Warning: Permanently added '3.85.163.47' (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/10587614-fedora-43-x86_64 --chroot fedora-43-x86_64 Version: 1.8 PID: 12661 Logging PID: 12663 Task: {'allow_user_ssh': False, 'appstream': False, 'background': False, 'build_id': 10587614, 'buildroot_pkgs': [], 'chroot': 'fedora-43-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-43-x86_64/', 'id': 'copr_base', 'name': 'Copr repository', 'priority': None}], 'sandbox': 'mhough/neurofedora--mhough', 'source_json': {}, 'source_type': None, 'ssh_public_keys': None, 'storage': 0, 'submitter': 'mhough', 'tags': [], 'task_id': '10587614-fedora-43-x86_64', 'timeout': 18000, '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-iq4kkpz3/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-iq4kkpz3/ucsc-kent-utils', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-iq4kkpz3/ucsc-kent-utils'... Running: git checkout 332fa7a6f988c08af202fe2c499b8a0264b9d1fc -- cmd: ['git', 'checkout', '332fa7a6f988c08af202fe2c499b8a0264b9d1fc', '--'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-iq4kkpz3/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-iq4kkpz3/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 24.1M 100 24.1M 0 0 11.3M 0 0:00:02 0:00:02 --:--:-- 11.3M INFO: Reading stdout from command: md5sum kent-core-492.tar.gz tail: /var/lib/copr-rpmbuild/main.log: file truncated Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-iq4kkpz3/ucsc-kent-utils/ucsc-kent-utils.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-iq4kkpz3/ucsc-kent-utils --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1781120563.631826 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 6.7 starting (python version = 3.14.2, NVR = mock-6.7-1.fc43), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-iq4kkpz3/ucsc-kent-utils/ucsc-kent-utils.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-iq4kkpz3/ucsc-kent-utils --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1781120563.631826 -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-iq4kkpz3/ucsc-kent-utils/ucsc-kent-utils.spec) Config(fedora-43-x86_64) Start: clean chroot Finish: clean chroot Mock Version: 6.7 INFO: Mock Version: 6.7 Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-43-x86_64-bootstrap-1781120563.631826/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:43 INFO: Pulling image: registry.fedoraproject.org/fedora:43 INFO: Tagging container image as mock-bootstrap-4dc612c3-6ed7-4d2b-b507-d2b4bd2109ce INFO: Checking that f621b79d0940e1a41fdadd2d68cb3643bc4a397e348b1aa62cfcc13c08cadb4c image matches host's architecture INFO: Copy content of container f621b79d0940e1a41fdadd2d68cb3643bc4a397e348b1aa62cfcc13c08cadb4c to /var/lib/mock/fedora-43-x86_64-bootstrap-1781120563.631826/root INFO: mounting f621b79d0940e1a41fdadd2d68cb3643bc4a397e348b1aa62cfcc13c08cadb4c with podman image mount INFO: image f621b79d0940e1a41fdadd2d68cb3643bc4a397e348b1aa62cfcc13c08cadb4c as /var/lib/containers/storage/overlay/c499add3827bc9f1d779dc0a1ba66f4c0670bca5b79a2a076044a175f10af333/merged INFO: umounting image f621b79d0940e1a41fdadd2d68cb3643bc4a397e348b1aa62cfcc13c08cadb4c (/var/lib/containers/storage/overlay/c499add3827bc9f1d779dc0a1ba66f4c0670bca5b79a2a076044a175f10af333/merged) with podman image umount INFO: Removing image mock-bootstrap-4dc612c3-6ed7-4d2b-b507-d2b4bd2109ce 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-43-x86_64-1781120563.631826/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-6.0.1-1.fc43.x86_64 rpm-sequoia-1.10.2-2.fc43.x86_64 dnf5-5.2.18.0-4.fc43.x86_64 dnf5-plugins-5.2.18.0-4.fc43.x86_64 Start: installing minimal buildroot with dnf5 Updating and loading repositories: Copr repository 100% | 87.6 KiB/s | 30.4 KiB | 00m00s updates 100% | 13.6 MiB/s | 11.0 MiB | 00m01s fedora 100% | 28.8 MiB/s | 35.4 MiB | 00m01s Repositories loaded. Package Arch Version Repository Size Installing group/module packages: bash x86_64 5.3.0-2.fc43 fedora 8.4 MiB bzip2 x86_64 1.0.8-21.fc43 fedora 95.3 KiB coreutils x86_64 9.7-8.fc43 updates 5.4 MiB cpio x86_64 2.15-6.fc43 fedora 1.1 MiB diffutils x86_64 3.12-3.fc43 fedora 1.6 MiB fedora-release-common noarch 43-27 updates 20.6 KiB findutils x86_64 1:4.10.0-6.fc43 fedora 1.8 MiB gawk x86_64 5.3.2-2.fc43 fedora 1.8 MiB glibc-minimal-langpack x86_64 2.42-13.fc43 updates 0.0 B grep x86_64 3.12-2.fc43 fedora 1.0 MiB gzip x86_64 1.13-4.fc43 fedora 388.8 KiB info x86_64 7.2-7.fc43 updates 353.9 KiB patch x86_64 2.8-2.fc43 fedora 222.8 KiB redhat-rpm-config noarch 343-14.fc43 updates 182.9 KiB rpm-build x86_64 6.0.1-1.fc43 updates 287.5 KiB sed x86_64 4.9-5.fc43 fedora 857.3 KiB shadow-utils x86_64 2:4.18.0-3.fc43 fedora 3.9 MiB tar x86_64 2:1.35-6.fc43 fedora 2.9 MiB unzip x86_64 6.0-67.fc43 fedora 386.3 KiB util-linux x86_64 2.41.4-7.fc43 updates 3.5 MiB which x86_64 2.23-3.fc43 fedora 83.5 KiB xz x86_64 1:5.8.1-4.fc43 updates 1.3 MiB Installing dependencies: add-determinism x86_64 0.6.0-3.fc43 updates 2.3 MiB alternatives x86_64 1.33-3.fc43 updates 62.2 KiB ansible-srpm-macros noarch 1-18.1.fc43 fedora 35.7 KiB audit-libs x86_64 4.1.4-1.fc43 updates 378.8 KiB binutils x86_64 2.45.1-4.fc43 updates 27.3 MiB build-reproducibility-srpm-macros noarch 0.6.0-3.fc43 updates 735.0 B bzip2-libs x86_64 1.0.8-21.fc43 fedora 80.6 KiB ca-certificates noarch 2025.2.80_v9.0.304-1.2.fc43 updates 2.7 MiB cmake-srpm-macros noarch 3.31.11-1.fc43 updates 524.0 B coreutils-common x86_64 9.7-8.fc43 updates 11.3 MiB crypto-policies noarch 20251125-1.git63291f8.fc43 updates 147.1 KiB curl x86_64 8.15.0-7.fc43 updates 461.4 KiB cyrus-sasl-lib x86_64 2.1.28-33.fc43 fedora 2.3 MiB debugedit x86_64 5.2-3.fc43 fedora 214.0 KiB dwz x86_64 0.16-2.fc43 fedora 287.1 KiB ed x86_64 1.22.2-1.fc43 fedora 148.1 KiB efi-srpm-macros noarch 6-4.fc43 fedora 40.1 KiB elfutils x86_64 0.195-1.fc43 updates 2.9 MiB elfutils-debuginfod-client x86_64 0.195-1.fc43 updates 84.1 KiB elfutils-default-yama-scope noarch 0.195-1.fc43 updates 1.8 KiB elfutils-libelf x86_64 0.195-1.fc43 updates 1.2 MiB elfutils-libs x86_64 0.195-1.fc43 updates 691.5 KiB fedora-gpg-keys noarch 43-1 fedora 131.2 KiB fedora-release noarch 43-27 updates 0.0 B fedora-release-identity-basic noarch 43-27 updates 631.0 B fedora-repos noarch 43-1 fedora 4.9 KiB file x86_64 5.46-9.fc43 updates 100.2 KiB file-libs x86_64 5.46-9.fc43 updates 11.9 MiB filesystem x86_64 3.18-50.fc43 fedora 112.0 B filesystem-srpm-macros noarch 3.18-50.fc43 fedora 38.2 KiB fonts-srpm-macros noarch 1:2.0.5-23.fc43 fedora 55.8 KiB forge-srpm-macros noarch 0.4.0-3.fc43 fedora 38.9 KiB fpc-srpm-macros noarch 1.3-15.fc43 fedora 144.0 B gap-srpm-macros noarch 2-1.fc43 fedora 2.1 KiB gdb-minimal x86_64 17.1-4.fc43 updates 13.6 MiB gdbm-libs x86_64 1:1.23-10.fc43 fedora 129.9 KiB ghc-srpm-macros noarch 1.9.2-3.fc43 fedora 779.0 B glibc x86_64 2.42-13.fc43 updates 6.7 MiB glibc-common x86_64 2.42-13.fc43 updates 1.0 MiB glibc-gconv-extra x86_64 2.42-13.fc43 updates 7.2 MiB gmp x86_64 1:6.3.0-4.fc43 fedora 811.2 KiB gnat-srpm-macros noarch 7-1.fc43 updates 1.0 KiB gnome-srpm-macros noarch 1.0-1.fc43 updates 3.5 KiB gnulib-l10n noarch 20241231-1.fc43 fedora 655.0 KiB gnupg2 x86_64 2.4.9-5.fc43 updates 6.6 MiB gnupg2-dirmngr x86_64 2.4.9-5.fc43 updates 618.4 KiB gnupg2-gpg-agent x86_64 2.4.9-5.fc43 updates 671.4 KiB gnupg2-gpgconf x86_64 2.4.9-5.fc43 updates 250.0 KiB gnupg2-keyboxd x86_64 2.4.9-5.fc43 updates 201.4 KiB gnupg2-verify x86_64 2.4.9-5.fc43 updates 348.5 KiB gnutls x86_64 3.8.13-1.fc43 updates 3.8 MiB go-srpm-macros noarch 3.8.0-1.fc43 fedora 61.9 KiB gpgverify noarch 2.2-3.fc43 fedora 8.7 KiB ima-evm-utils-libs x86_64 1.6.2-6.fc43 fedora 60.7 KiB jansson x86_64 2.14-3.fc43 fedora 89.1 KiB java-srpm-macros noarch 1-7.fc43 fedora 870.0 B json-c x86_64 0.18-7.fc43 fedora 82.7 KiB kernel-srpm-macros noarch 1.0-27.fc43 fedora 1.9 KiB keyutils-libs x86_64 1.6.3-6.fc43 fedora 54.3 KiB krb5-libs x86_64 1.22.2-4.fc43 updates 2.3 MiB libacl x86_64 2.3.2-4.fc43 fedora 35.9 KiB libarchive x86_64 3.8.4-1.fc43 updates 955.3 KiB libassuan x86_64 2.5.7-4.fc43 fedora 163.8 KiB libattr x86_64 2.5.2-6.fc43 fedora 24.4 KiB libblkid x86_64 2.41.4-7.fc43 updates 262.4 KiB libbrotli x86_64 1.2.0-1.fc43 updates 865.4 KiB libcap x86_64 2.76-4.fc43 updates 209.1 KiB libcap-ng x86_64 0.9.3-1.fc43 updates 69.0 KiB libcom_err x86_64 1.47.3-2.fc43 fedora 63.1 KiB libcurl x86_64 8.15.0-7.fc43 updates 907.1 KiB libeconf x86_64 0.7.9-2.fc43 fedora 64.9 KiB libevent x86_64 2.1.12-16.fc43 fedora 883.1 KiB libfdisk x86_64 2.41.4-7.fc43 updates 380.4 KiB libffi x86_64 3.5.2-1.fc43 updates 83.8 KiB libfsverity x86_64 1.6-3.fc43 fedora 28.5 KiB libgcc x86_64 15.2.1-7.fc43 updates 266.6 KiB libgcrypt x86_64 1.11.1-4.fc43 updates 1.6 MiB libgomp x86_64 15.2.1-7.fc43 updates 541.5 KiB libgpg-error x86_64 1.55-2.fc43 fedora 915.3 KiB libidn2 x86_64 2.3.8-2.fc43 fedora 552.5 KiB libksba x86_64 1.6.7-4.fc43 fedora 398.5 KiB liblastlog2 x86_64 2.41.4-7.fc43 updates 33.9 KiB libmount x86_64 2.41.4-7.fc43 updates 372.7 KiB libnghttp2 x86_64 1.66.0-2.fc43 fedora 162.2 KiB libpkgconf x86_64 2.3.0-3.fc43 fedora 78.1 KiB libpsl x86_64 0.21.5-6.fc43 fedora 76.4 KiB libselinux x86_64 3.9-5.fc43 fedora 193.1 KiB libsemanage x86_64 3.9-4.fc43 fedora 308.5 KiB libsepol x86_64 3.9-2.fc43 fedora 822.0 KiB libsmartcols x86_64 2.41.4-7.fc43 updates 180.5 KiB libssh x86_64 0.11.4-1.fc43 updates 571.8 KiB libssh-config noarch 0.11.4-1.fc43 updates 277.0 B libstdc++ x86_64 15.2.1-7.fc43 updates 2.8 MiB libtasn1 x86_64 4.21.0-1.fc43 updates 176.7 KiB libtool-ltdl x86_64 2.5.4-8.fc43 updates 70.1 KiB libunistring x86_64 1.1-10.fc43 fedora 1.7 MiB libusb1 x86_64 1.0.30-1.fc43 updates 176.0 KiB libuuid x86_64 2.41.4-7.fc43 updates 37.4 KiB libverto x86_64 0.3.2-11.fc43 fedora 25.4 KiB libxcrypt x86_64 4.5.2-1.fc43 updates 285.3 KiB libxml2 x86_64 2.12.10-5.fc43 fedora 1.7 MiB libzstd x86_64 1.5.7-2.fc43 fedora 799.9 KiB lua-libs x86_64 5.4.8-4.fc43 updates 281.9 KiB lua-srpm-macros noarch 1-16.fc43 fedora 1.3 KiB lz4-libs x86_64 1.10.0-3.fc43 fedora 161.4 KiB mpfr x86_64 4.2.2-2.fc43 fedora 832.8 KiB ncurses-base noarch 6.5-7.20250614.fc43 fedora 328.1 KiB ncurses-libs x86_64 6.5-7.20250614.fc43 fedora 946.3 KiB nettle x86_64 3.10.1-2.fc43 fedora 790.6 KiB npth x86_64 1.8-3.fc43 fedora 49.6 KiB ocaml-srpm-macros noarch 11-2.fc43 fedora 1.9 KiB openblas-srpm-macros noarch 2-20.fc43 fedora 112.0 B openldap x86_64 2.6.13-1.fc43 updates 658.1 KiB openssl-libs x86_64 1:3.5.4-3.fc43 updates 8.9 MiB p11-kit x86_64 0.26.2-1.fc43 updates 2.5 MiB p11-kit-trust x86_64 0.26.2-1.fc43 updates 466.5 KiB package-notes-srpm-macros noarch 0.18-1.fc43 updates 1.6 KiB pam-libs x86_64 1.7.1-4.fc43 updates 126.8 KiB pcre2 x86_64 10.47-1.fc43 updates 702.6 KiB pcre2-syntax noarch 10.47-1.fc43 updates 281.9 KiB perl-srpm-macros noarch 1-60.fc43 fedora 861.0 B pkgconf x86_64 2.3.0-3.fc43 fedora 88.5 KiB pkgconf-m4 noarch 2.3.0-3.fc43 fedora 14.4 KiB pkgconf-pkg-config x86_64 2.3.0-3.fc43 fedora 989.0 B popt x86_64 1.19-9.fc43 fedora 132.8 KiB publicsuffix-list-dafsa noarch 20260116-1.fc43 updates 70.4 KiB pyproject-srpm-macros noarch 1.22.2-1.fc43 updates 3.2 KiB python-srpm-macros noarch 3.14-5.fc43 fedora 51.5 KiB qt5-srpm-macros noarch 5.15.18-1.fc43 updates 500.0 B qt6-srpm-macros noarch 6.10.3-1.fc43 updates 472.0 B readline x86_64 8.3-2.fc43 fedora 511.7 KiB rpm x86_64 6.0.1-1.fc43 updates 3.1 MiB rpm-build-libs x86_64 6.0.1-1.fc43 updates 264.4 KiB rpm-libs x86_64 6.0.1-1.fc43 updates 933.7 KiB rpm-sequoia x86_64 1.10.2-2.fc43 updates 2.4 MiB rpm-sign-libs x86_64 6.0.1-1.fc43 updates 39.7 KiB rust-srpm-macros noarch 28.4-1.fc43 updates 5.5 KiB setup noarch 2.15.0-26.fc43 fedora 725.0 KiB sqlite-libs x86_64 3.50.2-2.fc43 fedora 1.5 MiB systemd-libs x86_64 258.8-1.fc43 updates 2.3 MiB systemd-standalone-sysusers x86_64 258.8-1.fc43 updates 293.4 KiB tpm2-tss x86_64 4.1.3-8.fc43 fedora 1.6 MiB tree-sitter-srpm-macros noarch 0.4.2-1.fc43 fedora 8.3 KiB util-linux-core x86_64 2.41.4-7.fc43 updates 1.5 MiB xxhash-libs x86_64 0.8.3-3.fc43 fedora 90.2 KiB xz-libs x86_64 1:5.8.1-4.fc43 updates 217.8 KiB zig-srpm-macros noarch 1-5.fc43 fedora 1.1 KiB zip x86_64 3.0-44.fc43 fedora 694.5 KiB zlib-ng-compat x86_64 2.3.3-2.fc43 updates 161.7 KiB zstd x86_64 1.5.7-2.fc43 fedora 1.7 MiB Installing groups: Buildsystem building group Transaction Summary: Installing: 172 packages Total size of inbound packages is 59 MiB. Need to download 59 MiB. After this operation, 200 MiB extra will be used (install 200 MiB, remove 0 B). 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37.9 KiB | 00m00s [130/172] build-reproducibility-srpm-ma 100% | 11.7 MiB/s | 11.9 KiB | 00m00s [131/172] curl-0:8.15.0-7.fc43.x86_64 100% | 55.4 MiB/s | 226.9 KiB | 00m00s [132/172] add-determinism-0:0.6.0-3.fc4 100% | 174.5 MiB/s | 893.7 KiB | 00m00s [133/172] gnat-srpm-macros-0:7-1.fc43.n 100% | 2.1 MiB/s | 8.7 KiB | 00m00s [134/172] package-notes-srpm-macros-0:0 100% | 3.1 MiB/s | 9.5 KiB | 00m00s [135/172] pyproject-srpm-macros-0:1.22. 100% | 3.8 MiB/s | 15.5 KiB | 00m00s [136/172] qt5-srpm-macros-0:5.15.18-1.f 100% | 2.1 MiB/s | 8.6 KiB | 00m00s [137/172] qt6-srpm-macros-0:6.10.3-1.fc 100% | 2.2 MiB/s | 9.1 KiB | 00m00s [138/172] rust-srpm-macros-0:28.4-1.fc4 100% | 5.3 MiB/s | 10.8 KiB | 00m00s [139/172] ca-certificates-0:2025.2.80_v 100% | 136.0 MiB/s | 974.5 KiB | 00m00s [140/172] crypto-policies-0:20251125-1. 100% | 13.6 MiB/s | 97.8 KiB | 00m00s [141/172] libgcrypt-0:1.11.1-4.fc43.x86 100% | 116.4 MiB/s | 596.0 KiB | 00m00s [142/172] libidn2-0:2.3.8-2.fc43.x86_64 100% | 42.7 MiB/s | 174.9 KiB | 00m00s [143/172] libunistring-0:1.1-10.fc43.x8 100% | 75.7 MiB/s | 542.9 KiB | 00m00s [144/172] gnutls-0:3.8.13-1.fc43.x86_64 100% | 126.2 MiB/s | 1.4 MiB | 00m00s [145/172] nettle-0:3.10.1-2.fc43.x86_64 100% | 51.8 MiB/s | 424.2 KiB | 00m00s [146/172] openldap-0:2.6.13-1.fc43.x86_ 100% | 50.7 MiB/s | 259.7 KiB | 00m00s [147/172] cyrus-sasl-lib-0:2.1.28-33.fc 100% | 109.9 MiB/s | 787.9 KiB | 00m00s [148/172] gdbm-libs-1:1.23-10.fc43.x86_ 100% | 11.1 MiB/s | 56.8 KiB | 00m00s [149/172] elfutils-default-yama-scope-0 100% | 10.9 MiB/s | 11.2 KiB | 00m00s [150/172] libevent-0:2.1.12-16.fc43.x86 100% | 36.0 MiB/s | 257.8 KiB | 00m00s [151/172] libffi-0:3.5.2-1.fc43.x86_64 100% | 13.4 MiB/s | 41.1 KiB | 00m00s [152/172] alternatives-0:1.33-3.fc43.x8 100% | 19.8 MiB/s | 40.6 KiB | 00m00s [153/172] p11-kit-trust-0:0.26.2-1.fc43 100% | 34.3 MiB/s | 140.4 KiB | 00m00s [154/172] p11-kit-0:0.26.2-1.fc43.x86_6 100% | 104.9 MiB/s | 537.2 KiB | 00m00s [155/172] libtool-ltdl-0:2.5.4-8.fc43.x 100% | 11.8 MiB/s | 36.2 KiB | 00m00s [156/172] fedora-release-0:43-27.noarch 100% | 5.6 MiB/s | 11.5 KiB | 00m00s [157/172] libtasn1-0:4.21.0-1.fc43.x86_ 100% | 18.2 MiB/s | 74.5 KiB | 00m00s [158/172] xxhash-libs-0:0.8.3-3.fc43.x8 100% | 18.8 MiB/s | 38.5 KiB | 00m00s [159/172] systemd-standalone-sysusers-0 100% | 20.7 MiB/s | 148.5 KiB | 00m00s [160/172] fedora-release-identity-basic 100% | 1.7 MiB/s | 12.3 KiB | 00m00s [161/172] libcurl-0:8.15.0-7.fc43.x86_6 100% | 65.6 MiB/s | 403.1 KiB | 00m00s [162/172] gdb-minimal-0:17.1-4.fc43.x86 100% | 235.5 MiB/s | 4.5 MiB | 00m00s [163/172] libssh-0:0.11.4-1.fc43.x86_64 100% | 22.8 MiB/s | 233.3 KiB | 00m00s [164/172] libnghttp2-0:1.66.0-2.fc43.x8 100% | 11.8 MiB/s | 72.5 KiB | 00m00s [165/172] libssh-config-0:0.11.4-1.fc43 100% | 9.0 MiB/s | 9.2 KiB | 00m00s [166/172] libpsl-0:0.21.5-6.fc43.x86_64 100% | 31.7 MiB/s | 65.0 KiB | 00m00s [167/172] publicsuffix-list-dafsa-0:202 100% | 58.9 MiB/s | 60.3 KiB | 00m00s [168/172] keyutils-libs-0:1.6.3-6.fc43. 100% | 10.2 MiB/s | 31.4 KiB | 00m00s [169/172] libcom_err-0:1.47.3-2.fc43.x8 100% | 8.7 MiB/s | 26.8 KiB | 00m00s [170/172] krb5-libs-0:1.22.2-4.fc43.x86 100% | 125.4 MiB/s | 770.4 KiB | 00m00s [171/172] libverto-0:0.3.2-11.fc43.x86_ 100% | 10.1 MiB/s | 20.7 KiB | 00m00s [172/172] libbrotli-0:1.2.0-1.fc43.x86_ 100% | 85.3 MiB/s | 349.3 KiB | 00m00s -------------------------------------------------------------------------------- [172/172] Total 100% | 173.4 MiB/s | 59.3 MiB | 00m00s Running transaction Importing OpenPGP key 0x31645531: UserID : "Fedora (43) " Fingerprint: C6E7F081CF80E13146676E88829B606631645531 From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-43-primary The key was successfully imported. [ 1/174] Verify package files 100% | 807.0 B/s | 172.0 B | 00m00s [ 2/174] Prepare transaction 100% | 4.2 KiB/s | 172.0 B | 00m00s [ 3/174] Installing libgcc-0:15.2.1-7. 100% | 262.0 MiB/s | 268.3 KiB | 00m00s [ 4/174] Installing publicsuffix-list- 100% | 0.0 B/s | 71.1 KiB | 00m00s [ 5/174] Installing libssh-config-0:0. 100% | 0.0 B/s | 816.0 B | 00m00s [ 6/174] Installing fedora-release-ide 100% | 0.0 B/s | 888.0 B | 00m00s [ 7/174] Installing fedora-gpg-keys-0: 100% | 58.3 MiB/s | 179.0 KiB | 00m00s [ 8/174] Installing fedora-repos-0:43- 100% | 0.0 B/s | 5.7 KiB | 00m00s [ 9/174] Installing fedora-release-com 100% | 24.3 MiB/s | 24.8 KiB | 00m00s [ 10/174] Installing fedora-release-0:4 100% | 17.3 KiB/s | 124.0 B | 00m00s >>> Running sysusers scriptlet: setup-0:2.15.0-26.fc43.noarch >>> Finished sysusers scriptlet: setup-0:2.15.0-26.fc43.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. >>> [ 11/174] Installing setup-0:2.15.0-26. 100% | 51.0 MiB/s | 730.6 KiB | 00m00s >>> [RPM] /etc/hosts created as /etc/hosts.rpmnew [ 12/174] Installing filesystem-0:3.18- 100% | 3.0 MiB/s | 212.8 KiB | 00m00s [ 13/174] Installing rust-srpm-macros-0 100% | 0.0 B/s | 6.4 KiB | 00m00s [ 14/174] Installing qt6-srpm-macros-0: 100% | 0.0 B/s | 748.0 B | 00m00s [ 15/174] Installing qt5-srpm-macros-0: 100% | 0.0 B/s | 776.0 B | 00m00s [ 16/174] Installing package-notes-srpm 100% | 0.0 B/s | 2.1 KiB | 00m00s [ 17/174] Installing gnat-srpm-macros-0 100% | 0.0 B/s | 1.3 KiB | 00m00s [ 18/174] Installing pkgconf-m4-0:2.3.0 100% | 0.0 B/s | 14.8 KiB | 00m00s [ 19/174] Installing pcre2-syntax-0:10. 100% | 277.7 MiB/s | 284.3 KiB | 00m00s [ 20/174] Installing gnulib-l10n-0:2024 100% | 215.5 MiB/s | 661.9 KiB | 00m00s [ 21/174] Installing coreutils-common-0 100% | 418.2 MiB/s | 11.3 MiB | 00m00s [ 22/174] Installing ncurses-base-0:6.5 100% | 86.3 MiB/s | 353.5 KiB | 00m00s [ 23/174] Installing bash-0:5.3.0-2.fc4 100% | 290.7 MiB/s | 8.4 MiB | 00m00s [ 24/174] Installing glibc-common-0:2.4 100% | 67.9 MiB/s | 1.0 MiB | 00m00s [ 25/174] Installing glibc-gconv-extra- 100% | 303.4 MiB/s | 7.3 MiB | 00m00s [ 26/174] Installing glibc-0:2.42-13.fc 100% | 197.2 MiB/s | 6.7 MiB | 00m00s [ 27/174] Installing ncurses-libs-0:6.5 100% | 310.1 MiB/s | 952.8 KiB | 00m00s [ 28/174] Installing glibc-minimal-lang 100% | 0.0 B/s | 124.0 B | 00m00s [ 29/174] Installing zlib-ng-compat-0:2 100% | 158.7 MiB/s | 162.6 KiB | 00m00s [ 30/174] Installing bzip2-libs-0:1.0.8 100% | 0.0 B/s | 81.7 KiB | 00m00s [ 31/174] Installing libgpg-error-0:1.5 100% | 64.3 MiB/s | 921.1 KiB | 00m00s [ 32/174] Installing libstdc++-0:15.2.1 100% | 406.3 MiB/s | 2.8 MiB | 00m00s [ 33/174] Installing xz-libs-1:5.8.1-4. 100% | 213.8 MiB/s | 218.9 KiB | 00m00s [ 34/174] Installing libassuan-0:2.5.7- 100% | 161.7 MiB/s | 165.6 KiB | 00m00s [ 35/174] Installing libgcrypt-0:1.11.1 100% | 393.7 MiB/s | 1.6 MiB | 00m00s [ 36/174] Installing readline-0:8.3-2.f 100% | 501.8 MiB/s | 513.9 KiB | 00m00s [ 37/174] Installing gmp-1:6.3.0-4.fc43 100% | 397.2 MiB/s | 813.5 KiB | 00m00s [ 38/174] Installing libuuid-0:2.41.4-7 100% | 0.0 B/s | 38.5 KiB | 00m00s [ 39/174] Installing popt-0:1.19-9.fc43 100% | 68.1 MiB/s | 139.4 KiB | 00m00s [ 40/174] Installing npth-0:1.8-3.fc43. 100% | 0.0 B/s | 50.7 KiB | 00m00s [ 41/174] Installing libblkid-0:2.41.4- 100% | 257.4 MiB/s | 263.6 KiB | 00m00s [ 42/174] Installing libzstd-0:1.5.7-2. 100% | 391.2 MiB/s | 801.1 KiB | 00m00s [ 43/174] Installing elfutils-libelf-0: 100% | 386.0 MiB/s | 1.2 MiB | 00m00s [ 44/174] Installing sqlite-libs-0:3.50 100% | 379.1 MiB/s | 1.5 MiB | 00m00s [ 45/174] Installing libxcrypt-0:4.5.2- 100% | 281.3 MiB/s | 288.0 KiB | 00m00s [ 46/174] Installing gnupg2-gpgconf-0:2 100% | 20.5 MiB/s | 252.1 KiB | 00m00s [ 47/174] Installing libattr-0:2.5.2-6. 100% | 0.0 B/s | 25.4 KiB | 00m00s [ 48/174] Installing libacl-0:2.3.2-4.f 100% | 0.0 B/s | 36.8 KiB | 00m00s [ 49/174] Installing libunistring-0:1.1 100% | 431.7 MiB/s | 1.7 MiB | 00m00s [ 50/174] Installing libidn2-0:2.3.8-2. 100% | 181.9 MiB/s | 558.7 KiB | 00m00s [ 51/174] Installing libtasn1-0:4.21.0- 100% | 24.9 MiB/s | 178.6 KiB | 00m00s [ 52/174] Installing crypto-policies-0: 100% | 42.0 MiB/s | 172.2 KiB | 00m00s [ 53/174] Installing dwz-0:0.16-2.fc43. 100% | 21.7 MiB/s | 288.5 KiB | 00m00s [ 54/174] Installing gnupg2-verify-0:2. 100% | 28.5 MiB/s | 349.9 KiB | 00m00s [ 55/174] Installing mpfr-0:4.2.2-2.fc4 100% | 271.6 MiB/s | 834.4 KiB | 00m00s [ 56/174] Installing gawk-0:5.3.2-2.fc4 100% | 113.5 MiB/s | 1.8 MiB | 00m00s [ 57/174] Installing libksba-0:1.6.7-4. 100% | 391.7 MiB/s | 401.1 KiB | 00m00s [ 58/174] Installing unzip-0:6.0-67.fc4 100% | 31.7 MiB/s | 389.8 KiB | 00m00s [ 59/174] Installing file-libs-0:5.46-9 100% | 697.7 MiB/s | 11.9 MiB | 00m00s [ 60/174] Installing file-0:5.46-9.fc43 100% | 9.0 MiB/s | 101.7 KiB | 00m00s [ 61/174] Installing libeconf-0:0.7.9-2 100% | 0.0 B/s | 66.5 KiB | 00m00s [ 62/174] Installing libsepol-0:3.9-2.f 100% | 401.8 MiB/s | 822.9 KiB | 00m00s [ 63/174] Installing lz4-libs-0:1.10.0- 100% | 158.6 MiB/s | 162.5 KiB | 00m00s [ 64/174] Installing json-c-0:0.18-7.fc 100% | 0.0 B/s | 84.0 KiB | 00m00s [ 65/174] Installing pcre2-0:10.47-1.fc 100% | 343.8 MiB/s | 704.1 KiB | 00m00s [ 66/174] Installing libselinux-0:3.9-5 100% | 189.8 MiB/s | 194.4 KiB | 00m00s [ 67/174] Installing grep-0:3.12-2.fc43 100% | 71.6 MiB/s | 1.0 MiB | 00m00s [ 68/174] Installing findutils-1:4.10.0 100% | 116.1 MiB/s | 1.9 MiB | 00m00s [ 69/174] Installing sed-0:4.9-5.fc43.x 100% | 60.4 MiB/s | 865.5 KiB | 00m00s [ 70/174] Installing xz-1:5.8.1-4.fc43. 100% | 88.8 MiB/s | 1.3 MiB | 00m00s [ 71/174] Installing libmount-0:2.41.4- 100% | 365.1 MiB/s | 373.8 KiB | 00m00s [ 72/174] Installing libsmartcols-0:2.4 100% | 177.2 MiB/s | 181.5 KiB | 00m00s [ 73/174] Installing libcap-ng-0:0.9.3- 100% | 69.2 MiB/s | 70.9 KiB | 00m00s [ 74/174] Installing audit-libs-0:4.1.4 100% | 372.4 MiB/s | 381.4 KiB | 00m00s [ 75/174] Installing pam-libs-0:1.7.1-4 100% | 126.1 MiB/s | 129.1 KiB | 00m00s [ 76/174] Installing libcap-0:2.76-4.fc 100% | 17.4 MiB/s | 214.3 KiB | 00m00s [ 77/174] Installing systemd-libs-0:258 100% | 389.4 MiB/s | 2.3 MiB | 00m00s [ 78/174] Installing lua-libs-0:5.4.8-4 100% | 276.7 MiB/s | 283.3 KiB | 00m00s [ 79/174] Installing libffi-0:3.5.2-1.f 100% | 83.2 MiB/s | 85.2 KiB | 00m00s [ 80/174] Installing p11-kit-0:0.26.2-1 100% | 139.4 MiB/s | 2.5 MiB | 00m00s [ 81/174] Installing alternatives-0:1.3 100% | 5.7 MiB/s | 63.8 KiB | 00m00s [ 82/174] Installing p11-kit-trust-0:0. 100% | 22.9 MiB/s | 468.2 KiB | 00m00s [ 83/174] Installing openssl-libs-1:3.5 100% | 405.3 MiB/s | 8.9 MiB | 00m00s [ 84/174] Installing coreutils-0:9.7-8. 100% | 165.2 MiB/s | 5.5 MiB | 00m00s [ 85/174] Installing ca-certificates-0: 100% | 2.1 MiB/s | 2.5 MiB | 00m01s [ 86/174] Installing gzip-0:1.13-4.fc43 100% | 29.6 MiB/s | 394.4 KiB | 00m00s [ 87/174] Installing libfsverity-0:1.6- 100% | 0.0 B/s | 29.5 KiB | 00m00s [ 88/174] Installing rpm-sequoia-0:1.10 100% | 396.5 MiB/s | 2.4 MiB | 00m00s [ 89/174] Installing libevent-0:2.1.12- 100% | 288.7 MiB/s | 886.8 KiB | 00m00s [ 90/174] Installing util-linux-core-0: 100% | 87.1 MiB/s | 1.5 MiB | 00m00s [ 91/174] Installing libusb1-0:1.0.30-1 100% | 19.3 MiB/s | 177.7 KiB | 00m00s >>> Running sysusers scriptlet: tpm2-tss-0:4.1.3-8.fc43.x86_64 >>> Finished sysusers scriptlet: tpm2-tss-0:4.1.3-8.fc43.x86_64 >>> Scriptlet output: >>> Creating group 'tss' with GID 59. >>> Creating user 'tss' (Account used for TPM access) with UID 59 and GID 59. >>> [ 92/174] Installing tpm2-tss-0:4.1.3-8 100% | 314.4 MiB/s | 1.6 MiB | 00m00s [ 93/174] Installing ima-evm-utils-libs 100% | 60.5 MiB/s | 62.0 KiB | 00m00s [ 94/174] Installing gnupg2-gpg-agent-0 100% | 33.0 MiB/s | 675.4 KiB | 00m00s [ 95/174] Installing systemd-standalone 100% | 23.9 MiB/s | 294.0 KiB | 00m00s [ 96/174] Installing rpm-libs-0:6.0.1-1 100% | 304.5 MiB/s | 935.3 KiB | 00m00s [ 97/174] Installing libsemanage-0:3.9- 100% | 303.0 MiB/s | 310.2 KiB | 00m00s [ 98/174] Installing tar-2:1.35-6.fc43. 100% | 155.7 MiB/s | 3.0 MiB | 00m00s [ 99/174] Installing zstd-0:1.5.7-2.fc4 100% | 114.0 MiB/s | 1.7 MiB | 00m00s [100/174] Installing zip-0:3.0-44.fc43. 100% | 52.5 MiB/s | 698.4 KiB | 00m00s [101/174] Installing gnupg2-keyboxd-0:2 100% | 33.0 MiB/s | 202.7 KiB | 00m00s [102/174] Installing libpsl-0:0.21.5-6. 100% | 75.7 MiB/s | 77.5 KiB | 00m00s [103/174] Installing liblastlog2-0:2.41 100% | 7.0 MiB/s | 36.0 KiB | 00m00s [104/174] Installing libfdisk-0:2.41.4- 100% | 186.2 MiB/s | 381.4 KiB | 00m00s [105/174] Installing nettle-0:3.10.1-2. 100% | 387.5 MiB/s | 793.7 KiB | 00m00s [106/174] Installing gnutls-0:3.8.13-1. 100% | 376.7 MiB/s | 3.8 MiB | 00m00s [107/174] Installing libxml2-0:2.12.10- 100% | 106.5 MiB/s | 1.7 MiB | 00m00s [108/174] Installing libarchive-0:3.8.4 100% | 311.6 MiB/s | 957.2 KiB | 00m00s [109/174] Installing bzip2-0:1.0.8-21.f 100% | 8.1 MiB/s | 99.8 KiB | 00m00s [110/174] Installing add-determinism-0: 100% | 143.9 MiB/s | 2.3 MiB | 00m00s [111/174] Installing build-reproducibil 100% | 0.0 B/s | 1.0 KiB | 00m00s [112/174] Installing cpio-0:2.15-6.fc43 100% | 78.5 MiB/s | 1.1 MiB | 00m00s [113/174] Installing diffutils-0:3.12-3 100% | 104.1 MiB/s | 1.6 MiB | 00m00s [114/174] Installing ed-0:1.22.2-1.fc43 100% | 13.3 MiB/s | 150.4 KiB | 00m00s [115/174] Installing patch-0:2.8-2.fc43 100% | 19.9 MiB/s | 224.3 KiB | 00m00s [116/174] Installing jansson-0:2.14-3.f 100% | 88.3 MiB/s | 90.5 KiB | 00m00s [117/174] Installing libgomp-0:15.2.1-7 100% | 265.1 MiB/s | 542.9 KiB | 00m00s [118/174] Installing libpkgconf-0:2.3.0 100% | 0.0 B/s | 79.2 KiB | 00m00s [119/174] Installing pkgconf-0:2.3.0-3. 100% | 8.1 MiB/s | 91.0 KiB | 00m00s [120/174] Installing pkgconf-pkg-config 100% | 161.2 KiB/s | 1.8 KiB | 00m00s [121/174] Installing gdbm-libs-1:1.23-1 100% | 128.5 MiB/s | 131.6 KiB | 00m00s [122/174] Installing cyrus-sasl-lib-0:2 100% | 143.5 MiB/s | 2.3 MiB | 00m00s [123/174] Installing libtool-ltdl-0:2.5 100% | 69.6 MiB/s | 71.2 KiB | 00m00s [124/174] Installing openldap-0:2.6.13- 100% | 323.2 MiB/s | 661.9 KiB | 00m00s [125/174] Installing gnupg2-dirmngr-0:2 100% | 31.9 MiB/s | 621.1 KiB | 00m00s [126/174] Installing gnupg2-0:2.4.9-5.f 100% | 243.1 MiB/s | 6.6 MiB | 00m00s [127/174] Installing rpm-sign-libs-0:6. 100% | 0.0 B/s | 40.6 KiB | 00m00s [128/174] Installing gpgverify-0:2.2-3. 100% | 0.0 B/s | 9.4 KiB | 00m00s [129/174] Installing xxhash-libs-0:0.8. 100% | 89.4 MiB/s | 91.6 KiB | 00m00s [130/174] Installing libnghttp2-0:1.66. 100% | 159.5 MiB/s | 163.3 KiB | 00m00s [131/174] Installing keyutils-libs-0:1. 100% | 0.0 B/s | 55.7 KiB | 00m00s [132/174] Installing libcom_err-0:1.47. 100% | 0.0 B/s | 64.2 KiB | 00m00s [133/174] Installing libverto-0:0.3.2-1 100% | 26.6 MiB/s | 27.2 KiB | 00m00s [134/174] Installing krb5-libs-0:1.22.2 100% | 333.1 MiB/s | 2.3 MiB | 00m00s [135/174] Installing libssh-0:0.11.4-1. 100% | 280.2 MiB/s | 573.9 KiB | 00m00s [136/174] Installing libbrotli-0:1.2.0- 100% | 282.4 MiB/s | 867.7 KiB | 00m00s [137/174] Installing libcurl-0:8.15.0-7 100% | 295.6 MiB/s | 908.2 KiB | 00m00s [138/174] Installing curl-0:8.15.0-7.fc 100% | 21.6 MiB/s | 463.8 KiB | 00m00s [139/174] Installing rpm-0:6.0.1-1.fc43 100% | 83.1 MiB/s | 2.6 MiB | 00m00s [140/174] Installing cmake-srpm-macros- 100% | 0.0 B/s | 804.0 B | 00m00s [141/174] Installing efi-srpm-macros-0: 100% | 0.0 B/s | 41.1 KiB | 00m00s [142/174] Installing java-srpm-macros-0 100% | 0.0 B/s | 1.1 KiB | 00m00s [143/174] Installing lua-srpm-macros-0: 100% | 0.0 B/s | 1.9 KiB | 00m00s [144/174] Installing tree-sitter-srpm-m 100% | 0.0 B/s | 9.3 KiB | 00m00s [145/174] Installing zig-srpm-macros-0: 100% | 0.0 B/s | 1.7 KiB | 00m00s [146/174] Installing filesystem-srpm-ma 100% | 0.0 B/s | 38.9 KiB | 00m00s [147/174] Installing elfutils-default-y 100% | 408.6 KiB/s | 2.0 KiB | 00m00s [148/174] Installing elfutils-libs-0:0. 100% | 225.7 MiB/s | 693.3 KiB | 00m00s [149/174] Installing elfutils-debuginfo 100% | 6.5 MiB/s | 86.4 KiB | 00m00s [150/174] Installing elfutils-0:0.195-1 100% | 163.3 MiB/s | 2.9 MiB | 00m00s [151/174] Installing binutils-0:2.45.1- 100% | 342.2 MiB/s | 27.4 MiB | 00m00s [152/174] Installing gdb-minimal-0:17.1 100% | 302.4 MiB/s | 13.6 MiB | 00m00s [153/174] Installing debugedit-0:5.2-3. 100% | 17.7 MiB/s | 217.3 KiB | 00m00s [154/174] Installing rpm-build-libs-0:6 100% | 259.0 MiB/s | 265.2 KiB | 00m00s [155/174] Installing perl-srpm-macros-0 100% | 0.0 B/s | 1.1 KiB | 00m00s [156/174] Installing openblas-srpm-macr 100% | 0.0 B/s | 392.0 B | 00m00s [157/174] Installing ocaml-srpm-macros- 100% | 0.0 B/s | 2.1 KiB | 00m00s [158/174] Installing kernel-srpm-macros 100% | 0.0 B/s | 2.3 KiB | 00m00s [159/174] Installing ghc-srpm-macros-0: 100% | 0.0 B/s | 1.0 KiB | 00m00s [160/174] Installing gap-srpm-macros-0: 100% | 0.0 B/s | 2.7 KiB | 00m00s [161/174] Installing fpc-srpm-macros-0: 100% | 0.0 B/s | 420.0 B | 00m00s [162/174] Installing ansible-srpm-macro 100% | 0.0 B/s | 36.2 KiB | 00m00s [163/174] Installing gnome-srpm-macros- 100% | 0.0 B/s | 4.1 KiB | 00m00s [164/174] Installing rpm-build-0:6.0.1- 100% | 22.3 MiB/s | 296.4 KiB | 00m00s [165/174] Installing pyproject-srpm-mac 100% | 0.0 B/s | 3.8 KiB | 00m00s [166/174] Installing redhat-rpm-config- 100% | 92.3 MiB/s | 189.1 KiB | 00m00s [167/174] Installing forge-srpm-macros- 100% | 0.0 B/s | 40.3 KiB | 00m00s [168/174] Installing fonts-srpm-macros- 100% | 0.0 B/s | 57.0 KiB | 00m00s [169/174] Installing go-srpm-macros-0:3 100% | 0.0 B/s | 63.0 KiB | 00m00s [170/174] Installing python-srpm-macros 100% | 25.8 MiB/s | 52.8 KiB | 00m00s [171/174] Installing util-linux-0:2.41. 100% | 105.2 MiB/s | 3.6 MiB | 00m00s [172/174] Installing shadow-utils-2:4.1 100% | 147.0 MiB/s | 4.0 MiB | 00m00s [173/174] Installing which-0:2.23-3.fc4 100% | 7.0 MiB/s | 85.7 KiB | 00m00s [174/174] Installing info-0:7.2-7.fc43. 100% | 226.4 KiB/s | 354.3 KiB | 00m02s Complete! Finish: installing minimal buildroot with dnf5 Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: add-determinism-0.6.0-3.fc43.x86_64 alternatives-1.33-3.fc43.x86_64 ansible-srpm-macros-1-18.1.fc43.noarch audit-libs-4.1.4-1.fc43.x86_64 bash-5.3.0-2.fc43.x86_64 binutils-2.45.1-4.fc43.x86_64 build-reproducibility-srpm-macros-0.6.0-3.fc43.noarch bzip2-1.0.8-21.fc43.x86_64 bzip2-libs-1.0.8-21.fc43.x86_64 ca-certificates-2025.2.80_v9.0.304-1.2.fc43.noarch cmake-srpm-macros-3.31.11-1.fc43.noarch coreutils-9.7-8.fc43.x86_64 coreutils-common-9.7-8.fc43.x86_64 cpio-2.15-6.fc43.x86_64 crypto-policies-20251125-1.git63291f8.fc43.noarch curl-8.15.0-7.fc43.x86_64 cyrus-sasl-lib-2.1.28-33.fc43.x86_64 debugedit-5.2-3.fc43.x86_64 diffutils-3.12-3.fc43.x86_64 dwz-0.16-2.fc43.x86_64 ed-1.22.2-1.fc43.x86_64 efi-srpm-macros-6-4.fc43.noarch elfutils-0.195-1.fc43.x86_64 elfutils-debuginfod-client-0.195-1.fc43.x86_64 elfutils-default-yama-scope-0.195-1.fc43.noarch elfutils-libelf-0.195-1.fc43.x86_64 elfutils-libs-0.195-1.fc43.x86_64 fedora-gpg-keys-43-1.noarch fedora-release-43-27.noarch fedora-release-common-43-27.noarch fedora-release-identity-basic-43-27.noarch fedora-repos-43-1.noarch file-5.46-9.fc43.x86_64 file-libs-5.46-9.fc43.x86_64 filesystem-3.18-50.fc43.x86_64 filesystem-srpm-macros-3.18-50.fc43.noarch findutils-4.10.0-6.fc43.x86_64 fonts-srpm-macros-2.0.5-23.fc43.noarch forge-srpm-macros-0.4.0-3.fc43.noarch fpc-srpm-macros-1.3-15.fc43.noarch gap-srpm-macros-2-1.fc43.noarch gawk-5.3.2-2.fc43.x86_64 gdb-minimal-17.1-4.fc43.x86_64 gdbm-libs-1.23-10.fc43.x86_64 ghc-srpm-macros-1.9.2-3.fc43.noarch glibc-2.42-13.fc43.x86_64 glibc-common-2.42-13.fc43.x86_64 glibc-gconv-extra-2.42-13.fc43.x86_64 glibc-minimal-langpack-2.42-13.fc43.x86_64 gmp-6.3.0-4.fc43.x86_64 gnat-srpm-macros-7-1.fc43.noarch gnome-srpm-macros-1.0-1.fc43.noarch gnulib-l10n-20241231-1.fc43.noarch gnupg2-2.4.9-5.fc43.x86_64 gnupg2-dirmngr-2.4.9-5.fc43.x86_64 gnupg2-gpg-agent-2.4.9-5.fc43.x86_64 gnupg2-gpgconf-2.4.9-5.fc43.x86_64 gnupg2-keyboxd-2.4.9-5.fc43.x86_64 gnupg2-verify-2.4.9-5.fc43.x86_64 gnutls-3.8.13-1.fc43.x86_64 go-srpm-macros-3.8.0-1.fc43.noarch gpg-pubkey-c6e7f081cf80e13146676e88829b606631645531-66b6dccf gpgverify-2.2-3.fc43.noarch grep-3.12-2.fc43.x86_64 gzip-1.13-4.fc43.x86_64 ima-evm-utils-libs-1.6.2-6.fc43.x86_64 info-7.2-7.fc43.x86_64 jansson-2.14-3.fc43.x86_64 java-srpm-macros-1-7.fc43.noarch json-c-0.18-7.fc43.x86_64 kernel-srpm-macros-1.0-27.fc43.noarch keyutils-libs-1.6.3-6.fc43.x86_64 krb5-libs-1.22.2-4.fc43.x86_64 libacl-2.3.2-4.fc43.x86_64 libarchive-3.8.4-1.fc43.x86_64 libassuan-2.5.7-4.fc43.x86_64 libattr-2.5.2-6.fc43.x86_64 libblkid-2.41.4-7.fc43.x86_64 libbrotli-1.2.0-1.fc43.x86_64 libcap-2.76-4.fc43.x86_64 libcap-ng-0.9.3-1.fc43.x86_64 libcom_err-1.47.3-2.fc43.x86_64 libcurl-8.15.0-7.fc43.x86_64 libeconf-0.7.9-2.fc43.x86_64 libevent-2.1.12-16.fc43.x86_64 libfdisk-2.41.4-7.fc43.x86_64 libffi-3.5.2-1.fc43.x86_64 libfsverity-1.6-3.fc43.x86_64 libgcc-15.2.1-7.fc43.x86_64 libgcrypt-1.11.1-4.fc43.x86_64 libgomp-15.2.1-7.fc43.x86_64 libgpg-error-1.55-2.fc43.x86_64 libidn2-2.3.8-2.fc43.x86_64 libksba-1.6.7-4.fc43.x86_64 liblastlog2-2.41.4-7.fc43.x86_64 libmount-2.41.4-7.fc43.x86_64 libnghttp2-1.66.0-2.fc43.x86_64 libpkgconf-2.3.0-3.fc43.x86_64 libpsl-0.21.5-6.fc43.x86_64 libselinux-3.9-5.fc43.x86_64 libsemanage-3.9-4.fc43.x86_64 libsepol-3.9-2.fc43.x86_64 libsmartcols-2.41.4-7.fc43.x86_64 libssh-0.11.4-1.fc43.x86_64 libssh-config-0.11.4-1.fc43.noarch libstdc++-15.2.1-7.fc43.x86_64 libtasn1-4.21.0-1.fc43.x86_64 libtool-ltdl-2.5.4-8.fc43.x86_64 libunistring-1.1-10.fc43.x86_64 libusb1-1.0.30-1.fc43.x86_64 libuuid-2.41.4-7.fc43.x86_64 libverto-0.3.2-11.fc43.x86_64 libxcrypt-4.5.2-1.fc43.x86_64 libxml2-2.12.10-5.fc43.x86_64 libzstd-1.5.7-2.fc43.x86_64 lua-libs-5.4.8-4.fc43.x86_64 lua-srpm-macros-1-16.fc43.noarch lz4-libs-1.10.0-3.fc43.x86_64 mpfr-4.2.2-2.fc43.x86_64 ncurses-base-6.5-7.20250614.fc43.noarch ncurses-libs-6.5-7.20250614.fc43.x86_64 nettle-3.10.1-2.fc43.x86_64 npth-1.8-3.fc43.x86_64 ocaml-srpm-macros-11-2.fc43.noarch openblas-srpm-macros-2-20.fc43.noarch openldap-2.6.13-1.fc43.x86_64 openssl-libs-3.5.4-3.fc43.x86_64 p11-kit-0.26.2-1.fc43.x86_64 p11-kit-trust-0.26.2-1.fc43.x86_64 package-notes-srpm-macros-0.18-1.fc43.noarch pam-libs-1.7.1-4.fc43.x86_64 patch-2.8-2.fc43.x86_64 pcre2-10.47-1.fc43.x86_64 pcre2-syntax-10.47-1.fc43.noarch perl-srpm-macros-1-60.fc43.noarch pkgconf-2.3.0-3.fc43.x86_64 pkgconf-m4-2.3.0-3.fc43.noarch pkgconf-pkg-config-2.3.0-3.fc43.x86_64 popt-1.19-9.fc43.x86_64 publicsuffix-list-dafsa-20260116-1.fc43.noarch pyproject-srpm-macros-1.22.2-1.fc43.noarch python-srpm-macros-3.14-5.fc43.noarch qt5-srpm-macros-5.15.18-1.fc43.noarch qt6-srpm-macros-6.10.3-1.fc43.noarch readline-8.3-2.fc43.x86_64 redhat-rpm-config-343-14.fc43.noarch rpm-6.0.1-1.fc43.x86_64 rpm-build-6.0.1-1.fc43.x86_64 rpm-build-libs-6.0.1-1.fc43.x86_64 rpm-libs-6.0.1-1.fc43.x86_64 rpm-sequoia-1.10.2-2.fc43.x86_64 rpm-sign-libs-6.0.1-1.fc43.x86_64 rust-srpm-macros-28.4-1.fc43.noarch sed-4.9-5.fc43.x86_64 setup-2.15.0-26.fc43.noarch shadow-utils-4.18.0-3.fc43.x86_64 sqlite-libs-3.50.2-2.fc43.x86_64 systemd-libs-258.8-1.fc43.x86_64 systemd-standalone-sysusers-258.8-1.fc43.x86_64 tar-1.35-6.fc43.x86_64 tpm2-tss-4.1.3-8.fc43.x86_64 tree-sitter-srpm-macros-0.4.2-1.fc43.noarch unzip-6.0-67.fc43.x86_64 util-linux-2.41.4-7.fc43.x86_64 util-linux-core-2.41.4-7.fc43.x86_64 which-2.23-3.fc43.x86_64 xxhash-libs-0.8.3-3.fc43.x86_64 xz-5.8.1-4.fc43.x86_64 xz-libs-5.8.1-4.fc43.x86_64 zig-srpm-macros-1-5.fc43.noarch zip-3.0-44.fc43.x86_64 zlib-ng-compat-2.3.3-2.fc43.x86_64 zstd-1.5.7-2.fc43.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.fc43.src.rpm Finish: rpmbuild -bs INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-43-x86_64-1781120563.631826/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-iq4kkpz3/ucsc-kent-utils/ucsc-kent-utils.spec) Config(child) 0 minutes 18 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.fc43.src.rpm) Config(fedora-43-x86_64) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-43-x86_64-bootstrap-1781120563.631826/root. INFO: reusing tmpfs at /var/lib/mock/fedora-43-x86_64-bootstrap-1781120563.631826/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-43-x86_64-1781120563.631826/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-6.0.1-1.fc43.x86_64 rpm-sequoia-1.10.2-2.fc43.x86_64 dnf5-5.2.18.0-4.fc43.x86_64 dnf5-plugins-5.2.18.0-4.fc43.x86_64 Finish: chroot init Start: build phase for ucsc-kent-utils-492-1.fc43.src.rpm Start: build setup for ucsc-kent-utils-492-1.fc43.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.fc43.src.rpm Updating and loading repositories: Copr repository 100% | 486.0 B/s | 1.5 KiB | 00m03s fedora 100% | 8.1 KiB/s | 27.2 KiB | 00m03s updates 100% | 3.8 KiB/s | 12.4 KiB | 00m03s Repositories loaded. Package Arch Version Repository Size Installing: bzip2-devel x86_64 1.0.8-21.fc43 fedora 309.8 KiB gcc x86_64 15.2.1-7.fc43 updates 112.0 MiB gcc-c++ x86_64 15.2.1-7.fc43 updates 41.4 MiB libcurl-devel x86_64 8.15.0-7.fc43 updates 1.3 MiB libpng-devel x86_64 2:1.6.58-1.fc43 updates 1.1 MiB libuuid-devel x86_64 2.41.4-7.fc43 updates 41.1 KiB make x86_64 1:4.4.1-11.fc43 fedora 1.8 MiB mariadb-connector-c-devel x86_64 3.4.8-1.fc43 updates 191.9 KiB openssl-devel x86_64 1:3.5.4-3.fc43 updates 4.6 MiB python3-devel x86_64 3.14.5-1.fc43 updates 2.0 MiB xz-devel x86_64 1:5.8.1-4.fc43 updates 258.8 KiB zlib-ng-compat-devel x86_64 2.3.3-2.fc43 updates 107.0 KiB Installing dependencies: annobin-docs noarch 12.99-1.fc43 fedora 98.9 KiB annobin-plugin-gcc x86_64 12.99-1.fc43 fedora 1.0 MiB brotli x86_64 1.2.0-1.fc43 updates 33.6 KiB brotli-devel x86_64 1.2.0-1.fc43 updates 65.9 KiB cmake-filesystem x86_64 3.31.11-1.fc43 updates 0.0 B cpp x86_64 15.2.1-7.fc43 updates 38.0 MiB expat x86_64 2.8.1-1.fc43 updates 315.4 KiB gcc-plugin-annobin x86_64 15.2.1-7.fc43 updates 57.2 KiB glibc-devel x86_64 2.42-13.fc43 updates 2.3 MiB kernel-headers x86_64 7.0.6-100.fc43 updates 6.9 MiB keyutils-libs-devel x86_64 1.6.3-6.fc43 fedora 48.2 KiB krb5-devel x86_64 1.22.2-4.fc43 updates 709.9 KiB libcom_err-devel x86_64 1.47.3-2.fc43 fedora 16.7 KiB libidn2-devel x86_64 2.3.8-2.fc43 fedora 149.1 KiB libkadm5 x86_64 1.22.2-4.fc43 updates 213.7 KiB libmpc x86_64 1.3.1-8.fc43 fedora 160.6 KiB libnghttp2-devel x86_64 1.66.0-2.fc43 fedora 286.3 KiB libpng x86_64 2:1.6.58-1.fc43 updates 245.7 KiB libpsl-devel x86_64 0.21.5-6.fc43 fedora 110.2 KiB libselinux-devel x86_64 3.9-5.fc43 fedora 127.3 KiB libsepol-devel x86_64 3.9-2.fc43 fedora 121.4 KiB libssh-devel x86_64 0.11.4-1.fc43 updates 178.0 KiB libstdc++-devel x86_64 15.2.1-7.fc43 updates 37.3 MiB libverto-devel x86_64 0.3.2-11.fc43 fedora 25.7 KiB libxcrypt-devel x86_64 4.5.2-1.fc43 updates 31.1 KiB mariadb-connector-c x86_64 3.4.8-1.fc43 updates 516.2 KiB mariadb-connector-c-config noarch 3.4.8-1.fc43 updates 497.0 B mpdecimal x86_64 4.0.1-2.fc43 fedora 217.2 KiB pcre2-devel x86_64 10.47-1.fc43 updates 2.1 MiB pcre2-utf16 x86_64 10.47-1.fc43 updates 639.2 KiB pcre2-utf32 x86_64 10.47-1.fc43 updates 611.1 KiB publicsuffix-list noarch 20260116-1.fc43 updates 342.2 KiB pyproject-rpm-macros noarch 1.22.2-1.fc43 updates 147.2 KiB python-pip-wheel noarch 25.1.1-18.fc43 fedora 1.2 MiB python-rpm-macros noarch 3.14-5.fc43 fedora 23.2 KiB python3 x86_64 3.14.5-1.fc43 updates 28.7 KiB python3-libs x86_64 3.14.5-1.fc43 updates 43.2 MiB python3-packaging noarch 25.0-7.fc43 fedora 607.4 KiB python3-rpm-generators noarch 14-13.fc43 fedora 81.7 KiB python3-rpm-macros noarch 3.14-5.fc43 fedora 6.5 KiB tzdata noarch 2026b-1.fc43 updates 1.6 MiB Transaction Summary: Installing: 53 packages Total size of inbound packages is 97 MiB. Need to download 97 MiB. After this operation, 305 MiB extra will be used (install 305 MiB, remove 0 B). [ 1/53] bzip2-devel-0:1.0.8-21.fc43.x86 100% | 13.9 MiB/s | 213.4 KiB | 00m00s [ 2/53] make-1:4.4.1-11.fc43.x86_64 100% | 27.2 MiB/s | 585.2 KiB | 00m00s [ 3/53] gcc-c++-0:15.2.1-7.fc43.x86_64 100% | 212.1 MiB/s | 15.3 MiB | 00m00s [ 4/53] libcurl-devel-0:8.15.0-7.fc43.x 100% | 13.4 MiB/s | 918.9 KiB | 00m00s [ 5/53] libuuid-devel-0:2.41.4-7.fc43.x 100% | 7.7 MiB/s | 31.4 KiB | 00m00s [ 6/53] libpng-devel-2:1.6.58-1.fc43.x8 100% | 42.3 MiB/s | 303.1 KiB | 00m00s [ 7/53] mariadb-connector-c-devel-0:3.4 100% | 8.0 MiB/s | 57.0 KiB | 00m00s [ 8/53] python3-devel-0:3.14.5-1.fc43.x 100% | 71.3 MiB/s | 437.8 KiB | 00m00s [ 9/53] xz-devel-1:5.8.1-4.fc43.x86_64 100% | 13.0 MiB/s | 66.7 KiB | 00m00s [10/53] zlib-ng-compat-devel-0:2.3.3-2. 100% | 6.2 MiB/s | 37.8 KiB | 00m00s [11/53] libmpc-0:1.3.1-8.fc43.x86_64 100% | 13.7 MiB/s | 70.4 KiB | 00m00s [12/53] gcc-0:15.2.1-7.fc43.x86_64 100% | 227.1 MiB/s | 39.7 MiB | 00m00s [13/53] cpp-0:15.2.1-7.fc43.x86_64 100% | 161.7 MiB/s | 12.9 MiB | 00m00s [14/53] libpng-2:1.6.58-1.fc43.x86_64 100% | 4.0 MiB/s | 125.8 KiB | 00m00s [15/53] mpdecimal-0:4.0.1-2.fc43.x86_64 100% | 13.5 MiB/s | 97.1 KiB | 00m00s [16/53] python-pip-wheel-0:25.1.1-18.fc 100% | 150.6 MiB/s | 1.2 MiB | 00m00s [17/53] expat-0:2.8.1-1.fc43.x86_64 100% | 20.3 MiB/s | 124.5 KiB | 00m00s [18/53] cmake-filesystem-0:3.31.11-1.fc 100% | 1.9 MiB/s | 13.4 KiB | 00m00s [19/53] tzdata-0:2026b-1.fc43.noarch 100% | 116.0 MiB/s | 712.7 KiB | 00m00s [20/53] python3-libs-0:3.14.5-1.fc43.x8 100% | 209.9 MiB/s | 9.9 MiB | 00m00s [21/53] python3-0:3.14.5-1.fc43.x86_64 100% | 2.5 MiB/s | 28.7 KiB | 00m00s [22/53] mariadb-connector-c-config-0:3. 100% | 2.2 MiB/s | 9.0 KiB | 00m00s [23/53] mariadb-connector-c-0:3.4.8-1.f 100% | 33.8 MiB/s | 207.6 KiB | 00m00s [24/53] brotli-devel-0:1.2.0-1.fc43.x86 100% | 11.2 MiB/s | 34.4 KiB | 00m00s [25/53] brotli-0:1.2.0-1.fc43.x86_64 100% | 5.8 MiB/s | 23.8 KiB | 00m00s [26/53] openssl-devel-1:3.5.4-3.fc43.x8 100% | 17.5 MiB/s | 3.0 MiB | 00m00s 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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.fc43.src.rpm Updating and loading repositories: Copr repository 100% | 3.2 KiB/s | 1.5 KiB | 00m00s fedora 100% | 32.3 KiB/s | 27.2 KiB | 00m01s updates 100% | 23.3 KiB/s | 12.4 KiB | 00m01s Repositories loaded. Nothing to do. Package "bzip2-devel-1.0.8-21.fc43.x86_64" is already installed. Package "gcc-15.2.1-7.fc43.x86_64" is already installed. Package "gcc-c++-15.2.1-7.fc43.x86_64" is already installed. Package "libcurl-devel-8.15.0-7.fc43.x86_64" is already installed. Package "libpng-devel-2:1.6.58-1.fc43.x86_64" is already installed. Package "libuuid-devel-2.41.4-7.fc43.x86_64" is already installed. Package "make-1:4.4.1-11.fc43.x86_64" is already installed. Package "mariadb-connector-c-devel-3.4.8-1.fc43.x86_64" is already installed. Package "openssl-devel-1:3.5.4-3.fc43.x86_64" is already installed. Package "python3-devel-3.14.5-1.fc43.x86_64" is already installed. Package "xz-devel-1:5.8.1-4.fc43.x86_64" is already installed. Package "zlib-ng-compat-devel-2.3.3-2.fc43.x86_64" is already installed. Finish: build setup for ucsc-kent-utils-492-1.fc43.src.rpm Start: rpmbuild ucsc-kent-utils-492-1.fc43.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.wH3Gx3 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.qupOB9 + 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/lib/rpm/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/lib/rpm/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.XJtoDv + 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 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-D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_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 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-m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_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 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-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 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-mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_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 gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_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 gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_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 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-fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_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 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-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 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-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 gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_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 -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o fieldedTable.o -c fieldedTable.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/usr/include/libpng16 -o filePath.o -c filePath.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_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 -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_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/mgHelveticaBold24.o -c font/mgHelveticaBold24.c gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_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 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-D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_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 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-Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_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 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-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 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-DMACHTYPE_x86_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 gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_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_20’ 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 gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_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 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-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 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-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 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-Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_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 gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_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 ‘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 gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-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 gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-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 gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-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 gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-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 gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-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_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:2187:9: warning: ‘strncpy’ specified bound 4096 equals destination size [-Wstringop-truncation] 2187 | strncpy(fd->refUrl, refUrl, sizeof(fd->refUrl)); | ^ 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 gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -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 gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -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 gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -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 ‘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 gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -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 gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -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 gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -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 gcc -O -g -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -std=c99 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -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 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 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 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 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)); | ^ libScan.c:126:9: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation] 126 | strncpy(lib->authorId, row[2], sizeof(lib->authorId)); | ^ 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 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 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 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 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 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 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; | ^ ../lib/hgFind.c:3923:16: warning: ‘end’ may be used uninitialized [-Wmaybe-uninitialized] 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:970, 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 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 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 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 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 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 ‘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 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:970, 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 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 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 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 ‘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:970, 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 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:970, 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 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.mxNAuK + 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/ + find /builddir/build/BUILD/ucsc-kent-utils-492-build/BUILDROOT/usr/bin -type f + 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 + 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.fc43 --unique-debug-suffix -492-1.fc43.x86_64 --unique-debug-src-base ucsc-kent-utils-492-1.fc43.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.fc43.x86_64 find-debuginfo: done + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + /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-determinism --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 Reading /builddir/build/BUILD/ucsc-kent-utils-492-build/SPECPARTS/rpm-debuginfo.specpart Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.PzFnwz + 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.fc43.x86_64 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.t8vlHx + 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.fc43 ucsc-kent-utils(x86-64) = 492-1.fc43 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.3()(64bit) libcrypto.so.3(OPENSSL_3.0.0)(64bit) libcurl.so.4()(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgcc_s.so.1(GCC_3.3.1)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.29)(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.3()(64bit) libssl.so.3(OPENSSL_3.0.0)(64bit) libz.so.1()(64bit) libz.so.1(ZLIB_1.2.0)(64bit) rtld(GNU_HASH) Processing files: ucsc-kent-utils-debugsource-492-1.fc43.x86_64 Provides: ucsc-kent-utils-debugsource = 492-1.fc43 ucsc-kent-utils-debugsource(x86-64) = 492-1.fc43 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.fc43.x86_64 Provides: debuginfo(build-id) = 01b336dd73c08cb3b1f3cb0cc89a2a57c3e8faf6 debuginfo(build-id) = 02014bc374a15c568f2d92829baba62c47ca5c41 debuginfo(build-id) = 021714a86458c25e70ed91c6077e4bdcef82f1df debuginfo(build-id) = 02a6fadce11fdb2c498d2cd9d6f7e859b0a55ec1 debuginfo(build-id) = 02aad03f2eadff335b45d104bae4b450963a44d2 debuginfo(build-id) = 02e7857c1ca41e23e6b640836d92616f70e3a7df debuginfo(build-id) = 02eff5948da9f2741da1016b91cfbd63528bda15 debuginfo(build-id) = 056439e54ed8d9b678d26bfcf3737d3cf6b31230 debuginfo(build-id) = 05ee58579ed51271e70de2f0be8f6d65389a272a debuginfo(build-id) = 0782a9d0807cffbfb2dcf9fa00dddfd82d6d1c3e debuginfo(build-id) = 080ca34adc0b4e90e545b70a23e9ba489cca4abc debuginfo(build-id) = 08518c3ea6688518421740aef9467a91c1382833 debuginfo(build-id) = 085f623bbd77f2e23a76f998f1eb92ec6ca77492 debuginfo(build-id) = 0988a2a288bc72e20ac97e553835042cdb9cf767 debuginfo(build-id) = 09a72e0e32d704f1e1084c59276bd2347a8c345e debuginfo(build-id) = 0a23d899bf1729f5ee14d42dd431127c37e060ed debuginfo(build-id) = 0aa9932e8f02c051fbb4dfe99035e9102e717b37 debuginfo(build-id) = 0aeed895557746740c0a8fc089fc51eda26582a3 debuginfo(build-id) = 0af09cf18bcb41b0848ca62d97eba706bacb6a59 debuginfo(build-id) = 0b3ee9324d24b9ca0232b573dddabe0a97b3bf1e debuginfo(build-id) = 0b61ff073626c73cf9d5cd5b735b8078c92b58f0 debuginfo(build-id) = 0c1bc093d45e39cb6dfad7f91df38cd5dedfe4b3 debuginfo(build-id) = 0c50176b94c5bdf754f3fe97cd5c44acdef2fcd5 debuginfo(build-id) = 0d388c435e34ba28b3ea7609dcfde508ed7ac1f4 debuginfo(build-id) = 0d50a4f23878c730db0b0ecba6565ee8ecd3152c debuginfo(build-id) = 0d5f3c556d814595ab115e4a8f727471ae340a33 debuginfo(build-id) = 0e4f1942f00801982cd42e433cb180f91e882455 debuginfo(build-id) = 0e55f2d3fabcf7a30f7fdbc935704be04c8e3b8e debuginfo(build-id) = 0e7e3161f8945927134a8140eedc9a2e3362c19c debuginfo(build-id) = 0ec2bce425d1b7d8c61e233ac71846a20fc7b45a debuginfo(build-id) = 0f44901bbf60ab1f5fc111cb5a12e38dbb152b09 debuginfo(build-id) = 0f91a438c1b773d65b2bc20f27db95e2637be583 debuginfo(build-id) = 10284ae4970a16ac0b8fb8115e88940ef5a4a398 debuginfo(build-id) = 107836f3f2096600c3c1031f48dbc49279d57cff debuginfo(build-id) = 11395774c3237a3d500991d83e476558af731d4a debuginfo(build-id) = 11739a21213dfcb1abf037c78a4207cac216529e debuginfo(build-id) = 119de28fc982c0c1c9d035d0bb0fcfa2cd75a6de debuginfo(build-id) = 120f9652c889881e53c9c8b9e294e24a6d5d2265 debuginfo(build-id) = 1225e29f183eb29291e696f45b37610d82ff33ff debuginfo(build-id) = 127fdfc0dc94a80deffd5d096d7d213dec6603f6 debuginfo(build-id) = 12fb205d7a0a120d1fd7524332dc9a4302900c8d debuginfo(build-id) = 13332b2f7e29f390f2e568ec878464c7a2d6aac2 debuginfo(build-id) = 133ec58ff281e5823405c3ed87f0d4dfdc3fd2a9 debuginfo(build-id) = 135d8179e45a990afd6dafde13c52a859dee6142 debuginfo(build-id) = 13ff183436dbcb7cb1cd15597eef9a5af02a19ea debuginfo(build-id) = 140da947392f9177cb2260d418aa78ba632a2fd0 debuginfo(build-id) = 1435b6dd4d3f808b8e91d4225aa1de43ba0e2511 debuginfo(build-id) = 146226ed52c5c781f19825815d5dd469c56b2708 debuginfo(build-id) = 14c8a3258626ccdc5ec35f3009d38d5f5105e3cd debuginfo(build-id) = 14ccd6f96101336732bedb1ee873fb930882c39f debuginfo(build-id) = 1533f1665ff6c24d2330578ecdd02aab67e08fc3 debuginfo(build-id) = 15a43e8585a4fe92bdd5953296c56371416e36bf debuginfo(build-id) = 15bf19a27d4e3ff2c271027a498c357d872e337f debuginfo(build-id) = 16e5d3c359dfad3430bf4f815cce962df4e24b0f debuginfo(build-id) = 16ee90779fd26de2598cf8dcdb6ccc491fe205c2 debuginfo(build-id) = 173da7ed8d5241033dab72c547ca4f6801a27de2 debuginfo(build-id) = 17531039ed27b2b3e8a1ef2f4e577692122ada69 debuginfo(build-id) = 179ec14a637e5338736b1ac0bb85ae477330e643 debuginfo(build-id) = 17bd9f521b736d22b42fc390c6b4babd3b1ce092 debuginfo(build-id) = 17ff5466a037739b36a354d1aac74e9ccc2c1bee debuginfo(build-id) = 18117c0ebd10d55f452d14398e1ec1997e41bd45 debuginfo(build-id) = 187c637e3a465e20a2b36aefeef2672ef7475cb9 debuginfo(build-id) = 18d74e49fde553ccc40d2d6d75c549e5d7a6f038 debuginfo(build-id) = 1938329f40bbe106b6bfb8f906f058665e77d33f debuginfo(build-id) = 194a28b53bb406a7a2bab663c7bda9a08baa5104 debuginfo(build-id) = 195513ce1fa17aa63a67ef3771dbe82d60190252 debuginfo(build-id) = 19614fa2c1e2947e840f367903e9ed9095f2d8d5 debuginfo(build-id) = 19ba543cee843f5a5b229662a6dc5dc236928061 debuginfo(build-id) = 19cc8f73c40fd9af9208c90022f8d0182360a9e5 debuginfo(build-id) = 1a0fd0eebe0bf280352e7a5f860bced074894cf0 debuginfo(build-id) = 1a247675194dcf723532004938896087512d84f5 debuginfo(build-id) = 1aab2eedfc7938d4a4854fa396a72d574cd39bda debuginfo(build-id) = 1ab17bd5bf937c0a3e4851b7a1d3807bb114191f debuginfo(build-id) = 1ac03ebdcdeaacf3b03451a4b5a16d6e3fe8467b debuginfo(build-id) = 1acf1708c1293e31501d30e1640954f841b858f8 debuginfo(build-id) = 1b1892d48a33fa36263136e55219e9290d99f54e debuginfo(build-id) = 1b5e78e3bb64982998c6f716168bd933439b78cc debuginfo(build-id) = 1b747c2f93003424d1ee1027ebdbfba2fdd8ebcf debuginfo(build-id) = 1b96520ac46961d6ca0178e45232a44e5f96ede4 debuginfo(build-id) = 1c369ee2a863105495e028259c536946462f6cc5 debuginfo(build-id) = 1d1cbd69099806c426cc0fc6bcb1a5f8c06573d1 debuginfo(build-id) = 1d5abb083aad3dfb58c30285d19a9d4d44006242 debuginfo(build-id) = 1da971926ec991a87d091f19364b887d11768890 debuginfo(build-id) = 1e56c172dd20e5945cb1e52c7390236c9eefcfcf debuginfo(build-id) = 1efc072a208c06b8f024b3a18efc08d061801045 debuginfo(build-id) = 1fcb1349620d4542860151d1f4bb27d220f8e860 debuginfo(build-id) = 201a00aa5cc70f424b92fd15b3cce9b4b50829e8 debuginfo(build-id) = 2025e551e0ef1c7555ca76dc346a4e5a8f5708d7 debuginfo(build-id) = 2111d7e0e1805ecee2eb23cf065fafca4b8c66dd debuginfo(build-id) = 2120e9ae94660ea154f30c0e7206696ef97bd5ee debuginfo(build-id) = 21363b59850fc1621837536b24fd4c6aceb48e08 debuginfo(build-id) = 217348131a50451fea28217dfbab1a5ce1e26fbc debuginfo(build-id) = 21950f75d3949601c80d507c0548e6955128672a debuginfo(build-id) = 219f185ab11fa0a9301209fbc82c22a6b2e92be8 debuginfo(build-id) = 2221030ce4325a56afe3f1447560c70362032f0d debuginfo(build-id) = 2237a19c2f314e041552edb692ee7a577a934ff0 debuginfo(build-id) = 22d8d2dbd548ed6474aa09200a40c2aebaa66d05 debuginfo(build-id) = 2354446a9b20e07de0d30271f2416c40a528ca49 debuginfo(build-id) = 236d4b93ea19ef86630b1d310642930359636acc debuginfo(build-id) = 23a0ed11462be69148cb67b14af2e340af4677db debuginfo(build-id) = 23b7ba89eb0fa5ed9768014b7744c7ffa4bf870b debuginfo(build-id) = 23cbb943326af9082bf29420b0282a0fdb7d2ada debuginfo(build-id) = 23f9e377cd7256f1eb91fcbdffdc7df8a05ef723 debuginfo(build-id) = 24529e70d5bb6e48e602d51ee3b61fe270cc95eb debuginfo(build-id) = 25092dac3e722f02d932c2a32b4e69499e5afabe debuginfo(build-id) = 25e872facc77679df6705c48e3c0ebc06e4583ee debuginfo(build-id) = 25f72df023bc9ba8855b34ccaaac2871a38f5a18 debuginfo(build-id) = 262b621ddeed0b4e91d881078b897a2072e4b202 debuginfo(build-id) = 2685b096878097bb8e213326e2f84f46d56106ef debuginfo(build-id) = 26d70112a6e1a80ee1ced1f150392f8dadab6be1 debuginfo(build-id) = 27950f82d133d9a1cb54b27416a74c192f78fe0f debuginfo(build-id) = 27cf9ba7430a1a9e86d49712d4233a379708001a debuginfo(build-id) = 27e7094af5fb7dd55f88de1fd9ff6d8aadf36916 debuginfo(build-id) = 285750438706aee83cfe9fe7c152058e265d4ab3 debuginfo(build-id) = 29537bb693b414a722100166f6a3a905b2f1d2c1 debuginfo(build-id) = 2973c685a0bc99bddf141fdf3e502c98ac71f806 debuginfo(build-id) = 29c1e489b21660fd3b28ba7587b0a5710a2ed708 debuginfo(build-id) = 2a9f15a079e7747897a7f7bcf583dde86578d422 debuginfo(build-id) = 2bb96b402603c9ee60eda5876ddcda7bf796d671 debuginfo(build-id) = 2ca7125b6d6258b2548c924fead2bc82bada3856 debuginfo(build-id) = 2caf32095632274bf571c9688804fd4bf5d6746e debuginfo(build-id) = 2ced66c818e8b062f2ba26a0e55c1554381232b2 debuginfo(build-id) = 2cedc7317075845c0dfb50a350d800ccd5eeb83b debuginfo(build-id) = 2d3e198376aaedd2500996b7bd0de21e5048ea87 debuginfo(build-id) = 2d9aa39bfb326602390bf2672322e5e25c54936f debuginfo(build-id) = 2dbd759c14b488311560ea86891d406fd26a5d7c debuginfo(build-id) = 2de1e1e7627af62cec7e0bbe90104a4097403471 debuginfo(build-id) = 2dee9db20a453c2a07692935406ebe7fc3b7e9a6 debuginfo(build-id) = 2e003fded1912ede28a4e5e1aae1440fb031939a debuginfo(build-id) = 2e83e058501604ff7af12262920a747f5e4bbaf2 debuginfo(build-id) = 2ea4b79aa31161c628127f3f0dba6e175c44d159 debuginfo(build-id) = 2ebb0905d56fcf3f0a17f52f3328f5855490bbfb debuginfo(build-id) = 2ef308e8da241199e8924c1c400aa77dbf020b57 debuginfo(build-id) = 2f3dc3ac3d9222c9d743067c69c8b5cc285ebcd6 debuginfo(build-id) = 2ffd1c13f8d19c58ded398fa525771d6ec276f4e debuginfo(build-id) = 307ac541381b0f9f1eb6f6dd12e05ceca2341d42 debuginfo(build-id) = 30b2b54df9bacc19c54928d3c3d562530691a55c debuginfo(build-id) = 30eae41d41ece37569ece4a5653c95c915db4f55 debuginfo(build-id) = 311ec6fd706ddf236a055186671e75f2e1dcbaad debuginfo(build-id) = 3184f8c77f9052cd620a575ba29761572f2488b8 debuginfo(build-id) = 32908d6f44529c0a3f04905cd4d4c0fc25288619 debuginfo(build-id) = 330ee38ec6c1beb2b8c3a3ba7b2d455d19bab0c4 debuginfo(build-id) = 331e6caeba8f64d0718e87c2429c74b3237ae2a1 debuginfo(build-id) = 33745489bcda6817891b70937ca3af7ac754a699 debuginfo(build-id) = 338b9c617de22fbf4c34c75aaba2e3328dd68458 debuginfo(build-id) = 34169cc27eb3811980e3b6ce9d6a5307fcd72d74 debuginfo(build-id) = 344028f53686d9dfef79a1fe4dcd234e0d838b91 debuginfo(build-id) = 356d80fb9bcfd9660d419ced62e7a376ccb26067 debuginfo(build-id) = 36a7284a8db8c931ac049c618573b825acfcc8a4 debuginfo(build-id) = 36b77128821d3007aa75b6e631e1e076bff2e1f8 debuginfo(build-id) = 379a12825ceeb67c85a0278d624f0decc3e011f2 debuginfo(build-id) = 37d38b8a45d3305590885ea44cb1a897a2386f69 debuginfo(build-id) = 3813268f099bbdc3d533368bbe9e39dc8153a663 debuginfo(build-id) = 3846551c7a0739183fe4adb81bb35f3b58004307 debuginfo(build-id) = 39e10b6973b9c20e520ab70851c4c643c834564b debuginfo(build-id) = 39e38d808f2cd5b33dfde5cca21cae5bb071ae0e debuginfo(build-id) = 3a10ab8e381e74c71b392fb04279fd9c67243c88 debuginfo(build-id) = 3a3ee4e6bc11d5734d505e1c8d6e257022522d18 debuginfo(build-id) = 3a5310de602b33602741105dbc07c008a2887fea debuginfo(build-id) = 3a70c15f58dac093a45f8cbad74583a161db2bad debuginfo(build-id) = 3b4e39080030d2843d5189f177ff1313bbeb73f6 debuginfo(build-id) = 3b52c5fbac804d2c04c1b68c2697561db73d7967 debuginfo(build-id) = 3b63ccdc44301caa486c32a0f7f5d07b8a0d071c debuginfo(build-id) = 3b846235d7c745133f50a358afd91aeeb9f2fa9b debuginfo(build-id) = 3ce46808bad50b37a0b69962265892626f02c858 debuginfo(build-id) = 3cfdd2f1fb0984940d5dee75dac0aaf2294aa94b debuginfo(build-id) = 3d73af394dbef3c2d960c41b4a9f9ba37ce8cf60 debuginfo(build-id) = 3d7dd6fcbbbfbec893539b17b941604f66bbcd78 debuginfo(build-id) = 3ecd6af4cb29cf53424a7ed27fb91aff2794762e debuginfo(build-id) = 3f006482299cf88388b05424e6178343d5836525 debuginfo(build-id) = 3f035d3d798cbedc75e3cb1c2a130de3f2a7d4ef debuginfo(build-id) = 3f082bedc4fff5787b558ffed99f71ce268a1b9a debuginfo(build-id) = 401c4d26a3be9ddc8ccddeab3617654e1b8f38c7 debuginfo(build-id) = 40418a03946c5047c65e848185153ed85647839b debuginfo(build-id) = 405b1feec9bf500bfed1d649bbb24c33336fc6cf debuginfo(build-id) = 40b8321b2b9e4f487d43d884cffd638af5193809 debuginfo(build-id) = 40bef230ccab548908f64a815c17ee9b6d75c4ea debuginfo(build-id) = 412101da7450bbb4a0a24f0ecba83bb92c7ffc0c debuginfo(build-id) = 41231af4b8c2a7894c1d5f1e2855e61a3330b2e5 debuginfo(build-id) = 4238aae9ae5f5cd0702e566420c49ee010aa6f9e debuginfo(build-id) = 424f8680456a9de01d42ab7e3ead1c62882cdd1a debuginfo(build-id) = 42ad45acae0e6b111aa41cddfceb5d03ead09b29 debuginfo(build-id) = 42afba5cc93d0abd49c651e269467345c8b0e2a7 debuginfo(build-id) = 43ffe283ea45303365c16bc72691e990d6e95e58 debuginfo(build-id) = 44279c6033038a0fb57f2521cf2513c98ce0ad38 debuginfo(build-id) = 4491494797c1ebe635935696fe00b18177ec33f3 debuginfo(build-id) = 44bf929d41dba433a7183f37c1e7c360e79eb91a debuginfo(build-id) = 4534cac3f98b01d2aa4933f2b44e71a2d9c47d5b debuginfo(build-id) = 463f2a5a92e0b41a9e2b0201e4543a770410554b debuginfo(build-id) = 4656ea8088538527a0ef48ef6da0f6be5417db8f debuginfo(build-id) = 469132f726d214ec40ab4af642a8fa512481d628 debuginfo(build-id) = 46a3bc73f46dd246119809f480d14d8378b193c2 debuginfo(build-id) = 46ca33a3e736c27666bd6496c03ffc885a05fcd2 debuginfo(build-id) = 47583f529ef95a807bf1d4be460ba931f493214b debuginfo(build-id) = 4786f78d3b297bcd7aa8bdc0819a6769123adf93 debuginfo(build-id) = 478f8d07b730662b76a2ad0f3d12d878142084ad debuginfo(build-id) = 482a0580186fafa2ce46a873346b1f27bf6c3f00 debuginfo(build-id) = 4957387402f7613a902cd7674c1f78770f77d344 debuginfo(build-id) = 498bbe8ec2828b270f9c9a270aaa4ebca76b2ef7 debuginfo(build-id) = 4a0902d2c4c71d1043066f0cd8d5ee2f3670d691 debuginfo(build-id) = 4a15d4618720b35a329f10d823ee10641a114a83 debuginfo(build-id) = 4a9fdc1b016266bd2118c8e561a663bc0fdf17f4 debuginfo(build-id) = 4bae908dc7b0673f31a575846cd3a7de5357c636 debuginfo(build-id) = 4c2276888a45db20b3ec2bf0dfc3de1ca389f27d debuginfo(build-id) = 4c3a9f5e8f75b3888820da44c73deca6065a4b6b debuginfo(build-id) = 4c7a4cee4a2b94fb9e7dafbf440e458db5e7813a debuginfo(build-id) = 4cd2d295aa5b295a84fd747cbe61936071aad746 debuginfo(build-id) = 4ceb5bdc3fff7f8eb36c941841891628c34772b9 debuginfo(build-id) = 4d2d22b0a3ca49d02e0a0b7e1325d9c8ced1c6b8 debuginfo(build-id) = 4d8cc81934281d19792ad40c566b03b80cdd4cbe debuginfo(build-id) = 4dea4c588e994a4ee3f3bd3f4266ccdd4c85bfb0 debuginfo(build-id) = 4e2b47857e5969d9520aa5a99f639bad295992b3 debuginfo(build-id) = 4e7ae315d1fe7f4a8b8e3b7d1073f136bf559ad4 debuginfo(build-id) = 4edf404abddf7f60f1a0337b999b6d11e40b80b6 debuginfo(build-id) = 5020a2f06c5f0dffd25915fb0443868af26eb2de debuginfo(build-id) = 50699faa93dc414df1d77a7e4c8ad36225d242f3 debuginfo(build-id) = 50e30756961502f48fa9cb48f0e2b2ce93c3efa2 debuginfo(build-id) = 511e5c0b1a0c587b56764e1cf2a5de5c644d4a32 debuginfo(build-id) = 52132667c9e383caffce1c4190a393f7453720d4 debuginfo(build-id) = 521d4243a7e398c54fe7fb79765120774418a87b debuginfo(build-id) = 5445630a8bf56802b685c68634aeaabcadc4c107 debuginfo(build-id) = 545e558e80b14cdbefb5df0da5d8d53c5c8c9d72 debuginfo(build-id) = 546b12df7261008019fa946874b77eaa86c85c42 debuginfo(build-id) = 55813a7d392f6f27e6ae25922cebf580894ee247 debuginfo(build-id) = 55e05ac73be58f3be6c55782c111437e07e5fb40 debuginfo(build-id) = 55e08a7abd8fc9ebcaa613d99d1c7a80cef9ad60 debuginfo(build-id) = 55e8a276adb217921e9a7dffff32a7202aa08027 debuginfo(build-id) = 570d63faa22b587d6da0538fc5d7e64ca6c8b121 debuginfo(build-id) = 573102343e04d1855d213fd162452fc9a1dd9ce1 debuginfo(build-id) = 574186366829d15d0de82a718912ef728dd6eba4 debuginfo(build-id) = 583024edf618f91acb426ff1e717b5311a8eed0b debuginfo(build-id) = 584e7fe69189684fb856453c8896fa254bec2fa0 debuginfo(build-id) = 5857695ae3ec7b8748c1f4fa9e7f331383136965 debuginfo(build-id) = 58df8d942620f1b45eed22d7f9cb7f7c927970b0 debuginfo(build-id) = 59c44942d43e98bac31ef7d921b3c2750f117a97 debuginfo(build-id) = 5a396e9266b1108ae5dcc0aa3e5b86a9737f40da debuginfo(build-id) = 5a7ad929392a3773414e5dc8025fcc5e64755efd debuginfo(build-id) = 5a8ed82152b29e44c500a940c3f444c15e2fa102 debuginfo(build-id) = 5b3427929db24a731930c40b682c3f6b9be7b7b5 debuginfo(build-id) = 5b8d53a5e67eba16415b669a5d40738689e65522 debuginfo(build-id) = 5bcbd15597627be72540af0fc6d1e80d975e4fc1 debuginfo(build-id) = 5bed68dbfde5ab7bbb6c62a18ae63dbfbc2d9c17 debuginfo(build-id) = 5cbfe9a829edb9b9c2873e101db245f04e8a5192 debuginfo(build-id) = 5cf78d8c7c59fbeedd3e37aa3e08d15912d3974d debuginfo(build-id) = 5eba3a99d572a617d68f53a650c41ddf10c39378 debuginfo(build-id) = 5f2d651dc071b0af7f5ef34726fe0a4749f039c4 debuginfo(build-id) = 6036307f2a7ee5a4f4d371fb7af753e232e08dd7 debuginfo(build-id) = 60ae82d90b0b8e93adf45d9a0f9b76ed40872d76 debuginfo(build-id) = 6161a15ca215b65a409e94a7f62f5ed70183d45d debuginfo(build-id) = 627b51e6e8c89b5d078827a0fd48afa5ccc38b07 debuginfo(build-id) = 629f5b4c509c6bcb0b5b1d1ae16455da12ec621b debuginfo(build-id) = 62ac66037c3cf437f8b804743af51016a8be1ab3 debuginfo(build-id) = 6334a94cef7c375c96cd7ab1da5ba4050c54f99c debuginfo(build-id) = 63502e1512ba75b0510c1949ac11a7f8c00d3df1 debuginfo(build-id) = 63b0c91c6044a2ea4174e29486b5d0acb12c121f debuginfo(build-id) = 65ac0d909c9d5b7c768e7134827f724a42005ba4 debuginfo(build-id) = 66276423b304461d33743d8e80f37a21de461c38 debuginfo(build-id) = 66fcf634ed191b3d00d198ace1a36429f74c7e42 debuginfo(build-id) = 679058cf240f09a8c37137953e06ed655b347682 debuginfo(build-id) = 6845fd281ce707eb06054a6ea28cc540c9adde9e debuginfo(build-id) = 68b752975378fa94229c1b6fd9d3f9cb21d08919 debuginfo(build-id) = 68f1704019590a0b813e2fb197c15c0af65588e8 debuginfo(build-id) = 6a048d9762955eef538439baeb411efcfed080e0 debuginfo(build-id) = 6a36f86e2df895503f3c52b1151a08e6ed55c185 debuginfo(build-id) = 6a8bd2a34a122ea6460c3e9c37ff476d43f80821 debuginfo(build-id) = 6a95f761b682f7ecd3c9074451043e86c2bcfb23 debuginfo(build-id) = 6ae6d533a6825260d298c295b9cc1c63f0d1cb78 debuginfo(build-id) = 6b4fe83b75885e80c035745ef310c303cb831723 debuginfo(build-id) = 6b7c29f5a59cd63fddda7ec387d7c9d3e0dec24e debuginfo(build-id) = 6b7e1df16f8664a4a1717d1739b4e2a607e613ff debuginfo(build-id) = 6be6b41fa18fe41e5a76fb14f17d0101ebbda27f debuginfo(build-id) = 6bea4a3ba6d29e13af16b5384a50ef5597a6fd62 debuginfo(build-id) = 6c55db56ec5594a08eec7410096f624d812846f7 debuginfo(build-id) = 6c6aefcd91f6bec1d6dc14782758b5a8f67409ca debuginfo(build-id) = 6c7865c53aff790478986c6284b95e5a2d9ef3b5 debuginfo(build-id) = 6c9ed276084d6a160943db388cc42fbdec062cd5 debuginfo(build-id) = 6d0d562830618017fe107ae65bb88cccf6809eee debuginfo(build-id) = 6d1e94daef36d09f7a0cd059fef6898cb577ba83 debuginfo(build-id) = 6d5a7db72adb47f607d46c50d27c22ba6dc69601 debuginfo(build-id) = 6dc0bf027d975b90973c2d574e5f1eee4faac8c9 debuginfo(build-id) = 6e569c1d58e6d5e0680ebf96d240fe627470bba6 debuginfo(build-id) = 6eae92829795c089b5393573efe7188c58349e0c debuginfo(build-id) = 6ebfcc34da4c9e96802adfe6b05a96c46a008095 debuginfo(build-id) = 6f1c1f042772bb29ae58aff468edc070624cd8fe debuginfo(build-id) = 6f59258ef8048dfcb7ee293687d99cf2dcdcab00 debuginfo(build-id) = 6f924743d4bfbdc9d334d7a29e8ed776a8ce0004 debuginfo(build-id) = 6fa5c8e27d30460c13de722b5bb2f568eb2548ce debuginfo(build-id) = 6fb621512a2efee4e57dc85cc20667469f334cda debuginfo(build-id) = 70c415002d1adf390a4e480933e928896cb40990 debuginfo(build-id) = 710af733aaffc76d3dbc4b86a3cbc91e481fc3d0 debuginfo(build-id) = 711d937ed66439061dbe909c9ee56023ffaad5e8 debuginfo(build-id) = 7124b17823e30bb70e883a83dd34db95b01493c7 debuginfo(build-id) = 714b4d34a0e8729197d10b0cf6fa75e24dfa169f debuginfo(build-id) = 715d23e6bae663307071311505381a5eea5fa864 debuginfo(build-id) = 7187cbbe4af4503653829c78bb4fe61f332c457e debuginfo(build-id) = 71d8ce905295e501d1b9d5d9ba36434df98e30a3 debuginfo(build-id) = 71de186502a5ff1a408c04a42d363036ed75e1d0 debuginfo(build-id) = 7246ae76c1d5c4f2f38b460076f4c940e4ce5c94 debuginfo(build-id) = 72be00e0da74d9cf420718600e0144cc886995ce debuginfo(build-id) = 73e10635cafcd8e664498e627e5dd56bc5959f94 debuginfo(build-id) = 73fa48f57eea646710e4bb64c21836e04c19b0d3 debuginfo(build-id) = 74cde6a7d7188d3cbe234537776c5f22700a3308 debuginfo(build-id) = 74d7c209fade5665532f1eea2acc13f82e24028c debuginfo(build-id) = 756bdc802da634263b831185e22f28bd07983e3e debuginfo(build-id) = 75890618c7ec6b7d6e5ab636ebf5e1201f4bc35e debuginfo(build-id) = 7590a378cfd6e50f0e895f4e07cfda8ac5aa231a debuginfo(build-id) = 75e2d0c5296de198569025098eef3b7a565b40f6 debuginfo(build-id) = 761eecf4a397e549cfe9022b7883e4694fc853d3 debuginfo(build-id) = 764c96f7ae898d2af388bf4631f2c3e9ea137f73 debuginfo(build-id) = 76cb1050dddaff924024d877ea89de9bdadfdee5 debuginfo(build-id) = 7759b4757a57194b86a1fde2e04f0a32b9982d51 debuginfo(build-id) = 781a468faa56966e24fc6905a410952e61416807 debuginfo(build-id) = 79e1846e7f5a37ad0dbda4355407e27813e0fe44 debuginfo(build-id) = 7a46877ad6c19cf5ed98e1f8c9d24223485cf9c4 debuginfo(build-id) = 7abbf2d1a41e6b6ffe9849c5e80bcdd7baacb57b debuginfo(build-id) = 7b4437a779777e71b5de0159ac8978d6d4c0280f debuginfo(build-id) = 7b841368ea5ed11aebaf2e7686a966a58d6d958b debuginfo(build-id) = 7b945f7af19e4f69a39e46e23f03a44d619a0842 debuginfo(build-id) = 7ba15efb68cd482d1da83ef822299ef6e7e06a94 debuginfo(build-id) = 7ca7296924751a3024b02c77bca4011c249db02f debuginfo(build-id) = 7cfe7420fcc78beafe9a2ea9885005ab0d149505 debuginfo(build-id) = 7d4de77f92d6f60c86466764b42fe22c68f51cd8 debuginfo(build-id) = 7d9cb0d1b08fd0a82389d636d5f7d015511d4874 debuginfo(build-id) = 7e2547f8446b340239ba25ac823f3fd93df3df2e debuginfo(build-id) = 7e71dce91a1ed89eaebc5ee99d82c2c579451d15 debuginfo(build-id) = 7ed0c4349b6703d5ca1c023485538ae9488c325e debuginfo(build-id) = 7f6018d6d0477d4d945f9723e09ca6abb9ae3e7e debuginfo(build-id) = 7fa0a95252211d957082d311310987f2a707d347 debuginfo(build-id) = 7fb848f3184d1d0e2c00dd7150eb49ec7b66ea99 debuginfo(build-id) = 7fec7b33c2b45bda5dbaebfca88fb32f7518df9a debuginfo(build-id) = 80a1a2eb9b0abc5a13c42b82c87378525d434cd2 debuginfo(build-id) = 8156605741c206647229f5854b8b93f1c38e65b9 debuginfo(build-id) = 819109fb0637a87c575029a35a5de3154f9d0ba3 debuginfo(build-id) = 81e770cf7ae84c6200aff0d07a4a9c745c043195 debuginfo(build-id) = 81ea4e876f01726e19e2a5b79fdfd8db32d4076a debuginfo(build-id) = 82b8bca5bade3bcd9d50496a8b03a03bdb959324 debuginfo(build-id) = 8308464ffc1b11352882bc78a4d01bf5ec63cb59 debuginfo(build-id) = 8329320fb13475e81535b869af228c9e2f079e1c debuginfo(build-id) = 8370d2a579cc13f7180becc969574d977642fc24 debuginfo(build-id) = 83d540323b1f54983e942a0c6b682feecd06cd21 debuginfo(build-id) = 8422bf08bcb3c299ad81ed578f9630f24d2519e1 debuginfo(build-id) = 8518d4474d7bf1d957bc344231550b2c5f87c7bc debuginfo(build-id) = 8594b31666741d0b3c58accb08874ae9fb8a1fad debuginfo(build-id) = 8603b63a68e773a90852d68bf67a273e2153fdf9 debuginfo(build-id) = 867ba07021c83f60077ddf8fdc63dd612084a18e debuginfo(build-id) = 86e374455919ee0192aa38250df835f156dc0bee debuginfo(build-id) = 870efa6e0e23944a7d02758ccbd26a882c8322f8 debuginfo(build-id) = 87f99300a8fd7bc7742ecb1b932803bbcafca15c debuginfo(build-id) = 88052b08acd1a9dd8d3eb14c10f6cf14c8f02b6d debuginfo(build-id) = 88361749051512e7885b1ecc5da668403b2940d2 debuginfo(build-id) = 88d67f878b2009d414304c7458018367cce1b783 debuginfo(build-id) = 88d8b490d506f67f6e1d532ae7dbd040f77a5c7d debuginfo(build-id) = 88ddb4b125957288c8fc8cc41959c8b02499c7ac debuginfo(build-id) = 88fdea382cc0bab271f4f2c842aeb0cc8a80b5a9 debuginfo(build-id) = 893d8da796d3b37f12e900f3a9ebe687e4560d66 debuginfo(build-id) = 899bfb6aa119aef6c07266c2307d6936371f1b5f debuginfo(build-id) = 8a9ac95a98295394e86fa8208f7d61644c2419cb debuginfo(build-id) = 8ad9c96c397062f83e97f66a2b3f8e4ad2b63697 debuginfo(build-id) = 8b56b630f2f57cc74473cc4c63e67f27310dc848 debuginfo(build-id) = 8bb705ac929befbfd3dcec44b0165418d1a11567 debuginfo(build-id) = 8bbc463b1ecdb9f7ae323f9d7dcd3bd8cc6a287b debuginfo(build-id) = 8bf79a7c2f61f9ac2512ac85f6d2ce13cb9b6464 debuginfo(build-id) = 8c55945b358023eb7c228c997c544068433240fa debuginfo(build-id) = 8cbb431bafffdac5936442588f70a73bacd04cec debuginfo(build-id) = 8ceff83b2ab6c733be2ec07b2e16bd97e7a012fc debuginfo(build-id) = 8d3a8720ced759d1d711f113719afe16afe3931b debuginfo(build-id) = 8dd2f1d5a7561f20726ca492981d0fed0f8e991e debuginfo(build-id) = 8e6021ba4bbef417f1e786cb6eddeea785981db2 debuginfo(build-id) = 8ea3373e7f1ab0a281261762928e19dd4a747327 debuginfo(build-id) = 8eb7b00226dcb42b40e18457bbeda718f55927a0 debuginfo(build-id) = 8f0616b475294600472d5c78f2926e4fd97b81fd debuginfo(build-id) = 8ff18c45d39a37085d634d658c817e81c1c63a8b debuginfo(build-id) = 914cffbdf684d28e3c7c83357750297c8f1c392b debuginfo(build-id) = 9195a7a78b4127cf44baf51b6486fa4426945fee debuginfo(build-id) = 91f214a38c7b16e6888344d9fe7fe52485d353a3 debuginfo(build-id) = 9222d053ed3af7c11771c45fca8c22eb6b3feaa9 debuginfo(build-id) = 922cb652977e42f407277e9389a16d78a70798b4 debuginfo(build-id) = 922dac6fd933d94bff4d43802b571afcca346bbd debuginfo(build-id) = 925d5ae3f35bf83bcfdaf7c897a72cba7067570f debuginfo(build-id) = 929d9aceb760cd3e67d2ff9770f7eadcc3d781fb debuginfo(build-id) = 92e7e570b2721464bbb19e6afbdcf2da8f86d3df debuginfo(build-id) = 9318e7e24b73c9fc25f4a73dd178ab10faa9315b debuginfo(build-id) = 9346e0027aea5cabe82dadf4cb83e6418df6912c debuginfo(build-id) = 939f09fdfc0ed4b4b848b0b3af44080ca305a33e debuginfo(build-id) = 940f95c3e6a5b1899e3684c053227b63c89fcc1c debuginfo(build-id) = 9468a7c9b6ae55383123988361768dad574c540e debuginfo(build-id) = 94b791356571dbe39f2b430d8a2fac8209841fca debuginfo(build-id) = 94c0a2b1bc770075e84f87748b4ac7348011b7cd debuginfo(build-id) = 94e79d4156ca6738471cb56635d00bd1a70054e0 debuginfo(build-id) = 95062f1517a20908db389adbecbbdfcff7ecd962 debuginfo(build-id) = 954053bfd55fe3bed5910415bbdc41d9030f6a21 debuginfo(build-id) = 9589853fd0a337d6ac216b78b2760231df889812 debuginfo(build-id) = 958e16b43517d039e899f28685064cee00896295 debuginfo(build-id) = 960ea1ffa2f240a55073059d5eb5e994922a0702 debuginfo(build-id) = 96727905868fdc8a284c67e4a9291e85b4199fb4 debuginfo(build-id) = 9752482ad36e347319a098aef6ff47045d940b77 debuginfo(build-id) = 975bf867e5590be515b31ee1aac2897c4f664738 debuginfo(build-id) = 9775246f962aa4ca3cdd031092a14bca422a7da7 debuginfo(build-id) = 979a38fd6f8ece9e5076cedcd93707844c363650 debuginfo(build-id) = 9809c9da969fa0ef97f461375589942c7498565c debuginfo(build-id) = 980cfc87d088bd6b0851a0ded6950179a6b00997 debuginfo(build-id) = 9878f7629a93bd380b4c2807049965e75f33f254 debuginfo(build-id) = 98e018bd4ddca71f954e0243f743e408eda5e2ae debuginfo(build-id) = 98f2e1b81573ea4da9c669a0a6c92b5dfd725f91 debuginfo(build-id) = 9942d8fa7ceca00cea14f91d319ece74e574942e debuginfo(build-id) = 995350a84266b292535db1ff3fae141d6349f3d6 debuginfo(build-id) = 99fe35adbd821a243188e01199ba7fb68965c8a0 debuginfo(build-id) = 9a0fded563bb79e8122c0490d8283869188c0bca debuginfo(build-id) = 9ac198b6915ce90b9a4f0a59796fac5a91f5ae13 debuginfo(build-id) = 9b03c9f6b5ee5ad1ba092fc6a1912c11bac051bb debuginfo(build-id) = 9b24ef33b09b52849c78d61f2f2186456f726a37 debuginfo(build-id) = 9b4fe399aad081e9da5d48b57cd54c38083d63ee debuginfo(build-id) = 9bbe215d54260e3f66ae1c3d573d2d800c6d4a45 debuginfo(build-id) = 9c7cab4c78321e8bac03f61ce31518fb11e6133b debuginfo(build-id) = 9cb97ba723249dc63b5dd2b6cb4c309d761ce2c7 debuginfo(build-id) = 9ce6e2d4890c69fa44b6e14322572a90e8a38cc9 debuginfo(build-id) = 9d608c7566b843459aec07cf0393ba10893b2ea0 debuginfo(build-id) = 9d7c9eaf4ca08e0b11a363da415c565d8177598f debuginfo(build-id) = 9de91dafecfc804341f7979011276033c62ab447 debuginfo(build-id) = 9e0de280a7e647dbc344db81b0b58747bf36a136 debuginfo(build-id) = 9e80e87c784136c562a67013f9bd7da72b41c2f4 debuginfo(build-id) = 9e9e5d249539e867926db844d31259cdbe4285a3 debuginfo(build-id) = 9f110a7f690d80f300955d4224cc9fb54bb4804b debuginfo(build-id) = 9f35b5cb58b6685c9ce9d23fd066dcba79fc82ab debuginfo(build-id) = 9f76bf20e0bedd8a034f94d28304b9d2d0bca178 debuginfo(build-id) = 9ff4f444ea3462ff042d0f201a9770b0e87cd1d0 debuginfo(build-id) = 9ffecd6197a674f620e98e19f7014f5572f8595b debuginfo(build-id) = a006384856f10ebab0d2bd74c7b87db886db1530 debuginfo(build-id) = a07cfcf510baa0fa34dc7f68d65362e514028d4c debuginfo(build-id) = a082ca48e9c1245e7ca10f078c9e2db9dc9067ca debuginfo(build-id) = a19370fbb6ed95a3b7ac00baa6b5854df2412cd4 debuginfo(build-id) = a23311105f048ad35530798644561879a2099837 debuginfo(build-id) = a2427d60b4a71423e7de59a91b7a1a89a9c371fa debuginfo(build-id) = a299a1cf14fa84cf31742b71bacb03cb5f51ff07 debuginfo(build-id) = a29a745d4522a29fddeb2455d1fe686c8a802075 debuginfo(build-id) = a39c1a8bc6cab9995cfcd24f0491505ae2f2cd98 debuginfo(build-id) = a3cb281b8d6d949cc3708e3c19545bdc9869b2cd debuginfo(build-id) = a4b24fb7539e4e73f76cbd88a9917ae131d443e3 debuginfo(build-id) = a4c31889d696c6a1eaabfdfe52488e2c2c972c5c debuginfo(build-id) = a582038433d74d6b3b7d5371ae7aa2ef56680c84 debuginfo(build-id) = a59a22699e50a0ff3bd0ef8bf52fcf691576de01 debuginfo(build-id) = a5c98ad1040ac7ff225100ce0c654f5d54e73cbb debuginfo(build-id) = a6b234011a99a69b5b8d22865f8a9db897196fc1 debuginfo(build-id) = a6d0c350b49b368898e28739383ef7f6dadfd770 debuginfo(build-id) = a7e27e98fcf16138d6962f7ebc8cd10b6dcaa7d2 debuginfo(build-id) = a845bd0a29da8d158c582a19c0ce4b863c9e1c9c debuginfo(build-id) = a87b333041561658d45ae8e5ab8ec4379fcdd6ed debuginfo(build-id) = a913efb2f1496fb8ebf882c567fe39652cc49294 debuginfo(build-id) = a969da8a428df61b82aebec87e1a49b3527a4c28 debuginfo(build-id) = aa4bab27bcd55c8377f98c837a82b3332f35ac48 debuginfo(build-id) = aa6a3e98ec81f32b067d2bfc419610a12124e313 debuginfo(build-id) = aaca5ba0b576cc2f591972d52891fd82a13b8fe3 debuginfo(build-id) = aadb45558e880db94a856d4f1fa327dbfecd2f5c debuginfo(build-id) = ab133b64c899071598c789a59db0bc7b91af910d debuginfo(build-id) = ab5873a787c93cfe5e92219242ff3c34524f0dd6 debuginfo(build-id) = ac49a3a3eb75f7852cf35ab73adf3bd81910bf53 debuginfo(build-id) = ac72bddef1f9d8caab6783d3c770b5d69070abfd debuginfo(build-id) = ac9ccb9e555a2a4bf76cb33848906bbcd93d8f9e debuginfo(build-id) = acfbf1b582f1b5c507cc69009e1e43b2fae02391 debuginfo(build-id) = ad975d84f86fea9ffe44875e32e448ba8f0c27b2 debuginfo(build-id) = ade60f3545e16642b4a7c0115dbc399fc90c8f76 debuginfo(build-id) = adf3c24106cec59c6c901b2cb1f56bbbec23a29c debuginfo(build-id) = af3b4383050bf6a0a9127223f22c877ce1ce303a debuginfo(build-id) = af97ff53fbbb0f0afebce46197b82fc0cf0502ea debuginfo(build-id) = b07f4613303d692c73b13a1d15310e068a09c004 debuginfo(build-id) = b0b9fb0259dad1fafcd418c8739b0fca8acbc83e debuginfo(build-id) = b1c089ef5749618aa5f2c2b58ff0257e4e0e9dd5 debuginfo(build-id) = b1e99afc3260cbe5d61aaf6288e9d12fe5b2153c debuginfo(build-id) = b2133640d7edb4ded40ffd584a0ef717ac77e92f debuginfo(build-id) = b256ee81b7f3ab279c10142a8117a04aa4adf39d debuginfo(build-id) = b2692799445f7b79b87676f8f2397390a0b022ac debuginfo(build-id) = b281fe21d382bcd6d685de33e798c8b24b04ce6d debuginfo(build-id) = b28e079eed5e75c1090215416aef01ecf6dc004d debuginfo(build-id) = b32a624e4b2809fc58faa76175ceb8f56a8b76af debuginfo(build-id) = b359c02fb70ce576ff3a2910e79f343deff141db debuginfo(build-id) = b38df7ef4797ddba93843881cd0c192ae2bf2825 debuginfo(build-id) = b3b4648cfb9534418146e23d039d0a738f09d36b debuginfo(build-id) = b4327bc560416f9f6f96f6f89e01fb3bb13e3315 debuginfo(build-id) = b484baa2e422959c1e9f2dcd91f3730d284b6146 debuginfo(build-id) = b4afbc36a32008fddfb5cbd42c21ddff5be30943 debuginfo(build-id) = b4c5fd6848117cc2124b6bfdf2ba9fea342b96ba debuginfo(build-id) = b5104433290bcb40865e0e0034919abd08399078 debuginfo(build-id) = b518fd8087fb13659e745cc31574cf948bd8e45a debuginfo(build-id) = b5b27e7f6019f74b69c7bd524b4275c9ba58b74d debuginfo(build-id) = b6088828b6ddc787a040c224ef29a622600c3d6f debuginfo(build-id) = b70d72008bba10b31d743ccd4ae6cac180818e50 debuginfo(build-id) = b741ea993361bd984711b473ecb2b19d76518bb4 debuginfo(build-id) = b7994faf9255e6e02466b6562e3b34e329b7518f debuginfo(build-id) = b7cd2efa2d85278a0fae1f003d5c7c01de1e4e1c debuginfo(build-id) = b7da59f38a95df0d0ce91908b88433123c8269d6 debuginfo(build-id) = b81444dde115a4c363123089c4c57c41a54311bf debuginfo(build-id) = b823a1bdd4004eade66a8adb3ca6484b3ae45f10 debuginfo(build-id) = b82bf7f44d3051a3c174ec190eece19e758c7aca debuginfo(build-id) = b8919a6da2dd1326ddacc7f32bc7d48bf7500200 debuginfo(build-id) = b95a222993cb3e2ccac25baf453020ec23d229b5 debuginfo(build-id) = b9bf82eed7509b3173c8418f2bc4022c8c760d51 debuginfo(build-id) = b9cedd7681520e7627f420ee4d53916825fda7aa debuginfo(build-id) = b9dca6a9a88588d3abf3aaf433594be6a129d460 debuginfo(build-id) = ba8c3f154d696ab8a4cbdd02be130aa5834120dc debuginfo(build-id) = bb5b1de194ebba6a9e3c49e115ff8df166c7010e debuginfo(build-id) = bb8605870a161614fd533e05a396e99b475c901d debuginfo(build-id) = bbd7e67a964fe92a1e46eef02648658810987e84 debuginfo(build-id) = bc4c4b6a2e699b678ae9953382f3740e1bc0ac88 debuginfo(build-id) = bcfc111fdfe75ea290a7debae148628b502cf21f debuginfo(build-id) = bd729b400bff74ea732e36024573e5fd9e8f3364 debuginfo(build-id) = bd7c1b24196ba086df22b29964e2f15f9d6fa5e7 debuginfo(build-id) = bdd846d461a1828bc37bfcee6c26ce4cddd1e914 debuginfo(build-id) = bddbda094b906d4118db1d7413830de3df3c4c8e debuginfo(build-id) = be10ee3b724d278ef880aea5431fbb7c4b2b4193 debuginfo(build-id) = be987e377971e4d74aaf8388124a6a6ac7e95c61 debuginfo(build-id) = bed9cd6eac8c0f34e3ba2fa23b4ed25e2b8cca1c debuginfo(build-id) = bf3a9186e553c7f27660fdb7433784fbb109befb debuginfo(build-id) = bf52c6e4f804a6d5eb986395f2b9d8a3704ce195 debuginfo(build-id) = bfd7bbfd7d74438e6476f025a36706177438a435 debuginfo(build-id) = bfed0b037d770908a609dadcd44da2bb47bb49cb debuginfo(build-id) = bff20655aba16a70f3238323c3a710ae281ed818 debuginfo(build-id) = c098191faa9ba3e8f31e03a31a7a2d432c92dfd6 debuginfo(build-id) = c0a5a2fefb961bbc967c2f53c6a49d15f0276ed5 debuginfo(build-id) = c1a5c1de6fc795c755a95aa6408cd564aa5498d3 debuginfo(build-id) = c1c4e0c497eb355d5e493afa4927663381862515 debuginfo(build-id) = c23f886ea73edf23e3410d14e6167f686ba30453 debuginfo(build-id) = c2dd016dc1de934c6635f17ced41b5fd243812ab debuginfo(build-id) = c37bf5aa903468a76933888bcf6be175a449571a debuginfo(build-id) = c3f2eb41a0ea6e84161e3b64816a8d9d0fa26bcd debuginfo(build-id) = c452595f311ff8b11fe762772803d8433d6b9ec9 debuginfo(build-id) = c47670efb0b211c0980cbea5df4a10486018563a debuginfo(build-id) = c4cd2ace959d3eba660c746c251833e77da8c34e debuginfo(build-id) = c5ed7fa2dfce536c4260d32af5635a19cf168891 debuginfo(build-id) = c6020e6985b92ff368be1be4eb2a2e35fb77e0ed debuginfo(build-id) = c60c40598e5711df0603ffb4d778f45a656cad59 debuginfo(build-id) = c6dcb37083fd094ad44e6d55bb59343f4d58f6fe debuginfo(build-id) = c74bd87a34552908f6f906545cedd104886bfc98 debuginfo(build-id) = c77c5c8905ac16f7e5f0e608733e23b66eaca020 debuginfo(build-id) = c8180b0f258a976efc4daa04fb3a0d017e394c5b debuginfo(build-id) = c85d8949145e7ccaf319588804420c65491d8bfa debuginfo(build-id) = c865cfb4f42a9559ebfd5aaa665d8b77a2605236 debuginfo(build-id) = c890998d16bf4219c6b2df8dd45c89d354b45735 debuginfo(build-id) = c97631d34d81015cd483516a5969578ec3680230 debuginfo(build-id) = ca14a73adabf74ecf78f22cd2c2ac960ef1848c9 debuginfo(build-id) = ca191ff013bcf3899875f0b50029eddd29e2bd04 debuginfo(build-id) = ca378271948e2923209ddaaa7aefdfc0ff679b5b debuginfo(build-id) = ca58528f1d72ba5ebf2c3ecea87c03a7a3073cb3 debuginfo(build-id) = ca6a1db429ef330609ec39007b7da656999a4bb7 debuginfo(build-id) = ca8c4bbd4b4d1abe5f6e95f3de3d079bd5ad9baf debuginfo(build-id) = cab9a42589d3e86f42e14654b245ff02ec5c15ad debuginfo(build-id) = cb37008022fa952b0a45f77cead6821f6333cfb4 debuginfo(build-id) = cb60d322906cd6f7925ed544a0450db99fd566be debuginfo(build-id) = cb7de76a2eeaf7beb44e0ef597397f30c798c36b debuginfo(build-id) = cb9740d70c08f09ad7e409e03805b978c5b8e9e5 debuginfo(build-id) = cbb9d2a89659074a4517f41fd5369fe412e3f2aa debuginfo(build-id) = cc56638d9f2b90f7d02666949a7a487c0c14a942 debuginfo(build-id) = ccf0aaec0a578cfc9e385971d02ac5060fb054ea debuginfo(build-id) = cd02d532b70760f02f117288963abf4b28786b1c debuginfo(build-id) = cd984b8a800e190666f351fad30ef360699f7b59 debuginfo(build-id) = d00521927cb896ae55a359332dabad5c52241f24 debuginfo(build-id) = d00913602a33ecfe5bf3301ad083df1f366b6624 debuginfo(build-id) = d00cf3e8137489450401819023d57fc1a1f3f532 debuginfo(build-id) = d0dbb0efc8944446bc4e80bd6912e0691f0e9ea3 debuginfo(build-id) = d0ffedae8d976d5e4382dd300b564ddd6002a5df debuginfo(build-id) = d19cfd6695bc50cac5675166798e043643fbab5d debuginfo(build-id) = d19d4c72d71732bef7292b2493defda7c6b17e9b debuginfo(build-id) = d1f942c27a06d8e65335aaf55ebdbd6c23f1adce debuginfo(build-id) = d1fb9d441f4bf963dc1797e4901a18146152fd4a debuginfo(build-id) = d29f91217ae2c340b254e08da892179b4c8ee9e5 debuginfo(build-id) = d40fb2fb69cafe98077f61ed59e962f53e3fffe6 debuginfo(build-id) = d41d55b3e06b5b2aa6e369517bd85e6d544a1639 debuginfo(build-id) = d43f513d6a62dcdcea39247af2bac2fb17996823 debuginfo(build-id) = d522f971f5c57d365ed293fac4f0839728595731 debuginfo(build-id) = d57c06b91a913f750fe7492017bfae91c2b66e11 debuginfo(build-id) = d608b707e06514d20e23731ca916337546488a48 debuginfo(build-id) = d663f755b1c840fe244fd5b1b3282b5210315a54 debuginfo(build-id) = d69ddd9b2c6f78d109eb8bd32660ed015e3a0223 debuginfo(build-id) = d6cb3e801dc5fdde6aebed1c82b26ce27b7ace2d debuginfo(build-id) = d6e5012da44b8feb43118fcc5f1e390867ade108 debuginfo(build-id) = d7509011721a8d858ee378424ff90b29dab2dee9 debuginfo(build-id) = d7577aa848795000692bbbb0eadf27f51591f70c debuginfo(build-id) = d78a7dd981ac1f970b599956da5b4f344fb69a95 debuginfo(build-id) = d8dd3aca512b2a7a67413aa7e464f5ebe0f725c6 debuginfo(build-id) = d97b75c756db87cda061225fd2b8c10a188e9e17 debuginfo(build-id) = d99de69f59f15ce0c8ddad53a78caa9014f22550 debuginfo(build-id) = da00b5f1c9f100ad35d509cc4713d44e711d8331 debuginfo(build-id) = da31d387d0043fd2daf4f45f4e28283424352d25 debuginfo(build-id) = dae3fb77316feb4d5a3740307846c0fd9159e2ff debuginfo(build-id) = dc021f00d71f2559473e6fb41f1982fe2966172c debuginfo(build-id) = dc036a79d697219334bdf5441de341f138dfe2a3 debuginfo(build-id) = dd65ebddfe4c59dac641c2694493f732b2e4bcdd debuginfo(build-id) = de32bb9a2da9f1fd237d9b339f814925b01eddea debuginfo(build-id) = deefdd934b85194bf5d5eaa5287b752fe4a0ce89 debuginfo(build-id) = df0af7c0ba3c4537dd62c578c9c549629a3b2af2 debuginfo(build-id) = dfa870f7850e3677aac4daef72447dcb9df3f7ef debuginfo(build-id) = e01380fbea8a119d6a7cedc94fbbf3fcd258cfa3 debuginfo(build-id) = e06509a31a26cff42f11461af96f73ec589e45fc debuginfo(build-id) = e0d4e494954f874207a5c25abef08089ec58e741 debuginfo(build-id) = e1228196a909b99f641dffc8604bbdfe9693297a debuginfo(build-id) = e1a76e8fdb41e0863fc423aa2d18b8ffa1a45ac6 debuginfo(build-id) = e21d0e97bc10b3707565b80c79955fc2c5a3022f debuginfo(build-id) = e22b4bc12aac9b9335fd3b0d00946e68a691b59b debuginfo(build-id) = e235c766de56709540613f017c11a5d5c9896c55 debuginfo(build-id) = e256e73df6ecab4c2a13f43fcccd25503350385f debuginfo(build-id) = e27fb7b2e0afcd261c2c23acacf41b5fa201aa0b debuginfo(build-id) = e2a4211545b54981ddc120a1db593adac9859a75 debuginfo(build-id) = e2d6b396c3ded5743a71933cf083c591ec82955f debuginfo(build-id) = e3038cd5d3a82a2990ca471851f17ccac582d717 debuginfo(build-id) = e31574f339aabbc17de601ec7d3d2992ed6c464e debuginfo(build-id) = e319f7ed7737bf0994aa847b7615c2ddf85857b8 debuginfo(build-id) = e38262c9ee58941fcbf1c0b6f4408cddecb0feb1 debuginfo(build-id) = e39dea23674bb271b1a49a4a3110e56eb41bf56d debuginfo(build-id) = e46f10d3dd61c1f20d92d2f19a5b73c26627d3ba debuginfo(build-id) = e48e96a9b554b92374ceef06a163a20914e6547b debuginfo(build-id) = e495d49ce4eef1b8acfffbaa91e348de0ddf1484 debuginfo(build-id) = e55256e9eb126d758990947d12eb0a1f10499ae4 debuginfo(build-id) = e58a8040e886136b9a300d0ffbf9abe0aff07619 debuginfo(build-id) = e5f7be9cb43e259c217a046feb0b629e9faa607c debuginfo(build-id) = e6d9acd8e6c29afcb949e3a57ca5e82a8db71542 debuginfo(build-id) = e6f88599f299b200ed3dd638740cd5569b390441 debuginfo(build-id) = e6ffcee24a5f575b5d9980162e823dd0121c34a0 debuginfo(build-id) = e7418bc24015921b913561648a45895dd52dc26d debuginfo(build-id) = e7543f7075262de128022cbd70b7cdefa3ff15e4 debuginfo(build-id) = e754e1c6da3405cc53919a5d42a62c714e7dead0 debuginfo(build-id) = e7eeaebef867d32969ccc160b2a83481b6f0885f debuginfo(build-id) = e8121cdb45eb82a82b87ab949146f77305037780 debuginfo(build-id) = e857a9a3f8eb8c26bac287fb3f14bbcbf7e3860a debuginfo(build-id) = e89d4f6c7cc7b252ecc07154c8e6689e036c9a6c debuginfo(build-id) = e8dfb223b295e77a1f0649f4bb5d8b7a3b09d24d debuginfo(build-id) = e936419547d086c80efc57adb5da1642a27f1536 debuginfo(build-id) = e96288f259d8b69236b7914030a8e8b1d5cd748c debuginfo(build-id) = e9a1fad578696f5637c3cb4c4c4ebb620ecc331b debuginfo(build-id) = eb409a9d0b349b2bea9ffdc8e16d288ac9e37cf7 debuginfo(build-id) = eb6194265617582555d6bffef58b35e2766c53c9 debuginfo(build-id) = eb96ca573357e63949b11e0a22c339c420d52d2b debuginfo(build-id) = eba6b0254bdda00391bfed9fb2bc148dec0d4a2d debuginfo(build-id) = ebc4eb1631124c0cba6dfdd42fa64817fcd17438 debuginfo(build-id) = ec838e7384c82ea818ddb9f2d6a22cf9a36dbe65 debuginfo(build-id) = eca3344c6558e6af80e0c495304600705983e28c debuginfo(build-id) = ece44c5e5caa57994ce66d8a8b116e994497207d debuginfo(build-id) = ed21fd71835d39bb28abbabff2e020ee1045350b debuginfo(build-id) = edb2b4d461cbd126b710032567bfe81d5cb0a1ff debuginfo(build-id) = edcfa8475fbad1f8dde96140d733efbe70d38587 debuginfo(build-id) = ee06f73022b112220487c805dcf6f4360273a2c4 debuginfo(build-id) = ef0625badffb2e0a7b1c968d6b46e6c98c165ba9 debuginfo(build-id) = ef2e79b4517267bcc028ac51d10ec53a2dfc3ab7 debuginfo(build-id) = ef3bef9c926124134985423cd8639dba693ca688 debuginfo(build-id) = ef4ae05c123cc30d55f80ec8a3fd19b1961aead3 debuginfo(build-id) = ef85653e25a5becad7532a86623e874c1ae7d13c debuginfo(build-id) = ef94979c0665d060ee387c2346639ce8fcb92dcf debuginfo(build-id) = efe19fd11e2b3bcd278e4f5a16ff75ee1d0d69d4 debuginfo(build-id) = f0c4df90d07e2881fba614eaf64d9c7913dcf41e debuginfo(build-id) = f0d66e51245767212f989898d867c2634893bce6 debuginfo(build-id) = f0e7886d40bda1db2b3f9344fd1a2f07a0bf1959 debuginfo(build-id) = f1d951beb091ece67c106491846f9ca230eebc55 debuginfo(build-id) = f24ccc8483b99db9189023eac3bad47e830a1592 debuginfo(build-id) = f2accde545ff332518082b09fba95fadeb5d3332 debuginfo(build-id) = f2e1da9a8baa6cea3eaa160cadda75c8b8086612 debuginfo(build-id) = f303c9c00050c3f164b0179cb8d9c8fd8bf001c5 debuginfo(build-id) = f3514b4ff50ac2012c030bf993b44036b7aeb23f debuginfo(build-id) = f36001d8e86d068da202f46599ca1d0fee03d75a debuginfo(build-id) = f3afb2f82235b990034ad7cf8fa2fda82bddd1f5 debuginfo(build-id) = f402325d62904ab36e49ae2ff90aae98d9befc2f debuginfo(build-id) = f46334e31963b30dbf11a7b3a2b1a1d12d190120 debuginfo(build-id) = f57451f3e5d2ed78faac143a40f1402af8d8d642 debuginfo(build-id) = f6141ababb7b381effa6093e64962446e01dc30a debuginfo(build-id) = f6e1e05af96cf62a622dc45c134e5021f68eec59 debuginfo(build-id) = f6f442b418db7ebf1363e6c76d9ac011f11b8059 debuginfo(build-id) = f709318162ac9b5e383ad84e52d8769b4a50249e debuginfo(build-id) = f71dda6383f619e0b3ca351e83f2140986e00d22 debuginfo(build-id) = f73e213767215d5f7d4b075976596c0704fb2741 debuginfo(build-id) = f7dc5e1f1151160f2f794aa72aceb5e73ca93269 debuginfo(build-id) = f80e6d4b032727c41621ae3490ef4137ada97f13 debuginfo(build-id) = f82555a53b3a8997bb0fba62f350c43aef4879ef debuginfo(build-id) = f82ac2052d0bc5ca817b4ed7c893a068f1e74fff debuginfo(build-id) = f833df7b1376531a0cc7e4e61f952f514d9706ab debuginfo(build-id) = f8acb2454a5a8b97a42bf89ee97273fc8de56910 debuginfo(build-id) = f94f28880d37fbdeed470a80615bedb36f0a4c2d debuginfo(build-id) = f95ecd4a97eb5fe78f1a7ae74c6872271f03b272 debuginfo(build-id) = f9d15485cc135ca8600e91ea3ce590aee8ad25b0 debuginfo(build-id) = fa2b2094d8cbd3cfb0f100eafeaea1fc54cd53c6 debuginfo(build-id) = fa674aee17defe527299ef22f4c20416cce9998b debuginfo(build-id) = fa85cdffd441372f0fe3b4f0f6e6b8c9d88f6339 debuginfo(build-id) = face0b48aa1675087076cea805b068a725a3fba6 debuginfo(build-id) = fb1426305156e6484f84951c97ef128cfdfd9eb3 debuginfo(build-id) = fb1c4e750e1f64d52292fdeb3c899ac141773829 debuginfo(build-id) = fc6e127731484beff92ff32dd9a91eb7b7116d59 debuginfo(build-id) = fd55bf4483cb99e5612575271a37c932c66084ab debuginfo(build-id) = fda4138227c0bfc70e75bcd5f3da37ec4545f929 debuginfo(build-id) = fddd09b8793d1dbf39ff33202bb8548bc0ed1ed4 debuginfo(build-id) = fe6c8a4b49be29be0b6a5424649e0635fa82c98e debuginfo(build-id) = ff0de497b9e7eb435a6a0c92206b11089836d68a debuginfo(build-id) = ff4cd504c67de75dc8bd0872681e83e186a34fe0 debuginfo(build-id) = ffcc7d9dae3c03136e7fa467775d5b1a42b8941c debuginfo(build-id) = ffdb7f523fcd229ce6d606d9d191a00823328010 ucsc-kent-utils-debuginfo = 492-1.fc43 ucsc-kent-utils-debuginfo(x86-64) = 492-1.fc43 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.fc43 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.fc43.x86_64.rpm Wrote: /builddir/build/RPMS/ucsc-kent-utils-492-1.fc43.x86_64.rpm Wrote: /builddir/build/RPMS/ucsc-kent-utils-debuginfo-492-1.fc43.x86_64.rpm Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.O8P4MY + umask 022 + cd /builddir/build/BUILD/ucsc-kent-utils-492-build + test -d /builddir/build/BUILD/ucsc-kent-utils-492-build + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w /builddir/build/BUILD/ucsc-kent-utils-492-build + rm -rf /builddir/build/BUILD/ucsc-kent-utils-492-build + RPM_EC=0 ++ jobs -p + exit 0 Finish: rpmbuild ucsc-kent-utils-492-1.fc43.src.rpm Finish: build phase for ucsc-kent-utils-492-1.fc43.src.rpm INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-43-x86_64-1781120563.631826/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.fc43.src.rpm) Config(child) 32 minutes 40 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", "epoch": null, "version": "492", "release": "1.fc43", "arch": "x86_64" }, { "name": "ucsc-kent-utils-debuginfo", "epoch": null, "version": "492", "release": "1.fc43", "arch": "x86_64" }, { "name": "ucsc-kent-utils-debugsource", "epoch": null, "version": "492", "release": "1.fc43", "arch": "x86_64" }, { "name": "ucsc-kent-utils", "epoch": null, "version": "492", "release": "1.fc43", "arch": "src" } ] } RPMResults finished