bbiAlias.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o bbiRead.o -c bbiRead.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o bbiWrite.o -c bbiWrite.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o bedTabix.o -c bedTabix.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o bigBed.o -c bigBed.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o bigBedCmdSupport.o -c bigBedCmdSupport.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o binRange.o -c binRange.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o bits.o -c bits.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o blastOut.o -c blastOut.c blastOut.c: In function ‘ncbiBlastOut’: blastOut.c:555:9: warning: variable ‘ii’ set but not used [-Wunused-but-set-variable=] 555 | int ii = 0; | ^~ gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o blastParse.o -c blastParse.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o boxClump.o -c boxClump.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o boxLump.o -c boxLump.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o bPlusTree.o -c bPlusTree.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o cacheTwoBit.o -c cacheTwoBit.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o bwgCreate.o -c bwgCreate.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o bwgQuery.o -c bwgQuery.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o bwgValsOnChrom.o -c bwgValsOnChrom.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o cda.o -c cda.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o chain.o -c chain.c chain.c: In function ‘chainReadUsedSwapLf’: chain.c:401:20: warning: variable ‘count’ set but not used [-Wunused-but-set-variable=] 401 | int usedCount = 0, count = 0; | ^~~~~ chain.c:401:5: warning: variable ‘usedCount’ set but not used [-Wunused-but-set-variable=] 401 | int usedCount = 0, count = 0; | ^~~~~~~~~ gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o chainBlock.o -c chainBlock.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o chainConnect.o -c chainConnect.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o chainToAxt.o -c chainToAxt.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o chainToPsl.o -c chainToPsl.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o cheapcgi.o -c cheapcgi.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o cirTree.o -c cirTree.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o codebias.o -c codebias.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o colHash.o -c colHash.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o common.o -c common.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o correlate.o -c correlate.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o crTree.o -c crTree.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o csv.o -c csv.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o dgRange.o -c dgRange.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o diGraph.o -c diGraph.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o dlist.o -c dlist.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o dnaLoad.o -c dnaLoad.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o dnaMarkov.o -c dnaMarkov.c dnaMarkov.c: In function ‘dnaMarkTriple’: dnaMarkov.c:111:5: warning: variable ‘total’ set but not used [-Wunused-but-set-variable=] 111 | int total = 0; | ^~~~~ gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o dnaMotif.o -c dnaMotif.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o dnaseq.o -c dnaseq.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o dnautil.o -c dnautil.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o dtdParse.o -c dtdParse.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o dyOut.o -c dyOut.c dyOut.c: In function ‘dyOutPointerFromToken’: dyOut.c:47:5: warning: variable ‘ix’ set but not used [-Wunused-but-set-variable=] 47 | int ix = 0; | ^~ gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o dystring.o -c dystring.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o elmTree.o -c elmTree.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o emblParse.o -c emblParse.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o errCatch.o -c errCatch.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o errAbort.o -c errAbort.c errAbort.c: In function ‘getThreadVars’: errAbort.c:382:5: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 382 | write(STDERR_FILENO, errMsg, strlen(errMsg)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o fa.o -c fa.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o ffAli.o -c ffAli.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o ffScore.o -c ffScore.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic 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-Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o fixColor.o -c fixColor.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o flydna.o -c flydna.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o fof.o -c fof.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o font/mgCourier10.o -c font/mgCourier10.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o font/mgCourier12.o -c font/mgCourier12.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o font/mgCourier14.o -c font/mgCourier14.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o font/mgCourier18.o -c font/mgCourier18.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o font/mgCourier24.o -c font/mgCourier24.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o font/mgCourier34.o -c font/mgCourier34.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o font/mgCourier8.o -c font/mgCourier8.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o font/mgHelvetica10.o -c font/mgHelvetica10.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o font/mgHelvetica12.o -c font/mgHelvetica12.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o font/mgHelvetica14.o -c font/mgHelvetica14.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o font/mgHelvetica18.o -c font/mgHelvetica18.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o font/mgHelvetica24.o -c font/mgHelvetica24.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o font/mgHelvetica34.o -c font/mgHelvetica34.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o font/mgHelvetica8.o -c font/mgHelvetica8.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o font/mgHelveticaBold10.o -c font/mgHelveticaBold10.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o font/mgHelveticaBold12.o -c font/mgHelveticaBold12.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o font/mgHelveticaBold14.o -c font/mgHelveticaBold14.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o font/mgHelveticaBold18.o -c font/mgHelveticaBold18.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit 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-Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o font/mgHelveticaBold34.o -c font/mgHelveticaBold34.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o font/mgHelveticaBold8.o -c font/mgHelveticaBold8.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o font/mgSixhi6.o -c font/mgSixhi6.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o font/mgSail8.o -c font/mgSail8.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o font/mgTimes10.o -c font/mgTimes10.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o font/mgTimes12.o -c font/mgTimes12.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o font/mgTimes14.o -c font/mgTimes14.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o font/mgTimes18.o -c font/mgTimes18.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o font/mgTimes24.o -c font/mgTimes24.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o font/mgTimes34.o -c font/mgTimes34.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o font/mgTimes8.o -c font/mgTimes8.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o font/mgMenlo12.o -c font/mgMenlo12.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o fq.o -c fq.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o freeType.o -c freeType.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o fuzzyShow.o -c fuzzyShow.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o gapCalc.o -c gapCalc.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o gdf.o -c gdf.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o gemfont.o -c gemfont.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o genomeRangeTree.o -c genomeRangeTree.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o gfNet.o -c gfNet.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o gff.o -c gff.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o gff3.o -c gff3.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o gfxPoly.o -c gfxPoly.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o gifLabel.o -c gifLabel.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o hacTree.o -c hacTree.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o hash.o -c hash.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o hex.o -c hex.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o histogram.o -c histogram.c histogram.c: In function ‘histoGram’: histogram.c:165:10: warning: variable ‘missed’ set but not used [-Wunused-but-set-variable=] 165 | unsigned missed = 0; | ^~~~~~ gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o hmmPfamParse.o -c hmmPfamParse.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o hmmstats.o -c hmmstats.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o htmlColor.o -c htmlColor.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o htmlPage.o -c htmlPage.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o htmshell.o -c htmshell.c htmshell.c: In function ‘htmlEncodeTextExtended’: htmshell.c:323:13: warning: ‘strncpy’ output may be truncated copying 5 bytes from a string of length 5 [-Wstringop-truncation] 323 | strncpy(out, newString, size); | ^ htmshell.c:323:13: warning: ‘strncpy’ output may be truncated copying between 4 and 6 bytes from a string of length 6 [-Wstringop-truncation] gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o hmac.o -c hmac.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o https.o -c https.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o intExp.o -c intExp.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o intValTree.o -c intValTree.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o internet.o -c internet.c internet.c: In function ‘internetParseOneSubnetCidr’: internet.c:508:5: warning: dangling pointer ‘ip_19’ to ‘expIp’ may be used [-Wdangling-pointer=] 508 | errAbort("internetIpStringToIp6 failed for %s", ip); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ internet.c:464:10: note: ‘expIp’ declared here 464 | char expIp[17]; | ^~~~~ gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o itsa.o -c itsa.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o iupac.o -c iupac.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o jointalign.o -c jointalign.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o jpegSize.o -c jpegSize.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o jsonParse.o -c jsonParse.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o jsonQuery.o -c jsonQuery.c jsonQuery.c: In function ‘jsonPathPopHead’: jsonQuery.c:50:18: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 50 | char *pDot = strchr(pathIn, '.'); | ^~~~~~ jsonQuery.c:51:22: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 51 | char *pBracket = strchr(pathIn, '['); | ^~~~~~ gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o jsonWrite.o -c jsonWrite.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o keys.o -c keys.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o knetUdc.o -c knetUdc.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o kxTok.o -c kxTok.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o linefile.o -c linefile.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o lineFileOnBigBed.o -c lineFileOnBigBed.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o localmem.o -c localmem.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o log.o -c log.c log.c: In function ‘logDaemonize’: log.c:345:5: warning: ignoring return value of ‘dup’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 345 | dup(nullFd); // Stdout goes also to /dev/null | ^~~~~~~~~~~ log.c:346:5: warning: ignoring return value of ‘dup’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 346 | dup(nullFd); // Stderr goes also to /dev/null | ^~~~~~~~~~~ gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o longTabix.o -c longTabix.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o longToList.o -c longToList.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o maf.o -c maf.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o mafFromAxt.o -c mafFromAxt.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o mafScore.o -c mafScore.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o mailViaPipe.o -c mailViaPipe.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o md5.o -c md5.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o matrixMarket.o -c matrixMarket.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o memalloc.o -c memalloc.c memalloc.c: In function ‘carefulAlloc’: memalloc.c:321:5: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 321 | write(STDERR_FILENO, errMsg, strlen(errMsg)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o memgfx.o -c memgfx.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o meta.o -c meta.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o metaWig.o -c metaWig.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o mgCircle.o -c mgCircle.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o mgPolygon.o -c mgPolygon.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o mime.o -c mime.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o mmHash.o -c mmHash.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o net.o -c net.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o nib.o -c nib.c nib.c: In function ‘nibInput’: nib.c:225:22: warning: array subscript [-134217728, -1] is outside array bounds of ‘DNA[]’ [-Warray-bounds=] 225 | *d++ = valToNtTbl[(bVal>>4)]; | ~~~~~~~~~~^~~~~~~~~~~ In file included from nib.c:8: ../inc/dnautil.h:71:12: note: at offset [-134217728, -1] into object ‘valToNtMasked’ of size 256 71 | extern DNA valToNtMasked[256]; | ^~~~~~~~~~~~~ ../inc/dnautil.h:57:12: note: at offset [-134217728, -1] into object ‘valToNt’ of size [0, 9223372036854775807] 57 | extern DNA valToNt[]; | ^~~~~~~ gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o nibTwo.o -c nibTwo.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o nt4.o -c nt4.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o numObscure.o -c numObscure.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o obscure.o -c obscure.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o oldGff.o -c oldGff.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o oligoTm.o -c oligoTm.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o options.o -c options.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o osunix.o -c osunix.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o pairHmm.o -c pairHmm.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o pairDistance.o -c pairDistance.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o paraFetch.o -c paraFetch.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o peakCluster.o -c peakCluster.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o phyloTree.o -c phyloTree.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o pipeline.o -c pipeline.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o portimpl.o -c portimpl.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o pngwrite.o -c pngwrite.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o psGfx.o -c psGfx.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o psPoly.o -c psPoly.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o pscmGfx.o -c pscmGfx.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o psl.o -c psl.c psl.c: In function ‘pslTrimToTargetRange’: psl.c:1423:9: warning: variable ‘qE’ set but not used [-Wunused-but-set-variable=] 1423 | int qE = qS + sz; | ^~ psl.c: In function ‘pslTrimToQueryRange’: psl.c:1509:9: warning: variable ‘tE’ set but not used [-Wunused-but-set-variable=] 1509 | int tE = tS + sz; | ^~ gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o pslGenoShow.o -c pslGenoShow.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o pslShow.o -c pslShow.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o pslTbl.o -c pslTbl.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o pslTransMap.o -c pslTransMap.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o pthreadDoList.o -c pthreadDoList.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o pthreadWrap.o -c pthreadWrap.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o qa.o -c qa.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o quickHeap.o -c quickHeap.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o quotedP.o -c quotedP.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o ra.o -c ra.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o rainbow.o -c rainbow.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o raToStruct.o -c raToStruct.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o rbTree.o -c rbTree.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o rangeTree.o -c rangeTree.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o regexHelper.o -c regexHelper.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o repMask.o -c repMask.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o rle.o -c rle.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o rnautil.o -c rnautil.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o rqlEval.o -c rqlEval.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o rqlParse.o -c rqlParse.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o rqlToSql.o -c rqlToSql.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o rudp.o -c rudp.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o scoreWindow.o -c scoreWindow.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o seg.o -c seg.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o seqOut.o -c seqOut.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o seqStats.o -c seqStats.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o servBrcMcw.o -c servBrcMcw.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o servCrunx.o -c servCrunx.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o servcis.o -c servcis.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o servcl.o -c servcl.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o servmsII.o -c servmsII.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o servpws.o -c servpws.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o shaRes.o -c shaRes.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o slog.o -c slog.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o snof.o -c snof.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o snofmake.o -c snofmake.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o snofsig.o -c snofsig.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o spaceSaver.o -c spaceSaver.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o spacedColumn.o -c spacedColumn.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o spacedSeed.o -c spacedSeed.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o sparseMatrix.o -c sparseMatrix.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o splatAli.o -c splatAli.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o sqlList.o -c sqlList.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o sqlNum.o -c sqlNum.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o sqlReserved.o -c sqlReserved.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o strex.o -c strex.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o subText.o -c subText.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o sufa.o -c sufa.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o sufx.o -c sufx.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o synQueue.o -c synQueue.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o tabRow.o -c tabRow.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o tagSchema.o -c tagSchema.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o tagStorm.o -c tagStorm.c tagStorm.c: In function ‘tagStormFromFile’: tagStorm.c:171:5: warning: variable ‘tagCount’ set but not used [-Wunused-but-set-variable=] 171 | int tagCount = 0; | ^~~~~~~~ tagStorm.c:170:5: warning: variable ‘stanzaCount’ set but not used [-Wunused-but-set-variable=] 170 | int stanzaCount = 0; | ^~~~~~~~~~~ gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o tagToJson.o -c tagToJson.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o tagToSql.o -c tagToSql.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o textOut.o -c textOut.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o tokenizer.o -c tokenizer.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o trix.o -c trix.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o twoBit.o -c twoBit.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o udc.o -c udc.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o uuid.o -c uuid.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o vcf.o -c vcf.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o vcfBits.o -c vcfBits.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o vGfx.o -c vGfx.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o vPng.o -c vPng.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o verbose.o -c verbose.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o vMatrix.o -c vMatrix.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o wildcmp.o -c wildcmp.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o windowsToAscii.o -c windowsToAscii.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o wormdna.o -c wormdna.c wormdna.c: In function ‘wormInfoForGene’: wormdna.c:614:5: warning: variable ‘lineCount’ set but not used [-Wunused-but-set-variable=] 614 | int lineCount = 0; | ^~~~~~~~~ wormdna.c: In function ‘wormIsGeneName’: wormdna.c:513:1: warning: ‘strncpy’ specified bound 128 equals destination size [-Wstringop-truncation] 513 | strncpy(buf, name, sizeof(buf)); | ^ wormdna.c: In function ‘wormParseChromRange’: wormdna.c:870:1: warning: ‘strncpy’ specified bound 128 equals destination size [-Wstringop-truncation] 870 | strncpy(buf, in, sizeof(buf)); | ^ gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o xAli.o -c xAli.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o xa.o -c xa.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o xap.o -c xap.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o xenshow.o -c xenshow.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o xmlEscape.o -c xmlEscape.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o xp.o -c xp.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o zlibFace.o -c zlibFace.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o curlWrap.o -c curlWrap.c ar rcus x86_64/jkweb.a aliType.o annoAssembly.o annoFilter.o annoFormatter.o annoFormatTab.o annoGrator.o annoGrateWig.o annoGratorQuery.o annoOption.o annoRow.o annoStreamer.o annoStreamBigBed.o annoStreamBigWig.o annoStreamTab.o annoStreamLongTabix.o annoStreamVcf.o apacheLog.o asParse.o aveStats.o axt.o axtAffine.o bamFile.o base64.o basicBed.o bbiAlias.o bbiRead.o bbiWrite.o bedTabix.o bigBed.o bigBedCmdSupport.o binRange.o bits.o blastOut.o blastParse.o boxClump.o boxLump.o bPlusTree.o cacheTwoBit.o bwgCreate.o bwgQuery.o bwgValsOnChrom.o cacheTwoBit.o cda.o chain.o chainBlock.o chainConnect.o chainToAxt.o chainToPsl.o cheapcgi.o cirTree.o codebias.o colHash.o common.o correlate.o crTree.o csv.o dgRange.o diGraph.o dlist.o dnaLoad.o dnaMarkov.o dnaMotif.o dnaseq.o dnautil.o dtdParse.o dyOut.o dystring.o elmTree.o emblParse.o errCatch.o errAbort.o fa.o ffAli.o ffScore.o fieldedTable.o filePath.o fixColor.o flydna.o fof.o font/mgCourier10.o font/mgCourier12.o font/mgCourier14.o font/mgCourier18.o font/mgCourier24.o font/mgCourier34.o font/mgCourier8.o font/mgHelvetica10.o font/mgHelvetica12.o font/mgHelvetica14.o font/mgHelvetica18.o font/mgHelvetica24.o font/mgHelvetica34.o font/mgHelvetica8.o font/mgHelveticaBold10.o font/mgHelveticaBold12.o font/mgHelveticaBold14.o font/mgHelveticaBold18.o font/mgHelveticaBold24.o font/mgHelveticaBold34.o font/mgHelveticaBold8.o font/mgSixhi6.o font/mgSail8.o font/mgTimes10.o font/mgTimes12.o font/mgTimes14.o font/mgTimes18.o font/mgTimes24.o font/mgTimes34.o font/mgTimes8.o font/mgMenlo12.o fq.o freeType.o fuzzyShow.o gapCalc.o gdf.o gemfont.o genomeRangeTree.o gfNet.o gff.o gff3.o gfxPoly.o gifLabel.o hacTree.o hash.o hex.o histogram.o hmmPfamParse.o hmmstats.o htmlColor.o htmlPage.o htmshell.o hmac.o https.o intExp.o intValTree.o internet.o itsa.o iupac.o jointalign.o jpegSize.o jsonParse.o jsonQuery.o jsonWrite.o keys.o knetUdc.o kxTok.o linefile.o lineFileOnBigBed.o localmem.o log.o longTabix.o longToList.o maf.o mafFromAxt.o mafScore.o mailViaPipe.o md5.o matrixMarket.o memalloc.o memgfx.o meta.o metaWig.o mgCircle.o mgPolygon.o mime.o mmHash.o net.o nib.o nibTwo.o nt4.o numObscure.o obscure.o oldGff.o oligoTm.o options.o osunix.o pairHmm.o pairDistance.o paraFetch.o peakCluster.o phyloTree.o pipeline.o portimpl.o pngwrite.o psGfx.o psPoly.o pscmGfx.o psl.o pslGenoShow.o pslShow.o pslTbl.o pslTransMap.o pthreadDoList.o pthreadWrap.o qa.o quickHeap.o quotedP.o ra.o rainbow.o raToStruct.o rbTree.o rangeTree.o regexHelper.o repMask.o rle.o rnautil.o rqlEval.o rqlParse.o rqlToSql.o rudp.o scoreWindow.o seg.o seqOut.o seqStats.o servBrcMcw.o servCrunx.o servcis.o servcl.o servmsII.o servpws.o shaRes.o slog.o snof.o snofmake.o snofsig.o spaceSaver.o spacedColumn.o spacedSeed.o sparseMatrix.o splatAli.o sqlList.o sqlNum.o sqlReserved.o strex.o subText.o sufa.o sufx.o synQueue.o tabRow.o tagSchema.o tagStorm.o tagToJson.o tagToSql.o textOut.o tokenizer.o trix.o twoBit.o udc.o uuid.o vcf.o vcfBits.o vGfx.o vPng.o verbose.o vMatrix.o wildcmp.o windowsToAscii.o wormdna.o xAli.o xa.o xap.o xenshow.o xmlEscape.o xp.o zlibFace.o curlWrap.o make[2]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/lib' make -C parasol/lib make[2]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/parasol/lib' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o broadData.o -c broadData.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o paraLib.o -c paraLib.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o paraMessage.o -c paraMessage.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o machSpec.o -c machSpec.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o jobResult.o -c jobResult.c mkdir -p x86_64 ar rcu x86_64/paralib.a broadData.o paraLib.o paraMessage.o machSpec.o jobResult.o ranlib x86_64/paralib.a make[2]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/parasol/lib' make -C htslib make[2]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/htslib' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o kfunc.o -c kfunc.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o knetfile.o -c knetfile.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o kstring.o -c kstring.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o bgzf.o -c bgzf.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o faidx.o -c faidx.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o hfile.o -c hfile.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o hfile_net.o -c hfile_net.c echo '#define HTS_VERSION "1.3"' > version.h gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o hts.o -c hts.c hts.c: In function ‘hts_hopen’: hts.c:690:13: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 690 | if ((cp = strchr(mode, ','))) { | ^ gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o md5.o -c md5.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o regidx.o -c regidx.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o sam.o -c sam.c sam.c: In function ‘sam_open_mode_opts’: sam.c:1366:15: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 1366 | if ((opts = strchr(format, ','))) { | ^ gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o synced_bcf_reader.o -c synced_bcf_reader.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o vcf_sweep.o -c vcf_sweep.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o tbx.o -c tbx.c tbx.c: In function ‘tbx_parse1’: tbx.c:75:27: warning: variable ‘ncols’ set but not used [-Wunused-but-set-variable=] 75 | int i, b = 0, id = 1, ncols = 0; | ^~~~~ gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o vcf.o -c vcf.c vcf.c: In function ‘bcf_hdr_parse’: vcf.c:590:14: warning: variable ‘needs_sync’ set but not used [-Wunused-but-set-variable=] 590 | int len, needs_sync = 0; | ^~~~~~~~~~ vcf.c: In function ‘bcf_hdr_merge’: vcf.c:2352:50: warning: variable ‘ret’ set but not used [-Wunused-but-set-variable=] 2352 | int i, ndst_ori = dst->nhrec, need_sync = 0, ret = 0; | ^~~ gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o vcfutils.o -c vcfutils.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o cram/cram_codecs.o -c cram/cram_codecs.c cram/cram_codecs.c: In function ‘cram_huffman_encode_init’: cram/cram_codecs.c:1195:19: warning: variable ‘ntot’ set but not used [-Wunused-but-set-variable=] 1195 | int nvals, i, ntot = 0, max_val = 0, min_val = INT_MAX, k; | ^~~~ gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o cram/cram_decode.o -c cram/cram_decode.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o cram/cram_encode.o -c cram/cram_encode.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o cram/cram_external.o -c cram/cram_external.c cram/cram_external.c: In function ‘cram_block_compression_hdr_set_DS’: cram/cram_external.c:128:16: warning: the comparison will always evaluate as ‘true’ for the address of ‘codecs’ will never be NULL [-Waddress] 128 | if (!ch || !ch->codecs || !ch->codecs[ds]) | ^ In file included from ../htslib/cram/cram.h:47, from cram/cram_external.c:44: ../htslib/cram/cram_structs.h:301:24: note: ‘codecs’ declared here 301 | struct cram_codec *codecs[DS_END]; | ^~~~~~ cram/cram_external.c: In function ‘cram_block_compression_hdr_decoder2encoder’: cram/cram_external.c:167:16: warning: the comparison will always evaluate as ‘true’ for the address of ‘codecs’ will never be NULL [-Waddress] 167 | if (!ch || !ch->codecs) | ^ ../htslib/cram/cram_structs.h:301:24: note: ‘codecs’ declared here 301 | struct cram_codec *codecs[DS_END]; | ^~~~~~ gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o cram/cram_index.o -c cram/cram_index.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o cram/cram_io.o -c cram/cram_io.c cram/cram_io.c: In function ‘cram_dopen’: cram/cram_io.c:4209:29: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 4209 | fd->prefix = strdup((cp = strrchr(filename, '/')) ? cp+1 : filename); | ^ cram/cram_io.c: In function ‘cram_set_cache_url’: cram/cram_io.c:2185:9: warning: ‘strncpy’ specified bound 1024 equals destination size [-Wstringop-truncation] 2185 | strncpy(fd->cacheDir, cacheDir, sizeof(fd->cacheDir)); | ^ cram/cram_io.c: In function ‘cram_write_SAM_hdr’: cram/cram_io.c:3825:13: warning: ‘strncpy’ specified bound 4096 equals destination size [-Wstringop-truncation] 3825 | strncpy(out, in, PATH_MAX); | ^ cram/cram_io.c:3817:9: warning: ‘strncpy’ specified bound 4096 equals destination size [-Wstringop-truncation] 3817 | strncpy(out, in, PATH_MAX); | ^ cram/cram_io.c: In function ‘cram_dopen’: cram/cram_io.c:4200:9: warning: ‘strncpy’ specified bound 20 equals destination size [-Wstringop-truncation] 4200 | strncpy(def->file_id, filename, 20); | ^ gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o cram/cram_samtools.o -c cram/cram_samtools.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o cram/cram_stats.o -c cram/cram_stats.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o cram/files.o -c cram/files.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o cram/mFILE.o -c cram/mFILE.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o cram/open_trace_file.o -c cram/open_trace_file.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o cram/pooled_alloc.o -c cram/pooled_alloc.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o cram/rANS_static.o -c cram/rANS_static.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o cram/sam_header.o -c cram/sam_header.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o cram/string_alloc.o -c cram/string_alloc.c cram/string_alloc.c: In function ‘string_dup’: cram/string_alloc.c:151:5: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 151 | strncpy(str, instr, len); | ^ cram/string_alloc.c:143:12: note: length computed here 143 | return string_ndup(a_str, instr, strlen(instr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o cram/thread_pool.o -c cram/thread_pool.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o cram/vlen.o -c cram/vlen.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -DKNETFILE_HOOKS -DUCSC_CRAM -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o cram/zfio.o -c cram/zfio.c ar -rc libhts.a kfunc.o knetfile.o kstring.o bgzf.o faidx.o hfile.o hfile_net.o hts.o md5.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o cram/thread_pool.o cram/vlen.o cram/zfio.o ranlib libhts.a make[2]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/htslib' make -C hg/lib make[2]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/lib' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o adjacency.o -c adjacency.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o affyPairs.o -c affyPairs.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o agpFrag.o -c agpFrag.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o agpGap.o -c agpGap.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o alignSeqSizes.o -c alignSeqSizes.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o altGraphX.o -c altGraphX.c altGraphX.c: In function ‘altGraphXDrawPack’: altGraphX.c:1649:5: warning: variable ‘count’ set but not used [-Wunused-but-set-variable=] 1649 | int count =0; | ^~~~~ gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o asmAlias.o -c asmAlias.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o asmEquivalent.o -c asmEquivalent.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o asmSummary.o -c asmSummary.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o assemblyList.o -c assemblyList.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o autoUpgrade.o -c autoUpgrade.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o axtInfo.o -c axtInfo.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o barChartBed.o -c barChartBed.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o barChartCategory.o -c barChartCategory.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o barChartUi.o -c barChartUi.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o bed.o -c bed.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o bed12Source.o -c bed12Source.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o bedDetail.o -c bedDetail.c bedDetail.c: In function ‘bedDetailLineFileLoad’: bedDetail.c:340:6: warning: ‘strncpy’ specified bound 2 equals destination size [-Wstringop-truncation] 340 | strncpy(item->strand, row[5], sizeof(item->strand)); | ^ gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o bedMethyl.o -c bedMethyl.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o bigBedFind.o -c bigBedFind.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o bigBedLabel.o -c bigBedLabel.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o bigChain.o -c bigChain.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o bigDbSnp.o -c bigDbSnp.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o bigGenePred.o -c bigGenePred.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o bigLink.o -c bigLink.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o bigPsl.o -c bigPsl.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o blastTab.o -c blastTab.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o borf.o -c borf.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o botDelay.o -c botDelay.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o cart.o -c cart.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o cartDb.o -c cartDb.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o cartTrackDb.o -c cartTrackDb.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o cdsEvidence.o -c cdsEvidence.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o cdsOrtho.o -c cdsOrtho.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o cdsPick.o -c cdsPick.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o cgapSage/cgapSage.o -c cgapSage/cgapSage.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o cgapSage/cgapSageLib.o -c cgapSage/cgapSageLib.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o cgiApoptosis.o -c cgiApoptosis.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o chainCart.o -c chainCart.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o chainDb.o -c chainDb.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o chainLink.o -c chainLink.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o chainNet.o -c chainNet.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o chainNetDbLoad.o -c chainNetDbLoad.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o chromAlias.o -c chromAlias.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o chromBins.o -c chromBins.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o chromGraph.o -c chromGraph.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o chromGraphFactory.o -c chromGraphFactory.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o chromInfo.o -c chromInfo.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o chromInserts.o -c chromInserts.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o chromKeeper.o -c chromKeeper.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o clonePos.o -c clonePos.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o cpgIsland.o -c cpgIsland.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o ctgPos.o -c ctgPos.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o customAdjacency.o -c customAdjacency.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o customComposite.o -c customComposite.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o customFactory.o -c customFactory.c customFactory.c: In function ‘niceGeneName’: customFactory.c:1977:1: warning: ‘strncpy’ specified bound 128 equals destination size [-Wstringop-truncation] 1977 | strncpy(buf, name, sizeof(buf)); | ^ customFactory.c: In function ‘bedLoader’: customFactory.c:652:6: warning: ‘strncpy’ specified bound 2 equals destination size [-Wstringop-truncation] 652 | strncpy(bed->strand, row[5], sizeof(bed->strand)); | ^ gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o customPp.o -c customPp.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o customTrack.o -c customTrack.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o cv.o -c cv.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o cytoBand.o -c cytoBand.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o dbDb.o -c dbDb.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o decoration.o -c decoration.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o decoratorUi.o -c decoratorUi.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o defaultDb.o -c defaultDb.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o dnaMotifSql.o -c dnaMotifSql.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o dupTrack.o -c dupTrack.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o encode/encodeErge.o -c encode/encodeErge.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o encode/encodeErgeHssCellLines.o -c encode/encodeErgeHssCellLines.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o encode/encodeExp.o -c encode/encodeExp.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o encode/encodeHapMapAlleleFreq.o -c encode/encodeHapMapAlleleFreq.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o encode/encodeIndels.o -c encode/encodeIndels.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o encode/encodePeak.o -c encode/encodePeak.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o encode/encodeRegionInfoCustom.o -c encode/encodeRegionInfoCustom.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o encode/encodeRna.o -c encode/encodeRna.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o encode/encodeStanfordPromoters.o -c encode/encodeStanfordPromoters.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o encode/encodeStanfordPromotersAverage.o -c encode/encodeStanfordPromotersAverage.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o encode/peptideMapping.o -c encode/peptideMapping.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o encode/wgEncodeGencodeAnnotationRemark.o -c encode/wgEncodeGencodeAnnotationRemark.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o encode/wgEncodeGencodeAttrs.o -c encode/wgEncodeGencodeAttrs.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o encode/wgEncodeGencodeEntrezGene.o -c encode/wgEncodeGencodeEntrezGene.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o encode/wgEncodeGencodeExonSupport.o -c encode/wgEncodeGencodeExonSupport.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o encode/wgEncodeGencodeGeneSource.o -c encode/wgEncodeGencodeGeneSource.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o encode/wgEncodeGencodeGeneSymbol.o -c encode/wgEncodeGencodeGeneSymbol.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o encode/wgEncodeGencodePdb.o -c encode/wgEncodeGencodePdb.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o encode/wgEncodeGencodePubMed.o -c encode/wgEncodeGencodePubMed.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o encode/wgEncodeGencodeRefSeq.o -c encode/wgEncodeGencodeRefSeq.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o encode/wgEncodeGencodeTag.o -c encode/wgEncodeGencodeTag.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o encode/wgEncodeGencodeTranscriptSource.o -c encode/wgEncodeGencodeTranscriptSource.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o encode/wgEncodeGencodeTranscriptSupport.o -c encode/wgEncodeGencodeTranscriptSupport.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o encode/wgEncodeGencodeTranscriptionSupportLevel.o -c encode/wgEncodeGencodeTranscriptionSupportLevel.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o encode/wgEncodeGencodeUniProt.o -c encode/wgEncodeGencodeUniProt.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o encode3/encode3Valid.o -c encode3/encode3Valid.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o estOrientInfo.o -c estOrientInfo.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o expData.o -c expData.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o exportedDataHubs.o -c exportedDataHubs.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o expRecord.o -c expRecord.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o facetField.o -c facetField.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o facetedTable.o -c facetedTable.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o featureBits.o -c featureBits.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o findKGAlias.o -c findKGAlias.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o fakeCurl.o -c fakeCurl.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o findKGProtAlias.o -c findKGProtAlias.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o gbSeq.o -c gbSeq.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o gbExtFile.o -c gbExtFile.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o gcPercent.o -c gcPercent.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o genark.o -c genark.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o genbank.o -c genbank.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o genbankBlackList.o -c genbankBlackList.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o gencodeTracksCommon.o -c gencodeTracksCommon.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o gencodeAttrs.o -c gencodeAttrs.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o gencodeToRefSeq.o -c gencodeToRefSeq.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o geneGraph.o -c geneGraph.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o genePred.o -c genePred.c genePred.c: In function ‘assignFrame’: genePred.c:677:5: warning: variable ‘numFrameExons’ set but not used [-Wunused-but-set-variable=] 677 | int numFrameExons = 0; | ^~~~~~~~~~~~~ genePred.c:676:5: warning: variable ‘numCdsExons’ set but not used [-Wunused-but-set-variable=] 676 | int numCdsExons = 0; | ^~~~~~~~~~~ gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o genePredReader.o -c genePredReader.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o geoMirror.o -c geoMirror.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o ggCluster.o -c ggCluster.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o ggDump.o -c ggDump.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o ggGraph.o -c ggGraph.c ggGraph.c: In function ‘makeInitialGraph’: ggGraph.c:132:5: warning: variable ‘totalWithDupes’ set but not used [-Wunused-but-set-variable=] 132 | int totalWithDupes = 0; | ^~~~~~~~~~~~~~ gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o ggMrnaAli.o -c ggMrnaAli.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o ggTypes.o -c ggTypes.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o glDbRep.o -c glDbRep.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o googleAnalytics.o -c googleAnalytics.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o gpFx.o -c gpFx.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o grp.o -c grp.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o gtexAse.o -c gtexAse.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o gtexDonor.o -c gtexDonor.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o gtexGeneBed.o -c gtexGeneBed.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o gtexInfo.o -c gtexInfo.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o gtexSample.o -c gtexSample.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o gtexSampleData.o -c gtexSampleData.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o gtexTissue.o -c gtexTissue.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o gtexTissueMedian.o -c gtexTissueMedian.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o gtexUi.o -c gtexUi.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o hCommon.o -c hCommon.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o hPrint.o -c hPrint.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o hVarSubst.o -c hVarSubst.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o hapmapAllelesOrtho.o -c hapmapAllelesOrtho.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o hapmapPhaseIIISummary.o -c hapmapPhaseIIISummary.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o hapmapSnps.o -c hapmapSnps.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o hdb.o -c hdb.c hdb.c: In function ‘getGencodeVersion’: hdb.c:5921:11: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 5921 | char *p = strrchr(name, 'V'); | ^~~~~~~ hdb.c: In function ‘hGetCtBedRange’: hdb.c:2300:13: warning: ‘strncpy’ specified bound 2 equals destination size [-Wstringop-truncation] 2300 | strncpy(bedItem->strand, row[4], 2); | ^ gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o hgColors.o -c hgColors.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o hgConfig.o -c hgConfig.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o hgFind.o -c hgFind.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o hgFindSpec.o -c hgFindSpec.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o hgFindSpecCustom.o -c hgFindSpecCustom.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o hgHgvs.o -c hgHgvs.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o hgHgvsParse.o -c hgHgvsParse.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o hgMaf.o -c hgMaf.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o hgRelate.o -c hgRelate.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o hic.o -c hic.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o hicUi.o -c hicUi.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o hubConnect.o -c hubConnect.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o hubPublic.o -c hubPublic.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o hubSearchText.o -c hubSearchText.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o hubSpace.o -c hubSpace.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o hubSpaceKeys.o -c hubSpaceKeys.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o hubSpaceQuotas.o -c hubSpaceQuotas.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o hui.o -c hui.c hui.c: In function ‘wigMafSpeciesTable’: hui.c:7970:5: warning: variable ‘i’ set but not used [-Wunused-but-set-variable=] 7970 | int i,j; | ^ gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o imageClone.o -c imageClone.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o indelShift.o -c indelShift.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o interact.o -c interact.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o interactUi.o -c interactUi.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o itemAttr.o -c itemAttr.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o jksql.o -c jksql.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o joiner.o -c joiner.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o jsHelper.o -c jsHelper.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o kgAlias.o -c kgAlias.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o kgProtAlias.o -c kgProtAlias.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o kgXref.o -c kgXref.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o knownInfo.o -c knownInfo.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o knownMore.o -c knownMore.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o lav.o -c lav.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o lfs.o -c lfs.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o liftOver.o -c liftOver.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o liftOverChain.o -c liftOverChain.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o liftUp.o -c liftUp.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o longRange.o -c longRange.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o lrg.o -c lrg.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o lsSnpPdb.o -c lsSnpPdb.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o mafFrames.o -c mafFrames.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o mafGene.o -c mafGene.c mafGene.c: In function ‘copyMafs’: mafGene.c:745:9: warning: variable ‘thisSize’ set but not used [-Wunused-but-set-variable=] 745 | int thisSize = 0; | ^~~~~~~~ gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o mafSummary.o -c mafSummary.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o makeItemsItem.o -c makeItemsItem.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o mdb.o -c mdb.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o microarray.o -c microarray.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o minChromSize.o -c minChromSize.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o namedSessionDb.o -c namedSessionDb.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o netAlign.o -c netAlign.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o netCart.o -c netCart.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o pepPred.o -c pepPred.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o pgPhenoAssoc.o -c pgPhenoAssoc.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o pgSnp.o -c pgSnp.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o pslReader.o -c pslReader.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o qaSeq.o -c qaSeq.c qaSeq.c: In function ‘qaFastReadNext’: qaSeq.c:195:1: warning: ‘strncpy’ specified bound 256 equals destination size [-Wstringop-truncation] 195 | strncpy(name, s, sizeof(name)); | ^ gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o quickLift.o -c quickLift.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o quickLiftChain.o -c quickLiftChain.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o rankProp.o -c rankProp.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o refLink.o -c refLink.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o refSeqStatus.o -c refSeqStatus.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o rikenCluster.o -c rikenCluster.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o rmskAlign.o -c rmskAlign.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o rmskJoined.o -c rmskJoined.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o rmskOut.o -c rmskOut.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o rmskOut2.o -c rmskOut2.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o rnaGene.o -c rnaGene.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o sage.o -c sage.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o sageCounts.o -c sageCounts.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o samAlignment.o -c samAlignment.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o sample.o -c sample.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o sanger22extra.o -c sanger22extra.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o scoredRef.o -c scoredRef.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o sessionData.o -c sessionData.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o seqWindow.o -c seqWindow.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o snakeUi.o -c snakeUi.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o snp.o -c snp.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o snpExceptions.o -c snpExceptions.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o soTerm.o -c soTerm.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o spDb.o -c spDb.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o sqlProg.o -c sqlProg.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o sqlSanity.o -c sqlSanity.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o stanMad.o -c stanMad.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o stsAlias.o -c stsAlias.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o stsInfo2.o -c stsInfo2.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o stsMap.o -c stsMap.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o stsMarker.o -c stsMarker.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o tableStatus.o -c tableStatus.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o tablesTables.o -c tablesTables.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o tagRepo.o -c tagRepo.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o tfbsCons.o -c tfbsCons.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o tigrCmrGene.o -c tigrCmrGene.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o traceInfo.o -c traceInfo.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o trackDb.o -c trackDb.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o trackDbCache.o -c trackDbCache.c trackDbCache.c: In function ‘cloneTdbListToSharedMem’: trackDbCache.c:350:1: warning: ignoring return value of ‘ftruncate’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 350 | ftruncate(fd, 0); | ^~~~~~~~~~~~~~~~ trackDbCache.c:351:1: warning: ignoring return value of ‘ftruncate’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 351 | ftruncate(fd, size); | ^~~~~~~~~~~~~~~~~~~ trackDbCache.c:391:1: warning: ignoring return value of ‘ftruncate’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 391 | ftruncate(fd, memUsed); | ^~~~~~~~~~~~~~~~~~~~~~ gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o trackDbCustom.o -c trackDbCustom.c trackDbCustom.c: In function ‘trackDbPrioritizeContainerItems’: trackDbCustom.c:1069:5: warning: variable ‘countOfSortedContainers’ set but not used [-Wunused-but-set-variable=] 1069 | int countOfSortedContainers = 0; | ^~~~~~~~~~~~~~~~~~~~~~~ gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o trackHub.o -c trackHub.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o trackVersion.o -c trackVersion.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o trashDir.o -c trashDir.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o txAliDiff.o -c txAliDiff.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o txCluster.o -c txCluster.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o txCommon.o -c txCommon.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o txEdgeBed.o -c txEdgeBed.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o txGraph.o -c txGraph.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o txInfo.o -c txInfo.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o txRnaAccs.o -c txRnaAccs.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o userdata.o -c userdata.c userdata.c: In function ‘prefixUserFile’: userdata.c:225:5: warning: ignoring return value of ‘realpath’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 225 | realpath(path, canonicalPath); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ userdata.c: In function ‘removeFileForUser’: userdata.c:470:1: warning: ignoring return value of ‘realpath’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 470 | realpath(fname, canonicalPath); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o variantProjector.o -c variantProjector.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o vcfUi.o -c vcfUi.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o vegaInfo.o -c vegaInfo.c sed -e 's/\\/\\\\/g; s/"/\\"/g; s/^/"/; s/$/\\n"/;' jWestHeader.html > jWestHeader.h sed -e 's/\\/\\\\/g; s/"/\\"/g; s/^/"/; s/$/\\n"/;' jWestBanner.html > jWestBanner.h gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o web.o -c web.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o wigAsciiToBinary.o -c wigAsciiToBinary.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o wigDataStream.o -c wigDataStream.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o wiggle.o -c wiggle.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o wiggleCart.o -c wiggleCart.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o wiggleUtils.o -c wiggleUtils.c wiggleUtils.c: In function ‘minSpan’: wiggleUtils.c:167:5: warning: variable ‘spanCount’ set but not used [-Wunused-but-set-variable=] 167 | int spanCount = 0; | ^~~~~~~~~ wiggleUtils.c: In function ‘spanInUse’: wiggleUtils.c:264:5: warning: variable ‘spanCount’ set but not used [-Wunused-but-set-variable=] 264 | int spanCount = 0; | ^~~~~~~~~ wiggleUtils.c: In function ‘wigReadDataRow’: wiggleUtils.c:457:5: warning: variable ‘noData’ set but not used [-Wunused-but-set-variable=] 457 | int noData = 0; | ^~~~~~ wiggleUtils.c: In function ‘wigFetchData’: wiggleUtils.c:786:5: warning: variable ‘spanCount’ set but not used [-Wunused-but-set-variable=] 786 | int spanCount = 0; | ^~~~~~~~~ wiggleUtils.c:777:5: warning: variable ‘rowCount’ set but not used [-Wunused-but-set-variable=] 777 | int rowCount = 0; | ^~~~~~~~ gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o wikiLink.o -c wikiLink.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o wikiTrack.o -c wikiTrack.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o bigRmskAlignBed.o -c bigRmskAlignBed.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -I/usr/include/mysql -o bigRmskBed.o -c bigRmskBed.c mkdir -p ../../lib/x86_64 ar rcus ../../lib/x86_64/jkhgap.a adjacency.o affyPairs.o agpFrag.o agpGap.o alignSeqSizes.o altGraphX.o asmAlias.o asmEquivalent.o asmSummary.o assemblyList.o autoUpgrade.o axtInfo.o barChartBed.o barChartCategory.o barChartUi.o bed.o bed12Source.o bedDetail.o bedMethyl.o bigBedFind.o bigBedLabel.o bigChain.o bigDbSnp.o bigGenePred.o bigLink.o bigPsl.o blastTab.o borf.o botDelay.o cart.o cartDb.o cartTrackDb.o cdsEvidence.o cdsOrtho.o cdsPick.o cgapSage/cgapSage.o cgapSage/cgapSageLib.o cgiApoptosis.o chainCart.o chainDb.o chainLink.o chainNet.o chainNetDbLoad.o chromAlias.o chromBins.o chromGraph.o chromGraphFactory.o chromInfo.o chromInserts.o chromKeeper.o clonePos.o cpgIsland.o ctgPos.o customAdjacency.o customComposite.o customFactory.o customPp.o customTrack.o cv.o cytoBand.o dbDb.o decoration.o decoratorUi.o defaultDb.o dnaMotifSql.o dupTrack.o encode/encodeErge.o encode/encodeErgeHssCellLines.o encode/encodeExp.o encode/encodeHapMapAlleleFreq.o encode/encodeIndels.o encode/encodePeak.o encode/encodeRegionInfoCustom.o encode/encodeRna.o encode/encodeStanfordPromoters.o encode/encodeStanfordPromotersAverage.o encode/peptideMapping.o encode/wgEncodeGencodeAnnotationRemark.o encode/wgEncodeGencodeAttrs.o encode/wgEncodeGencodeEntrezGene.o encode/wgEncodeGencodeExonSupport.o encode/wgEncodeGencodeGeneSource.o encode/wgEncodeGencodeGeneSymbol.o encode/wgEncodeGencodePdb.o encode/wgEncodeGencodePubMed.o encode/wgEncodeGencodeRefSeq.o encode/wgEncodeGencodeTag.o encode/wgEncodeGencodeTranscriptSource.o encode/wgEncodeGencodeTranscriptSupport.o encode/wgEncodeGencodeTranscriptionSupportLevel.o encode/wgEncodeGencodeUniProt.o encode3/encode3Valid.o estOrientInfo.o expData.o exportedDataHubs.o expRecord.o facetField.o facetedTable.o featureBits.o findKGAlias.o fakeCurl.o findKGProtAlias.o gbSeq.o gbExtFile.o gcPercent.o genark.o genbank.o genbankBlackList.o gencodeTracksCommon.o gencodeAttrs.o gencodeToRefSeq.o geneGraph.o genePred.o genePredReader.o geoMirror.o ggCluster.o ggDump.o ggGraph.o ggMrnaAli.o ggTypes.o glDbRep.o googleAnalytics.o gpFx.o grp.o gtexAse.o gtexDonor.o gtexGeneBed.o gtexInfo.o gtexSample.o gtexSampleData.o gtexTissue.o gtexTissueMedian.o gtexUi.o hCommon.o hPrint.o hVarSubst.o hapmapAllelesOrtho.o hapmapPhaseIIISummary.o hapmapSnps.o hdb.o hgColors.o hgConfig.o hgFind.o hgFindSpec.o hgFindSpecCustom.o hgHgvs.o hgHgvsParse.o hgMaf.o hgRelate.o hic.o hicUi.o hubConnect.o hubPublic.o hubSearchText.o hubSpace.o hubSpaceKeys.o hubSpaceQuotas.o hui.o imageClone.o indelShift.o interact.o interactUi.o itemAttr.o jksql.o joiner.o jsHelper.o kgAlias.o kgProtAlias.o kgXref.o knownInfo.o knownMore.o lav.o lfs.o liftOver.o liftOverChain.o liftUp.o longRange.o lrg.o lsSnpPdb.o mafFrames.o mafGene.o mafSummary.o makeItemsItem.o mdb.o microarray.o minChromSize.o namedSessionDb.o netAlign.o netCart.o pepPred.o pgPhenoAssoc.o pgSnp.o pslReader.o qaSeq.o quickLift.o quickLiftChain.o rankProp.o refLink.o refSeqStatus.o rikenCluster.o rmskAlign.o rmskJoined.o rmskOut.o rmskOut2.o rnaGene.o sage.o sageCounts.o samAlignment.o sample.o sanger22extra.o scoredRef.o sessionData.o seqWindow.o snakeUi.o snp.o snpExceptions.o soTerm.o spDb.o sqlProg.o sqlSanity.o stanMad.o stsAlias.o stsInfo2.o stsMap.o stsMarker.o tableStatus.o tablesTables.o tagRepo.o tfbsCons.o tigrCmrGene.o traceInfo.o trackDb.o trackDbCache.o trackDbCustom.o trackHub.o trackVersion.o trashDir.o txAliDiff.o txCluster.o txCommon.o txEdgeBed.o txGraph.o txInfo.o txRnaAccs.o userdata.o variantProjector.o vcfUi.o vegaInfo.o web.o wigAsciiToBinary.o wigDataStream.o wiggle.o wiggleCart.o wiggleUtils.o wikiLink.o wikiTrack.o bigRmskAlignBed.o bigRmskBed.o make[2]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/lib' cd optimalLeaf && make make[2]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/optimalLeaf' g++ -c -g Tree.cc g++ -c -g Leaf.cc g++ -c -g readFile.cc g++ -c -g SimMat.cc g++ -c -g bestArr.cc mkdir x86_64 ar rcus ../lib/x86_64/optimalLeaf.a Tree.o Leaf.o readFile.o SimMat.o bestArr.o make[2]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/optimalLeaf' mkdir -p /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin cd hg && make utils make[2]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg' make[2]: hostname: No such file or directory cd lib && make make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/lib' mkdir -p ../../lib/x86_64 ar rcus ../../lib/x86_64/jkhgap.a adjacency.o affyPairs.o agpFrag.o agpGap.o alignSeqSizes.o altGraphX.o asmAlias.o asmEquivalent.o asmSummary.o assemblyList.o autoUpgrade.o axtInfo.o barChartBed.o barChartCategory.o barChartUi.o bed.o bed12Source.o bedDetail.o bedMethyl.o bigBedFind.o bigBedLabel.o bigChain.o bigDbSnp.o bigGenePred.o bigLink.o bigPsl.o blastTab.o borf.o botDelay.o cart.o cartDb.o cartTrackDb.o cdsEvidence.o cdsOrtho.o cdsPick.o cgapSage/cgapSage.o cgapSage/cgapSageLib.o cgiApoptosis.o chainCart.o chainDb.o chainLink.o chainNet.o chainNetDbLoad.o chromAlias.o chromBins.o chromGraph.o chromGraphFactory.o chromInfo.o chromInserts.o chromKeeper.o clonePos.o cpgIsland.o ctgPos.o customAdjacency.o customComposite.o customFactory.o customPp.o customTrack.o cv.o cytoBand.o dbDb.o decoration.o decoratorUi.o defaultDb.o dnaMotifSql.o dupTrack.o encode/encodeErge.o encode/encodeErgeHssCellLines.o encode/encodeExp.o encode/encodeHapMapAlleleFreq.o encode/encodeIndels.o encode/encodePeak.o encode/encodeRegionInfoCustom.o encode/encodeRna.o encode/encodeStanfordPromoters.o encode/encodeStanfordPromotersAverage.o encode/peptideMapping.o encode/wgEncodeGencodeAnnotationRemark.o encode/wgEncodeGencodeAttrs.o encode/wgEncodeGencodeEntrezGene.o encode/wgEncodeGencodeExonSupport.o encode/wgEncodeGencodeGeneSource.o encode/wgEncodeGencodeGeneSymbol.o encode/wgEncodeGencodePdb.o encode/wgEncodeGencodePubMed.o encode/wgEncodeGencodeRefSeq.o encode/wgEncodeGencodeTag.o encode/wgEncodeGencodeTranscriptSource.o encode/wgEncodeGencodeTranscriptSupport.o encode/wgEncodeGencodeTranscriptionSupportLevel.o encode/wgEncodeGencodeUniProt.o encode3/encode3Valid.o estOrientInfo.o expData.o exportedDataHubs.o expRecord.o facetField.o facetedTable.o featureBits.o findKGAlias.o fakeCurl.o findKGProtAlias.o gbSeq.o gbExtFile.o gcPercent.o genark.o genbank.o genbankBlackList.o gencodeTracksCommon.o gencodeAttrs.o gencodeToRefSeq.o geneGraph.o genePred.o genePredReader.o geoMirror.o ggCluster.o ggDump.o ggGraph.o ggMrnaAli.o ggTypes.o glDbRep.o googleAnalytics.o gpFx.o grp.o gtexAse.o gtexDonor.o gtexGeneBed.o gtexInfo.o gtexSample.o gtexSampleData.o gtexTissue.o gtexTissueMedian.o gtexUi.o hCommon.o hPrint.o hVarSubst.o hapmapAllelesOrtho.o hapmapPhaseIIISummary.o hapmapSnps.o hdb.o hgColors.o hgConfig.o hgFind.o hgFindSpec.o hgFindSpecCustom.o hgHgvs.o hgHgvsParse.o hgMaf.o hgRelate.o hic.o hicUi.o hubConnect.o hubPublic.o hubSearchText.o hubSpace.o hubSpaceKeys.o hubSpaceQuotas.o hui.o imageClone.o indelShift.o interact.o interactUi.o itemAttr.o jksql.o joiner.o jsHelper.o kgAlias.o kgProtAlias.o kgXref.o knownInfo.o knownMore.o lav.o lfs.o liftOver.o liftOverChain.o liftUp.o longRange.o lrg.o lsSnpPdb.o mafFrames.o mafGene.o mafSummary.o makeItemsItem.o mdb.o microarray.o minChromSize.o namedSessionDb.o netAlign.o netCart.o pepPred.o pgPhenoAssoc.o pgSnp.o pslReader.o qaSeq.o quickLift.o quickLiftChain.o rankProp.o refLink.o refSeqStatus.o rikenCluster.o rmskAlign.o rmskJoined.o rmskOut.o rmskOut2.o rnaGene.o sage.o sageCounts.o samAlignment.o sample.o sanger22extra.o scoredRef.o sessionData.o seqWindow.o snakeUi.o snp.o snpExceptions.o soTerm.o spDb.o sqlProg.o sqlSanity.o stanMad.o stsAlias.o stsInfo2.o stsMap.o stsMarker.o tableStatus.o tablesTables.o tagRepo.o tfbsCons.o tigrCmrGene.o traceInfo.o trackDb.o trackDbCache.o trackDbCustom.o trackHub.o trackVersion.o trashDir.o txAliDiff.o txCluster.o txCommon.o txEdgeBed.o txGraph.o txInfo.o txRnaAccs.o userdata.o variantProjector.o vcfUi.o vegaInfo.o web.o wigAsciiToBinary.o wigDataStream.o wiggle.o wiggleCart.o wiggleUtils.o wikiLink.o wikiTrack.o bigRmskAlignBed.o bigRmskBed.o make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/lib' if test -d affyTransciptome ; then cd affyTransciptome && echo affyTransciptome && make ; fi affyTransciptome make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/affyTransciptome' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -Wimplicit -I../inc -I../../inc -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/affyPairsToSample affyPairsToSample.c ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lmariadb -lz -lpthread -lm -lssl -lcrypto gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -Wimplicit -I../inc -I../../inc -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/normalizeSampleFile normalizeSampleFile.c ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lmariadb -lz -lpthread -lm -lssl -lcrypto gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -Wimplicit -I../inc -I../../inc -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/avgTranscriptomeExps avgTranscriptomeExps.c ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lmariadb -lz -lpthread -lm -lssl -lcrypto gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -Wimplicit -I../inc -I../../inc -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/maxTranscriptomeExps maxTranscriptomeExps.c ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lmariadb -lz -lpthread -lm -lssl -lcrypto gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -Wimplicit -I../inc -I../../inc -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/scaleSampleFiles scaleSampleFiles.c ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lmariadb -lz -lpthread -lm -lssl -lcrypto gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -Wimplicit -I../inc -I../../inc -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/averageZoomLevels averageZoomLevels.c ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lmariadb -lz -lpthread -lm -lssl -lcrypto gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -Wimplicit -I../inc -I../../inc -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/groupSamples groupSamples.c ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lmariadb -lz -lpthread -lm -lssl -lcrypto make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/affyTransciptome' if test -d agpCloneCheck ; then cd agpCloneCheck && echo agpCloneCheck && make ; fi agpCloneCheck make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/agpCloneCheck' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o agpCloneCheck.o -c agpCloneCheck.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/agpCloneCheck agpCloneCheck.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/agpCloneCheck make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/agpCloneCheck' if test -d agpCloneList ; then cd agpCloneList && echo agpCloneList && make ; fi agpCloneList make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/agpCloneList' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o agpCloneList.o -c agpCloneList.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/agpCloneList agpCloneList.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/agpCloneList make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/agpCloneList' if test -d agpAllToFaFile ; then cd agpAllToFaFile && echo agpAllToFaFile && make ; fi agpAllToFaFile make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/agpAllToFaFile' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o agpAllToFaFile.o -c agpAllToFaFile.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/agpAllToFaFile agpAllToFaFile.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/agpAllToFaFile make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/agpAllToFaFile' if test -d agpMergeChromScaf ; then cd agpMergeChromScaf && echo agpMergeChromScaf && make ; fi agpMergeChromScaf make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/agpMergeChromScaf' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o agpMergeChromScaf.o -c agpMergeChromScaf.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/agpMergeChromScaf \ agpMergeChromScaf.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm agpMergeChromScaf.c: In function ‘agpMergeChromScaf’: agpMergeChromScaf.c:149:12: warning: ‘gap’ may be used uninitialized [-Wmaybe-uninitialized] 149 | gap->chromStart += 1; | ^ agpMergeChromScaf.c:59:16: note: ‘gap’ was declared here 59 | struct agpGap *gap; | ^ true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/agpMergeChromScaf make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/agpMergeChromScaf' if test -d agpToFa ; then cd agpToFa && echo agpToFa && make ; fi agpToFa make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/agpToFa' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o agpToFa.o -c agpToFa.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/agpToFa agpToFa.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/agpToFa make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/agpToFa' if test -d agpToGl ; then cd agpToGl && echo agpToGl && make ; fi agpToGl make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/agpToGl' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o agpToGl.o -c agpToGl.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/agpToGl agpToGl.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/agpToGl make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/agpToGl' if test -d altSplice ; then cd altSplice && echo altSplice && make ; fi altSplice make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/altSplice' cd lib && make make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/altSplice/lib' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o spliceGraph.o -c spliceGraph.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o exonGraph.o -c exonGraph.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o heap.o -c heap.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o altSpliceSite.o -c altSpliceSite.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o pfamDat.o -c pfamDat.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o affyProbe.o -c affyProbe.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o altProbe.o -c altProbe.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o dMatrix.o -c dMatrix.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o splice.o -c splice.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o mouseAPSetEventMap.o -c mouseAPSetEventMap.c ar rcu ./x86_64/libSpliceGraph.a spliceGraph.o exonGraph.o heap.o altSpliceSite.o pfamDat.o affyProbe.o altProbe.o dMatrix.o splice.o mouseAPSetEventMap.o ranlib ./x86_64/libSpliceGraph.a make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/altSplice/lib' cd altSplice && make make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/altSplice/altSplice' gcc -O -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 \ -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/sequenceForBed sequenceForBed.c ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a ../lib/x86_64/libSpliceGraph.a -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lmariadb -lz -lpthread -lm -lssl -lcrypto gcc -O -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 \ -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/altAnalysis altAnalysis.c ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a ../lib/x86_64/libSpliceGraph.a -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lmariadb -lz -lpthread -lm -lssl -lcrypto gcc -O -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 \ -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/altSplice altSplice.c ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a ../lib/x86_64/libSpliceGraph.a -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lmariadb -lz -lpthread -lm -lssl -lcrypto altSplice.c: In function ‘convertBedsToGps’: altSplice.c:784:20: warning: the comparison will always evaluate as ‘false’ for the address of ‘strand’ will never be NULL [-Waddress] 784 | if(bedList->strand == NULL) | ^~ In file included from ../../inc/genePred.h:12, from ../../inc/bed.h:18, from ../../inc/altGraphX.h:16, from altSplice.c:62: ../../../inc/basicBed.h:28:10: note: ‘strand’ declared here 28 | char strand[2]; /* + or -. */ | ^~~~~~ gcc -O -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 \ -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/orthoSplice orthoSplice.c ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a ../lib/x86_64/libSpliceGraph.a -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lmariadb -lz -lpthread -lm -lssl -lcrypto gcc -O -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 \ -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/agxToBed agxToBed.c ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a ../lib/x86_64/libSpliceGraph.a -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lmariadb -lz -lpthread -lm -lssl -lcrypto gcc -O -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 \ -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/altSummary altSummary.c ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a ../lib/x86_64/libSpliceGraph.a -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lmariadb -lz -lpthread -lm -lssl -lcrypto gcc -O -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 \ -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bedInGraph bedInGraph.c ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a ../lib/x86_64/libSpliceGraph.a -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lmariadb -lz -lpthread -lm -lssl -lcrypto gcc -O -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 \ -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/consForBed consForBed.c ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a ../lib/x86_64/libSpliceGraph.a -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lmariadb -lz -lpthread -lm -lssl -lcrypto gcc -O -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 \ -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/altPaths altPaths.c ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a ../lib/x86_64/libSpliceGraph.a -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lmariadb -lz -lpthread -lm -lssl -lcrypto gcc -O -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 \ -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bedToExons bedToExons.c ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a ../lib/x86_64/libSpliceGraph.a -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lmariadb -lz -lpthread -lm -lssl -lcrypto gcc -O -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 \ -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/genePredToPsl genePredToPsl.c ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a ../lib/x86_64/libSpliceGraph.a -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lmariadb -lz -lpthread -lm -lssl -lcrypto make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/altSplice/altSplice' make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/altSplice' if test -d bedOrBlocks ; then cd bedOrBlocks && echo bedOrBlocks && make ; fi bedOrBlocks make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/bedOrBlocks' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o bedOrBlocks.o -c bedOrBlocks.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bedOrBlocks bedOrBlocks.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bedOrBlocks make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/bedOrBlocks' if test -d bedSplitOnChrom ; then cd bedSplitOnChrom && echo bedSplitOnChrom && make ; fi bedSplitOnChrom make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/bedSplitOnChrom' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o bedSplitOnChrom.o -c bedSplitOnChrom.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bedSplitOnChrom bedSplitOnChrom.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bedSplitOnChrom make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/bedSplitOnChrom' if test -d borfBig ; then cd borfBig && echo borfBig && make ; fi borfBig make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/borfBig' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o borfBig.o -c borfBig.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/borfBig borfBig.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/borfBig make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/borfBig' if test -d ctgFaToFa ; then cd ctgFaToFa && echo ctgFaToFa && make ; fi ctgFaToFa make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/ctgFaToFa' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o ctgFaToFa.o -c ctgFaToFa.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/ctgFaToFa ctgFaToFa.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/ctgFaToFa make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/ctgFaToFa' if test -d ctgToChromFa ; then cd ctgToChromFa && echo ctgToChromFa && make ; fi ctgToChromFa make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/ctgToChromFa' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o ctgToChromFa.o -c ctgToChromFa.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/ctgToChromFa ctgToChromFa.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/ctgToChromFa make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/ctgToChromFa' if test -d embossToPsl ; then cd embossToPsl && echo embossToPsl && make ; fi embossToPsl make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/embossToPsl' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o embossToPsl.o -c embossToPsl.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/embossToPsl embossToPsl.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/embossToPsl make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/embossToPsl' if test -d fakeFinContigs ; then cd fakeFinContigs && echo fakeFinContigs && make ; fi fakeFinContigs make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/fakeFinContigs' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o fakeFinContigs.o -c fakeFinContigs.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/fakeFinContigs fakeFinContigs.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/fakeFinContigs make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/fakeFinContigs' if test -d fakeOut ; then cd fakeOut && echo fakeOut && make ; fi fakeOut make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/fakeOut' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o fakeOut.o -c fakeOut.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/fakeOut fakeOut.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/fakeOut make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/fakeOut' if test -d ffaToFa ; then cd ffaToFa && echo ffaToFa && make ; fi ffaToFa make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/ffaToFa' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o ffaToFa.o -c ffaToFa.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/ffaToFa ffaToFa.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/ffaToFa make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/ffaToFa' if test -d fishClones ; then cd fishClones && echo fishClones && make ; fi fishClones make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/fishClones' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o fishClones.o -c fishClones.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/fishClones fishClones.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/fishClones make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/fishClones' if test -d fqToQa ; then cd fqToQa && echo fqToQa && make ; fi fqToQa make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/fqToQa' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o fqToQa.o -c fqToQa.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/fqToQa fqToQa.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/fqToQa make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/fqToQa' if test -d fqToQac ; then cd fqToQac && echo fqToQac && make ; fi fqToQac make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/fqToQac' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o fqToQac.o -c fqToQac.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/fqToQac fqToQac.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/fqToQac make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/fqToQac' if test -d fragPart ; then cd fragPart && echo fragPart && make ; fi fragPart make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/fragPart' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o fragPart.o -c fragPart.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/fragPart fragPart.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/fragPart make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/fragPart' if test -d gbGetEntries ; then cd gbGetEntries && echo gbGetEntries && make ; fi gbGetEntries make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/gbGetEntries' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o gbGetEntries.o -c gbGetEntries.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/gbGetEntries gbGetEntries.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/gbGetEntries make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/gbGetEntries' if test -d gbOneAcc ; then cd gbOneAcc && echo gbOneAcc && make ; fi gbOneAcc make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/gbOneAcc' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o gbOneAcc.o -c gbOneAcc.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/gbOneAcc gbOneAcc.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/gbOneAcc make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/gbOneAcc' if test -d gbToFaRa ; then cd gbToFaRa && echo gbToFaRa && make ; fi gbToFaRa make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/gbToFaRa' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o gbToFaRa.o -c gbToFaRa.c gbToFaRa.c: In function ‘procOneGbFile’: gbToFaRa.c:1394:25: warning: ‘strncpy’ specified bound 32 equals destination size [-Wstringop-truncation] 1394 | strncpy(ae->accession, accession, sizeof(ae->accession)); | ^ gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/gbToFaRa gbToFaRa.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/gbToFaRa make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/gbToFaRa' if test -d geneBounds ; then cd geneBounds && echo geneBounds && make ; fi geneBounds make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds' cd lib && make make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/lib' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o improbRunInfo.o -c improbRunInfo.c echo all done in hg/geneBounds/lib/ all done in hg/geneBounds/lib/ make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/lib' cd assessLibs && echo assessLibs && make assessLibs make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/assessLibs' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o assessLibs.o -c assessLibs.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/assessLibs assessLibs.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/assessLibs make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/assessLibs' cd averagExp && echo averagExp && make averagExp make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/averagExp' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o averagExp.o -c averagExp.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/averagExp averagExp.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/averagExp make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/averagExp' cd axtForEst && echo axtForEst && make axtForEst make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/axtForEst' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o axtForEst.o -c axtForEst.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/axtForEst axtForEst.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/axtForEst make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/axtForEst' cd bedCons && echo bedCons && make bedCons make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/bedCons' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o bedCons.o -c bedCons.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bedCons bedCons.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bedCons make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/bedCons' cd checkableBorf && echo checkableBorf && make checkableBorf make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/checkableBorf' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o checkableBorf.o -c checkableBorf.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/checkableBorf checkableBorf.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/checkableBorf make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/checkableBorf' cd clusterGenes && echo clusterGenes && make clusterGenes make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/clusterGenes' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o clusterGenes.o -c clusterGenes.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/clusterGenes clusterGenes.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/clusterGenes make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/clusterGenes' cd clusterPsl && echo clusterPsl && make clusterPsl make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/clusterPsl' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o clusterPsl.o -c clusterPsl.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/clusterPsl clusterPsl.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/clusterPsl make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/clusterPsl' cd clusterRna && echo clusterRna && make clusterRna make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/clusterRna' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o clusterRna.o -c clusterRna.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/clusterRna clusterRna.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/clusterRna make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/clusterRna' cd dnaMotifFind && echo dnaMotifFind && make dnaMotifFind make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/dnaMotifFind' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o dnaMotifFind.o -c dnaMotifFind.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/dnaMotifFind dnaMotifFind.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/dnaMotifFind make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/dnaMotifFind' cd eisenInput && echo eisenInput && make eisenInput make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/eisenInput' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o eisenInput.o -c eisenInput.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/eisenInput eisenInput.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/eisenInput make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/eisenInput' cd emblMatrixToMotif && echo emblMatrixToMotif && make emblMatrixToMotif make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/emblMatrixToMotif' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o emblMatrixToMotif.o -c emblMatrixToMotif.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/emblMatrixToMotif emblMatrixToMotif.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/emblMatrixToMotif make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/emblMatrixToMotif' cd estLibStats && echo estLibStats && make estLibStats make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/estLibStats' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o estLibStats.o -c estLibStats.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/estLibStats estLibStats.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/estLibStats make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/estLibStats' cd expToRna && echo expToRna && make expToRna make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/expToRna' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o expToRna.o -c expToRna.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/expToRna expToRna.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/expToRna make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/expToRna' cd iriToControlTable && echo iriToControlTable && make iriToControlTable make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/iriToControlTable' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o iriToControlTable.o -c iriToControlTable.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/iriToControlTable iriToControlTable.o ../lib/improbRunInfo.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/iriToControlTable make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/iriToControlTable' cd iriToDnaMotif && echo iriToDnaMotif && make iriToDnaMotif make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/iriToDnaMotif' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o iriToDnaMotif.o -c iriToDnaMotif.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/iriToDnaMotif iriToDnaMotif.o ../lib/improbRunInfo.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/iriToDnaMotif make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/iriToDnaMotif' cd liftPromoHits && echo liftPromoHits && make liftPromoHits make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/liftPromoHits' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o liftPromoHits.o -c liftPromoHits.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/liftPromoHits liftPromoHits.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/liftPromoHits make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/liftPromoHits' cd motifLogo && echo motifLogo && make motifLogo make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/motifLogo' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o motifLogo.o -c motifLogo.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/motifLogo motifLogo.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/motifLogo make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/motifLogo' cd motifSig && echo motifSig && make motifSig make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/motifSig' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o motifSig.o -c motifSig.c motifSig.c: In function ‘readMotif’: motifSig.c:73:1: warning: ‘strncpy’ specified bound 257 equals destination size [-Wstringop-truncation] 73 | strncpy(m->consensus, words[5], sizeof(m->consensus)); | ^ gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/motifSig motifSig.o ../lib/improbRunInfo.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/motifSig make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/motifSig' cd orf && echo orf && make orf make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/orf' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o orf.o -c orf.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/orf orf.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/orf make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/orf' cd orfStats && echo orfStats && make orfStats make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/orfStats' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o orfStats.o -c orfStats.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/orfStats orfStats.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/orfStats make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/orfStats' cd polyInfo && echo polyInfo && make polyInfo make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/polyInfo' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o polyInfo.o -c polyInfo.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/polyInfo polyInfo.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/polyInfo make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/polyInfo' cd promoSeqFromCluster && echo promoSeqFromCluster && make promoSeqFromCluster make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/promoSeqFromCluster' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o promoSeqFromCluster.o -c promoSeqFromCluster.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/promoSeqFromCluster promoSeqFromCluster.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/promoSeqFromCluster make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/promoSeqFromCluster' cd raToCds && echo raToCds && make raToCds make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/raToCds' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o raToCds.o -c raToCds.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/raToCds raToCds.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/raToCds make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/raToCds' cd twinOrf && echo twinOrf && make twinOrf make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/twinOrf' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o twinOrf.o -c twinOrf.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/twinOrf twinOrf.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/twinOrf make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/twinOrf' cd twinOrf2 && echo twinOrf2 && make twinOrf2 make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/twinOrf2' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o twinOrf2.o -c twinOrf2.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/twinOrf2 twinOrf2.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/twinOrf2 make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/twinOrf2' cd twinOrf3 && echo twinOrf3 && make twinOrf3 make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/twinOrf3' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o twinOrf3.o -c twinOrf3.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/twinOrf3 twinOrf3.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/twinOrf3 make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/twinOrf3' cd twinOrfStats && echo twinOrfStats && make twinOrfStats make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/twinOrfStats' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o twinOrfStats.o -c twinOrfStats.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/twinOrfStats twinOrfStats.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/twinOrfStats make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/twinOrfStats' cd twinOrfStats2 && echo twinOrfStats2 && make twinOrfStats2 make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/twinOrfStats2' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o twinOrfStats2.o -c twinOrfStats2.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/twinOrfStats2 twinOrfStats2.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/twinOrfStats2 make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/twinOrfStats2' cd twinOrfStats3 && echo twinOrfStats3 && make twinOrfStats3 make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/twinOrfStats3' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o twinOrfStats3.o -c twinOrfStats3.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/twinOrfStats3 twinOrfStats3.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/twinOrfStats3 make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/twinOrfStats3' make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds' if test -d getFeatDna ; then cd getFeatDna && echo getFeatDna && make ; fi getFeatDna make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/getFeatDna' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o getFeatDna.o -c getFeatDna.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/getFeatDna getFeatDna.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/getFeatDna make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/getFeatDna' if test -d gpStats ; then cd gpStats && echo gpStats && make ; fi gpStats make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/gpStats' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o gpStats.o -c gpStats.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/gpStats gpStats.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/gpStats make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/gpStats' if test -d gpToGtf ; then cd gpToGtf && echo gpToGtf && make ; fi gpToGtf make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/gpToGtf' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o gpToGtf.o -c gpToGtf.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/gpToGtf gpToGtf.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/gpToGtf make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/gpToGtf' if test -d gpcrParser ; then cd gpcrParser && echo gpcrParser && make ; fi gpcrParser make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/gpcrParser' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o gpcrParser.o -c gpcrParser.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/gpcrParser gpcrParser.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/gpcrParser make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/gpcrParser' if test -d gsBig ; then cd gsBig && echo gsBig && make ; fi gsBig make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/gsBig' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o gsBig.o -c gsBig.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/gsBig gsBig.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/gsBig make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/gsBig' if test -d hgTablesTest ; then cd hgTablesTest && echo hgTablesTest && make ; fi if test -d hgChroms ; then cd hgChroms && echo hgChroms && make ; fi hgChroms make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/hgChroms' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o hgChroms.o -c hgChroms.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgChroms hgChroms.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgChroms make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/hgChroms' if test -d hgGetAnn ; then cd hgGetAnn && echo hgGetAnn && make ; fi hgGetAnn make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/hgGetAnn' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o hgGetAnn.o -c hgGetAnn.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgGetAnn hgGetAnn.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgGetAnn make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/hgGetAnn' if test -d hgKnownGeneList ; then cd hgKnownGeneList && echo hgKnownGeneList && make ; fi hgKnownGeneList make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/hgKnownGeneList' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o hgKnownGeneList.o -c hgKnownGeneList.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgKnownGeneList hgKnownGeneList.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgKnownGeneList make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/hgKnownGeneList' if test -d hgSelect ; then cd hgSelect && echo hgSelect && make ; fi hgSelect make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/hgSelect' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o hgSelect.o -c hgSelect.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgSelect hgSelect.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgSelect make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/hgSelect' if test -d hgsqladmin ; then cd hgsqladmin && echo hgsqladmin && make ; fi hgsqladmin make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/hgsqladmin' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o hgsqladmin.o -c hgsqladmin.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgsqladmin hgsqladmin.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgsqladmin make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/hgsqladmin' if test -d hgsqlimport ; then cd hgsqlimport && echo hgsqlimport && make ; fi hgsqlimport make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/hgsqlimport' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o hgsqlimport.o -c hgsqlimport.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgsqlimport hgsqlimport.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgsqlimport make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/hgsqlimport' if test -d hgsqlSwapTables ; then cd hgsqlSwapTables && echo hgsqlSwapTables && make ; fi hgsqlSwapTables make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/hgsqlSwapTables' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o hgsqlSwapTables.o -c hgsqlSwapTables.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgsqlSwapTables hgsqlSwapTables.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgsqlSwapTables make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/hgsqlSwapTables' if test -d hgsqlTableDate ; then cd hgsqlTableDate && echo hgsqlTableDate && make ; fi hgsqlTableDate make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/hgsqlTableDate' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o hgsqlTableDate.o -c hgsqlTableDate.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgsqlTableDate hgsqlTableDate.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgsqlTableDate make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/hgsqlTableDate' if test -d intronEnds ; then cd intronEnds && echo intronEnds && make ; fi intronEnds make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/intronEnds' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o intronEnds.o -c intronEnds.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/intronEnds intronEnds.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/intronEnds make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/intronEnds' if test -d lib ; then cd lib && echo lib && make ; fi lib make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/lib' mkdir -p ../../lib/x86_64 ar rcus ../../lib/x86_64/jkhgap.a adjacency.o affyPairs.o agpFrag.o agpGap.o alignSeqSizes.o altGraphX.o asmAlias.o asmEquivalent.o asmSummary.o assemblyList.o autoUpgrade.o axtInfo.o barChartBed.o barChartCategory.o barChartUi.o bed.o bed12Source.o bedDetail.o bedMethyl.o bigBedFind.o bigBedLabel.o bigChain.o bigDbSnp.o bigGenePred.o bigLink.o bigPsl.o blastTab.o borf.o botDelay.o cart.o cartDb.o cartTrackDb.o cdsEvidence.o cdsOrtho.o cdsPick.o cgapSage/cgapSage.o cgapSage/cgapSageLib.o cgiApoptosis.o chainCart.o chainDb.o chainLink.o chainNet.o chainNetDbLoad.o chromAlias.o chromBins.o chromGraph.o chromGraphFactory.o chromInfo.o chromInserts.o chromKeeper.o clonePos.o cpgIsland.o ctgPos.o customAdjacency.o customComposite.o customFactory.o customPp.o customTrack.o cv.o cytoBand.o dbDb.o decoration.o decoratorUi.o defaultDb.o dnaMotifSql.o dupTrack.o encode/encodeErge.o encode/encodeErgeHssCellLines.o encode/encodeExp.o encode/encodeHapMapAlleleFreq.o encode/encodeIndels.o encode/encodePeak.o encode/encodeRegionInfoCustom.o encode/encodeRna.o encode/encodeStanfordPromoters.o encode/encodeStanfordPromotersAverage.o encode/peptideMapping.o encode/wgEncodeGencodeAnnotationRemark.o encode/wgEncodeGencodeAttrs.o encode/wgEncodeGencodeEntrezGene.o encode/wgEncodeGencodeExonSupport.o encode/wgEncodeGencodeGeneSource.o encode/wgEncodeGencodeGeneSymbol.o encode/wgEncodeGencodePdb.o encode/wgEncodeGencodePubMed.o encode/wgEncodeGencodeRefSeq.o encode/wgEncodeGencodeTag.o encode/wgEncodeGencodeTranscriptSource.o encode/wgEncodeGencodeTranscriptSupport.o encode/wgEncodeGencodeTranscriptionSupportLevel.o encode/wgEncodeGencodeUniProt.o encode3/encode3Valid.o estOrientInfo.o expData.o exportedDataHubs.o expRecord.o facetField.o facetedTable.o featureBits.o findKGAlias.o fakeCurl.o findKGProtAlias.o gbSeq.o gbExtFile.o gcPercent.o genark.o genbank.o genbankBlackList.o gencodeTracksCommon.o gencodeAttrs.o gencodeToRefSeq.o geneGraph.o genePred.o genePredReader.o geoMirror.o ggCluster.o ggDump.o ggGraph.o ggMrnaAli.o ggTypes.o glDbRep.o googleAnalytics.o gpFx.o grp.o gtexAse.o gtexDonor.o gtexGeneBed.o gtexInfo.o gtexSample.o gtexSampleData.o gtexTissue.o gtexTissueMedian.o gtexUi.o hCommon.o hPrint.o hVarSubst.o hapmapAllelesOrtho.o hapmapPhaseIIISummary.o hapmapSnps.o hdb.o hgColors.o hgConfig.o hgFind.o hgFindSpec.o hgFindSpecCustom.o hgHgvs.o hgHgvsParse.o hgMaf.o hgRelate.o hic.o hicUi.o hubConnect.o hubPublic.o hubSearchText.o hubSpace.o hubSpaceKeys.o hubSpaceQuotas.o hui.o imageClone.o indelShift.o interact.o interactUi.o itemAttr.o jksql.o joiner.o jsHelper.o kgAlias.o kgProtAlias.o kgXref.o knownInfo.o knownMore.o lav.o lfs.o liftOver.o liftOverChain.o liftUp.o longRange.o lrg.o lsSnpPdb.o mafFrames.o mafGene.o mafSummary.o makeItemsItem.o mdb.o microarray.o minChromSize.o namedSessionDb.o netAlign.o netCart.o pepPred.o pgPhenoAssoc.o pgSnp.o pslReader.o qaSeq.o quickLift.o quickLiftChain.o rankProp.o refLink.o refSeqStatus.o rikenCluster.o rmskAlign.o rmskJoined.o rmskOut.o rmskOut2.o rnaGene.o sage.o sageCounts.o samAlignment.o sample.o sanger22extra.o scoredRef.o sessionData.o seqWindow.o snakeUi.o snp.o snpExceptions.o soTerm.o spDb.o sqlProg.o sqlSanity.o stanMad.o stsAlias.o stsInfo2.o stsMap.o stsMarker.o tableStatus.o tablesTables.o tagRepo.o tfbsCons.o tigrCmrGene.o traceInfo.o trackDb.o trackDbCache.o trackDbCustom.o trackHub.o trackVersion.o trashDir.o txAliDiff.o txCluster.o txCommon.o txEdgeBed.o txGraph.o txInfo.o txRnaAccs.o userdata.o variantProjector.o vcfUi.o vegaInfo.o web.o wigAsciiToBinary.o wigDataStream.o wiggle.o wiggleCart.o wiggleUtils.o wikiLink.o wikiTrack.o bigRmskAlignBed.o bigRmskBed.o make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/lib' if test -d liftAcross ; then cd liftAcross && echo liftAcross && make ; fi liftAcross make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/liftAcross' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o liftAcross.o -c liftAcross.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/liftAcross liftAcross.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/liftAcross make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/liftAcross' if test -d liftAgp ; then cd liftAgp && echo liftAgp && make ; fi liftAgp make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/liftAgp' gcc -O -g -I../inc -I../../inc -o liftAgp liftAgp.c ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lmariadb -lz -lpthread -lm -lssl -lcrypto -lm mv liftAgp /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/ make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/liftAgp' if test -d liftFrags ; then cd liftFrags && echo liftFrags && make ; fi liftFrags make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/liftFrags' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o liftFrags.o -c liftFrags.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/liftFrags liftFrags.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/liftFrags make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/liftFrags' if test -d lfsOverlap ; then cd lfsOverlap && echo lfsOverlap && make ; fi lfsOverlap make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/lfsOverlap' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o lfsOverlap.o -c lfsOverlap.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/lfsOverlap lfsOverlap.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/lfsOverlap make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/lfsOverlap' if test -d makeDb ; then cd makeDb && echo makeDb && make ; fi makeDb make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb' cd hgAar && echo hgAar && make hgAar make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgAar' rm -f /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/aarToAxt cp -f aarToAxt /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/aarToAxt make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgAar' cd hgAddLiftOverChain && echo hgAddLiftOverChain && make hgAddLiftOverChain make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgAddLiftOverChain' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hgAddLiftOverChain.o -c hgAddLiftOverChain.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgAddLiftOverChain hgAddLiftOverChain.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgAddLiftOverChain make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgAddLiftOverChain' cd hgClonePos && echo hgClonePos && make hgClonePos make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgClonePos' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hgClonePos.o -c hgClonePos.c hgClonePos.c: In function ‘addStageInfo’: hgClonePos.c:182:8: warning: ‘strncpy’ specified bound 256 equals destination size [-Wstringop-truncation] 182 | strncpy(cloneName, words[1], sizeof(cloneName)); | ^ gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o gsSeqInfo.o -c gsSeqInfo.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgClonePos hgClonePos.o gsSeqInfo.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgClonePos make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgClonePos' cd hgCountAlign && echo hgCountAlign && make hgCountAlign make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgCountAlign' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hgCountAlign.o -c hgCountAlign.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o align.o -c align.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o slidingWin.o -c slidingWin.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o winCounts.o -c winCounts.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgCountAlign hgCountAlign.o align.o slidingWin.o winCounts.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgCountAlign make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgCountAlign' cd hgCtgPos && echo hgCtgPos && make hgCtgPos make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgCtgPos' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hgCtgPos.o -c hgCtgPos.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o liftSpec.o -c liftSpec.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgCtgPos hgCtgPos.o liftSpec.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgCtgPos make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgCtgPos' cd hgDeleteChrom && echo hgDeleteChrom && make hgDeleteChrom make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgDeleteChrom' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hgDeleteChrom.o -c hgDeleteChrom.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgDeleteChrom hgDeleteChrom.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgDeleteChrom make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgDeleteChrom' cd hgExperiment && echo hgExperiment && make hgExperiment make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgExperiment' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hgExperiment.o -c hgExperiment.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgExperiment hgExperiment.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgExperiment make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgExperiment' cd hgExtFileCheck && echo hgExtFileCheck && make hgExtFileCheck make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgExtFileCheck' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hgExtFileCheck.o -c hgExtFileCheck.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgExtFileCheck hgExtFileCheck.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgExtFileCheck make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgExtFileCheck' cd hgFakeAgp && echo hgFakeAgp && make hgFakeAgp make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgFakeAgp' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hgFakeAgp.o -c hgFakeAgp.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgFakeAgp hgFakeAgp.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgFakeAgp make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgFakeAgp' cd hgGeneBands && echo hgGeneBands && make hgGeneBands make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgGeneBands' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hgGeneBands.o -c hgGeneBands.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgGeneBands hgGeneBands.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgGeneBands make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgGeneBands' cd hgGenericMicroarray && echo hgGenericMicroarray && make hgGenericMicroarray make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgGenericMicroarray' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hgGenericMicroarray.o -c hgGenericMicroarray.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgGenericMicroarray hgGenericMicroarray.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgGenericMicroarray make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgGenericMicroarray' cd hgPar && echo hgPar && make hgPar make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgPar' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hgPar.o -c hgPar.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o parSpec.o -c parSpec.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgPar hgPar.o parSpec.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lmariadb -lz -lpthread -lm -lssl -lcrypto -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgPar make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgPar' cd hgKgGetText && echo hgKgGetText && make hgKgGetText make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgKgGetText' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hgKgGetText.o -c hgKgGetText.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgKgGetText hgKgGetText.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgKgGetText make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgKgGetText' cd hgKgMrna && echo hgKgMrna && make hgKgMrna make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgKgMrna' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hgKgMrna.o -c hgKgMrna.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgKgMrna hgKgMrna.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgKgMrna make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgKgMrna' cd hgKnownMore && echo hgKnownMore && make hgKnownMore make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgKnownMore' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hgKnownMore.o -c hgKnownMore.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hugoMulti.o -c hugoMulti.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgKnownMore hgKnownMore.o hugoMulti.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgKnownMore make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgKnownMore' cd hgKnownMore.oo21 && echo hgKnownMore.oo21 && make hgKnownMore.oo21 make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgKnownMore.oo21' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hgKnownMore.o -c hgKnownMore.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hugoMulti.o -c hugoMulti.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgKnownMore hgKnownMore.o hugoMulti.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgKnownMore make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgKnownMore.oo21' cd hgLoadBlastTab && echo hgLoadBlastTab && make hgLoadBlastTab make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgLoadBlastTab' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hgLoadBlastTab.o -c hgLoadBlastTab.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgLoadBlastTab hgLoadBlastTab.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgLoadBlastTab make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgLoadBlastTab' cd hgLoadChromGraph && echo hgLoadChromGraph && make hgLoadChromGraph make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgLoadChromGraph' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hgLoadChromGraph.o -c hgLoadChromGraph.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgLoadChromGraph hgLoadChromGraph.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgLoadChromGraph make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgLoadChromGraph' cd hgLoadGenePred && echo hgLoadGenePred && make hgLoadGenePred make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgLoadGenePred' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hgLoadGenePred.o -c hgLoadGenePred.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgLoadGenePred hgLoadGenePred.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgLoadGenePred make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgLoadGenePred' cd hgLoadItemAttr && echo hgLoadItemAttr && make hgLoadItemAttr make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgLoadItemAttr' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hgLoadItemAttr.o -c hgLoadItemAttr.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgLoadItemAttr hgLoadItemAttr.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgLoadItemAttr make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgLoadItemAttr' cd hgLoadMafFrames && echo hgLoadMafFrames && make hgLoadMafFrames make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgLoadMafFrames' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hgLoadMafFrames.o -c hgLoadMafFrames.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgLoadMafFrames hgLoadMafFrames.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgLoadMafFrames make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgLoadMafFrames' cd hgLoadPsl && echo hgLoadPsl && make hgLoadPsl make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgLoadPsl' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hgLoadPsl.o -c hgLoadPsl.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgLoadPsl hgLoadPsl.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgLoadPsl make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgLoadPsl' cd hgLoadSeq && echo hgLoadSeq && make hgLoadSeq make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgLoadSeq' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hgLoadSeq.o -c hgLoadSeq.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgLoadSeq hgLoadSeq.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgLoadSeq make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgLoadSeq' cd hgLoadSample && echo hgLoadSample && make hgLoadSample make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgLoadSample' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hgLoadSample.o -c hgLoadSample.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgLoadSample hgLoadSample.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgLoadSample make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgLoadSample' cd hgLoadSqlTab && echo hgLoadSqlTab && make hgLoadSqlTab make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgLoadSqlTab' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hgLoadSqlTab.o -c hgLoadSqlTab.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgLoadSqlTab hgLoadSqlTab.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgLoadSqlTab make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgLoadSqlTab' cd hgMapMicroarray && echo hgMapMicroarray && make hgMapMicroarray make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgMapMicroarray' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hgMapMicroarray.o -c hgMapMicroarray.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgMapMicroarray hgMapMicroarray.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgMapMicroarray make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgMapMicroarray' cd hgMedianMicroarray && echo hgMedianMicroarray && make hgMedianMicroarray make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgMedianMicroarray' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hgMedianMicroarray.o -c hgMedianMicroarray.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgMedianMicroarray hgMedianMicroarray.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgMedianMicroarray make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgMedianMicroarray' cd hgNibSeq && echo hgNibSeq && make hgNibSeq make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgNibSeq' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hgNibSeq.o -c hgNibSeq.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgNibSeq hgNibSeq.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgNibSeq make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgNibSeq' cd hgPepPred && echo hgPepPred && make hgPepPred make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgPepPred' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hgPepPred.o -c hgPepPred.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgPepPred hgPepPred.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgPepPred make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgPepPred' cd hgRatioMicroarray && echo hgRatioMicroarray && make hgRatioMicroarray make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgRatioMicroarray' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hgRatioMicroarray.o -c hgRatioMicroarray.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgRatioMicroarray hgRatioMicroarray.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgRatioMicroarray make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgRatioMicroarray' cd hgDropSplitTable && echo hgDropSplitTable && make hgDropSplitTable make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgDropSplitTable' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hgDropSplitTable.o -c hgDropSplitTable.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgDropSplitTable hgDropSplitTable.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgDropSplitTable make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgDropSplitTable' cd hgRenameSplitTable && echo hgRenameSplitTable && make hgRenameSplitTable make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgRenameSplitTable' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hgRenameSplitTable.o -c hgRenameSplitTable.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgRenameSplitTable hgRenameSplitTable.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgRenameSplitTable make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgRenameSplitTable' cd hgSanger20 && echo hgSanger20 && make hgSanger20 make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgSanger20' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hgSanger20.o -c hgSanger20.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgSanger20 hgSanger20.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgSanger20 make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgSanger20' cd hgSanger22 && echo hgSanger22 && make hgSanger22 make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgSanger22' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hgSanger22.o -c hgSanger22.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgSanger22 hgSanger22.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgSanger22 make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgSanger22' cd hgStanfordMicroarray && echo hgStanfordMicroarray && make hgStanfordMicroarray make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgStanfordMicroarray' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hgStanfordMicroarray.o -c hgStanfordMicroarray.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgStanfordMicroarray hgStanfordMicroarray.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgStanfordMicroarray make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgStanfordMicroarray' cd hgStsAlias && echo hgStsAlias && make hgStsAlias make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgStsAlias' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hgStsAlias.o -c hgStsAlias.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgStsAlias hgStsAlias.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgStsAlias make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgStsAlias' cd hgStsMarkers && echo hgStsMarkers && make hgStsMarkers make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgStsMarkers' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hgStsMarkers.o -c hgStsMarkers.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgStsMarkers hgStsMarkers.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgStsMarkers make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgStsMarkers' cd hgTomRough && echo hgTomRough && make hgTomRough make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgTomRough' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hgTomRough.o -c hgTomRough.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o tomRough.o -c tomRough.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgTomRough hgTomRough.o tomRough.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lmariadb -lz -lpthread -lm -lssl -lcrypto -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgTomRough make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgTomRough' cd hgTpf && echo hgTpf && make hgTpf make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgTpf' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hgTpf.o -c hgTpf.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgTpf hgTpf.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgTpf make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgTpf' cd hgTraceInfo && echo hgTraceInfo && make hgTraceInfo make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgTraceInfo' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hgTraceInfo.o -c hgTraceInfo.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgTraceInfo hgTraceInfo.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgTraceInfo make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgTraceInfo' cd hgWaba && echo hgWaba && make hgWaba make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgWaba' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hgWaba.o -c hgWaba.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgWaba hgWaba.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgWaba make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgWaba' cd hgMrnaRefseq && echo hgMrnaRefseq && make hgMrnaRefseq make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgMrnaRefseq' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hgMrnaRefseq.o -c hgMrnaRefseq.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgMrnaRefseq hgMrnaRefseq.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgMrnaRefseq make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgMrnaRefseq' cd mdbUpdate && echo mdbUpdate && make mdbUpdate make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/mdbUpdate' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o mdbUpdate.o -c mdbUpdate.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/mdbUpdate mdbUpdate.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm -lmariadb -lz -lpthread -lm -lssl -lcrypto true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/mdbUpdate gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o mdbPrint.o -c mdbPrint.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/mdbPrint mdbPrint.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm -lmariadb -lz -lpthread -lm -lssl -lcrypto true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/mdbPrint make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/mdbUpdate' cd schema && echo schema && make schema make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/schema' ( cd joinerCheck && echo joinerCheck && make ) joinerCheck make[5]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/schema/joinerCheck' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../../htslib -I/usr/include/libpng16 -o joinerCheck.o -c joinerCheck.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/joinerCheck joinerCheck.o ../../../../lib/x86_64/jkhgap.a ../../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/joinerCheck make[5]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/schema/joinerCheck' ( cd joinerRoute && echo joinerRoute && make ) joinerRoute make[5]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/schema/joinerRoute' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../../htslib -I/usr/include/libpng16 -o joinerRoute.o -c joinerRoute.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/joinerRoute joinerRoute.o ../../../../lib/x86_64/jkhgap.a ../../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/joinerRoute make[5]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/schema/joinerRoute' ( cd joinableFields && echo joinableFields && make ) joinableFields make[5]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/schema/joinableFields' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../../htslib -I/usr/include/libpng16 -o joinableFields.o -c joinableFields.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/joinableFields joinableFields.o ../../../../lib/x86_64/jkhgap.a ../../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/joinableFields make[5]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/schema/joinableFields' ( cd makeTableDescriptions && echo makeTableDescriptions && make ) makeTableDescriptions make[5]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/schema/makeTableDescriptions' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../../htslib -I/usr/include/libpng16 -o makeTableDescriptions.o -c makeTableDescriptions.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/makeTableDescriptions makeTableDescriptions.o ../../../../lib/x86_64/jkhgap.a ../../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/makeTableDescriptions make[5]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/schema/makeTableDescriptions' ( cd dbFindFieldsWith && echo dbFindFieldsWith && make ) dbFindFieldsWith make[5]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/schema/dbFindFieldsWith' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../../htslib -I/usr/include/libpng16 -o dbFindFieldsWith.o -c dbFindFieldsWith.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/dbFindFieldsWith dbFindFieldsWith.o ../../../../lib/x86_64/jkhgap.a ../../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/dbFindFieldsWith make[5]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/schema/dbFindFieldsWith' ( cd dbSnoop && echo dbSnoop && make ) dbSnoop make[5]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/schema/dbSnoop' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../../htslib -I/usr/include/libpng16 -o dbSnoop.o -c dbSnoop.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/dbSnoop dbSnoop.o ../../../../lib/x86_64/jkhgap.a ../../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/dbSnoop make[5]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/schema/dbSnoop' make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/schema' cd tfbsConsLoc && echo tfbsConsLoc && make tfbsConsLoc make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/tfbsConsLoc' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o tfbsConsLoc.o -c tfbsConsLoc.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o matt-maf.o -c matt-maf.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o tfbsConsLocUtil.o -c tfbsConsLocUtil.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o seq.o -c seq.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o util.o -c util.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/tfbsConsLoc tfbsConsLoc.o matt-maf.o tfbsConsLocUtil.o seq.o util.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/tfbsConsLoc make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/tfbsConsLoc' cd tfbsConsSort && echo tfbsConsSort && make tfbsConsSort make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/tfbsConsSort' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o tfbsConsSort.o -c tfbsConsSort.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/tfbsConsSort tfbsConsSort.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/tfbsConsSort make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/tfbsConsSort' cd outside && echo outside && make outside make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside' ( cd allenBrain/allenCollectSeq && echo allenBrain/allenCollectSeq && make ) allenBrain/allenCollectSeq make[5]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/allenBrain/allenCollectSeq' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../../../htslib -I/usr/include/libpng16 -o allenCollectSeq.o -c allenCollectSeq.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/allenCollectSeq allenCollectSeq.o ../../../../../lib/x86_64/jkhgap.a ../../../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/allenCollectSeq make[5]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/allenBrain/allenCollectSeq' ( cd exonerateGffDoctor && echo exonerateGffDoctor && make ) exonerateGffDoctor make[5]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/exonerateGffDoctor' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../../htslib -I/usr/include/libpng16 -o exonerateGffDoctor.o -c exonerateGffDoctor.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/exonerateGffDoctor exonerateGffDoctor.o ../../../../lib/x86_64/jkhgap.a ../../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/exonerateGffDoctor make[5]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/exonerateGffDoctor' ( cd hgAvidShortBed && echo hgAvidShortBed && make ) hgAvidShortBed make[5]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/hgAvidShortBed' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../../htslib -I/usr/include/libpng16 -o hgAvidShortBed.o -c hgAvidShortBed.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgAvidShortBed hgAvidShortBed.o ../../../../lib/x86_64/jkhgap.a ../../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgAvidShortBed make[5]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/hgAvidShortBed' ( cd hgBioCyc && echo hgBioCyc && make ) hgBioCyc make[5]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/hgBioCyc' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../../htslib -I/usr/include/libpng16 -o hgBioCyc.o -c hgBioCyc.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgBioCyc hgBioCyc.o ../../../../lib/x86_64/jkhgap.a ../../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgBioCyc make[5]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/hgBioCyc' ( cd hgCGAP && echo hgCGAP && make ) hgCGAP make[5]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/hgCGAP' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../../htslib -I/usr/include/libpng16 -o hgCGAP.o -c hgCGAP.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgCGAP hgCGAP.o ../../../../lib/x86_64/jkhgap.a ../../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgCGAP make[5]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/hgCGAP' ( cd hgExonerate && echo hgExonerate && make ) hgExonerate make[5]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/hgExonerate' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../../htslib -I/usr/include/libpng16 -o hgExonerate.o -c hgExonerate.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgExonerate hgExonerate.o ../../../../lib/x86_64/jkhgap.a ../../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgExonerate make[5]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/hgExonerate' ( cd hgFiberglass && echo hgFiberglass && make ) hgFiberglass make[5]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/hgFiberglass' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../../htslib -I/usr/include/libpng16 -o hgFiberglass.o -c hgFiberglass.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgFiberglass hgFiberglass.o ../../../../lib/x86_64/jkhgap.a ../../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgFiberglass make[5]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/hgFiberglass' ( cd hgFlyBase && echo hgFlyBase && make ) hgFlyBase make[5]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/hgFlyBase' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../../htslib -I/usr/include/libpng16 -o hgFlyBase.o -c hgFlyBase.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgFlyBase hgFlyBase.o ../../../../lib/x86_64/jkhgap.a ../../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgFlyBase make[5]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/hgFlyBase' ( cd hgGnfMicroarray && echo hgGnfMicroarray && make ) hgGnfMicroarray make[5]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/hgGnfMicroarray' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../../htslib -I/usr/include/libpng16 -o hgGnfMicroarray.o -c hgGnfMicroarray.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgGnfMicroarray hgGnfMicroarray.o ../../../../lib/x86_64/jkhgap.a ../../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgGnfMicroarray make[5]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/hgGnfMicroarray' ( cd hgGtex && echo hgGtex && make ) hgGtex make[5]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/hgGtex' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../../htslib -I/usr/include/libpng16 -o hgGtex.o -c hgGtex.c hgGtex.c: In function ‘hgGtexTissues’: hgGtex.c:616:5: warning: variable ‘i’ set but not used [-Wunused-but-set-variable=] 616 | int i; | ^ gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgGtex hgGtex.o ../../../../lib/x86_64/jkhgap.a ../../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgGtex make[5]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/hgGtex' ( cd hgGtexAse && echo hgGtexAse && make ) hgGtexAse make[5]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/hgGtexAse' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../../htslib -I/usr/include/libpng16 -o hgGtexAse.o -c hgGtexAse.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgGtexAse hgGtexAse.o ../../../../lib/x86_64/jkhgap.a ../../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgGtexAse make[5]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/hgGtexAse' ( cd hgGtexExonBed && echo hgGtexExonBed && make ) hgGtexExonBed make[5]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/hgGtexExonBed' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../../htslib -I/usr/include/libpng16 -o hgGtexExonBed.o -c hgGtexExonBed.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgGtexExonBed hgGtexExonBed.o ../../../../lib/x86_64/jkhgap.a ../../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgGtexExonBed make[5]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/hgGtexExonBed' ( cd hgGtexGeneBed && echo hgGtexGeneBed && make ) hgGtexGeneBed make[5]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/hgGtexGeneBed' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../../htslib -I/usr/include/libpng16 -o hgGtexGeneBed.o -c hgGtexGeneBed.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgGtexGeneBed hgGtexGeneBed.o ../../../../lib/x86_64/jkhgap.a ../../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgGtexGeneBed make[5]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/hgGtexGeneBed' ( cd hgJaxQtl && echo hgJaxQtl && make ) hgJaxQtl make[5]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/hgJaxQtl' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../../htslib -I/usr/include/libpng16 -o hgJaxQtl.o -c hgJaxQtl.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgJaxQtl hgJaxQtl.o ../../../../lib/x86_64/jkhgap.a ../../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgJaxQtl make[5]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/hgJaxQtl' ( cd hgKegg && echo hgKegg && make ) hgKegg make[5]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/hgKegg' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../../htslib -I/usr/include/libpng16 -o hgKegg.o -c hgKegg.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgKegg hgKegg.o ../../../../lib/x86_64/jkhgap.a ../../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgKegg make[5]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/hgKegg' ( cd hgKegg2 && echo hgKegg2 && make ) hgKegg2 make[5]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/hgKegg2' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../../htslib -I/usr/include/libpng16 -o hgKegg2.o -c hgKegg2.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgKegg2 hgKegg2.o ../../../../lib/x86_64/jkhgap.a ../../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgKegg2 make[5]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/hgKegg2' ( cd hgKegg3 && echo hgKegg3 && make ) hgKegg3 make[5]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/hgKegg3' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../../htslib -I/usr/include/libpng16 -o hgKegg3.o -c hgKegg3.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgKegg3 hgKegg3.o ../../../../lib/x86_64/jkhgap.a ../../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgKegg3 make[5]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/hgKegg3' ( cd hgLoadEranModules && echo hgLoadEranModules && make ) hgLoadEranModules make[5]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/hgLoadEranModules' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../../htslib -I/usr/include/libpng16 -o hgLoadEranModules.o -c hgLoadEranModules.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../../htslib -I/usr/include/libpng16 -o esMotif.o -c esMotif.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgLoadEranModules hgLoadEranModules.o esMotif.o ../../../../lib/x86_64/jkhgap.a ../../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgLoadEranModules make[5]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/hgLoadEranModules' ( cd hgLsSnpPdbLoad && echo hgLsSnpPdbLoad && make ) hgLsSnpPdbLoad make[5]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/hgLsSnpPdbLoad' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../../htslib -I/usr/include/libpng16 -o hgLsSnpPdbLoad.o -c hgLsSnpPdbLoad.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgLsSnpPdbLoad hgLsSnpPdbLoad.o ../../../../lib/x86_64/jkhgap.a ../../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgLsSnpPdbLoad make[5]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/hgLsSnpPdbLoad' ( cd hgPhMouse && echo hgPhMouse && make ) hgPhMouse make[5]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/hgPhMouse' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../../htslib -I/usr/include/libpng16 -o hgPhMouse.o -c hgPhMouse.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgPhMouse hgPhMouse.o ../../../../lib/x86_64/jkhgap.a ../../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgPhMouse make[5]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/hgPhMouse' ( cd hgRnaGenes && echo hgRnaGenes && make ) hgRnaGenes make[5]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/hgRnaGenes' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../../htslib -I/usr/include/libpng16 -o hgRnaGenes.o -c hgRnaGenes.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgRnaGenes hgRnaGenes.o ../../../../lib/x86_64/jkhgap.a ../../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgRnaGenes make[5]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/hgRnaGenes' ( cd hgSoftPromoter && echo hgSoftPromoter && make ) hgSoftPromoter make[5]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/hgSoftPromoter' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../../htslib -I/usr/include/libpng16 -o hgSoftPromoter.o -c hgSoftPromoter.c hgSoftPromoter.c: In function ‘simplifyName’: hgSoftPromoter.c:35:5: warning: ‘strncpy’ specified bound 256 equals destination size [-Wstringop-truncation] 35 | strncpy(simple, softName, sizeof(simple)); | ^ gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgSoftPromoter hgSoftPromoter.o ../../../../lib/x86_64/jkhgap.a ../../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgSoftPromoter make[5]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/hgSoftPromoter' ( cd hgSoftberryHom && echo hgSoftberryHom && make ) hgSoftberryHom make[5]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/hgSoftberryHom' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../../htslib -I/usr/include/libpng16 -o hgSoftberryHom.o -c hgSoftberryHom.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgSoftberryHom hgSoftberryHom.o ../../../../lib/x86_64/jkhgap.a ../../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgSoftberryHom make[5]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/hgSoftberryHom' ( cd hgSuperfam && echo hgSuperfam && make ) hgSuperfam make[5]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/hgSuperfam' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../../htslib -I/usr/include/libpng16 -o hgSuperfam.o -c hgSuperfam.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgSuperfam hgSuperfam.o ../../../../lib/x86_64/jkhgap.a ../../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgSuperfam make[5]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/hgSuperfam' ( cd nibb/nibbImageProbes && echo nibb/nibbImageProbes && make ) nibb/nibbImageProbes make[5]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/nibb/nibbImageProbes' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../../../htslib -I/usr/include/libpng16 -o nibbImageProbes.o -c nibbImageProbes.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/nibbImageProbes nibbImageProbes.o ../../../../../lib/x86_64/jkhgap.a ../../../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/nibbImageProbes make[5]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/nibb/nibbImageProbes' ( cd nibb/nibbNameFix && echo nibb/nibbNameFix && make ) nibb/nibbNameFix make[5]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/nibb/nibbNameFix' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../../../htslib -I/usr/include/libpng16 -o nibbNameFix.o -c nibbNameFix.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/nibbNameFix nibbNameFix.o ../../../../../lib/x86_64/jkhgap.a ../../../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/nibbNameFix make[5]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/nibb/nibbNameFix' ( cd nibb/nibbParseImageDir && echo nibb/nibbParseImageDir && make ) nibb/nibbParseImageDir make[5]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/nibb/nibbParseImageDir' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../../../htslib -I/usr/include/libpng16 -o nibbParseImageDir.o -c nibbParseImageDir.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/nibbParseImageDir nibbParseImageDir.o ../../../../../lib/x86_64/jkhgap.a ../../../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/nibbParseImageDir make[5]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/nibb/nibbParseImageDir' ( cd nibb/nibbPrepImages && echo nibb/nibbPrepImages && make ) nibb/nibbPrepImages make[5]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/nibb/nibbPrepImages' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../../../htslib -I/usr/include/libpng16 -o nibbPrepImages.o -c nibbPrepImages.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/nibbPrepImages nibbPrepImages.o ../../../../../lib/x86_64/jkhgap.a ../../../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/nibbPrepImages make[5]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/nibb/nibbPrepImages' ( cd samHit && echo samHit && make ) samHit make[5]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/samHit' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../../htslib -I/usr/include/libpng16 -o samHit.o -c samHit.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/samHit samHit.o ../../../../lib/x86_64/jkhgap.a ../../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/samHit make[5]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/samHit' ( cd sanger22gtf && echo sanger22gtf && make ) sanger22gtf make[5]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/sanger22gtf' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../../htslib -I/usr/include/libpng16 -o sanger22gtf.o -c sanger22gtf.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/sanger22gtf sanger22gtf.o ../../../../lib/x86_64/jkhgap.a ../../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/sanger22gtf make[5]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/sanger22gtf' ( cd vegaBuildInfo && echo vegaBuildInfo && make ) vegaBuildInfo make[5]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/vegaBuildInfo' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../../htslib -I/usr/include/libpng16 -o vegaBuildInfo.o -c vegaBuildInfo.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/vegaBuildInfo vegaBuildInfo.o ../../../../lib/x86_64/jkhgap.a ../../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/vegaBuildInfo make[5]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/vegaBuildInfo' ( cd yeast/checkSgdSync && echo yeast/checkSgdSync && make ) yeast/checkSgdSync make[5]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/yeast/checkSgdSync' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../../../htslib -I/usr/include/libpng16 -o checkSgdSync.o -c checkSgdSync.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/checkSgdSync checkSgdSync.o ../../../../../lib/x86_64/jkhgap.a ../../../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/checkSgdSync make[5]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/yeast/checkSgdSync' ( cd yeast/fixHarbisonMotifs && echo yeast/fixHarbisonMotifs && make ) yeast/fixHarbisonMotifs make[5]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/yeast/fixHarbisonMotifs' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../../../htslib -I/usr/include/libpng16 -o fixHarbisonMotifs.o -c fixHarbisonMotifs.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/fixHarbisonMotifs fixHarbisonMotifs.o ../../../../../lib/x86_64/jkhgap.a ../../../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/fixHarbisonMotifs make[5]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/yeast/fixHarbisonMotifs' ( cd yeast/hgSgdGff3 && echo yeast/hgSgdGff3 && make ) yeast/hgSgdGff3 make[5]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/yeast/hgSgdGff3' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../../../htslib -I/usr/include/libpng16 -o hgSgdGff3.o -c hgSgdGff3.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgSgdGff3 hgSgdGff3.o ../../../../../lib/x86_64/jkhgap.a ../../../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgSgdGff3 make[5]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/yeast/hgSgdGff3' ( cd yeast/hgSgdGfp && echo yeast/hgSgdGfp && make ) yeast/hgSgdGfp make[5]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/yeast/hgSgdGfp' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../../../htslib -I/usr/include/libpng16 -o hgSgdGfp.o -c hgSgdGfp.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgSgdGfp hgSgdGfp.o ../../../../../lib/x86_64/jkhgap.a ../../../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgSgdGfp make[5]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/yeast/hgSgdGfp' ( cd yeast/hgSgdPep && echo yeast/hgSgdPep && make ) yeast/hgSgdPep make[5]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/yeast/hgSgdPep' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../../../htslib -I/usr/include/libpng16 -o hgSgdPep.o -c hgSgdPep.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgSgdPep hgSgdPep.o ../../../../../lib/x86_64/jkhgap.a ../../../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgSgdPep make[5]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/yeast/hgSgdPep' ( cd yeast/hgYeastRegCode && echo yeast/hgYeastRegCode && make ) yeast/hgYeastRegCode make[5]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/yeast/hgYeastRegCode' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../../../htslib -I/usr/include/libpng16 -o hgYeastRegCode.o -c hgYeastRegCode.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgYeastRegCode hgYeastRegCode.o ../../../../../lib/x86_64/jkhgap.a ../../../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgYeastRegCode make[5]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside/yeast/hgYeastRegCode' make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/outside' cd trackDbRaFormat && echo trackDbRaFormat && make trackDbRaFormat make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/trackDbRaFormat' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o trackDbRaFormat.o -c trackDbRaFormat.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/trackDbRaFormat trackDbRaFormat.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/trackDbRaFormat make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/trackDbRaFormat' cd trackDbPatch && echo trackDbPatch && make trackDbPatch make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/trackDbPatch' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o trackDbPatch.o -c trackDbPatch.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/trackDbPatch trackDbPatch.o ../../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/trackDbPatch' cd trackDbToTxt && echo trackDbToTxt && make trackDbToTxt make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/trackDbToTxt' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o trackDbToTxt.o -c trackDbToTxt.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/trackDbToTxt trackDbToTxt.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/trackDbToTxt make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/trackDbToTxt' cd dbDbToHubTxt && echo dbDbToHubTxt && make dbDbToHubTxt make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/dbDbToHubTxt' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o dbDbToHubTxt.o -c dbDbToHubTxt.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/dbDbToHubTxt dbDbToHubTxt.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/dbDbToHubTxt make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/dbDbToHubTxt' cd hgBbiDbLink && echo hgBbiDbLink && make hgBbiDbLink make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgBbiDbLink' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hgBbiDbLink.o -c hgBbiDbLink.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgBbiDbLink hgBbiDbLink.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgBbiDbLink make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgBbiDbLink' cd hgFindSpec && echo hgFindSpec && make hgFindSpec make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgFindSpec' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hgFindSpec.o -c hgFindSpec.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgFindSpec hgFindSpec.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgFindSpec make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgFindSpec' cd hgGoldGapGl && echo hgGoldGapGl && make hgGoldGapGl make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgGoldGapGl' make default PROG=hgGoldGapGl make[5]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgGoldGapGl' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hgGoldGapGl.o -c hgGoldGapGl.c hgGoldGapGl.c: In function ‘makeCloneVerHash’: hgGoldGapGl.c:341:5: warning: ‘strncpy’ specified bound 32 equals destination size [-Wstringop-truncation] 341 | strncpy(acc, row[0], sizeof(acc)); | ^ gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o ntContig.o -c ntContig.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgGoldGapGl hgGoldGapGl.o ntContig.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgGoldGapGl make[5]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgGoldGapGl' make default PROG=hgLoadGap make[5]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgGoldGapGl' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hgLoadGap.o -c hgLoadGap.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgLoadGap hgLoadGap.o ntContig.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgLoadGap make[5]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgGoldGapGl' make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgGoldGapGl' cd hgLoadBed && echo hgLoadBed && make hgLoadBed make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgLoadBed' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hgLoadBed.o -c hgLoadBed.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgLoadBed hgLoadBed.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgLoadBed make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgLoadBed' cd hgLoadChain && echo hgLoadChain && make hgLoadChain make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgLoadChain' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hgLoadChain.o -c hgLoadChain.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgLoadChain hgLoadChain.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgLoadChain make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgLoadChain' cd hgLoadMaf && echo hgLoadMaf && make hgLoadMaf make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgLoadMaf' make default PROG=hgLoadMaf make[5]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgLoadMaf' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hgLoadMaf.o -c hgLoadMaf.c hgLoadMaf.c: In function ‘hgLoadMaf’: hgLoadMaf.c:126:16: warning: storing the address of local variable ‘extFileDir’ in ‘pathPrefix’ [-Wdangling-pointer=] 126 | pathPrefix = extFileDir; | ~~~~~~~~~~~^~~~~~~~~~~~ hgLoadMaf.c:105:6: note: ‘extFileDir’ declared here 105 | char extFileDir[PATH_LEN]; | ^~~~~~~~~~ hgLoadMaf.c:46:7: note: ‘pathPrefix’ declared here 46 | char *pathPrefix = NULL; /* extFile directory */ | ^~~~~~~~~~ gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgLoadMaf hgLoadMaf.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgLoadMaf make[5]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgLoadMaf' make default PROG=hgLoadMafSummary make[5]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgLoadMaf' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hgLoadMafSummary.o -c hgLoadMafSummary.c hgLoadMafSummary.c: In function ‘hgLoadMafSummary’: hgLoadMafSummary.c:263:6: warning: variable ‘mafCount’ set but not used [-Wunused-but-set-variable=] 263 | long mafCount = 0, allMafCount = 0; | ^~~~~~~~ gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgLoadMafSummary hgLoadMafSummary.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgLoadMafSummary make[5]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgLoadMaf' make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgLoadMaf' cd hgLoadNet && echo hgLoadNet && make hgLoadNet make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgLoadNet' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hgLoadNet.o -c hgLoadNet.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgLoadNet hgLoadNet.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgLoadNet make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgLoadNet' cd hgLoadOut && echo hgLoadOut && make hgLoadOut make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgLoadOut' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hgLoadOut.o -c hgLoadOut.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgLoadOut hgLoadOut.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgLoadOut make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgLoadOut' cd hgLoadOutJoined && echo hgLoadOutJoined && make hgLoadOutJoined make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgLoadOutJoined' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hgLoadOutJoined.o -c hgLoadOutJoined.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgLoadOutJoined hgLoadOutJoined.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgLoadOutJoined make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgLoadOutJoined' cd hgGcPercent && echo hgGcPercent && make hgGcPercent make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgGcPercent' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hgGcPercent.o -c hgGcPercent.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgGcPercent hgGcPercent.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgGcPercent make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgGcPercent' cd hgLoadWiggle && echo hgLoadWiggle && make hgLoadWiggle make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgLoadWiggle' make default PROG=hgLoadWiggle make[5]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgLoadWiggle' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hgLoadWiggle.o -c hgLoadWiggle.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgLoadWiggle hgLoadWiggle.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgLoadWiggle mkdir -p /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/ cp -f fixStepToBedGraph.pl /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/fixStepToBedGraph.pl mkdir -p /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/ cp -f varStepToBedGraph.pl /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/varStepToBedGraph.pl make[5]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgLoadWiggle' make default PROG=hgWiggle make[5]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgLoadWiggle' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hgWiggle.o -c hgWiggle.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgWiggle hgWiggle.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgWiggle make[5]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgLoadWiggle' make default PROG=wigEncode make[5]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgLoadWiggle' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o wigEncode.o -c wigEncode.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/wigEncode wigEncode.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/wigEncode make[5]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgLoadWiggle' make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgLoadWiggle' cd hgTrackDb && echo hgTrackDb && make hgTrackDb make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgTrackDb' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hgTrackDb.o -c hgTrackDb.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgTrackDb hgTrackDb.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgTrackDb make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/hgTrackDb' cd ldHgGene && echo ldHgGene && make ldHgGene make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/ldHgGene' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o ldHgGene.o -c ldHgGene.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/ldHgGene ldHgGene.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/ldHgGene make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb/ldHgGene' make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/makeDb' if test -d mdToNcbiLift ; then cd mdToNcbiLift && echo mdToNcbiLift && make ; fi mdToNcbiLift make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mdToNcbiLift' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o mdToNcbiLift.o -c mdToNcbiLift.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/mdToNcbiLift mdToNcbiLift.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/mdToNcbiLift make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mdToNcbiLift' if test -d mouseStuff ; then cd mouseStuff && echo mouseStuff && make ; fi mouseStuff make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff' if test -d axtAndBed ; then cd axtAndBed && echo axtAndBed && make ; fi axtAndBed make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/axtAndBed' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o axtAndBed.o -c axtAndBed.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/axtAndBed axtAndBed.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/axtAndBed make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/axtAndBed' if test -d axtBest ; then cd axtBest && echo axtBest && make ; fi axtBest make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/axtBest' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o axtBest.o -c axtBest.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/axtBest axtBest.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/axtBest make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/axtBest' if test -d axtCalcMatrix ; then cd axtCalcMatrix && echo axtCalcMatrix && make ; fi axtCalcMatrix make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/axtCalcMatrix' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o axtCalcMatrix.o -c axtCalcMatrix.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/axtCalcMatrix axtCalcMatrix.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/axtCalcMatrix make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/axtCalcMatrix' if test -d axtDropOverlap ; then cd axtDropOverlap && echo axtDropOverlap && make ; fi axtDropOverlap make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/axtDropOverlap' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o axtDropOverlap.o -c axtDropOverlap.c axtDropOverlap.c: In function ‘axtDropOverlap’: axtDropOverlap.c:61:5: warning: variable ‘totLines’ set but not used [-Wunused-but-set-variable=] 61 | int totLines = 0; | ^~~~~~~~ axtDropOverlap.c:60:5: warning: variable ‘totSkip’ set but not used [-Wunused-but-set-variable=] 60 | int totSkip = 0; | ^~~~~~~ axtDropOverlap.c:59:5: warning: variable ‘totMatch’ set but not used [-Wunused-but-set-variable=] 59 | int totMatch = 0; | ^~~~~~~~ gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/axtDropOverlap axtDropOverlap.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/axtDropOverlap make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/axtDropOverlap' if test -d axtDropSelf ; then cd axtDropSelf && echo axtDropSelf && make ; fi axtDropSelf make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/axtDropSelf' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o axtDropSelf.o -c axtDropSelf.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/axtDropSelf axtDropSelf.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/axtDropSelf make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/axtDropSelf' if test -d axtFilter ; then cd axtFilter && echo axtFilter && make ; fi axtFilter make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/axtFilter' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o axtFilter.o -c axtFilter.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/axtFilter axtFilter.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/axtFilter make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/axtFilter' if test -d axtIndex ; then cd axtIndex && echo axtIndex && make ; fi axtIndex make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/axtIndex' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o axtIndex.o -c axtIndex.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/axtIndex axtIndex.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/axtIndex make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/axtIndex' if test -d axtPretty ; then cd axtPretty && echo axtPretty && make ; fi axtPretty make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/axtPretty' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o axtPretty.o -c axtPretty.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/axtPretty axtPretty.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/axtPretty make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/axtPretty' if test -d axtQueryCount ; then cd axtQueryCount && echo axtQueryCount && make ; fi axtQueryCount make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/axtQueryCount' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o axtQueryCount.o -c axtQueryCount.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/axtQueryCount axtQueryCount.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/axtQueryCount make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/axtQueryCount' if test -d axtRecipBest ; then cd axtRecipBest && echo axtRecipBest && make ; fi axtRecipBest make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/axtRecipBest' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o axtRecipBest.o -c axtRecipBest.c axtRecipBest.c: In function ‘axtRecipBest’: axtRecipBest.c:223:13: warning: variable ‘filesInMidFile’ set but not used [-Wunused-but-set-variable=] 223 | int filesInMidFile = 0; | ^~~~~~~~~~~~~~ axtRecipBest.c:196:5: warning: variable ‘totalT’ set but not used [-Wunused-but-set-variable=] 196 | int totalT = 0; | ^~~~~~ gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/axtRecipBest axtRecipBest.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/axtRecipBest make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/axtRecipBest' if test -d axtRescore ; then cd axtRescore && echo axtRescore && make ; fi axtRescore make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/axtRescore' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o axtRescore.o -c axtRescore.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/axtRescore axtRescore.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/axtRescore make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/axtRescore' if test -d axtSplitByTarget ; then cd axtSplitByTarget && echo axtSplitByTarget && make ; fi axtSplitByTarget make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/axtSplitByTarget' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o axtSplitByTarget.o -c axtSplitByTarget.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/axtSplitByTarget axtSplitByTarget.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/axtSplitByTarget make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/axtSplitByTarget' if test -d axtToBed ; then cd axtToBed && echo axtToBed && make ; fi axtToBed make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/axtToBed' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o axtToBed.o -c axtToBed.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/axtToBed axtToBed.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/axtToBed make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/axtToBed' if test -d axtToChain ; then cd axtToChain && echo axtToChain && make ; fi axtToChain make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/axtToChain' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o axtToChain.o -c axtToChain.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/axtToChain axtToChain.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/axtToChain make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/axtToChain' if test -d calcGap ; then cd calcGap && echo calcGap && make ; fi calcGap make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/calcGap' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o calcGap.o -c calcGap.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/calcGap calcGap.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/calcGap make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/calcGap' if test -d chainDbToFile ; then cd chainDbToFile && echo chainDbToFile && make ; fi chainDbToFile make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/chainDbToFile' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o chainDbToFile.o -c chainDbToFile.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/chainDbToFile chainDbToFile.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/chainDbToFile make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/chainDbToFile' if test -d gcForBed ; then cd gcForBed && echo gcForBed && make ; fi gcForBed make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/gcForBed' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o gcForBed.o -c gcForBed.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/gcForBed gcForBed.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/gcForBed make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/gcForBed' if test -d knownVsBlat ; then cd knownVsBlat && echo knownVsBlat && make ; fi knownVsBlat make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/knownVsBlat' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o knownVsBlat.o -c knownVsBlat.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o blatStats.o -c blatStats.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/knownVsBlat knownVsBlat.o blatStats.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm -lmariadb -lz -lpthread -lm -lssl -lcrypto true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/knownVsBlat gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o kvsSummary.o -c kvsSummary.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/kvsSummary kvsSummary.o blatStats.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm -lmariadb -lz -lpthread -lm -lssl -lcrypto true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/kvsSummary make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/knownVsBlat' if test -d libScan ; then cd libScan && echo libScan && make ; fi libScan make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/libScan' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o libScan.o -c libScan.c libScan.c: In function ‘libScan’: libScan.c:131:13: warning: ‘strncpy’ specified bound 12 equals destination size [-Wstringop-truncation] 131 | strncpy(lib->sampleAcc, row[3], sizeof(lib->sampleAcc)); | ^ libScan.c:125:9: warning: ‘strncpy’ specified bound 12 equals destination size [-Wstringop-truncation] 125 | strncpy(lib->sampleAcc, row[3], sizeof(lib->sampleAcc)); | ^ gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/libScan libScan.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/libScan make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/libScan' if test -d mousePoster ; then cd mousePoster && echo mousePoster && make ; fi mousePoster make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/mousePoster' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o mousePoster.o -c mousePoster.c mousePoster.c: In function ‘makeLocusLinkToJaxHash’: mousePoster.c:211:5: warning: variable ‘count’ set but not used [-Wunused-but-set-variable=] 211 | int count = 0; | ^~~~~ mousePoster.c: In function ‘parseMorbidMap’: mousePoster.c:244:15: warning: variable ‘syns’ set but not used [-Wunused-but-set-variable=] 244 | int loci = 0, syns = 0; | ^~~~ mousePoster.c:244:5: warning: variable ‘loci’ set but not used [-Wunused-but-set-variable=] 244 | int loci = 0, syns = 0; | ^~~~ mousePoster.c: In function ‘makeDiseaseOrthoHash’: mousePoster.c:272:5: warning: variable ‘count’ set but not used [-Wunused-but-set-variable=] 272 | int count = 0; | ^~~~~ gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/mousePoster mousePoster.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/mousePoster make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/mousePoster' if test -d netStats ; then cd netStats && echo netStats && make ; fi netStats make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/netStats' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o netStats.o -c netStats.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/netStats netStats.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/netStats make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/netStats' if test -d netToBedWithId ; then cd netToBedWithId && echo netToBedWithId && make ; fi netToBedWithId make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/netToBedWithId' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o netToBedWithId.o -c netToBedWithId.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/netToBedWithId netToBedWithId.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/netToBedWithId make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/netToBedWithId' if test -d orthologBySynteny ; then cd orthologBySynteny && echo orthologBySynteny && make ; fi orthologBySynteny make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/orthologBySynteny' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o orthologBySynteny.o -c orthologBySynteny.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/orthologBySynteny orthologBySynteny.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/orthologBySynteny make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/orthologBySynteny' if test -d phToPsl ; then cd phToPsl && echo phToPsl && make ; fi phToPsl make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/phToPsl' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o phToPsl.o -c phToPsl.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/phToPsl phToPsl.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/phToPsl make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/phToPsl' if test -d regionPicker ; then cd regionPicker && echo regionPicker && make ; fi regionPicker make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/regionPicker' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o regionPicker.o -c regionPicker.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/regionPicker regionPicker.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl In function ‘memset’, inlined from ‘zeroBytes’ at ../../../inc/common.h:327:1, inlined from ‘bitClear’ at ../../../lib/bits.c:224:1, inlined from ‘statsOnSpan’ at regionPicker.c:339:1, inlined from ‘regionPicker’ at regionPicker.c:703:6, inlined from ‘main’ at regionPicker.c:732:1: /usr/include/bits/string_fortified.h:59:10: warning: ‘__builtin_memset’ specified size between 18446744073441116160 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] 59 | return __builtin___memset_chk (__dest, __ch, __len, | ^ true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/regionPicker make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/regionPicker' if test -d rikenBestInCluster ; then cd rikenBestInCluster && echo rikenBestInCluster && make ; fi rikenBestInCluster make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/rikenBestInCluster' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o rikenBestInCluster.o -c rikenBestInCluster.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/rikenBestInCluster rikenBestInCluster.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/rikenBestInCluster make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/rikenBestInCluster' if test -d simpleChain ; then cd simpleChain && echo simpleChain && make ; fi simpleChain make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/simpleChain' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o simpleChain.o -c simpleChain.c simpleChain.c: In function ‘simpleChain’: simpleChain.c:450:9: warning: variable ‘count’ set but not used [-Wunused-but-set-variable=] 450 | int count = 0; | ^~~~~ gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/simpleChain simpleChain.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/simpleChain make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/simpleChain' if test -d splitSim ; then cd splitSim && echo splitSim && make ; fi splitSim make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/splitSim' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o splitSim.o -c splitSim.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/splitSim splitSim.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/splitSim make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/splitSim' if test -d subsetAxt ; then cd subsetAxt && echo subsetAxt && make ; fi subsetAxt make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/subsetAxt' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o subsetAxt.o -c subsetAxt.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/subsetAxt subsetAxt.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/subsetAxt make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/subsetAxt' if test -d subsetTraces ; then cd subsetTraces && echo subsetTraces && make ; fi subsetTraces make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/subsetTraces' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o subsetTraces.o -c subsetTraces.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/subsetTraces subsetTraces.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/subsetTraces make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/subsetTraces' if test -d whyConserved ; then cd whyConserved && echo whyConserved && make ; fi whyConserved make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/whyConserved' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o whyConserved.o -c whyConserved.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/whyConserved whyConserved.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm -lmariadb -lz -lpthread -lm -lssl -lcrypto true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/whyConserved gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o trackOverlap.o -c trackOverlap.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/trackOverlap trackOverlap.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm -lmariadb -lz -lpthread -lm -lssl -lcrypto true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/trackOverlap make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/whyConserved' if test -d axtChain ; then cd axtChain && echo axtChain && make ; fi axtChain make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/axtChain' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o axtChain.o -c axtChain.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/axtChain axtChain.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/axtChain make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/axtChain' if test -d axtSort ; then cd axtSort && echo axtSort && make ; fi axtSort make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/axtSort' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o axtSort.o -c axtSort.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/axtSort axtSort.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/axtSort make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/axtSort' if test -d axtSwap ; then cd axtSwap && echo axtSwap && make ; fi axtSwap make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/axtSwap' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o axtSwap.o -c axtSwap.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/axtSwap axtSwap.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/axtSwap make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/axtSwap' if test -d axtToMaf ; then cd axtToMaf && echo axtToMaf && make ; fi axtToMaf make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/axtToMaf' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o axtToMaf.o -c axtToMaf.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/axtToMaf axtToMaf.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/axtToMaf make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/axtToMaf' if test -d axtToPsl ; then cd axtToPsl && echo axtToPsl && make ; fi axtToPsl make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/axtToPsl' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o axtToPsl.o -c axtToPsl.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/axtToPsl axtToPsl.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/axtToPsl make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/axtToPsl' if test -d bedCoverage ; then cd bedCoverage && echo bedCoverage && make ; fi bedCoverage make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/bedCoverage' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o bedCoverage.o -c bedCoverage.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bedCoverage bedCoverage.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bedCoverage make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/bedCoverage' if test -d chainAntiRepeat ; then cd chainAntiRepeat && echo chainAntiRepeat && make ; fi chainAntiRepeat make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/chainAntiRepeat' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o chainAntiRepeat.o -c chainAntiRepeat.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/chainAntiRepeat chainAntiRepeat.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/chainAntiRepeat make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/chainAntiRepeat' if test -d chainBridge ; then cd chainBridge && echo chainBridge && make ; fi if test -d chainCleaner ; then cd chainCleaner && echo chainCleaner && make ; fi chainCleaner make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/chainCleaner' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o chainCleaner.o -c chainCleaner.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/chainCleaner chainCleaner.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/chainCleaner make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/chainCleaner' if test -d chainFilter ; then cd chainFilter && echo chainFilter && make ; fi chainFilter make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/chainFilter' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o chainFilter.o -c chainFilter.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/chainFilter chainFilter.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/chainFilter make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/chainFilter' if test -d chainMergeSort ; then cd chainMergeSort && echo chainMergeSort && make ; fi chainMergeSort make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/chainMergeSort' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o chainMergeSort.o -c chainMergeSort.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/chainMergeSort chainMergeSort.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/chainMergeSort make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/chainMergeSort' if test -d chainNet ; then cd chainNet && echo chainNet && make ; fi chainNet make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/chainNet' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o chainNet.o -c chainNet.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/chainNet chainNet.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/chainNet make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/chainNet' if test -d chainPreNet ; then cd chainPreNet && echo chainPreNet && make ; fi chainPreNet make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/chainPreNet' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o chainPreNet.o -c chainPreNet.c chainPreNet.c: In function ‘setupChroms’: chainPreNet.c:74:5: warning: variable ‘chromCount’ set but not used [-Wunused-but-set-variable=] 74 | int chromCount = 0; | ^~~~~~~~~~ gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/chainPreNet chainPreNet.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/chainPreNet make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/chainPreNet' if test -d chainScore ; then cd chainScore && echo chainScore && make ; fi chainScore make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/chainScore' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o chainScore.o -c chainScore.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/chainScore chainScore.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/chainScore make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/chainScore' if test -d chainSort ; then cd chainSort && echo chainSort && make ; fi chainSort make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/chainSort' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o chainSort.o -c chainSort.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/chainSort chainSort.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/chainSort make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/chainSort' if test -d chainSplit ; then cd chainSplit && echo chainSplit && make ; fi chainSplit make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/chainSplit' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o chainSplit.o -c chainSplit.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/chainSplit chainSplit.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/chainSplit make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/chainSplit' if test -d chainStitchId ; then cd chainStitchId && echo chainStitchId && make ; fi chainStitchId make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/chainStitchId' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o chainStitchId.o -c chainStitchId.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/chainStitchId chainStitchId.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/chainStitchId make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/chainStitchId' if test -d chainSwap ; then cd chainSwap && echo chainSwap && make ; fi chainSwap make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/chainSwap' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o chainSwap.o -c chainSwap.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/chainSwap chainSwap.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/chainSwap make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/chainSwap' if test -d chainToAxt ; then cd chainToAxt && echo chainToAxt && make ; fi chainToAxt make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/chainToAxt' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o chainToAxt.o -c chainToAxt.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/chainToAxt chainToAxt.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/chainToAxt make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/chainToAxt' if test -d chainToPsl ; then cd chainToPsl && echo chainToPsl && make ; fi chainToPsl make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/chainToPsl' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o chainToPsl.o -c chainToPsl.c chainToPsl.c: In function ‘aliStringToPsl’: chainToPsl.c:48:17: warning: variable ‘tbSize’ set but not used [-Wunused-but-set-variable=] 48 | int qbSize = 0, tbSize = 0; /* sum of block sizes */ | ^~~~~~ chainToPsl.c:48:5: warning: variable ‘qbSize’ set but not used [-Wunused-but-set-variable=] 48 | int qbSize = 0, tbSize = 0; /* sum of block sizes */ | ^~~~~~ gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/chainToPsl chainToPsl.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/chainToPsl make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/chainToPsl' if test -d chainToPslBasic ; then cd chainToPslBasic && echo chainToPslBasic && make ; fi chainToPslBasic make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/chainToPslBasic' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o chainToPslBasic.o -c chainToPslBasic.c chainToPslBasic.c: In function ‘chainToPsl’: chainToPslBasic.c:63:5: warning: variable ‘iBlk’ set but not used [-Wunused-but-set-variable=] 63 | int iBlk = 0; | ^~~~ gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/chainToPslBasic chainToPslBasic.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/chainToPslBasic make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/chainToPslBasic' if test -d lavToAxt ; then cd lavToAxt && echo lavToAxt && make ; fi lavToAxt make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/lavToAxt' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o lavToAxt.o -c lavToAxt.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/lavToAxt lavToAxt.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/lavToAxt make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/lavToAxt' if test -d lavToPsl ; then cd lavToPsl && echo lavToPsl && make ; fi lavToPsl make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/lavToPsl' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o lavToPsl.o -c lavToPsl.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/lavToPsl lavToPsl.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/lavToPsl make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/lavToPsl' if test -d mafCoverage ; then cd mafCoverage && echo mafCoverage && make ; fi mafCoverage make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/mafCoverage' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o mafCoverage.o -c mafCoverage.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/mafCoverage mafCoverage.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/mafCoverage make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/mafCoverage' if test -d mafFetch ; then cd mafFetch && echo mafFetch && make ; fi mafFetch make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/mafFetch' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o mafFetch.o -c mafFetch.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/mafFetch mafFetch.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/mafFetch make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/mafFetch' if test -d mafRanges ; then cd mafRanges && echo mafRanges && make ; fi mafRanges make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/mafRanges' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o mafRanges.o -c mafRanges.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/mafRanges mafRanges.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/mafRanges make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/mafRanges' if test -d mafNoAlign ; then cd mafNoAlign && echo mafNoAlign && make ; fi mafNoAlign make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/mafNoAlign' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o mafNoAlign.o -c mafNoAlign.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/mafNoAlign mafNoAlign.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/mafNoAlign make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/mafNoAlign' if test -d mafToAxt ; then cd mafToAxt && echo mafToAxt && make ; fi mafToAxt make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/mafToAxt' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o mafToAxt.o -c mafToAxt.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/mafToAxt mafToAxt.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/mafToAxt make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/mafToAxt' if test -d mafToPsl ; then cd mafToPsl && echo mafToPsl && make ; fi mafToPsl make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/mafToPsl' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o mafToPsl.o -c mafToPsl.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/mafToPsl mafToPsl.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/mafToPsl make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/mafToPsl' if test -d netChainSubset ; then cd netChainSubset && echo netChainSubset && make ; fi netChainSubset make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/netChainSubset' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o netChainSubset.o -c netChainSubset.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/netChainSubset netChainSubset.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/netChainSubset make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/netChainSubset' if test -d netClass ; then cd netClass && echo netClass && make ; fi netClass make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/netClass' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o netClass.o -c netClass.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/netClass netClass.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/netClass make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/netClass' if test -d netFilter ; then cd netFilter && echo netFilter && make ; fi netFilter make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/netFilter' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o netFilter.o -c netFilter.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/netFilter netFilter.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/netFilter make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/netFilter' if test -d netSplit ; then cd netSplit && echo netSplit && make ; fi netSplit make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/netSplit' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o netSplit.o -c netSplit.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/netSplit netSplit.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/netSplit make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/netSplit' if test -d netSyntenic ; then cd netSyntenic && echo netSyntenic && make ; fi netSyntenic make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/netSyntenic' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o netSyntenic.o -c netSyntenic.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/netSyntenic netSyntenic.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/netSyntenic make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/netSyntenic' if test -d netToAxt ; then cd netToAxt && echo netToAxt && make ; fi netToAxt make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/netToAxt' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o netToAxt.o -c netToAxt.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/netToAxt netToAxt.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/netToAxt make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/netToAxt' if test -d netToBed ; then cd netToBed && echo netToBed && make ; fi netToBed make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/netToBed' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o netToBed.o -c netToBed.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/netToBed netToBed.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/netToBed make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/netToBed' if test -d pslMrnaCover ; then cd pslMrnaCover && echo pslMrnaCover && make ; fi pslMrnaCover make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/pslMrnaCover' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o pslMrnaCover.o -c pslMrnaCover.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslMrnaCover pslMrnaCover.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslMrnaCover make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff/pslMrnaCover' make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mouseStuff' if test -d near/hgCeOrfToGene ; then cd near/hgCeOrfToGene && echo near/hgCeOrfToGene && make ; fi if test -d near/hgClusterGenes ; then cd near/hgClusterGenes && echo near/hgClusterGenes && make ; fi if test -d near/hgEmblProtLinks ; then cd near/hgEmblProtLinks && echo near/hgEmblProtLinks && make ; fi if test -d near/hgExpDistance ; then cd near/hgExpDistance && echo near/hgExpDistance && make ; fi if test -d near/hgGoAssociation ; then cd near/hgGoAssociation && echo near/hgGoAssociation && make ; fi if test -d near/hgKnownToSuper ; then cd near/hgKnownToSuper && echo near/hgKnownToSuper && make ; fi if test -d near/hgMapToGene ; then cd near/hgMapToGene && echo near/hgMapToGene && make ; fi if test -d near/hgMapViaSwissProt ; then cd near/hgMapViaSwissProt && echo near/hgMapViaSwissProt && make ; fi if test -d near/hgProtIdToGenePred ; then cd near/hgProtIdToGenePred && echo near/hgProtIdToGenePred && make ; fi if test -d near/hgWormLinks ; then cd near/hgWormLinks && echo near/hgWormLinks && make ; fi if test -d near/pepPredToFa ; then cd near/pepPredToFa && echo near/pepPredToFa && make ; fi if test -d near/hgNearTest ; then cd near/hgNearTest && echo near/hgNearTest && make ; fi if test -d near/hgNetDist ; then cd near/hgNetDist && echo near/hgNetDist && make ; fi if test -d near/knownToHprd ; then cd near/knownToHprd && echo near/knownToHprd && make ; fi if test -d nci60 ; then cd nci60 && echo nci60 && make ; fi nci60 make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/nci60' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -Wimplicit -I../inc -I../../inc -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/findStanAlignments findStanAlignments.c ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm -lmariadb -lz -lpthread -lm -lssl -lcrypto true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/findStanAlignments gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -Wimplicit -I../inc -I../../inc -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/stanToBedAndExpRecs stanToBedAndExpRecs.c ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm -lmariadb -lz -lpthread -lm -lssl -lcrypto stanToBedAndExpRecs.c: In function ‘pslToBed’: stanToBedAndExpRecs.c:73:1: warning: ‘strncpy’ output may be truncated copying 2 bytes from a string of length 2 [-Wstringop-truncation] 73 | strncpy(bed->strand, psl->strand, sizeof(bed->strand)); | ^ true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/stanToBedAndExpRecs make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/nci60' if test -d orthoMap ; then cd orthoMap && echo orthoMap && make ; fi orthoMap make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/orthoMap' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o orthoEval.o -c orthoEval.c gcc -I../inc -I../../inc -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/mgcFastaForBed mgcFastaForBed.c orthoEval.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lmariadb -lz -lpthread -lm -lssl -lcrypto gcc -I../inc -I../../inc -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/agxToIntronBeds agxToIntronBeds.c orthoEval.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lmariadb -lz -lpthread -lm -lssl -lcrypto gcc -I../inc -I../../inc -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bedToFrames bedToFrames.c orthoEval.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lmariadb -lz -lpthread -lm -lssl -lcrypto gcc -I../inc -I../../inc -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/orthoMap orthoMap.c orthoEval.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lmariadb -lz -lpthread -lm -lssl -lcrypto gcc -I../inc -I../../inc -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/orthoEvaluate orthoEvaluate.c orthoEval.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lmariadb -lz -lpthread -lm -lssl -lcrypto gcc -I../inc -I../../inc -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/orthoPickIntron orthoPickIntron.c orthoEval.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lmariadb -lz -lpthread -lm -lssl -lcrypto make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/orthoMap' if test -d patCount ; then cd patCount && echo patCount && make ; fi patCount make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/patCount' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o patCount.o -c patCount.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/patCount patCount.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/patCount make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/patCount' if test -d perf ; then cd perf && echo perf && make ; fi perf make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/perf' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o hgTracksRandom.o -c hgTracksRandom.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgTracksRandom hgTracksRandom.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm -lmariadb -lz -lpthread -lm -lssl -lcrypto make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/perf' if test -d pslCoverage ; then cd pslCoverage && echo pslCoverage && make ; fi pslCoverage make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/pslCoverage' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o pslCoverage.o -c pslCoverage.c pslCoverage.c: In function ‘doOneAcc’: pslCoverage.c:132:5: warning: variable ‘goodAliCount’ set but not used [-Wunused-but-set-variable=] 132 | int goodAliCount = 0; | ^~~~~~~~~~~~ pslCoverage.c: In function ‘summarizeProbeList’: pslCoverage.c:251:5: warning: variable ‘totalBases’ set but not used [-Wunused-but-set-variable=] 251 | int totalBases = 0; | ^~~~~~~~~~ gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslCoverage pslCoverage.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslCoverage make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/pslCoverage' if test -d pslDiff ; then cd pslDiff && echo pslDiff && make ; fi pslDiff make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/pslDiff' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o pslSets.o -c pslSets.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o pslDiff.o -c pslDiff.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslDiff pslSets.o pslDiff.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lmariadb -lz -lpthread -lm -lssl -lcrypto -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslDiff make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/pslDiff' if test -d pslFilterPrimers ; then cd pslFilterPrimers && echo pslFilterPrimers && make ; fi pslFilterPrimers make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/pslFilterPrimers' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o pslFilterPrimers.o -c pslFilterPrimers.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslFilterPrimers pslFilterPrimers.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslFilterPrimers make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/pslFilterPrimers' if test -d pslGlue ; then cd pslGlue && echo pslGlue && make ; fi pslGlue make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/pslGlue' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o pslGlue.o -c pslGlue.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslGlue pslGlue.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslGlue make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/pslGlue' if test -d pslHitPercent ; then cd pslHitPercent && echo pslHitPercent && make ; fi pslHitPercent make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/pslHitPercent' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o pslHitPercent.o -c pslHitPercent.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslHitPercent pslHitPercent.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslHitPercent make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/pslHitPercent' if test -d pslIntronsOnly ; then cd pslIntronsOnly && echo pslIntronsOnly && make ; fi pslIntronsOnly make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/pslIntronsOnly' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o pslIntronsOnly.o -c pslIntronsOnly.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslIntronsOnly pslIntronsOnly.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslIntronsOnly make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/pslIntronsOnly' if test -d pslQuickFilter ; then cd pslQuickFilter && echo pslQuickFilter && make ; fi pslQuickFilter make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/pslQuickFilter' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o pslQuickFilter.o -c pslQuickFilter.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslQuickFilter pslQuickFilter.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslQuickFilter make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/pslQuickFilter' if test -d pslSimp ; then cd pslSimp && echo pslSimp && make ; fi pslSimp make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/pslSimp' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o pslSimp.o -c pslSimp.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslSimp pslSimp.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslSimp make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/pslSimp' if test -d pslSortAcc ; then cd pslSortAcc && echo pslSortAcc && make ; fi pslSortAcc make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/pslSortAcc' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o pslSortAcc.o -c pslSortAcc.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslSortAcc pslSortAcc.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslSortAcc make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/pslSortAcc' if test -d pslSplitOnTarget ; then cd pslSplitOnTarget && echo pslSplitOnTarget && make ; fi pslSplitOnTarget make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/pslSplitOnTarget' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o pslSplitOnTarget.o -c pslSplitOnTarget.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslSplitOnTarget pslSplitOnTarget.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslSplitOnTarget make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/pslSplitOnTarget' if test -d pslUnpile ; then cd pslUnpile && echo pslUnpile && make ; fi pslUnpile make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/pslUnpile' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o pslUnpile.o -c pslUnpile.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslUnpile pslUnpile.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslUnpile make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/pslUnpile' if test -d qa ; then cd qa && echo qa && make ; fi qa make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/qa' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/apacheMonitor apacheMonitor.c ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lmariadb -lz -lpthread -lm -lssl -lcrypto -lm gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/checkCardinality checkCardinality.c ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lmariadb -lz -lpthread -lm -lssl -lcrypto -lm gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/countNib countNib.c ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lmariadb -lz -lpthread -lm -lssl -lcrypto -lm gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/dumpNib dumpNib.c ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lmariadb -lz -lpthread -lm -lssl -lcrypto -lm gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/gbSeqCheck gbSeqCheck.c ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lmariadb -lz -lpthread -lm -lssl -lcrypto -lm gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/reviewIndexes reviewIndexes.c ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lmariadb -lz -lpthread -lm -lssl -lcrypto -lm gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/seqCheck seqCheck.c ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lmariadb -lz -lpthread -lm -lssl -lcrypto -lm gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/getChroms getChroms.c ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lmariadb -lz -lpthread -lm -lssl -lcrypto -lm gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/checkChain checkChain.c ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lmariadb -lz -lpthread -lm -lssl -lcrypto -lm gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/testSearch testSearch.c ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lmariadb -lz -lpthread -lm -lssl -lcrypto -lm In function ‘hgPositionsFind’, inlined from ‘searchAndCompare’ at testSearch.c:262:15: ../lib/hgFind.c:3930:23: warning: ‘start’ may be used uninitialized [-Wmaybe-uninitialized] 3930 | start = start + relStart; | ^ ../lib/hgFind.c: In function ‘searchAndCompare’: ../lib/hgFind.c:3923:9: note: ‘start’ was declared here 3923 | int start, end; | ^ In function ‘hgPositionsFind’, inlined from ‘searchAndCompare’ at testSearch.c:262:15: ../lib/hgFind.c:3931:12: warning: ‘end’ may be used uninitialized [-Wmaybe-uninitialized] 3931 | if (end > chromSize) | ^ ../lib/hgFind.c: In function ‘searchAndCompare’: ../lib/hgFind.c:3923:16: note: ‘end’ was declared here 3923 | int start, end; | ^ In function ‘hgPositionsFind’, inlined from ‘searchAndCompare’ at testSearch.c:262:15: ../lib/hgFind.c:3936:5: warning: ‘chrom’ may be used uninitialized [-Wmaybe-uninitialized] 3936 | singlePos(hgp, "Chromosome Range", NULL, "chromInfo", originalTerm, | ^ ../lib/hgFind.c: In function ‘searchAndCompare’: ../lib/hgFind.c:3922:11: note: ‘chrom’ was declared here 3922 | char *chrom; | ^ gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/timePosTable timePosTable.c ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lmariadb -lz -lpthread -lm -lssl -lcrypto -lm make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/qa' if test -d ratStuff ; then cd ratStuff && echo ratStuff && make ; fi ratStuff make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/ratStuff' cd stageMultiz && echo stageMultiz && make stageMultiz make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/ratStuff/stageMultiz' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o stageMultiz.o -c stageMultiz.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/stageMultiz stageMultiz.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/stageMultiz make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/ratStuff/stageMultiz' cd mafAddIRows && echo mafAddIRows && make mafAddIRows make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/ratStuff/mafAddIRows' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o mafAddIRows.o -c mafAddIRows.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/mafAddIRows mafAddIRows.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/mafAddIRows make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/ratStuff/mafAddIRows' cd mafAddQRows && echo mafAddQRows && make mafAddQRows make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/ratStuff/mafAddQRows' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o mafAddQRows.o -c mafAddQRows.c mafAddQRows.c: In function ‘loadQualityData.isra.0’: mafAddQRows.c:230:1: warning: ‘strncpy’ specified bound 1024 equals destination size [-Wstringop-truncation] 230 | strncpy(buffer, mc->src, sizeof(buffer)); | ^ gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/mafAddQRows mafAddQRows.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/mafAddQRows make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/ratStuff/mafAddQRows' cd mafFilter && echo mafFilter && make mafFilter make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/ratStuff/mafFilter' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o mafFilter.o -c mafFilter.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/mafFilter mafFilter.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/mafFilter make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/ratStuff/mafFilter' cd mafFrag && echo mafFrag && make mafFrag make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/ratStuff/mafFrag' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o mafFrag.o -c mafFrag.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/mafFrag mafFrag.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/mafFrag make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/ratStuff/mafFrag' cd mafFrags && echo mafFrags && make mafFrags make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/ratStuff/mafFrags' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o mafFrags.o -c mafFrags.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/mafFrags mafFrags.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/mafFrags make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/ratStuff/mafFrags' cd mafGene && echo mafGene && make mafGene make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/ratStuff/mafGene' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o mafGene.o -c mafGene.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/mafGene mafGene.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/mafGene make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/ratStuff/mafGene' cd mafMeFirst && echo mafMeFirst && make mafMeFirst make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/ratStuff/mafMeFirst' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o mafMeFirst.o -c mafMeFirst.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/mafMeFirst mafMeFirst.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/mafMeFirst make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/ratStuff/mafMeFirst' cd mafSpeciesList && echo mafSpeciesList && make mafSpeciesList make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/ratStuff/mafSpeciesList' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o mafSpeciesList.o -c mafSpeciesList.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/mafSpeciesList mafSpeciesList.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/mafSpeciesList make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/ratStuff/mafSpeciesList' cd mafSpeciesSubset && echo mafSpeciesSubset && make mafSpeciesSubset make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/ratStuff/mafSpeciesSubset' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o mafSpeciesSubset.o -c mafSpeciesSubset.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/mafSpeciesSubset mafSpeciesSubset.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/mafSpeciesSubset make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/ratStuff/mafSpeciesSubset' cd mafSplit && echo mafSplit && make mafSplit make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/ratStuff/mafSplit' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o mafSplit.o -c mafSplit.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/mafSplit mafSplit.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/mafSplit make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/ratStuff/mafSplit' cd mafSplitPos && echo mafSplitPos && make mafSplitPos make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/ratStuff/mafSplitPos' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o mafSplitPos.o -c mafSplitPos.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/mafSplitPos mafSplitPos.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/mafSplitPos make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/ratStuff/mafSplitPos' cd mafsInRegion && echo mafsInRegion && make mafsInRegion make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/ratStuff/mafsInRegion' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o mafsInRegion.o -c mafsInRegion.c In file included from mafsInRegion.c:6: mafsInRegion.c: In function ‘extractMafs’: ../../../inc/common.h:801:31: warning: ‘strcmp’ reading 1 or more bytes from a region of size 0 [-Wstringop-overread] 801 | #define differentString(a,b) (strcmp(a,b)) | ~^~~~~~~~~~~~ cc1: note: source object is likely at address zero gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/mafsInRegion mafsInRegion.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/mafsInRegion make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/ratStuff/mafsInRegion' cd mafOrder && echo mafOrder && make mafOrder make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/ratStuff/mafOrder' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o mafOrder.o -c mafOrder.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/mafOrder mafOrder.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/mafOrder make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/ratStuff/mafOrder' make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/ratStuff' if test -d relPairs ; then cd relPairs && echo relPairs && make ; fi relPairs make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/relPairs' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o relPairs.o -c relPairs.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/relPairs relPairs.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/relPairs make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/relPairs' if test -d recycleDb ; then cd recycleDb && echo recycleDb && make ; fi recycleDb make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/recycleDb' cd bedUp && make make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/recycleDb/bedUp' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o bedUp.o -c bedUp.c bedUp.c: In function ‘unpackPslName’: bedUp.c:60:1: warning: ‘strncpy’ specified bound 128 equals destination size [-Wstringop-truncation] 60 | strncpy(buf, pslName, sizeof(buf)); | ^ gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bedUp bedUp.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bedUp make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/recycleDb/bedUp' cd bedDown && make make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/recycleDb/bedDown' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o bedDown.o -c bedDown.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bedDown bedDown.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bedDown make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/recycleDb/bedDown' make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/recycleDb' if test -d rnaStructure ; then cd rnaStructure && echo rnaStructure && make ; fi rnaStructure make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/rnaStructure' ( cd hgLoadRnaFold && echo hgLoadRnaFold && make ) hgLoadRnaFold make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/rnaStructure/hgLoadRnaFold' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hgLoadRnaFold.o -c hgLoadRnaFold.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgLoadRnaFold hgLoadRnaFold.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgLoadRnaFold make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/rnaStructure/hgLoadRnaFold' ( cd rnaFoldBig && echo rnaFoldBig && make ) rnaFoldBig make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/rnaStructure/rnaFoldBig' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o rnaFoldBig.o -c rnaFoldBig.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/rnaFoldBig rnaFoldBig.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/rnaFoldBig make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/rnaStructure/rnaFoldBig' ( cd utrFa && echo utrFa && make ) utrFa make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/rnaStructure/utrFa' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o utrFa.o -c utrFa.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/utrFa utrFa.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/utrFa make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/rnaStructure/utrFa' make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/rnaStructure' if test -d sage ; then cd sage && echo sage && make ; fi sage make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/sage' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o addAveMedScoreToPsls.o -c addAveMedScoreToPsls.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o createSageSummary.o -c createSageSummary.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -o addAveMedScoreToPsls addAveMedScoreToPsls.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm -lmariadb -lz -lpthread -lm -lssl -lcrypto gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -o createSageSummary createSageSummary.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm -lmariadb -lz -lpthread -lm -lssl -lcrypto rm -f /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/addAveMedScoreToPsls mv addAveMedScoreToPsls /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/ rm -f /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/createSageSummary mv createSageSummary /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/ make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/sage' if test -d scanRa ; then cd scanRa && echo scanRa && make ; fi scanRa make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/scanRa' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o scanRa.o -c scanRa.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/scanRa scanRa.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/scanRa make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/scanRa' if test -d semiNorm ; then cd semiNorm && echo semiNorm && make ; fi semiNorm make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/semiNorm' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o semiNorm.o -c semiNorm.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/semiNorm semiNorm.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/semiNorm make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/semiNorm' if test -d sim4big ; then cd sim4big && echo sim4big && make ; fi sim4big make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/sim4big' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o sim4big.o -c sim4big.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/sim4big sim4big.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/sim4big make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/sim4big' if test -d snpException ; then cd snpException && echo snpException && make ; fi snpException make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/snpException' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o snpException.o -c snpException.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/snpException snpException.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/snpException make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/snpException' if test -d snp ; then cd snp && echo snp && make ; fi snp make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/snp' make -C snpLoad make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/snp/snpLoad' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o snpNcbiToUcsc.o -c snpNcbiToUcsc.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/snpNcbiToUcsc snpNcbiToUcsc.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lmariadb -lz -lpthread -lm -lssl -lcrypto -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/snpNcbiToUcsc gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hapmapPhaseIIISummary.o -c hapmapPhaseIIISummary.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hapmapPhaseIIISummary hapmapPhaseIIISummary.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lmariadb -lz -lpthread -lm -lssl -lcrypto -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hapmapPhaseIIISummary make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/snp/snpLoad' make -C snpMask make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/snp/snpMask' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o snpMaskSingle.o -c snpMaskSingle.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/snpMaskSingle snpMaskSingle.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lmariadb -lz -lpthread -lm -lssl -lcrypto -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/snpMaskSingle gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o snpMaskAddInsertions.o -c snpMaskAddInsertions.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/snpMaskAddInsertions snpMaskAddInsertions.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lmariadb -lz -lpthread -lm -lssl -lcrypto -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/snpMaskAddInsertions gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o snpMaskCutDeletions.o -c snpMaskCutDeletions.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/snpMaskCutDeletions snpMaskCutDeletions.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lmariadb -lz -lpthread -lm -lssl -lcrypto -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/snpMaskCutDeletions make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/snp/snpMask' make -C snpValid make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/snp/snpValid' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o snpValid.o -c snpValid.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/snpValid snpValid.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/snpValid make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/snp/snpValid' make -C dbSnpJsonToTab make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/snp/dbSnpJsonToTab' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o dbSnpJsonToTab.o -c dbSnpJsonToTab.c dbSnpJsonToTab.c: In function ‘parseSpdis’: dbSnpJsonToTab.c:217:45: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 217 | errAbort("Invalid deleted_sequence '%s' in spdi for %s", del, name); | ^~ dbSnpJsonToTab.c:217:45: warning: ‘%s’ directive argument is null [-Wformat-overflow=] gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/dbSnpJsonToTab dbSnpJsonToTab.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/dbSnpJsonToTab make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/snp/dbSnpJsonToTab' make -C checkBigDbSnp make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/snp/checkBigDbSnp' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o checkBigDbSnp.o -c checkBigDbSnp.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/checkBigDbSnp checkBigDbSnp.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/checkBigDbSnp make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/snp/checkBigDbSnp' make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/snp' if test -d spideyToPsl ; then cd spideyToPsl && echo spideyToPsl && make ; fi spideyToPsl make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/spideyToPsl' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o spideyToPsl.o -c spideyToPsl.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/spideyToPsl spideyToPsl.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/spideyToPsl make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/spideyToPsl' if test -d splitFa ; then cd splitFa && echo splitFa && make ; fi splitFa make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/splitFa' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o splitFa.o -c splitFa.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/splitFa splitFa.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/splitFa make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/splitFa' if test -d splitFaIntoContigs ; then cd splitFaIntoContigs && echo splitFaIntoContigs && make ; fi splitFaIntoContigs make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/splitFaIntoContigs' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o splitFaIntoContigs.o -c splitFaIntoContigs.c splitFaIntoContigs.c: In function ‘splitFaIntoContigs’: splitFaIntoContigs.c:273:25: warning: ‘.fa’ directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 273 | sprintf(filename, "%s/%s.fa", destDir, chromName); | ^~~ In file included from /usr/include/stdio.h:974, from ../../inc/common.h:30, from splitFaIntoContigs.c:9: In function ‘sprintf’, inlined from ‘writeChromFaFile’ at splitFaIntoContigs.c:273:1, inlined from ‘splitFaIntoContigs’ at splitFaIntoContigs.c:514:5: /usr/include/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output 5 or more bytes (assuming 1028) into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ splitFaIntoContigs.c: In function ‘splitFaIntoContigs’: splitFaIntoContigs.c:240:25: warning: ‘.agp’ directive writing 4 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 240 | sprintf(filename, "%s/%s.agp", destDir, chromName); | ^~~~ In function ‘sprintf’, inlined from ‘writeChromAgpFile’ at splitFaIntoContigs.c:240:1, inlined from ‘splitFaIntoContigs’ at splitFaIntoContigs.c:515:5: /usr/include/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output 6 or more bytes (assuming 1029) into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/splitFaIntoContigs splitFaIntoContigs.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/splitFaIntoContigs make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/splitFaIntoContigs' if test -d test ; then cd test && echo test && make ; fi test make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/test' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o test.o -c test.c gcc -O -g -o test test.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lmariadb -lz -lpthread -lm -lssl -lcrypto -lm make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/test' if test -d txCds ; then cd txCds && echo txCds && make ; fi txCds make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txCds' ( cd txCdsBadBed && echo txCdsBadBed && make ) txCdsBadBed make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txCds/txCdsBadBed' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o txCdsBadBed.o -c txCdsBadBed.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txCdsBadBed txCdsBadBed.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txCdsBadBed make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txCds/txCdsBadBed' ( cd txCdsCluster && echo txCdsCluster && make ) txCdsCluster make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txCds/txCdsCluster' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o txCdsCluster.o -c txCdsCluster.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txCdsCluster txCdsCluster.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txCdsCluster make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txCds/txCdsCluster' ( cd txCdsEvFromBed && echo txCdsEvFromBed && make ) txCdsEvFromBed make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txCds/txCdsEvFromBed' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o txCdsEvFromBed.o -c txCdsEvFromBed.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txCdsEvFromBed txCdsEvFromBed.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txCdsEvFromBed make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txCds/txCdsEvFromBed' ( cd txCdsEvFromBorf && echo txCdsEvFromBorf && make ) txCdsEvFromBorf make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txCds/txCdsEvFromBorf' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o txCdsEvFromBorf.o -c txCdsEvFromBorf.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txCdsEvFromBorf txCdsEvFromBorf.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txCdsEvFromBorf make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txCds/txCdsEvFromBorf' ( cd txCdsEvFromProtein && echo txCdsEvFromProtein && make ) txCdsEvFromProtein make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txCds/txCdsEvFromProtein' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o txCdsEvFromProtein.o -c txCdsEvFromProtein.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txCdsEvFromProtein txCdsEvFromProtein.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txCdsEvFromProtein make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txCds/txCdsEvFromProtein' ( cd txCdsEvFromRna && echo txCdsEvFromRna && make ) txCdsEvFromRna make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txCds/txCdsEvFromRna' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o txCdsEvFromRna.o -c txCdsEvFromRna.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txCdsEvFromRna txCdsEvFromRna.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txCdsEvFromRna make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txCds/txCdsEvFromRna' ( cd txCdsGoodBed && echo txCdsGoodBed && make ) txCdsGoodBed make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txCds/txCdsGoodBed' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o txCdsGoodBed.o -c txCdsGoodBed.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txCdsGoodBed txCdsGoodBed.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txCdsGoodBed make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txCds/txCdsGoodBed' ( cd txCdsOrfInfo && echo txCdsOrfInfo && make ) txCdsOrfInfo make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txCds/txCdsOrfInfo' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o txCdsOrfInfo.o -c txCdsOrfInfo.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txCdsOrfInfo txCdsOrfInfo.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txCdsOrfInfo make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txCds/txCdsOrfInfo' ( cd txCdsOrtho && echo txCdsOrtho && make ) txCdsOrtho make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txCds/txCdsOrtho' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o txCdsOrtho.o -c txCdsOrtho.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txCdsOrtho txCdsOrtho.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txCdsOrtho make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txCds/txCdsOrtho' ( cd txCdsPick && echo txCdsPick && make ) txCdsPick make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txCds/txCdsPick' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o txCdsPick.o -c txCdsPick.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txCdsPick txCdsPick.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txCdsPick make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txCds/txCdsPick' ( cd txCdsPredict && echo txCdsPredict && make ) txCdsPredict make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txCds/txCdsPredict' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o txCdsPredict.o -c txCdsPredict.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txCdsPredict txCdsPredict.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txCdsPredict make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txCds/txCdsPredict' ( cd txCdsRaExceptions && echo txCdsRaExceptions && make ) txCdsRaExceptions make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txCds/txCdsRaExceptions' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o txCdsRaExceptions.o -c txCdsRaExceptions.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txCdsRaExceptions txCdsRaExceptions.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txCdsRaExceptions make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txCds/txCdsRaExceptions' ( cd txCdsRefBestEvOnly && echo txCdsRefBestEvOnly && make ) txCdsRefBestEvOnly make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txCds/txCdsRefBestEvOnly' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o txCdsRefBestEvOnly.o -c txCdsRefBestEvOnly.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txCdsRefBestEvOnly txCdsRefBestEvOnly.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txCdsRefBestEvOnly make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txCds/txCdsRefBestEvOnly' ( cd txCdsRepick && echo txCdsRepick && make ) txCdsRepick make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txCds/txCdsRepick' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o txCdsRepick.o -c txCdsRepick.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txCdsRepick txCdsRepick.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txCdsRepick make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txCds/txCdsRepick' ( cd txCdsSuspect && echo txCdsSuspect && make ) txCdsSuspect make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txCds/txCdsSuspect' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o txCdsSuspect.o -c txCdsSuspect.c txCdsSuspect.c: In function ‘txCdsSuspect’: txCdsSuspect.c:203:5: warning: variable ‘txWithCdsCount’ set but not used [-Wunused-but-set-variable=] 203 | int txWithCdsCount = 0; | ^~~~~~~~~~~~~~ gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txCdsSuspect txCdsSuspect.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txCdsSuspect make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txCds/txCdsSuspect' ( cd txCdsSvmInput && echo txCdsSvmInput && make ) txCdsSvmInput make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txCds/txCdsSvmInput' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o txCdsSvmInput.o -c txCdsSvmInput.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txCdsSvmInput txCdsSvmInput.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txCdsSvmInput make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txCds/txCdsSvmInput' ( cd txCdsToGene && echo txCdsToGene && make ) txCdsToGene make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txCds/txCdsToGene' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o txCdsToGene.o -c txCdsToGene.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txCdsToGene txCdsToGene.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txCdsToGene make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txCds/txCdsToGene' ( cd txCdsWeed && echo txCdsWeed && make ) txCdsWeed make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txCds/txCdsWeed' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o txCdsWeed.o -c txCdsWeed.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txCdsWeed txCdsWeed.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txCdsWeed make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txCds/txCdsWeed' ( cd txInfoAssemble && echo txInfoAssemble && make ) txInfoAssemble make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txCds/txInfoAssemble' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o txInfoAssemble.o -c txInfoAssemble.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txInfoAssemble txInfoAssemble.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txInfoAssemble make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txCds/txInfoAssemble' make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txCds' if test -d txGene ; then cd txGene && echo txGene && make ; fi txGene make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGene' make -C txGenbankData make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGene/txGenbankData' cp -p txGenbankData /builddir/bin/scripts/txGenbankData.tmp mv -f /builddir/bin/scripts/txGenbankData.tmp /builddir/bin/scripts/txGenbankData make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGene/txGenbankData' make -C txGeneAccession make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGene/txGeneAccession' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o txGeneAccession.o -c txGeneAccession.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txGeneAccession txGeneAccession.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txGeneAccession make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGene/txGeneAccession' make -C txGeneAlias make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGene/txGeneAlias' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o txGeneAlias.o -c txGeneAlias.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txGeneAlias txGeneAlias.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txGeneAlias make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGene/txGeneAlias' make -C txGeneAltProt make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGene/txGeneAltProt' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o txGeneAltProt.o -c txGeneAltProt.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txGeneAltProt txGeneAltProt.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txGeneAltProt make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGene/txGeneAltProt' make -C txGeneCanonical make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGene/txGeneCanonical' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o txGeneCanonical.o -c txGeneCanonical.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txGeneCanonical txGeneCanonical.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txGeneCanonical make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGene/txGeneCanonical' make -C txGeneCdsMap make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGene/txGeneCdsMap' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o txGeneCdsMap.o -c txGeneCdsMap.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txGeneCdsMap txGeneCdsMap.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txGeneCdsMap make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGene/txGeneCdsMap' make -C txGeneColor make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGene/txGeneColor' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o txGeneColor.o -c txGeneColor.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txGeneColor txGeneColor.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txGeneColor make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGene/txGeneColor' make -C txGeneExplainUpdate1 make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGene/txGeneExplainUpdate1' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o txGeneExplainUpdate1.o -c txGeneExplainUpdate1.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txGeneExplainUpdate1 txGeneExplainUpdate1.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txGeneExplainUpdate1 make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGene/txGeneExplainUpdate1' make -C txGeneFromBed make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGene/txGeneFromBed' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o txGeneFromBed.o -c txGeneFromBed.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txGeneFromBed txGeneFromBed.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txGeneFromBed make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGene/txGeneFromBed' make -C txGeneProtAndRna make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGene/txGeneProtAndRna' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o txGeneProtAndRna.o -c txGeneProtAndRna.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txGeneProtAndRna txGeneProtAndRna.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txGeneProtAndRna make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGene/txGeneProtAndRna' make -C txGeneSeparateNoncoding make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGene/txGeneSeparateNoncoding' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o txGeneSeparateNoncoding.o -c txGeneSeparateNoncoding.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txGeneSeparateNoncoding txGeneSeparateNoncoding.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txGeneSeparateNoncoding make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGene/txGeneSeparateNoncoding' make -C txGeneValidation make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGene/txGeneValidation' mkdir -p /builddir/bin/scripts cp checkRandomLinesExist.py compareModifiedFileSizes.csh compareTableSizesFromDbSnoop.py /builddir/bin/scripts/ make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGene/txGeneValidation' make -C txGeneXref make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGene/txGeneXref' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o txGeneXref.o -c txGeneXref.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txGeneXref txGeneXref.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txGeneXref make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGene/txGeneXref' make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGene' if test -d txGraph ; then cd txGraph && echo txGraph && make ; fi txGraph make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGraph' make -C agxToTxg make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGraph/agxToTxg' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o agxToTxg.o -c agxToTxg.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/agxToTxg agxToTxg.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/agxToTxg make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGraph/agxToTxg' make -C bedToTxEdges make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGraph/bedToTxEdges' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o bedToTxEdges.o -c bedToTxEdges.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bedToTxEdges bedToTxEdges.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bedToTxEdges make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGraph/bedToTxEdges' make -C txAbFragFind make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGraph/txAbFragFind' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o txAbFragFind.o -c txAbFragFind.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txAbFragFind txAbFragFind.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txAbFragFind make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGraph/txAbFragFind' make -C txBedToGraph make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGraph/txBedToGraph' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o txBedToGraph.o -c txBedToGraph.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o makeGraph.o -c makeGraph.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txBedToGraph txBedToGraph.o makeGraph.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txBedToGraph make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGraph/txBedToGraph' make -C txOrtho make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGraph/txOrtho' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o txOrtho.o -c txOrtho.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txOrtho txOrtho.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txOrtho make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGraph/txOrtho' make -C txPslFilter make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGraph/txPslFilter' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o txPslFilter.o -c txPslFilter.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txPslFilter txPslFilter.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txPslFilter make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGraph/txPslFilter' make -C txPslToBed make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGraph/txPslToBed' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o txPslToBed.o -c txPslToBed.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txPslToBed txPslToBed.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txPslToBed make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGraph/txPslToBed' make -C txReadRa make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGraph/txReadRa' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o txReadRa.o -c txReadRa.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txReadRa txReadRa.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txReadRa make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGraph/txReadRa' make -C txWalk make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGraph/txWalk' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o txWalk.o -c txWalk.c txWalk.c: In function ‘makeTrackerList’: txWalk.c:151:5: warning: variable ‘i’ set but not used [-Wunused-but-set-variable=] 151 | int i; | ^ gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txWalk txWalk.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txWalk make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGraph/txWalk' make -C txgAddEvidence make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGraph/txgAddEvidence' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o txgAddEvidence.o -c txgAddEvidence.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txgAddEvidence txgAddEvidence.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txgAddEvidence make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGraph/txgAddEvidence' make -C txgAnalyze make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGraph/txgAnalyze' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o txgAnalyze.o -c txgAnalyze.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txgAnalyze txgAnalyze.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txgAnalyze make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGraph/txgAnalyze' make -C txgGoodEdges make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGraph/txgGoodEdges' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o txgGoodEdges.o -c txgGoodEdges.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txgGoodEdges txgGoodEdges.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txgGoodEdges make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGraph/txgGoodEdges' make -C txgToAgx make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGraph/txgToAgx' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o txgToAgx.o -c txgToAgx.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txgToAgx txgToAgx.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txgToAgx make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGraph/txgToAgx' make -C txgToXml make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGraph/txgToXml' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o txgToXml.o -c txgToXml.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txgToXml txgToXml.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txgToXml make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGraph/txgToXml' make -C txgTrim make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGraph/txgTrim' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o txgTrim.o -c txgTrim.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txgTrim txgTrim.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/txgTrim make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGraph/txgTrim' make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/txGraph' if test -d utils ; then cd utils && echo utils && make ; fi utils make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils' if test -d refreshNamedSessionCustomTracks ; then cd refreshNamedSessionCustomTracks && echo refreshNamedSessionCustomTracks && make ; fi refreshNamedSessionCustomTracks make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/refreshNamedSessionCustomTracks' gcc -DCGI_BIN=\"/usr/local/apache/cgi-bin\" -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o refreshNamedSessionCustomTracks.o -c refreshNamedSessionCustomTracks.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/refreshNamedSessionCustomTracks refreshNamedSessionCustomTracks.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/refreshNamedSessionCustomTracks make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/refreshNamedSessionCustomTracks' if test -d automation ; then cd automation && echo automation && make ; fi automation make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/automation' mkdir -p /builddir/bin/scripts rm -f /builddir/bin/scripts/Encode.pm echo cp -p Encode.pm /builddir/bin/scripts cp -p Encode.pm /builddir/bin/scripts cp -p Encode.pm /builddir/bin/scripts chmod 664 /builddir/bin/scripts/Encode.pm rm -f /builddir/bin/scripts/HgAutomate.pm echo cp -p HgAutomate.pm /builddir/bin/scripts cp -p HgAutomate.pm /builddir/bin/scripts cp -p HgAutomate.pm /builddir/bin/scripts chmod 664 /builddir/bin/scripts/HgAutomate.pm rm -f /builddir/bin/scripts/HgDb.pm echo cp -p HgDb.pm /builddir/bin/scripts cp -p HgDb.pm /builddir/bin/scripts cp -p HgDb.pm /builddir/bin/scripts chmod 664 /builddir/bin/scripts/HgDb.pm rm -f /builddir/bin/scripts/RAFile.pm echo cp -p RAFile.pm /builddir/bin/scripts cp -p RAFile.pm /builddir/bin/scripts cp -p RAFile.pm /builddir/bin/scripts chmod 664 /builddir/bin/scripts/RAFile.pm rm -f /builddir/bin/scripts/SafePipe.pm echo cp -p SafePipe.pm /builddir/bin/scripts cp -p SafePipe.pm /builddir/bin/scripts cp -p SafePipe.pm /builddir/bin/scripts chmod 664 /builddir/bin/scripts/SafePipe.pm rm -f /builddir/bin/scripts/EnsGeneAutomate.pm echo cp -p EnsGeneAutomate.pm /builddir/bin/scripts cp -p EnsGeneAutomate.pm /builddir/bin/scripts cp -p EnsGeneAutomate.pm /builddir/bin/scripts chmod 664 /builddir/bin/scripts/EnsGeneAutomate.pm rm -f /builddir/bin/scripts/HgRemoteScript.pm echo cp -p HgRemoteScript.pm /builddir/bin/scripts cp -p HgRemoteScript.pm /builddir/bin/scripts cp -p HgRemoteScript.pm /builddir/bin/scripts chmod 664 /builddir/bin/scripts/HgRemoteScript.pm rm -f /builddir/bin/scripts/HgStepManager.pm echo cp -p HgStepManager.pm /builddir/bin/scripts cp -p HgStepManager.pm /builddir/bin/scripts cp -p HgStepManager.pm /builddir/bin/scripts chmod 664 /builddir/bin/scripts/HgStepManager.pm rm -f /builddir/bin/scripts/AsmHub.pm echo cp -p AsmHub.pm /builddir/bin/scripts cp -p AsmHub.pm /builddir/bin/scripts cp -p AsmHub.pm /builddir/bin/scripts chmod 664 /builddir/bin/scripts/AsmHub.pm rm -f /builddir/bin/scripts/addQuickLift.py echo cp -p addQuickLift.py /builddir/bin/scripts cp -p addQuickLift.py /builddir/bin/scripts cp -p addQuickLift.py /builddir/bin/scripts chmod +x /builddir/bin/scripts/addQuickLift.py rm -f /builddir/bin/scripts/asmHubAllGaps.pl echo cp -p asmHubAllGaps.pl /builddir/bin/scripts cp -p asmHubAllGaps.pl /builddir/bin/scripts cp -p asmHubAllGaps.pl /builddir/bin/scripts chmod +x /builddir/bin/scripts/asmHubAllGaps.pl rm -f /builddir/bin/scripts/asmHubAssembly.pl echo cp -p asmHubAssembly.pl /builddir/bin/scripts cp -p asmHubAssembly.pl /builddir/bin/scripts cp -p asmHubAssembly.pl /builddir/bin/scripts chmod +x /builddir/bin/scripts/asmHubAssembly.pl rm -f /builddir/bin/scripts/asmHubAugustusGene.pl echo cp -p asmHubAugustusGene.pl /builddir/bin/scripts cp -p asmHubAugustusGene.pl /builddir/bin/scripts cp -p asmHubAugustusGene.pl /builddir/bin/scripts chmod +x /builddir/bin/scripts/asmHubAugustusGene.pl rm -f /builddir/bin/scripts/asmHubChainNetTrackDb.pl echo cp -p asmHubChainNetTrackDb.pl /builddir/bin/scripts cp -p asmHubChainNetTrackDb.pl /builddir/bin/scripts cp -p asmHubChainNetTrackDb.pl /builddir/bin/scripts chmod +x /builddir/bin/scripts/asmHubChainNetTrackDb.pl rm -f /builddir/bin/scripts/asmHubCpG.pl echo cp -p asmHubCpG.pl /builddir/bin/scripts cp -p asmHubCpG.pl /builddir/bin/scripts cp -p asmHubCpG.pl /builddir/bin/scripts chmod +x /builddir/bin/scripts/asmHubCpG.pl rm -f /builddir/bin/scripts/asmHubEnsGene.pl echo cp -p asmHubEnsGene.pl /builddir/bin/scripts cp -p asmHubEnsGene.pl /builddir/bin/scripts cp -p asmHubEnsGene.pl /builddir/bin/scripts chmod +x /builddir/bin/scripts/asmHubEnsGene.pl rm -f /builddir/bin/scripts/asmHubGap.pl echo cp -p asmHubGap.pl /builddir/bin/scripts cp -p asmHubGap.pl /builddir/bin/scripts cp -p asmHubGap.pl /builddir/bin/scripts chmod +x /builddir/bin/scripts/asmHubGap.pl rm -f /builddir/bin/scripts/asmHubGatewayPage.pl echo cp -p asmHubGatewayPage.pl /builddir/bin/scripts cp -p asmHubGatewayPage.pl /builddir/bin/scripts cp -p asmHubGatewayPage.pl /builddir/bin/scripts chmod +x /builddir/bin/scripts/asmHubGatewayPage.pl rm -f /builddir/bin/scripts/asmHubGc5Percent.pl echo cp -p asmHubGc5Percent.pl /builddir/bin/scripts cp -p asmHubGc5Percent.pl /builddir/bin/scripts cp -p asmHubGc5Percent.pl /builddir/bin/scripts chmod +x /builddir/bin/scripts/asmHubGc5Percent.pl rm -f /builddir/bin/scripts/asmHubHtml.pl echo cp -p asmHubHtml.pl /builddir/bin/scripts cp -p asmHubHtml.pl /builddir/bin/scripts cp -p asmHubHtml.pl /builddir/bin/scripts chmod +x /builddir/bin/scripts/asmHubHtml.pl rm -f /builddir/bin/scripts/asmHubRepeatMasker.sh echo cp -p asmHubRepeatMasker.sh /builddir/bin/scripts cp -p asmHubRepeatMasker.sh /builddir/bin/scripts cp -p asmHubRepeatMasker.sh /builddir/bin/scripts chmod +x /builddir/bin/scripts/asmHubRepeatMasker.sh rm -f /builddir/bin/scripts/asmHubRmsk.pl echo cp -p asmHubRmsk.pl /builddir/bin/scripts cp -p asmHubRmsk.pl /builddir/bin/scripts cp -p asmHubRmsk.pl /builddir/bin/scripts chmod +x /builddir/bin/scripts/asmHubRmsk.pl rm -f /builddir/bin/scripts/asmHubRmskJoinAlign.pl echo cp -p asmHubRmskJoinAlign.pl /builddir/bin/scripts cp -p asmHubRmskJoinAlign.pl /builddir/bin/scripts cp -p asmHubRmskJoinAlign.pl /builddir/bin/scripts chmod +x /builddir/bin/scripts/asmHubRmskJoinAlign.pl rm -f /builddir/bin/scripts/asmHubSimpleRepeat.pl echo cp -p asmHubSimpleRepeat.pl /builddir/bin/scripts cp -p asmHubSimpleRepeat.pl /builddir/bin/scripts cp -p asmHubSimpleRepeat.pl /builddir/bin/scripts chmod +x /builddir/bin/scripts/asmHubSimpleRepeat.pl rm -f /builddir/bin/scripts/asmHubTrackDb.sh echo cp -p asmHubTrackDb.sh /builddir/bin/scripts cp -p asmHubTrackDb.sh /builddir/bin/scripts cp -p asmHubTrackDb.sh /builddir/bin/scripts chmod +x /builddir/bin/scripts/asmHubTrackDb.sh rm -f /builddir/bin/scripts/asmHubWindowMasker.pl echo cp -p asmHubWindowMasker.pl /builddir/bin/scripts cp -p asmHubWindowMasker.pl /builddir/bin/scripts cp -p asmHubWindowMasker.pl /builddir/bin/scripts chmod +x /builddir/bin/scripts/asmHubWindowMasker.pl rm -f /builddir/bin/scripts/blastz-make-joblist echo cp -p blastz-make-joblist /builddir/bin/scripts cp -p blastz-make-joblist /builddir/bin/scripts cp -p blastz-make-joblist /builddir/bin/scripts chmod +x /builddir/bin/scripts/blastz-make-joblist rm -f /builddir/bin/scripts/blastz-normalizeLav echo cp -p blastz-normalizeLav /builddir/bin/scripts cp -p blastz-normalizeLav /builddir/bin/scripts cp -p blastz-normalizeLav /builddir/bin/scripts chmod +x /builddir/bin/scripts/blastz-normalizeLav rm -f /builddir/bin/scripts/blastz-run-ucsc echo cp -p blastz-run-ucsc /builddir/bin/scripts cp -p blastz-run-ucsc /builddir/bin/scripts cp -p blastz-run-ucsc /builddir/bin/scripts chmod +x /builddir/bin/scripts/blastz-run-ucsc rm -f /builddir/bin/scripts/doAssemblyHub.pl echo cp -p doAssemblyHub.pl /builddir/bin/scripts cp -p doAssemblyHub.pl /builddir/bin/scripts cp -p doAssemblyHub.pl /builddir/bin/scripts chmod +x /builddir/bin/scripts/doAssemblyHub.pl rm -f /builddir/bin/scripts/doAugustus.pl echo cp -p doAugustus.pl /builddir/bin/scripts cp -p doAugustus.pl /builddir/bin/scripts cp -p doAugustus.pl /builddir/bin/scripts chmod +x /builddir/bin/scripts/doAugustus.pl rm -f /builddir/bin/scripts/doBlastzChainNet.pl echo cp -p doBlastzChainNet.pl /builddir/bin/scripts cp -p doBlastzChainNet.pl /builddir/bin/scripts cp -p doBlastzChainNet.pl /builddir/bin/scripts chmod +x /builddir/bin/scripts/doBlastzChainNet.pl rm -f /builddir/bin/scripts/doCpgIslands.pl echo cp -p doCpgIslands.pl /builddir/bin/scripts cp -p doCpgIslands.pl /builddir/bin/scripts cp -p doCpgIslands.pl /builddir/bin/scripts chmod +x /builddir/bin/scripts/doCpgIslands.pl rm -f /builddir/bin/scripts/doEnsGeneUpdate.pl echo cp -p doEnsGeneUpdate.pl /builddir/bin/scripts cp -p doEnsGeneUpdate.pl /builddir/bin/scripts cp -p doEnsGeneUpdate.pl /builddir/bin/scripts chmod +x /builddir/bin/scripts/doEnsGeneUpdate.pl rm -f /builddir/bin/scripts/doGenscan.pl echo cp -p doGenscan.pl /builddir/bin/scripts cp -p doGenscan.pl /builddir/bin/scripts cp -p doGenscan.pl /builddir/bin/scripts chmod +x /builddir/bin/scripts/doGenscan.pl rm -f /builddir/bin/scripts/doHgNearBlastp.pl echo cp -p doHgNearBlastp.pl /builddir/bin/scripts cp -p doHgNearBlastp.pl /builddir/bin/scripts cp -p doHgNearBlastp.pl /builddir/bin/scripts chmod +x /builddir/bin/scripts/doHgNearBlastp.pl rm -f /builddir/bin/scripts/doIdKeys.pl echo cp -p doIdKeys.pl /builddir/bin/scripts cp -p doIdKeys.pl /builddir/bin/scripts cp -p doIdKeys.pl /builddir/bin/scripts chmod +x /builddir/bin/scripts/doIdKeys.pl rm -f /builddir/bin/scripts/ensemblInfo.pl echo cp -p ensemblInfo.pl /builddir/bin/scripts cp -p ensemblInfo.pl /builddir/bin/scripts cp -p ensemblInfo.pl /builddir/bin/scripts chmod +x /builddir/bin/scripts/ensemblInfo.pl rm -f /builddir/bin/scripts/synBlastp.csh echo cp -p synBlastp.csh /builddir/bin/scripts cp -p synBlastp.csh /builddir/bin/scripts cp -p synBlastp.csh /builddir/bin/scripts chmod +x /builddir/bin/scripts/synBlastp.csh rm -f /builddir/bin/scripts/doRecipBest.pl echo cp -p doRecipBest.pl /builddir/bin/scripts cp -p doRecipBest.pl /builddir/bin/scripts cp -p doRecipBest.pl /builddir/bin/scripts chmod +x /builddir/bin/scripts/doRecipBest.pl rm -f /builddir/bin/scripts/doRepeatMasker.pl echo cp -p doRepeatMasker.pl /builddir/bin/scripts cp -p doRepeatMasker.pl /builddir/bin/scripts cp -p doRepeatMasker.pl /builddir/bin/scripts chmod +x /builddir/bin/scripts/doRepeatMasker.pl rm -f /builddir/bin/scripts/doRepeatModeler.pl echo cp -p doRepeatModeler.pl /builddir/bin/scripts cp -p doRepeatModeler.pl /builddir/bin/scripts cp -p doRepeatModeler.pl /builddir/bin/scripts chmod +x /builddir/bin/scripts/doRepeatModeler.pl rm -f /builddir/bin/scripts/doWindowMasker.pl echo cp -p doWindowMasker.pl /builddir/bin/scripts cp -p doWindowMasker.pl /builddir/bin/scripts cp -p doWindowMasker.pl /builddir/bin/scripts chmod +x /builddir/bin/scripts/doWindowMasker.pl rm -f /builddir/bin/scripts/doSimpleRepeat.pl echo cp -p doSimpleRepeat.pl /builddir/bin/scripts cp -p doSimpleRepeat.pl /builddir/bin/scripts cp -p doSimpleRepeat.pl /builddir/bin/scripts chmod +x /builddir/bin/scripts/doSimpleRepeat.pl rm -f /builddir/bin/scripts/doSameSpeciesLiftOver.pl echo cp -p doSameSpeciesLiftOver.pl /builddir/bin/scripts cp -p doSameSpeciesLiftOver.pl /builddir/bin/scripts cp -p doSameSpeciesLiftOver.pl /builddir/bin/scripts chmod +x /builddir/bin/scripts/doSameSpeciesLiftOver.pl rm -f /builddir/bin/scripts/ensVersions echo cp -p ensVersions /builddir/bin/scripts cp -p ensVersions /builddir/bin/scripts cp -p ensVersions /builddir/bin/scripts chmod +x /builddir/bin/scripts/ensVersions rm -f /builddir/bin/scripts/extractNestedRepeats.pl echo cp -p extractNestedRepeats.pl /builddir/bin/scripts cp -p extractNestedRepeats.pl /builddir/bin/scripts cp -p extractNestedRepeats.pl /builddir/bin/scripts chmod +x /builddir/bin/scripts/extractNestedRepeats.pl rm -f /builddir/bin/scripts/extractGtf.pl echo cp -p extractGtf.pl /builddir/bin/scripts cp -p extractGtf.pl /builddir/bin/scripts cp -p extractGtf.pl /builddir/bin/scripts chmod +x /builddir/bin/scripts/extractGtf.pl rm -f /builddir/bin/scripts/kmerPairs.pl echo cp -p kmerPairs.pl /builddir/bin/scripts cp -p kmerPairs.pl /builddir/bin/scripts cp -p kmerPairs.pl /builddir/bin/scripts chmod +x /builddir/bin/scripts/kmerPairs.pl rm -f /builddir/bin/scripts/kmerCollapsePairedEnds.pl echo cp -p kmerCollapsePairedEnds.pl /builddir/bin/scripts cp -p kmerCollapsePairedEnds.pl /builddir/bin/scripts cp -p kmerCollapsePairedEnds.pl /builddir/bin/scripts chmod +x /builddir/bin/scripts/kmerCollapsePairedEnds.pl rm -f /builddir/bin/scripts/kmerPrint.pl echo cp -p kmerPrint.pl /builddir/bin/scripts cp -p kmerPrint.pl /builddir/bin/scripts cp -p kmerPrint.pl /builddir/bin/scripts chmod +x /builddir/bin/scripts/kmerPrint.pl rm -f /builddir/bin/scripts/kmerPrint.py echo cp -p kmerPrint.py /builddir/bin/scripts cp -p kmerPrint.py /builddir/bin/scripts cp -p kmerPrint.py /builddir/bin/scripts chmod +x /builddir/bin/scripts/kmerPrint.py rm -f /builddir/bin/scripts/liftRMAlign.pl echo cp -p liftRMAlign.pl /builddir/bin/scripts cp -p liftRMAlign.pl /builddir/bin/scripts cp -p liftRMAlign.pl /builddir/bin/scripts chmod +x /builddir/bin/scripts/liftRMAlign.pl rm -f /builddir/bin/scripts/makeDownloads.pl echo cp -p makeDownloads.pl /builddir/bin/scripts cp -p makeDownloads.pl /builddir/bin/scripts cp -p makeDownloads.pl /builddir/bin/scripts chmod +x /builddir/bin/scripts/makeDownloads.pl rm -f /builddir/bin/scripts/makeGenomeDb.pl echo cp -p makeGenomeDb.pl /builddir/bin/scripts cp -p makeGenomeDb.pl /builddir/bin/scripts cp -p makeGenomeDb.pl /builddir/bin/scripts chmod +x /builddir/bin/scripts/makeGenomeDb.pl rm -f /builddir/bin/scripts/makePushQSql.pl echo cp -p makePushQSql.pl /builddir/bin/scripts cp -p makePushQSql.pl /builddir/bin/scripts cp -p makePushQSql.pl /builddir/bin/scripts chmod +x /builddir/bin/scripts/makePushQSql.pl rm -f /builddir/bin/scripts/monthlyUpdateIgtc.csh echo cp -p monthlyUpdateIgtc.csh /builddir/bin/scripts cp -p monthlyUpdateIgtc.csh /builddir/bin/scripts cp -p monthlyUpdateIgtc.csh /builddir/bin/scripts chmod +x /builddir/bin/scripts/monthlyUpdateIgtc.csh rm -f /builddir/bin/scripts/simplePartition.pl echo cp -p simplePartition.pl /builddir/bin/scripts cp -p simplePartition.pl /builddir/bin/scripts cp -p simplePartition.pl /builddir/bin/scripts chmod +x /builddir/bin/scripts/simplePartition.pl rm -f /builddir/bin/scripts/partitionSequence.pl echo cp -p partitionSequence.pl /builddir/bin/scripts cp -p partitionSequence.pl /builddir/bin/scripts cp -p partitionSequence.pl /builddir/bin/scripts chmod +x /builddir/bin/scripts/partitionSequence.pl rm -f /builddir/bin/scripts/updateIgtc.pl echo cp -p updateIgtc.pl /builddir/bin/scripts cp -p updateIgtc.pl /builddir/bin/scripts cp -p updateIgtc.pl /builddir/bin/scripts chmod +x /builddir/bin/scripts/updateIgtc.pl rm -f /builddir/bin/scripts/unigene.csh echo cp -p unigene.csh /builddir/bin/scripts cp -p unigene.csh /builddir/bin/scripts cp -p unigene.csh /builddir/bin/scripts chmod +x /builddir/bin/scripts/unigene.csh make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/automation' if test -d blatServersCheck ; then cd blatServersCheck && echo blatServersCheck && make ; fi if test -d buildReleaseLog ; then cd buildReleaseLog && echo buildReleaseLog && make ; fi buildReleaseLog make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/buildReleaseLog' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o buildReleaseLog.o -c buildReleaseLog.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o htmlOut.o -c htmlOut.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/buildReleaseLog buildReleaseLog.o htmlOut.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/buildReleaseLog make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/buildReleaseLog' if test -d checkUrlsInTable ; then cd checkUrlsInTable && echo checkUrlsInTable && make ; fi checkUrlsInTable make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/checkUrlsInTable' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o checkUrlsInTable.o -c checkUrlsInTable.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/checkUrlsInTable checkUrlsInTable.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/checkUrlsInTable make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/checkUrlsInTable' if test -d geoMirrorNode ; then cd geoMirrorNode && echo geoMirrorNode && make ; fi geoMirrorNode make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/geoMirrorNode' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o geoMirrorNode.o -c geoMirrorNode.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/geoMirrorNode geoMirrorNode.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lmariadb -lz -lpthread -lm -lssl -lcrypto true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/geoMirrorNode make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/geoMirrorNode' if test -d hubCrawl ; then cd hubCrawl && echo hubCrawl && make ; fi hubCrawl make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/hubCrawl' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hubCrawl.o -c hubCrawl.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hubCrawl hubCrawl.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hubCrawl make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/hubCrawl' if test -d makeTrackIndex ; then cd makeTrackIndex && echo makeTrackIndex && make ; fi makeTrackIndex make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/makeTrackIndex' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o makeTrackIndex.o -c makeTrackIndex.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/makeTrackIndex makeTrackIndex.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lmariadb -lz -lpthread -lm -lssl -lcrypto true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/makeTrackIndex make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/makeTrackIndex' if test -d mysqlSecurityCheck ; then cd mysqlSecurityCheck && echo mysqlSecurityCheck && make ; fi mysqlSecurityCheck make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/mysqlSecurityCheck' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o mysqlSecurityCheck.o -c mysqlSecurityCheck.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/mysqlSecurityCheck mysqlSecurityCheck.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/mysqlSecurityCheck make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/mysqlSecurityCheck' if test -d phyloRenameAndPrune ; then cd phyloRenameAndPrune && echo phyloRenameAndPrune && make ; fi phyloRenameAndPrune make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/phyloRenameAndPrune' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o phyloRenameAndPrune.o -c phyloRenameAndPrune.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/phyloRenameAndPrune phyloRenameAndPrune.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/phyloRenameAndPrune make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/phyloRenameAndPrune' if test -d pslFixCdsJoinGap ; then cd pslFixCdsJoinGap && echo pslFixCdsJoinGap && make ; fi pslFixCdsJoinGap make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/pslFixCdsJoinGap' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o pslFixCdsJoinGap.o -c pslFixCdsJoinGap.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslFixCdsJoinGap pslFixCdsJoinGap.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslFixCdsJoinGap make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/pslFixCdsJoinGap' if test -d pslMismatchGapToBed ; then cd pslMismatchGapToBed && echo pslMismatchGapToBed && make ; fi pslMismatchGapToBed make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/pslMismatchGapToBed' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o pslMismatchGapToBed.o -c pslMismatchGapToBed.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslMismatchGapToBed pslMismatchGapToBed.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslMismatchGapToBed make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/pslMismatchGapToBed' if test -d pslUniq ; then cd pslUniq && echo pslUniq && make ; fi pslUniq make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/pslUniq' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o pslUniq.o -c pslUniq.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslUniq pslUniq.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslUniq make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/pslUniq' if test -d refSeqGet ; then cd refSeqGet && echo refSeqGet && make ; fi refSeqGet make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/refSeqGet' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o refSeqVerInfo.o -c refSeqVerInfo.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o refSeqGet.o -c refSeqGet.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/refSeqGet refSeqVerInfo.o refSeqGet.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lmariadb -lz -lpthread -lm -lssl -lcrypto true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/refSeqGet make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/refSeqGet' if test -d safePush ; then cd safePush && echo safePush && make ; fi safePush make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/safePush' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o safePush.o -c safePush.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/safePush safePush.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/safePush make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/safePush' if test -d scaffoldFaToAgp ; then cd scaffoldFaToAgp && echo scaffoldFaToAgp && make ; fi scaffoldFaToAgp make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/scaffoldFaToAgp' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o scaffoldFaToAgp.o -c scaffoldFaToAgp.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/scaffoldFaToAgp scaffoldFaToAgp.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/scaffoldFaToAgp make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/scaffoldFaToAgp' if test -d toDev64 ; then cd toDev64 && echo toDev64 && make ; fi toDev64 make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/toDev64' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o toDev64.o -c toDev64.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/toDev64 toDev64.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/toDev64 make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/toDev64' if test -d vcfRenameAndPrune ; then cd vcfRenameAndPrune && echo vcfRenameAndPrune && make ; fi vcfRenameAndPrune make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/vcfRenameAndPrune' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o vcfRenameAndPrune.o -c vcfRenameAndPrune.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/vcfRenameAndPrune vcfRenameAndPrune.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/vcfRenameAndPrune make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/vcfRenameAndPrune' if test -d vcfToHgvs ; then cd vcfToHgvs && echo vcfToHgvs && make ; fi vcfToHgvs make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/vcfToHgvs' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o vcfToHgvs.o -c vcfToHgvs.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/vcfToHgvs vcfToHgvs.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/vcfToHgvs make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/vcfToHgvs' if test -d wigBedToStep ; then cd wigBedToStep && echo wigBedToStep && make ; fi wigBedToStep make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/wigBedToStep' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o wigBedToStep.o -c wigBedToStep.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/wigBedToStep wigBedToStep.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/wigBedToStep make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/wigBedToStep' if test -d bedExtendRanges ; then cd bedExtendRanges && echo bedExtendRanges && make ; fi bedExtendRanges make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/bedExtendRanges' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o bedExtendRanges.o -c bedExtendRanges.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bedExtendRanges bedExtendRanges.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bedExtendRanges make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/bedExtendRanges' if test -d bedToPsl ; then cd bedToPsl && echo bedToPsl && make ; fi bedToPsl make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/bedToPsl' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o bedToPsl.o -c bedToPsl.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bedToPsl bedToPsl.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bedToPsl make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/bedToPsl' if test -d bedWeedOverlapping ; then cd bedWeedOverlapping && echo bedWeedOverlapping && make ; fi bedWeedOverlapping make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/bedWeedOverlapping' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o bedWeedOverlapping.o -c bedWeedOverlapping.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bedWeedOverlapping bedWeedOverlapping.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bedWeedOverlapping make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/bedWeedOverlapping' if test -d bedMergeAdjacent ; then cd bedMergeAdjacent && echo bedMergeAdjacent && make ; fi bedMergeAdjacent make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/bedMergeAdjacent' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o bedMergeAdjacent.o -c bedMergeAdjacent.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bedMergeAdjacent bedMergeAdjacent.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bedMergeAdjacent make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/bedMergeAdjacent' if test -d bedPartition ; then cd bedPartition && echo bedPartition && make ; fi bedPartition make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/bedPartition' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o bedPartition.o -c bedPartition.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bedPartition bedPartition.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bedPartition make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/bedPartition' if test -d bigChainBreaks ; then cd bigChainBreaks && echo bigChainBreaks && make ; fi bigChainBreaks make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/bigChainBreaks' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o bigChainBreaks.o -c bigChainBreaks.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bigChainBreaks bigChainBreaks.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bigChainBreaks make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/bigChainBreaks' if test -d bigChainToChain ; then cd bigChainToChain && echo bigChainToChain && make ; fi bigChainToChain make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/bigChainToChain' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o bigChainToChain.o -c bigChainToChain.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bigChainToChain bigChainToChain.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bigChainToChain make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/bigChainToChain' if test -d bigGenePredToGenePred ; then cd bigGenePredToGenePred && echo bigGenePredToGenePred && make ; fi bigGenePredToGenePred make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/bigGenePredToGenePred' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o bigGenePredToGenePred.o -c bigGenePredToGenePred.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bigGenePredToGenePred bigGenePredToGenePred.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bigGenePredToGenePred make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/bigGenePredToGenePred' if test -d bigMafToMaf ; then cd bigMafToMaf && echo bigMafToMaf && make ; fi bigMafToMaf make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/bigMafToMaf' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o bigMafToMaf.o -c bigMafToMaf.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bigMafToMaf bigMafToMaf.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bigMafToMaf make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/bigMafToMaf' if test -d bigPslToPsl ; then cd bigPslToPsl && echo bigPslToPsl && make ; fi bigPslToPsl make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/bigPslToPsl' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o bigPslToPsl.o -c bigPslToPsl.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bigPslToPsl bigPslToPsl.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bigPslToPsl make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/bigPslToPsl' if test -d binFromRange ; then cd binFromRange && echo binFromRange && make ; fi binFromRange make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/binFromRange' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o binFromRange.o -c binFromRange.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/binFromRange binFromRange.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/binFromRange make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/binFromRange' if test -d chainToBigChain ; then cd chainToBigChain && echo chainToBigChain && make ; fi chainToBigChain make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/chainToBigChain' gcc -ggdb -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o chainToBigChain.o -c chainToBigChain.c gcc -ggdb -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/chainToBigChain chainToBigChain.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/chainToBigChain make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/chainToBigChain' if test -d chromGraphFromBin ; then cd chromGraphFromBin && echo chromGraphFromBin && make ; fi chromGraphFromBin make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/chromGraphFromBin' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o chromGraphFromBin.o -c chromGraphFromBin.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/chromGraphFromBin chromGraphFromBin.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/chromGraphFromBin make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/chromGraphFromBin' if test -d chromGraphToBin ; then cd chromGraphToBin && echo chromGraphToBin && make ; fi chromGraphToBin make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/chromGraphToBin' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o chromGraphToBin.o -c chromGraphToBin.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/chromGraphToBin chromGraphToBin.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/chromGraphToBin make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/chromGraphToBin' if test -d crTreeIndexBed ; then cd crTreeIndexBed && echo crTreeIndexBed && make ; fi crTreeIndexBed make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/crTreeIndexBed' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o crTreeIndexBed.o -c crTreeIndexBed.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/crTreeIndexBed crTreeIndexBed.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/crTreeIndexBed make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/crTreeIndexBed' if test -d crTreeSearchBed ; then cd crTreeSearchBed && echo crTreeSearchBed && make ; fi crTreeSearchBed make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/crTreeSearchBed' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o crTreeSearchBed.o -c crTreeSearchBed.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/crTreeSearchBed crTreeSearchBed.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/crTreeSearchBed make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/crTreeSearchBed' if test -d faToVcf ; then cd faToVcf && echo faToVcf && make ; fi faToVcf make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/faToVcf' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o faToVcf.o -c faToVcf.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/faToVcf faToVcf.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/faToVcf make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/faToVcf' if test -d gapToLift ; then cd gapToLift && echo gapToLift && make ; fi gapToLift make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/gapToLift' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o gapToLift.o -c gapToLift.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/gapToLift gapToLift.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/gapToLift make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/gapToLift' if test -d genePredFilter ; then cd genePredFilter && echo genePredFilter && make ; fi genePredFilter make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/genePredFilter' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o genePredFilter.o -c genePredFilter.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/genePredFilter genePredFilter.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/genePredFilter make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/genePredFilter' if test -d genePredToBigGenePred ; then cd genePredToBigGenePred && echo genePredToBigGenePred && make ; fi genePredToBigGenePred make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/genePredToBigGenePred' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o genePredToBigGenePred.o -c genePredToBigGenePred.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/genePredToBigGenePred genePredToBigGenePred.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/genePredToBigGenePred make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/genePredToBigGenePred' if test -d genePredToProt ; then cd genePredToProt && echo genePredToProt && make ; fi genePredToProt make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/genePredToProt' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o genePredToProt.o -c genePredToProt.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/genePredToProt genePredToProt.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/genePredToProt make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/genePredToProt' if test -d gencodeVersionForGenes ; then cd gencodeVersionForGenes && echo gencodeVersionForGenes && make ; fi gencodeVersionForGenes make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/gencodeVersionForGenes' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o gencodeVersionForGenes.o -c gencodeVersionForGenes.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/gencodeVersionForGenes gencodeVersionForGenes.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/gencodeVersionForGenes make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/gencodeVersionForGenes' if test -d gff3ToGenePred ; then cd gff3ToGenePred && echo gff3ToGenePred && make ; fi gff3ToGenePred make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/gff3ToGenePred' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o gff3ToGenePred.o -c gff3ToGenePred.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/gff3ToGenePred gff3ToGenePred.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/gff3ToGenePred make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/gff3ToGenePred' if test -d gff3ToPsl ; then cd gff3ToPsl && echo gff3ToPsl && make ; fi gff3ToPsl make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/gff3ToPsl' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o gff3ToPsl.o -c gff3ToPsl.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/gff3ToPsl gff3ToPsl.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lmariadb -lz -lpthread -lm -lssl -lcrypto true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/gff3ToPsl make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/gff3ToPsl' if test -d gtfToGenePred ; then cd gtfToGenePred && echo gtfToGenePred && make ; fi gtfToGenePred make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/gtfToGenePred' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o gtfToGenePred.o -c gtfToGenePred.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/gtfToGenePred gtfToGenePred.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/gtfToGenePred make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/gtfToGenePred' if test -d hicInfo ; then cd hicInfo && echo hicInfo && make ; fi hicInfo make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/hicInfo' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hicInfo.o -c hicInfo.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hicInfo hicInfo.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hicInfo make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/hicInfo' if test -d hgvsToVcf ; then cd hgvsToVcf && echo hgvsToVcf && make ; fi hgvsToVcf make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/hgvsToVcf' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hgvsToVcf.o -c hgvsToVcf.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgvsToVcf hgvsToVcf.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgvsToVcf make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/hgvsToVcf' if test -d hubCheck ; then cd hubCheck && echo hubCheck && make ; fi hubCheck make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/hubCheck' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hubCheck.o -c hubCheck.c hubCheck.c: In function ‘hubCheckTrack’: hubCheck.c:924:5: warning: variable ‘trackDbErrorCount’ set but not used [-Wunused-but-set-variable=] 924 | int trackDbErrorCount = 0; | ^~~~~~~~~~~~~~~~~ gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hubCheck hubCheck.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hubCheck make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/hubCheck' if test -d hubClone ; then cd hubClone && echo hubClone && make ; fi hubClone make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/hubClone' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hubClone.o -c hubClone.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hubClone hubClone.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hubClone make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/hubClone' if test -d hubPublicCheck ; then cd hubPublicCheck && echo hubPublicCheck && make ; fi hubPublicCheck make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/hubPublicCheck' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o hubPublicCheck.o -c hubPublicCheck.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hubPublicCheck hubPublicCheck.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hubPublicCheck make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/hubPublicCheck' if test -d mafToBigMaf ; then cd mafToBigMaf && echo mafToBigMaf && make ; fi mafToBigMaf make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/mafToBigMaf' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o mafToBigMaf.o -c mafToBigMaf.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/mafToBigMaf mafToBigMaf.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/mafToBigMaf make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/mafToBigMaf' if test -d makeTableList ; then cd makeTableList && echo makeTableList && make ; fi makeTableList make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/makeTableList' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o makeTableList.o -c makeTableList.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/makeTableList makeTableList.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/makeTableList make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/makeTableList' if test -d oligoMatch ; then cd oligoMatch && echo oligoMatch && make ; fi oligoMatch make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/oligoMatch' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o oligoMatch.o -c oligoMatch.c oligoMatch.c: In function ‘oligoMatch’: oligoMatch.c:73:5: warning: variable ‘count’ set but not used [-Wunused-but-set-variable=] 73 | int count = 0; | ^~~~~ gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/oligoMatch oligoMatch.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/oligoMatch make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/oligoMatch' if test -d overlapSelect ; then cd overlapSelect && echo overlapSelect && make ; fi overlapSelect make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/overlapSelect' echo '/* GENERATED CODE, DO NOT EDIT */' > usage.h.tmp ../../../utils/stringify/stringifyEz -static -var=usageMsg usage.txt >> usage.h.tmp mv -f usage.h.tmp usage.h gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o overlapSelect.o -c overlapSelect.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o rowReader.o -c rowReader.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o chromAnn.o -c chromAnn.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o chromAnnMap.o -c chromAnnMap.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o selectTable.o -c selectTable.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o coordCols.o -c coordCols.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/overlapSelect overlapSelect.o rowReader.o chromAnn.o chromAnnMap.o selectTable.o coordCols.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/overlapSelect make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/overlapSelect' if test -d positionalTblCheck ; then cd positionalTblCheck && echo positionalTblCheck && make ; fi positionalTblCheck make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/positionalTblCheck' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o positionalTblCheck.o -c positionalTblCheck.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/positionalTblCheck positionalTblCheck.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/positionalTblCheck make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/positionalTblCheck' if test -d pslLiftSubrangeBlat ; then cd pslLiftSubrangeBlat && echo pslLiftSubrangeBlat && make ; fi pslLiftSubrangeBlat make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/pslLiftSubrangeBlat' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o pslLiftSubrangeBlat.o -c pslLiftSubrangeBlat.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslLiftSubrangeBlat pslLiftSubrangeBlat.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslLiftSubrangeBlat make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/pslLiftSubrangeBlat' if test -d pslToBigPsl ; then cd pslToBigPsl && echo pslToBigPsl && make ; fi pslToBigPsl make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/pslToBigPsl' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o pslToBigPsl.o -c pslToBigPsl.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslToBigPsl pslToBigPsl.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslToBigPsl make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/pslToBigPsl' if test -d raSqlQuery ; then cd raSqlQuery && echo raSqlQuery && make ; fi raSqlQuery make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/raSqlQuery' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o raSqlQuery.o -c raSqlQuery.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o raRecord.o -c raRecord.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/raSqlQuery raSqlQuery.o raRecord.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lmariadb -lz -lpthread -lm -lssl -lcrypto true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/raSqlQuery make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/raSqlQuery' if test -d rmskAlignToPsl ; then cd rmskAlignToPsl && echo rmskAlignToPsl && make ; fi rmskAlignToPsl make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/rmskAlignToPsl' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o rmskAlignToPsl.o -c rmskAlignToPsl.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/rmskAlignToPsl rmskAlignToPsl.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/rmskAlignToPsl make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/rmskAlignToPsl' if test -d tdbQuery ; then cd tdbQuery && echo tdbQuery && make ; fi tdbQuery make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/tdbQuery' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o tdbQuery.o -c tdbQuery.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o tdbRecord.o -c tdbRecord.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/tdbQuery tdbQuery.o tdbRecord.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/tdbQuery make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/tdbQuery' if test -d transMapPslToGenePred ; then cd transMapPslToGenePred && echo transMapPslToGenePred && make ; fi transMapPslToGenePred make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/transMapPslToGenePred' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o transMapPslToGenePred.o -c transMapPslToGenePred.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/transMapPslToGenePred transMapPslToGenePred.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/transMapPslToGenePred make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/transMapPslToGenePred' if test -d twoBitMask ; then cd twoBitMask && echo twoBitMask && make ; fi twoBitMask make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/twoBitMask' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o twoBitMask.o -c twoBitMask.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/twoBitMask twoBitMask.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/twoBitMask make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/twoBitMask' if test -d vcfToBed ; then cd vcfToBed && echo vcfToBed && make ; fi vcfToBed make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/vcfToBed' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o vcfToBed.o -c vcfToBed.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/vcfToBed vcfToBed.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl In function ‘parseColumnHeaderRow’, inlined from ‘vcfFileHeaderFromLineFile’ at ../../../lib/vcf.c:530:1, inlined from ‘vcfTabixFileAndIndexMayOpenExt’ at ../../../lib/vcf.c:1054:24, inlined from ‘vcfTabixFileAndIndexMayOpen’ at ../../../lib/vcf.c:1070:8, inlined from ‘vcfToBed’ at vcfToBed.c:225:12: ../../../lib/vcf.c:416:1: warning: ‘chopByChar’ accessing 8 bytes in a region of size 0 [-Wstringop-overflow=] 416 | chopTabs(line+1, words); | ^ ../../../lib/vcf.c:416:1: note: referencing argument 3 of type ‘char *[0:]’ ../../../lib/common.c: In function ‘vcfToBed’: ../../../lib/common.c:2299:5: note: in a call to function ‘chopByChar’ 2299 | int chopByChar(char *in, char chopper, char *outArray[], int outSize) | ^ true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/vcfToBed make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/vcfToBed' if test -d fixTrackDb ; then cd fixTrackDb && echo fixTrackDb && make ; fi fixTrackDb make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/fixTrackDb' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o fixTrackDb.o -c fixTrackDb.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/fixTrackDb fixTrackDb.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/fixTrackDb make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils/fixTrackDb' chmod +x archiveTracks.sh rm -f /builddir/bin/scripts/archiveTracks.sh cp -p archiveTracks.sh /builddir/bin/scripts/archiveTracks.sh chmod +x dbNsfpToBed.pl rm -f /builddir/bin/scripts/dbNsfpToBed.pl cp -p dbNsfpToBed.pl /builddir/bin/scripts/dbNsfpToBed.pl chmod +x dumpDb.pl rm -f /builddir/bin/scripts/dumpDb.pl cp -p dumpDb.pl /builddir/bin/scripts/dumpDb.pl chmod +x mergeOverlapBed4.pl rm -f /builddir/bin/scripts/mergeOverlapBed4.pl cp -p mergeOverlapBed4.pl /builddir/bin/scripts/mergeOverlapBed4.pl chmod +x mergeSortedBed3Plus.pl rm -f /builddir/bin/scripts/mergeSortedBed3Plus.pl cp -p mergeSortedBed3Plus.pl /builddir/bin/scripts/mergeSortedBed3Plus.pl chmod +x mysqlRowSizes.pl rm -f /builddir/bin/scripts/mysqlRowSizes.pl cp -p mysqlRowSizes.pl /builddir/bin/scripts/mysqlRowSizes.pl chmod +x vai.pl rm -f /builddir/bin/scripts/vai.pl cp -p vai.pl /builddir/bin/scripts/vai.pl make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/utils' if test -d uniqSize ; then cd uniqSize && echo uniqSize && make ; fi uniqSize make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/uniqSize' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o uniqSize.o -c uniqSize.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/uniqSize uniqSize.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/uniqSize make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/uniqSize' if test -d updateStsInfo ; then cd updateStsInfo && echo updateStsInfo && make ; fi updateStsInfo make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/updateStsInfo' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o updateStsInfo.o -c updateStsInfo.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/updateStsInfo updateStsInfo.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/updateStsInfo make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/updateStsInfo' if test -d visiGene/knownToVisiGene ; then cd visiGene/knownToVisiGene && echo visiGene/knownToVisiGene && make ; fi if test -d autoDtd ; then cd autoDtd && echo autoDtd && make ; fi autoDtd make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/autoDtd' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o autoDtd.o -c autoDtd.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/autoDtd autoDtd.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/autoDtd make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/autoDtd' if test -d autoSql ; then cd autoSql && echo autoSql && make ; fi autoSql make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/autoSql' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o autoSql.o -c autoSql.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/autoSql autoSql.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/autoSql make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/autoSql' if test -d autoXml ; then cd autoXml && echo autoXml && make ; fi autoXml make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/autoXml' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o autoXml.o -c autoXml.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/autoXml autoXml.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/autoXml make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/autoXml' if test -d bedSort ; then cd bedSort && echo bedSort && make ; fi bedSort make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/bedSort' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o bedSort.o -c bedSort.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bedSort bedSort.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bedSort make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/bedSort' if test -d liftUp ; then cd liftUp && echo liftUp && make ; fi liftUp make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/liftUp' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o liftUp.o -c liftUp.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/liftUp liftUp.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/liftUp make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/liftUp' if test -d liftOver ; then cd liftOver && echo liftOver && make ; fi if test -d bedIntersect ; then cd bedIntersect && echo bedIntersect && make ; fi bedIntersect make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/bedIntersect' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o bedIntersect.o -c bedIntersect.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bedIntersect bedIntersect.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bedIntersect make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/bedIntersect' if test -d bedItemOverlapCount ; then cd bedItemOverlapCount && echo bedItemOverlapCount && make ; fi bedItemOverlapCount make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/bedItemOverlapCount' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o bedItemOverlapCount.o -c bedItemOverlapCount.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bedItemOverlapCount bedItemOverlapCount.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bedItemOverlapCount make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/bedItemOverlapCount' if test -d bedToGenePred ; then cd bedToGenePred && echo bedToGenePred && make ; fi bedToGenePred make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/bedToGenePred' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o bedToGenePred.o -c bedToGenePred.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bedToGenePred bedToGenePred.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bedToGenePred make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/bedToGenePred' if test -d blastToPsl ; then cd blastToPsl && echo blastToPsl && make ; fi blastToPsl make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/blastToPsl' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o blastToPsl.o -c blastToPsl.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o pslBuild.o -c pslBuild.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/blastToPsl blastToPsl.o pslBuild.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lmariadb -lz -lpthread -lm -lssl -lcrypto -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/blastToPsl gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o blastXmlToPsl.o -c blastXmlToPsl.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o ncbiBlast.o -c ncbiBlast.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/blastXmlToPsl blastXmlToPsl.o ncbiBlast.o pslBuild.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lmariadb -lz -lpthread -lm -lssl -lcrypto -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/blastXmlToPsl make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/blastToPsl' if test -d checkCoverageGaps ; then cd checkCoverageGaps && echo checkCoverageGaps && make ; fi checkCoverageGaps make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/checkCoverageGaps' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o checkCoverageGaps.o -c checkCoverageGaps.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/checkCoverageGaps checkCoverageGaps.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/checkCoverageGaps make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/checkCoverageGaps' if test -d checkTableCoords ; then cd checkTableCoords && echo checkTableCoords && make ; fi checkTableCoords make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/checkTableCoords' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o checkTableCoords.o -c checkTableCoords.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/checkTableCoords checkTableCoords.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/checkTableCoords make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/checkTableCoords' if test -d dbTrash ; then cd dbTrash && echo dbTrash && make ; fi dbTrash make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/dbTrash' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o dbTrash.o -c dbTrash.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/dbTrash dbTrash.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/dbTrash make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/dbTrash' if test -d encode3/validateFiles ; then cd encode3/validateFiles && echo encode3/validateFiles && make ; fi if test -d encode3/validateManifest ; then cd encode3/validateManifest && echo encode3/validateManifest && make ; fi if test -d estOrient ; then cd estOrient && echo estOrient && make ; fi estOrient make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/estOrient' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o estOrient.o -c estOrient.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/estOrient estOrient.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/estOrient make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/estOrient' if test -d featureBits ; then cd featureBits && echo featureBits && make ; fi featureBits make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/featureBits' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o featureBits.o -c featureBits.c featureBits.c: In function ‘featureBits’: featureBits.c:993:12: warning: variable ‘totalBases’ set but not used [-Wunused-but-set-variable=] 993 | double totalBases = 0; | ^~~~~~~~~~ featureBits.c:992:9: warning: variable ‘totalItems’ set but not used [-Wunused-but-set-variable=] 992 | int totalItems = 0; | ^~~~~~~~~~ featureBits.c: In function ‘chromFileName.part.0’: featureBits.c:312:9: warning: ‘strncpy’ specified bound 512 equals destination size [-Wstringop-truncation] 312 | strncpy(fileName, track, 512); | ^ featureBits.c: In function ‘chromFileName’: featureBits.c:297:5: warning: ‘strncpy’ specified bound 512 equals destination size [-Wstringop-truncation] 297 | strncpy(fileName, track, 512); | ^ featureBits.c: In function ‘fbOrPsl’: featureBits.c:297:5: warning: ‘strncpy’ specified bound 512 equals destination size [-Wstringop-truncation] featureBits.c: In function ‘fbOrBed’: featureBits.c:297:5: warning: ‘strncpy’ specified bound 512 equals destination size [-Wstringop-truncation] featureBits.c: In function ‘fbOrBigBed’: featureBits.c:297:5: warning: ‘strncpy’ specified bound 512 equals destination size [-Wstringop-truncation] featureBits.c: In function ‘fbOrChain’: featureBits.c:297:5: warning: ‘strncpy’ specified bound 512 equals destination size [-Wstringop-truncation] featureBits.c: In function ‘isolateTrackPartOfSpec’: featureBits.c:509:1: warning: ‘strncpy’ specified bound 512 equals destination size [-Wstringop-truncation] 509 | strncpy(track, spec, 512); | ^ featureBits.c: In function ‘orTable’: featureBits.c:509:1: warning: ‘strncpy’ specified bound 512 equals destination size [-Wstringop-truncation] featureBits.c: In function ‘chromFeatureSeq’: featureBits.c:509:1: warning: ‘strncpy’ specified bound 512 equals destination size [-Wstringop-truncation] featureBits.c: In function ‘checkInputExists’: featureBits.c:509:1: warning: ‘strncpy’ specified bound 512 equals destination size [-Wstringop-truncation] gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/featureBits featureBits.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/featureBits make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/featureBits' if test -d geneBounds/clusterGenes ; then cd geneBounds/clusterGenes && echo geneBounds/clusterGenes && make ; fi geneBounds/clusterGenes make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/clusterGenes' gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/clusterGenes clusterGenes.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/clusterGenes make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/geneBounds/clusterGenes' if test -d genePredHisto ; then cd genePredHisto && echo genePredHisto && make ; fi genePredHisto make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/genePredHisto' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o genePredHisto.o -c genePredHisto.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/genePredHisto genePredHisto.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/genePredHisto make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/genePredHisto' if test -d genePredSingleCover ; then cd genePredSingleCover && echo genePredSingleCover && make ; fi genePredSingleCover make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/genePredSingleCover' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o genePredSingleCover.o -c genePredSingleCover.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o geneScore.o -c geneScore.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/genePredSingleCover genePredSingleCover.o geneScore.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/genePredSingleCover make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/genePredSingleCover' if test -d genePredToBed ; then cd genePredToBed && echo genePredToBed && make ; fi genePredToBed make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/genePredToBed' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o genePredToBed.o -c genePredToBed.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/genePredToBed genePredToBed.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/genePredToBed make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/genePredToBed' if test -d genePredToFakePsl ; then cd genePredToFakePsl && echo genePredToFakePsl && make ; fi genePredToFakePsl make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/genePredToFakePsl' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o genePredToFakePsl.o -c genePredToFakePsl.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/genePredToFakePsl genePredToFakePsl.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/genePredToFakePsl make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/genePredToFakePsl' if test -d genePredToMafFrames ; then cd genePredToMafFrames && echo genePredToMafFrames && make ; fi genePredToMafFrames make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/genePredToMafFrames' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o genePredToMafFrames.o -c genePredToMafFrames.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o orgGenes.o -c orgGenes.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o mkMafFrames.o -c mkMafFrames.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o splitMultiMappings.o -c splitMultiMappings.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o finishMafFrames.o -c finishMafFrames.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/genePredToMafFrames genePredToMafFrames.o orgGenes.o mkMafFrames.o splitMultiMappings.o finishMafFrames.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/genePredToMafFrames make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/genePredToMafFrames' if test -d getRna ; then cd getRna && echo getRna && make ; fi getRna make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/getRna' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o getRna.o -c getRna.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/getRna getRna.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/getRna make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/getRna' if test -d getRnaPred ; then cd getRnaPred && echo getRnaPred && make ; fi getRnaPred make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/getRnaPred' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o getRnaPred.o -c getRnaPred.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/getRnaPred getRnaPred.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/getRnaPred make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/getRnaPred' if test -d gigAssembler/checkAgpAndFa ; then cd gigAssembler/checkAgpAndFa && echo gigAssembler/checkAgpAndFa && make ; fi gigAssembler/checkAgpAndFa make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/gigAssembler/checkAgpAndFa' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o checkAgpAndFa.o -c checkAgpAndFa.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/checkAgpAndFa checkAgpAndFa.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/checkAgpAndFa make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/gigAssembler/checkAgpAndFa' if test -d hgSpeciesRna ; then cd hgSpeciesRna && echo hgSpeciesRna && make ; fi hgSpeciesRna make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/hgSpeciesRna' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o hgSpeciesRna.o -c hgSpeciesRna.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgSpeciesRna hgSpeciesRna.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgSpeciesRna make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/hgSpeciesRna' if test -d hgsql ; then cd hgsql && echo hgsql && make ; fi hgsql make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/hgsql' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o hgsql.o -c hgsql.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgsql hgsql.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgsql make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/hgsql' if test -d hgsqldump ; then cd hgsqldump && echo hgsqldump && make ; fi hgsqldump make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/hgsqldump' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o hgsqldump.o -c hgsqldump.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgsqldump hgsqldump.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hgsqldump make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/hgsqldump' if test -d maskOutFa ; then cd maskOutFa && echo maskOutFa && make ; fi maskOutFa make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/maskOutFa' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o maskOutFa.o -c maskOutFa.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/maskOutFa maskOutFa.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/maskOutFa make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/maskOutFa' if test -d mrnaToGene ; then cd mrnaToGene && echo mrnaToGene && make ; fi mrnaToGene make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mrnaToGene' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o mrnaToGene.o -c mrnaToGene.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/mrnaToGene mrnaToGene.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/mrnaToGene make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/mrnaToGene' if test -d ratStuff/mafsInRegion ; then cd ratStuff/mafsInRegion && echo ratStuff/mafsInRegion && make ; fi ratStuff/mafsInRegion make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/ratStuff/mafsInRegion' make[3]: Nothing to be done for 'default'. make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/ratStuff/mafsInRegion' if test -d ratStuff/mafSpeciesSubset ; then cd ratStuff/mafSpeciesSubset && echo ratStuff/mafSpeciesSubset && make ; fi ratStuff/mafSpeciesSubset make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/ratStuff/mafSpeciesSubset' make[3]: Nothing to be done for 'default'. make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/ratStuff/mafSpeciesSubset' if test -d ratStuff/mafToSnpBed ; then cd ratStuff/mafToSnpBed && echo ratStuff/mafToSnpBed && make ; fi ratStuff/mafToSnpBed make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/ratStuff/mafToSnpBed' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o mafToSnpBed.o -c mafToSnpBed.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/mafToSnpBed mafToSnpBed.o ../../../lib/x86_64/jkhgap.a ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/mafToSnpBed make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/ratStuff/mafToSnpBed' if test -d pslCDnaFilter ; then cd pslCDnaFilter && echo pslCDnaFilter && make ; fi pslCDnaFilter make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/pslCDnaFilter' echo '/* GENERATED CODE, DO NOT EDIT */' > usage.h.tmp ../../utils/stringify/stringifyEz -static -var=usageMsg usage.txt >> usage.h.tmp mv -f usage.h.tmp usage.h echo '/* GENERATED CODE, DO NOT EDIT */' > algo.h.tmp ../../utils/stringify/stringifyEz -static -var=usageMsg algo.txt >> algo.h.tmp mv -f algo.h.tmp algo.h gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o pslCDnaFilter.o -c pslCDnaFilter.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o cDnaAligns.o -c cDnaAligns.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o cDnaStats.o -c cDnaStats.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o cDnaReader.o -c cDnaReader.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o overlapFilter.o -c overlapFilter.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o globalNearBestFilter.o -c globalNearBestFilter.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o localNearBestFilter.o -c localNearBestFilter.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o polyASize.o -c polyASize.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o hapRegions.o -c hapRegions.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslCDnaFilter pslCDnaFilter.o cDnaAligns.o cDnaStats.o cDnaReader.o overlapFilter.o globalNearBestFilter.o localNearBestFilter.o polyASize.o hapRegions.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslCDnaFilter make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/pslCDnaFilter' if test -d genePredCheck ; then cd genePredCheck && echo genePredCheck && make ; fi genePredCheck make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/genePredCheck' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o genePredCheck.o -c genePredCheck.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/genePredCheck genePredCheck.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/genePredCheck make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/genePredCheck' if test -d genePredToGtf ; then cd genePredToGtf && echo genePredToGtf && make ; fi genePredToGtf make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/genePredToGtf' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o genePredToGtf.o -c genePredToGtf.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/genePredToGtf genePredToGtf.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/genePredToGtf make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/genePredToGtf' if test -d pslCat ; then cd pslCat && echo pslCat && make ; fi pslCat make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/pslCat' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o pslCat.o -c pslCat.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslCat pslCat.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslCat make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/pslCat' if test -d pslCheck ; then cd pslCheck && echo pslCheck && make ; fi pslCheck make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/pslCheck' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o pslCheck.o -c pslCheck.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslCheck pslCheck.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslCheck make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/pslCheck' if test -d pslDropOverlap ; then cd pslDropOverlap && echo pslDropOverlap && make ; fi pslDropOverlap make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/pslDropOverlap' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o pslDropOverlap.o -c pslDropOverlap.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslDropOverlap pslDropOverlap.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslDropOverlap make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/pslDropOverlap' if test -d pslFilter ; then cd pslFilter && echo pslFilter && make ; fi pslFilter make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/pslFilter' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o pslFilter.o -c pslFilter.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslFilter pslFilter.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslFilter make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/pslFilter' if test -d pslHisto ; then cd pslHisto && echo pslHisto && make ; fi pslHisto make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/pslHisto' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o pslHisto.o -c pslHisto.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslHisto pslHisto.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslHisto make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/pslHisto' if test -d pslPairs ; then cd pslPairs && echo pslPairs && make ; fi pslPairs make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/pslPairs' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o pslPairs.o -c pslPairs.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslPairs pslPairs.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslPairs make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/pslPairs' if test -d pslPartition ; then cd pslPartition && echo pslPartition && make ; fi pslPartition make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/pslPartition' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o pslPartition.o -c pslPartition.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslPartition pslPartition.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslPartition make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/pslPartition' if test -d pslPretty ; then cd pslPretty && echo pslPretty && make ; fi pslPretty make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/pslPretty' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o pslPretty.o -c pslPretty.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslPretty pslPretty.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslPretty make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/pslPretty' if test -d pslRecalcMatch ; then cd pslRecalcMatch && echo pslRecalcMatch && make ; fi pslRecalcMatch make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/pslRecalcMatch' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o pslRecalcMatch.o -c pslRecalcMatch.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslRecalcMatch pslRecalcMatch.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslRecalcMatch make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/pslRecalcMatch' if test -d pslReps ; then cd pslReps && echo pslReps && make ; fi pslReps make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/pslReps' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o pslReps.o -c pslReps.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslReps pslReps.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslReps make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/pslReps' if test -d pslSelect ; then cd pslSelect && echo pslSelect && make ; fi pslSelect make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/pslSelect' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o pslSelect.o -c pslSelect.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslSelect pslSelect.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslSelect make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/pslSelect' if test -d pslSomeRecords ; then cd pslSomeRecords && echo pslSomeRecords && make ; fi pslSomeRecords make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/pslSomeRecords' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o pslSomeRecords.o -c pslSomeRecords.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslSomeRecords pslSomeRecords.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslSomeRecords make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/pslSomeRecords' if test -d pslSort ; then cd pslSort && echo pslSort && make ; fi pslSort make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/pslSort' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o pslSort.o -c pslSort.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslSort pslSort.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslSort make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/pslSort' if test -d pslStats ; then cd pslStats && echo pslStats && make ; fi pslStats make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/pslStats' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o pslStats.o -c pslStats.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslStats pslStats.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslStats make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/pslStats' if test -d pslToBed ; then cd pslToBed && echo pslToBed && make ; fi pslToBed make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/pslToBed' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o pslToBed.o -c pslToBed.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslToBed pslToBed.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslToBed make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/pslToBed' if test -d pslToChain ; then cd pslToChain && echo pslToChain && make ; fi pslToChain make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/pslToChain' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o pslToChain.o -c pslToChain.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslToChain pslToChain.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslToChain make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/pslToChain' if test -d pslxToFa ; then cd pslxToFa && echo pslxToFa && make ; fi pslxToFa make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/pslxToFa' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o pslxToFa.o -c pslxToFa.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslxToFa pslxToFa.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslxToFa make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/pslxToFa' if test -d qaToQac ; then cd qaToQac && echo qaToQac && make ; fi qaToQac make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/qaToQac' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o qaToQac.o -c qaToQac.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/qaToQac qaToQac.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/qaToQac make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/qaToQac' if test -d qacAgpLift ; then cd qacAgpLift && echo qacAgpLift && make ; fi qacAgpLift make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/qacAgpLift' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o qacAgpLift.o -c qacAgpLift.c qacAgpLift.c: In function ‘qacAgpLift’: qacAgpLift.c:163:5: warning: variable ‘count’ set but not used [-Wunused-but-set-variable=] 163 | int count = 0; | ^~~~~ gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/qacAgpLift qacAgpLift.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/qacAgpLift make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/qacAgpLift' if test -d qacToQa ; then cd qacToQa && echo qacToQa && make ; fi qacToQa make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/qacToQa' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o qacToQa.o -c qacToQa.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/qacToQa qacToQa.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/qacToQa make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/qacToQa' if test -d qacToWig ; then cd qacToWig && echo qacToWig && make ; fi qacToWig make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/qacToWig' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o qacToWig.o -c qacToWig.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/qacToWig qacToWig.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/qacToWig make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/qacToWig' if test -d sqlToXml ; then cd sqlToXml && echo sqlToXml && make ; fi sqlToXml make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/sqlToXml' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o sqlToXml.o -c sqlToXml.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/sqlToXml sqlToXml.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/sqlToXml make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/sqlToXml' if test -d trfBig ; then cd trfBig && echo trfBig && make ; fi trfBig make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/trfBig' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o trfBig.o -c trfBig.c trfBig.c: In function ‘trfBig’: trfBig.c:123:25: warning: ‘.2.7.7.80.10.50.’ directive writing 16 bytes into a region of size between 1 and 512 [-Wformat-overflow=] 123 | sprintf(trfRootName, "%s.2.7.7.80.10.50.%d", faFile, maxPeriod); | ^~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:974, from ../../inc/common.h:30, from trfBig.c:5: In function ‘sprintf’, inlined from ‘makeTrfRootName’ at trfBig.c:123:1, inlined from ‘trfBig’ at trfBig.c:219:2: /usr/include/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 18 and 539 bytes into a destination of size 512 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ trfBig.c: In function ‘trfBig’: trfBig.c:123:25: warning: ‘.2.7.7.80.10.50.’ directive writing 16 bytes into a region of size between 1 and 512 [-Wformat-overflow=] 123 | sprintf(trfRootName, "%s.2.7.7.80.10.50.%d", faFile, maxPeriod); | ^~~~~~~~~~~~~~~~ In function ‘sprintf’, inlined from ‘makeTrfRootName’ at trfBig.c:123:1, inlined from ‘trfBig’ at trfBig.c:256:6: /usr/include/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 18 and 539 bytes into a destination of size 512 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/trfBig trfBig.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/trfBig make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/trfBig' if test -d xmlCat ; then cd xmlCat && echo xmlCat && make ; fi xmlCat make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/xmlCat' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o xmlCat.o -c xmlCat.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/xmlCat xmlCat.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/xmlCat make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/xmlCat' if test -d xmlToSql ; then cd xmlToSql && echo xmlToSql && make ; fi xmlToSql make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/xmlToSql' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o xmlToSql.o -c xmlToSql.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o elStat.o -c elStat.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o rename.o -c rename.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o tables.o -c tables.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/xmlToSql xmlToSql.o elStat.o rename.o tables.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/xmlToSql make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg/xmlToSql' make[2]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/hg' make -C utils make[2]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils' cd addCols && echo addCols && make addCols make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/addCols' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o addCols.o -c addCols.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/addCols addCols.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/addCols make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/addCols' cd ave && echo ave && make ave make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/ave' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o ave.o -c ave.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/ave ave.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/ave make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/ave' cd aveCols && echo aveCols && make aveCols make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/aveCols' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o aveCols.o -c aveCols.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/aveCols aveCols.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/aveCols make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/aveCols' cd bamToPsl && echo bamToPsl && make bamToPsl make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/bamToPsl' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o bamToPsl.o -c bamToPsl.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bamToPsl bamToPsl.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bamToPsl make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/bamToPsl' cd bedClip && echo bedClip && make bedClip make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/bedClip' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o bedClip.o -c bedClip.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bedClip bedClip.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bedClip make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/bedClip' cd bedGraphToBigWig && echo bedGraphToBigWig && make bedGraphToBigWig make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/bedGraphToBigWig' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o bedGraphToBigWig.o -c bedGraphToBigWig.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bedGraphToBigWig bedGraphToBigWig.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bedGraphToBigWig make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/bedGraphToBigWig' cd bedJoinTabOffset && echo bedJoinTabOffset && make bedJoinTabOffset make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/bedJoinTabOffset' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o bedJoinTabOffset.o -c bedJoinTabOffset.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bedJoinTabOffset bedJoinTabOffset.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bedJoinTabOffset make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/bedJoinTabOffset' cd bedToBigBed && echo bedToBigBed && make bedToBigBed make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/bedToBigBed' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o bedToBigBed.o -c bedToBigBed.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bedToBigBed bedToBigBed.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bedToBigBed make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/bedToBigBed' cd bigBedInfo && echo bigBedInfo && make bigBedInfo make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/bigBedInfo' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o bigBedInfo.o -c bigBedInfo.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bigBedInfo bigBedInfo.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bigBedInfo make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/bigBedInfo' cd bigBedNamedItems && echo bigBedNamedItems && make bigBedNamedItems make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/bigBedNamedItems' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o bigBedNamedItems.o -c bigBedNamedItems.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bigBedNamedItems bigBedNamedItems.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bigBedNamedItems make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/bigBedNamedItems' cd bigBedSummary && echo bigBedSummary && make bigBedSummary make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/bigBedSummary' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o bigBedSummary.o -c bigBedSummary.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bigBedSummary bigBedSummary.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bigBedSummary make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/bigBedSummary' cd bigBedToBed && echo bigBedToBed && make bigBedToBed make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/bigBedToBed' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o bigBedToBed.o -c bigBedToBed.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bigBedToBed bigBedToBed.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bigBedToBed make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/bigBedToBed' cd bedCommonRegions && echo bedCommonRegions && make bedCommonRegions make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/bedCommonRegions' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o bedCommonRegions.o -c bedCommonRegions.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bedCommonRegions bedCommonRegions.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bedCommonRegions make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/bedCommonRegions' cd bedGeneParts && echo bedGeneParts && make bedGeneParts make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/bedGeneParts' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o bedGeneParts.o -c bedGeneParts.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bedGeneParts bedGeneParts.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bedGeneParts make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/bedGeneParts' cd bedGraphPack && echo bedGraphPack && make bedGraphPack make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/bedGraphPack' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o bedGraphPack.o -c bedGraphPack.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bedGraphPack bedGraphPack.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bedGraphPack make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/bedGraphPack' cd bedPileUps && echo bedPileUps && make bedPileUps make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/bedPileUps' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o bedPileUps.o -c bedPileUps.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bedPileUps bedPileUps.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bedPileUps make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/bedPileUps' cd bedRemoveOverlap && echo bedRemoveOverlap && make bedRemoveOverlap make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/bedRemoveOverlap' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o bedRemoveOverlap.o -c bedRemoveOverlap.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bedRemoveOverlap bedRemoveOverlap.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bedRemoveOverlap make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/bedRemoveOverlap' cd bedRestrictToPositions && echo bedRestrictToPositions && make bedRestrictToPositions make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/bedRestrictToPositions' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o bedRestrictToPositions.o -c bedRestrictToPositions.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bedRestrictToPositions bedRestrictToPositions.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bedRestrictToPositions make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/bedRestrictToPositions' cd bigWigAverageOverBed && echo bigWigAverageOverBed && make bigWigAverageOverBed make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/bigWigAverageOverBed' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o bigWigAverageOverBed.o -c bigWigAverageOverBed.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bigWigAverageOverBed bigWigAverageOverBed.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bigWigAverageOverBed make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/bigWigAverageOverBed' cd bigWigCat && echo bigWigCat && make bigWigCat make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/bigWigCat' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o bigWigCat.o -c bigWigCat.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bigWigCat bigWigCat.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bigWigCat make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/bigWigCat' cd bigWigCorrelate && echo bigWigCorrelate && make bigWigCorrelate make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/bigWigCorrelate' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o bigWigCorrelate.o -c bigWigCorrelate.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bigWigCorrelate bigWigCorrelate.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bigWigCorrelate make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/bigWigCorrelate' cd bigWigCluster && echo bigWigCluster && make bigWigCluster make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/bigWigCluster' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o bigWigCluster.o -c bigWigCluster.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bigWigCluster bigWigCluster.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bigWigCluster make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/bigWigCluster' cd bigWigInfo && echo bigWigInfo && make bigWigInfo make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/bigWigInfo' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o bigWigInfo.o -c bigWigInfo.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bigWigInfo bigWigInfo.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bigWigInfo make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/bigWigInfo' cd bigWigMerge && echo bigWigMerge && make bigWigMerge make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/bigWigMerge' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o bigWigMerge.o -c bigWigMerge.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bigWigMerge bigWigMerge.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bigWigMerge make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/bigWigMerge' cd bigWigSummary && echo bigWigSummary && make bigWigSummary make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/bigWigSummary' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o bigWigSummary.o -c bigWigSummary.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bigWigSummary bigWigSummary.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bigWigSummary make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/bigWigSummary' cd bigWigToBedGraph && echo bigWigToBedGraph && make bigWigToBedGraph make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/bigWigToBedGraph' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o bigWigToBedGraph.o -c bigWigToBedGraph.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bigWigToBedGraph bigWigToBedGraph.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bigWigToBedGraph make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/bigWigToBedGraph' cd bigWigToWig && echo bigWigToWig && make bigWigToWig make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/bigWigToWig' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o bigWigToWig.o -c bigWigToWig.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bigWigToWig bigWigToWig.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bigWigToWig make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/bigWigToWig' cd calc && echo calc && make calc make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/calc' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o calc.o -c calc.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/calc calc.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/calc make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/calc' cd catDir && echo catDir && make catDir make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/catDir' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o catDir.o -c catDir.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/catDir catDir.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/catDir make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/catDir' cd catUncomment && echo catUncomment && make catUncomment make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/catUncomment' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o catUncomment.o -c catUncomment.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/catUncomment catUncomment.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/catUncomment make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/catUncomment' cd chopFaLines && echo chopFaLines && make chopFaLines make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/chopFaLines' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o chopFaLines.o -c chopFaLines.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/chopFaLines chopFaLines.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/chopFaLines make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/chopFaLines' cd colTransform && echo colTransform && make colTransform make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/colTransform' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o colTransform.o -c colTransform.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/colTransform colTransform.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/colTransform make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/colTransform' cd countChars && echo countChars && make countChars make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/countChars' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o countChars.o -c countChars.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/countChars countChars.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/countChars make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/countChars' cd endsInLf && echo endsInLf && make endsInLf make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/endsInLf' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o endsInLf.o -c endsInLf.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/endsInLf endsInLf.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/endsInLf make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/endsInLf' cd clusterMatrixToBarChartBed && echo clusterMatrixToBarChartBed && make clusterMatrixToBarChartBed make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/clusterMatrixToBarChartBed' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o clusterMatrixToBarChartBed.o -c clusterMatrixToBarChartBed.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/clusterMatrixToBarChartBed clusterMatrixToBarChartBed.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/clusterMatrixToBarChartBed make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/clusterMatrixToBarChartBed' cd cpgIslandExt && echo cpgIslandExt && make cpgIslandExt make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/cpgIslandExt' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o cpg_lh.o -c cpg_lh.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o readseq.o -c readseq.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/cpg_lh cpg_lh.o readseq.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/cpg_lh make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/cpgIslandExt' cd faAlign && echo faAlign && make faAlign make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/faAlign' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o faAlign.o -c faAlign.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/faAlign faAlign.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/faAlign make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/faAlign' cd fastqToFa && echo fastqToFa && make fastqToFa make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/fastqToFa' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o fastqToFa.o -c fastqToFa.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/fastqToFa fastqToFa.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/fastqToFa make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/fastqToFa' cd fastqStatsAndSubsample && echo fastqStatsAndSubsample && make fastqStatsAndSubsample make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/fastqStatsAndSubsample' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o fastqStatsAndSubsample.o -c fastqStatsAndSubsample.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/fastqStatsAndSubsample fastqStatsAndSubsample.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/fastqStatsAndSubsample make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/fastqStatsAndSubsample' cd faCmp && echo faCmp && make faCmp make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/faCmp' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o faCmp.o -c faCmp.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/faCmp faCmp.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/faCmp make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/faCmp' cd faCount && echo faCount && make faCount make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/faCount' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o faCount.o -c faCount.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/faCount faCount.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/faCount make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/faCount' cd faFilterN && echo faFilterN && make faFilterN make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/faFilterN' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o faFilterN.o -c faFilterN.c faFilterN.c: In function ‘faFilterN’: faFilterN.c:130:19: warning: variable ‘passCount’ set but not used [-Wunused-but-set-variable=] 130 | int seqCount = 0, passCount = 0; | ^~~~~~~~~ faFilterN.c:130:5: warning: variable ‘seqCount’ set but not used [-Wunused-but-set-variable=] 130 | int seqCount = 0, passCount = 0; | ^~~~~~~~ gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/faFilterN faFilterN.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/faFilterN make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/faFilterN' cd faFilter && echo faFilter && make faFilter make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/faFilter' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o faFilter.o -c faFilter.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/faFilter faFilter.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/faFilter make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/faFilter' cd faFrag && echo faFrag && make faFrag make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/faFrag' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o faFrag.o -c faFrag.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/faFrag faFrag.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/faFrag make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/faFrag' cd faNoise && echo faNoise && make faNoise make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/faNoise' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o faNoise.o -c faNoise.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/faNoise faNoise.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/faNoise make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/faNoise' cd faOneRecord && echo faOneRecord && make faOneRecord make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/faOneRecord' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o faOneRecord.o -c faOneRecord.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/faOneRecord faOneRecord.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/faOneRecord make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/faOneRecord' cd faPolyASizes && echo faPolyASizes && make faPolyASizes make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/faPolyASizes' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o faPolyASizes.o -c faPolyASizes.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/faPolyASizes faPolyASizes.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/faPolyASizes make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/faPolyASizes' cd faRandomize && echo faRandomize && make faRandomize make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/faRandomize' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o faRandomize.o -c faRandomize.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/faRandomize faRandomize.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/faRandomize make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/faRandomize' cd faRc && echo faRc && make faRc make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/faRc' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o faRc.o -c faRc.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/faRc faRc.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/faRc make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/faRc' cd faSize && echo faSize && make faSize make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/faSize' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o faSize.o -c faSize.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/faSize faSize.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/faSize make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/faSize' cd faSomeRecords && echo faSomeRecords && make faSomeRecords make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/faSomeRecords' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o faSomeRecords.o -c faSomeRecords.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/faSomeRecords faSomeRecords.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/faSomeRecords make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/faSomeRecords' cd faSplit && echo faSplit && make faSplit make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/faSplit' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o faSplit.o -c faSplit.c faSplit.c: In function ‘splitByBase’: faSplit.c:159:5: warning: ‘strncpy’ specified bound 128 equals destination size [-Wstringop-truncation] 159 | strncpy(seqName, line, sizeof(seqName)); | ^ gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/faSplit faSplit.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/faSplit make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/faSplit' cd faToFastq && echo faToFastq && make faToFastq make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/faToFastq' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o faToFastq.o -c faToFastq.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/faToFastq faToFastq.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/faToFastq make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/faToFastq' cd faToTab && echo faToTab && make faToTab make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/faToTab' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o faToTab.o -c faToTab.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/faToTab faToTab.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/faToTab make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/faToTab' cd faToTwoBit && echo faToTwoBit && make faToTwoBit make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/faToTwoBit' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o faToTwoBit.o -c faToTwoBit.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/faToTwoBit faToTwoBit.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/faToTwoBit make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/faToTwoBit' cd faTrans && echo faTrans && make faTrans make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/faTrans' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o faTrans.o -c faTrans.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/faTrans faTrans.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/faTrans make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/faTrans' cd findMotif && echo findMotif && make findMotif make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/findMotif' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o findMotif.o -c findMotif.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/findMotif findMotif.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/findMotif make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/findMotif' cd headRest && echo headRest && make headRest make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/headRest' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o headRest.o -c headRest.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/headRest headRest.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/headRest make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/headRest' cd htmlCheck && echo htmlCheck && make htmlCheck make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/htmlCheck' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o htmlCheck.o -c htmlCheck.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/htmlCheck htmlCheck.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/htmlCheck make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/htmlCheck' cd matrixClusterColumns && echo matrixClusterColumns && make matrixClusterColumns make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/matrixClusterColumns' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o matrixClusterColumns.o -c matrixClusterColumns.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/matrixClusterColumns matrixClusterColumns.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/matrixClusterColumns make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/matrixClusterColumns' cd matrixMarketToTsv && echo matrixMarketToTsv && make matrixMarketToTsv make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/matrixMarketToTsv' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o matrixMarketToTsv.o -c matrixMarketToTsv.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/matrixMarketToTsv matrixMarketToTsv.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/matrixMarketToTsv make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/matrixMarketToTsv' cd matrixNormalize && echo matrixNormalize && make matrixNormalize make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/matrixNormalize' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o matrixNormalize.o -c matrixNormalize.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/matrixNormalize matrixNormalize.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/matrixNormalize make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/matrixNormalize' cd matrixToBarChartBed && echo matrixToBarChartBed && make matrixToBarChartBed make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/matrixToBarChartBed' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o matrixToBarChartBed.o -c matrixToBarChartBed.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/matrixToBarChartBed matrixToBarChartBed.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/matrixToBarChartBed make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/matrixToBarChartBed' cd newProg && echo newProg && make newProg make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/newProg' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o newProg.o -c newProg.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/newProg newProg.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/newProg make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/newProg' cd newPythonProg && echo newPythonProg && make newPythonProg make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/newPythonProg' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o newPythonProg.o -c newPythonProg.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/newPythonProg newPythonProg.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/newPythonProg make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/newPythonProg' cd nibFrag && echo nibFrag && make nibFrag make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/nibFrag' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o nibFrag.o -c nibFrag.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/nibFrag nibFrag.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/nibFrag make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/nibFrag' cd nibSize && echo nibSize && make nibSize make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/nibSize' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o nibSize.o -c nibSize.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/nibSize nibSize.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/nibSize make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/nibSize' cd paraFetch && echo paraFetch && make paraFetch make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/paraFetch' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o paraFetch.o -c paraFetch.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/paraFetch paraFetch.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/paraFetch make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/paraFetch' cd paraSync && echo paraSync && make paraSync make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/paraSync' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o paraSync.o -c paraSync.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/paraSync paraSync.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/paraSync make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/paraSync' cd pslMap && echo pslMap && make pslMap make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/pslMap' echo '/* GENERATED CODE, DO NOT EDIT */' > usage.msg.tmp sed -Ee 's/^.*$/"&\\n"/' usage.txt >> usage.msg.tmp mv -f usage.msg.tmp usage.msg gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o pslMap.o -c pslMap.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslMap pslMap.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslMap make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/pslMap' cd pslMapPostChain && echo pslMapPostChain && make pslMapPostChain make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/pslMapPostChain' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o pslMapPostChain.o -c pslMapPostChain.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslMapPostChain pslMapPostChain.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslMapPostChain make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/pslMapPostChain' cd pslPosTarget && echo pslPosTarget && make pslPosTarget make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/pslPosTarget' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o pslPosTarget.o -c pslPosTarget.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslPosTarget pslPosTarget.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslPosTarget make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/pslPosTarget' cd pslProtToRnaCoords && echo pslProtToRnaCoords && make pslProtToRnaCoords make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/pslProtToRnaCoords' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o pslProtToRnaCoords.o -c pslProtToRnaCoords.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslProtToRnaCoords pslProtToRnaCoords.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslProtToRnaCoords make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/pslProtToRnaCoords' cd pslRc && echo pslRc && make pslRc make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/pslRc' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o pslRc.o -c pslRc.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslRc pslRc.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslRc make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/pslRc' cd pslRemoveFrameShifts && echo pslRemoveFrameShifts && make pslRemoveFrameShifts make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/pslRemoveFrameShifts' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o pslRemoveFrameShifts.o -c pslRemoveFrameShifts.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslRemoveFrameShifts pslRemoveFrameShifts.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslRemoveFrameShifts make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/pslRemoveFrameShifts' cd pslScore && echo pslScore && make pslScore make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/pslScore' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o pslScore.o -c pslScore.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslScore pslScore.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslScore make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/pslScore' cd pslSpliceJunctions && echo pslSpliceJunctions && make pslSpliceJunctions make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/pslSpliceJunctions' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o pslSpliceJunctions.o -c pslSpliceJunctions.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslSpliceJunctions pslSpliceJunctions.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslSpliceJunctions make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/pslSpliceJunctions' cd pslSwap && echo pslSwap && make pslSwap make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/pslSwap' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o pslSwap.o -c pslSwap.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslSwap pslSwap.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslSwap make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/pslSwap' cd pslToPslx && echo pslToPslx && make pslToPslx make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/pslToPslx' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o pslToPslx.o -c pslToPslx.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslToPslx pslToPslx.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslToPslx make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/pslToPslx' cd randomLines && echo randomLines && make randomLines make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/randomLines' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o randomLines.o -c randomLines.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/randomLines randomLines.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/randomLines make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/randomLines' cd raToTab && echo raToTab && make raToTab make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/raToTab' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o raToTab.o -c raToTab.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/raToTab raToTab.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/raToTab make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/raToTab' cd raToLines && echo raToLines && make raToLines make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/raToLines' cd raToLines && make make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/raToLines/raToLines' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o raToLines.o -c raToLines.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/raToLines raToLines.o ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/raToLines make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/raToLines/raToLines' cd linesToRa && make make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/raToLines/linesToRa' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o linesToRa.o -c linesToRa.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/linesToRa linesToRa.o ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/linesToRa make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/raToLines/linesToRa' make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/raToLines' cd rmFaDups && echo rmFaDups && make rmFaDups make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/rmFaDups' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o rmFaDups.o -c rmFaDups.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/rmFaDups rmFaDups.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/rmFaDups make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/rmFaDups' cd rowsToCols && echo rowsToCols && make rowsToCols make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/rowsToCols' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o rowsToCols.o -c rowsToCols.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/rowsToCols rowsToCols.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/rowsToCols make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/rowsToCols' cd sizeof && echo sizeof && make sizeof make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/sizeof' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o sizeof.o -c sizeof.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/sizeof sizeof.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/sizeof make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/sizeof' cd spacedToTab && echo spacedToTab && make spacedToTab make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/spacedToTab' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o spacedToTab.o -c spacedToTab.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/spacedToTab spacedToTab.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/spacedToTab make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/spacedToTab' cd splitFile && echo splitFile && make splitFile make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/splitFile' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o splitFile.o -c splitFile.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/splitFile splitFile.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/splitFile make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/splitFile' cd splitFileByColumn && echo splitFileByColumn && make splitFileByColumn make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/splitFileByColumn' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o splitFileByColumn.o -c splitFileByColumn.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/splitFileByColumn splitFileByColumn.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/splitFileByColumn make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/splitFileByColumn' cd strexCalc && echo strexCalc && make strexCalc make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/strexCalc' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o strexCalc.o -c strexCalc.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/strexCalc strexCalc.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/strexCalc make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/strexCalc' cd stringify && echo stringify && make stringify make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/stringify' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o stringify.o -c stringify.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/stringify stringify.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/stringify make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/stringify' cd subChar && echo subChar && make subChar make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/subChar' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o subChar.o -c subChar.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/subChar subChar.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/subChar make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/subChar' cd subColumn && echo subColumn && make subColumn make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/subColumn' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o subColumn.o -c subColumn.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/subColumn subColumn.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/subColumn make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/subColumn' cd tabFmt && echo tabFmt && make tabFmt make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/tabFmt' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o tabFmt.o -c tabFmt.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/tabFmt tabFmt.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/tabFmt make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/tabFmt' cd tailLines && echo tailLines && make tailLines make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/tailLines' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o tailLines.o -c tailLines.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/tailLines tailLines.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/tailLines make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/tailLines' cd textHistogram && echo textHistogram && make textHistogram make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/textHistogram' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o textHistogram.o -c textHistogram.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/textHistogram textHistogram.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/textHistogram make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/textHistogram' cd tickToDate && echo tickToDate && make tickToDate make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/tickToDate' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o tickToDate.o -c tickToDate.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/tickToDate tickToDate.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/tickToDate make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/tickToDate' cd timing && echo timing && make timing make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/timing' cd gmtime && make make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/timing/gmtime' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o gmtime.o -c gmtime.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/gmtime gmtime.o ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/gmtime make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/timing/gmtime' cd mktime && make make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/timing/mktime' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o mktime.o -c mktime.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/mktime mktime.o ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/mktime make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/timing/mktime' cd localtime && make make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/timing/localtime' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../../htslib -I/usr/include/libpng16 -o localtime.o -c localtime.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/localtime localtime.o ../../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/localtime make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/timing/localtime' make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/timing' cd toLower && echo toLower && make toLower make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/toLower' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o toLower.o -c toLower.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/toLower toLower.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/toLower make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/toLower' cd toUpper && echo toUpper && make toUpper make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/toUpper' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o toUpper.o -c toUpper.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/toUpper toUpper.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/toUpper make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/toUpper' cd trackDbIndexBb && echo trackDbIndexBb && make trackDbIndexBb make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/trackDbIndexBb' rm -f /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/trackDbIndexBb cp -p trackDbIndexBb /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/trackDbIndexBb make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/trackDbIndexBb' cd twoBitDup && echo twoBitDup && make twoBitDup make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/twoBitDup' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o twoBitDup.o -c twoBitDup.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/twoBitDup twoBitDup.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/twoBitDup make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/twoBitDup' cd twoBitInfo && echo twoBitInfo && make twoBitInfo make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/twoBitInfo' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o twoBitInfo.o -c twoBitInfo.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/twoBitInfo twoBitInfo.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/twoBitInfo make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/twoBitInfo' cd twoBitToFa && echo twoBitToFa && make twoBitToFa make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/twoBitToFa' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o twoBitToFa.o -c twoBitToFa.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/twoBitToFa twoBitToFa.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/twoBitToFa make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/twoBitToFa' cd wigCorrelate && echo wigCorrelate && make wigCorrelate make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/wigCorrelate' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o wigCorrelate.o -c wigCorrelate.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/wigCorrelate wigCorrelate.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/wigCorrelate make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/wigCorrelate' cd wigToBigWig && echo wigToBigWig && make wigToBigWig make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/wigToBigWig' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o wigToBigWig.o -c wigToBigWig.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/wigToBigWig wigToBigWig.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/wigToBigWig make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/wigToBigWig' cd wordLine && echo wordLine && make wordLine make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/wordLine' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o wordLine.o -c wordLine.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/wordLine wordLine.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/wordLine make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/wordLine' cd aNotB && echo aNotB && make aNotB make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/aNotB' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o aNotB.o -c aNotB.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/aNotB aNotB.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/aNotB make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/aNotB' cd ccCp && echo ccCp && make ccCp make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/ccCp' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o ccCp.o -c ccCp.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/ccCp ccCp.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/ccCp make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/ccCp' cd convolve && echo convolve && make convolve make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/convolve' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o convolve.o -c convolve.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/convolve convolve.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/convolve make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/convolve' cd detab && echo detab && make detab make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/detab' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o detab.o -c detab.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/detab detab.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/detab make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/detab' cd dnsInfo && echo dnsInfo && make dnsInfo make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/dnsInfo' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o dnsInfo.o -c dnsInfo.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/dnsInfo dnsInfo.o ../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm -lresolv true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/dnsInfo make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/dnsInfo' cd faFlyBaseToUcsc && echo faFlyBaseToUcsc && make faFlyBaseToUcsc make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/faFlyBaseToUcsc' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o faFlyBaseToUcsc.o -c faFlyBaseToUcsc.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/faFlyBaseToUcsc faFlyBaseToUcsc.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/faFlyBaseToUcsc make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/faFlyBaseToUcsc' cd faGapLocs && echo faGapLocs && make faGapLocs make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/faGapLocs' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o faGapLocs.o -c faGapLocs.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/faGapLocs faGapLocs.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/faGapLocs make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/faGapLocs' cd faGapSizes && echo faGapSizes && make faGapSizes make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/faGapSizes' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o faGapSizes.o -c faGapSizes.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/faGapSizes faGapSizes.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/faGapSizes make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/faGapSizes' cd faNcbiToUcsc && echo faNcbiToUcsc && make faNcbiToUcsc make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/faNcbiToUcsc' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o faNcbiToUcsc.o -c faNcbiToUcsc.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/faNcbiToUcsc faNcbiToUcsc.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/faNcbiToUcsc make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/faNcbiToUcsc' cd faRenameRecords && echo faRenameRecords && make faRenameRecords make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/faRenameRecords' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o faRenameRecords.o -c faRenameRecords.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/faRenameRecords faRenameRecords.o ../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/faRenameRecords make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/faRenameRecords' cd faSimplify && echo faSimplify && make faSimplify make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/faSimplify' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o faSimplify.o -c faSimplify.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/faSimplify faSimplify.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/faSimplify make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/faSimplify' cd faToNib && echo faToNib && make faToNib make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/faToNib' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o faToNib.o -c faToNib.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/faToNib faToNib.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/faToNib make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/faToNib' cd faTrimPolyA && echo faTrimPolyA && make faTrimPolyA make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/faTrimPolyA' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o faTrimPolyA.o -c faTrimPolyA.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/faTrimPolyA faTrimPolyA.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/faTrimPolyA make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/faTrimPolyA' cd faTrimRead && echo faTrimRead && make faTrimRead make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/faTrimRead' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o faTrimRead.o -c faTrimRead.c faTrimRead.c: In function ‘faTrimRead’: faTrimRead.c:228:5: warning: variable ‘seqCount’ set but not used [-Wunused-but-set-variable=] 228 | int seqCount = 0; | ^~~~~~~~ gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/faTrimRead faTrimRead.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/faTrimRead make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/faTrimRead' cd fixCr && echo fixCr && make fixCr make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/fixCr' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o fixCr.o -c fixCr.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/fixCr fixCr.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/fixCr make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/fixCr' cd gapSplit && echo gapSplit && make gapSplit make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/gapSplit' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o gapSplit.o -c gapSplit.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/gapSplit gapSplit.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/gapSplit make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/gapSplit' cd gitTools && echo gitTools && make gitTools make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/gitTools' chmod a+rx gitFiles rm -f /builddir/bin/scripts/gitFiles cp -pf gitFiles /builddir/bin/scripts/gitFiles chmod a+rx gilt rm -f /builddir/bin/scripts/gilt cp -pf gilt /builddir/bin/scripts/gilt chmod a+rx gitu rm -f /builddir/bin/scripts/gitu cp -pf gitu /builddir/bin/scripts/gitu make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/gitTools' cd gffPeek && echo gffPeek && make gffPeek make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/gffPeek' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o gffPeek.o -c gffPeek.c gffPeek.c: In function ‘gffPeek’: gffPeek.c:93:5: warning: variable ‘badCount’ set but not used [-Wunused-but-set-variable=] 93 | int badCount = 0; | ^~~~~~~~ gffPeek.c:92:5: warning: variable ‘commentCount’ set but not used [-Wunused-but-set-variable=] 92 | int commentCount = 0; | ^~~~~~~~~~~~ gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/gffPeek gffPeek.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/gffPeek make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/gffPeek' cd git-reports && echo git-reports && make git-reports make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/git-reports' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o git-reports.o -c git-reports.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/git-reports git-reports.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/git-reports make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/git-reports' cd htmlPics && echo htmlPics && make htmlPics make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/htmlPics' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o htmlPics.o -c htmlPics.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/htmlPics htmlPics.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/htmlPics make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/htmlPics' cd jkUniq && echo jkUniq && make jkUniq make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/jkUniq' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o jkUniq.o -c jkUniq.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/jkUniq jkUniq.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/jkUniq make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/jkUniq' cd lineCount && echo lineCount && make lineCount make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/lineCount' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o lineCount.o -c lineCount.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/lineCount lineCount.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/lineCount make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/lineCount' cd nt4Frag && echo nt4Frag && make nt4Frag make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/nt4Frag' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o nt4Frag.o -c nt4Frag.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/nt4Frag nt4Frag.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/nt4Frag make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/nt4Frag' cd pslToXa && echo pslToXa && make pslToXa make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/pslToXa' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o pslToXa.o -c pslToXa.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslToXa pslToXa.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/pslToXa make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/pslToXa' cd scrambleFa && echo scrambleFa && make scrambleFa make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/scrambleFa' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o scrambleFa.o -c scrambleFa.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/scrambleFa scrambleFa.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/scrambleFa make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/scrambleFa' cd subs && echo subs && make subs make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/subs' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o subs.o -c subs.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/subs subs.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/subs make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/subs' cd tabToMmHash && echo tabToMmHash && make tabToMmHash make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/tabToMmHash' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o tabToMmHash.o -c tabToMmHash.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/tabToMmHash tabToMmHash.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/tabToMmHash make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/tabToMmHash' cd tableSum && echo tableSum && make tableSum make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/tableSum' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o tableSum.o -c tableSum.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/tableSum tableSum.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/tableSum make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/tableSum' cd textHist2 && echo textHist2 && make textHist2 make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/textHist2' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o textHist2.o -c textHist2.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/textHist2 textHist2.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/textHist2 make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/textHist2' cd udcCleanup && echo udcCleanup && make udcCleanup make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/udcCleanup' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o udcCleanup.o -c udcCleanup.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/udcCleanup udcCleanup.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/udcCleanup make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/udcCleanup' cd undupFa && echo undupFa && make undupFa make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/undupFa' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o undupFa.o -c undupFa.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/undupFa undupFa.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/undupFa make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/undupFa' cd upper && echo upper && make upper make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/upper' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o upper.o -c upper.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/upper upper.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/upper make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/upper' cd vcfFilter && echo vcfFilter && make vcfFilter make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/vcfFilter' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o vcfFilter.o -c vcfFilter.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/vcfFilter vcfFilter.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/vcfFilter make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/vcfFilter' cd venn && echo venn && make venn make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/venn' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o venn.o -c venn.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/venn venn.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/venn make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/venn' cd verticalSplitSqlTable && echo verticalSplitSqlTable && make verticalSplitSqlTable make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/verticalSplitSqlTable' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o verticalSplitSqlTable.o -c verticalSplitSqlTable.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/verticalSplitSqlTable verticalSplitSqlTable.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/verticalSplitSqlTable make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/verticalSplitSqlTable' cd weedLines && echo weedLines && make weedLines make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/weedLines' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o weedLines.o -c weedLines.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/weedLines weedLines.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/weedLines make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils/weedLines' cp -p bedJoinTabOffset.py/bedJoinTabOffset.py /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin cp -p expMatrixToBarchartBed/expMatrixToBarchartBed /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin cp -p barChartMaxLimit/barChartMaxLimit /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin cp -p ucscApiClient/ucscApiClient /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin cp -p tdbRename/tdbRename /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin cp -p tdbSort/tdbSort /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin cp -p webSync/webSync /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin cp -p chromToUcsc/chromToUcsc /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin cp -p bigHeat/bigHeat /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin cp -p bigGuessDb/bigGuessDb /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin make[2]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/utils' make -C ameme make[2]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/ameme' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o ameme.o -c ameme.c ameme.c: In function ‘findSeedsFragTime’: ameme.c:164:8: warning: variable ‘acc’ set but not used [-Wunused-but-set-variable=] 164 | double acc; | ^~~ ameme.c: In function ‘readSeqMaybeMakeFrame’: ameme.c:295:51: warning: ‘%s’ directive output may be truncated writing 6 bytes into a region of size between 1 and 512 [-Wformat-truncation=] 295 | snprintf(codFileName, sizeof(codFileName), "%s%s", amemeDir(), "ce.cod"); | ^~ ~~~~~~~~ In file included from /usr/include/stdio.h:974, from ../inc/common.h:30, from ameme.c:2: In function ‘snprintf’, inlined from ‘readSeqMaybeMakeFrame’ at ameme.c:295:5: /usr/include/bits/stdio2.h:68:10: note: ‘__snprintf_chk’ output between 7 and 518 bytes into a destination of size 512 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ ameme.c: In function ‘impDoMiddle’: ameme.c:2488:25: warning: ‘%s’ directive writing between 8 and 10 bytes into a region of size between 1 and 512 [-Wformat-overflow=] 2488 | sprintf(retPathName, "%s%s", dir, fileName); | ^~ In function ‘sprintf’, inlined from ‘makePremadeBgPathName’ at ameme.c:2488:1, inlined from ‘impDoMiddle’ at ameme.c:2820:9: /usr/include/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 9 and 522 bytes into a destination of size 512 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o fragFind.o -c fragFind.c fragFind.c: In function ‘makeProfile’: fragFind.c:437:5: warning: variable ‘seqCount’ set but not used [-Wunused-but-set-variable=] 437 | int seqCount = 0; | ^~~~~~~~ gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/ameme ameme.o fragFind.o ../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/ameme make[2]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/ameme' make -C index make[2]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/index' cd bptForTwoBit && make make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/index/bptForTwoBit' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o bptForTwoBit.o -c bptForTwoBit.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bptForTwoBit bptForTwoBit.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bptForTwoBit make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/index/bptForTwoBit' cd bptLookupStringToBits64 && make make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/index/bptLookupStringToBits64' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o bptLookupStringToBits64.o -c bptLookupStringToBits64.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bptLookupStringToBits64 bptLookupStringToBits64.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bptLookupStringToBits64 make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/index/bptLookupStringToBits64' cd bptMakeStringToBits64 && make make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/index/bptMakeStringToBits64' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o bptMakeStringToBits64.o -c bptMakeStringToBits64.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bptMakeStringToBits64 bptMakeStringToBits64.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bptMakeStringToBits64 make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/index/bptMakeStringToBits64' cd indexfa && make make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/index/indexfa' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o indexfa.o -c indexfa.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/indexfa indexfa.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/indexfa make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/index/indexfa' cd indexgl && make make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/index/indexgl' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o indexgl.o -c indexgl.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/indexgl indexgl.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/indexgl make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/index/indexgl' cd ixali && make make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/index/ixali' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o ixali.o -c ixali.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/ixali ixali.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/ixali make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/index/ixali' cd ixIxx && make make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/index/ixIxx' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o ixIxx.o -c ixIxx.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/ixIxx ixIxx.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/ixIxx make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/index/ixIxx' cd ixword1 && make make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/index/ixword1' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o ixword1.o -c ixword1.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/ixword1 ixword1.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/ixword1 make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/index/ixword1' cd ixword3 && make make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/index/ixword3' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o ixword3.o -c ixword3.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/ixword3 ixword3.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/ixword3 make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/index/ixword3' cd makepgo && make make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/index/makepgo' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o makepgo.o -c makepgo.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/makepgo makepgo.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/makepgo make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/index/makepgo' cd stToXao && make make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/index/stToXao' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o stToXao.o -c stToXao.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/stToXao stToXao.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/stToXao make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/index/stToXao' cd trixContextIndex && make make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/index/trixContextIndex' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o trixContextIndex.o -c trixContextIndex.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/trixContextIndex trixContextIndex.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/trixContextIndex make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/index/trixContextIndex' cd trixSearch && make make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/index/trixSearch' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o trixSearch.o -c trixSearch.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/trixSearch trixSearch.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/trixSearch make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/index/trixSearch' cd trixMultiSearch && make make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/index/trixMultiSearch' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o trixMultiSearch.o -c trixMultiSearch.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/trixMultiSearch trixMultiSearch.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/trixMultiSearch make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/index/trixMultiSearch' make[2]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/index' make -C dnaDust make[2]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/dnaDust' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o dnadust.o -c dnadust.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/dnadust dnadust.o ../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/dnadust make[2]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/dnaDust' make -C protDust make[2]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/protDust' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o protDust.o -c protDust.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/protDust protDust.o ../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/protDust make[2]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/protDust' make -C weblet make[2]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/weblet' cd bottleneck && make make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/weblet/bottleneck' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o bottleneck.o -c bottleneck.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bottleneck bottleneck.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/bottleneck make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/weblet/bottleneck' cd counter && make make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/weblet/counter' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o counter.o -c counter.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/counter counter.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/counter make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/weblet/counter' cd hitreport && make make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/weblet/hitreport' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o hitreport.o -c hitreport.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hitreport hitreport.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/hitreport make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/weblet/hitreport' make[2]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/weblet' make -C aladdin make[2]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/aladdin' cd aladdin && make make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/aladdin/aladdin' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o aladdin.o -c aladdin.c aladdin.c: In function ‘makeMarkovModels’: aladdin.c:985:26: warning: ‘%s’ directive writing 16 bytes into a region of size between 1 and 512 [-Wformat-overflow=] 985 | sprintf(fileName, "%s%s", dir, "ceLongIntron3.fa"); | ^~ ~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:974, from ../../inc/common.h:30, from aladdin.c:2: In function ‘sprintf’, inlined from ‘makeMarkovModels’ at aladdin.c:985:5: /usr/include/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 17 and 528 bytes into a destination of size 512 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ aladdin.c: In function ‘makeMarkovModels’: aladdin.c:987:26: warning: ‘%s’ directive writing 11 bytes into a region of size between 1 and 512 [-Wformat-overflow=] 987 | sprintf(fileName, "%s%s", dir, "cecoding.fa"); | ^~ ~~~~~~~~~~~~~ In function ‘sprintf’, inlined from ‘makeMarkovModels’ at aladdin.c:987:5: /usr/include/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 12 and 523 bytes into a destination of size 512 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ aladdin.c: In function ‘makeMarkovModels’: aladdin.c:989:26: warning: ‘%s’ directive writing 7 bytes into a region of size between 1 and 512 [-Wformat-overflow=] 989 | sprintf(fileName, "%s%s", dir, "ceig.fa"); | ^~ ~~~~~~~~~ In function ‘sprintf’, inlined from ‘makeMarkovModels’ at aladdin.c:989:5: /usr/include/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 8 and 519 bytes into a destination of size 512 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ aladdin.c: In function ‘makeMarkovModels’: aladdin.c:991:26: warning: ‘%s’ directive writing 7 bytes into a region of size between 1 and 512 [-Wformat-overflow=] 991 | sprintf(fileName, "%s%s", dir, "ceig.fa"); | ^~ ~~~~~~~~~ In function ‘sprintf’, inlined from ‘makeMarkovModels’ at aladdin.c:991:5: /usr/include/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 8 and 519 bytes into a destination of size 512 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ aladdin.c: In function ‘makeMarkovModels’: aladdin.c:993:26: warning: ‘%s’ directive writing 14 bytes into a region of size between 1 and 512 [-Wformat-overflow=] 993 | sprintf(fileName, "%s%s", dir, "cepromoCons.fa"); | ^~ ~~~~~~~~~~~~~~~~ In function ‘sprintf’, inlined from ‘makeMarkovModels’ at aladdin.c:993:5: /usr/include/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 15 and 526 bytes into a destination of size 512 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/aladdin aladdin.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/aladdin make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/aladdin/aladdin' make[2]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/aladdin' make -C primeMate make[2]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/primeMate' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o primeMate.o -c primeMate.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/primeMate primeMate.o ../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/primeMate make[2]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/primeMate' make -C fuse make[2]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/fuse' make -C udcFuse make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/fuse/udcFuse' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o udcFuse.o -c udcFuse.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/udcFuse udcFuse.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/udcFuse make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/fuse/udcFuse' make[2]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/fuse' make -C meta make[2]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/meta' cd metaFlatten && make make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/meta/metaFlatten' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o metaFlatten.o -c metaFlatten.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/metaFlatten metaFlatten.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/metaFlatten make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/meta/metaFlatten' cd metaHoist && make make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/meta/metaHoist' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o metaHoist.o -c metaHoist.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/metaHoist metaHoist.o ../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/metaHoist make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/meta/metaHoist' cd metaReformat && make make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/meta/metaReformat' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o metaReformat.o -c metaReformat.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/metaReformat metaReformat.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl -lm true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/metaReformat make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/meta/metaReformat' make[2]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/meta' make -C tagStorm make[2]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/tagStorm' make buildUtils make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/tagStorm' cd tagStormHoist && make make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/tagStorm/tagStormHoist' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o tagStormHoist.o -c tagStormHoist.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/tagStormHoist tagStormHoist.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/tagStormHoist make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/tagStorm/tagStormHoist' cd tagStormReformat && make make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/tagStorm/tagStormReformat' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o tagStormReformat.o -c tagStormReformat.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/tagStormReformat tagStormReformat.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/tagStormReformat make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/tagStorm/tagStormReformat' cd tagStormFromTab && make make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/tagStorm/tagStormFromTab' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o tagStormFromTab.o -c tagStormFromTab.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/tagStormFromTab tagStormFromTab.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/tagStormFromTab make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/tagStorm/tagStormFromTab' cd jsonToTagStorm && make make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/tagStorm/jsonToTagStorm' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o jsonToTagStorm.o -c jsonToTagStorm.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/jsonToTagStorm jsonToTagStorm.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/jsonToTagStorm make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/tagStorm/jsonToTagStorm' cd tagStormInfo && make make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/tagStorm/tagStormInfo' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o tagStormInfo.o -c tagStormInfo.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/tagStormInfo tagStormInfo.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/tagStormInfo make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/tagStorm/tagStormInfo' cd tagStormJoinTab && make make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/tagStorm/tagStormJoinTab' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o tagStormJoinTab.o -c tagStormJoinTab.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/tagStormJoinTab tagStormJoinTab.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/tagStormJoinTab make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/tagStorm/tagStormJoinTab' cd tagStormToHtml && make make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/tagStorm/tagStormToHtml' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o tagStormToHtml.o -c tagStormToHtml.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/tagStormToHtml tagStormToHtml.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/tagStormToHtml make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/tagStorm/tagStormToHtml' cd tagStormToJson && make make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/tagStorm/tagStormToJson' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o tagStormToJson.o -c tagStormToJson.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/tagStormToJson tagStormToJson.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/tagStormToJson make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/tagStorm/tagStormToJson' cd tagStormDeleteTags && make make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/tagStorm/tagStormDeleteTags' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o tagStormDeleteTags.o -c tagStormDeleteTags.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/tagStormDeleteTags tagStormDeleteTags.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/tagStormDeleteTags make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/tagStorm/tagStormDeleteTags' cd tagStormRenameTags && make make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/tagStorm/tagStormRenameTags' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o tagStormRenameTags.o -c tagStormRenameTags.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/tagStormRenameTags tagStormRenameTags.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/tagStormRenameTags make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/tagStorm/tagStormRenameTags' cd tagStormRenameVals && make make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/tagStorm/tagStormRenameVals' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o tagStormRenameVals.o -c tagStormRenameVals.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/tagStormRenameVals tagStormRenameVals.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/tagStormRenameVals make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/tagStorm/tagStormRenameVals' cd tagStormToCsv && make make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/tagStorm/tagStormToCsv' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o tagStormToCsv.o -c tagStormToCsv.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/tagStormToCsv tagStormToCsv.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/tagStormToCsv make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/tagStorm/tagStormToCsv' cd tagStormToTab && make make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/tagStorm/tagStormToTab' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o tagStormToTab.o -c tagStormToTab.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/tagStormToTab tagStormToTab.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/tagStormToTab make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/tagStorm/tagStormToTab' cd tagStormToSql && make make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/tagStorm/tagStormToSql' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o tagStormToSql.o -c tagStormToSql.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/tagStormToSql tagStormToSql.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/tagStormToSql make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/tagStorm/tagStormToSql' cd tagStormCheck && make make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/tagStorm/tagStormCheck' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o tagStormCheck.o -c tagStormCheck.c tagStormCheck.c: In function ‘tagStormCheck’: tagStormCheck.c:323:5: warning: variable ‘schemaSize’ set but not used [-Wunused-but-set-variable=] 323 | int schemaSize = 0; | ^~~~~~~~~~ gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/tagStormCheck tagStormCheck.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/tagStormCheck make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/tagStorm/tagStormCheck' cd tagStormArrayToCsv && make make[4]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/tagStorm/tagStormArrayToCsv' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o tagStormArrayToCsv.o -c tagStormArrayToCsv.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/tagStormArrayToCsv tagStormArrayToCsv.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/tagStormArrayToCsv make[4]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/tagStorm/tagStormArrayToCsv' make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/tagStorm' make[2]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/tagStorm' make -C tabFile make[2]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/tabFile' cd tabInfo && echo tabInfo && make tabInfo make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/tabFile/tabInfo' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o tabInfo.o -c tabInfo.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/tabInfo tabInfo.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/tabInfo make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/tabFile/tabInfo' cd tabQuery && echo tabQuery && make tabQuery make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/tabFile/tabQuery' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o tabQuery.o -c tabQuery.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/tabQuery tabQuery.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/tabQuery make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/tabFile/tabQuery' cd tabRepeatedFieldsToArrayField && echo tabRepeatedFieldsToArrayField && make tabRepeatedFieldsToArrayField make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/tabFile/tabRepeatedFieldsToArrayField' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o tabRepeatedFieldsToArrayField.o -c tabRepeatedFieldsToArrayField.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/tabRepeatedFieldsToArrayField tabRepeatedFieldsToArrayField.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/tabRepeatedFieldsToArrayField make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/tabFile/tabRepeatedFieldsToArrayField' cd tabToHtml && echo tabToHtml && make tabToHtml make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/tabFile/tabToHtml' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o tabToHtml.o -c tabToHtml.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/tabToHtml tabToHtml.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/tabToHtml make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/tabFile/tabToHtml' cd tabToTabDir && echo tabToTabDir && make tabToTabDir make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/tabFile/tabToTabDir' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o tabToTabDir.o -c tabToTabDir.c gcc -O -g -o /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/tabToTabDir tabToTabDir.o ../../lib/x86_64/jkweb.a -lmariadb -lz -lpthread -lm -lssl -lcrypto -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin/tabToTabDir make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/tabFile/tabToTabDir' make[2]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/tabFile' make -C parasol make[2]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/parasol' mkdir -p bin cd lib && make make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/parasol/lib' mkdir -p x86_64 ar rcu x86_64/paralib.a broadData.o paraLib.o paraMessage.o machSpec.o jobResult.o ranlib x86_64/paralib.a make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/parasol/lib' cd gensub2 && echo gensub2 && make gensub2 make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/parasol/gensub2' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o gensub2.o -c gensub2.c mkdir -p ../bin gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -o ../bin/gensub2 gensub2.o ../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true ../bin/gensub2 make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/parasol/gensub2' cd para && echo para && make para make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/parasol/para' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o para.o -c para.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o jobDb.o -c jobDb.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -o ../bin/para para.o jobDb.o ../lib/x86_64/paralib.a ../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true ../bin/para make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/parasol/para' cd paraHub && echo paraHub && make paraHub make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/parasol/paraHub' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o paraHub.o -c paraHub.c paraHub.c: In function ‘startHub’: paraHub.c:3399:8: warning: ignoring return value of ‘nice’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3399 | (void) nice(-40); // ignore return value | ^~~~~~~~~ gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o spoke.o -c spoke.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o heartbeat.o -c heartbeat.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o queue.o -c queue.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o sockSuck.o -c sockSuck.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -ggdb -o ../bin/paraHub paraHub.o spoke.o heartbeat.o queue.o sockSuck.o ../lib/x86_64/paralib.a ../../lib/x86_64/jkweb.a -lpthread -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/parasol/paraHub' cd paraHubStop && echo paraHubStop && make paraHubStop make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/parasol/paraHubStop' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o paraHubStop.o -c paraHubStop.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -o ../bin/paraHubStop paraHubStop.o ../lib/x86_64/paralib.a ../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true ../bin/paraHubStop make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/parasol/paraHubStop' cd paraNode && echo paraNode && make paraNode make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/parasol/paraNode' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o paraNode.o -c paraNode.c mkdir -p ../bin gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -o ../bin/paraNode paraNode.o ../lib/x86_64/paralib.a ../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true ../bin/paraNode make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/parasol/paraNode' cd paraNodeStart && echo paraNodeStart && make paraNodeStart make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/parasol/paraNodeStart' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o paraNodeStart.o -c paraNodeStart.c paraNodeStart.c: In function ‘paraNodeStart’: paraNodeStart.c:100:12: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 100 | (void) system(dy->string); // ignore return value | ^~~~~~~~~~~~~~~~~~ gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -o ../bin/paraNodeStart paraNodeStart.o ../lib/x86_64/paralib.a ../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true ../bin/paraNodeStart make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/parasol/paraNodeStart' cd paraNodeStatus && echo paraNodeStatus && make paraNodeStatus make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/parasol/paraNodeStatus' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o paraNodeStatus.o -c paraNodeStatus.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -o ../bin/paraNodeStatus paraNodeStatus.o ../lib/x86_64/paralib.a ../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true ../bin/paraNodeStatus make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/parasol/paraNodeStatus' cd paraNodeStop && echo paraNodeStop && make paraNodeStop make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/parasol/paraNodeStop' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o paraNodeStop.o -c paraNodeStop.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -o ../bin/paraNodeStop paraNodeStop.o ../lib/x86_64/paralib.a ../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true ../bin/paraNodeStop chmod 744 ../bin/paraNodeStop make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/parasol/paraNodeStop' cd paraTestJob && echo paraTestJob && make paraTestJob make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/parasol/paraTestJob' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o paraTestJob.o -c paraTestJob.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -o ../bin/paraTestJob paraTestJob.o ../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true ../bin/paraTestJob make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/parasol/paraTestJob' cd parasol && echo parasol && make parasol make[3]: Entering directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/parasol/parasol' gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/usr/include/libpng16 -o parasol.o -c parasol.c parasol.c: In function ‘getResultsFile’: parasol.c:108:8: warning: ignoring return value of ‘getcwd’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 108 | (void) getcwd(curDir, sizeof(curDir)); // ignore return value | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ parasol.c: In function ‘addJob’: parasol.c:268:8: warning: ignoring return value of ‘getcwd’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 268 | (void) getcwd(curDir, sizeof(curDir)); // ignore return value | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -o ../bin/parasol parasol.o ../lib/x86_64/paralib.a ../../lib/x86_64/jkweb.a -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lz -lbz2 -ldl -lm -lc -lcurl true ../bin/parasol make[3]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/parasol/parasol' make[2]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src/parasol' make[1]: Leaving directory '/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/src' + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.uhDf9f + umask 022 + cd /builddir/build/BUILD/ucsc-kent-utils-492-build + '[' /builddir/build/BUILD/ucsc-kent-utils-492-build/BUILDROOT '!=' / ']' + rm -rf /builddir/build/BUILD/ucsc-kent-utils-492-build/BUILDROOT ++ dirname /builddir/build/BUILD/ucsc-kent-utils-492-build/BUILDROOT + mkdir -p /builddir/build/BUILD/ucsc-kent-utils-492-build + mkdir /builddir/build/BUILD/ucsc-kent-utils-492-build/BUILDROOT + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd kent-core-492 + mkdir -p /builddir/build/BUILD/ucsc-kent-utils-492-build/BUILDROOT/usr/bin + install -m 0755 bin/aNotB bin/aarToAxt bin/addAveMedScoreToPsls bin/addCols bin/affyPairsToSample bin/agpAllToFaFile bin/agpCloneCheck bin/agpCloneList bin/agpMergeChromScaf bin/agpToFa bin/agpToGl bin/agxToBed bin/agxToIntronBeds bin/agxToTxg bin/aladdin bin/allenCollectSeq bin/altAnalysis bin/altPaths bin/altSplice bin/altSummary bin/ameme bin/apacheMonitor bin/assessLibs bin/autoDtd bin/autoSql bin/autoXml bin/ave bin/aveCols bin/averagExp bin/averageZoomLevels bin/avgTranscriptomeExps bin/axtAndBed bin/axtBest bin/axtCalcMatrix bin/axtChain bin/axtDropOverlap bin/axtDropSelf bin/axtFilter bin/axtForEst bin/axtIndex bin/axtPretty bin/axtQueryCount bin/axtRecipBest bin/axtRescore bin/axtSort bin/axtSplitByTarget bin/axtSwap bin/axtToBed bin/axtToChain bin/axtToMaf bin/axtToPsl bin/bamToPsl bin/barChartMaxLimit bin/bedClip bin/bedCommonRegions bin/bedCons bin/bedCoverage bin/bedDown bin/bedExtendRanges bin/bedGeneParts bin/bedGraphPack bin/bedGraphToBigWig bin/bedInGraph bin/bedIntersect bin/bedItemOverlapCount bin/bedJoinTabOffset bin/bedJoinTabOffset.py bin/bedMergeAdjacent bin/bedOrBlocks bin/bedPartition bin/bedPileUps bin/bedRemoveOverlap bin/bedRestrictToPositions bin/bedSort bin/bedSplitOnChrom bin/bedToBigBed bin/bedToExons bin/bedToFrames bin/bedToGenePred bin/bedToPsl bin/bedToTxEdges bin/bedUp bin/bedWeedOverlapping bin/bigBedInfo bin/bigBedNamedItems bin/bigBedSummary bin/bigBedToBed bin/bigChainBreaks bin/bigChainToChain bin/bigGenePredToGenePred bin/bigGuessDb bin/bigHeat bin/bigMafToMaf bin/bigPslToPsl bin/bigWigAverageOverBed bin/bigWigCat bin/bigWigCluster bin/bigWigCorrelate bin/bigWigInfo bin/bigWigMerge bin/bigWigSummary bin/bigWigToBedGraph bin/bigWigToWig bin/binFromRange bin/blastToPsl bin/blastXmlToPsl bin/borfBig bin/bottleneck bin/bptForTwoBit bin/bptLookupStringToBits64 bin/bptMakeStringToBits64 bin/buildReleaseLog bin/calc bin/calcGap bin/catDir bin/catUncomment bin/ccCp bin/chainAntiRepeat bin/chainCleaner bin/chainDbToFile bin/chainFilter bin/chainMergeSort bin/chainNet bin/chainPreNet bin/chainScore bin/chainSort bin/chainSplit bin/chainStitchId bin/chainSwap bin/chainToAxt bin/chainToBigChain bin/chainToPsl bin/chainToPslBasic bin/checkAgpAndFa bin/checkBigDbSnp bin/checkCardinality bin/checkChain bin/checkCoverageGaps bin/checkSgdSync bin/checkTableCoords bin/checkUrlsInTable bin/checkableBorf bin/chopFaLines bin/chromGraphFromBin bin/chromGraphToBin bin/chromToUcsc bin/clusterGenes bin/clusterMatrixToBarChartBed bin/clusterPsl bin/clusterRna bin/colTransform bin/consForBed bin/convolve bin/countChars bin/countNib bin/counter bin/cpg_lh bin/crTreeIndexBed bin/crTreeSearchBed bin/createSageSummary bin/ctgFaToFa bin/ctgToChromFa bin/dbDbToHubTxt bin/dbFindFieldsWith bin/dbSnoop bin/dbSnpJsonToTab bin/dbTrash bin/detab bin/dnaMotifFind bin/dnadust bin/dnsInfo bin/dumpNib bin/eisenInput bin/emblMatrixToMotif bin/embossToPsl bin/endsInLf bin/estLibStats bin/estOrient bin/exonerateGffDoctor bin/expMatrixToBarchartBed bin/expToRna bin/faAlign bin/faCmp bin/faCount bin/faFilter bin/faFilterN bin/faFlyBaseToUcsc bin/faFrag bin/faGapLocs bin/faGapSizes bin/faNcbiToUcsc bin/faNoise bin/faOneRecord bin/faPolyASizes bin/faRandomize bin/faRc bin/faRenameRecords bin/faSimplify bin/faSize bin/faSomeRecords bin/faSplit bin/faToFastq bin/faToNib bin/faToTab bin/faToTwoBit bin/faToVcf bin/faTrans bin/faTrimPolyA bin/faTrimRead bin/fakeFinContigs bin/fakeOut bin/fastqStatsAndSubsample bin/fastqToFa bin/featureBits bin/ffaToFa bin/findMotif bin/findStanAlignments bin/fishClones bin/fixCr bin/fixHarbisonMotifs bin/fixStepToBedGraph.pl bin/fixTrackDb bin/fqToQa bin/fqToQac bin/fragPart bin/gapSplit bin/gapToLift bin/gbGetEntries bin/gbOneAcc bin/gbSeqCheck bin/gbToFaRa bin/gcForBed bin/gencodeVersionForGenes bin/genePredCheck bin/genePredFilter bin/genePredHisto bin/genePredSingleCover bin/genePredToBed bin/genePredToBigGenePred bin/genePredToFakePsl bin/genePredToGtf bin/genePredToMafFrames bin/genePredToProt bin/genePredToPsl bin/geoMirrorNode bin/getChroms bin/getFeatDna bin/getRna bin/getRnaPred bin/gff3ToGenePred bin/gff3ToPsl bin/gffPeek bin/git-reports bin/gmtime bin/gpStats bin/gpToGtf bin/gpcrParser bin/groupSamples bin/gsBig bin/gtfToGenePred bin/hapmapPhaseIIISummary bin/headRest bin/hgAddLiftOverChain bin/hgAvidShortBed bin/hgBbiDbLink bin/hgBioCyc bin/hgCGAP bin/hgChroms bin/hgClonePos bin/hgCountAlign bin/hgCtgPos bin/hgDeleteChrom bin/hgDropSplitTable bin/hgExonerate bin/hgExperiment bin/hgExtFileCheck bin/hgFakeAgp bin/hgFiberglass bin/hgFindSpec bin/hgFlyBase bin/hgGcPercent bin/hgGeneBands bin/hgGenericMicroarray bin/hgGetAnn bin/hgGnfMicroarray bin/hgGoldGapGl bin/hgGtex bin/hgGtexAse bin/hgGtexExonBed bin/hgGtexGeneBed bin/hgJaxQtl bin/hgKegg bin/hgKegg2 bin/hgKegg3 bin/hgKgGetText bin/hgKgMrna bin/hgKnownGeneList bin/hgKnownMore bin/hgLoadBed bin/hgLoadBlastTab bin/hgLoadChain bin/hgLoadChromGraph bin/hgLoadEranModules bin/hgLoadGap bin/hgLoadGenePred bin/hgLoadItemAttr bin/hgLoadMaf bin/hgLoadMafFrames bin/hgLoadMafSummary bin/hgLoadNet bin/hgLoadOut bin/hgLoadOutJoined bin/hgLoadPsl bin/hgLoadRnaFold bin/hgLoadSample bin/hgLoadSeq bin/hgLoadSqlTab bin/hgLoadWiggle bin/hgLsSnpPdbLoad bin/hgMapMicroarray bin/hgMedianMicroarray bin/hgMrnaRefseq bin/hgNibSeq bin/hgPar bin/hgPepPred bin/hgPhMouse bin/hgRatioMicroarray bin/hgRenameSplitTable bin/hgRnaGenes bin/hgSanger20 bin/hgSanger22 bin/hgSelect bin/hgSgdGff3 bin/hgSgdGfp bin/hgSgdPep bin/hgSoftPromoter bin/hgSoftberryHom bin/hgSpeciesRna bin/hgStanfordMicroarray bin/hgStsAlias bin/hgStsMarkers bin/hgSuperfam bin/hgTomRough bin/hgTpf bin/hgTraceInfo bin/hgTrackDb bin/hgTracksRandom bin/hgWaba bin/hgWiggle bin/hgYeastRegCode bin/hgsql bin/hgsqlSwapTables bin/hgsqlTableDate bin/hgsqladmin bin/hgsqldump bin/hgsqlimport bin/hgvsToVcf bin/hicInfo bin/hitreport bin/htmlCheck bin/htmlPics bin/hubCheck bin/hubClone bin/hubCrawl bin/hubPublicCheck bin/indexfa bin/indexgl bin/intronEnds bin/iriToControlTable bin/iriToDnaMotif bin/ixIxx bin/ixali bin/ixword1 bin/ixword3 bin/jkUniq bin/joinableFields bin/joinerCheck bin/joinerRoute bin/jsonToTagStorm bin/knownVsBlat bin/kvsSummary bin/lavToAxt bin/lavToPsl bin/ldHgGene bin/lfsOverlap bin/libScan bin/liftAcross bin/liftAgp bin/liftFrags bin/liftPromoHits bin/liftUp bin/lineCount bin/linesToRa bin/localtime bin/mafAddIRows bin/mafAddQRows bin/mafCoverage bin/mafFetch bin/mafFilter bin/mafFrag bin/mafFrags bin/mafGene bin/mafMeFirst bin/mafNoAlign bin/mafOrder bin/mafRanges bin/mafSpeciesList bin/mafSpeciesSubset bin/mafSplit bin/mafSplitPos bin/mafToAxt bin/mafToBigMaf bin/mafToPsl bin/mafToSnpBed bin/mafsInRegion bin/makeTableDescriptions bin/makeTableList bin/makeTrackIndex bin/makepgo bin/maskOutFa bin/matrixClusterColumns bin/matrixMarketToTsv bin/matrixNormalize bin/matrixToBarChartBed bin/maxTranscriptomeExps bin/mdToNcbiLift bin/mdbPrint bin/mdbUpdate bin/metaFlatten bin/metaHoist bin/metaReformat bin/mgcFastaForBed bin/mktime bin/motifLogo bin/motifSig bin/mousePoster bin/mrnaToGene bin/mysqlSecurityCheck bin/netChainSubset bin/netClass bin/netFilter bin/netSplit bin/netStats bin/netSyntenic bin/netToAxt bin/netToBed bin/netToBedWithId bin/newProg bin/newPythonProg bin/nibFrag bin/nibSize bin/nibbImageProbes bin/nibbNameFix bin/nibbParseImageDir bin/nibbPrepImages bin/normalizeSampleFile bin/nt4Frag bin/oligoMatch bin/orf bin/orfStats bin/orthoEvaluate bin/orthoMap bin/orthoPickIntron bin/orthoSplice bin/orthologBySynteny bin/overlapSelect bin/paraFetch bin/paraSync bin/patCount bin/phToPsl bin/phyloRenameAndPrune bin/polyInfo bin/positionalTblCheck bin/primeMate bin/promoSeqFromCluster bin/protDust bin/pslCDnaFilter bin/pslCat bin/pslCheck bin/pslCoverage bin/pslDiff bin/pslDropOverlap bin/pslFilter bin/pslFilterPrimers bin/pslFixCdsJoinGap bin/pslGlue bin/pslHisto bin/pslHitPercent bin/pslIntronsOnly bin/pslLiftSubrangeBlat bin/pslMap bin/pslMapPostChain bin/pslMismatchGapToBed bin/pslMrnaCover bin/pslPairs bin/pslPartition bin/pslPosTarget bin/pslPretty bin/pslProtToRnaCoords bin/pslQuickFilter bin/pslRc bin/pslRecalcMatch bin/pslRemoveFrameShifts bin/pslReps bin/pslScore bin/pslSelect bin/pslSimp bin/pslSomeRecords bin/pslSort bin/pslSortAcc bin/pslSpliceJunctions bin/pslSplitOnTarget bin/pslStats bin/pslSwap bin/pslToBed bin/pslToBigPsl bin/pslToChain bin/pslToPslx bin/pslToXa bin/pslUniq bin/pslUnpile bin/pslxToFa bin/qaToQac bin/qacAgpLift bin/qacToQa bin/qacToWig bin/raSqlQuery bin/raToCds bin/raToLines bin/raToTab bin/randomLines bin/refSeqGet bin/refreshNamedSessionCustomTracks bin/regionPicker bin/relPairs bin/reviewIndexes bin/rikenBestInCluster bin/rmFaDups bin/rmskAlignToPsl bin/rnaFoldBig bin/rowsToCols bin/safePush bin/samHit bin/sanger22gtf bin/scaffoldFaToAgp bin/scaleSampleFiles bin/scanRa bin/scrambleFa bin/semiNorm bin/seqCheck bin/sequenceForBed bin/sim4big bin/simpleChain bin/sizeof bin/snpException bin/snpMaskAddInsertions bin/snpMaskCutDeletions bin/snpMaskSingle bin/snpNcbiToUcsc bin/snpValid bin/spacedToTab bin/spideyToPsl bin/splitFa bin/splitFaIntoContigs bin/splitFile bin/splitFileByColumn bin/splitSim bin/sqlToXml bin/stToXao bin/stageMultiz bin/stanToBedAndExpRecs bin/strexCalc bin/stringify bin/subChar bin/subColumn bin/subs bin/subsetAxt bin/subsetTraces bin/tabFmt bin/tabInfo bin/tabQuery bin/tabRepeatedFieldsToArrayField bin/tabToHtml bin/tabToMmHash bin/tabToTabDir bin/tableSum bin/tagStormArrayToCsv bin/tagStormCheck bin/tagStormDeleteTags bin/tagStormFromTab bin/tagStormHoist bin/tagStormInfo bin/tagStormJoinTab bin/tagStormReformat bin/tagStormRenameTags bin/tagStormRenameVals bin/tagStormToCsv bin/tagStormToHtml bin/tagStormToJson bin/tagStormToSql bin/tagStormToTab bin/tailLines bin/tdbQuery bin/tdbRename bin/tdbSort bin/testSearch bin/textHist2 bin/textHistogram bin/tfbsConsLoc bin/tfbsConsSort bin/tickToDate bin/timePosTable bin/toDev64 bin/toLower bin/toUpper bin/trackDbIndexBb bin/trackDbPatch bin/trackDbRaFormat bin/trackDbToTxt bin/trackOverlap bin/transMapPslToGenePred bin/trfBig bin/trixContextIndex bin/trixMultiSearch bin/trixSearch bin/twinOrf bin/twinOrf2 bin/twinOrf3 bin/twinOrfStats bin/twinOrfStats2 bin/twinOrfStats3 bin/twoBitDup bin/twoBitInfo bin/twoBitMask bin/twoBitToFa bin/txAbFragFind bin/txBedToGraph bin/txCdsBadBed bin/txCdsCluster bin/txCdsEvFromBed bin/txCdsEvFromBorf bin/txCdsEvFromProtein bin/txCdsEvFromRna bin/txCdsGoodBed bin/txCdsOrfInfo bin/txCdsOrtho bin/txCdsPick bin/txCdsPredict bin/txCdsRaExceptions bin/txCdsRefBestEvOnly bin/txCdsRepick bin/txCdsSuspect bin/txCdsSvmInput bin/txCdsToGene bin/txCdsWeed bin/txGeneAccession bin/txGeneAlias bin/txGeneAltProt bin/txGeneCanonical bin/txGeneCdsMap bin/txGeneColor bin/txGeneExplainUpdate1 bin/txGeneFromBed bin/txGeneProtAndRna bin/txGeneSeparateNoncoding bin/txGeneXref bin/txInfoAssemble bin/txOrtho bin/txPslFilter bin/txPslToBed bin/txReadRa bin/txWalk bin/txgAddEvidence bin/txgAnalyze bin/txgGoodEdges bin/txgToAgx bin/txgToXml bin/txgTrim bin/ucscApiClient bin/udcCleanup bin/udcFuse bin/undupFa bin/uniqSize bin/updateStsInfo bin/upper bin/utrFa bin/varStepToBedGraph.pl bin/vcfFilter bin/vcfRenameAndPrune bin/vcfToBed bin/vcfToHgvs bin/vegaBuildInfo bin/venn bin/verticalSplitSqlTable bin/webSync bin/weedLines bin/whyConserved bin/wigBedToStep bin/wigCorrelate bin/wigEncode bin/wigToBigWig bin/wordLine bin/xmlCat bin/xmlToSql /builddir/build/BUILD/ucsc-kent-utils-492-build/BUILDROOT/usr/bin/ + xargs grep -lE '^#!.*python' + xargs sed -i '1s|#!.*python.*|#!/usr/bin/python3|' + find /builddir/build/BUILD/ucsc-kent-utils-492-build/BUILDROOT/usr/bin -type f + find /builddir/build/BUILD/ucsc-kent-utils-492-build/BUILDROOT/usr/bin -type f + xargs grep -lE '^#!.*perl' + xargs sed -i '1s|#!.*perl|#!/usr/bin/perl|' + /usr/bin/find-debuginfo -j4 --strict-build-id -m -i --build-id-seed 492-1.fc46 --unique-debug-suffix -492-1.fc46.x86_64 --unique-debug-src-base ucsc-kent-utils-492-1.fc46.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 --remove-section .gnu.build.attributes -S debugsourcefiles.list /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492 find-debuginfo: starting Extracting debug info from 690 files DWARF-compressing 690 files sepdebugcrcfix: Updated 690 CRC32s, 0 CRC32s did match. Creating .debug symlinks for symlinks to ELF files Copying sources found by 'debugedit -l' to /usr/src/debug/ucsc-kent-utils-492-1.fc46.x86_64 find-debuginfo: done + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + COMPRESS='gzip -9 -n' + COMPRESS_EXT=.gz + /usr/lib/rpm/brp-compress + /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip + /usr/lib/rpm/check-rpaths + /usr/lib/rpm/redhat/brp-mangle-shebangs + /usr/lib/rpm/brp-remove-la-files + /usr/lib/rpm/redhat/brp-python-rpm-in-distinfo + env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j4 + /usr/lib/rpm/redhat/brp-python-hardlink + /usr/bin/add-det --brp -j4 /builddir/build/BUILD/ucsc-kent-utils-492-build/BUILDROOT Scanned 701 directories and 2970 files, processed 0 inodes, 0 modified (0 replaced + 0 rewritten), 0 unsupported format, 0 errors + /usr/bin/linkdupes --brp /builddir/build/BUILD/ucsc-kent-utils-492-build/BUILDROOT/usr Scanned 700 directories and 2970 files, considered 2970 files, read 427 files, linked 0 files, 0 errors sum of sizes of linked files: 0 bytes Reading /builddir/build/BUILD/ucsc-kent-utils-492-build/SPECPARTS/rpm-debuginfo.specpart Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.VntMc3 + umask 022 + cd /builddir/build/BUILD/ucsc-kent-utils-492-build + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd kent-core-492 ++ uname -m ++ sed 's/-.*//' + export MACHTYPE=x86_64 + MACHTYPE=x86_64 ++ pwd + export BINDIR=/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin + BINDIR=/builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/bin + RPM_EC=0 ++ jobs -p + exit 0 Processing files: ucsc-kent-utils-492-1.fc46.x86_64 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.nAxlgD + umask 022 + cd /builddir/build/BUILD/ucsc-kent-utils-492-build + cd kent-core-492 + LICENSEDIR=/builddir/build/BUILD/ucsc-kent-utils-492-build/BUILDROOT/usr/share/licenses/ucsc-kent-utils + export LC_ALL=C.UTF-8 + LC_ALL=C.UTF-8 + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILD/ucsc-kent-utils-492-build/BUILDROOT/usr/share/licenses/ucsc-kent-utils + cp -pr /builddir/build/BUILD/ucsc-kent-utils-492-build/kent-core-492/LICENSE /builddir/build/BUILD/ucsc-kent-utils-492-build/BUILDROOT/usr/share/licenses/ucsc-kent-utils + RPM_EC=0 ++ jobs -p + exit 0 Provides: ucsc-kent-utils = 492-1.fc46 ucsc-kent-utils(x86-64) = 492-1.fc46 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: /usr/bin/awk /usr/bin/perl /usr/bin/python3 libbz2.so.1()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.11)(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.15)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.28)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.2)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.38)(64bit) libc.so.6(GLIBC_2.4)(64bit) libcrypto.so.4()(64bit) libcrypto.so.4(OPENSSL_4.0.0)(64bit) libcurl.so.4()(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.29)(64bit) libm.so.6(GLIBC_2.43)(64bit) libmariadb.so.3()(64bit) libmariadb.so.3(libmysqlclient_18)(64bit) libpng16.so.16()(64bit) libpng16.so.16(PNG16_0)(64bit) libresolv.so.2()(64bit) libssl.so.4()(64bit) libssl.so.4(OPENSSL_4.0.0)(64bit) libz.so.1()(64bit) libz.so.1(ZLIB_1.2.0)(64bit) rtld(GNU_HASH) Processing files: ucsc-kent-utils-debugsource-492-1.fc46.x86_64 Provides: ucsc-kent-utils-debugsource = 492-1.fc46 ucsc-kent-utils-debugsource(x86-64) = 492-1.fc46 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: ucsc-kent-utils-debuginfo-492-1.fc46.x86_64 Provides: debuginfo(build-id) = 00b0f177d1803ddec52edc388fb6756a31d31f85 debuginfo(build-id) = 01119b68af3cfef24005e903ce4cf56480518587 debuginfo(build-id) = 01c7dac6ecb4d2bf13394c114502f12ab0121c3c debuginfo(build-id) = 03e40b36898cfef11d7f5a02a259fe6e3e9e9b5c debuginfo(build-id) = 03e5dcb02a879e264d9a897d97e1da11f110957b debuginfo(build-id) = 04b1bc27bdeb28fca10202d25258f8b6a9c5d9ab debuginfo(build-id) = 04c09459130afdb08360fb95322afc94631564a8 debuginfo(build-id) = 056a7c6cb04af53ecbf9503a5780ef4da1064318 debuginfo(build-id) = 05e5e114582d82464b102cf9d36e4d017c1321e4 debuginfo(build-id) = 06936d4a63532a4212775ec81a10cc61140ed4a3 debuginfo(build-id) = 07e303f097b44ecf6373fc6436bce07820a51bf8 debuginfo(build-id) = 0834ea5daf3fe961b432d765a7b491fa29e5575c debuginfo(build-id) = 086eb0cb8fd3f0b8346a69b124c2cab28990fc69 debuginfo(build-id) = 08d184a236a5afd98dcf080ae6152170129f461c debuginfo(build-id) = 08d683ad1f5dade3adf7763a666e73f5bcdb45d6 debuginfo(build-id) = 08ef8de75b9be21c168e35dc1f003c8323284a03 debuginfo(build-id) = 09b8795268ae616ec7c5fe1472ad8c6d90bff0ce debuginfo(build-id) = 0af4fe94c53b01e14eff827b1ce7d9c01df90f9f debuginfo(build-id) = 0b20bfef2d44fab90441a7b9607635db56077075 debuginfo(build-id) = 0b2c8a26ab2cea50d8ccca432160da0f1d722f29 debuginfo(build-id) = 0b6c400a04f8bab5ebdadbf3c94c12ffc8be5e41 debuginfo(build-id) = 0baab2f21ae8f2997f4b8b61c7eb3ede4174f95b debuginfo(build-id) = 0c0f28d41b8bc0cf0e7ae69b0b53807ac3d29fca debuginfo(build-id) = 0c31d044fb0a50f6e666cec68a49d02ae4eb58da debuginfo(build-id) = 0c8665e7455a83a48c5e47dd914cc4fb1e548cac debuginfo(build-id) = 0c93dcba3dd431b327d81fbac14c6cf5e296722a debuginfo(build-id) = 0e57294c058a13419e30864a01c6788f377f8ed9 debuginfo(build-id) = 0eae405fa3ff7d7d318eb0d466a0271a8dc360b7 debuginfo(build-id) = 0f0a8187ef287ba4b01df79d4ed69edc2d26e162 debuginfo(build-id) = 0fb0e2eade5581f8d8341a31167f268fbd6c52fb debuginfo(build-id) = 106e3a0ad1e16370fa0f2ba0da7e99d3840289c5 debuginfo(build-id) = 1082c92f2c490b3a059f8de819314b837d2460ff debuginfo(build-id) = 11368b14c47e4d934aa984ad38c2892d0fa1c358 debuginfo(build-id) = 11dd2950b9dfdba8ae0753a43f2030bf83049fa1 debuginfo(build-id) = 11f3391198dba20d7582d51483a072ad2fbb388f debuginfo(build-id) = 11f46a6ce5a77338bd4f95974099af92074561f3 debuginfo(build-id) = 12662f4ad1153e8db5911f0e5445d8cf6ce11d39 debuginfo(build-id) = 131d2da9b68a7f0456ae67b486b9fdde5e6b88c6 debuginfo(build-id) = 13965dac734c0e782a9f0b4e63bb82946f14fbe1 debuginfo(build-id) = 13acdf30cd897f6e645a15ffaa3ab83476a8a385 debuginfo(build-id) = 14045d81dbdcaef74802aaf50e8cc0a1cc3d79f8 debuginfo(build-id) = 142d53f05b05be746c7c7f7342b27c2dd039d733 debuginfo(build-id) = 14777037cdd43b7736579d67cfde069d10bc02ea debuginfo(build-id) = 14e40522787809291808ba9d0c70c2fc27a9d232 debuginfo(build-id) = 14f7e65e41116303dc00d0d328811e995f4e1618 debuginfo(build-id) = 15247200191c2c531f1afe4c003805b0b9fe11f0 debuginfo(build-id) = 1544c943f8e91829e73b7b92c7633b997e9c62e2 debuginfo(build-id) = 154504ac2144ef934c4faefae13b72b4b47f4128 debuginfo(build-id) = 159e2289526c74a9150d9f64335ebc0b85dc0a0d debuginfo(build-id) = 15adce55bf5c771a7a72d16ef568e4fa06cb9407 debuginfo(build-id) = 1692b9e73ce1e7d5312583a35cd6fd6fe06c3da4 debuginfo(build-id) = 16a894e7b085d685308f8dd96ff9e681bb498d5f debuginfo(build-id) = 16fefe315643168ec04b3ad1c0cc16ec9753cbea debuginfo(build-id) = 170bf77ce43ef436a0f1b19d6f260a6c2b67a029 debuginfo(build-id) = 17165cb33c204f961d52dacb6d145f79b8d97122 debuginfo(build-id) = 17273caf8013ded37d8f7494ec4ab036b5a34faa debuginfo(build-id) = 17646acff76d2f63114c85fdd5c3543cc41a84c8 debuginfo(build-id) = 17755e4ea54f35734b9d780b67bf064a94d20d0c debuginfo(build-id) = 179841cb782208f7458065bc7d3b20f143abbd90 debuginfo(build-id) = 17c569758e427360833f29205fbd38be22aeb3bf debuginfo(build-id) = 183a9b98f393926a031bb2b9cf56280ec0c87769 debuginfo(build-id) = 18e268a0f3373c1d90fb7bd80ddb0e55eaf8d862 debuginfo(build-id) = 18f142799d7f231e4ea888ac19d6b7223f2818ce debuginfo(build-id) = 1919dbef865eb92bb7ac1185d0e3fa22f50bcc18 debuginfo(build-id) = 1959efdd65d15bbf97684731c547413e9ad71631 debuginfo(build-id) = 19647f32648db7b500d8d2ebb11a9dc055533d1c debuginfo(build-id) = 19a3812ed2832325d01490a08fdd2723acb23304 debuginfo(build-id) = 19c0051cd781a99d7fe185fe1fa8c72a3942d333 debuginfo(build-id) = 19c7a718b3a763692b763402be80ee9f1d8eb3be debuginfo(build-id) = 1a15811cb20f887a89de14addc2e3abdf40b190d debuginfo(build-id) = 1a5d0105518d5190bbddb575fa005e55c10e2c84 debuginfo(build-id) = 1a65c77765c620a69dcf6e52d89e9a61cdfd3ec2 debuginfo(build-id) = 1b72879da350093b93f81e596c8fa25a12fa2bef debuginfo(build-id) = 1bb01d8a8214b005234d6cb86c5f18e7e193919e debuginfo(build-id) = 1bea3ae48ce0e86647bc04ce89d47ff8e36f25e3 debuginfo(build-id) = 1cf817e165a90141ca6a2f3a07d4495e7f04df93 debuginfo(build-id) = 1d6a059d2d6e51769b833c76a8668c75d0104aca debuginfo(build-id) = 1d9226627817b6db787751325fd88010f4b62232 debuginfo(build-id) = 1dda379fa5f75dd27e9bf23a269654bd7d1a090b debuginfo(build-id) = 1e85118fa2476a2e5d28e00a122fe26a4615f4cc debuginfo(build-id) = 1f4f3fdc2fe96028a442700008baf20542738191 debuginfo(build-id) = 1f50d890dedc1aa66e02bac9b9ed5cb4f2f1243a debuginfo(build-id) = 1f5159bf50e84eb3949d53e29095ad7dc5085ce3 debuginfo(build-id) = 1f970945e001181147de41b2a41ffcbc19a1a567 debuginfo(build-id) = 20acfa9973cf7211270c14ce621995158ed801e2 debuginfo(build-id) = 228be8c0e0dc371a03bd09381142f741ad3c2e7b debuginfo(build-id) = 22fff9519771428b54a35a67805f2dce2c5637e4 debuginfo(build-id) = 235bb41a9460cf4e4f5518451998128937966dc5 debuginfo(build-id) = 23918e14f879443dad14c7a29efd08550f916346 debuginfo(build-id) = 24d9cd9a545209922713968d3f209da27b190b60 debuginfo(build-id) = 2525b96c4a7bc223171b84a95eaef8676a08fdb8 debuginfo(build-id) = 25362570ff394b313298398c1ae90074ec295b71 debuginfo(build-id) = 2592edc36e41910447d0087a56f1f6fa598ed5ca debuginfo(build-id) = 260eeb75b787c97c53598224faf4022ef6a6631b debuginfo(build-id) = 261af749e5a2d2ea2c7f4c3758649a6a43e11443 debuginfo(build-id) = 266d199910ab92be3285d584d65bf8edb24a3727 debuginfo(build-id) = 274bdf0c51d192c9a96c08295d41afa20eabe84c debuginfo(build-id) = 27bd05fca03f70c3f81df5915517d1b7f7fa0f92 debuginfo(build-id) = 27ea828724c6a30320f1dc27e0f06835e08a054b debuginfo(build-id) = 281815562ca35ed157ec4a4126886ad6ec669a46 debuginfo(build-id) = 2984866aa8d3162284ae43607c12b48d8c3976dd debuginfo(build-id) = 29fe23a24048981b391c10ec3621e9c3c73fcce3 debuginfo(build-id) = 2af0e842a3f9e1b3fd72764db23dce028d76ec3b debuginfo(build-id) = 2b09accd4ff91398bd5d14f6daf76c4c301b6258 debuginfo(build-id) = 2b119f5f33e1d4ea8ee21c935f7d585fcdf292e2 debuginfo(build-id) = 2b900c7ca17911b66bad163763eb08f4d5367b84 debuginfo(build-id) = 2c384eb0367bb7ac6836dfebd614e7c7436c87a8 debuginfo(build-id) = 2c39abda059e8a210ab2248e32d940ccac30f309 debuginfo(build-id) = 2c3cab09d147ac05fc102086bae83f063bd251a0 debuginfo(build-id) = 2dfa396c92e8b687058c712270eff98454cb9116 debuginfo(build-id) = 2e47522a05f862a6c3b85ac9be7f32f33b416f05 debuginfo(build-id) = 2e68d59b9fa0e2ad81e33b516b2b986ce64993de debuginfo(build-id) = 2f381799470155ad0c5267ab22022c4dba9aebd3 debuginfo(build-id) = 2f94fb79f00bdede998bfb5e12c79b3d149f785a debuginfo(build-id) = 2fce614cbcca9ffa5ecaf7ba5db9019b1d2069cf debuginfo(build-id) = 30f3ee880e0e5e616cd1f6874da90877aff174fc debuginfo(build-id) = 3109de77c01357c7798b4c2f2e31ddf813741df6 debuginfo(build-id) = 31ec3349f5c88133a54fe2396a1b7d60338efb14 debuginfo(build-id) = 32448efc2ee1e63a57161b20455a5aec1f9b6c10 debuginfo(build-id) = 330e4031f767414bc3e31f954f17013166b263ce debuginfo(build-id) = 33db27289b4b72986b65f2797e321aace2dcd3e4 debuginfo(build-id) = 347534732502be8449a51a22d093eb04c79e9640 debuginfo(build-id) = 34f4067ebce5b54f4d2ab0852566c7d0ea3020d3 debuginfo(build-id) = 35e41ccb35cc3df3f3cfb81575a8def9c408b8fc debuginfo(build-id) = 35e7fab2785cc482d49d9a0e9a0885527f394548 debuginfo(build-id) = 35ea6c298be37f8f0ea68c58ba1c7fe50637fab5 debuginfo(build-id) = 3668cdc5c4f6471b8a909a86e1eb3e9517302248 debuginfo(build-id) = 36a3d78e7b7bbe21c9cadb08a1649c55d708a55a debuginfo(build-id) = 36b6d613096f379205896d61589bc0b3cd4ff4a4 debuginfo(build-id) = 3713791dd67b97da62d78e7c9b729db9d7340c0e debuginfo(build-id) = 37a72e3b87d057a42b56bd206d241b225b173f04 debuginfo(build-id) = 384cd4af5a021ca0eddb24864831fe1ea31304fa debuginfo(build-id) = 38e35c931dd6b1eb2e65fcf842f184b7adf3c108 debuginfo(build-id) = 395909d208b3003e12b2ae3e3cb5f0d3923aae52 debuginfo(build-id) = 3a25e4b964208f4d7032ff4107ac287d3557b862 debuginfo(build-id) = 3b2442957f27c5b97c54767209faf90f6bfdc424 debuginfo(build-id) = 3b2cbed961205de1de737bb94549dab77414da53 debuginfo(build-id) = 3bbd091ffeb9faef700f9588e97e671689fb4afb debuginfo(build-id) = 3bcf83c2283bbf4c6fbfc93a0e767aad2008a6ec debuginfo(build-id) = 3cacd68a915c71e2bc2cd08723f2c77896e9228a debuginfo(build-id) = 3cc902d93c4aaa431c7a844510a9b6887bafa5b7 debuginfo(build-id) = 3d6260b714922a8cbcac5489a3c60e451a941f0c debuginfo(build-id) = 3dfe1c4e8abfc55739197902f592f7a1d3554312 debuginfo(build-id) = 3e0a0397ff0e4d00c30f1193408de8683e0fded3 debuginfo(build-id) = 3e0c15066ba5c599db38ba1aa97b586f5106049d debuginfo(build-id) = 3e2a7efb81868f34fe349bf0a8b7b9694d6f21f4 debuginfo(build-id) = 3e87476a8f9d6727ae1fc791b5c8bf8b213b7e30 debuginfo(build-id) = 3eed8d8f36413127ef087e50528bd2b1137a88ad debuginfo(build-id) = 3fb0496215f5811fcce5a9936a3df83fb22fe3af debuginfo(build-id) = 4015dbde50b80339a3e20bae16794793d0591c10 debuginfo(build-id) = 40168995212eb2b0f53c1c5aa26fff3210b6d049 debuginfo(build-id) = 403e62024f1a1614f23272782c8a23df7db12c14 debuginfo(build-id) = 4050919a8285aa5c537c3bf385a716e471912070 debuginfo(build-id) = 409828bcb2a4399dc5e56fe286e1da7a9fca3c59 debuginfo(build-id) = 40a8f1248090d52af22dc641e05d8dc3113a3eaf debuginfo(build-id) = 40ac8a7b88a9766daa644a23b03be8b219c5765f debuginfo(build-id) = 40c3cf0801fc2e57ba0cb1bc2c2c8d11b063377b debuginfo(build-id) = 418a287222dec318430b2789eb6bb95063a6b211 debuginfo(build-id) = 4197576c40542a9567bb02e2460e65b1f054e06c debuginfo(build-id) = 42cf7d6923cde3e39425722524b7cc9bda232424 debuginfo(build-id) = 42e49628abb73e2f2865d0b54896a8b77e5b90c4 debuginfo(build-id) = 432316c1d6313928a30cb108cdb87d1c1dbdd4ae debuginfo(build-id) = 43611c92ac17469a4e5019207e48ba0a7beb9119 debuginfo(build-id) = 43928c285a7266ca03806278ae9fad0a1a3cc863 debuginfo(build-id) = 43e824254fc3e0f01082bb9a3e05ad956d2cffb8 debuginfo(build-id) = 44278a5d743f14c2e36a8674be05a59a0b6203cc debuginfo(build-id) = 442a8ee18ed56be8a20a656a4ea3bc579a691141 debuginfo(build-id) = 4474c6c56a6437ce9911376142292c42f07f8450 debuginfo(build-id) = 448a6230bad58db6ce3356844ed778eb7f245211 debuginfo(build-id) = 4565e1f6f6fd227b6604bb6baca839c31e7fb38e debuginfo(build-id) = 45c30c57b4e81ee8ce839b66335841b46c948d02 debuginfo(build-id) = 45d67ab3f2fefe1e513bb45281a6528ca36593ee debuginfo(build-id) = 4651a6b1fbce7385daf5476f3419f7b1a545c557 debuginfo(build-id) = 4665038a8c004fd95fff60852cecbee1e9266cd6 debuginfo(build-id) = 47121f312906ea62d1491761da005165b6b7e6be debuginfo(build-id) = 491717c430fba874e586cd088d386f9591ad8414 debuginfo(build-id) = 491e4c614e10722feb8bf22f9bbcb6f90a147025 debuginfo(build-id) = 493997c1854991749bd89065a16095a8b84c159c debuginfo(build-id) = 493bc5654695c55aa07463b091ec3a448ea4233c debuginfo(build-id) = 499904f1d02c449c93c93e625a3e36a1b8d0dd71 debuginfo(build-id) = 4a4305221b1c9884b572ea39ab24754846a1479b debuginfo(build-id) = 4b129404f79f21604be2586d61d07b67b74827e0 debuginfo(build-id) = 4bf11f7d2552540b0c78083be6accaf64df85712 debuginfo(build-id) = 4c1621d3e6919be3f65e3b422f9da0b2ea7d2ab6 debuginfo(build-id) = 4c3b371ab1e0e82a1f820c2fe037101087c890af debuginfo(build-id) = 4c5d6e6074053fad11ee077194d480a3c3884531 debuginfo(build-id) = 4c5eccafcd9c4ad4c783768b246078039683a235 debuginfo(build-id) = 4d68b17d61f06958a82e2d0d449c27c3c73a6edb debuginfo(build-id) = 4d6b5945b7235b8e026bf16ae359f46f9610eba4 debuginfo(build-id) = 4d7b006677734dafbcdbed0a85ad869287cb5d40 debuginfo(build-id) = 4d91fab417bc9af6a7f86e7fe6de7fc679e50dc3 debuginfo(build-id) = 4dd24dc5caf4e2fa151eb4edc63149f528e8d218 debuginfo(build-id) = 4ef53b153f6fee2e88e0175111946a7397782457 debuginfo(build-id) = 4fac693415565c73cd3e2bd695b6bfbd8d9e6d9b debuginfo(build-id) = 4fc6dd10da445a272a2e4ee1d8e278f5cfb26958 debuginfo(build-id) = 51c7976056837e7ca4dd8c87974e34413ffe93ff debuginfo(build-id) = 520d1bd2b104f38bed9296c90857345dcb36fb0a debuginfo(build-id) = 522ca334e1f1f8c7bc1511664e1876c0089616af debuginfo(build-id) = 52ce9f1df9d4b36c3e5aef6c41a4574bd65669f8 debuginfo(build-id) = 531ee660a27bb6901fcb5d704b6ec9bc43c06c66 debuginfo(build-id) = 532f7eb4badd5b0110d0e03896ef3972e772e495 debuginfo(build-id) = 53356e514e9e056435345f01dccf35cc292b0c79 debuginfo(build-id) = 5389c4893d6c2bb1e0aaef95012d62bd64c91f75 debuginfo(build-id) = 53b0740adf4e7789be616e5f105f0f0123821094 debuginfo(build-id) = 53b6cfb3a92ac1598a1845fc645a8bf5f6d0e438 debuginfo(build-id) = 547a45d5bdc6ab53e326e61ef31949ce38a4bf0c debuginfo(build-id) = 54bd955c8b6772bf907ae9b569500ef5d0c171db debuginfo(build-id) = 54cddbddfa5688fc513937b2a2f9b0d786d81f97 debuginfo(build-id) = 54e2c11b543f7ab992969f2acf8a480905c3cae5 debuginfo(build-id) = 553f3df790fd3f155daaf2b49b32b5b9428ea786 debuginfo(build-id) = 5580c6800662fe40e2d8609c8e077badca81abc9 debuginfo(build-id) = 55fe2dd2d5427a656a5aec61d30f0f4fc982eb9f debuginfo(build-id) = 5616500e098ab6234e2f9c51466662d26d269837 debuginfo(build-id) = 5677b62e1ffcd9275aea38dc3e92d140d34af8b6 debuginfo(build-id) = 567c48bf796e3f82b9cae0b37776c881a31ac2eb debuginfo(build-id) = 56a4f7e7f9857719f7d319d8ddf74be6f2d5ad29 debuginfo(build-id) = 572e21ca0bea05e400f91f427de087d2df2b90a5 debuginfo(build-id) = 57e3cc4246591a43ddb4f8ad0d9901e63744f08d debuginfo(build-id) = 57f20f401701bf6bfa459baa5f636b1962cfd301 debuginfo(build-id) = 581b9556cf401348b862d46c2f3095ab3125d0e1 debuginfo(build-id) = 5842041a9966c22c79de1c76992add8af9825de2 debuginfo(build-id) = 5842498ad99b34ca7fb4fc38413808778db27c5d debuginfo(build-id) = 588d3dcf3309aa5d5125bb901819f31de5cff713 debuginfo(build-id) = 58eedf3a8dddd50530b6914ecfdcec67639515bc debuginfo(build-id) = 5981ad49f6b56f55fca872dc0af0da52156100f3 debuginfo(build-id) = 59eef9c69dbedcf4217656684dc21e744990ec40 debuginfo(build-id) = 5b3423064faf34b854f53213535eb9c3622e0bc5 debuginfo(build-id) = 5b5f4d58a0d8af991592e64a131d8e7b86996f1c debuginfo(build-id) = 5c98b72377d9ec9467391d2166dfe657666d673b debuginfo(build-id) = 5db08d9e2e063e140ca7e7694034e2621c04977a debuginfo(build-id) = 5db0ea3d8aa0c36a5f2e480e118230ef437d36e1 debuginfo(build-id) = 5efe145433ac0fd7a2f8607865ef63e497781fda debuginfo(build-id) = 5f8560ba28944c3ef43a7ea26be919859add125f debuginfo(build-id) = 5f96a281dfb926b49933a35f34f6c7e43832136b debuginfo(build-id) = 5fb036193c59f840e6874b718f72c6a689ae7787 debuginfo(build-id) = 5fcf4f8ad4cfc05258f7f56f7f2728810484e76c debuginfo(build-id) = 5fd9d535871b8cca90e219acaf95a95912fb6899 debuginfo(build-id) = 603360da3b42f671831f24ea81640cfffc45b77a debuginfo(build-id) = 60788e5029aca66ad85bb4af07d2f10b0f72d13e debuginfo(build-id) = 608ffc22e53a8bdcd2bd6bf9e6560cd8c761a08e debuginfo(build-id) = 61d020eabbc7b9fa93288f8853c884035a478e45 debuginfo(build-id) = 621014f9402fcde0e2d4965c5030c2d8b7d7b5f5 debuginfo(build-id) = 6214eade0d995479d37e24760973253420a911bc debuginfo(build-id) = 62688c876f6e428dc6d8ebbae501ed262c983808 debuginfo(build-id) = 630ab0c12a3f00491d8c3e6cd9c6b8857d57a952 debuginfo(build-id) = 637ef7c53f15e0e8f63de6f66f71609e46bef4f9 debuginfo(build-id) = 63efb4255210565124de05f8e28ba45341881633 debuginfo(build-id) = 6507af8c674ab961aa60befcebb66a4ee5591c10 debuginfo(build-id) = 6529fb7acdfd24b4daf0e5c959ee1549cd957dd3 debuginfo(build-id) = 652cbe3a83c20af988c83ad70c8174b5dac5f8ba debuginfo(build-id) = 654a06c1d1ea97104a79c98516291d5c796f96ed debuginfo(build-id) = 65d6320c23861ce37ba99e6ec6c99535fa056c66 debuginfo(build-id) = 65f95f2781754186feb967fcb49ce757bd14282a debuginfo(build-id) = 662a633767c0f6434e764a0199d007570aa6ba0d debuginfo(build-id) = 6708fce4cc4fcf499e127d37a3683665c4d35869 debuginfo(build-id) = 67158b7aefa86b66b28ab92a6527b924f5bfa131 debuginfo(build-id) = 6717c8a94e2d9756a3a8627c7519672d945100e0 debuginfo(build-id) = 675d62f5461d1e57ee27a29e7bc942dbb8a886d6 debuginfo(build-id) = 678648664be6aaadb08e2c47830a35683a3a93e4 debuginfo(build-id) = 67c7e86df239336eadcc80ae103a9befbd4a0fe3 debuginfo(build-id) = 6810bcf45f63fa28b0a0874df74d942ea3d678ca debuginfo(build-id) = 68565b307de6e2591f519acaf206c47e40f77de2 debuginfo(build-id) = 685a3ad2cb7f13ebc82b5cbac6a506c3df681459 debuginfo(build-id) = 68a2e73adbaf39a8f29095a37a693eeb567b28e9 debuginfo(build-id) = 6a07cf4f703b507b6edf2ebe5b4d76b0999922b9 debuginfo(build-id) = 6a981d93c05d7a2db7aa6e0f24d8536ea2ccae8c debuginfo(build-id) = 6acef4e476a488f147f85326983eefa6d1c977b6 debuginfo(build-id) = 6b2eddea421bfd73bc3b83d24e749215acdaadb0 debuginfo(build-id) = 6b6ecaf42e65dd042c1aaa40e4f78f456cc8bdd1 debuginfo(build-id) = 6c28ad20076b451a450fedeecd58ffc8aff223ef debuginfo(build-id) = 6c2e4acac88ab5320d30c3fb43f688e031a94670 debuginfo(build-id) = 6c7506c69c868a9fed4a816da73a073c01fda16b debuginfo(build-id) = 6c9a5bd5e1d17f20e2e6ef27ba8ff140ba21cfb9 debuginfo(build-id) = 6ca9c439a66a21bcf42affbbeffd314e0ba9c7db debuginfo(build-id) = 6d059b76481ae379a1247727bb08d71e27dabb98 debuginfo(build-id) = 6d0ab6a2e3a23b942eff6bb83a0bbed352106bf2 debuginfo(build-id) = 6e9bfa1b109e3bad277c008455b45171cc8b1dc7 debuginfo(build-id) = 6ed8e920486cbf6a04eb2dfdad491a6446d714aa debuginfo(build-id) = 6f3bf3c2588d632bbb974467e14407656af55c3f debuginfo(build-id) = 6f759b0c6d47839e99ebc74129659fa3709b2160 debuginfo(build-id) = 6fc4fada1ae7e16c5addd060726e9fb584f39a29 debuginfo(build-id) = 6fdcb1d7c63aee63d157ed03b0788ea9125b3338 debuginfo(build-id) = 707d96662143cd4a3a10edd514fd0a161382f605 debuginfo(build-id) = 709885d18294933ad7aa43d668517ec85894a74d debuginfo(build-id) = 70d18998c65f40c9e350f101cb712f1cfd8f282c debuginfo(build-id) = 714eacf44fd045397146bebd7068632a770397af debuginfo(build-id) = 71c5bddf385f437464e2fe7cf8f5969c00c6a5bd debuginfo(build-id) = 72605d4359522c90493aa5296ff12973580d96b5 debuginfo(build-id) = 72bf44a27c314696021d91572566e8132d69f390 debuginfo(build-id) = 73059704fe789b9416df2aacf2d3b26a742aece0 debuginfo(build-id) = 733a3e164da38779d373e102745c4253651478bf debuginfo(build-id) = 73e4405ae9192079dfbd76f20b91dab1b290b24a debuginfo(build-id) = 7418a740111dd7002864aeaf17d36799b6a35de0 debuginfo(build-id) = 745b6dc87a2699a627f41b5134fc5e7c1ea8d88c debuginfo(build-id) = 74c092a4693b876d6baea8cbe744eb23ae7e8388 debuginfo(build-id) = 74ffdb6d3334dffad65a353b326fcbd112502dfd debuginfo(build-id) = 7500483bbc373d2a4b86fc7e145c61aab240f6f9 debuginfo(build-id) = 752166f09dc92568976f5942cfda039618687751 debuginfo(build-id) = 756ee87c3f91bc990e1685c77d8f7e15c53ee46f debuginfo(build-id) = 75ca13b3e6a43438cac1f55745092402472377de debuginfo(build-id) = 7668a2296be41b8c01203cb4a97aae70180d3bcd debuginfo(build-id) = 7678117c0b37abc0559ddfba8b334243de6644c3 debuginfo(build-id) = 7680e9745c98522a2c3deaa4b5fda7ccf79ad807 debuginfo(build-id) = 76909ac7df81e32a640d721cc76a69140b8772ae debuginfo(build-id) = 77277643a148f4d7c8ac72ee023ce5383bcd7729 debuginfo(build-id) = 777ab63114d99cc4775fd52ba5df4c4878a55cb9 debuginfo(build-id) = 779eb8575ee28f2657c0122d16fd79c9277dc905 debuginfo(build-id) = 77dfa279f9f359d7321829248ff35c3049e78f10 debuginfo(build-id) = 78792d26f46b049eefb9667052e53b114a2e6b55 debuginfo(build-id) = 787be2c3a738323d856e8f679ba71c205bcc24a4 debuginfo(build-id) = 78bc3c349b2a3e0983839a43c71efc8976c15e0e debuginfo(build-id) = 78faa1c3e50fd058d677c15c5a023edbe15fd8c1 debuginfo(build-id) = 79addfee0259f1d245fd1a5fe2e6a71fa3ba37a4 debuginfo(build-id) = 79b5b03268356dba6757ccb9013848157c2f1850 debuginfo(build-id) = 79c584db2f9199b0cb5c43b75e3ef3b35f2ea3a4 debuginfo(build-id) = 79c79e3a088d1fc8567a1ba53775bb70628a228f debuginfo(build-id) = 7a194a5463190d390c8f0d9b26b266de018d893b debuginfo(build-id) = 7a1d4eaf3df1c557b5204af6bcdde2c9127e4aa0 debuginfo(build-id) = 7a5ed2e95a78cf72b8573f93bffdd032002ccb48 debuginfo(build-id) = 7af2d601cf41c162e2b1cb1798b8da809c6d553c debuginfo(build-id) = 7b8ede0063e99048d915087d131487408faff971 debuginfo(build-id) = 7c7d6517168518a017e0ed83e73eb6d6808328a5 debuginfo(build-id) = 7c97ed2ae4c097116e27560e8731db90610faec4 debuginfo(build-id) = 7ca4d27cfaac518f0ffee01e652ffa3af63ef05a debuginfo(build-id) = 7d5bf0ebdbae9bdebd993378eab688bca3c9dab4 debuginfo(build-id) = 7d78a71f6f7fcab73b769a83ee01cd0617d98bed debuginfo(build-id) = 7d9ad0e3c9373774d97ac2ab098d24854f2b6f19 debuginfo(build-id) = 7e679c3873cbbc9eaf6871d4bce9c41173d137fd debuginfo(build-id) = 7e7e1580fd3bbd1516b257bb68afa391eeb2e6b3 debuginfo(build-id) = 7fff07a863689469397fe97c73e4491cf650e246 debuginfo(build-id) = 80095e7b278ab21eb6d70aaa405456ae70a147e1 debuginfo(build-id) = 80e23f3c55c45b08b7752a3da7397766d6d301fb debuginfo(build-id) = 80f9a3e5d91f0e1ff4cb13721947b20d2fa18e2f debuginfo(build-id) = 81124f323886b0359a912cc5e442a9436c2ae209 debuginfo(build-id) = 817b115ff12b91114d16a00070b7621f7a64f3f3 debuginfo(build-id) = 81848119cf949bee51028d2bb1c0d883df77d42a debuginfo(build-id) = 81cf85e8685b43f19a7828c8a26d9b6f822c0d9d debuginfo(build-id) = 82112d495becc07066eb7705b5a3d97b7a6e435e debuginfo(build-id) = 827242a0cef72019b7753714c7d3568432fdbdbc debuginfo(build-id) = 834f930a06bf3211a782e25a743fcdd3a972da25 debuginfo(build-id) = 8376b5e76517516968e82ba4513ebcb5f0bf3a81 debuginfo(build-id) = 83c8b0ebb62746604b8d9d8d1a77e9ff099c880d debuginfo(build-id) = 841e73576b8521898c83b449fc48a74e9287afd6 debuginfo(build-id) = 84806388b44963bdaa0a3564bd9a8ff7a54eab40 debuginfo(build-id) = 84a5092e5641ab911cb0be3c77061519a59d5514 debuginfo(build-id) = 84e664c39d322e6dd59581d2127620a31cd496af debuginfo(build-id) = 85492c7951455cd52c747988d56cfbf4fa96584c debuginfo(build-id) = 858982384b427130223a14149e5c3a15993c77a4 debuginfo(build-id) = 85fad235c2df15a2007e8301ce9c72913a076f86 debuginfo(build-id) = 861d455c2b830488d6a285d574271c46bc4279df debuginfo(build-id) = 86699ec047b6ea9444ad57ef0d13eea140e2b790 debuginfo(build-id) = 86f46f6f0a8b82c8edc7a333daa25ae8ce66bdc4 debuginfo(build-id) = 870e0fa5f9c614d9b6ec6c0f3fe647485021f8f2 debuginfo(build-id) = 870f02d22c5b68eb68730d260c0936ccc6c3bc26 debuginfo(build-id) = 873a8ebdad8f9a590670260e696cd6ad2a037b07 debuginfo(build-id) = 876c14e5c1492ad23256007a400f43db87b1c6f8 debuginfo(build-id) = 87c92400612b2702e03709073421e0c906a6764d debuginfo(build-id) = 87cf837bda62372606e9aac77aaebcb2b1a42faa debuginfo(build-id) = 88991a51d6bf21de4910fc71d41d610176f59b2b debuginfo(build-id) = 892c5bf44b4efb0f8671ddc95955873a98a1202b debuginfo(build-id) = 89569b6a10815f44ca937e3d8efad76e058faf81 debuginfo(build-id) = 897cbf2ab54fb96ff0f3865eb010bcadfeef7e2d debuginfo(build-id) = 89912de0a092d0226dcbad3cb0ac305600be8d03 debuginfo(build-id) = 89b3a367c3ed4a72cac161006eb0855ed528d70b debuginfo(build-id) = 8a09e2a91f9b42c2de39f4c2294965db9278e0e0 debuginfo(build-id) = 8a953e009e417cf7399a1994ecb3b8af961844ad debuginfo(build-id) = 8a9e7f937894423b97ec6faf63be3556a546b1d5 debuginfo(build-id) = 8b25452a964508b1b66c7dcf28a504e480fe8770 debuginfo(build-id) = 8b3f6e65691a74843dec78b681a4981ffcbd96b5 debuginfo(build-id) = 8bc6b1ecdfb3d329c8d436152008fdb7848630f5 debuginfo(build-id) = 8c06cdd9021dcb57a5b4a01b0a5d217d00dc3648 debuginfo(build-id) = 8c612510ed1893234569d7d21c1ff8e1bba0c4cf debuginfo(build-id) = 8c936af9217ad74dda05a82d3ed3c7b6bb7e6a23 debuginfo(build-id) = 8cae33878e412a88a8b44d1a165661dd8fc16373 debuginfo(build-id) = 8cbb4bc12e38749a5ab36e8fe1751a9177ff6b4e debuginfo(build-id) = 8e1a83f954174255de80c719062e55e02720fe68 debuginfo(build-id) = 8e2e07063672c1724f84a0e34a7c74bede3d0eb2 debuginfo(build-id) = 8ea531067b4f03cb5b66208faa114171f045ec25 debuginfo(build-id) = 8ec5c89a372693f8ed38849668c3b426523cbcc6 debuginfo(build-id) = 8ee4266a1cde8b7d76e51b7c639932e9c4f060ca debuginfo(build-id) = 8f2ac77ab9065c9eee1d8308ff83f1ed281706f9 debuginfo(build-id) = 8f3dae23dd03e143970cf0eaf0b8ec09ab545b73 debuginfo(build-id) = 8fbf78f5a27ee50138c0a29b4739fd33b51fae93 debuginfo(build-id) = 9041549f32064e5fa84a2d2ef43cfe0dc7dd7380 debuginfo(build-id) = 90539982c3629666fc6694e5992be9f1c10ac756 debuginfo(build-id) = 90f46e1644079b3bcec059b74b6bd99e28c37661 debuginfo(build-id) = 914f34023a909c257c2f9bc37a002e532cfc1485 debuginfo(build-id) = 91dd951c173a4627c951b1869aa2cf613dc85601 debuginfo(build-id) = 92b3dff7a4ee34d37926dbc56f51d2f4f02c42f3 debuginfo(build-id) = 92beefe598d9f7e17adc97a480ee066df76a65c0 debuginfo(build-id) = 92ce43846e14054a8990f20cfc0e5f7bb7a84135 debuginfo(build-id) = 92fa4dd4f29ab99a93be81f908a04a7b96af362d debuginfo(build-id) = 931a86b345c73331983c502f7a7592dbaa0e6be7 debuginfo(build-id) = 94072cc62ddcadd235b0364dc941af63183f1055 debuginfo(build-id) = 944aaf268aa14e0f7e6d001d5bffedb1a5edc22a debuginfo(build-id) = 9464e56daaf1e5f5f1453fa46d87424c00dc993d debuginfo(build-id) = 9480e8a7fefdc9255e2eaa493080ed0b24a4ce85 debuginfo(build-id) = 9485159f98473ded0fcdb948451bf9fcd328c3dc debuginfo(build-id) = 94baf3ed2426ff462148752b8f556a81d1fcfd6c debuginfo(build-id) = 952074b036341e94a120d99ab3d76b234a4858dd debuginfo(build-id) = 956e58e1d366d674a639004a25962edf6434996e debuginfo(build-id) = 95ab6b5fda3886a3b0087f92e13fa15dd2b3e1ec debuginfo(build-id) = 95bad444ae9eb3f1112621618cbbe4a0f3b7e800 debuginfo(build-id) = 95ecce5a4152931db3a3a82ca7e2fcfb35c2cbff debuginfo(build-id) = 963404ae7bee28e607e1fb801d6b316ebe89bab2 debuginfo(build-id) = 97b8c41542bd1524e1a9fda0c158287ac1f39630 debuginfo(build-id) = 9852c7d9efbcd1ebfa884a67e56b4650b1ba40df debuginfo(build-id) = 985ebafb54cdd6daa64100c760fd5b16cbcd0a68 debuginfo(build-id) = 98957dac1c1a65c526670a48a42c145dac8a8375 debuginfo(build-id) = 98a403b303d8426400c245de9b7e74a23e5770e8 debuginfo(build-id) = 99d3685e15cc25d15f1e11ee2496cdbdb270f762 debuginfo(build-id) = 99d9204f609edb5093257957dcdfc9f9ca7ad597 debuginfo(build-id) = 9a5c04a3ce571fda21038c61c5bb6db66c0e6111 debuginfo(build-id) = 9aa85a76ac7191bbc37f99dd6fc8667588d2f224 debuginfo(build-id) = 9ab605d2e3c029c60d9e5f737dcf7e94d659584b debuginfo(build-id) = 9b096dd8abb0b2db83c136f33007936b7f0961dd debuginfo(build-id) = 9b2a550a96e0528163601d79a74ada6a1eb9c53e debuginfo(build-id) = 9bddff08fdf1acfbabc15610e0883884cb7c1442 debuginfo(build-id) = 9c994e03874feac0d4fc335bee86e757eb2309ba debuginfo(build-id) = 9c9ce4eb7123da6446392e9d84eb7d401e71fe18 debuginfo(build-id) = 9ca989fbc0d476fdd8968169f1ac638a03209ce2 debuginfo(build-id) = 9d622fb93619b7e0ce712a09e2f351fbc6697b33 debuginfo(build-id) = 9dace3c996be36057652076228cff74e01080a12 debuginfo(build-id) = 9e2ebc456b57cf2f95751cc45439aca6ae8c6ee3 debuginfo(build-id) = 9ec952e4e26c018fe513e0a1aadb8d86a07c914b debuginfo(build-id) = 9f2969da62bc5825f98e088b5bd20fe610070a0f debuginfo(build-id) = 9f4089a9458ec82e5c25c4034558b0ad6621e639 debuginfo(build-id) = a0238f7f8b7902b4c2fd37674e093e33b773e910 debuginfo(build-id) = a067482a7b9c21bcd41f1a263b45d4667e29599e debuginfo(build-id) = a2118f9dc3e7b70dd5134994a542951d5f0eb103 debuginfo(build-id) = a28b6e3b03654289c7b3ea8b6d357886c0637aba debuginfo(build-id) = a2bb5fc65171730e59e623d69ab08470ce56c72d debuginfo(build-id) = a2d8f3e2282ae67229ae7961ba3e7beb92d907bf debuginfo(build-id) = a2f10fd99145de23931c78d74c6294ec565031c6 debuginfo(build-id) = a35b5730d9b0631417dd4ce4f5b392e702413135 debuginfo(build-id) = a3a0c76e37f9fbc7749b1006863c890319fe4f58 debuginfo(build-id) = a479c93996cac8cd0d3303de855e7b8b0c3a3fe1 debuginfo(build-id) = a515905d76c103ade63aeffffd3d6118416147b6 debuginfo(build-id) = a57c8ce073632192b99571e0e8b6a73302041b7e debuginfo(build-id) = a5a304d109e290b7651136a895a3b5f794bf1feb debuginfo(build-id) = a636fc330a988b0084f19380e6e5e47110458668 debuginfo(build-id) = a6c6978560054e5b80dc4165ff5f9de40b9bf191 debuginfo(build-id) = a6d337fa783ef0aea4ee6fc9d1bf4a550319923d debuginfo(build-id) = a72c4e0c706f7144cd03d6bd870a73bbd53e2312 debuginfo(build-id) = a7a9c94a9d20b56d7397fd55ae29e229c4cd5c24 debuginfo(build-id) = a82892b7657e745cad8b9bf3f24dd4ee8f98bd6b debuginfo(build-id) = a849b1cf76266f4e9e4038868aa771f3acb14f3d debuginfo(build-id) = a86f2f13103926599616fd8e8479ed4dc0589b51 debuginfo(build-id) = a8882dcdd2302910f2b774625381359ebbb74728 debuginfo(build-id) = a8c1abcf6ef0d3ea0f4c349f1de75e63364b507b debuginfo(build-id) = a8ceff8c50fbb7c9f348fb71abd0803e43d4de06 debuginfo(build-id) = a92e9ad145c0e6df614478b3defd4aeb75f1eb54 debuginfo(build-id) = a9a4ebf6165c3f7da586e98b114a0b0886cb2479 debuginfo(build-id) = a9d531711df2e42279a246d77173f5096c8060d4 debuginfo(build-id) = aabba9eea8aa73b0d65f0738c0f674a453b90924 debuginfo(build-id) = aae2b8bbf827bcdbce0ccbf7c7bdc94238739d8c debuginfo(build-id) = ab1dfefd3c157af26029d0681c4b196393ca49f1 debuginfo(build-id) = ab91008ddd96f449faf0d36821a7b98e5440f51f debuginfo(build-id) = ac270f3a31bb5754e6916348652ece31cfb689f4 debuginfo(build-id) = ad2dd3226cfd26e091e758dae904849ebc5a828a debuginfo(build-id) = ada8a572fbb6d2c4b0da2bf2190b573c528ce066 debuginfo(build-id) = adef597ca40da6abd61d6b061acc68e5024b3000 debuginfo(build-id) = ae1666f992a9a07310bf166b883943149bcabbbe debuginfo(build-id) = ae18fa05e2bb781ea9e16c4d47ffedfb84156080 debuginfo(build-id) = ae819f66df9c015bd7804af2d6f57f8f6bd7f2f0 debuginfo(build-id) = af03fb55be46e5e61d833371c3cc0a4d8dd77bca debuginfo(build-id) = af065a7c0c0b2603c2180e16764eff11f6c871d9 debuginfo(build-id) = af587f721989d750bf2f41e1b105ae225b65ec20 debuginfo(build-id) = b0a33f33469c65df960376e76faed7c9251594df debuginfo(build-id) = b163970c56fe8d20e8406beba72f86a9e6aaa0e4 debuginfo(build-id) = b2366f021a3555a1317f2c6b693f6401cb8742e1 debuginfo(build-id) = b29b1fc4eb4bbbe8a463de47a256d0d2ed7d1a88 debuginfo(build-id) = b2ba33cda95a38e8fc6288b2e9370ef1a033c1aa debuginfo(build-id) = b2d098b1f6b0648b721f5b5f2735ee3420e1720f debuginfo(build-id) = b2d3d87ee956bccd85eda38931809f54bc725c36 debuginfo(build-id) = b2e8ed32f00b29dbecb3132135e1f907f47cf5bf debuginfo(build-id) = b33855a7e829028fecbd52b83b7d66c2768f917b debuginfo(build-id) = b3baacb26291c3e72410793db054da557bcb7884 debuginfo(build-id) = b4152721bc4113d811384cc41bded43c92191ab0 debuginfo(build-id) = b47b71efac4fd474629f4980c0ab031722209142 debuginfo(build-id) = b48848298fefac6a7e2b409f7532f4ced99911d3 debuginfo(build-id) = b48e28463b805fca1ca6e130ef4fb68e10448039 debuginfo(build-id) = b491d25f3e935693c765beaa346412eaba026303 debuginfo(build-id) = b56c674e1d63f32fc32404dba31cdbf67ad9bc2a debuginfo(build-id) = b59a1b60874ddcab8f37bfab3f625aa939ed5296 debuginfo(build-id) = b6d00169d0bbe58f4fed913cb03896029091560c debuginfo(build-id) = b6e05a64cd98dff077f53388800e3745b6aebb8e debuginfo(build-id) = b733138db3b795042f679ad7d1c8023d61abcbc4 debuginfo(build-id) = b8e5d13a16649ad6a7b84f2c3c07f2978133ff3d debuginfo(build-id) = b8e87061932c1ddd579e715a59586c51483a46ee debuginfo(build-id) = b8fdee40f0fd733a63b66afd071364f31afe749e debuginfo(build-id) = ba2e2d821954044a48ed085dea7fc3f7e1ef5bc0 debuginfo(build-id) = ba5807cb7f0c7c33f972462d0824649e1ef2c185 debuginfo(build-id) = baeb435990bee6c33d413b8c999c0471a1be55a7 debuginfo(build-id) = bb5481121539e897c5a09245be5134d40ab432ff debuginfo(build-id) = bb6e0e7bec615b2f61cd1729633fa7c3bd4b3f4b debuginfo(build-id) = bba751d58fc138d00b871f1eb982ce81e9029922 debuginfo(build-id) = bc304dbbad004d6eea16a0afacfdaec725c5abd8 debuginfo(build-id) = bc3105ff883de268b0199b5fd8ca76ea8862ab23 debuginfo(build-id) = bc5cdc14b8414d41041c0b5870a0eaf30e0dd4ac debuginfo(build-id) = bc8f2913d00f94efd6aecf21ad96eca9950e9d24 debuginfo(build-id) = bc97df7298c180b4306d7e16db7134f1210d2f39 debuginfo(build-id) = bd6571275b8bfea06a371ef79b5ee57f65c4a500 debuginfo(build-id) = bdcab171dcc41b906826f08f0632d25fecb5825a debuginfo(build-id) = be560d491be54e4c7a8587b33f4238208aaaaf8f debuginfo(build-id) = be87caa76b035f9b70c99f9928adb0f1fc4192bd debuginfo(build-id) = bec5f5a942ff7a373de2b4e96fd95e6b6469b941 debuginfo(build-id) = bef3e80a91962a2c5787c5fa21b80c2c4908d4b6 debuginfo(build-id) = bf10f736dd303a8ac249348d4c7ea1c12abaa946 debuginfo(build-id) = bf6012f11f0940d6b6e412b0f8b81ba3502a230f debuginfo(build-id) = c04ca30c174fa10976bd678d0beba9f423b65a93 debuginfo(build-id) = c1267a9686dd91a7e2f3d11f43ed16c639a65cb0 debuginfo(build-id) = c17e0e9429095637e727198d0b781c38479d95c4 debuginfo(build-id) = c19768cd814df423a15e1b0243e0e582cbf3c569 debuginfo(build-id) = c3124c77f563ed689b17ef59c2a2107f33a6e3d4 debuginfo(build-id) = c31429588db2277eb0b1af7b748efade90352403 debuginfo(build-id) = c35bf08cb7d3c43418fbe50f27e92a4d79767b69 debuginfo(build-id) = c4139b8ead52db89d7f03129fd642603bd758fa6 debuginfo(build-id) = c4579351069898a8270d1d4445e618d8f2980dc2 debuginfo(build-id) = c47250c7b64932f8b6f3ce4dc2eac66f429e6fbc debuginfo(build-id) = c4b88f8137407467fbfa9c07788c90880da5a393 debuginfo(build-id) = c503a3414dd9f62a612381dea7f4d88593e0460d debuginfo(build-id) = c5a961bd30324a40f9bdedaaf8cf877df6a6e976 debuginfo(build-id) = c67088a24b093869b7c85df657c0b00cbb2f583e debuginfo(build-id) = c7621f4142a735e55c9704e5b7f8d858d1f7345c debuginfo(build-id) = c76d7a610e1d2ec88dea0126b2974dcd72840b2e debuginfo(build-id) = c81cb606f9714530b36141e8ed91270a4a216977 debuginfo(build-id) = c834f246006ab895292e9eb009d7186e3b9eaaa2 debuginfo(build-id) = c8830403caa0177021b1f02df82d2a2b01302878 debuginfo(build-id) = c92299f13ee8debd7867502db62efe963e4e43ba debuginfo(build-id) = c95894935eaf2699e51e5a817558b11819743a5e debuginfo(build-id) = ca72319fd09cc39df3a0dd13199a25e674e8e150 debuginfo(build-id) = cab7cc63d5557811750619abb044ce81c0e90408 debuginfo(build-id) = cb1c91ce89c8dd41ce100947a9c618bd1208f54a debuginfo(build-id) = cb94169111807ce8a05a3bec252ec533f89c5191 debuginfo(build-id) = cbcc9fd35e052a1f84d73f89b8dcbda58e99c867 debuginfo(build-id) = cbdcc43ace69eb6a8d42b0d6c853f36c8b3eb32a debuginfo(build-id) = cc02e7b68f495e4d4f3ada12c7e46c0c79b197d4 debuginfo(build-id) = cc03c20e9f6b6aa89255c29a06d85fa6f1c62292 debuginfo(build-id) = cc476237115477f7fc1e5e3c04e918a0a67201df debuginfo(build-id) = cc8b3b747b6d92f350c9105857c92edcdec9506f debuginfo(build-id) = ccfe42c13643ebfe62e09f9a5ce474244ccf77d2 debuginfo(build-id) = cd2e790426054b18cb36fc2e0a68cd3a2bd38f64 debuginfo(build-id) = cd33bfea7bab46f022be615cf67496f8be496e58 debuginfo(build-id) = cd64eeefd28e07d55781c8c8002709607c13b507 debuginfo(build-id) = cd712a1720fd55b0856ad316a7021c5eca8a5392 debuginfo(build-id) = cdb18b1c44e0957afe04351ccf7617e70db24f54 debuginfo(build-id) = cdec9e4ccace78c5b9c25882453a567bfb580a23 debuginfo(build-id) = ce22933812d06ffd7c139a7982dd039f84abbb1e debuginfo(build-id) = ce2d0b1d03bcff6538bf51941c520ff4ba236eb6 debuginfo(build-id) = ce49bda5847cc14fb416f69c7ad62097c0fc7f46 debuginfo(build-id) = ceb16aa93b68bd6d8823cc239c761402f5266b09 debuginfo(build-id) = cf4ac8ca4c518b20ce6b1310ff42533ee062ec5b debuginfo(build-id) = cf5d6981ce8a918efb18d83b0af2a4cb50eaaf13 debuginfo(build-id) = cfc5e82470cbda5846896957e8310e40d1750755 debuginfo(build-id) = d02c653fc75253bb735581b2d248bf45d024e5c2 debuginfo(build-id) = d0f92565bb7fe5eee64f08680d50e3064ca80a42 debuginfo(build-id) = d1ffe8df9a2da336d49644b8402c227564fe32df debuginfo(build-id) = d20e799c2fac803868d50d18a9fb9b2b36cde497 debuginfo(build-id) = d2fc9a5ef8ee01e7aa02c70ea31b92f9619b44f6 debuginfo(build-id) = d32fa714b97ed7f3e540f71703d22ffabdb2038f debuginfo(build-id) = d34be146b3d7802f1cc59554a06f5bd02593e97d debuginfo(build-id) = d3ad3ca0ee404b9f71bb84c736c805951274f9dc debuginfo(build-id) = d5882b81029979d9d05dcc3e97a894d79a23c4a4 debuginfo(build-id) = d5f0d949fbd0bcebf3f388c7dfd348a2d04f4adf debuginfo(build-id) = d633f50b5f589d962dcdac9d2dd29cdb151d279e debuginfo(build-id) = d65e0402300fc9ac879e6cbaf513b8fb2c7b2bfd debuginfo(build-id) = d682c062193eb80f69f08437d18781b7338a5643 debuginfo(build-id) = d713fd5881d762f42b489dc27f8f4bbfed201ed4 debuginfo(build-id) = d71bcfe8eabbe580ab1941a82ec83e5ce760a78d debuginfo(build-id) = d756d33c353e911dc755719720f5e6458fd52e4c debuginfo(build-id) = d786190446b3c36eb96a8b99c932482a27ea6898 debuginfo(build-id) = d815d8af9183d1c2e7cb100cc2f211df14fe4d15 debuginfo(build-id) = d86b49c48b2ace331a3ef7c0486587d540a61a0b debuginfo(build-id) = d8f29018e5b1ff24b0747ff8f7b5efaad8f5672f debuginfo(build-id) = d8f7d3e9ecd3747a83ff80d4983ea509c00f534f debuginfo(build-id) = d964426ec74e228c29852556994c83fdfea36388 debuginfo(build-id) = da18e7e5a63afe7e993c919e7edd2cb7e1f818d2 debuginfo(build-id) = da21f401ba54a670280d8086af792f9fab265756 debuginfo(build-id) = db909266b30c510ba131f28b24e3b3e585eda0ff debuginfo(build-id) = dbd161e068c47a32452e12a905c1ced8fc7e65d0 debuginfo(build-id) = dc009459bdc431d584b28f2054e477e010ec1a5c debuginfo(build-id) = dc17aeab5c802c4992c3670c0a4310e40627c040 debuginfo(build-id) = dc44028794f7b6ea541a600e3b23771ffd692929 debuginfo(build-id) = dc5a9af87564447ad556dcc269689c8f115c760f debuginfo(build-id) = dd35e3ed60d234a787e851d42bed60a038ffd7f2 debuginfo(build-id) = dd9c1017ca18c603c796b918bf639b3a7a3ddcf4 debuginfo(build-id) = ddc324b461eb2e53c1bcf1f600f5f0fcaf7a8d7e debuginfo(build-id) = dddb3f1054f248eefd7e2997b1aad33fc454a33b debuginfo(build-id) = ddf41592e1aafde9c97624e57385fc964f12a668 debuginfo(build-id) = de0b3c64bfd11e1c42c3be4076d61b863fca19e8 debuginfo(build-id) = de42b923e248ed3c0c0ab4626f0b4a18e0ca7226 debuginfo(build-id) = de5d1cfeea86078044de5b0d770a47c504178b76 debuginfo(build-id) = de6d61c1d4507541bfdb2b5d3891af49bb83e942 debuginfo(build-id) = dec365b8d5454fc266545974af6f8c896522ec0d debuginfo(build-id) = df34703723bd9b0b934f7a410a4f95b0ea384eac debuginfo(build-id) = df4c6cf7a96aa5a2d6ca7162a3a1c94bb6a24943 debuginfo(build-id) = df6c42b96527f0be052ea47f41355aa8d96c8427 debuginfo(build-id) = dfed23c0da00507a856fa5b021d49e91fefe534a debuginfo(build-id) = e05100bcea831f11f911f7338ef1e09368931477 debuginfo(build-id) = e074e0da00b8c07590f2ff3ba690a5fec7bdba47 debuginfo(build-id) = e07b87b19995f10215ce868dacf8720acfed2fef debuginfo(build-id) = e0a8f8b2a0736bc729a35f352fcda3967d9dc435 debuginfo(build-id) = e0d137c24158df825551140750dd128f1235ed46 debuginfo(build-id) = e105df8d8ce284bd6c541660c76a7a0628cd731f debuginfo(build-id) = e12a09b30ed32fbfb3b2aabc5118c064e69e4ace debuginfo(build-id) = e158e6df1f8baf8ecc2f4dd8af7ca9ad8ad381da debuginfo(build-id) = e16f63d00635242ac22af2da6cc83cb5d6935d24 debuginfo(build-id) = e1744d8f963e625b88d0f7ee7c0c9572f63695f3 debuginfo(build-id) = e1c5f70fa6df6ed34aa6289e3193a35423a9fafb debuginfo(build-id) = e2149097e023612336dfd168d5a461cbb791236e debuginfo(build-id) = e238f7e2af41fbf3da81684c8eda7fd70a9c6a0a debuginfo(build-id) = e29a3d0c6771be4e7de7e463ae062e17c014fab7 debuginfo(build-id) = e3483b37366a09baf2c8e14bae2a3d8b237a572e debuginfo(build-id) = e35bd2d6f43a2b63f0c2c93af1a207e20cbb9427 debuginfo(build-id) = e3a1efe64bdb843359362b18ad226dd063b82989 debuginfo(build-id) = e3d1d08dd83d674e7e5020ef2860e6b34e22c84d debuginfo(build-id) = e3d27e93d8601db41a8abb749efde270a6363bde debuginfo(build-id) = e40637e799166a765d960be9cd3a8ecaf1110a1d debuginfo(build-id) = e4521a076e2e20be613d7a83213a0e6257c92eb3 debuginfo(build-id) = e4654a4d54e60845d3ee87a574d606d2300c83ef debuginfo(build-id) = e49c73480556a1814199a8a5bab235bb87c4f0c5 debuginfo(build-id) = e4d8f15dded125693975768e5490acbc5f852713 debuginfo(build-id) = e5575eee8237517cb1a51b998595b458e695bb8c debuginfo(build-id) = e5b877af78f0e1719dee8b764e9fa7ebaa384949 debuginfo(build-id) = e5d0c0e7d929afafe562a1a6a2635d82039bda3b debuginfo(build-id) = e5d75e4ebdc04437b78f49cf4123371ae89b0f59 debuginfo(build-id) = e5da9956a6fd8d797a2578a3834aedce33a35b2d debuginfo(build-id) = e60e89f73a9db332309d969ea37a409a23875b0b debuginfo(build-id) = e6f7660e64b826fd00b68f47641632c644b8744c debuginfo(build-id) = e774b1b60fdbc8ad7c8896c07adcc147d10fe2a8 debuginfo(build-id) = e7f238b189eae5ea4188096dcc109114fb10d1d0 debuginfo(build-id) = e80b30a6a0bf9e59af9a09af45988335def022ff debuginfo(build-id) = e8388f2a4e86dcdb9401003a0bf1683792cf802c debuginfo(build-id) = e86cba46cfb0feca1f5463a0d3984dd6c6b35d91 debuginfo(build-id) = e9826a5261ba4645b3594488dd5b784cb0a13e9a debuginfo(build-id) = e9a6a7c601c8c0f3b305c655bb5a0f5a9445f75a debuginfo(build-id) = ea30a7b932a12a6cc16fc56419f1bac794dbb4c4 debuginfo(build-id) = eaa76fefc1307cc9101273e8012a84b82173d449 debuginfo(build-id) = eaa8b602dd01ca11ec24eed2729b0cf029dc4542 debuginfo(build-id) = eb1737b5aaa856e89534294b559f4b566c6f93ab debuginfo(build-id) = eb243668c8d2c2f0321d265046a52951666f4639 debuginfo(build-id) = ec14ce7b4fc5698c6f496a465a00ff7455d6069a debuginfo(build-id) = ec3a378e5df031d341b9af31ff2f2c4388deb859 debuginfo(build-id) = ec404d9feea96330d752175475e5c38eddebfa2b debuginfo(build-id) = ec62171f9a5b03e467b3ce191aa38cba128e0523 debuginfo(build-id) = edebbcea98a87c02d58ab7b9570eb58fddd9153b debuginfo(build-id) = edfbd5359a16889cb71efcef3e1790865a451f90 debuginfo(build-id) = ee20b4d07be412f880a4e1bbb24e95a81416ba44 debuginfo(build-id) = ee4b76f5c7f7237a9809087d283add3613df9513 debuginfo(build-id) = ee625b0604b1428e8a02455e92b155a6f14932e9 debuginfo(build-id) = eed5b64fb1bb6e6178e10c24ceb46dee0871e970 debuginfo(build-id) = ef42ce60047eaa79be45d3f716f4d93a4e5d60e1 debuginfo(build-id) = ef45a0115d23b1da4e5cd252c535f1ede7de6673 debuginfo(build-id) = f153b1a0807f80da3cf64b78c4e723e7522dcf4a debuginfo(build-id) = f25a2a99744f7c8dbd09eee54c2fe23d3f4dd3da debuginfo(build-id) = f2dfcb94f301fbb081618a22b7cbd5795a0e96b5 debuginfo(build-id) = f3484eef3fc78fb0cc9912ac42465527b28bfae8 debuginfo(build-id) = f3dd09db74d475520ddb79d48ae6d13820881387 debuginfo(build-id) = f3fc503a01cdef2c627c5e63552e679327cd513d debuginfo(build-id) = f4726e948375bc4d9fefa00d853e946055f6c1d2 debuginfo(build-id) = f4bfd76ba725821adda546927c09323566b73f6c debuginfo(build-id) = f516687455c754f590644e626f136fe60154d285 debuginfo(build-id) = f53967bdd24a1ee5c7b0c1939a807539f1f97741 debuginfo(build-id) = f58ecba1f2d21b0b194d651f59b4ff2aeaf8d3b4 debuginfo(build-id) = f6f52b5b36e5b81cbf4371048103953821fac995 debuginfo(build-id) = f7026cdaddf15af123be0ecac05177b17f52000a debuginfo(build-id) = f797d8cf7da48dee5d9a7520358fca806ad9d153 debuginfo(build-id) = f79fd6cae7a5d40c69b7bcdafb82163c2ad22aaa debuginfo(build-id) = f7fdaa973886c1af1e176d4b35221b15891c8f4c debuginfo(build-id) = f921b50de6f1e9c0303f1d179d25951901f2ddc1 debuginfo(build-id) = f9622e928b41822b80bb87f5fdf512bbff25ad3c debuginfo(build-id) = f9b98a1dcf58dceb5a913e5b28c99d060fba8f10 debuginfo(build-id) = fa0adaeeb90ec03f8e70b8bf71be45b35af16cd3 debuginfo(build-id) = fa1ecadd428213a039a766f622ce1370066e16c7 debuginfo(build-id) = fa388a5856ee42f1c66e472a1d944d31b25edc1c debuginfo(build-id) = fa806d662e95b99ec339e8835575c2d010cb416c debuginfo(build-id) = fabdd3fa1dc06e2f3039a0d3faf4637a2b57dc57 debuginfo(build-id) = fade6231b4f58f6b0bfd443adacc4c3590303ed2 debuginfo(build-id) = fb3b560f9ec2cfee868a5a8b42825a312ef9ad98 debuginfo(build-id) = fb7c364579490294c40c211dda609d06b6d91c37 debuginfo(build-id) = fbeb9ec54891d06b1795e026fb8049d4211b6bad debuginfo(build-id) = fc0c50a0437d1844735b69f9a9aad9ba6e32c67b debuginfo(build-id) = fc4e435530bcb21fa4f6d2f8cc09b503c2b9ddda debuginfo(build-id) = fdd0955ef59459b84c6923739f7a9c8584830f2f debuginfo(build-id) = fe5ec1c4c09dc2690caf28b6f5d22fbd1165e523 debuginfo(build-id) = ff0468c25321de826bf84c3f95ef96f28f3118de debuginfo(build-id) = ff513a95e16d5b70f7775cfddadd5937e3ac79ea debuginfo(build-id) = ffbf0c463a60526b55134523325b224b83081ccd debuginfo(build-id) = ffcbc6c771c63189d01551886bab2da045e6e6ef ucsc-kent-utils-debuginfo = 492-1.fc46 ucsc-kent-utils-debuginfo(x86-64) = 492-1.fc46 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: ucsc-kent-utils-debugsource(x86-64) = 492-1.fc46 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILD/ucsc-kent-utils-492-build/BUILDROOT Wrote: /builddir/build/RPMS/ucsc-kent-utils-debugsource-492-1.fc46.x86_64.rpm Wrote: /builddir/build/RPMS/ucsc-kent-utils-492-1.fc46.x86_64.rpm Wrote: /builddir/build/RPMS/ucsc-kent-utils-debuginfo-492-1.fc46.x86_64.rpm Finish: rpmbuild ucsc-kent-utils-492-1.fc46.src.rpm Finish: build phase for ucsc-kent-utils-492-1.fc46.src.rpm INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-x86_64-1793082781.422399/root/var/log/dnf5.log INFO: chroot_scan: creating tarball /var/lib/copr-rpmbuild/results/chroot_scan.tar.gz /bin/tar: Removing leading `/' from member names INFO: Done(/var/lib/copr-rpmbuild/results/ucsc-kent-utils-492-1.fc46.src.rpm) Config(child) 32 minutes 32 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot Finish: run Running RPMResults tool Package info: { "packages": [ { "name": "ucsc-kent-utils-debuginfo", "epoch": null, "version": "492", "release": "1.fc46", "arch": "x86_64" }, { "name": "ucsc-kent-utils-debugsource", "epoch": null, "version": "492", "release": "1.fc46", "arch": "x86_64" }, { "name": "ucsc-kent-utils", "epoch": null, "version": "492", "release": "1.fc46", "arch": "x86_64" }, { "name": "ucsc-kent-utils", "epoch": null, "version": "492", "release": "1.fc46", "arch": "src" } ] } RPMResults finished