Warning: Permanently added '54.234.80.53' (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/11058182-fedora-rawhide-x86_64 --chroot fedora-rawhide-x86_64 Version: 1.10 PID: 40867 Logging PID: 40869 Task: {'allow_user_ssh': False, 'appstream': False, 'background': True, 'build_id': 11058182, 'buildroot_pkgs': ['fedora-clang-default-cc'], 'chroot': 'fedora-rawhide-x86_64', 'enable_net': False, 'fedora_review': False, 'git_hash': '49f27db1f1a2a0ebbc1c4e903458121869bcfc42', 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/@fedora-llvm-team/clang-monthly-fedora-rebuild/htslib', 'isolation': 'default', 'memory_reqs': 2048, 'package_name': 'htslib', 'package_version': '1.24-1', 'project_dirname': 'clang-monthly-fedora-rebuild', 'project_name': 'clang-monthly-fedora-rebuild', 'project_owner': '@fedora-llvm-team', 'repo_priority': None, 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/@fedora-llvm-team/clang-monthly-fedora-rebuild/fedora-rawhide-x86_64/', 'id': 'copr_base', 'name': 'Copr repository', 'priority': None, 'repo_gpgcheck': False}, {'baseurl': 'https://download.copr.fedorainfracloud.org/results/tstellar/fedora-clang-default-cc/fedora-rawhide-x86_64/', 'id': 'copr_tstellar_fedora_clang_default_cc', 'name': 'Additional repo copr_tstellar_fedora_clang_default_cc', 'repo_gpgcheck': False}, {'baseurl': 'https://download.copr.fedorainfracloud.org/results/@fedora-llvm-team/llvm-snapshots-big-merge-20260928/fedora-rawhide-x86_64/', 'id': 'copr_fedora_llvm_team_llvm_snapshots_big_merge_20260928', 'module_hotfixes': True, 'name': 'Additional repo copr_fedora_llvm_team_llvm_snapshots_big_merge_20260928', 'repo_gpgcheck': False}], 'sandbox': '@fedora-llvm-team/clang-monthly-fedora-rebuild--kkleine', 'source_json': {}, 'source_type': None, 'ssh_public_keys': None, 'storage': 0, 'submitter': 'kkleine', 'tags': [], 'task_id': '11058182-fedora-rawhide-x86_64', 'timeout': 90000, 'uses_devel_repo': False, 'with_opts': [], 'without_opts': ['toolchain_clang', 'clang_lto']} Running: git clone https://copr-dist-git.fedorainfracloud.org/git/@fedora-llvm-team/clang-monthly-fedora-rebuild/htslib /var/lib/copr-rpmbuild/workspace/workdir-4354l277/htslib --depth 500 --no-single-branch --recursive cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/@fedora-llvm-team/clang-monthly-fedora-rebuild/htslib', '/var/lib/copr-rpmbuild/workspace/workdir-4354l277/htslib', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-4354l277/htslib'... Running: git checkout 49f27db1f1a2a0ebbc1c4e903458121869bcfc42 -- cmd: ['git', 'checkout', '49f27db1f1a2a0ebbc1c4e903458121869bcfc42', '--'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-4354l277/htslib rc: 0 stdout: stderr: Note: switching to '49f27db1f1a2a0ebbc1c4e903458121869bcfc42'. 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 49f27db automatic import of htslib Running: dist-git-client sources cmd: ['dist-git-client', 'sources'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-4354l277/htslib 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 htslib-1.24.tar.bz2 INFO: Reading stdout from command: curl --help all INFO: Calling: curl -H Pragma: -H 'Accept-Encoding: identity' -o htslib-1.24.tar.bz2 --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/@fedora-llvm-team/clang-monthly-fedora-rebuild/htslib/htslib-1.24.tar.bz2/md5/7e4cb4e4c18440b54bd043fcdc3c72e9/htslib-1.24.tar.bz2 % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 4.77M 100 4.77M 0 0 63.70M 0 0 INFO: Reading stdout from command: md5sum htslib-1.24.tar.bz2 tail: /var/lib/copr-rpmbuild/main.log: file truncated Running (timeout=90000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-4354l277/htslib/htslib.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-4354l277/htslib --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1790841053.256992 -r /var/lib/copr-rpmbuild/results/configs/child.cfg --without toolchain_clang --without clang_lto INFO: mock.py version 6.8 starting (python version = 3.14.5, NVR = mock-6.8-1.fc44), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-4354l277/htslib/htslib.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-4354l277/htslib --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1790841053.256992 -r /var/lib/copr-rpmbuild/results/configs/child.cfg --without toolchain_clang --without clang_lto 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-4354l277/htslib/htslib.spec) Config(fedora-rawhide-x86_64) Start: clean chroot Finish: clean chroot Mock Version: 6.8 INFO: Mock Version: 6.8 Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1790841053.256992/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata INFO: Guessed host environment type: unknown INFO: Using container image: registry.fedoraproject.org/fedora:rawhide INFO: Pulling image: registry.fedoraproject.org/fedora:rawhide INFO: Tagging container image as mock-bootstrap-80f6aa7c-2301-42cc-9698-a2225ad301ef INFO: Checking that f302ae09c5da88a921a2279f1716b78a40453a136311e1bc90339822f97dd102 image matches host's architecture INFO: Copy content of container f302ae09c5da88a921a2279f1716b78a40453a136311e1bc90339822f97dd102 to /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1790841053.256992/root INFO: mounting f302ae09c5da88a921a2279f1716b78a40453a136311e1bc90339822f97dd102 with podman image mount INFO: image f302ae09c5da88a921a2279f1716b78a40453a136311e1bc90339822f97dd102 as /var/lib/containers/storage/overlay/1d1ad910df2ed4d61ba1e22d635a40fe26ed19598464fab648317385c585d8e1/merged INFO: umounting image f302ae09c5da88a921a2279f1716b78a40453a136311e1bc90339822f97dd102 (/var/lib/containers/storage/overlay/1d1ad910df2ed4d61ba1e22d635a40fe26ed19598464fab648317385c585d8e1/merged) with podman image umount INFO: Removing image mock-bootstrap-80f6aa7c-2301-42cc-9698-a2225ad301ef INFO: Package manager dnf5 detected and used (fallback) INFO: Not updating bootstrap chroot, bootstrap_image_ready=True Start(bootstrap): creating root cache Finish(bootstrap): creating root cache Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-1790841053.256992/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin INFO: Package manager dnf5 detected and used (direct choice) INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-6.1.0-1.fc46.x86_64 rpm-sequoia-1.10.3-1.fc46.x86_64 dnf5-5.4.6.0-1.fc46.x86_64 dnf5-plugins-5.4.6.0-1.fc46.x86_64 Start: installing minimal buildroot with dnf5 Updating and loading repositories: fedora 100% | 84.1 KiB/s | 24.5 KiB | 00m00s Additional repo copr_tstellar_fedora_c 100% | 10.6 KiB/s | 1.5 KiB | 00m00s Additional repo copr_fedora_llvm_team_ 100% | 10.9 KiB/s | 1.5 KiB | 00m00s Copr repository 100% | 10.7 KiB/s | 1.5 KiB | 00m00s Repositories loaded. Package Arch Version Repository Size Installing group/module packages: bash x86_64 0:5.3.15-2.fc46 copr_base 8.5 MiB bzip2 x86_64 0:1.0.8-24.fc46 copr_base 90.6 KiB coreutils x86_64 0:9.12-1.fc46 fedora 6.3 MiB cpio x86_64 0:2.15-10.fc46 copr_base 1.1 MiB diffutils x86_64 0:3.12-6.fc45 fedora 1.6 MiB fedora-release-common noarch 0:46-0.1 fedora 4.6 KiB findutils x86_64 1:4.11.0-2.fc46 copr_base 2.0 MiB gawk x86_64 0:5.4.1-1.fc46 copr_base 2.2 MiB glibc-minimal-langpack x86_64 0:2.44.9000-4.fc46 fedora 0.0 B grep x86_64 0:3.12-4.fc45 fedora 1.0 MiB gzip x86_64 0:1.14-4.fc46 copr_base 409.6 KiB info x86_64 0:7.3-3.fc46 copr_base 395.6 KiB patch x86_64 0:2.8-6.fc46 fedora 226.6 KiB redhat-rpm-config noarch 0:345-4.fc46 fedora 184.2 KiB rpm-build x86_64 0:6.1.0-1.fc46 fedora 312.1 KiB sed x86_64 0:4.10-2.fc45 fedora 866.5 KiB shadow-utils x86_64 2:4.20.0-1.fc46 copr_base 4.0 MiB tar x86_64 2:1.35-9.fc45 fedora 3.0 MiB unzip x86_64 0:6.0-71.fc45 fedora 441.8 KiB util-linux x86_64 0:2.42.4-2.fc46 fedora 3.7 MiB which x86_64 0:2.25-2.fc46 copr_base 79.0 KiB xz x86_64 1:5.8.4-1.fc46 fedora 1.4 MiB Installing dependencies: R-srpm-macros noarch 0:1.3.7-3.fc45 fedora 3.5 KiB add-determinism x86_64 0:0.7.3-3.fc45 fedora 2.2 MiB alternatives x86_64 0:1.33-6.fc46 copr_base 61.9 KiB ansible-srpm-macros noarch 0:1-22.fc45 fedora 35.7 KiB audit-libs x86_64 0:4.2.1-2.fc45 fedora 390.5 KiB binutils x86_64 0:2.47.50-12.fc46 fedora 24.4 MiB build-reproducibility-srpm-macros noarch 0:0.7.3-3.fc45 fedora 1.2 KiB bzip2-libs x86_64 0:1.0.8-24.fc46 copr_base 92.3 KiB ca-certificates noarch 0:2026.2.90_v9.0.317-1.fc46 fedora 2.6 MiB cmake-srpm-macros noarch 0:4.3.0-5.fc45 fedora 524.0 B coreutils-common x86_64 0:9.12-1.fc46 fedora 11.5 MiB crypto-policies noarch 0:20260713-2.gitc42da77.fc45 fedora 134.3 KiB curl x86_64 0:8.23.0~rc2-1.fc46 fedora 485.6 KiB cyrus-sasl-lib x86_64 0:2.1.28-37.fc45 fedora 2.3 MiB debugedit x86_64 0:5.3-3.fc46 copr_base 220.3 KiB dwz x86_64 0:0.17-3.fc45 fedora 291.1 KiB ed x86_64 0:1.22.6-1.fc46 copr_base 166.9 KiB efi-srpm-macros noarch 0:6-9.fc45 fedora 40.3 KiB elfutils x86_64 0:0.196-1.fc46 fedora 3.2 MiB elfutils-debuginfod-client x86_64 0:0.196-1.fc46 fedora 79.9 KiB elfutils-libelf x86_64 0:0.196-1.fc46 fedora 1.4 MiB elfutils-libs x86_64 0:0.196-1.fc46 fedora 719.6 KiB erlang-srpm-macros noarch 0:0.3.11-2.fc45 fedora 1.9 KiB fedora-gpg-keys noarch 0:46-0.3 fedora 130.3 KiB fedora-release noarch 0:46-0.1 fedora 0.0 B fedora-release-identity-basic noarch 0:46-0.1 fedora 664.0 B fedora-repos noarch 0:46-0.3 fedora 4.9 KiB fedora-repos-rawhide noarch 0:46-0.3 fedora 2.2 KiB file x86_64 0:5.48-3.fc46 fedora 101.9 KiB file-libs x86_64 0:5.48-3.fc46 fedora 12.3 MiB filesystem x86_64 0:3.18-59.fc45 fedora 112.0 B filesystem-srpm-macros noarch 0:3.18-59.fc45 fedora 38.2 KiB fips-provider x86_64 0:1.5.3-1.fc46 fedora 4.8 MiB fonts-srpm-macros noarch 1:5.0.0-4.fc45 fedora 55.8 KiB forge-srpm-macros noarch 0:0.4.0-5.fc45 fedora 38.9 KiB fpc-srpm-macros noarch 0:1.3-17.fc45 fedora 144.0 B gap-srpm-macros noarch 0:2-3.fc45 fedora 2.1 KiB gdb-minimal x86_64 0:17.2-6.fc46 fedora 14.2 MiB gdbm-libs x86_64 1:1.23-12.fc46 copr_base 133.7 KiB ghc-srpm-macros noarch 0:1.10-2.fc45 fedora 792.0 B glibc x86_64 0:2.44.9000-4.fc46 fedora 7.2 MiB glibc-common x86_64 0:2.44.9000-4.fc46 fedora 1.0 MiB glibc-gconv-extra x86_64 0:2.44.9000-4.fc46 fedora 7.7 MiB gmp x86_64 1:6.3.0-6.fc45 fedora 815.2 KiB gnat-srpm-macros noarch 0:7-3.fc45 fedora 1.0 KiB gnome-srpm-macros noarch 0:1.0-2.fc45 fedora 3.5 KiB gnulib-l10n noarch 0:20241231-4.fc46 copr_base 655.0 KiB gnupg2 x86_64 0:2.4.9-18.fc46 copr_base 6.6 MiB gnupg2-dirmngr x86_64 0:2.4.9-18.fc46 copr_base 680.0 KiB gnupg2-gpg-agent x86_64 0:2.4.9-18.fc46 copr_base 729.9 KiB gnupg2-gpgconf x86_64 0:2.4.9-18.fc46 copr_base 266.9 KiB gnupg2-keyboxd x86_64 0:2.4.9-18.fc46 copr_base 222.2 KiB gnupg2-verify x86_64 0:2.4.9-18.fc46 copr_base 399.2 KiB gnutls x86_64 0:3.8.13-5.fc46 fedora 3.8 MiB go-srpm-macros noarch 0:3.8.0-3.fc45 fedora 61.9 KiB gpgverify noarch 0:2.2-5.fc45 fedora 8.7 KiB ima-evm-utils-libs x86_64 0:1.6.2-12.fc46 copr_base 56.4 KiB jansson x86_64 0:2.14-5.fc46 copr_base 101.1 KiB java-srpm-macros noarch 0:1-9.fc45 fedora 870.0 B json-c x86_64 0:0.18-9.fc46 copr_base 86.4 KiB kernel-srpm-macros noarch 0:1.0-30.fc45 fedora 1.9 KiB keyutils-libs x86_64 0:1.6.3-8.fc46 copr_base 50.0 KiB krb5-libs x86_64 0:1.22.2-9.fc45 fedora 2.4 MiB libacl x86_64 0:2.4.0-2.fc45 fedora 43.9 KiB libarchive x86_64 0:3.8.9-2.fc46 fedora 1.0 MiB libassuan x86_64 0:2.5.7-6.fc46 copr_base 168.0 KiB libattr x86_64 0:2.6.0-2.fc46 copr_base 24.1 KiB libblkid x86_64 0:2.42.4-2.fc46 fedora 282.3 KiB libbrotli x86_64 0:1.2.0-6.fc46 copr_base 876.8 KiB libcap x86_64 0:2.78-2.fc45 fedora 208.2 KiB libcap-ng x86_64 0:0.9.6-1.fc46 fedora 68.8 KiB libcbor x86_64 0:0.14.0-3.fc45 fedora 83.5 KiB libcom_err x86_64 0:1.47.4-2.fc46 copr_base 62.8 KiB libcurl x86_64 0:8.23.0~rc2-1.fc46 fedora 1.1 MiB libeconf x86_64 0:0.7.9-4.fc46 copr_base 69.0 KiB libevent x86_64 0:2.1.13-1.fc46 fedora 980.7 KiB libfdisk x86_64 0:2.42.4-2.fc46 fedora 392.3 KiB libffi x86_64 0:3.8.0-1.fc46 fedora 95.5 KiB libfido2 x86_64 0:1.17.0-5.fc46 copr_base 257.4 KiB libfsverity x86_64 0:1.7-4.fc45 fedora 24.4 KiB libgcc x86_64 0:16.2.1-2.fc46.1 fedora 270.7 KiB libgcrypt x86_64 0:1.12.4-1.fc46 fedora 1.7 MiB libgomp x86_64 0:16.2.1-2.fc46.1 fedora 577.5 KiB libgpg-error x86_64 0:1.61-2.fc46 copr_base 966.4 KiB libidn2 x86_64 0:2.3.8-4.fc46 copr_base 556.3 KiB libksba x86_64 0:1.8.1-1.fc46 copr_base 428.9 KiB liblastlog2 x86_64 0:2.42.4-2.fc46 fedora 37.6 KiB libmount x86_64 0:2.42.4-2.fc46 fedora 408.9 KiB libnghttp2 x86_64 0:1.69.0-6.fc46 fedora 166.1 KiB libnghttp3 x86_64 0:1.18.0-1.fc46 copr_base 183.7 KiB libpfm x86_64 0:4.13.0-23.fc45 fedora 1.7 MiB libpkgconf x86_64 0:2.5.1-2.fc46 copr_base 85.8 KiB libpsl x86_64 0:0.23.3-1.fc46 fedora 80.4 KiB libselinux x86_64 0:3.11-5.fc46 fedora 205.2 KiB libselinux-utils x86_64 0:3.11-5.fc46 fedora 306.0 KiB libsemanage x86_64 0:3.11-4.fc46 fedora 320.6 KiB libsepol x86_64 0:3.11-2.fc46 copr_base 944.4 KiB libsmartcols x86_64 0:2.42.4-2.fc46 fedora 188.5 KiB libssh x86_64 0:0.12.2-1.fc45 fedora 725.7 KiB libssh-config noarch 0:0.12.2-1.fc45 fedora 277.0 B libstdc++ x86_64 0:16.2.1-2.fc46.1 fedora 3.1 MiB libtasn1 x86_64 0:4.21.0-2.fc46 copr_base 188.6 KiB libtool-ltdl x86_64 0:2.6.2-1.fc46 fedora 70.0 KiB libunistring x86_64 0:1.1-12.fc46 copr_base 1.7 MiB libusb1 x86_64 0:1.0.30-2.fc45 fedora 180.1 KiB libuuid x86_64 0:2.42.4-2.fc46 fedora 37.2 KiB libverto x86_64 0:0.3.2-13.fc45 fedora 25.3 KiB libxcrypt x86_64 0:4.5.2-4.fc45 fedora 293.2 KiB libxml2 x86_64 0:2.15.4-1.fc46 fedora 1.7 MiB libzstd x86_64 0:1.5.7-6.fc46 copr_base 963.2 KiB linkdupes x86_64 0:0.7.3-3.fc45 fedora 782.1 KiB lua-libs x86_64 0:5.5.1-2.fc46 fedora 298.0 KiB lua-srpm-macros noarch 0:1-18.fc45 fedora 1.3 KiB lz4-libs x86_64 0:1.10.0-5.fc46 copr_base 173.1 KiB meson-srpm-macros noarch 0:1.12.1-2.fc46 fedora 1.7 KiB mpfr x86_64 0:4.2.2-4.fc45 fedora 849.2 KiB ncurses-base noarch 0:6.6-3.fc46 copr_base 329.7 KiB ncurses-libs x86_64 0:6.6-3.fc46 copr_base 959.0 KiB nettle x86_64 0:4.0-5.fc45 fedora 801.9 KiB ngtcp2 x86_64 0:1.22.1-3.fc45 fedora 334.3 KiB ngtcp2-crypto-ossl x86_64 0:1.22.1-3.fc45 fedora 51.6 KiB npth x86_64 0:1.8-5.fc46 copr_base 53.3 KiB ocaml-srpm-macros noarch 0:11-4.fc45 fedora 1.9 KiB openblas-srpm-macros noarch 0:2-22.fc45 fedora 112.0 B openldap x86_64 0:2.6.14-1.fc46 fedora 678.9 KiB openssl-libs x86_64 1:4.0.3-1.fc46 fedora 6.7 MiB p11-kit x86_64 0:0.26.5-1.fc46 copr_base 2.6 MiB p11-kit-trust x86_64 0:0.26.5-1.fc46 copr_base 511.9 KiB package-notes-srpm-macros noarch 0:0.20-2.fc45 fedora 1.6 KiB pam-libs x86_64 0:1.7.2-4.fc46 copr_base 134.4 KiB pcre2 x86_64 0:10.47-1.fc46.2 copr_base 765.7 KiB pcre2-syntax noarch 0:10.47-1.fc46.2 copr_base 281.9 KiB perl-srpm-macros noarch 0:1-65.fc45 fedora 861.0 B pkgconf x86_64 0:2.5.1-2.fc46 copr_base 94.8 KiB pkgconf-m4 noarch 0:2.5.1-2.fc46 copr_base 14.3 KiB pkgconf-pkg-config x86_64 0:2.5.1-2.fc46 copr_base 989.0 B policycoreutils x86_64 0:3.11-2.fc46 copr_base 882.1 KiB popt x86_64 0:1.19-11.fc46 copr_base 132.5 KiB publicsuffix-list-dafsa noarch 0:20260624-2.fc45 fedora 71.3 KiB pyproject-srpm-macros noarch 0:1.23.2-1.fc45 fedora 3.4 KiB python-srpm-macros noarch 0:3.15-2.fc45 fedora 51.6 KiB qt5-srpm-macros noarch 0:5.15.18-3.fc45 fedora 500.0 B qt6-srpm-macros noarch 0:6.11.2-1.fc46 fedora 472.0 B readline x86_64 0:8.3-6.fc46 copr_base 535.4 KiB redhat-systemd-presets noarch 0:102-3.fc45 fedora 1.0 KiB redhat-systemd-presets-common noarch 0:102-3.fc45 fedora 16.9 KiB rpm x86_64 0:6.1.0-1.fc46 fedora 3.1 MiB rpm-build-libs x86_64 0:6.1.0-1.fc46 fedora 288.3 KiB rpm-libs x86_64 0:6.1.0-1.fc46 fedora 1.1 MiB rpm-plugin-selinux x86_64 0:6.1.0-1.fc46 fedora 11.9 KiB rpm-sequoia x86_64 0:1.10.3-1.fc46 fedora 2.4 MiB rpm-sign-libs x86_64 0:6.1.0-1.fc46 fedora 39.6 KiB rust-srpm-macros noarch 0:28.5-2.fc45 fedora 5.5 KiB selinux-policy noarch 0:45.20-1.fc46 fedora 32.1 KiB selinux-policy-targeted noarch 0:45.20-1.fc46 fedora 19.0 MiB setup noarch 0:2.15.1-2.fc45 fedora 725.6 KiB sqlite-libs x86_64 0:3.53.4-1.fc45 fedora 1.6 MiB systemd-libs x86_64 0:262-3.fc46 fedora 2.8 MiB systemd-standalone-sysusers x86_64 0:262-3.fc46 fedora 981.3 KiB tpm2-tss x86_64 0:4.2.0-1.fc46 copr_base 1.7 MiB tree-sitter-srpm-macros noarch 0:0.4.6-2.fc45 fedora 8.6 KiB util-linux-core x86_64 0:2.42.4-2.fc46 fedora 1.5 MiB xxhash-libs x86_64 0:0.8.4-1.fc46 fedora 94.0 KiB xz-libs x86_64 1:5.8.4-1.fc46 fedora 221.7 KiB zig-srpm-macros noarch 0:1-9.fc45 fedora 1.3 KiB zip x86_64 0:3.0-46.fc45 fedora 694.1 KiB zlib-ng-compat x86_64 0:2.3.3-6.fc46 copr_base 173.4 KiB zstd x86_64 0:1.5.7-6.fc46 copr_base 491.6 KiB Installing groups: Buildsystem building group Transaction Summary: Installing: 190 packages Total size of inbound packages is 71 MiB. Need to download 0 B. After this operation, 231 MiB extra will be used (install 231 MiB, remove 0 B). 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B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [190/190] Total 100% | 0.0 B/s | 0.0 B | 00m00s Running transaction Importing OpenPGP key 0x91211FCE: UserID : "Fedora (46) " Fingerprint: D924B10D3E810DABDD8B56B596E7E91491211FCE From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-46-primary The key was successfully imported. Importing OpenPGP key 0x91211FCE: UserID : "Fedora (46) " Fingerprint: D924B10D3E810DABDD8B56B596E7E91491211FCE From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-46-primary The key was successfully imported. Importing OpenPGP key 0xF577861E: UserID : "Fedora (45) " Fingerprint: 4F50A6114CD5C6976A7F1179655A4B02F577861E From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-45-primary The key was successfully imported. Importing OpenPGP key 0x9488FB64: UserID : "Fedora (47) " Fingerprint: B2E766FA50CA6FA2D5ED06FC09D879E09488FB64 From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-47-primary The key was successfully imported. [ 1/192] Verify package files 100% | 618.0 B/s | 190.0 B | 00m00s >>> Running %pretrans scriptlet: filesystem-0:3.18-59.fc45.x86_64 >>> Finished %pretrans scriptlet: filesystem-0:3.18-59.fc45.x86_64 >>> [RPM] /var/lib/mock/fedora-rawhide-x86_64-1790841053.256992/root/var/cache/dnf/copr_base-64ab9e188b99823d/packages/bzip2-1.0.8-24.fc46.x86_64.rpm: Header OpenPGP V4 RSA/SHA256 signature, key ID 5291f7fa5c4b3009: NOKEY >>> [RPM] failed to open /var/lib/mock/fedora-rawhide-x86_64-1790841053.256992/root/etc/group for id/name lookup: No such file or directory [ 2/192] Prepare transaction 100% | 2.9 KiB/s | 190.0 B | 00m00s [ 3/192] Installing libgcc-0:16.2.1-2. 100% | 133.0 MiB/s | 272.4 KiB | 00m00s [ 4/192] Installing redhat-systemd-pre 100% | 0.0 B/s | 1.5 KiB | 00m00s [ 5/192] Installing redhat-systemd-pre 100% | 0.0 B/s | 18.1 KiB | 00m00s [ 6/192] Installing libssh-config-0:0. 100% | 0.0 B/s | 816.0 B | 00m00s [ 7/192] Installing publicsuffix-list- 100% | 0.0 B/s | 72.0 KiB | 00m00s [ 8/192] Installing fedora-release-ide 100% | 0.0 B/s | 920.0 B | 00m00s [ 9/192] Installing fedora-gpg-keys-0: 100% | 44.4 MiB/s | 181.7 KiB | 00m00s [ 10/192] Installing fedora-repos-rawhi 100% | 0.0 B/s | 2.5 KiB | 00m00s [ 11/192] Installing fedora-repos-0:46- 100% | 0.0 B/s | 5.9 KiB | 00m00s [ 12/192] Installing fedora-release-com 100% | 7.8 MiB/s | 8.0 KiB | 00m00s [ 13/192] Installing fedora-release-0:4 100% | 15.1 KiB/s | 124.0 B | 00m00s >>> Running sysusers scriptlet: setup-0:2.15.1-2.fc45.noarch >>> Finished sysusers scriptlet: setup-0:2.15.1-2.fc45.noarch >>> Scriptlet output: >>> Creating group 'adm' with GID 4. >>> Creating group 'audio' with GID 63. >>> Creating group 'cdrom' with GID 11. >>> Creating group 'clock' with GID 103. >>> Creating group 'dialout' with GID 18. >>> Creating group 'disk' with GID 6. >>> Creating group 'floppy' with GID 19. >>> Creating group 'ftp' with GID 50. >>> Creating group 'games' with GID 20. >>> Creating group 'input' with GID 104. >>> Creating group 'kmem' with GID 9. >>> Creating group 'kvm' with GID 36. >>> Creating group 'lock' with GID 54. >>> Creating group 'lp' with GID 7. >>> Creating group 'mail' with GID 12. >>> Creating group 'man' with GID 15. >>> Creating group 'mem' with GID 8. >>> Creating group 'nobody' with GID 65534. >>> Creating group 'render' with GID 105. >>> Creating group 'root' with GID 0. >>> Creating group 'sgx' with GID 106. >>> Creating group 'sys' with GID 3. >>> Creating group 'tape' with GID 33. >>> Creating group 'tty' with GID 5. >>> Creating group 'users' with GID 100. >>> Creating group 'utmp' with GID 22. >>> Creating group 'video' with GID 39. >>> Creating group 'wheel' with GID 10. >>> Creating user 'adm' (adm) with UID 3 and GID 4. >>> Creating group 'bin' with GID 1. >>> Creating user 'bin' (bin) with UID 1 and GID 1. >>> Creating group 'daemon' with GID 2. >>> Creating user 'daemon' (daemon) with UID 2 and GID 2. >>> Creating user 'ftp' (FTP User) with UID 14 and GID 50. >>> Creating user 'games' (games) with UID 12 and GID 100. >>> Creating user 'halt' (halt) with UID 7 and GID 0. >>> Creating user 'lp' (lp) with UID 4 and GID 7. >>> Creating user 'mail' (mail) with UID 8 and GID 12. >>> Creating user 'nobody' (Kernel Overflow User) with UID 65534 and GID 65534. >>> Creating user 'operator' (operator) with UID 11 and GID 0. >>> Creating user 'root' (Super User) with UID 0 and GID 0. >>> Creating user 'shutdown' (shutdown) with UID 6 and GID 0. >>> Creating user 'sync' (sync) with UID 5 and GID 0. >>> [ 14/192] Installing setup-0:2.15.1-2.f 100% | 35.7 MiB/s | 731.3 KiB | 00m00s >>> [RPM] /etc/hosts created as /etc/hosts.rpmnew [ 15/192] Installing filesystem-0:3.18- 100% | 2.3 MiB/s | 253.6 KiB | 00m00s [ 16/192] Installing gnulib-l10n-0:2024 100% | 161.6 MiB/s | 661.9 KiB | 00m00s [ 17/192] Installing coreutils-common-0 100% | 350.3 MiB/s | 11.6 MiB | 00m00s [ 18/192] Installing pcre2-syntax-0:10. 100% | 277.7 MiB/s | 284.3 KiB | 00m00s [ 19/192] Installing pkgconf-m4-0:2.5.1 100% | 0.0 B/s | 14.7 KiB | 00m00s [ 20/192] Installing ncurses-base-0:6.6 100% | 69.4 MiB/s | 355.3 KiB | 00m00s [ 21/192] Installing glibc-common-0:2.4 100% | 41.4 MiB/s | 1.0 MiB | 00m00s [ 22/192] Installing glibc-gconv-extra- 100% | 251.2 MiB/s | 7.8 MiB | 00m00s [ 23/192] Installing glibc-0:2.44.9000- 100% | 138.1 MiB/s | 7.2 MiB | 00m00s [ 24/192] Installing ncurses-libs-0:6.6 100% | 188.4 MiB/s | 964.9 KiB | 00m00s [ 25/192] Installing bash-0:5.3.15-2.fc 100% | 180.4 MiB/s | 8.5 MiB | 00m00s [ 26/192] Installing glibc-minimal-lang 100% | 0.0 B/s | 124.0 B | 00m00s [ 27/192] Installing zlib-ng-compat-0:2 100% | 170.1 MiB/s | 174.2 KiB | 00m00s [ 28/192] Installing bzip2-libs-0:1.0.8 100% | 91.2 MiB/s | 93.4 KiB | 00m00s [ 29/192] Installing libgpg-error-0:1.6 100% | 43.2 MiB/s | 972.2 KiB | 00m00s [ 30/192] Installing readline-0:8.3-6.f 100% | 262.5 MiB/s | 537.6 KiB | 00m00s [ 31/192] Installing libstdc++-0:16.2.1 100% | 385.8 MiB/s | 3.1 MiB | 00m00s [ 32/192] Installing libzstd-0:1.5.7-6. 100% | 314.0 MiB/s | 964.5 KiB | 00m00s [ 33/192] Installing elfutils-libelf-0: 100% | 360.7 MiB/s | 1.4 MiB | 00m00s [ 34/192] Installing libgcrypt-0:1.12.4 100% | 333.2 MiB/s | 1.7 MiB | 00m00s [ 35/192] Installing libassuan-0:2.5.7- 100% | 165.9 MiB/s | 169.8 KiB | 00m00s [ 36/192] Installing libacl-0:2.4.0-2.f 100% | 0.0 B/s | 44.7 KiB | 00m00s [ 37/192] Installing gmp-1:6.3.0-6.fc45 100% | 266.1 MiB/s | 817.4 KiB | 00m00s [ 38/192] Installing systemd-libs-0:262 100% | 346.3 MiB/s | 2.8 MiB | 00m00s [ 39/192] Installing libuuid-0:2.42.4-2 100% | 0.0 B/s | 38.2 KiB | 00m00s [ 40/192] Installing xz-libs-1:5.8.4-1. 100% | 217.6 MiB/s | 222.8 KiB | 00m00s [ 41/192] Installing popt-0:1.19-11.fc4 100% | 67.9 MiB/s | 139.1 KiB | 00m00s [ 42/192] Installing sqlite-libs-0:3.53 100% | 323.8 MiB/s | 1.6 MiB | 00m00s [ 43/192] Installing npth-0:1.8-5.fc46. 100% | 0.0 B/s | 54.4 KiB | 00m00s [ 44/192] Installing elfutils-libs-0:0. 100% | 352.2 MiB/s | 721.3 KiB | 00m00s [ 45/192] Installing libblkid-0:2.42.4- 100% | 276.6 MiB/s | 283.3 KiB | 00m00s [ 46/192] Installing libsepol-0:3.11-2. 100% | 307.7 MiB/s | 945.4 KiB | 00m00s [ 47/192] Installing gnupg2-gpgconf-0:2 100% | 9.7 MiB/s | 269.0 KiB | 00m00s [ 48/192] Installing crypto-policies-0: 100% | 31.2 MiB/s | 159.5 KiB | 00m00s [ 49/192] Installing libxcrypt-0:4.5.2- 100% | 144.5 MiB/s | 295.9 KiB | 00m00s [ 50/192] Installing pcre2-0:10.47-1.fc 100% | 249.7 MiB/s | 767.1 KiB | 00m00s [ 51/192] Installing libselinux-0:3.11- 100% | 201.6 MiB/s | 206.4 KiB | 00m00s [ 52/192] Installing grep-0:3.12-4.fc45 100% | 40.1 MiB/s | 1.0 MiB | 00m00s [ 53/192] Installing sed-0:4.10-2.fc45. 100% | 38.8 MiB/s | 874.9 KiB | 00m00s [ 54/192] Installing findutils-1:4.11.0 100% | 79.3 MiB/s | 2.0 MiB | 00m00s [ 55/192] Installing libtasn1-0:4.21.0- 100% | 186.0 MiB/s | 190.5 KiB | 00m00s [ 56/192] Installing libunistring-0:1.1 100% | 347.6 MiB/s | 1.7 MiB | 00m00s [ 57/192] Installing libidn2-0:2.3.8-4. 100% | 183.1 MiB/s | 562.5 KiB | 00m00s [ 58/192] Installing json-c-0:0.18-9.fc 100% | 85.6 MiB/s | 87.7 KiB | 00m00s [ 59/192] Installing xz-1:5.8.4-1.fc46. 100% | 57.0 MiB/s | 1.4 MiB | 00m00s [ 60/192] Installing libmount-0:2.42.4- 100% | 200.2 MiB/s | 410.0 KiB | 00m00s [ 61/192] Installing gnupg2-verify-0:2. 100% | 20.6 MiB/s | 400.6 KiB | 00m00s [ 62/192] Installing mpfr-0:4.2.2-4.fc4 100% | 277.0 MiB/s | 850.9 KiB | 00m00s [ 63/192] Installing gawk-0:5.4.1-1.fc4 100% | 87.9 MiB/s | 2.2 MiB | 00m00s [ 64/192] Installing dwz-0:0.17-3.fc45. 100% | 15.0 MiB/s | 292.5 KiB | 00m00s [ 65/192] Installing libksba-0:1.8.1-1. 100% | 210.7 MiB/s | 431.5 KiB | 00m00s [ 66/192] Installing unzip-0:6.0-71.fc4 100% | 21.7 MiB/s | 445.3 KiB | 00m00s [ 67/192] Installing file-libs-0:5.48-3 100% | 587.8 MiB/s | 12.3 MiB | 00m00s [ 68/192] Installing file-0:5.48-3.fc46 100% | 5.3 MiB/s | 103.4 KiB | 00m00s [ 69/192] Installing diffutils-0:3.12-6 100% | 68.0 MiB/s | 1.6 MiB | 00m00s [ 70/192] Installing libsmartcols-0:2.4 100% | 185.2 MiB/s | 189.6 KiB | 00m00s [ 71/192] Installing lua-libs-0:5.5.1-2 100% | 292.4 MiB/s | 299.4 KiB | 00m00s [ 72/192] Installing libeconf-0:0.7.9-4 100% | 69.0 MiB/s | 70.6 KiB | 00m00s [ 73/192] Installing libcap-ng-0:0.9.6- 100% | 69.0 MiB/s | 70.6 KiB | 00m00s [ 74/192] Installing audit-libs-0:4.2.1 100% | 191.9 MiB/s | 393.1 KiB | 00m00s [ 75/192] Installing pam-libs-0:1.7.2-4 100% | 133.6 MiB/s | 136.9 KiB | 00m00s [ 76/192] Installing libcap-0:2.78-2.fc 100% | 10.4 MiB/s | 213.3 KiB | 00m00s [ 77/192] Installing libsemanage-0:3.11 100% | 157.4 MiB/s | 322.4 KiB | 00m00s [ 78/192] Installing libattr-0:2.6.0-2. 100% | 24.5 MiB/s | 25.1 KiB | 00m00s [ 79/192] Installing libffi-0:3.8.0-1.f 100% | 94.6 MiB/s | 96.9 KiB | 00m00s [ 80/192] Installing p11-kit-0:0.26.5-1 100% | 92.1 MiB/s | 2.6 MiB | 00m00s [ 81/192] Installing alternatives-0:1.3 100% | 3.1 MiB/s | 63.4 KiB | 00m00s [ 82/192] Installing p11-kit-trust-0:0. 100% | 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coreutils-0:9.12-1 100% | 144.4 MiB/s | 6.4 MiB | 00m00s [ 96/192] Installing ca-certificates-0: 100% | 2.0 MiB/s | 2.5 MiB | 00m01s [ 97/192] Installing util-linux-0:2.42. 100% | 76.7 MiB/s | 3.8 MiB | 00m00s [ 98/192] Installing policycoreutils-0: 100% | 23.4 MiB/s | 910.5 KiB | 00m00s [ 99/192] Installing selinux-policy-0:4 100% | 1.2 MiB/s | 34.5 KiB | 00m00s [100/192] Installing selinux-policy-tar 100% | 191.8 MiB/s | 15.2 MiB | 00m00s [101/192] Installing gzip-0:1.14-4.fc46 100% | 17.6 MiB/s | 415.1 KiB | 00m00s [102/192] Installing libfsverity-0:1.7- 100% | 24.8 MiB/s | 25.4 KiB | 00m00s [103/192] Installing rpm-sequoia-0:1.10 100% | 349.6 MiB/s | 2.4 MiB | 00m00s [104/192] Installing libevent-0:2.1.13- 100% | 320.5 MiB/s | 984.5 KiB | 00m00s [105/192] Installing ngtcp2-crypto-ossl 100% | 0.0 B/s | 52.5 KiB | 00m00s [106/192] Installing libusb1-0:1.0.30-2 100% | 12.7 MiB/s | 181.8 KiB | 00m00s >>> Running sysusers scriptlet: tpm2-tss-0:4.2.0-1.fc46.x86_64 >>> Finished sysusers scriptlet: tpm2-tss-0:4.2.0-1.fc46.x86_64 >>> Scriptlet output: >>> Creating group 'tss' with GID 59. >>> Creating user 'tss' (Account used for TPM access) with UID 59 and GID 59. >>> [107/192] Installing tpm2-tss-0:4.2.0-1 100% | 241.0 MiB/s | 1.7 MiB | 00m00s [108/192] Installing gnupg2-gpg-agent-0 100% | 23.9 MiB/s | 733.7 KiB | 00m00s [109/192] Installing ima-evm-utils-libs 100% | 56.4 MiB/s | 57.7 KiB | 00m00s [110/192] Installing nettle-0:4.0-5.fc4 100% | 262.0 MiB/s | 805.0 KiB | 00m00s [111/192] Installing gnutls-0:3.8.13-5. 100% | 348.9 MiB/s | 3.8 MiB | 00m00s [112/192] Installing zstd-0:1.5.7-6.fc4 100% | 23.0 MiB/s | 495.2 KiB | 00m00s [113/192] Installing libxml2-0:2.15.4-1 100% | 68.9 MiB/s | 1.7 MiB | 00m00s [114/192] Installing bzip2-0:1.0.8-24.f 100% | 4.9 MiB/s | 95.1 KiB | 00m00s [115/192] Installing add-determinism-0: 100% | 90.0 MiB/s | 2.2 MiB | 00m00s [116/192] Installing build-reproducibil 100% | 0.0 B/s | 1.5 KiB | 00m00s [117/192] Installing filesystem-srpm-ma 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cyrus-sasl-lib-0:2 100% | 89.9 MiB/s | 2.3 MiB | 00m00s [131/192] Installing openldap-0:2.6.14- 100% | 222.2 MiB/s | 682.7 KiB | 00m00s [132/192] Installing gnupg2-dirmngr-0:2 100% | 22.2 MiB/s | 682.8 KiB | 00m00s [133/192] Installing gnupg2-0:2.4.9-18. 100% | 147.8 MiB/s | 6.7 MiB | 00m00s [134/192] Installing gpgverify-0:2.2-5. 100% | 0.0 B/s | 9.4 KiB | 00m00s [135/192] Installing jansson-0:2.14-5.f 100% | 100.1 MiB/s | 102.5 KiB | 00m00s [136/192] Installing systemd-standalone 100% | 43.6 MiB/s | 981.8 KiB | 00m00s [137/192] Installing rpm-libs-0:6.1.0-1 100% | 274.8 MiB/s | 1.1 MiB | 00m00s [138/192] Installing rpm-sign-libs-0:6. 100% | 39.5 MiB/s | 40.5 KiB | 00m00s [139/192] Installing rpm-build-libs-0:6 100% | 282.4 MiB/s | 289.2 KiB | 00m00s [140/192] Installing xxhash-libs-0:0.8. 100% | 93.1 MiB/s | 95.4 KiB | 00m00s [141/192] Installing libverto-0:0.3.2-1 100% | 26.4 MiB/s | 27.1 KiB | 00m00s [142/192] Installing libcbor-0:0.14.0-3 100% | 82.9 MiB/s | 84.9 KiB | 00m00s [143/192] Installing libfido2-0:1.17.0- 100% | 252.8 MiB/s | 258.9 KiB | 00m00s [144/192] Installing libbrotli-0:1.2.0- 100% | 286.2 MiB/s | 879.1 KiB | 00m00s [145/192] Installing libnghttp2-0:1.69. 100% | 163.3 MiB/s | 167.3 KiB | 00m00s [146/192] Installing libnghttp3-0:1.18. 100% | 180.7 MiB/s | 185.1 KiB | 00m00s [147/192] Installing keyutils-libs-0:1. 100% | 50.2 MiB/s | 51.4 KiB | 00m00s [148/192] Installing libcom_err-0:1.47. 100% | 62.5 MiB/s | 64.0 KiB | 00m00s [149/192] Installing krb5-libs-0:1.22.2 100% | 298.4 MiB/s | 2.4 MiB | 00m00s [150/192] Installing libssh-0:0.12.2-1. 100% | 236.9 MiB/s | 727.8 KiB | 00m00s [151/192] Installing libcurl-0:8.23.0~r 100% | 270.5 MiB/s | 1.1 MiB | 00m00s [152/192] Installing elfutils-debuginfo 100% | 4.0 MiB/s | 82.2 KiB | 00m00s [153/192] Installing elfutils-0:0.196-1 100% | 109.5 MiB/s | 3.2 MiB | 00m00s [154/192] Installing binutils-0:2.47.50 100% | 269.1 MiB/s | 24.5 MiB | 00m00s [155/192] Installing gdb-minimal-0:17.2 100% | 221.3 MiB/s | 14.2 MiB | 00m00s [156/192] Installing debugedit-0:5.3-3. 100% | 10.9 MiB/s | 223.6 KiB | 00m00s [157/192] Installing curl-0:8.23.0~rc2- 100% | 16.4 MiB/s | 488.2 KiB | 00m00s [158/192] Installing rpm-0:6.1.0-1.fc46 100% | 59.6 MiB/s | 2.5 MiB | 00m00s [159/192] Installing cmake-srpm-macros- 100% | 0.0 B/s | 804.0 B | 00m00s [160/192] Installing efi-srpm-macros-0: 100% | 40.3 MiB/s | 41.3 KiB | 00m00s [161/192] Installing java-srpm-macros-0 100% | 186.8 KiB/s | 1.1 KiB | 00m00s [162/192] Installing lua-srpm-macros-0: 100% | 0.0 B/s | 1.9 KiB | 00m00s [163/192] Installing tree-sitter-srpm-m 100% | 0.0 B/s | 9.6 KiB | 00m00s [164/192] Installing zig-srpm-macros-0: 100% | 0.0 B/s | 1.9 KiB | 00m00s [165/192] Installing rust-srpm-macros-0 100% | 0.0 B/s | 6.4 KiB | 00m00s [166/192] Installing qt6-srpm-macros-0: 100% | 0.0 B/s | 748.0 B | 00m00s [167/192] Installing qt5-srpm-macros-0: 100% | 0.0 B/s | 776.0 B | 00m00s [168/192] Installing perl-srpm-macros-0 100% | 0.0 B/s | 1.1 KiB | 00m00s [169/192] Installing package-notes-srpm 100% | 0.0 B/s | 2.1 KiB | 00m00s [170/192] Installing openblas-srpm-macr 100% | 0.0 B/s | 392.0 B | 00m00s [171/192] Installing ocaml-srpm-macros- 100% | 0.0 B/s | 2.1 KiB | 00m00s [172/192] Installing meson-srpm-macros- 100% | 0.0 B/s | 1.9 KiB | 00m00s [173/192] Installing kernel-srpm-macros 100% | 0.0 B/s | 2.3 KiB | 00m00s [174/192] Installing gnome-srpm-macros- 100% | 0.0 B/s | 4.1 KiB | 00m00s [175/192] Installing gnat-srpm-macros-0 100% | 0.0 B/s | 1.3 KiB | 00m00s [176/192] Installing ghc-srpm-macros-0: 100% | 0.0 B/s | 1.0 KiB | 00m00s [177/192] Installing gap-srpm-macros-0: 100% | 0.0 B/s | 2.7 KiB | 00m00s [178/192] Installing fpc-srpm-macros-0: 100% | 0.0 B/s | 420.0 B | 00m00s [179/192] Installing ansible-srpm-macro 100% | 35.4 MiB/s | 36.2 KiB | 00m00s [180/192] Installing redhat-rpm-config- 100% | 93.0 MiB/s | 190.4 KiB | 00m00s [181/192] Installing forge-srpm-macros- 100% | 39.3 MiB/s | 40.3 KiB | 00m00s [182/192] Installing rpm-build-0:6.1.0- 100% | 14.3 MiB/s | 322.1 KiB | 00m00s [183/192] Installing erlang-srpm-macros 100% | 2.4 MiB/s | 2.5 KiB | 00m00s [184/192] Installing pyproject-srpm-mac 100% | 0.0 B/s | 4.0 KiB | 00m00s [185/192] Installing fonts-srpm-macros- 100% | 55.7 MiB/s | 57.0 KiB | 00m00s [186/192] Installing go-srpm-macros-0:3 100% | 61.6 MiB/s | 63.0 KiB | 00m00s [187/192] Installing R-srpm-macros-0:1. 100% | 0.0 B/s | 4.4 KiB | 00m00s [188/192] Installing python-srpm-macros 100% | 51.7 MiB/s | 52.9 KiB | 00m00s [189/192] Installing rpm-plugin-selinux 100% | 0.0 B/s | 12.9 KiB | 00m00s [190/192] Installing which-0:2.25-2.fc4 100% | 4.0 MiB/s | 81.2 KiB | 00m00s [191/192] Installing shadow-utils-2:4.2 100% | 110.0 MiB/s | 4.1 MiB | 00m00s [192/192] Installing info-0:7.3-3.fc46. 100% | 48.8 KiB/s | 396.0 KiB | 00m08s Warning: skipped OpenPGP checks for 58 packages from repository: copr_base Complete! Updating and loading repositories: fedora 100% | 153.0 KiB/s | 24.5 KiB | 00m00s Additional repo copr_tstellar_fedora_c 100% | 14.7 KiB/s | 1.5 KiB | 00m00s Additional repo copr_fedora_llvm_team_ 100% | 14.9 KiB/s | 1.5 KiB | 00m00s Copr repository 100% | 14.5 KiB/s | 1.5 KiB | 00m00s Repositories loaded. Package Arch Version Repository Size Installing: fedora-clang-default-cc noarch 0:1-1.fc43 copr_tstellar_fedora_clang_default_cc 17.0 B Installing dependencies: annobin-docs noarch 0:13.32-1.fc46 fedora 99.7 KiB annobin-plugin-gcc x86_64 0:13.32-1.fc46 fedora 724.5 KiB clang x86_64 0:24.0.0~pre20260928.g6909c17f146832-6.fc46 copr_fedora_llvm_team_llvm_snapshots_big_merge_20260928 70.5 MiB clang-libs x86_64 0:24.0.0~pre20260928.g6909c17f146832-6.fc46 copr_fedora_llvm_team_llvm_snapshots_big_merge_20260928 112.2 MiB clang-resource-filesystem x86_64 0:24.0.0~pre20260928.g6909c17f146832-6.fc46 copr_fedora_llvm_team_llvm_snapshots_big_merge_20260928 15.3 KiB compiler-rt x86_64 0:24.0.0~pre20260928.g6909c17f146832-6.fc46 copr_fedora_llvm_team_llvm_snapshots_big_merge_20260928 44.1 MiB cpp x86_64 0:16.2.1-2.fc46.1 fedora 42.6 MiB expat x86_64 0:2.8.3-1.fc46 copr_base 342.1 KiB gcc x86_64 0:16.2.1-2.fc46.1 fedora 121.8 MiB gcc-c++ x86_64 0:16.2.1-2.fc46.1 fedora 46.8 MiB gcc-plugin-annobin x86_64 0:16.2.1-2.fc46.1 fedora 57.1 KiB glibc-devel x86_64 0:2.44.9000-4.fc46 fedora 2.3 MiB kernel-headers x86_64 0:7.3.0-0.rc5.45.fc46 fedora 7.1 MiB libatomic x86_64 0:16.2.1-2.fc46.1 fedora 45.6 KiB libedit x86_64 0:3.1-60.20260512cvs.fc46 copr_base 256.8 KiB libmpc x86_64 0:1.4.1-2.fc46 copr_base 164.7 KiB libomp x86_64 0:24.0.0~pre20260928.g6909c17f146832-6.fc46 copr_fedora_llvm_team_llvm_snapshots_big_merge_20260928 3.3 MiB libstdc++-devel x86_64 0:16.2.1-2.fc46.1 fedora 41.2 MiB libxcrypt-devel x86_64 0:4.5.2-4.fc45 fedora 31.0 KiB lld x86_64 0:24.0.0~pre20260928.g6909c17f146832-6.fc46 copr_fedora_llvm_team_llvm_snapshots_big_merge_20260928 42.8 KiB lld-libs x86_64 0:24.0.0~pre20260928.g6909c17f146832-6.fc46 copr_fedora_llvm_team_llvm_snapshots_big_merge_20260928 6.3 MiB llvm x86_64 0:24.0.0~pre20260928.g6909c17f146832-6.fc46 copr_fedora_llvm_team_llvm_snapshots_big_merge_20260928 135.7 MiB llvm-filesystem x86_64 0:24.0.0~pre20260928.g6909c17f146832-6.fc46 copr_fedora_llvm_team_llvm_snapshots_big_merge_20260928 0.0 B llvm-libs x86_64 0:24.0.0~pre20260928.g6909c17f146832-6.fc46 copr_fedora_llvm_team_llvm_snapshots_big_merge_20260928 150.9 MiB make x86_64 1:4.4.1-13.fc46 copr_base 1.8 MiB mpdecimal x86_64 0:4.0.1-4.fc46 copr_base 249.0 KiB python-pip-wheel noarch 0:26.2.1-1.fc46 fedora 1.3 MiB python3 x86_64 0:3.15.0~rc2-1.fc46 fedora 28.7 KiB python3-libs x86_64 0:3.15.0~rc2-1.fc46 fedora 48.2 MiB tzdata noarch 0:2026c-2.fc46 fedora 1.2 MiB Transaction Summary: Installing: 31 packages Total size of inbound packages is 215 MiB. Need to download 0 B. After this operation, 839 MiB extra will be used (install 839 MiB, remove 0 B). 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-------------------------------------------------------------------------------- [31/31] Total 100% | 0.0 B/s | 0.0 B | 00m00s Running transaction [ 1/33] Verify package files 100% | 34.0 B/s | 31.0 B | 00m01s [ 2/33] Prepare transaction 100% | 659.0 B/s | 31.0 B | 00m00s [ 3/33] Installing libmpc-0:1.4.1-2.fc4 100% | 40.6 MiB/s | 166.4 KiB | 00m00s [ 4/33] Installing libstdc++-devel-0:16 100% | 409.2 MiB/s | 41.3 MiB | 00m00s [ 5/33] Installing clang-resource-files 100% | 16.3 MiB/s | 16.7 KiB | 00m00s [ 6/33] Installing cpp-0:16.2.1-2.fc46. 100% | 273.0 MiB/s | 42.6 MiB | 00m00s [ 7/33] Installing annobin-docs-0:13.32 100% | 32.8 MiB/s | 100.8 KiB | 00m00s [ 8/33] Installing kernel-headers-0:7.3 100% | 185.1 MiB/s | 7.2 MiB | 00m00s [ 9/33] Installing glibc-devel-0:2.44.9 100% | 149.9 MiB/s | 2.4 MiB | 00m00s [10/33] Installing libxcrypt-devel-0:4. 100% | 32.5 MiB/s | 33.3 KiB | 00m00s [11/33] Installing make-1:4.4.1-13.fc46 100% | 72.7 MiB/s | 1.8 MiB | 00m00s [12/33] Installing libatomic-0:16.2.1-2 100% | 22.8 MiB/s | 46.7 KiB | 00m00s [13/33] Installing gcc-0:16.2.1-2.fc46. 100% | 334.9 MiB/s | 121.9 MiB | 00m00s [14/33] Installing gcc-c++-0:16.2.1-2.f 100% | 272.3 MiB/s | 46.8 MiB | 00m00s [15/33] Installing tzdata-0:2026c-2.fc4 100% | 43.0 MiB/s | 1.5 MiB | 00m00s [16/33] Installing mpdecimal-0:4.0.1-4. 100% | 122.3 MiB/s | 250.5 KiB | 00m00s [17/33] Installing expat-0:2.8.3-1.fc46 100% | 16.8 MiB/s | 344.2 KiB | 00m00s [18/33] Installing python-pip-wheel-0:2 100% | 158.5 MiB/s | 1.3 MiB | 00m00s [19/33] Installing python3-libs-0:3.15. 100% | 289.4 MiB/s | 48.6 MiB | 00m00s [20/33] Installing python3-0:3.15.0~rc2 100% | 1.5 MiB/s | 30.5 KiB | 00m00s [21/33] Installing compiler-rt-0:24.0.0 100% | 603.7 MiB/s | 44.1 MiB | 00m00s [22/33] Installing libedit-0:3.1-60.202 100% | 126.2 MiB/s | 258.5 KiB | 00m00s [23/33] Installing llvm-filesystem-0:24 100% | 0.0 B/s | 1.1 KiB | 00m00s [24/33] Installing llvm-libs-0:24.0.0~p 100% | 370.7 MiB/s | 150.9 MiB | 00m00s [25/33] Installing clang-libs-0:24.0.0~ 100% | 345.3 MiB/s | 112.2 MiB | 00m00s [26/33] Installing clang-0:24.0.0~pre20 100% | 446.3 MiB/s | 70.5 MiB | 00m00s [27/33] Installing llvm-0:24.0.0~pre202 100% | 324.8 MiB/s | 135.7 MiB | 00m00s [28/33] Installing libomp-0:24.0.0~pre2 100% | 332.1 MiB/s | 3.3 MiB | 00m00s [29/33] Installing lld-libs-0:24.0.0~pr 100% | 299.0 MiB/s | 6.3 MiB | 00m00s [30/33] Installing lld-0:24.0.0~pre2026 100% | 1.5 MiB/s | 45.9 KiB | 00m00s [31/33] Installing fedora-clang-default 100% | 281.2 KiB/s | 288.0 B | 00m00s [32/33] Installing annobin-plugin-gcc-0 100% | 47.3 MiB/s | 726.2 KiB | 00m00s [33/33] Installing gcc-plugin-annobin-0 100% | 493.1 KiB/s | 58.7 KiB | 00m00s Warning: skipped OpenPGP checks for 16 packages from repositories: copr_base, copr_fedora_llvm_team_llvm_snapshots_big_merge_20260928, copr_tstellar_fedora_clang_default_cc Complete! Finish: installing minimal buildroot with dnf5 Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: R-srpm-macros-1.3.7-3.fc45.noarch add-determinism-0.7.3-3.fc45.x86_64 alternatives-1.33-6.fc46.x86_64 annobin-docs-13.32-1.fc46.noarch annobin-plugin-gcc-13.32-1.fc46.x86_64 ansible-srpm-macros-1-22.fc45.noarch audit-libs-4.2.1-2.fc45.x86_64 bash-5.3.15-2.fc46.x86_64 binutils-2.47.50-12.fc46.x86_64 build-reproducibility-srpm-macros-0.7.3-3.fc45.noarch bzip2-1.0.8-24.fc46.x86_64 bzip2-libs-1.0.8-24.fc46.x86_64 ca-certificates-2026.2.90_v9.0.317-1.fc46.noarch clang-24.0.0~pre20260928.g6909c17f146832-6.fc46.x86_64 clang-libs-24.0.0~pre20260928.g6909c17f146832-6.fc46.x86_64 clang-resource-filesystem-24.0.0~pre20260928.g6909c17f146832-6.fc46.x86_64 cmake-srpm-macros-4.3.0-5.fc45.noarch compiler-rt-24.0.0~pre20260928.g6909c17f146832-6.fc46.x86_64 coreutils-9.12-1.fc46.x86_64 coreutils-common-9.12-1.fc46.x86_64 cpio-2.15-10.fc46.x86_64 cpp-16.2.1-2.fc46.1.x86_64 crypto-policies-20260713-2.gitc42da77.fc45.noarch curl-8.23.0~rc2-1.fc46.x86_64 cyrus-sasl-lib-2.1.28-37.fc45.x86_64 debugedit-5.3-3.fc46.x86_64 diffutils-3.12-6.fc45.x86_64 dwz-0.17-3.fc45.x86_64 ed-1.22.6-1.fc46.x86_64 efi-srpm-macros-6-9.fc45.noarch elfutils-0.196-1.fc46.x86_64 elfutils-debuginfod-client-0.196-1.fc46.x86_64 elfutils-libelf-0.196-1.fc46.x86_64 elfutils-libs-0.196-1.fc46.x86_64 erlang-srpm-macros-0.3.11-2.fc45.noarch expat-2.8.3-1.fc46.x86_64 fedora-clang-default-cc-1-1.fc43.noarch fedora-gpg-keys-46-0.3.noarch fedora-release-46-0.1.noarch fedora-release-common-46-0.1.noarch fedora-release-identity-basic-46-0.1.noarch fedora-repos-46-0.3.noarch fedora-repos-rawhide-46-0.3.noarch file-5.48-3.fc46.x86_64 file-libs-5.48-3.fc46.x86_64 filesystem-3.18-59.fc45.x86_64 filesystem-srpm-macros-3.18-59.fc45.noarch findutils-4.11.0-2.fc46.x86_64 fips-provider-1.5.3-1.fc46.x86_64 fonts-srpm-macros-5.0.0-4.fc45.noarch forge-srpm-macros-0.4.0-5.fc45.noarch fpc-srpm-macros-1.3-17.fc45.noarch gap-srpm-macros-2-3.fc45.noarch gawk-5.4.1-1.fc46.x86_64 gcc-16.2.1-2.fc46.1.x86_64 gcc-c++-16.2.1-2.fc46.1.x86_64 gcc-plugin-annobin-16.2.1-2.fc46.1.x86_64 gdb-minimal-17.2-6.fc46.x86_64 gdbm-libs-1.23-12.fc46.x86_64 ghc-srpm-macros-1.10-2.fc45.noarch glibc-2.44.9000-4.fc46.x86_64 glibc-common-2.44.9000-4.fc46.x86_64 glibc-devel-2.44.9000-4.fc46.x86_64 glibc-gconv-extra-2.44.9000-4.fc46.x86_64 glibc-minimal-langpack-2.44.9000-4.fc46.x86_64 gmp-6.3.0-6.fc45.x86_64 gnat-srpm-macros-7-3.fc45.noarch gnome-srpm-macros-1.0-2.fc45.noarch gnulib-l10n-20241231-4.fc46.noarch gnupg2-2.4.9-18.fc46.x86_64 gnupg2-dirmngr-2.4.9-18.fc46.x86_64 gnupg2-gpg-agent-2.4.9-18.fc46.x86_64 gnupg2-gpgconf-2.4.9-18.fc46.x86_64 gnupg2-keyboxd-2.4.9-18.fc46.x86_64 gnupg2-verify-2.4.9-18.fc46.x86_64 gnutls-3.8.13-5.fc46.x86_64 go-srpm-macros-3.8.0-3.fc45.noarch gpg-pubkey-4f50a6114cd5c6976a7f1179655a4b02f577861e-6888bc98 gpg-pubkey-b2e766fa50ca6fa2d5ed06fc09d879e09488fb64-6a6b46b4 gpg-pubkey-d924b10d3e810dabdd8b56b596e7e91491211fce-697c9899 gpgverify-2.2-5.fc45.noarch grep-3.12-4.fc45.x86_64 gzip-1.14-4.fc46.x86_64 ima-evm-utils-libs-1.6.2-12.fc46.x86_64 info-7.3-3.fc46.x86_64 jansson-2.14-5.fc46.x86_64 java-srpm-macros-1-9.fc45.noarch json-c-0.18-9.fc46.x86_64 kernel-headers-7.3.0-0.rc5.45.fc46.x86_64 kernel-srpm-macros-1.0-30.fc45.noarch keyutils-libs-1.6.3-8.fc46.x86_64 krb5-libs-1.22.2-9.fc45.x86_64 libacl-2.4.0-2.fc45.x86_64 libarchive-3.8.9-2.fc46.x86_64 libassuan-2.5.7-6.fc46.x86_64 libatomic-16.2.1-2.fc46.1.x86_64 libattr-2.6.0-2.fc46.x86_64 libblkid-2.42.4-2.fc46.x86_64 libbrotli-1.2.0-6.fc46.x86_64 libcap-2.78-2.fc45.x86_64 libcap-ng-0.9.6-1.fc46.x86_64 libcbor-0.14.0-3.fc45.x86_64 libcom_err-1.47.4-2.fc46.x86_64 libcurl-8.23.0~rc2-1.fc46.x86_64 libeconf-0.7.9-4.fc46.x86_64 libedit-3.1-60.20260512cvs.fc46.x86_64 libevent-2.1.13-1.fc46.x86_64 libfdisk-2.42.4-2.fc46.x86_64 libffi-3.8.0-1.fc46.x86_64 libfido2-1.17.0-5.fc46.x86_64 libfsverity-1.7-4.fc45.x86_64 libgcc-16.2.1-2.fc46.1.x86_64 libgcrypt-1.12.4-1.fc46.x86_64 libgomp-16.2.1-2.fc46.1.x86_64 libgpg-error-1.61-2.fc46.x86_64 libidn2-2.3.8-4.fc46.x86_64 libksba-1.8.1-1.fc46.x86_64 liblastlog2-2.42.4-2.fc46.x86_64 libmount-2.42.4-2.fc46.x86_64 libmpc-1.4.1-2.fc46.x86_64 libnghttp2-1.69.0-6.fc46.x86_64 libnghttp3-1.18.0-1.fc46.x86_64 libomp-24.0.0~pre20260928.g6909c17f146832-6.fc46.x86_64 libpfm-4.13.0-23.fc45.x86_64 libpkgconf-2.5.1-2.fc46.x86_64 libpsl-0.23.3-1.fc46.x86_64 libselinux-3.11-5.fc46.x86_64 libselinux-utils-3.11-5.fc46.x86_64 libsemanage-3.11-4.fc46.x86_64 libsepol-3.11-2.fc46.x86_64 libsmartcols-2.42.4-2.fc46.x86_64 libssh-0.12.2-1.fc45.x86_64 libssh-config-0.12.2-1.fc45.noarch libstdc++-16.2.1-2.fc46.1.x86_64 libstdc++-devel-16.2.1-2.fc46.1.x86_64 libtasn1-4.21.0-2.fc46.x86_64 libtool-ltdl-2.6.2-1.fc46.x86_64 libunistring-1.1-12.fc46.x86_64 libusb1-1.0.30-2.fc45.x86_64 libuuid-2.42.4-2.fc46.x86_64 libverto-0.3.2-13.fc45.x86_64 libxcrypt-4.5.2-4.fc45.x86_64 libxcrypt-devel-4.5.2-4.fc45.x86_64 libxml2-2.15.4-1.fc46.x86_64 libzstd-1.5.7-6.fc46.x86_64 linkdupes-0.7.3-3.fc45.x86_64 lld-24.0.0~pre20260928.g6909c17f146832-6.fc46.x86_64 lld-libs-24.0.0~pre20260928.g6909c17f146832-6.fc46.x86_64 llvm-24.0.0~pre20260928.g6909c17f146832-6.fc46.x86_64 llvm-filesystem-24.0.0~pre20260928.g6909c17f146832-6.fc46.x86_64 llvm-libs-24.0.0~pre20260928.g6909c17f146832-6.fc46.x86_64 lua-libs-5.5.1-2.fc46.x86_64 lua-srpm-macros-1-18.fc45.noarch lz4-libs-1.10.0-5.fc46.x86_64 make-4.4.1-13.fc46.x86_64 meson-srpm-macros-1.12.1-2.fc46.noarch mpdecimal-4.0.1-4.fc46.x86_64 mpfr-4.2.2-4.fc45.x86_64 ncurses-base-6.6-3.fc46.noarch ncurses-libs-6.6-3.fc46.x86_64 nettle-4.0-5.fc45.x86_64 ngtcp2-1.22.1-3.fc45.x86_64 ngtcp2-crypto-ossl-1.22.1-3.fc45.x86_64 npth-1.8-5.fc46.x86_64 ocaml-srpm-macros-11-4.fc45.noarch openblas-srpm-macros-2-22.fc45.noarch openldap-2.6.14-1.fc46.x86_64 openssl-libs-4.0.3-1.fc46.x86_64 p11-kit-0.26.5-1.fc46.x86_64 p11-kit-trust-0.26.5-1.fc46.x86_64 package-notes-srpm-macros-0.20-2.fc45.noarch pam-libs-1.7.2-4.fc46.x86_64 patch-2.8-6.fc46.x86_64 pcre2-10.47-1.fc46.2.x86_64 pcre2-syntax-10.47-1.fc46.2.noarch perl-srpm-macros-1-65.fc45.noarch pkgconf-2.5.1-2.fc46.x86_64 pkgconf-m4-2.5.1-2.fc46.noarch pkgconf-pkg-config-2.5.1-2.fc46.x86_64 policycoreutils-3.11-2.fc46.x86_64 popt-1.19-11.fc46.x86_64 publicsuffix-list-dafsa-20260624-2.fc45.noarch pyproject-srpm-macros-1.23.2-1.fc45.noarch python-pip-wheel-26.2.1-1.fc46.noarch python-srpm-macros-3.15-2.fc45.noarch python3-3.15.0~rc2-1.fc46.x86_64 python3-libs-3.15.0~rc2-1.fc46.x86_64 qt5-srpm-macros-5.15.18-3.fc45.noarch qt6-srpm-macros-6.11.2-1.fc46.noarch readline-8.3-6.fc46.x86_64 redhat-rpm-config-345-4.fc46.noarch redhat-systemd-presets-102-3.fc45.noarch redhat-systemd-presets-common-102-3.fc45.noarch rpm-6.1.0-1.fc46.x86_64 rpm-build-6.1.0-1.fc46.x86_64 rpm-build-libs-6.1.0-1.fc46.x86_64 rpm-libs-6.1.0-1.fc46.x86_64 rpm-plugin-selinux-6.1.0-1.fc46.x86_64 rpm-sequoia-1.10.3-1.fc46.x86_64 rpm-sign-libs-6.1.0-1.fc46.x86_64 rust-srpm-macros-28.5-2.fc45.noarch sed-4.10-2.fc45.x86_64 selinux-policy-45.20-1.fc46.noarch selinux-policy-targeted-45.20-1.fc46.noarch setup-2.15.1-2.fc45.noarch shadow-utils-4.20.0-1.fc46.x86_64 sqlite-libs-3.53.4-1.fc45.x86_64 systemd-libs-262-3.fc46.x86_64 systemd-standalone-sysusers-262-3.fc46.x86_64 tar-1.35-9.fc45.x86_64 tpm2-tss-4.2.0-1.fc46.x86_64 tree-sitter-srpm-macros-0.4.6-2.fc45.noarch tzdata-2026c-2.fc46.noarch unzip-6.0-71.fc45.x86_64 util-linux-2.42.4-2.fc46.x86_64 util-linux-core-2.42.4-2.fc46.x86_64 which-2.25-2.fc46.x86_64 xxhash-libs-0.8.4-1.fc46.x86_64 xz-5.8.4-1.fc46.x86_64 xz-libs-5.8.4-1.fc46.x86_64 zig-srpm-macros-1-9.fc45.noarch zip-3.0-46.fc45.x86_64 zlib-ng-compat-2.3.3-6.fc46.x86_64 zstd-1.5.7-6.fc46.x86_64 Start: buildsrpm Start: rpmbuild -bs Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1784246400 Wrote: /builddir/build/SRPMS/htslib-1.24-1.fc46.src.rpm Finish: rpmbuild -bs INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-x86_64-1790841053.256992/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-4354l277/htslib/htslib.spec) Config(child) 0 minutes 33 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/htslib-1.24-1.fc46.src.rpm) Config(fedora-rawhide-x86_64) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1790841053.256992/root. INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1790841053.256992/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-1790841053.256992/root. INFO: calling preinit hooks INFO: enabled root cache Start: unpacking root cache Finish: unpacking root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-6.1.0-1.fc46.x86_64 rpm-sequoia-1.10.3-1.fc46.x86_64 dnf5-5.4.6.0-1.fc46.x86_64 dnf5-plugins-5.4.6.0-1.fc46.x86_64 Finish: chroot init Start: build phase for htslib-1.24-1.fc46.src.rpm Start: build setup for htslib-1.24-1.fc46.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1784246400 Wrote: /builddir/build/SRPMS/htslib-1.24-1.fc46.src.rpm Updating and loading repositories: fedora 100% | 117.1 KiB/s | 24.5 KiB | 00m00s Additional repo copr_tstellar_fedora_c 100% | 12.3 KiB/s | 1.5 KiB | 00m00s Additional repo copr_fedora_llvm_team_ 100% | 12.7 KiB/s | 1.5 KiB | 00m00s Copr repository 100% | 12.7 KiB/s | 1.5 KiB | 00m00s Repositories loaded. Package "gcc-16.2.1-2.fc46.1.x86_64" is already installed. Package "make-1:4.4.1-13.fc46.x86_64" is already installed. Package Arch Version Repository Size Installing: bzip2-devel x86_64 0:1.0.8-24.fc46 copr_base 309.8 KiB libcurl-devel x86_64 0:8.23.0~rc2-1.fc46 fedora 1.4 MiB openssl-devel x86_64 1:4.0.3-1.fc46 fedora 4.7 MiB perl-Data-Dumper x86_64 0:2.192-528.fc45 fedora 115.5 KiB perl-FindBin noarch 0:1.54-527.fc45 fedora 6.8 KiB perl-Getopt-Long noarch 1:2.58-527.fc45 fedora 144.5 KiB perl-interpreter x86_64 4:5.44.0-527.fc45 fedora 119.8 KiB perl-lib x86_64 0:0.65-527.fc45 fedora 8.5 KiB xz-devel x86_64 1:5.8.4-1.fc46 fedora 258.8 KiB zlib-ng-compat-devel x86_64 0:2.3.3-6.fc46 copr_base 107.0 KiB Installing dependencies: brotli x86_64 0:1.2.0-6.fc46 copr_base 33.2 KiB brotli-devel x86_64 0:1.2.0-6.fc46 copr_base 65.9 KiB cmake-filesystem x86_64 0:4.3.0-5.fc45 fedora 0.0 B groff-base x86_64 0:1.24.1-2.fc46 copr_base 4.4 MiB keyutils-libs-devel x86_64 0:1.6.3-8.fc46 copr_base 48.2 KiB krb5-devel x86_64 0:1.22.2-9.fc45 fedora 709.9 KiB libcom_err-devel x86_64 0:1.47.4-2.fc46 copr_base 16.7 KiB libidn2-devel x86_64 0:2.3.8-4.fc46 copr_base 152.1 KiB libkadm5 x86_64 0:1.22.2-9.fc45 fedora 217.9 KiB libnghttp2-devel x86_64 0:1.69.0-6.fc46 fedora 288.0 KiB libnghttp3-devel x86_64 0:1.18.0-1.fc46 copr_base 119.4 KiB libpsl-devel x86_64 0:0.23.3-1.fc46 fedora 111.5 KiB libselinux-devel x86_64 0:3.11-5.fc46 fedora 121.9 KiB libsepol-devel x86_64 0:3.11-2.fc46 copr_base 120.7 KiB libssh-devel x86_64 0:0.12.2-1.fc45 fedora 204.2 KiB libverto-devel x86_64 0:0.3.2-13.fc45 fedora 25.7 KiB libzstd-devel x86_64 0:1.5.7-6.fc46 copr_base 217.6 KiB ncurses x86_64 0:6.6-3.fc46 copr_base 626.6 KiB ngtcp2-crypto-ossl-devel x86_64 0:1.22.1-3.fc45 fedora 7.5 KiB ngtcp2-devel x86_64 0:1.22.1-3.fc45 fedora 262.8 KiB pcre2-devel x86_64 0:10.47-1.fc46.2 copr_base 2.1 MiB pcre2-utf16 x86_64 0:10.47-1.fc46.2 copr_base 694.6 KiB pcre2-utf32 x86_64 0:10.47-1.fc46.2 copr_base 666.5 KiB perl-AutoLoader noarch 0:5.74-527.fc45 fedora 20.6 KiB perl-B x86_64 0:1.92-527.fc45 fedora 513.5 KiB perl-Carp noarch 0:1.54-527.fc45 fedora 46.6 KiB perl-Class-Struct noarch 0:0.68-527.fc45 fedora 25.4 KiB perl-Digest noarch 0:1.20-527.fc45 fedora 35.2 KiB perl-Digest-MD5 x86_64 0:2.59-527.fc45 fedora 59.5 KiB perl-DynaLoader x86_64 0:1.57-527.fc45 fedora 32.1 KiB perl-Encode x86_64 4:3.24-527.fc45 fedora 4.7 MiB perl-Errno x86_64 0:1.39-527.fc45 fedora 8.4 KiB perl-Exporter noarch 0:5.79-527.fc45 fedora 54.2 KiB perl-Fcntl x86_64 0:1.20-527.fc45 fedora 44.7 KiB perl-File-Basename noarch 0:2.86-527.fc45 fedora 14.0 KiB perl-File-Path noarch 0:2.18-527.fc45 fedora 63.4 KiB perl-File-Temp noarch 1:0.231.200-527.fc45 fedora 163.7 KiB perl-File-stat noarch 0:1.15-527.fc45 fedora 13.7 KiB perl-FileHandle noarch 0:2.05-527.fc45 fedora 9.4 KiB perl-Getopt-Std noarch 0:1.15-527.fc45 fedora 12.5 KiB perl-HTTP-Tiny noarch 0:0.096-528.fc45 fedora 162.4 KiB perl-IO x86_64 0:1.56-527.fc45 fedora 147.3 KiB perl-IO-Socket-IP noarch 0:0.44-527.fc45 fedora 100.5 KiB perl-IO-Socket-SSL noarch 0:2.099-2.fc45 fedora 726.9 KiB perl-IPC-Open3 noarch 0:1.24-527.fc45 fedora 27.7 KiB perl-MIME-Base32 noarch 0:1.303-26.fc45 fedora 30.7 KiB perl-MIME-Base64 x86_64 0:3.16-527.fc45 fedora 41.9 KiB perl-Net-SSLeay x86_64 0:1.96-5.fc45 fedora 1.3 MiB perl-POSIX x86_64 0:2.26-527.fc45 fedora 229.3 KiB perl-PathTools x86_64 0:3.95-527.fc45 fedora 180.0 KiB perl-Pod-Escapes noarch 1:1.07-527.fc45 fedora 24.9 KiB perl-Pod-Perldoc noarch 0:3.28.01-527.fc45 fedora 163.8 KiB perl-Pod-Simple noarch 1:3.48-527.fc45 fedora 565.2 KiB perl-Pod-Usage noarch 4:2.05-527.fc45 fedora 86.3 KiB perl-Scalar-List-Utils x86_64 5:1.70-527.fc45 fedora 144.8 KiB perl-SelectSaver noarch 0:1.03-527.fc45 fedora 2.1 KiB perl-Socket x86_64 4:2.043-1.fc46 fedora 121.7 KiB perl-Storable x86_64 1:3.41-527.fc45 fedora 234.9 KiB perl-Symbol noarch 0:1.09-527.fc45 fedora 6.8 KiB perl-Term-ANSIColor noarch 0:5.01-527.fc45 fedora 97.5 KiB perl-Term-Cap noarch 0:1.18-527.fc45 fedora 29.3 KiB perl-Text-ParseWords noarch 0:3.31-527.fc45 fedora 13.6 KiB perl-Text-Tabs+Wrap noarch 0:2024.001-527.fc45 fedora 22.6 KiB perl-Time-HiRes x86_64 4:1.9780-527.fc45 fedora 115.6 KiB perl-Time-Local noarch 2:1.350-527.fc45 fedora 69.0 KiB perl-URI noarch 0:5.37-1.fc46 fedora 275.5 KiB perl-Unicode-Normalize x86_64 0:1.32-527.fc45 fedora 486.1 KiB perl-base noarch 0:2.27-527.fc45 fedora 12.6 KiB perl-constant noarch 0:1.33-528.fc45 fedora 26.3 KiB perl-if noarch 0:0.61.000-527.fc45 fedora 5.8 KiB perl-libnet noarch 0:3.15-528.fc45 fedora 288.4 KiB perl-libs x86_64 4:5.44.0-527.fc45 fedora 12.0 MiB perl-locale noarch 0:1.13-527.fc45 fedora 6.1 KiB perl-mro x86_64 0:1.30-527.fc45 fedora 41.4 KiB perl-overload noarch 0:1.40-527.fc45 fedora 71.6 KiB perl-overloading noarch 0:0.03-527.fc45 fedora 4.8 KiB perl-parent noarch 1:0.244-527.fc45 fedora 10.3 KiB perl-podlators noarch 1:6.1.1-1.fc46 fedora 327.2 KiB perl-vars noarch 0:1.05-527.fc45 fedora 3.9 KiB publicsuffix-list noarch 0:20260624-2.fc45 fedora 345.9 KiB Transaction Summary: Installing: 90 packages Total size of inbound packages is 15 MiB. Need to download 6 MiB. After this operation, 42 MiB extra will be used (install 42 MiB, remove 0 B). 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pcre2-utf32-0:10.47-1.fc46.2.x8 100% | 55.0 MiB/s | 225.4 KiB | 00m00s -------------------------------------------------------------------------------- [90/90] Total 100% | 89.6 MiB/s | 6.5 MiB | 00m00s Running transaction [ 1/92] Verify package files 100% | 1.3 KiB/s | 90.0 B | 00m00s [ 2/92] Prepare transaction 100% | 1.2 KiB/s | 90.0 B | 00m00s [ 3/92] Installing cmake-filesystem-0:4 100% | 4.6 MiB/s | 9.4 KiB | 00m00s [ 4/92] Installing ngtcp2-devel-0:1.22. 100% | 257.9 MiB/s | 264.1 KiB | 00m00s [ 5/92] Installing libidn2-devel-0:2.3. 100% | 17.3 MiB/s | 159.8 KiB | 00m00s [ 6/92] Installing openssl-devel-1:4.0. 100% | 61.3 MiB/s | 5.6 MiB | 00m00s [ 7/92] Installing ngtcp2-crypto-ossl-d 100% | 7.9 MiB/s | 8.1 KiB | 00m00s [ 8/92] Installing zlib-ng-compat-devel 100% | 106.0 MiB/s | 108.6 KiB | 00m00s [ 9/92] Installing libzstd-devel-0:1.5. 100% | 214.0 MiB/s | 219.1 KiB | 00m00s [10/92] Installing pcre2-utf32-0:10.47- 100% | 325.8 MiB/s | 667.3 KiB | 00m00s [11/92] Installing 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Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1784246400 Wrote: /builddir/build/SRPMS/htslib-1.24-1.fc46.src.rpm Updating and loading repositories: fedora 100% | 96.0 KiB/s | 24.5 KiB | 00m00s Additional repo copr_tstellar_fedora_c 100% | 15.4 KiB/s | 1.5 KiB | 00m00s Additional repo copr_fedora_llvm_team_ 100% | 15.2 KiB/s | 1.5 KiB | 00m00s Copr repository 100% | 15.5 KiB/s | 1.5 KiB | 00m00s Repositories loaded. Nothing to do. Package "bzip2-devel-1.0.8-24.fc46.x86_64" is already installed. Package "gcc-16.2.1-2.fc46.1.x86_64" is already installed. Package "libcurl-devel-8.23.0~rc2-1.fc46.x86_64" is already installed. Package "make-1:4.4.1-13.fc46.x86_64" is already installed. Package "openssl-devel-1:4.0.3-1.fc46.x86_64" is already installed. Package "perl-Data-Dumper-2.192-528.fc45.x86_64" is already installed. Package "perl-FindBin-1.54-527.fc45.noarch" is already installed. Package "perl-Getopt-Long-1:2.58-527.fc45.noarch" is already installed. Package "perl-lib-0.65-527.fc45.x86_64" is already installed. Package "perl-interpreter-4:5.44.0-527.fc45.x86_64" is already installed. Package "xz-devel-1:5.8.4-1.fc46.x86_64" is already installed. Package "zlib-ng-compat-devel-2.3.3-6.fc46.x86_64" is already installed. Finish: build setup for htslib-1.24-1.fc46.src.rpm Start: rpmbuild htslib-1.24-1.fc46.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1784246400 Executing(mkbuilddir): /bin/sh -e /var/tmp/rpm-tmp.aCGpJO Creating(rpmbuild.env): /builddir/build/BUILD/htslib-1.24-build/rpmbuild.env RPM_SOURCE_DIR="/builddir/build/SOURCES" RPM_BUILD_DIR="/builddir/build/BUILD/htslib-1.24-build" RPM_OPT_FLAGS="-O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer" RPM_LD_FLAGS="-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 " RPM_ARCH="x86_64" RPM_OS="linux" RPM_BUILD_NCPUS="4" RPM_SPECPARTS_DIR="/builddir/build/BUILD/htslib-1.24-build/SPECPARTS" export RPM_SOURCE_DIR RPM_BUILD_DIR RPM_OPT_FLAGS RPM_ARCH RPM_OS RPM_BUILD_NCPUS RPM_SPECPARTS_DIR RPM_LD_FLAGS RPM_DOC_DIR="/usr/share/doc" export RPM_DOC_DIR RPM_PACKAGE_NAME="htslib" RPM_PACKAGE_VERSION="1.24" RPM_PACKAGE_RELEASE="1.fc46" export RPM_PACKAGE_NAME RPM_PACKAGE_VERSION RPM_PACKAGE_RELEASE LANG=C.UTF-8 export LANG unset CDPATH DISPLAY ||: unset DEBUGINFOD_URLS ||: unset RPM_CONFIG_DIR ||: RPM_BUILD_ROOT="/builddir/build/BUILD/htslib-1.24-build/BUILDROOT" export RPM_BUILD_ROOT PKG_CONFIG_PATH="${PKG_CONFIG_PATH}:/usr/lib64/pkgconfig:/usr/share/pkgconfig" export PKG_CONFIG_PATH CONFIG_SITE=${CONFIG_SITE:-NONE} export CONFIG_SITE Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.J7TxZd + umask 022 + cd /builddir/build/BUILD/htslib-1.24-build + cd /builddir/build/BUILD/htslib-1.24-build + rm -rf htslib-1.24 + /usr/bin/rpmuncompress -x /builddir/build/SOURCES/htslib-1.24.tar.bz2 + STATUS=0 + '[' 0 -ne 0 ']' + cd htslib-1.24 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.56yFSR + umask 022 + cd /builddir/build/BUILD/htslib-1.24-build + CFLAGS='-O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=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=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=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=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=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=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=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 --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=clang + export CC + CXX=clang++ + export CXX + cd htslib-1.24 + CFLAGS='-O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=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=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=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=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=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=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=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 --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=clang + export CC + CXX=clang++ + export CXX + '[' '-flto=thin -ffat-lto-objectsx' '!=' x ']' ++ find . -type f -name configure -print + for file in $(find . -type f -name configure -print) + /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\) = /__attribute__ ((used)) char (*f) () = /g' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\);/__attribute__ ((used)) char (*f) ();/g' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed -r --in-place=.backup 's/^char \$2 \(\);/__attribute__ ((used)) char \$2 ();/g' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed --in-place=.backup '1{$!N;$!N};$!N;s/int x = 1;\nint y = 0;\nint z;\nint nan;/volatile int x = 1; volatile int y = 0; volatile int z, nan;/;P;D' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed -r --in-place=.backup '/lt_cv_sys_global_symbol_to_cdecl=/s#(".*"|'\''.*'\'')#"sed -n -e '\''s/^T .* \\(.*\\)$/extern int \\1();/p'\'' -e '\''s/^$symcode* .* \\(.*\\)$/extern char \\1;/p'\''"#' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + '[' 1 = 1 ']' +++ dirname ./configure ++ find . -name config.guess -o -name config.sub + for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub) ++ basename ./config.guess + '[' -f /usr/lib/rpm/redhat/config.guess ']' + /usr/bin/rm -f ./config.guess ++ basename ./config.guess + /usr/bin/cp -fv /usr/lib/rpm/redhat/config.guess ./config.guess '/usr/lib/rpm/redhat/config.guess' -> './config.guess' + for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub) ++ basename ./config.sub + '[' -f /usr/lib/rpm/redhat/config.sub ']' + /usr/bin/rm -f ./config.sub ++ basename ./config.sub + /usr/bin/cp -fv /usr/lib/rpm/redhat/config.sub ./config.sub '/usr/lib/rpm/redhat/config.sub' -> './config.sub' + '[' 1 = 1 ']' + '[' x '!=' 'x-Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg' ']' ++ find . -name ltmain.sh ++ grep -q runstatedir=DIR ./configure ++ echo --runstatedir=/run + ./configure --build=x86_64-redhat-linux --host=x86_64-redhat-linux --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/bin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/libexec --localstatedir=/var --runstatedir=/run --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info 'CFLAGS=-O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer' 'LDFLAGS=-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 ' --prefix=/usr --libdir=/usr/lib64 --enable-plugins '--with-plugin-path=/usr/local/libexec/htslib:$(plugindir)' --enable-gcs --enable-libcurl --enable-s3 configure: WARNING: unrecognized options: --disable-dependency-tracking checking for x86_64-redhat-linux-gcc... clang checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether clang accepts -g... yes checking for clang option to enable C23 features... -std=gnu23 checking for x86_64-redhat-linux-ranlib... no checking for ranlib... ranlib checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for clang -std=gnu23 options to detect undeclared functions... none needed checking for clang -std=gnu23 options to ignore future-version functions... none needed checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for sys/param.h... yes checking whether _XOPEN_SOURCE is declared... no checking whether __get_cpuid_max is declared... yes checking whether __cpuid_count is declared... yes checking for x86intrin.h... yes checking C compiler flags needed for sse4.1... -msse4.1 -mssse3 -mpopcnt checking C compiler flags needed for avx2... -mavx2 -mpopcnt checking C compiler flags needed for avx512f... -mavx512f -mpopcnt checking for working __builtin_clz... yes checking for working __builtin_prefetch... yes checking for working __builtin_cpu_supports("ssse3")... yes checking for working __attribute__((target("ssse3")))... yes checking for x86_64-redhat-linux-pkg-config... no checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for clang -std=gnu23 option to support large files... none needed checking shared library type for x86_64-redhat-linux... plain .so checking whether the linker supports versioned symbols... yes checking whether the compiler accepts -fvisibility=hidden... yes checking build system type... x86_64-redhat-linux-gnu checking host system type... x86_64-redhat-linux-gnu checking for getpagesize... yes checking for working mmap... yes checking for gmtime_r... yes checking for fsync... yes checking for drand48... yes checking for srand48_deterministic... no checking for getauxval... yes checking for elf_aux_info... no checking for posix_memalign... yes checking whether fdatasync is declared... yes checking for fdatasync... yes checking for __attribute__((constructor))... yes checking for clock_gettime with CLOCK_PROCESS_CPUTIME_ID... yes checking for library containing dlsym... none required checking whether the compiler accepts -rdynamic... yes checking for library containing log... -lm checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing recv... none required checking for bzlib.h... yes checking for BZ2_bzBuffToBuffCompress in -lbz2... yes checking for lzma.h... yes checking for lzma_easy_buffer_encode in -llzma... yes checking whether htscodecs files are present... yes checking for libdeflate.h... no checking for libdeflate_deflate_compress in -ldeflate... no checking for curl/curl.h... yes checking for curl_easy_pause in -lcurl... yes checking for CCHmac... no checking for library containing HMAC... -lcrypto checking for fstatat... yes checking for CMSG_LEN... yes checking for epoll... yes (edge triggered) checking for sendfile... yes, Linux-style checking whether EHOSTDOWN is declared... yes checking whether ENONET is declared... yes checking whether AI_V4MAPPED is declared... yes checking whether AI_ADDRCONFIG is declared... yes checking whether the compiler accepts -Wextra... yes checking whether the compiler accepts -Wformat... yes checking whether the compiler accepts -Wformat=2... yes checking whether the compiler accepts -Wconversion... yes checking whether the compiler accepts -Wtrampolines... no checking whether the compiler accepts -Wstrict-aliasing... yes checking whether the compiler accepts -fstack-clash-protection... yes checking whether the compiler accepts -fstack-protector-strong... yes checking whether the compiler accepts -fcf-protection=full... yes checking whether the compiler accepts -mbranch-protection=standard... no checking whether the compiler accepts -fno-delete-null-pointer-checks... yes checking whether the compiler accepts -Wl,-z,noexecstack... yes checking whether the compiler accepts -Wl,-z,relro... yes checking whether the compiler accepts -Wl,-z,now... yes checking whether the compiler accepts -Wl,--as-needed... yes checking whether the compiler accepts -Wl,--no-copy-dt-needed-entries... yes checking whether the compiler accepts -Wl,-z,nodlopen... yes checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating htslib.pc.tmp config.status: creating config.h config.status: linking htscodecs_bundled.mk to htscodecs.mk configure: WARNING: unrecognized options: --disable-dependency-tracking + /usr/bin/make -O -j4 V=1 VERBOSE=1 clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o kfunc.o kfunc.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o kstring.o kstring.c kstring.c:468:10: warning: returning 'const void *' from a function with result type 'void *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] 468 | return memchr(str, pat[0], n); | ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/string.h:122:3: note: expanded from macro 'memchr' 122 | __glibc_const_generic (S, const void *, memchr (S, C, N)) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/sys/cdefs.h:847:3: note: expanded from macro '__glibc_const_generic' 847 | _Generic (0 ? (PTR) : (void *) 1, \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 848 | const void *: (CTYPE) (CALL), \ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 849 | default: CALL) | ~~~~~~~~~~~~~~ 1 warning generated. clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o errmod.o errmod.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o bcf_sr_sort.o bcf_sr_sort.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o bgzf.o bgzf.c echo '#define HTS_VERSION_TEXT "1.24"' > version.h printf '#define HTS_CC "%s"\n#define HTS_CPPFLAGS "%s"\n#define HTS_CFLAGS "%s"\n#define HTS_LDFLAGS "%s"\n#define HTS_LIBS "%s"\n' \ 'clang -std=gnu23' \ '' \ '-O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden' \ '-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic' \ '-llzma -lbz2 -lz -lm ' > config_vars.h clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o faidx.o faidx.c faidx.c:1067:15: warning: initializing 'char *' with an expression of type 'const char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] 1067 | char *fai_tmp = strstr(fa, HTS_IDX_DELIM); | ^ ~~~~~~~~~~~~~~~~~~~~~~~~~ 1 warning generated. clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o hts_os.o hts_os.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o md5.o md5.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o hts_expr.o hts_expr.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o multipart.o multipart.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o hfile.o hfile.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o probaln.o probaln.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o realn.o realn.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o region.o region.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o regidx.o regidx.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o header.o header.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o sam_mods.o sam_mods.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o vcf_sweep.o vcf_sweep.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o simd.o simd.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o textutils.o textutils.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o tbx.o tbx.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o synced_bcf_reader.o synced_bcf_reader.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o thread_pool.o thread_pool.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o cram/cram_codecs.o cram/cram_codecs.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o vcfutils.o vcfutils.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o sam.o sam.c sam.c:5222:15: warning: assigning to 'char *' from 'const char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] 5222 | if ((opts = strchr(format, ','))) { | ^ ~~~~~~~~~~~~~~~~~~~ 1 warning generated. clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o cram/cram_decode.o cram/cram_decode.c cram/cram_decode.c:1234:31: warning: initializing 'char *' with an expression of type 'const void *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] 1234 | char *N = memchr(refp, 'N', frag_len); | ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1 warning generated. clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o cram/cram_external.o cram/cram_external.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o cram/cram_index.o cram/cram_index.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o cram/cram_stats.o cram/cram_stats.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o cram/mFILE.o cram/mFILE.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o cram/open_trace_file.o cram/open_trace_file.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o cram/cram_encode.o cram/cram_encode.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o cram/string_alloc.o cram/string_alloc.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o cram/cram_io.o cram/cram_io.c cram/cram_io.c:2323:11: warning: initializing 'char *' with an expression of type 'const char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] 2323 | char *fn_delim = strstr(fn, HTS_IDX_DELIM); | ^ ~~~~~~~~~~~~~~~~~~~~~~~~~ cram/cram_io.c:5070:29: warning: assigning to 'char *' from 'const char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] 5070 | fd->prefix = strdup((cp = strrchr(filename, '/')) ? cp+1 : filename); | ^ ~~~~~~~~~~~~~~~~~~~~~~ 2 warnings generated. clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o vcf.o vcf.c vcf.c:168:17: warning: assigning to 'char *' from 'const char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] 168 | if (!(major = strstr(version, vcf))) { //bad format | ^ ~~~~~~~~~~~~~~~~~~~~ 1 warning generated. clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr_neon.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -mavx2 -mpopcnt -I. -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx2.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -mavx512f -mpopcnt -I. -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_avx512.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -msse4.1 -mssse3 -mpopcnt -I. -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_sse4.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static32x16pr.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o htscodecs/htscodecs/utils.o htscodecs/htscodecs/utils.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -DPLUGINPATH=\"/usr/local/libexec/htslib:/usr/libexec/htslib\" -c -o plugin.o plugin.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o kfunc.pico kfunc.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o kstring.pico kstring.c kstring.c:468:10: warning: returning 'const void *' from a function with result type 'void *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] 468 | return memchr(str, pat[0], n); | ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/string.h:122:3: note: expanded from macro 'memchr' 122 | __glibc_const_generic (S, const void *, memchr (S, C, N)) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/sys/cdefs.h:847:3: note: expanded from macro '__glibc_const_generic' 847 | _Generic (0 ? (PTR) : (void *) 1, \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 848 | const void *: (CTYPE) (CALL), \ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 849 | default: CALL) | ~~~~~~~~~~~~~~ 1 warning generated. clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o errmod.pico errmod.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o bcf_sr_sort.pico bcf_sr_sort.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o bgzf.pico bgzf.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o faidx.pico faidx.c faidx.c:1067:15: warning: initializing 'char *' with an expression of type 'const char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] 1067 | char *fai_tmp = strstr(fa, HTS_IDX_DELIM); | ^ ~~~~~~~~~~~~~~~~~~~~~~~~~ 1 warning generated. clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o hfile.pico hfile.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o hts_os.pico hts_os.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o hts_expr.pico hts_expr.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o md5.pico md5.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o multipart.pico multipart.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o probaln.pico probaln.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o header.pico header.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o realn.pico realn.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o region.pico region.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o regidx.pico regidx.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o sam_mods.pico sam_mods.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o simd.pico simd.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o vcf_sweep.pico vcf_sweep.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o hts.pico hts.c hts.c:942:25: warning: initializing 'char *' with an expression of type 'const char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] 942 | char *rmme = NULL, *fnidx = strstr(fn, HTS_IDX_DELIM); | ^ ~~~~~~~~~~~~~~~~~~~~~~~~~ hts.c:1478:13: warning: assigning to 'char *' from 'const char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] 1478 | if ((cp = strchr(mode, ','))) { | ^ ~~~~~~~~~~~~~~~~~ hts.c:4929:11: warning: initializing 'char *' with an expression of type 'const char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] 4929 | char *fnidx = strstr(fn, HTS_IDX_DELIM); | ^ ~~~~~~~~~~~~~~~~~~~~~~~~~ 3 warnings generated. clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o tbx.pico tbx.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o synced_bcf_reader.pico synced_bcf_reader.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o textutils.pico textutils.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o thread_pool.pico thread_pool.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o cram/cram_codecs.pico cram/cram_codecs.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o vcfutils.pico vcfutils.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o sam.pico sam.c sam.c:5222:15: warning: assigning to 'char *' from 'const char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] 5222 | if ((opts = strchr(format, ','))) { | ^ ~~~~~~~~~~~~~~~~~~~ 1 warning generated. clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o cram/cram_external.pico cram/cram_external.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o cram/cram_decode.pico cram/cram_decode.c cram/cram_decode.c:1234:31: warning: initializing 'char *' with an expression of type 'const void *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] 1234 | char *N = memchr(refp, 'N', frag_len); | ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1 warning generated. clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o cram/cram_index.pico cram/cram_index.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o cram/cram_stats.pico cram/cram_stats.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o cram/mFILE.pico cram/mFILE.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o cram/open_trace_file.pico cram/open_trace_file.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o cram/pooled_alloc.pico cram/pooled_alloc.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o cram/string_alloc.pico cram/string_alloc.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o cram/cram_encode.pico cram/cram_encode.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o cram/cram_io.pico cram/cram_io.c cram/cram_io.c:2323:11: warning: initializing 'char *' with an expression of type 'const char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] 2323 | char *fn_delim = strstr(fn, HTS_IDX_DELIM); | ^ ~~~~~~~~~~~~~~~~~~~~~~~~~ cram/cram_io.c:5070:29: warning: assigning to 'char *' from 'const char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] 5070 | fd->prefix = strdup((cp = strrchr(filename, '/')) ? cp+1 : filename); | ^ ~~~~~~~~~~~~~~~~~~~~~~ 2 warnings generated. clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/htscodecs.pico htscodecs/htscodecs/htscodecs.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o vcf.pico vcf.c vcf.c:168:17: warning: assigning to 'char *' from 'const char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] 168 | if (!(major = strstr(version, vcf))) { //bad format | ^ ~~~~~~~~~~~~~~~~~~~~ 1 warning generated. clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/pack.pico htscodecs/htscodecs/pack.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/arith_dynamic.pico htscodecs/htscodecs/arith_dynamic.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/fqzcomp_qual.pico htscodecs/htscodecs/fqzcomp_qual.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rANS_static4x16pr.pico htscodecs/htscodecs/rANS_static4x16pr.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr_neon.pico htscodecs/htscodecs/rANS_static32x16pr_neon.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -mavx2 -mpopcnt -I. -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.pico htscodecs/htscodecs/rANS_static32x16pr_avx2.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -mavx512f -mpopcnt -I. -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.pico htscodecs/htscodecs/rANS_static32x16pr_avx512.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -msse4.1 -mssse3 -mpopcnt -I. -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.pico htscodecs/htscodecs/rANS_static32x16pr_sse4.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rle.pico htscodecs/htscodecs/rle.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/utils.pico htscodecs/htscodecs/utils.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr.pico htscodecs/htscodecs/rANS_static32x16pr.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rANS_static.pico htscodecs/htscodecs/rANS_static.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -DPLUGINPATH=\"/usr/local/libexec/htslib:/usr/libexec/htslib\" -fpic -c -o plugin.pico plugin.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o htsfile.o htsfile.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o bgzip.o bgzip.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/tokenise_name3.pico htscodecs/htscodecs/tokenise_name3.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o annot-tsv.o annot-tsv.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o tabix.o tabix.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o hfile_gcs.pico hfile_gcs.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/fieldarith.o test/fieldarith.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/hts_endian.o test/hts_endian.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/hfile.o test/hfile.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/pileup.o test/pileup.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o hfile_libcurl.pico hfile_libcurl.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/pileup_mod.o test/pileup_mod.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/plugins-dlhts.o test/plugins-dlhts.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test_alloc.o test/test_alloc.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test_bgzf.o test/test_bgzf.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test_expr.o test/test_expr.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o hfile_s3.pico hfile_s3.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test_kfunc.o test/test_kfunc.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test_faidx.o test/test_faidx.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/sam.o test/sam.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test_mod.o test/test_mod.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test_realn.o test/test_realn.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test_nibbles.o test/test_nibbles.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test_khash.o test/test_khash.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test_time_funcs.o test/test_time_funcs.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test-regidx.o test/test-regidx.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test_str2int.o test/test_str2int.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test_index.o test/test_index.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test_kstring.o test/test_kstring.c In file included from test/test_kstring.c:38: test/../kstring.c:468:10: warning: returning 'const void *' from a function with result type 'void *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] 468 | return memchr(str, pat[0], n); | ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/string.h:122:3: note: expanded from macro 'memchr' 122 | __glibc_const_generic (S, const void *, memchr (S, C, N)) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/sys/cdefs.h:847:3: note: expanded from macro '__glibc_const_generic' 847 | _Generic (0 ? (PTR) : (void *) 1, \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 848 | const void *: (CTYPE) (CALL), \ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 849 | default: CALL) | ~~~~~~~~~~~~~~ 1 warning generated. clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test_view.o test/test_view.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test-bcf-sr.o test/test-bcf-sr.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test-bcf-translate.o test/test-bcf-translate.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/fuzz/hts_open_fuzzer.o test/fuzz/hts_open_fuzzer.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test-vcf-api.o test/test-vcf-api.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test_introspection.o test/test_introspection.c sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' htslib.pc.tmp > htslib_static.mk sed -e "s#@-includedir@#`pwd`#g;s#@-libdir@#`pwd`#g" htslib.pc.tmp > htslib-uninstalled.pc clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test-parse-reg.o test/test-parse-reg.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -c -o ref_cache/cmsg_wrap.o ref_cache/cmsg_wrap.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test_hfile_libcurl.o test/test_hfile_libcurl.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -c -o ref_cache/listener.o ref_cache/listener.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -c -o ref_cache/http_parser.o ref_cache/http_parser.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -c -o ref_cache/misc.o ref_cache/misc.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -c -o ref_cache/log_files.o ref_cache/log_files.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -c -o ref_cache/poll_wrap_epoll.o ref_cache/poll_wrap_epoll.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -c -o ref_cache/ping.o ref_cache/ping.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -c -o ref_cache/poll_wrap_poll.o ref_cache/poll_wrap_poll.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -c -o ref_cache/main.o ref_cache/main.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -c -o ref_cache/ref_files.o ref_cache/ref_files.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -c -o ref_cache/request_handler.o ref_cache/request_handler.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -c -o ref_cache/sendfile_wrap.o ref_cache/sendfile_wrap.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -c -o ref_cache/transaction.o ref_cache/transaction.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -c -o ref_cache/server.o ref_cache/server.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -c -o ref_cache/upstream.o ref_cache/upstream.c ref_cache/upstream.c:57:21: warning: variable 'curl_version_num' set but not used [-Wunused-but-set-global] 57 | static unsigned int curl_version_num; | ^ 1 warning generated. clang -std=gnu23 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o test/hts_endian test/hts_endian.o -llzma -lbz2 -lz -lm clang -std=gnu23 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o test/plugins-dlhts test/plugins-dlhts.o -llzma -lbz2 -lz -lm clang -std=gnu23 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o test/test_alloc test/test_alloc.o clang -std=gnu23 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o test/test_kstring test/test_kstring.o -lm clang -std=gnu23 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o test/test_time_funcs test/test_time_funcs.o clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o hts.o hts.c hts.c:942:25: warning: initializing 'char *' with an expression of type 'const char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] 942 | char *rmme = NULL, *fnidx = strstr(fn, HTS_IDX_DELIM); | ^ ~~~~~~~~~~~~~~~~~~~~~~~~~ hts.c:1478:13: warning: assigning to 'char *' from 'const char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] 1478 | if ((cp = strchr(mode, ','))) { | ^ ~~~~~~~~~~~~~~~~~ hts.c:4929:11: warning: initializing 'char *' with an expression of type 'const char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] 4929 | char *fnidx = strstr(fn, HTS_IDX_DELIM); | ^ ~~~~~~~~~~~~~~~~~~~~~~~~~ 3 warnings generated. ar -rc libhts.a kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o sam_mods.o simd.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.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_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o plugin.o ranlib libhts.a clang -std=gnu23 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -Wl,-z,noexecstack -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-copy-dt-needed-entries -Wl,-z,nodlopen -o ref_cache/ref-cache ref_cache/cmsg_wrap.o ref_cache/http_parser.o ref_cache/listener.o ref_cache/log_files.o ref_cache/main.o ref_cache/misc.o ref_cache/ping.o ref_cache/poll_wrap_epoll.o ref_cache/poll_wrap_poll.o ref_cache/ref_files.o ref_cache/request_handler.o ref_cache/sendfile_wrap.o ref_cache/server.o ref_cache/transaction.o ref_cache/upstream.o cram/pooled_alloc.o md5.o -lcurl clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test-bcf_set_variant_type.o test/test-bcf_set_variant_type.c In file included from test/test-bcf_set_variant_type.c:30: test/../vcf.c:168:17: warning: assigning to 'char *' from 'const char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] 168 | if (!(major = strstr(version, vcf))) { //bad format | ^ ~~~~~~~~~~~~~~~~~~~~ 1 warning generated. clang -std=gnu23 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o annot-tsv annot-tsv.o libhts.a -llzma -lbz2 -lz -lm -lpthread clang -std=gnu23 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o bgzip bgzip.o libhts.a -llzma -lbz2 -lz -lm -lpthread clang -std=gnu23 -shared -Wl,-soname,libhts.so.3 -Wl,-version-script,htslib.map -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o libhts.so kfunc.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico header.pico hfile.pico hts.pico hts_expr.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico region.pico sam.pico sam_mods.pico simd.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_stats.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/string_alloc.pico htscodecs/htscodecs/arith_dynamic.pico htscodecs/htscodecs/fqzcomp_qual.pico htscodecs/htscodecs/htscodecs.pico htscodecs/htscodecs/pack.pico htscodecs/htscodecs/rANS_static4x16pr.pico htscodecs/htscodecs/rANS_static32x16pr_avx2.pico htscodecs/htscodecs/rANS_static32x16pr_avx512.pico htscodecs/htscodecs/rANS_static32x16pr_sse4.pico htscodecs/htscodecs/rANS_static32x16pr_neon.pico htscodecs/htscodecs/rANS_static32x16pr.pico htscodecs/htscodecs/rANS_static.pico htscodecs/htscodecs/rle.pico htscodecs/htscodecs/tokenise_name3.pico htscodecs/htscodecs/utils.pico plugin.pico -llzma -lbz2 -lz -lm -lpthread ln -sf libhts.so libhts.so.3 clang -std=gnu23 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o htsfile htsfile.o libhts.a -llzma -lbz2 -lz -lm -lpthread clang -std=gnu23 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o test/fieldarith test/fieldarith.o libhts.a -llzma -lbz2 -lz -lm -lpthread clang -std=gnu23 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o test/hfile test/hfile.o libhts.a -llzma -lbz2 -lz -lm -lpthread clang -std=gnu23 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o tabix tabix.o libhts.a -llzma -lbz2 -lz -lm -lpthread clang -std=gnu23 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o test/pileup test/pileup.o libhts.a -llzma -lbz2 -lz -lm -lpthread clang -std=gnu23 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o test/pileup_mod test/pileup_mod.o libhts.a -llzma -lbz2 -lz -lm -lpthread clang -std=gnu23 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o test/sam test/sam.o libhts.a -llzma -lbz2 -lz -lm -lpthread clang -std=gnu23 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o test/test_kfunc test/test_kfunc.o libhts.a -llzma -lbz2 -lz -lm -lpthread clang -std=gnu23 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o test/test_khash test/test_khash.o libhts.a -llzma -lbz2 -lz -lm -lpthread clang -std=gnu23 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o test/test_bgzf test/test_bgzf.o libhts.a -llzma -lbz2 -lz -lm -lpthread clang -std=gnu23 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o test/test_expr test/test_expr.o libhts.a -llzma -lbz2 -lz -lm -lpthread clang -std=gnu23 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o test/test_faidx test/test_faidx.o libhts.a -llzma -lbz2 -lz -lm -lpthread clang -std=gnu23 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o test/test_mod test/test_mod.o libhts.a -llzma -lbz2 -lz -lm -lpthread clang -std=gnu23 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o test/test_nibbles test/test_nibbles.o libhts.a -llzma -lbz2 -lz -lm -lpthread clang -std=gnu23 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o test/test_realn test/test_realn.o libhts.a -llzma -lbz2 -lz -lm -lpthread clang -std=gnu23 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o test/test-regidx test/test-regidx.o libhts.a -llzma -lbz2 -lz -lm -lpthread clang -std=gnu23 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o test/test_str2int test/test_str2int.o libhts.a -llzma -lbz2 -lz -lm -lpthread clang -std=gnu23 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o test/test_view test/test_view.o libhts.a -llzma -lbz2 -lz -lm -lpthread clang -std=gnu23 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o test/test_index test/test_index.o libhts.a -llzma -lbz2 -lz -lm -lpthread clang -std=gnu23 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o test/test-vcf-api test/test-vcf-api.o libhts.a -llzma -lbz2 -lz -lm -lpthread clang -std=gnu23 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -llzma -lbz2 -lz -lm -lpthread clang -std=gnu23 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -llzma -lbz2 -lz -lm -lpthread clang -std=gnu23 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -llzma -lbz2 -lz -lm -lpthread clang -std=gnu23 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o test/test-parse-reg test/test-parse-reg.o libhts.a -llzma -lbz2 -lz -lm -lpthread clang -std=gnu23 -shared -Wl,-E -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o hfile_libcurl.so hfile_libcurl.pico libhts.so -llzma -lbz2 -lz -lm -lcurl -lpthread clang -std=gnu23 -shared -Wl,-E -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o hfile_gcs.so hfile_gcs.pico libhts.so -llzma -lbz2 -lz -lm -lpthread clang -std=gnu23 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o test/test_introspection test/test_introspection.o libhts.a -llzma -lbz2 -lz -lm -lpthread clang -std=gnu23 -shared -Wl,-E -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o hfile_s3.so hfile_s3.pico libhts.so -llzma -lbz2 -lz -lm -lcrypto -lcurl -lpthread clang -std=gnu23 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o test/test_hfile_libcurl test/test_hfile_libcurl.o libhts.a -llzma -lbz2 -lz -lm -lpthread clang -std=gnu23 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o test/test-bcf_set_variant_type test/test-bcf_set_variant_type.o libhts.a -llzma -lbz2 -lz -lm -lpthread + sed -i -E '/^(Libs|Requires)\.private:/d' htslib.pc.tmp + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.7NhXFF + umask 022 + cd /builddir/build/BUILD/htslib-1.24-build + '[' /builddir/build/BUILD/htslib-1.24-build/BUILDROOT '!=' / ']' + rm -rf /builddir/build/BUILD/htslib-1.24-build/BUILDROOT ++ dirname /builddir/build/BUILD/htslib-1.24-build/BUILDROOT + mkdir -p /builddir/build/BUILD/htslib-1.24-build + mkdir /builddir/build/BUILD/htslib-1.24-build/BUILDROOT + CFLAGS='-O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=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=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=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=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=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=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=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 --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=clang + export CC + CXX=clang++ + export CXX + cd htslib-1.24 + /usr/bin/make install DESTDIR=/builddir/build/BUILD/htslib-1.24-build/BUILDROOT 'INSTALL=/usr/bin/install -p' mkdir -p -m 755 /builddir/build/BUILD/htslib-1.24-build/BUILDROOT/usr/bin /builddir/build/BUILD/htslib-1.24-build/BUILDROOT/usr/include /builddir/build/BUILD/htslib-1.24-build/BUILDROOT/usr/include/htslib /builddir/build/BUILD/htslib-1.24-build/BUILDROOT/usr/lib64 /builddir/build/BUILD/htslib-1.24-build/BUILDROOT/usr/share/man/man1 /builddir/build/BUILD/htslib-1.24-build/BUILDROOT/usr/share/man/man5 /builddir/build/BUILD/htslib-1.24-build/BUILDROOT/usr/share/man/man7 /builddir/build/BUILD/htslib-1.24-build/BUILDROOT/usr/lib64/pkgconfig if test -n "/usr/libexec/htslib"; then mkdir -p -m 755 /builddir/build/BUILD/htslib-1.24-build/BUILDROOT/usr/libexec/htslib; fi /usr/bin/install -p -m 644 libhts.so /builddir/build/BUILD/htslib-1.24-build/BUILDROOT/usr/lib64/libhts.so.1.24 ln -sf libhts.so.1.24 /builddir/build/BUILD/htslib-1.24-build/BUILDROOT/usr/lib64/libhts.so ln -sf libhts.so.1.24 /builddir/build/BUILD/htslib-1.24-build/BUILDROOT/usr/lib64/libhts.so.3 sed -e 's#@-includedir@#/usr/include#g;s#@-libdir@#/usr/lib64#g;s#@-PACKAGE_VERSION@#1.24#g' htslib.pc.tmp > /builddir/build/BUILD/htslib-1.24-build/BUILDROOT/usr/lib64/pkgconfig/htslib.pc chmod 644 /builddir/build/BUILD/htslib-1.24-build/BUILDROOT/usr/lib64/pkgconfig/htslib.pc /usr/bin/install -p annot-tsv bgzip htsfile tabix ref_cache/ref-cache /builddir/build/BUILD/htslib-1.24-build/BUILDROOT/usr/bin if test -n "hfile_libcurl.so hfile_gcs.so hfile_s3.so"; then /usr/bin/install -p hfile_libcurl.so hfile_gcs.so hfile_s3.so /builddir/build/BUILD/htslib-1.24-build/BUILDROOT/usr/libexec/htslib; fi /usr/bin/install -p -m 644 htslib/*.h /builddir/build/BUILD/htslib-1.24-build/BUILDROOT/usr/include/htslib /usr/bin/install -p -m 644 libhts.a /builddir/build/BUILD/htslib-1.24-build/BUILDROOT/usr/lib64/libhts.a /usr/bin/install -p -m 644 annot-tsv.1 bgzip.1 htsfile.1 tabix.1 /builddir/build/BUILD/htslib-1.24-build/BUILDROOT/usr/share/man/man1 if test "xref_cache/ref-cache" != "x" ; then \ /usr/bin/install -p -m 644 ref_cache/ref-cache.1 /builddir/build/BUILD/htslib-1.24-build/BUILDROOT/usr/share/man/man1 ; \ fi /usr/bin/install -p -m 644 faidx.5 sam.5 vcf.5 /builddir/build/BUILD/htslib-1.24-build/BUILDROOT/usr/share/man/man5 /usr/bin/install -p -m 644 htslib-s3-plugin.7 /builddir/build/BUILD/htslib-1.24-build/BUILDROOT/usr/share/man/man7 + pushd /builddir/build/BUILD/htslib-1.24-build/BUILDROOT//usr/lib64 ~/build/BUILD/htslib-1.24-build/BUILDROOT/usr/lib64 ~/build/BUILD/htslib-1.24-build/htslib-1.24 + chmod 755 libhts.so.1.24 + popd ~/build/BUILD/htslib-1.24-build/htslib-1.24 + find /builddir/build/BUILD/htslib-1.24-build/BUILDROOT -name '*.la' -delete + rm -f /builddir/build/BUILD/htslib-1.24-build/BUILDROOT//usr/lib64/libhts.a + /usr/bin/find-debuginfo -j4 --strict-build-id -m -i --build-id-seed 1.24-1.fc46 --unique-debug-suffix -1.24-1.fc46.x86_64 --unique-debug-src-base htslib-1.24-1.fc46.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 --remove-section .gnu.build.attributes -S debugsourcefiles.list /builddir/build/BUILD/htslib-1.24-build/htslib-1.24 find-debuginfo: starting Extracting debug info from 9 files DWARF-compressing 9 files dwz: ./usr/bin/annot-tsv-1.24-1.fc46.x86_64.debug: Unknown debugging section .debug_addr dwz: ./usr/bin/bgzip-1.24-1.fc46.x86_64.debug: Unknown debugging section .debug_addr dwz: ./usr/bin/htsfile-1.24-1.fc46.x86_64.debug: Unknown debugging section .debug_addr dwz: ./usr/bin/ref-cache-1.24-1.fc46.x86_64.debug: Unknown debugging section .debug_addr dwz: ./usr/bin/tabix-1.24-1.fc46.x86_64.debug: Unknown debugging section .debug_addr dwz: ./usr/lib64/libhts.so.1.24-1.24-1.fc46.x86_64.debug: Unknown debugging section .debug_addr dwz: ./usr/libexec/htslib/hfile_gcs.so-1.24-1.fc46.x86_64.debug: Unknown debugging section .debug_addr dwz: ./usr/libexec/htslib/hfile_libcurl.so-1.24-1.fc46.x86_64.debug: Unknown debugging section .debug_addr dwz: ./usr/libexec/htslib/hfile_s3.so-1.24-1.fc46.x86_64.debug: Unknown debugging section .debug_addr dwz: Too few files for multifile optimization sepdebugcrcfix: Updated 0 CRC32s, 9 CRC32s did match. Creating .debug symlinks for symlinks to ELF files Copying sources found by 'debugedit -l' to /usr/src/debug/htslib-1.24-1.fc46.x86_64 find-debuginfo: done + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + COMPRESS='gzip -9 -n' + COMPRESS_EXT=.gz + /usr/lib/rpm/brp-compress + /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip + /usr/lib/rpm/check-rpaths + /usr/lib/rpm/redhat/brp-mangle-shebangs + /usr/lib/rpm/brp-remove-la-files + /usr/lib/rpm/redhat/brp-python-rpm-in-distinfo + env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j4 + /usr/lib/rpm/redhat/brp-python-hardlink + /usr/bin/add-det --brp -j4 /builddir/build/BUILD/htslib-1.24-build/BUILDROOT Scanned 29 directories and 206 files, processed 9 inodes, 0 modified (0 replaced + 0 rewritten), 0 unsupported format, 0 errors + /usr/bin/linkdupes --brp /builddir/build/BUILD/htslib-1.24-build/BUILDROOT/usr Scanned 28 directories and 206 files, considered 204 files, read 44 files, linked 22 files, 0 errors sum of sizes of linked files: 445258 bytes Reading /builddir/build/BUILD/htslib-1.24-build/SPECPARTS/rpm-debuginfo.specpart Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.gzactm + umask 022 + cd /builddir/build/BUILD/htslib-1.24-build + CFLAGS='-O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=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=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=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=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=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=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=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 --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=clang + export CC + CXX=clang++ + export CXX + cd htslib-1.24 + make test sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' htslib.pc.tmp > htslib_static.mk sed -e "s#@-includedir@#`pwd`#g;s#@-libdir@#`pwd`#g" htslib.pc.tmp > htslib-uninstalled.pc clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -Ihtscodecs -c -o htscodecs/tests/rANS_static_test.o htscodecs/tests/rANS_static_test.c clang -std=gnu23 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o htscodecs/tests/rans4x8 htscodecs/tests/rANS_static_test.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o -llzma -lbz2 -lz -lm -lm -lpthread cd htscodecs/tests && srcdir=. && export srcdir && ./rans4x8.test Testing rans4x8 -r -o0 on ./dat/q4 11674 Testing rans4x8 -r -o1 on ./dat/q4 10870 Testing rans4x8 -r -o0 on ./dat/q40+dir 50258 Testing rans4x8 -r -o1 on ./dat/q40+dir 50537 Testing rans4x8 -r -o0 on ./dat/q8 33099 Testing rans4x8 -r -o1 on ./dat/q8 31428 Testing rans4x8 -r -o0 on ./dat/qvar 32997 Testing rans4x8 -r -o1 on ./dat/qvar 32832 clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -Ihtscodecs -c -o htscodecs/tests/rANS_static4x16pr_test.o htscodecs/tests/rANS_static4x16pr_test.c clang -std=gnu23 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o htscodecs/tests/rans4x16pr htscodecs/tests/rANS_static4x16pr_test.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o -llzma -lbz2 -lz -lm -lm -lpthread cd htscodecs/tests && srcdir=. && export srcdir && ./rans4x16.test Testing rans4x16 -r -o0 on ./dat/q4 11660 Testing rans4x16 -r -o1 on ./dat/q4 10848 Testing rans4x16 -r -o64 on ./dat/q4 12878 Testing rans4x16 -r -o65 on ./dat/q4 10672 Testing rans4x16 -r -o128 on ./dat/q4 10902 Testing rans4x16 -r -o129 on ./dat/q4 10890 Testing rans4x16 -r -o192 on ./dat/q4 11225 Testing rans4x16 -r -o193 on ./dat/q4 10825 Testing rans4x16 -r -o8 on ./dat/q4 11731 Testing rans4x16 -r -o9 on ./dat/q4 11111 Testing rans4x16 -r -o4 on ./dat/q4 11746 11746 11746 11746 Testing rans4x16 -r -o5 on ./dat/q4 10932 10932 10932 10932 Testing rans4x16 -r -o0 on ./dat/q40+dir 50247 Testing rans4x16 -r -o1 on ./dat/q40+dir 49449 Testing rans4x16 -r -o8 on ./dat/q40+dir 50072 Testing rans4x16 -r -o9 on ./dat/q40+dir 50072 Testing rans4x16 -r -o4 on ./dat/q40+dir 50331 50331 50331 50331 Testing rans4x16 -r -o5 on ./dat/q40+dir 49537 49537 49537 49537 Testing rans4x16 -r -o0 on ./dat/q8 33088 Testing rans4x16 -r -o1 on ./dat/q8 31372 Testing rans4x16 -r -o64 on ./dat/q8 33458 Testing rans4x16 -r -o65 on ./dat/q8 31025 Testing rans4x16 -r -o128 on ./dat/q8 32237 Testing rans4x16 -r -o129 on ./dat/q8 31258 Testing rans4x16 -r -o192 on ./dat/q8 32024 Testing rans4x16 -r -o193 on ./dat/q8 31146 Testing rans4x16 -r -o4 on ./dat/q8 33176 33176 33176 33176 Testing rans4x16 -r -o5 on ./dat/q8 31458 31458 31458 31458 Testing rans4x16 -r -o69 on ./dat/qsimd 35 Testing rans4x16 -r -o4 on ./dat/qsimd 219 219 219 219 Testing rans4x16 -r -o5 on ./dat/qsimd 151 151 151 151 Testing rans4x16 -r -o0 on ./dat/qvar 32987 Testing rans4x16 -r -o1 on ./dat/qvar 32261 Testing rans4x16 -r -o32 on ./dat/qvar 62345 Testing rans4x16 -r -o4 on ./dat/qvar 33073 33073 33073 33073 Testing rans4x16 -r -o5 on ./dat/qvar 32353 32353 32353 32353 clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -Ihtscodecs -c -o htscodecs/tests/arith_dynamic_test.o htscodecs/tests/arith_dynamic_test.c clang -std=gnu23 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o htscodecs/tests/arith_dynamic htscodecs/tests/arith_dynamic_test.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o -llzma -lbz2 -lz -lm -lm -lpthread cd htscodecs/tests && srcdir=. && export srcdir && ./arith.test Testing arith_dynamic -r -o0 on ./dat/q4 11615 Testing arith_dynamic -r -o1 on ./dat/q4 10831 Testing arith_dynamic -r -o64 on ./dat/q4 13360 Testing arith_dynamic -r -o65 on ./dat/q4 10484 Testing arith_dynamic -r -o128 on ./dat/q4 10774 Testing arith_dynamic -r -o129 on ./dat/q4 10329 Testing arith_dynamic -r -o192 on ./dat/q4 11095 Testing arith_dynamic -r -o193 on ./dat/q4 10283 Testing arith_dynamic -r -o8 on ./dat/q4 11448 Testing arith_dynamic -r -o9 on ./dat/q4 11083 Testing arith_dynamic -r -o0 on ./dat/q40+dir 49949 Testing arith_dynamic -r -o1 on ./dat/q40+dir 49034 Testing arith_dynamic -r -o64 on ./dat/q40+dir 51242 Testing arith_dynamic -r -o65 on ./dat/q40+dir 49061 Testing arith_dynamic -r -o8 on ./dat/q40+dir 49820 Testing arith_dynamic -r -o9 on ./dat/q40+dir 49448 Testing arith_dynamic -r -o0 on ./dat/q8 32752 Testing arith_dynamic -r -o1 on ./dat/q8 31331 Testing arith_dynamic -r -o64 on ./dat/q8 35211 Testing arith_dynamic -r -o65 on ./dat/q8 30907 Testing arith_dynamic -r -o128 on ./dat/q8 32063 Testing arith_dynamic -r -o129 on ./dat/q8 31084 Testing arith_dynamic -r -o192 on ./dat/q8 32267 Testing arith_dynamic -r -o193 on ./dat/q8 30931 Testing arith_dynamic -r -o0 on ./dat/qvar 32597 Testing arith_dynamic -r -o1 on ./dat/qvar 31982 Testing arith_dynamic -r -o32 on ./dat/qvar 62345 Testing arith_dynamic -r -o64 on ./dat/qvar 33237 Testing arith_dynamic -r -o65 on ./dat/qvar 31993 Testing arith_dynamic -r -o1 on ./dat/u32 27005 Testing arith_dynamic -r -o65 on ./dat/u32 23864 Testing arith_dynamic -r -o9 on ./dat/u32 24811 Testing arith_dynamic -r -o4 on ./dat/u32 20849 clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -Ihtscodecs -c -o htscodecs/tests/tokenise_name3_test.o htscodecs/tests/tokenise_name3_test.c clang -std=gnu23 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o htscodecs/tests/tokenise_name3 htscodecs/tests/tokenise_name3_test.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o -llzma -lbz2 -lz -lm -lm -lpthread cd htscodecs/tests && srcdir=. && export srcdir && ./tok3.test Testing tokenise_name3 -r -1 on ./names/01.names 2708 Testing tokenise_name3 -r -3 on ./names/01.names 2429 Testing tokenise_name3 -r -5 on ./names/01.names 2264 Testing tokenise_name3 -r -7 on ./names/01.names 2264 Testing tokenise_name3 -r -9 on ./names/01.names 2234 Testing tokenise_name3 -r -11 on ./names/01.names 2449 Testing tokenise_name3 -r -13 on ./names/01.names 2085 Testing tokenise_name3 -r -15 on ./names/01.names 2071 Testing tokenise_name3 -r -17 on ./names/01.names 2070 Testing tokenise_name3 -r -19 on ./names/01.names 2051 Testing tokenise_name3 -r -1 on ./names/02.names 5390 Testing tokenise_name3 -r -3 on ./names/02.names 4955 Testing tokenise_name3 -r -5 on ./names/02.names 4923 Testing tokenise_name3 -r -7 on ./names/02.names 4923 Testing tokenise_name3 -r -9 on ./names/02.names 4918 Testing tokenise_name3 -r -11 on ./names/02.names 4838 Testing tokenise_name3 -r -13 on ./names/02.names 4757 Testing tokenise_name3 -r -15 on ./names/02.names 4743 Testing tokenise_name3 -r -17 on ./names/02.names 4716 Testing tokenise_name3 -r -19 on ./names/02.names 4700 Testing tokenise_name3 -r -1 on ./names/03.names 8854 Testing tokenise_name3 -r -3 on ./names/03.names 7782 Testing tokenise_name3 -r -5 on ./names/03.names 7771 Testing tokenise_name3 -r -7 on ./names/03.names 7771 Testing tokenise_name3 -r -9 on ./names/03.names 7521 Testing tokenise_name3 -r -11 on ./names/03.names 7395 Testing tokenise_name3 -r -13 on ./names/03.names 7252 Testing tokenise_name3 -r -15 on ./names/03.names 7252 Testing tokenise_name3 -r -17 on ./names/03.names 7225 Testing tokenise_name3 -r -19 on ./names/03.names 7075 Testing tokenise_name3 -r -1 on ./names/05.names 3787 Testing tokenise_name3 -r -3 on ./names/05.names 3564 Testing tokenise_name3 -r -5 on ./names/05.names 3536 Testing tokenise_name3 -r -7 on ./names/05.names 3536 Testing tokenise_name3 -r -9 on ./names/05.names 3534 Testing tokenise_name3 -r -11 on ./names/05.names 3411 Testing tokenise_name3 -r -13 on ./names/05.names 3397 Testing tokenise_name3 -r -15 on ./names/05.names 3383 Testing tokenise_name3 -r -17 on ./names/05.names 3383 Testing tokenise_name3 -r -19 on ./names/05.names 3377 Testing tokenise_name3 -r -1 on ./names/08.names 5579 Testing tokenise_name3 -r -3 on ./names/08.names 5274 Testing tokenise_name3 -r -5 on ./names/08.names 5246 Testing tokenise_name3 -r -7 on ./names/08.names 5213 Testing tokenise_name3 -r -9 on ./names/08.names 5160 Testing tokenise_name3 -r -11 on ./names/08.names 4915 Testing tokenise_name3 -r -13 on ./names/08.names 4901 Testing tokenise_name3 -r -15 on ./names/08.names 4887 Testing tokenise_name3 -r -17 on ./names/08.names 4844 Testing tokenise_name3 -r -19 on ./names/08.names 4805 Testing tokenise_name3 -r -1 on ./names/09.names 3740 Testing tokenise_name3 -r -3 on ./names/09.names 3539 Testing tokenise_name3 -r -5 on ./names/09.names 3539 Testing tokenise_name3 -r -7 on ./names/09.names 3528 Testing tokenise_name3 -r -9 on ./names/09.names 3493 Testing tokenise_name3 -r -11 on ./names/09.names 3431 Testing tokenise_name3 -r -13 on ./names/09.names 3394 Testing tokenise_name3 -r -15 on ./names/09.names 3394 Testing tokenise_name3 -r -17 on ./names/09.names 3386 Testing tokenise_name3 -r -19 on ./names/09.names 3366 Testing tokenise_name3 -r -1 on ./names/10.names 5210 Testing tokenise_name3 -r -3 on ./names/10.names 4782 Testing tokenise_name3 -r -5 on ./names/10.names 4752 Testing tokenise_name3 -r -7 on ./names/10.names 4752 Testing tokenise_name3 -r -9 on ./names/10.names 4744 Testing tokenise_name3 -r -11 on ./names/10.names 4566 Testing tokenise_name3 -r -13 on ./names/10.names 4520 Testing tokenise_name3 -r -15 on ./names/10.names 4506 Testing tokenise_name3 -r -17 on ./names/10.names 4494 Testing tokenise_name3 -r -19 on ./names/10.names 4476 Testing tokenise_name3 -r -1 on ./names/20.names 1783 Testing tokenise_name3 -r -3 on ./names/20.names 1668 Testing tokenise_name3 -r -5 on ./names/20.names 1640 Testing tokenise_name3 -r -7 on ./names/20.names 1640 Testing tokenise_name3 -r -9 on ./names/20.names 1632 Testing tokenise_name3 -r -11 on ./names/20.names 1645 Testing tokenise_name3 -r -13 on ./names/20.names 1625 Testing tokenise_name3 -r -15 on ./names/20.names 1611 Testing tokenise_name3 -r -17 on ./names/20.names 1609 Testing tokenise_name3 -r -19 on ./names/20.names 1600 Testing tokenise_name3 -r -1 on ./names/nv.names 5273 Testing tokenise_name3 -r -3 on ./names/nv.names 4968 Testing tokenise_name3 -r -5 on ./names/nv.names 4941 Testing tokenise_name3 -r -7 on ./names/nv.names 4941 Testing tokenise_name3 -r -9 on ./names/nv.names 4937 Testing tokenise_name3 -r -11 on ./names/nv.names 4864 Testing tokenise_name3 -r -13 on ./names/nv.names 4785 Testing tokenise_name3 -r -15 on ./names/nv.names 4772 Testing tokenise_name3 -r -17 on ./names/nv.names 4772 Testing tokenise_name3 -r -19 on ./names/nv.names 4767 Testing tokenise_name3 -r -1 on ./names/nv2.names 1060 Testing tokenise_name3 -r -3 on ./names/nv2.names 891 Testing tokenise_name3 -r -5 on ./names/nv2.names 863 Testing tokenise_name3 -r -7 on ./names/nv2.names 863 Testing tokenise_name3 -r -9 on ./names/nv2.names 855 Testing tokenise_name3 -r -11 on ./names/nv2.names 836 Testing tokenise_name3 -r -13 on ./names/nv2.names 799 Testing tokenise_name3 -r -15 on ./names/nv2.names 785 Testing tokenise_name3 -r -17 on ./names/nv2.names 779 Testing tokenise_name3 -r -19 on ./names/nv2.names 767 Testing tokenise_name3 -r -1 on ./names/rr.names 6605 Testing tokenise_name3 -r -3 on ./names/rr.names 6237 Testing tokenise_name3 -r -5 on ./names/rr.names 6237 Testing tokenise_name3 -r -7 on ./names/rr.names 6237 Testing tokenise_name3 -r -9 on ./names/rr.names 6230 Testing tokenise_name3 -r -11 on ./names/rr.names 6151 Testing tokenise_name3 -r -13 on ./names/rr.names 6025 Testing tokenise_name3 -r -15 on ./names/rr.names 6025 Testing tokenise_name3 -r -17 on ./names/rr.names 6023 Testing tokenise_name3 -r -19 on ./names/rr.names 5973 clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -Ihtscodecs -c -o htscodecs/tests/fqzcomp_qual_test.o htscodecs/tests/fqzcomp_qual_test.c clang -std=gnu23 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o htscodecs/tests/fqzcomp_qual htscodecs/tests/fqzcomp_qual_test.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o -llzma -lbz2 -lz -lm -lm -lpthread cd htscodecs/tests && srcdir=. && export srcdir && ./fqzcomp.test clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -Ihtscodecs -c -o htscodecs/tests/varint_test.o htscodecs/tests/varint_test.c clang -std=gnu23 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o htscodecs/tests/varint htscodecs/tests/varint_test.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o -llzma -lbz2 -lz -lm -lm -lpthread cd htscodecs/tests && ./varint test/hts_endian test/test_alloc test/test_expr test/test_kfunc test/test_khash test/test_kstring test/test_nibbles -v test/test_str2int test/test_time_funcs test/fieldarith test/fieldarith.sam test/hfile if test "xhfile_libcurl.so hfile_gcs.so hfile_s3.so" != "x"; then \ HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -g ./libhts.so; \ fi if test "xhfile_libcurl.so hfile_gcs.so hfile_s3.so" != "x"; then \ HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -l ./libhts.so; \ fi test/test_bgzf test/bgziptest.txt test/test-parse-reg -t test/colons.bam Expected error: [E::hts_parse_region] Range is ambiguous. Use {chr1:100-200} or {chr1}:100-200 instead Expected error: [E::hts_parse_region] Range is ambiguous. Use {chr1:100-200,chr3} or {chr1}:100-200,chr3 instead Expected error: [E::hts_parse_region] Mismatching braces in "{chr1" Expected error: [E::hts_parse_region] Unexpected string "x" after region Expected error: [E::hts_parse_region] Unexpected string "y" after region Expected error: [E::hts_parse_region] Unexpected string "chr3" after region cd test/faidx && ./test-faidx.sh faidx.tst Testing faidx... PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -e faidx.fa.expected.fai PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t fai_line_length -e 24 trailingblank2 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_has_seq -e 1 foo PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_has_seq -e 0 absent PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_iseq -e trailingblank3 3 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_seq_len -e 33 trailingblank1 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_seq_len64 -e 72 trailingblank2 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -e fastqs.fq.expected.fai PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t fai_line_length -e 63 FAKE0005_3 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t fai_line_length -e 144 SRR014849.203935_3 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_has_seq -e 1 SRR014849.203935_3 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_has_seq -e 0 absent PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_iseq -e FAKE0005_1 0 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_seq_len -e 453 FSRRS4401CM938_1 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_seq_len64 -e 309 FSRRS4401AOV6A_4 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai trailingblank2:28-33 trailingblank3:4-5 bar:4-5 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t fai_fetch trailingblank2:28-33 trailingblank3:4-5 bar:4-5 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_fetch_seq64 trailingblank2:28-33 trailingblank3:4-5 bar:4-5 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t fai_adjust_region trailingblank2:28-33 trailingblank3:4-5 bar:4-5 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q FAKE0006_1:4-12 FSRRS4401BE7HA_1:81-120 FAKE0010_2 SRR014849.50939_3:71-90 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t fai_fetch FAKE0006_1:4-12 FSRRS4401BE7HA_1:81-120 FAKE0010_2 SRR014849.50939_3:71-90 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t faidx_fetch_seq64 FAKE0006_1:4-12 FSRRS4401BE7HA_1:81-120 FAKE0010_2 SRR014849.50939_3:71-90 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai FAKE0006_1:4-12 FSRRS4401BE7HA_1:81-120 FAKE0010_2 SRR014849.50939_3:71-90 PASS : $test_faidx -i ce.fa.tmp.gz -f ce.fa.tmp.gz.fai -g ce.fa.tmp.gz.gzi -e ../ce.fa.fai PASS : $test_faidx -i ce.fa.tmp.gz -f ce.fa.tmp.gz.fai -g ce.fa.tmp.gz.gzi CHROMOSOME_I:5001-5125 CHROMOSOME_X:101-225 Expected passes: 25 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 cd test/sam_filter && ./filter.sh filter.tst Testing sam_filter... PASS : $tv -i 'filter=qname =~ "\.1" && cigar =~ "D"' ../ce#1000.sam PASS : $tv -i 'filter=rname=="CHROMOSOME_II"' ../ce#5b.sam PASS : $tv -i 'filter=rname=~"CHROMOSOME_II"' ../ce#5b.sam PASS : $tv -i 'filter=cigar=~"D"' ../ce#1000.sam PASS : $tv -i 'filter=seq =~ "(AT){2}"' ../ce#1000.sam PASS : $tv -i 'filter=library=="x"' ../xx#rg.sam PASS : $tv -i 'filter=library!="x"' ../xx#rg.sam PASS : $tv -i 'filter=pos % 23 == 11' ../ce#1000.sam | grep -E -cv '^@' PASS : $tv -i 'filter=qlen/(flag*mapq+pos)>5' ../ce#1000.sam | grep -E -cv '^@' PASS : $tv -i 'filter=[NM]>=10 || [MD]=~"A.*A.*A"' -t4 ../ce#1000.sam | grep -E -cv '^@' PASS : $tv -i 'filter=length(seq) != qlen' ../ce#5b.sam | grep -E -cv '^@' PASS : $tv -i 'filter=min(qual) >= 20' ../ce#1000.sam | grep -E -cv '^@' PASS : $tv -i 'filter=max(qual) <= 20' ../ce#1000.sam | grep -E -cv '^@' PASS : $tv -i 'filter=avg(qual) >= 20 && avg(qual) <= 30' ../ce#1000.sam | grep -E -cv '^@' PASS : $tv -i 'filter=sclen>=20' ../realn02.sam | grep -E -v '^@' PASS : $tv -i 'filter=rlen<50' ../realn02.sam | grep -E -v '^@' PASS : $tv -i 'filter=qlen>100' ../realn02.sam | grep -E -v '^@' PASS : $tv -i 'filter=hclen>=4' ../c1#clip.sam | grep -E -v '^@' Expected passes: 18 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 cd test/tabix && ./test-tabix.sh tabix.tst Testing tabix... PASS : $tabix -f -p vcf vcf_file.tbi.tmp.vcf.gz PASS : $tabix vcf_file.tbi.tmp.vcf.gz 1:3000151-3000151 PASS : $tabix -u vcf_file.tbi.tmp.vcf.gz 1:3000151-3000151 PASS : $tabix vcf_file.tbi.tmp.vcf.gz 2:3199812-3199812 PASS : $tabix -u vcf_file.tbi.tmp.vcf.gz 2:3199812-3199812 PASS : $tabix -f -C -p vcf vcf_file.csi.tmp.vcf.gz PASS : $tabix vcf_file.csi.tmp.vcf.gz 1:3000151-3000151 PASS : $tabix -u vcf_file.csi.tmp.vcf.gz 1:3000151-3000151 PASS : $tabix vcf_file.csi.tmp.vcf.gz 2:3199812-3199812 PASS : $tabix -u vcf_file.csi.tmp.vcf.gz 2:3199812-3199812 PASS : $tabix -f vcf_file.tmp.bcf PASS : $tabix vcf_file.tmp.bcf 1:3000151-3000151 PASS : $tabix -u vcf_file.tmp.bcf 1:3000151-3000151 PASS : $tabix vcf_file.tmp.bcf 2:3199812-3199812 PASS : $tabix -u vcf_file.tmp.bcf 2:3199812-3199812 PASS : $tabix -f -p vcf large_chr.tmp.vcf.gz (must exit non-zero) PASS : $tabix -f -C -p vcf large_chr.tmp.vcf.gz PASS : $tabix large_chr.tmp.vcf.gz chr20:1-2147483647 PASS : $tabix -u large_chr.tmp.vcf.gz chr20:1-2147483647 PASS : $tabix -f -p vcf vcf_overlaps.tmp.vcf.gz PASS : $tabix vcf_overlaps.tmp.vcf.gz chr1:1000002-1000002 chr1:1000007-1000007 chr2:1000001-1000001 chr2:1000009-1000009 chr3:1000002-1000002 chr3:1000006-1000006 PASS : $tabix -u vcf_overlaps.tmp.vcf.gz chr1:1000002-1000002 chr1:1000007-1000007 chr2:1000001-1000001 chr2:1000009-1000009 chr3:1000002-1000002 chr3:1000006-1000006 PASS : $tabix -R vcf_overlaps.tmp.regions vcf_overlaps.tmp.vcf.gz PASS : $tabix -u -R vcf_overlaps.tmp.regions vcf_overlaps.tmp.vcf.gz PASS : $tabix -T vcf_overlaps.tmp.regions vcf_overlaps.tmp.vcf.gz PASS : $tabix -f vcf_overlaps.tmp.bcf PASS : $tabix vcf_overlaps.tmp.bcf chr1:1000002-1000002 chr1:1000007-1000007 chr2:1000001-1000001 chr2:1000009-1000009 chr3:1000002-1000002 chr3:1000006-1000006 PASS : $tabix -u vcf_overlaps.tmp.bcf chr1:1000002-1000002 chr1:1000007-1000007 chr2:1000001-1000001 chr2:1000009-1000009 chr3:1000002-1000002 chr3:1000006-1000006 PASS : $tabix -R vcf_overlaps.tmp.regions vcf_overlaps.tmp.bcf PASS : $tabix -u -R vcf_overlaps.tmp.regions vcf_overlaps.tmp.bcf PASS : $tabix -T vcf_overlaps.tmp.regions vcf_overlaps.tmp.bcf PASS : $tabix -f -p bed bed_file.tbi.tmp.bed.gz PASS : $tabix bed_file.tbi.tmp.bed.gz Y:100200-100200 PASS : $tabix -u bed_file.tbi.tmp.bed.gz Y:100200-100200 PASS : $tabix -u bed_file.tbi.tmp.bed.gz Y:100201-100201 Y:100801-100801 PASS : $tabix -f -p gff gff_file.tbi.tmp.gff.gz PASS : $tabix gff_file.tbi.tmp.gff.gz X:2934832-2935190 PASS : $tabix -u gff_file.tbi.tmp.gff.gz X:2934832-2935190 PASS : $tabix -u gff_file.tbi.tmp.gff.gz X:2935191-2936741 X:2936864-2938094 X:2943200-2945997 PASS : $tabix --separate-regions bed_file.tbi.tmp.bed.gz X:1100-1400 Y:100000-100550 Z:100000-100005 PASS : $tabix -f -p bed bed_file.tbi.tmp.bed.gz -@ 2 PASS : $tabix vcf_file.tbi.tmp.vcf.gz 1:3000151-3000151 --threads 2 PASS : $tabix -u vcf_file.tbi.tmp.vcf.gz 1:3000151-3000151 --threads 2 Expected passes: 43 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 cd test/mpileup && ./test-pileup.sh mpileup.tst Testing (m)pileup... PASS : $pileup mp_D.sam PASS : $pileup -m mp_D.sam PASS : $pileup mp_DI.sam PASS : $pileup -m mp_DI.sam PASS : $pileup mp_I.sam PASS : $pileup -m mp_I.sam PASS : $pileup mp_P.sam PASS : $pileup -m mp_P.sam PASS : $pileup mp_ID.sam PASS : $pileup -m mp_ID.sam PASS : $pileup mp_N.sam PASS : $pileup -m mp_N.sam PASS : $pileup mp_N2.sam PASS : $pileup -m mp_N2.sam PASS : $pileup c1#pad1.sam PASS : $pileup -m c1#pad1.sam PASS : $pileup c1#pad2.sam PASS : $pileup -m c1#pad2.sam PASS : $pileup c1#pad3.sam PASS : $pileup -m c1#pad3.sam PASS : $pileup -m small.bam PASS : $pileup -m mp_overlap1.sam PASS : $pileup -m mp_overlap2.sam Expected passes: 23 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 cd test/fastq && ./test-fastq.sh Testing fastq support PASS : $tview minimal.fq PASS : $tview minimal.fa PASS : $tview multiline.fq PASS : $tview multiline.fa PASS : $tview -i fastq_aux longline.fq PASS : $tview single.fq PASS : $tview single.fa PASS : $tview -i fastq_aux single.fq PASS : $tview -i fastq_aux single.fa PASS : $tview interleaved.fq PASS : $tview interleaved.fa PASS : $tview -i fastq_aux interleaved.fq PASS : $tview -i fastq_aux interleaved.fa PASS : $tview -i fastq_casava interleaved_casava.fq PASS : $tview -i fastq_barcode=OX -i fastq_casava interleaved_casava.fq PASS : $tview -i fastq_casava interleaved_casava.fa PASS : $tview -i fastq_barcode=OX -i fastq_casava interleaved_casava.fa PASS : $tview -i fastq_casava filter_casava.fq PASS : $tview -i fastq_casava filter_casava.fa PASS : $tview -i fastq_aux r1.fq PASS : $tview -i fastq_aux r2.fq PASS : $tview -i fastq_aux r1.fa PASS : $tview -i fastq_aux r2.fa PASS : $tview -i fastq_name2 name2.fq PASS : $tview -i fastq_name2 name2.fa PASS : $tview -i fastq_umi=RX UMI.fq PASS : $tview -f minimal.sam PASS : $tview -F minimal.sam PASS : $tview -f -o fastq_aux single_aux.sam PASS : $tview -F -o fastq_aux single_aux.sam PASS : $tview -f -o fastq_aux -o fastq_rnum inter_aux.sam PASS : $tview -F -o fastq_aux -o fastq_rnum inter_aux.sam PASS : $tview -f -o fastq_casava inter_casava.sam PASS : $tview -f -o fastq_barcode=OX -o fastq_casava inter_casavaOX.sam PASS : $tview -F -o fastq_casava inter_casava.sam PASS : $tview -F -o fastq_barcode=OX -o fastq_casava inter_casavaOX.sam PASS : $tview -f -o fastq_casava filter_casava.sam PASS : $tview -F -o fastq_casava filter_casava.sam PASS : $tview -f -o fastq_aux -o fastq_rnum r1.sam PASS : $tview -f -o fastq_aux -o fastq_rnum r2.sam PASS : $tview -F -o fastq_aux -o fastq_rnum r1.sam PASS : $tview -F -o fastq_aux -o fastq_rnum r2.sam PASS : $tview -f -o fastq_rnum -o fastq_umi UMI.sam Expected passes: 43 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 cd test/base_mods && ./base-mods.sh base-mods.tst Testing base-modifications... PASS : $test_mod MM-chebi.sam PASS : $test_mod MM-double.sam PASS : $test_mod MM-multi.sam PASS : $test_mod MM-explicit.sam PASS : $test_mod -x MM-explicit.sam PASS : $test_mod -f 1 MM-explicit.sam PASS : $test_mod MM-not-all-modded.sam PASS : $pileup_mod < MM-pileup.sam PASS : $pileup_mod < MM-pileup2.sam PASS : $pileup_mod < MM-MNp.sam PASS : $pileup_mod < MM-MNf1.sam (must exit non-zero) PASS : $pileup_mod < MM-MNf2.sam (must exit non-zero) PASS : $test_mod < MM-MNf1.sam (must exit non-zero) PASS : $test_mod < MM-MNf2.sam (must exit non-zero) PASS : $test_mod < MM-bounds+.sam (must exit non-zero) PASS : $test_mod < MM-bounds-.sam (must exit non-zero) PASS : $test_mod -f 1 MM-variants.sam Expected passes: 17 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 cd test/tlen && ./tlen.sh tlen.tst Testing CRAM TLEN auto-creation... PASS : $test_view a7.cram PASS : $test_view a7b.cram PASS : $test_view a8.cram PASS : $test_view a8b.cram PASS : $test_view a9.cram PASS : $test_view a9b.cram PASS : $test_view b7.cram PASS : $test_view b7b.cram PASS : $test_view b8.cram PASS : $test_view b8b.cram PASS : $test_view c7.cram PASS : $test_view c7b.cram PASS : $test_view c8.cram PASS : $test_view c8b.cram PASS : $test_view d7.cram PASS : $test_view d7b.cram PASS : $test_view d4.cram PASS : $test_view d4b.cram PASS : $test_view d4c.cram PASS : $test_view d4d.cram PASS : $test_view d4e.cram PASS : $test_view d4f.cram PASS : $test_view d5.cram PASS : $test_view d5b.cram PASS : $test_view d5c.cram PASS : $test_view d5d.cram PASS : $test_view d5e.cram PASS : $test_view d5f.cram PASS : $test_view a4.cram PASS : $test_view a5.cram Expected passes: 30 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 REF_PATH=: test/sam test/ce.fa test/faidx/faidx.fa test/faidx/fastqs.fq (Expect trailing 'x' message for " -1,001x") [W::hts_parse_decimal] Ignoring unknown characters after -1,001[x] (Expect trailing 'k' message for "1.5e+3k") [W::hts_parse_decimal] Ignoring unknown characters after 1.5e+3[k] (Expect dropped fraction message for "12.3456k") [W::hts_parse_decimal] Discarding fractional part of 12.3456k [W::hts_parse_decimal] Discarding fractional part of 12.3456k (Expect invalid numeric message for "A") [W::hts_parse_decimal] Invalid numeric value A[truncated] (Expect invalid numeric message for "G") [W::hts_parse_decimal] Invalid numeric value G[truncated] (Expect invalid numeric message for " +/-") [W::hts_parse_decimal] Invalid numeric value +/-[truncated] (Expect invalid numeric message for " -.e+9999") [W::hts_parse_decimal] Invalid numeric value -.e+9999[truncated] test/test-regidx cd test && \ if test "xhfile_libcurl.so hfile_gcs.so hfile_s3.so" != "x"; then \ REF_PATH=: HTS_PATH=.. ./with-shlib.sh ./test.pl --ref-cache-bin ../ref_cache/ref-cache ${TEST_OPTS:-} ; \ else \ REF_PATH=: ./test.pl --ref-cache-bin ../ref_cache/ref-cache ${TEST_OPTS:-} ; \ fi bgzip round-trip no threads: .. ok bgzip text mode round-trip no threads: .. ok bgzip -b no threads: .. ok bgzip -b -I no threads: .. ok bgzip multifile no threads: .. ok bgzip --output no threads: .. ok bgzip round-trip 4 threads: .. ok bgzip text mode round-trip 4 threads: .. ok bgzip -b 4 threads: .. ok bgzip -b -I 4 threads: .. ok bgzip multifile 4 threads: .. ok bgzip --output 4 threads: .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view -l 0 -b -m 14 -x /tmp/ZoqikH74vH/index.bam.csi /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.sam > /tmp/ZoqikH74vH/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -c /tmp/ZoqikH74vH/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view -l 0 -b -m 0 -x /tmp/ZoqikH74vH/index.bam.bai /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.sam > /tmp/ZoqikH74vH/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -b /tmp/ZoqikH74vH/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view -l 0 -z -m 14 -x /tmp/ZoqikH74vH/index.sam.gz.csi /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.sam > /tmp/ZoqikH74vH/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -c /tmp/ZoqikH74vH/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view -l 0 -z -m 0 -x /tmp/ZoqikH74vH/index.sam.gz.bai /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.sam > /tmp/ZoqikH74vH/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -b /tmp/ZoqikH74vH/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view -l 0 -z -m 14 -x /tmp/ZoqikH74vH/index.sam.gz.csi /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index_dos.sam > /tmp/ZoqikH74vH/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -c /tmp/ZoqikH74vH/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view -l 0 -z -m 0 -x /tmp/ZoqikH74vH/index.sam.gz.bai /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index_dos.sam > /tmp/ZoqikH74vH/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -b /tmp/ZoqikH74vH/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view -l 0 -C -x /tmp/ZoqikH74vH/index.cram.crai /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.sam > /tmp/ZoqikH74vH/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index /tmp/ZoqikH74vH/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view -p /tmp/ZoqikH74vH/index3_rgn.sam /tmp/ZoqikH74vH/index3.cram CHROMOSOME_I:5000-5100 .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view -M -p /tmp/ZoqikH74vH/index3_rgnm.sam /tmp/ZoqikH74vH/index3.cram CHROMOSOME_I:5000-5100 .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view -l 0 -b -m 14 -x /tmp/ZoqikH74vH/index.bcf.csi /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.vcf > /tmp/ZoqikH74vH/index.bcf .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -c /tmp/ZoqikH74vH/index.bcf .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view -l 0 -z -m 14 -x /tmp/ZoqikH74vH/index.vcf.gz.csi /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.vcf > /tmp/ZoqikH74vH/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -c /tmp/ZoqikH74vH/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view -l 0 -z -m 0 -x /tmp/ZoqikH74vH/index.vcf.gz.tbi /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.vcf > /tmp/ZoqikH74vH/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -t /tmp/ZoqikH74vH/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/tabix /tmp/ZoqikH74vH/index.vcf.gz##idx##/tmp/ZoqikH74vH/index.vcf.gz.tbi 1:10000060-10000060 .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view /tmp/ZoqikH74vH/index2.bam 1:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view /tmp/ZoqikH74vH/index2.bam 1:2000000-2000000 .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view /tmp/ZoqikH74vH/index2.bam 2:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view /tmp/ZoqikH74vH/index2.bam 2:2000000-2000000 .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view -@4 -l 0 -b -m 14 -x /tmp/ZoqikH74vH/index.bam.csi /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.sam > /tmp/ZoqikH74vH/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -c /tmp/ZoqikH74vH/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view -@4 -l 0 -b -m 0 -x /tmp/ZoqikH74vH/index.bam.bai /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.sam > /tmp/ZoqikH74vH/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -b /tmp/ZoqikH74vH/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view -@4 -l 0 -z -m 14 -x /tmp/ZoqikH74vH/index.sam.gz.csi /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.sam > /tmp/ZoqikH74vH/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -c /tmp/ZoqikH74vH/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view -@4 -l 0 -z -m 0 -x /tmp/ZoqikH74vH/index.sam.gz.bai /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.sam > /tmp/ZoqikH74vH/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -b /tmp/ZoqikH74vH/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view -@4 -l 0 -z -m 14 -x /tmp/ZoqikH74vH/index.sam.gz.csi /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index_dos.sam > /tmp/ZoqikH74vH/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -c /tmp/ZoqikH74vH/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view -@4 -l 0 -z -m 0 -x /tmp/ZoqikH74vH/index.sam.gz.bai /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index_dos.sam > /tmp/ZoqikH74vH/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -b /tmp/ZoqikH74vH/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view -@4 -l 0 -C -x /tmp/ZoqikH74vH/index.cram.crai /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.sam > /tmp/ZoqikH74vH/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index /tmp/ZoqikH74vH/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view -@4 -p /tmp/ZoqikH74vH/index3_rgn.sam /tmp/ZoqikH74vH/index3.cram CHROMOSOME_I:5000-5100 .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view -@4 -M -p /tmp/ZoqikH74vH/index3_rgnm.sam /tmp/ZoqikH74vH/index3.cram CHROMOSOME_I:5000-5100 .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view -@4 -l 0 -b -m 14 -x /tmp/ZoqikH74vH/index.bcf.csi /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.vcf > /tmp/ZoqikH74vH/index.bcf .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -c /tmp/ZoqikH74vH/index.bcf .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view -@4 -l 0 -z -m 14 -x /tmp/ZoqikH74vH/index.vcf.gz.csi /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.vcf > /tmp/ZoqikH74vH/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -c /tmp/ZoqikH74vH/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view -@4 -l 0 -z -m 0 -x /tmp/ZoqikH74vH/index.vcf.gz.tbi /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.vcf > /tmp/ZoqikH74vH/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -t /tmp/ZoqikH74vH/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/tabix /tmp/ZoqikH74vH/index.vcf.gz##idx##/tmp/ZoqikH74vH/index.vcf.gz.tbi 1:10000060-10000060 .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view /tmp/ZoqikH74vH/index2.bam 1:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view /tmp/ZoqikH74vH/index2.bam 1:2000000-2000000 .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view /tmp/ZoqikH74vH/index2.bam 2:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view /tmp/ZoqikH74vH/index2.bam 2:2000000-2000000 .. ok test_view testing multi-ref CRAM modes: ./test_view -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=-1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ ./test_view -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=0 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ ./test_view -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ .. ok test_view testing multi-ref CRAM modes: ./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=-1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ ./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=0 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ ./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ .. ok test_view testing auxf#values.sam, ref auxf.fa: ./test_view -S -l0 -b auxf#values.sam > auxf#values.tmp.bam ./test_view auxf#values.tmp.bam > auxf#values.tmp.bam.sam_ ./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_ ./test_view -t auxf.fa -S -C -o VERSION=2.1 auxf#values.sam > auxf#values.tmp.cram ./test_view -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ ./test_view -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram ./test_view auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_ ./test_view -i reference=auxf.fa auxf#values_java.cram > auxf#values_java.tmp.sam_ ./compare_sam.pl -Baux -nomd auxf#values.sam auxf#values_java.tmp.sam_ .. ok test_view testing c1#bounds.sam, ref c1.fa: ./test_view -S -l0 -b c1#bounds.sam > c1#bounds.tmp.bam ./test_view c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_ ./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#bounds.sam > c1#bounds.tmp.cram ./test_view -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram ./test_view c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#clip.sam, ref c1.fa: ./test_view -S -l0 -b c1#clip.sam > c1#clip.tmp.bam ./test_view c1#clip.tmp.bam > c1#clip.tmp.bam.sam_ ./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#clip.sam > c1#clip.tmp.cram ./test_view -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.bam > c1#clip.tmp.bam.cram ./test_view c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#noseq.sam, ref c1.fa: ./test_view -S -l0 -b c1#noseq.sam > c1#noseq.tmp.bam ./test_view c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_ ./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#noseq.sam > c1#noseq.tmp.cram ./test_view -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram ./test_view c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad1.sam, ref c1.fa: ./test_view -S -l0 -b c1#pad1.sam > c1#pad1.tmp.bam ./test_view c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_ ./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad1.sam > c1#pad1.tmp.cram ./test_view -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram ./test_view c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad2.sam, ref c1.fa: ./test_view -S -l0 -b c1#pad2.sam > c1#pad2.tmp.bam ./test_view c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_ ./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad2.sam > c1#pad2.tmp.cram ./test_view -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram ./test_view c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad3.sam, ref c1.fa: ./test_view -S -l0 -b c1#pad3.sam > c1#pad3.tmp.bam ./test_view c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_ ./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad3.sam > c1#pad3.tmp.cram ./test_view -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram ./test_view c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#unknown.sam, ref c1.fa: ./test_view -S -l0 -b c1#unknown.sam > c1#unknown.tmp.bam ./test_view c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_ ./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#unknown.sam > c1#unknown.tmp.cram ./test_view -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram ./test_view c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_ .. ok test_view testing c2#pad.sam, ref c2.fa: ./test_view -S -l0 -b c2#pad.sam > c2#pad.tmp.bam ./test_view c2#pad.tmp.bam > c2#pad.tmp.bam.sam_ ./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_ ./test_view -t c2.fa -S -C -o VERSION=2.1 c2#pad.sam > c2#pad.tmp.cram ./test_view -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_ ./test_view -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.bam > c2#pad.tmp.bam.cram ./test_view c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#1.sam, ref ce.fa: ./test_view -S -l0 -b ce#1.sam > ce#1.tmp.bam ./test_view ce#1.tmp.bam > ce#1.tmp.bam.sam_ ./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#1.sam > ce#1.tmp.cram ./test_view -D ce#1.tmp.cram > ce#1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#1.tmp.bam > ce#1.tmp.bam.cram ./test_view ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#1000.sam, ref ce.fa: ./test_view -S -b ce#1000.sam > ce#1000.tmp.bam ./test_view ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ ./test_view -S -l0 -b ce#1000.sam > ce#1000.tmp.bam ./test_view ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#1000.sam > ce#1000.tmp.cram ./test_view -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1000.sam > ce#1000.tmp.cram ./test_view -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.bam > ce#1000.tmp.bam.cram ./test_view ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#2.sam, ref ce.fa: ./test_view -S -l0 -b ce#2.sam > ce#2.tmp.bam ./test_view ce#2.tmp.bam > ce#2.tmp.bam.sam_ ./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#2.sam > ce#2.tmp.cram ./test_view -D ce#2.tmp.cram > ce#2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#2.tmp.bam > ce#2.tmp.bam.cram ./test_view ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#5.sam, ref ce.fa: ./test_view -S -l0 -b ce#5.sam > ce#5.tmp.bam ./test_view ce#5.tmp.bam > ce#5.tmp.bam.sam_ ./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#5.sam > ce#5.tmp.cram ./test_view -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#5.tmp.bam > ce#5.tmp.bam.cram ./test_view ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#5b.sam, ref ce.fa: ./test_view -S -l0 -b ce#5b.sam > ce#5b.tmp.bam ./test_view ce#5b.tmp.bam > ce#5b.tmp.bam.sam_ ./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#5b.sam > ce#5b.tmp.cram ./test_view -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.bam > ce#5b.tmp.bam.cram ./test_view ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_ ./test_view -i reference=ce.fa ce#5b_java.cram > ce#5b_java.tmp.sam_ ./compare_sam.pl -Baux -nomd ce#5b.sam ce#5b_java.tmp.sam_ .. ok test_view testing ce#large_seq.sam, ref ce.fa: ./test_view -S -l0 -b ce#large_seq.sam > ce#large_seq.tmp.bam ./test_view ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_ ./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#large_seq.sam > ce#large_seq.tmp.cram ./test_view -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram ./test_view ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#supp.sam, ref ce.fa: ./test_view -S -l0 -b ce#supp.sam > ce#supp.tmp.bam ./test_view ce#supp.tmp.bam > ce#supp.tmp.bam.sam_ ./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#supp.sam > ce#supp.tmp.cram ./test_view -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.bam > ce#supp.tmp.bam.cram ./test_view ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#tag_depadded.sam, ref ce.fa: ./test_view -S -l0 -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam ./test_view ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_ ./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram ./test_view -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram ./test_view ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#tag_padded.sam, ref ce.fa: ./test_view -S -l0 -b ce#tag_padded.sam > ce#tag_padded.tmp.bam ./test_view ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_ ./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#tag_padded.sam > ce#tag_padded.tmp.cram ./test_view -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram ./test_view ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#unmap.sam, ref ce.fa: ./test_view -S -l0 -b ce#unmap.sam > ce#unmap.tmp.bam ./test_view ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_ ./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap.sam > ce#unmap.tmp.cram ./test_view -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram ./test_view ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#unmap1.sam, ref ce.fa: ./test_view -S -l0 -b ce#unmap1.sam > ce#unmap1.tmp.bam ./test_view ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_ ./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap1.sam > ce#unmap1.tmp.cram ./test_view -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram ./test_view ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#unmap2.sam, ref ce.fa: ./test_view -S -l0 -b ce#unmap2.sam > ce#unmap2.tmp.bam ./test_view ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_ ./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap2.sam > ce#unmap2.tmp.cram ./test_view -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram ./test_view ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_ .. ok test_view testing md#1.sam, ref md.fa: ./test_view -S -l0 -b md#1.sam > md#1.tmp.bam ./test_view md#1.tmp.bam > md#1.tmp.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.sam_ ./test_view -t md.fa -S -C -o VERSION=2.1 md#1.sam > md#1.tmp.cram ./test_view -D md#1.tmp.cram > md#1.tmp.cram.sam_ ./compare_sam.pl md#1.sam md#1.tmp.cram.sam_ ./test_view -t md.fa -C -o VERSION=3.0 md#1.tmp.bam > md#1.tmp.bam.cram ./test_view md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#blank.sam, ref xx.fa: ./test_view -S -l0 -b xx#blank.sam > xx#blank.tmp.bam ./test_view xx#blank.tmp.bam > xx#blank.tmp.bam.sam_ ./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#blank.sam > xx#blank.tmp.cram ./test_view -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.bam > xx#blank.tmp.bam.cram ./test_view xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#large_aux.sam, ref xx.fa: ./test_view -S -l0 -b xx#large_aux.sam > xx#large_aux.tmp.bam ./test_view xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_ ./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#large_aux.sam > xx#large_aux.tmp.cram ./test_view -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram ./test_view xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_ ./test_view -i reference=xx.fa xx#large_aux_java.cram > xx#large_aux_java.tmp.sam_ [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 30 vs 20 ./compare_sam.pl -Baux -nomd xx#large_aux.sam xx#large_aux_java.tmp.sam_ .. ok test_view testing xx#large_aux2.sam, ref xx.fa: ./test_view -S -l0 -b xx#large_aux2.sam > xx#large_aux2.tmp.bam ./test_view xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_ ./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#large_aux2.sam > xx#large_aux2.tmp.cram ./test_view -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram ./test_view xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#MD.sam, ref xx.fa: ./test_view -S -l0 -b xx#MD.sam > xx#MD.tmp.bam ./test_view xx#MD.tmp.bam > xx#MD.tmp.bam.sam_ ./compare_sam.pl xx#MD.sam xx#MD.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#MD.sam > xx#MD.tmp.cram ./test_view -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.bam > xx#MD.tmp.bam.cram ./test_view xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#MD2.sam, ref xx.fa: ./test_view -S -l0 -b xx#MD2.sam > xx#MD2.tmp.bam ./test_view xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_ ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#MD2.sam > xx#MD2.tmp.cram ./test_view -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram ./test_view xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#minimal.sam, ref xx.fa: ./test_view -S -l0 -b xx#minimal.sam > xx#minimal.tmp.bam ./test_view xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_ ./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#minimal.sam > xx#minimal.tmp.cram ./test_view -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram ./test_view xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#pair.sam, ref xx.fa: ./test_view -S -l0 -b xx#pair.sam > xx#pair.tmp.bam ./test_view xx#pair.tmp.bam > xx#pair.tmp.bam.sam_ ./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#pair.sam > xx#pair.tmp.cram ./test_view -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.bam > xx#pair.tmp.bam.cram ./test_view xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#repeated.sam, ref xx.fa: ./test_view -S -l0 -b xx#repeated.sam > xx#repeated.tmp.bam ./test_view xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_ ./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#repeated.sam > xx#repeated.tmp.cram ./test_view -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram ./test_view xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#repeated2.sam, ref xx.fa: ./test_view -S -l0 -b xx#repeated2.sam > xx#repeated2.tmp.bam ./test_view xx#repeated2.tmp.bam > xx#repeated2.tmp.bam.sam_ ./compare_sam.pl xx#repeated2.sam xx#repeated2.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#repeated2.sam > xx#repeated2.tmp.cram [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 100 vs 20 ./test_view -D xx#repeated2.tmp.cram > xx#repeated2.tmp.cram.sam_ [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 100 vs 20 ./compare_sam.pl -nomd xx#repeated2.sam xx#repeated2.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#repeated2.tmp.bam > xx#repeated2.tmp.bam.cram [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 100 vs 20 ./test_view xx#repeated2.tmp.bam.cram > xx#repeated2.tmp.bam.cram.bam.sam_ [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 100 vs 20 ./compare_sam.pl -nomd xx#repeated2.sam xx#repeated2.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#rg.sam, ref xx.fa: ./test_view -S -l0 -b xx#rg.sam > xx#rg.tmp.bam ./test_view xx#rg.tmp.bam > xx#rg.tmp.bam.sam_ ./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#rg.sam > xx#rg.tmp.cram ./test_view -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.bam > xx#rg.tmp.bam.cram ./test_view xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#tlen.sam, ref xx.fa: ./test_view -S -l0 -b xx#tlen.sam > xx#tlen.tmp.bam ./test_view xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_ ./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#tlen.sam > xx#tlen.tmp.cram ./test_view -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram ./test_view xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#tlen2.sam, ref xx.fa: ./test_view -S -l0 -b xx#tlen2.sam > xx#tlen2.tmp.bam ./test_view xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_ ./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#tlen2.sam > xx#tlen2.tmp.cram ./test_view -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram ./test_view xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#triplet.sam, ref xx.fa: ./test_view -S -l0 -b xx#triplet.sam > xx#triplet.tmp.bam ./test_view xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_ ./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#triplet.sam > xx#triplet.tmp.cram ./test_view -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram ./test_view xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#u.sam, ref xx.fa: ./test_view -S -l0 -b xx#u.sam > xx#u.tmp.bam ./test_view xx#u.tmp.bam > xx#u.tmp.bam.sam_ ./compare_sam.pl xx#u.sam xx#u.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#u.sam > xx#u.tmp.cram ./test_view -D xx#u.tmp.cram > xx#u.tmp.cram.sam_ ./compare_sam.pl -nomd xx#u.sam xx#u.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#u.tmp.bam > xx#u.tmp.bam.cram ./test_view xx#u.tmp.bam.cram > xx#u.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#u.sam xx#u.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#unsorted.sam, ref xx.fa: ./test_view -S -l0 -b xx#unsorted.sam > xx#unsorted.tmp.bam ./test_view xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_ ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#unsorted.sam > xx#unsorted.tmp.cram ./test_view -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram ./test_view xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_ .. ok test_view testing BAM records in multiple BGZF blocks: ./test_view -p bgzf_boundaries/bgzf_boundaries1.bam.tmp.sam bgzf_boundaries/bgzf_boundaries1.bam ./compare_sam.pl bgzf_boundaries/bgzf_boundaries1.bam.tmp.sam ce#1.sam ./test_view -p bgzf_boundaries/bgzf_boundaries2.bam.tmp.sam bgzf_boundaries/bgzf_boundaries2.bam ./compare_sam.pl bgzf_boundaries/bgzf_boundaries2.bam.tmp.sam ce#1.sam ./test_view -p bgzf_boundaries/bgzf_boundaries3.bam.tmp.sam bgzf_boundaries/bgzf_boundaries3.bam ./compare_sam.pl bgzf_boundaries/bgzf_boundaries3.bam.tmp.sam ce#1.sam ./test_view -b -l 0 -p bgzf_boundaries/large_rec.tmp.sam.bam bgzf_boundaries/large_rec.tmp.sam ./test_view -p bgzf_boundaries/large_rec.tmp.sam.bam.sam bgzf_boundaries/large_rec.tmp.sam.bam ./compare_sam.pl bgzf_boundaries/large_rec.tmp.sam bgzf_boundaries/large_rec.tmp.sam.bam.sam .. ok test_view testing embed_ref=2: ./test_view -C -p ce#1000_er.tmp.cram ce#1000.sam [W::cram_get_ref] Failed to populate reference "CHROMOSOME_I" [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam ./test_view -C -p c1#bounds_er.tmp.cram c1#bounds.sam [W::cram_get_ref] Failed to populate reference "c1" [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -p c1#bounds_er.tmp.cram.sam c1#bounds_er.tmp.cram ./compare_sam.pl c1#bounds.sam c1#bounds_er.tmp.cram.sam ./test_view -o embed_ref=2 -o seqs_per_slice=3 -o bases_per_slice=1000000 -C -p embed_MD.tmp.cram embed_MD.sam ./test_view -p embed_MD.tmp.cram.sam embed_MD.tmp.cram ./compare_sam.pl embed_MD.sam embed_MD.tmp.cram.sam ./test_view -o embed_ref=2 -o no_ref -C -p embed_del.tmp.cram embed_del.sam ./test_view -p embed_del.tmp.cram.sam embed_del.tmp.cram ./compare_sam.pl embed_del.sam embed_del.tmp.cram.sam .. ok test_view testing region queries: ./test_view -i reference=ce.fa range.cram CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp ./compare_sam.pl range.tmp range.out ./test_view range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp ./compare_sam.pl range.tmp range.out ./test_view -i reference=ce.fa -M range.cram CHROMOSOME_I:1122-1122 CHROMOSOME_II:1136-1136 CHROMOSOME_II:1241-1241 CHROMOSOME_II:1267-1267 CHROMOSOME_II:1326-1326 CHROMOSOME_II:1345-1345 CHROMOSOME_II:1353-1353 CHROMOSOME_II:1366-1366 CHROMOSOME_II:1416-1416 CHROMOSOME_II:1459-1459 CHROMOSOME_II:1536-1536 > range.tmp ./compare_sam.pl range.tmp range.out2 ./test_view -M range.bam CHROMOSOME_I:1122-1122 CHROMOSOME_II:1136-1136 CHROMOSOME_II:1241-1241 CHROMOSOME_II:1267-1267 CHROMOSOME_II:1326-1326 CHROMOSOME_II:1345-1345 CHROMOSOME_II:1353-1353 CHROMOSOME_II:1366-1366 CHROMOSOME_II:1416-1416 CHROMOSOME_II:1459-1459 CHROMOSOME_II:1536-1536 > range.tmp ./compare_sam.pl range.tmp range.out2 .. ok test_view testing BAM files with absent @SQ lines: ./test_view -p no_hdr_sq_1.tmp.sam no_hdr_sq_1.bam ./compare_sam.pl no_hdr_sq_1.tmp.sam no_hdr_sq_1.expected.sam ./test_view -p no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.bam CHROMOSOME_I ./compare_sam.pl no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.expected.sam .. ok test_view testing large (> 2Gbases) positions: ./test_view -z -p longrefs/longref.tmp.sam.gz -x longrefs/longref.tmp.sam.gz.csi.otf -m 14 longrefs/longref.sam ./test_view -p longrefs/longref.tmp.sam_ longrefs/longref.tmp.sam.gz ./compare_sam.pl longrefs/longref.sam longrefs/longref.tmp.sam_ test_view: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -c longrefs/longref.tmp.sam.gz .. ok ./test_view -p longrefs/longref_itr.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 ./compare_sam.pl longrefs/longref_itr.expected.sam longrefs/longref_itr.tmp.sam ./test_view -M -p longrefs/longref_multi.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 CHROMOSOME_I:10000000100-10000000110 ./compare_sam.pl longrefs/longref_multi.expected.sam longrefs/longref_multi.tmp.sam .. ok test_view testing auxf#values.sam, ref auxf.fa: ./test_view -@4 -S -l0 -b auxf#values.sam > auxf#values.tmp.bam ./test_view -@4 auxf#values.tmp.bam > auxf#values.tmp.bam.sam_ ./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_ ./test_view -@4 -t auxf.fa -S -C -o VERSION=2.1 auxf#values.sam > auxf#values.tmp.cram ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ ./test_view -@4 -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram ./test_view -@4 auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_ ./test_view -@4 -t auxf.fa -S -l7 -C -o VERSION=3.1 -o archive auxf#values.sam > auxf#values.tmp.cram ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ ./test_view -@4 -i reference=auxf.fa auxf#values_java.cram > auxf#values_java.tmp.sam_ ./compare_sam.pl -Baux -nomd auxf#values.sam auxf#values_java.tmp.sam_ .. ok test_view testing c1#bounds.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#bounds.sam > c1#bounds.tmp.bam ./test_view -@4 c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_ ./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#bounds.sam > c1#bounds.tmp.cram ./test_view -@4 -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram ./test_view -@4 c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#bounds_er.tmp.cram.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#bounds_er.tmp.cram.sam > c1#bounds_er.tmp.cram.tmp.bam ./test_view -@4 c1#bounds_er.tmp.cram.tmp.bam > c1#bounds_er.tmp.cram.tmp.bam.sam_ ./compare_sam.pl c1#bounds_er.tmp.cram.sam c1#bounds_er.tmp.cram.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#bounds_er.tmp.cram.sam > c1#bounds_er.tmp.cram.tmp.cram ./test_view -@4 -D c1#bounds_er.tmp.cram.tmp.cram > c1#bounds_er.tmp.cram.tmp.cram.sam_ ./compare_sam.pl -nomd c1#bounds_er.tmp.cram.sam c1#bounds_er.tmp.cram.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#bounds_er.tmp.cram.tmp.bam > c1#bounds_er.tmp.cram.tmp.bam.cram ./test_view -@4 c1#bounds_er.tmp.cram.tmp.bam.cram > c1#bounds_er.tmp.cram.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#bounds_er.tmp.cram.sam c1#bounds_er.tmp.cram.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#clip.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#clip.sam > c1#clip.tmp.bam ./test_view -@4 c1#clip.tmp.bam > c1#clip.tmp.bam.sam_ ./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#clip.sam > c1#clip.tmp.cram ./test_view -@4 -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.bam > c1#clip.tmp.bam.cram ./test_view -@4 c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#noseq.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#noseq.sam > c1#noseq.tmp.bam ./test_view -@4 c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_ ./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#noseq.sam > c1#noseq.tmp.cram ./test_view -@4 -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram ./test_view -@4 c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad1.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#pad1.sam > c1#pad1.tmp.bam ./test_view -@4 c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_ ./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad1.sam > c1#pad1.tmp.cram ./test_view -@4 -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram ./test_view -@4 c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad2.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#pad2.sam > c1#pad2.tmp.bam ./test_view -@4 c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_ ./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad2.sam > c1#pad2.tmp.cram ./test_view -@4 -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram ./test_view -@4 c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad3.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#pad3.sam > c1#pad3.tmp.bam ./test_view -@4 c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_ ./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad3.sam > c1#pad3.tmp.cram ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram ./test_view -@4 c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_ ./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=3.1 -o archive c1#pad3.sam > c1#pad3.tmp.cram ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ .. ok test_view testing c1#unknown.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#unknown.sam > c1#unknown.tmp.bam ./test_view -@4 c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_ ./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#unknown.sam > c1#unknown.tmp.cram ./test_view -@4 -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram ./test_view -@4 c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_ .. ok test_view testing c2#pad.sam, ref c2.fa: ./test_view -@4 -S -l0 -b c2#pad.sam > c2#pad.tmp.bam ./test_view -@4 c2#pad.tmp.bam > c2#pad.tmp.bam.sam_ ./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_ ./test_view -@4 -t c2.fa -S -C -o VERSION=2.1 c2#pad.sam > c2#pad.tmp.cram ./test_view -@4 -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_ ./test_view -@4 -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.bam > c2#pad.tmp.bam.cram ./test_view -@4 c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#1.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#1.sam > ce#1.tmp.bam ./test_view -@4 ce#1.tmp.bam > ce#1.tmp.bam.sam_ ./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1.sam > ce#1.tmp.cram ./test_view -@4 -D ce#1.tmp.cram > ce#1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1.tmp.bam > ce#1.tmp.bam.cram ./test_view -@4 ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#1000.sam, ref ce.fa: ./test_view -@4 -S -b ce#1000.sam > ce#1000.tmp.bam ./test_view -@4 ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ ./test_view -@4 -S -l0 -b ce#1000.sam > ce#1000.tmp.bam ./test_view -@4 ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1000.sam > ce#1000.tmp.cram ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1000.sam > ce#1000.tmp.cram ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.bam > ce#1000.tmp.bam.cram ./test_view -@4 ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.ms ./test_view -@4 ce#1000.tmp.bam.cram.ms > ce#1000.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#1000.sam > ce#1000.tmp.cram ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o normal ce#1000.sam > ce#1000.tmp.cram ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o small ce#1000.sam > ce#1000.tmp.cram ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#1000.sam > ce#1000.tmp.cram ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ .. ok test_view testing ce#1000_er.tmp.cram.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#1000_er.tmp.cram.sam > ce#1000_er.tmp.cram.tmp.bam ./test_view -@4 ce#1000_er.tmp.cram.tmp.bam > ce#1000_er.tmp.cram.tmp.bam.sam_ ./compare_sam.pl ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1000_er.tmp.cram.sam > ce#1000_er.tmp.cram.tmp.cram ./test_view -@4 -D ce#1000_er.tmp.cram.tmp.cram > ce#1000_er.tmp.cram.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1000_er.tmp.cram.tmp.bam > ce#1000_er.tmp.cram.tmp.bam.cram ./test_view -@4 ce#1000_er.tmp.cram.tmp.bam.cram > ce#1000_er.tmp.cram.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#2.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#2.sam > ce#2.tmp.bam ./test_view -@4 ce#2.tmp.bam > ce#2.tmp.bam.sam_ ./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#2.sam > ce#2.tmp.cram ./test_view -@4 -D ce#2.tmp.cram > ce#2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#2.tmp.bam > ce#2.tmp.bam.cram ./test_view -@4 ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#5.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#5.sam > ce#5.tmp.bam ./test_view -@4 ce#5.tmp.bam > ce#5.tmp.bam.sam_ ./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#5.sam > ce#5.tmp.cram ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5.tmp.bam > ce#5.tmp.bam.cram ./test_view -@4 ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.ms ./test_view -@4 ce#5.tmp.bam.cram.ms > ce#5.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#5.sam > ce#5.tmp.cram ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ .. ok test_view testing ce#5b.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#5b.sam > ce#5b.tmp.bam ./test_view -@4 ce#5b.tmp.bam > ce#5b.tmp.bam.sam_ ./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#5b.sam > ce#5b.tmp.cram ./test_view -@4 -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.bam > ce#5b.tmp.bam.cram ./test_view -@4 ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.ms ./test_view -@4 ce#5b.tmp.bam.cram.ms > ce#5b.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.sam_ ./test_view -@4 -i reference=ce.fa ce#5b_java.cram > ce#5b_java.tmp.sam_ ./compare_sam.pl -Baux -nomd ce#5b.sam ce#5b_java.tmp.sam_ .. ok test_view testing ce#large_seq.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#large_seq.sam > ce#large_seq.tmp.bam ./test_view -@4 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_ ./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#large_seq.sam > ce#large_seq.tmp.cram ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram ./test_view -@4 ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#large_seq.sam > ce#large_seq.tmp.cram ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ .. ok test_view testing ce#supp.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#supp.sam > ce#supp.tmp.bam ./test_view -@4 ce#supp.tmp.bam > ce#supp.tmp.bam.sam_ ./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#supp.sam > ce#supp.tmp.cram ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.bam > ce#supp.tmp.bam.cram ./test_view -@4 ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#supp.sam > ce#supp.tmp.cram ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ .. ok test_view testing ce#tag_depadded.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam ./test_view -@4 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_ ./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram ./test_view -@4 -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram ./test_view -@4 ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#tag_padded.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#tag_padded.sam > ce#tag_padded.tmp.bam ./test_view -@4 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_ ./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#tag_padded.sam > ce#tag_padded.tmp.cram ./test_view -@4 -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram ./test_view -@4 ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#unmap.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#unmap.sam > ce#unmap.tmp.bam ./test_view -@4 ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_ ./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap.sam > ce#unmap.tmp.cram ./test_view -@4 -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram ./test_view -@4 ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.ms ./test_view -@4 ce#unmap.tmp.bam.cram.ms > ce#unmap.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.sam_ .. ok test_view testing ce#unmap1.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#unmap1.sam > ce#unmap1.tmp.bam ./test_view -@4 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_ ./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap1.sam > ce#unmap1.tmp.cram ./test_view -@4 -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram ./test_view -@4 ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.ms ./test_view -@4 ce#unmap1.tmp.bam.cram.ms > ce#unmap1.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.sam_ .. ok test_view testing ce#unmap2.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#unmap2.sam > ce#unmap2.tmp.bam ./test_view -@4 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_ ./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap2.sam > ce#unmap2.tmp.cram ./test_view -@4 -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram ./test_view -@4 ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.ms ./test_view -@4 ce#unmap2.tmp.bam.cram.ms > ce#unmap2.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.sam_ .. ok test_view testing md#1.sam, ref md.fa: ./test_view -@4 -S -l0 -b md#1.sam > md#1.tmp.bam ./test_view -@4 md#1.tmp.bam > md#1.tmp.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.sam_ ./test_view -@4 -t md.fa -S -C -o VERSION=2.1 md#1.sam > md#1.tmp.cram ./test_view -@4 -D md#1.tmp.cram > md#1.tmp.cram.sam_ ./compare_sam.pl md#1.sam md#1.tmp.cram.sam_ ./test_view -@4 -t md.fa -C -o VERSION=3.0 md#1.tmp.bam > md#1.tmp.bam.cram ./test_view -@4 md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#blank.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#blank.sam > xx#blank.tmp.bam ./test_view -@4 xx#blank.tmp.bam > xx#blank.tmp.bam.sam_ ./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#blank.sam > xx#blank.tmp.cram ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.bam > xx#blank.tmp.bam.cram ./test_view -@4 xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.ms ./test_view -@4 xx#blank.tmp.bam.cram.ms > xx#blank.tmp.bam.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#blank.sam > xx#blank.tmp.cram ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ .. ok test_view testing xx#large_aux.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#large_aux.sam > xx#large_aux.tmp.bam ./test_view -@4 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_ ./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#large_aux.sam > xx#large_aux.tmp.cram ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram ./test_view -@4 xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#large_aux.sam > xx#large_aux.tmp.cram ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -i reference=xx.fa xx#large_aux_java.cram > xx#large_aux_java.tmp.sam_ [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 30 vs 20 ./compare_sam.pl -Baux -nomd xx#large_aux.sam xx#large_aux_java.tmp.sam_ .. ok test_view testing xx#large_aux2.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#large_aux2.sam > xx#large_aux2.tmp.bam ./test_view -@4 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_ ./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#large_aux2.sam > xx#large_aux2.tmp.cram ./test_view -@4 -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram ./test_view -@4 xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#MD.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#MD.sam > xx#MD.tmp.bam ./test_view -@4 xx#MD.tmp.bam > xx#MD.tmp.bam.sam_ ./compare_sam.pl xx#MD.sam xx#MD.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#MD.sam > xx#MD.tmp.cram ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.bam > xx#MD.tmp.bam.cram ./test_view -@4 xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#MD.sam > xx#MD.tmp.cram ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ .. ok test_view testing xx#MD2.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#MD2.sam > xx#MD2.tmp.bam ./test_view -@4 xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_ ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#MD2.sam > xx#MD2.tmp.cram ./test_view -@4 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram ./test_view -@4 xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#minimal.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#minimal.sam > xx#minimal.tmp.bam ./test_view -@4 xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_ ./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#minimal.sam > xx#minimal.tmp.cram ./test_view -@4 -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram ./test_view -@4 xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.ms ./test_view -@4 xx#minimal.tmp.bam.cram.ms > xx#minimal.tmp.bam.cram.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.sam_ .. ok test_view testing xx#pair.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#pair.sam > xx#pair.tmp.bam ./test_view -@4 xx#pair.tmp.bam > xx#pair.tmp.bam.sam_ ./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#pair.sam > xx#pair.tmp.cram ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.bam > xx#pair.tmp.bam.cram ./test_view -@4 xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#pair.sam > xx#pair.tmp.cram ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ .. ok test_view testing xx#repeated.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#repeated.sam > xx#repeated.tmp.bam ./test_view -@4 xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_ ./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#repeated.sam > xx#repeated.tmp.cram ./test_view -@4 -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram ./test_view -@4 xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#repeated2.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#repeated2.sam > xx#repeated2.tmp.bam ./test_view -@4 xx#repeated2.tmp.bam > xx#repeated2.tmp.bam.sam_ ./compare_sam.pl xx#repeated2.sam xx#repeated2.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#repeated2.sam > xx#repeated2.tmp.cram [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 100 vs 20 ./test_view -@4 -D xx#repeated2.tmp.cram > xx#repeated2.tmp.cram.sam_ [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 100 vs 20 ./compare_sam.pl -nomd xx#repeated2.sam xx#repeated2.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#repeated2.tmp.bam > xx#repeated2.tmp.bam.cram [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 100 vs 20 ./test_view -@4 xx#repeated2.tmp.bam.cram > xx#repeated2.tmp.bam.cram.bam.sam_ [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 100 vs 20 ./compare_sam.pl -nomd xx#repeated2.sam xx#repeated2.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#rg.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#rg.sam > xx#rg.tmp.bam ./test_view -@4 xx#rg.tmp.bam > xx#rg.tmp.bam.sam_ ./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#rg.sam > xx#rg.tmp.cram ./test_view -@4 -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.bam > xx#rg.tmp.bam.cram ./test_view -@4 xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#tlen.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#tlen.sam > xx#tlen.tmp.bam ./test_view -@4 xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_ ./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#tlen.sam > xx#tlen.tmp.cram ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram ./test_view -@4 xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.ms ./test_view -@4 xx#tlen.tmp.bam.cram.ms > xx#tlen.tmp.bam.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#tlen.sam > xx#tlen.tmp.cram ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ .. ok test_view testing xx#tlen2.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#tlen2.sam > xx#tlen2.tmp.bam ./test_view -@4 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_ ./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#tlen2.sam > xx#tlen2.tmp.cram ./test_view -@4 -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram ./test_view -@4 xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.ms ./test_view -@4 xx#tlen2.tmp.bam.cram.ms > xx#tlen2.tmp.bam.cram.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.sam_ .. ok test_view testing xx#triplet.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#triplet.sam > xx#triplet.tmp.bam ./test_view -@4 xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_ ./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#triplet.sam > xx#triplet.tmp.cram ./test_view -@4 -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram ./test_view -@4 xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.ms ./test_view -@4 xx#triplet.tmp.bam.cram.ms > xx#triplet.tmp.bam.cram.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.sam_ .. ok test_view testing xx#u.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#u.sam > xx#u.tmp.bam ./test_view -@4 xx#u.tmp.bam > xx#u.tmp.bam.sam_ ./compare_sam.pl xx#u.sam xx#u.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#u.sam > xx#u.tmp.cram ./test_view -@4 -D xx#u.tmp.cram > xx#u.tmp.cram.sam_ ./compare_sam.pl -nomd xx#u.sam xx#u.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#u.tmp.bam > xx#u.tmp.bam.cram ./test_view -@4 xx#u.tmp.bam.cram > xx#u.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#u.sam xx#u.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#unsorted.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#unsorted.sam > xx#unsorted.tmp.bam ./test_view -@4 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_ ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#unsorted.sam > xx#unsorted.tmp.cram ./test_view -@4 -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram ./test_view -@4 xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_ .. ok test_view testing BAM records in multiple BGZF blocks: ./test_view -@4 -p bgzf_boundaries/bgzf_boundaries1.bam.tmp.sam bgzf_boundaries/bgzf_boundaries1.bam ./compare_sam.pl bgzf_boundaries/bgzf_boundaries1.bam.tmp.sam ce#1.sam ./test_view -@4 -p bgzf_boundaries/bgzf_boundaries2.bam.tmp.sam bgzf_boundaries/bgzf_boundaries2.bam ./compare_sam.pl bgzf_boundaries/bgzf_boundaries2.bam.tmp.sam ce#1.sam ./test_view -@4 -p bgzf_boundaries/bgzf_boundaries3.bam.tmp.sam bgzf_boundaries/bgzf_boundaries3.bam ./compare_sam.pl bgzf_boundaries/bgzf_boundaries3.bam.tmp.sam ce#1.sam ./test_view -@4 -b -l 0 -p bgzf_boundaries/large_rec.tmp.sam.bam bgzf_boundaries/large_rec.tmp.sam ./test_view -@4 -p bgzf_boundaries/large_rec.tmp.sam.bam.sam bgzf_boundaries/large_rec.tmp.sam.bam ./compare_sam.pl bgzf_boundaries/large_rec.tmp.sam bgzf_boundaries/large_rec.tmp.sam.bam.sam .. ok test_view testing embed_ref=2: ./test_view -@4 -C -p ce#1000_er.tmp.cram ce#1000.sam [W::cram_get_ref] Failed to populate reference "CHROMOSOME_I" [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -@4 -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam ./test_view -@4 -C -p c1#bounds_er.tmp.cram c1#bounds.sam [W::cram_get_ref] Failed to populate reference "c1" [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -@4 -p c1#bounds_er.tmp.cram.sam c1#bounds_er.tmp.cram ./compare_sam.pl c1#bounds.sam c1#bounds_er.tmp.cram.sam ./test_view -@4 -o embed_ref=2 -o seqs_per_slice=3 -o bases_per_slice=1000000 -C -p embed_MD.tmp.cram embed_MD.sam ./test_view -@4 -p embed_MD.tmp.cram.sam embed_MD.tmp.cram ./compare_sam.pl embed_MD.sam embed_MD.tmp.cram.sam ./test_view -@4 -o embed_ref=2 -o no_ref -C -p embed_del.tmp.cram embed_del.sam ./test_view -@4 -p embed_del.tmp.cram.sam embed_del.tmp.cram ./compare_sam.pl embed_del.sam embed_del.tmp.cram.sam .. ok test_view testing region queries: ./test_view -@4 -i reference=ce.fa range.cram CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp ./compare_sam.pl range.tmp range.out ./test_view -@4 range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp ./compare_sam.pl range.tmp range.out ./test_view -@4 -i reference=ce.fa -M range.cram CHROMOSOME_I:1122-1122 CHROMOSOME_II:1136-1136 CHROMOSOME_II:1241-1241 CHROMOSOME_II:1267-1267 CHROMOSOME_II:1326-1326 CHROMOSOME_II:1345-1345 CHROMOSOME_II:1353-1353 CHROMOSOME_II:1366-1366 CHROMOSOME_II:1416-1416 CHROMOSOME_II:1459-1459 CHROMOSOME_II:1536-1536 > range.tmp ./compare_sam.pl range.tmp range.out2 ./test_view -@4 -M range.bam CHROMOSOME_I:1122-1122 CHROMOSOME_II:1136-1136 CHROMOSOME_II:1241-1241 CHROMOSOME_II:1267-1267 CHROMOSOME_II:1326-1326 CHROMOSOME_II:1345-1345 CHROMOSOME_II:1353-1353 CHROMOSOME_II:1366-1366 CHROMOSOME_II:1416-1416 CHROMOSOME_II:1459-1459 CHROMOSOME_II:1536-1536 > range.tmp ./compare_sam.pl range.tmp range.out2 .. ok test_view testing BAM files with absent @SQ lines: ./test_view -@4 -p no_hdr_sq_1.tmp.sam no_hdr_sq_1.bam ./compare_sam.pl no_hdr_sq_1.tmp.sam no_hdr_sq_1.expected.sam ./test_view -@4 -p no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.bam CHROMOSOME_I ./compare_sam.pl no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.expected.sam .. ok test_view testing large (> 2Gbases) positions: ./test_view -@4 -z -p longrefs/longref.tmp.sam.gz -x longrefs/longref.tmp.sam.gz.csi.otf -m 14 longrefs/longref.sam ./test_view -@4 -p longrefs/longref.tmp.sam_ longrefs/longref.tmp.sam.gz ./compare_sam.pl longrefs/longref.sam longrefs/longref.tmp.sam_ test_view: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -c longrefs/longref.tmp.sam.gz .. ok ./test_view -@4 -p longrefs/longref_itr.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 ./compare_sam.pl longrefs/longref_itr.expected.sam longrefs/longref_itr.tmp.sam ./test_view -@4 -M -p longrefs/longref_multi.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 CHROMOSOME_I:10000000100-10000000110 ./compare_sam.pl longrefs/longref_multi.expected.sam longrefs/longref_multi.tmp.sam .. ok test_MD testing xx#MD.sam, ref xx.fa: ./test_view -o store_nm=1 -o store_md=1 -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram ./test_view -i decode_md=0 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl xx#MD.sam xx#MD.tmp.cram.sam_ ./test_view -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram ./test_view -i decode_md=0 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -partialmd=2 xx#MD.sam xx#MD.tmp.cram.sam_ Checking for MD/NM in xx#MD.sam ./test_view -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram ./test_view -i decode_md=1 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -partialmd=1 xx#MD.sam xx#MD.tmp.cram.sam_ .. ok test_MD testing xx#MD2.sam, ref xx.fa: ./test_view -o store_nm=1 -o store_md=1 -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram ./test_view -i decode_md=0 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.cram.sam_ ./test_view -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram ./test_view -i decode_md=0 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl -partialmd=2 xx#MD2.sam xx#MD2.tmp.cram.sam_ ./test_view -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram ./test_view -i decode_md=1 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl -partialmd=1 xx#MD2.sam xx#MD2.tmp.cram.sam_ .. ok test_vcf_api: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-vcf-api /tmp/ZoqikH74vH/test-vcf-api.bcf .. ok test_bcf2vcf: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/tabix/vcf_file.bcf .. ok test_vcf_sweep: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-vcf-sweep /tmp/ZoqikH74vH/test-vcf-api.bcf .. ok test_vcf_various: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/htsfile -ch /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-vcf-hdr-in.vcf .. ok test_vcf_various: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/htsfile -c /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/formatcols.vcf .. ok test_vcf_various: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/htsfile -c /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/noroundtrip.vcf .. ok test_vcf_various: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/htsfile -c /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/formatmissing.vcf .. ok test_vcf_various: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/htsfile -c /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/vcf_meta_meta.vcf .. ok test_vcf_various: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/modhdr.vcf.gz chr22:1-2 .. ok test_vcf_44: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/htsfile -c /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/vcf44_1.vcf .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr.pl -t /tmp/ZoqikH74vH -s 74452500 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr.pl -t /tmp/ZoqikH74vH -s 34270147 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr.pl -t /tmp/ZoqikH74vH -s 11108528 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr.pl -t /tmp/ZoqikH74vH -s 42233895 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr.pl -t /tmp/ZoqikH74vH -s 8111117 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr.pl -t /tmp/ZoqikH74vH -s 85644070 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr.pl -t /tmp/ZoqikH74vH -s 49879942 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr.pl -t /tmp/ZoqikH74vH -s 47881429 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr.pl -t /tmp/ZoqikH74vH -s 69081244 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr.pl -t /tmp/ZoqikH74vH -s 83459376 .. ok test_bcf_sr_no_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr --no-index -p all --args /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/bcf-sr/merge.noidx.a.vcf /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/bcf-sr/merge.noidx.b.vcf /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/bcf-sr/merge.noidx.c.vcf 2> /tmp/ZoqikH74vH/no_index_1.err .. ok test_bcf_sr_no_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr --no-index -p all --args /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/bcf-sr/merge.noidx.a.vcf /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/bcf-sr/merge.noidx.hdr_order.vcf > /tmp/ZoqikH74vH/no_index_2.out 2> /tmp/ZoqikH74vH/no_index_2.err (expected fail) .. ok test_bcf_sr_no_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr --no-index -p all --args /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/bcf-sr/merge.noidx.a.vcf /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/bcf-sr/merge.noidx.rec_order.vcf > /tmp/ZoqikH74vH/no_index_3.out 2> /tmp/ZoqikH74vH/no_index_3.err (expected fail) .. ok test_bcf_sr_no_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr --no-index -p all --args /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/bcf-sr/merge.noidx.rec_order.vcf /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/bcf-sr/merge.noidx.a.vcf > /tmp/ZoqikH74vH/no_index_4.out 2> /tmp/ZoqikH74vH/no_index_4.err (expected fail) .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view -b -p /tmp/ZoqikH74vH/weird-chr-names.vcf.bcf -x /tmp/ZoqikH74vH/weird-chr-names.vcf.bcf.csi /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/bcf-sr/weird-chr-names.vcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr -O vcf -o /tmp/ZoqikH74vH/range_test_1.out.vcf -r '1' --args /tmp/ZoqikH74vH/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr -O vcf -o /tmp/ZoqikH74vH/range_test_2.out.vcf -r '1:1-2' --args /tmp/ZoqikH74vH/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr -O vcf -o /tmp/ZoqikH74vH/range_test_3.out.vcf -r '1:1,1:2' --args /tmp/ZoqikH74vH/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr -O vcf -o /tmp/ZoqikH74vH/range_test_4.out.vcf -r '1:1-1' --args /tmp/ZoqikH74vH/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr -O vcf -o /tmp/ZoqikH74vH/range_test_5.out.vcf -r '{1:1}' --args /tmp/ZoqikH74vH/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr -O vcf -o /tmp/ZoqikH74vH/range_test_6.out.vcf -r '{1:1}:1-2' --args /tmp/ZoqikH74vH/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr -O vcf -o /tmp/ZoqikH74vH/range_test_7.out.vcf -r '{1:1}:1,{1:1}:2' --args /tmp/ZoqikH74vH/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr -O vcf -o /tmp/ZoqikH74vH/range_test_8.out.vcf -r '{1:1}:1-1' --args /tmp/ZoqikH74vH/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr -O vcf -o /tmp/ZoqikH74vH/range_test_9.out.vcf -r '{1:1-1}' --args /tmp/ZoqikH74vH/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr -O vcf -o /tmp/ZoqikH74vH/range_test_10.out.vcf -r '{1:1-1}:1-2' --args /tmp/ZoqikH74vH/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr -O vcf -o /tmp/ZoqikH74vH/range_test_11.out.vcf -r '{1:1-1}:1,{1:1-1}:2' --args /tmp/ZoqikH74vH/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr -O vcf -o /tmp/ZoqikH74vH/range_test_12.out.vcf -r '{1:1-1}:1-1' --args /tmp/ZoqikH74vH/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr -O vcf -o /tmp/ZoqikH74vH/range_test_13.out.vcf -r '{1:1-1}-2' --args /tmp/ZoqikH74vH/weird-chr-names.vcf.bcf (expected fail) [E::_regions_init_string] Could not parse the region(s): {1:1-1}-2 Failed to set regions .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr -O vcf -o /tmp/ZoqikH74vH/range_test_14.out.vcf -t '1' --args /tmp/ZoqikH74vH/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr -O vcf -o /tmp/ZoqikH74vH/range_test_15.out.vcf -t '1:1-2' --args /tmp/ZoqikH74vH/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr -O vcf -o /tmp/ZoqikH74vH/range_test_16.out.vcf -t '1:1,1:2' --args /tmp/ZoqikH74vH/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr -O vcf -o /tmp/ZoqikH74vH/range_test_17.out.vcf -t '1:1-1' --args /tmp/ZoqikH74vH/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr -O vcf -o /tmp/ZoqikH74vH/range_test_18.out.vcf -t '{1:1}' --args /tmp/ZoqikH74vH/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr -O vcf -o /tmp/ZoqikH74vH/range_test_19.out.vcf -t '{1:1}:1-2' --args /tmp/ZoqikH74vH/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr -O vcf -o /tmp/ZoqikH74vH/range_test_20.out.vcf -t '{1:1}:1,{1:1}:2' --args /tmp/ZoqikH74vH/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr -O vcf -o /tmp/ZoqikH74vH/range_test_21.out.vcf -t '{1:1}:1-1' --args /tmp/ZoqikH74vH/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr -O vcf -o /tmp/ZoqikH74vH/range_test_22.out.vcf -t '{1:1-1}' --args /tmp/ZoqikH74vH/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr -O vcf -o /tmp/ZoqikH74vH/range_test_23.out.vcf -t '{1:1-1}:1-2' --args /tmp/ZoqikH74vH/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr -O vcf -o /tmp/ZoqikH74vH/range_test_24.out.vcf -t '{1:1-1}:1,{1:1-1}:2' --args /tmp/ZoqikH74vH/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr -O vcf -o /tmp/ZoqikH74vH/range_test_25.out.vcf -t '{1:1-1}:1-1' --args /tmp/ZoqikH74vH/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr -O vcf -o /tmp/ZoqikH74vH/range_test_26.out.vcf -t '{1:1-1}-2' --args /tmp/ZoqikH74vH/weird-chr-names.vcf.bcf (expected fail) [E::_regions_init_string] Could not parse the region(s): {1:1-1}-2 Failed to set targets .. ok .. ok test_command: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-translate - .. ok test_convert_padded_header: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view -t ce.fa -C /tmp/ZoqikH74vH/headernul0.bam .. ok test_convert_padded_header: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view -t ce.fa -C /tmp/ZoqikH74vH/headernul1.bam .. ok test_convert_padded_header: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view -t ce.fa -C /tmp/ZoqikH74vH/headernul678.bam .. ok test_rebgzip: Alternate zlib/deflate library detected test_rebgzip: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/bgzip -I /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/bgziptest.txt.tmp.gz.gzi -c -g /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/bgziptest.txt .. ok test-logging: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-logging.pl .. ok test_plugin_loading: HTS_PATH=/builddir/build/BUILD/htslib-1.24-build/htslib-1.24 /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/with-shlib.sh /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/htsfile https://localhost:99999/invalid_port .. ok test_realn: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_realn -f /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/realn01.fa -i /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/realn01.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_realn -f /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/realn02.fa -i /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/realn02.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_realn -a -f /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/realn01.fa -i /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/realn01.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_realn -a -f /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/realn02.fa -i /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/realn02.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_realn -e -f /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/realn01.fa -i /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/realn01.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_realn -e -f /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/realn02.fa -i /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/realn02.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_realn -r -f /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/realn02.fa -i /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/realn02-r.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_realn -a -f /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/realn02.fa -i /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/realn02_exp.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_realn -f /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/realn02.fa -i /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/realn02_exp-a.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_realn -f /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/realn03.fa -e -i /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/realn03.sam -o - .. ok test-bcf_set_variant_type: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf_set_variant_type .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -f smpl:overlap --allow-dups -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.1.txt -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.1.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -f smpl:overlap --allow-dups -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.1.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -f smpl:overlap --allow-dups -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -f smpl:overlap -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.1.txt -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.1.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -f smpl:overlap -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.1.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -f smpl:overlap -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -f smpl:overlap -c chr,beg,end -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.1.txt -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.1.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -f smpl:overlap -c chr,beg,end -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.1.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -f smpl:overlap -c chr,beg,end -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -f smpl,value:overlap,value -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.1.txt -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.1.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -f smpl,value:overlap,value -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.1.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -f smpl,value:overlap,value -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -f smpl:overlap -O 0.5 -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.1.txt -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.1.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -f smpl:overlap -O 0.5 -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.1.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -f smpl:overlap -O 0.5 -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -f smpl:overlap -rO 0.5 -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.1.txt -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.1.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -f smpl:overlap -rO 0.5 -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.1.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -f smpl:overlap -rO 0.5 -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -f smpl:overlap --allow-dups --max-annots 2 -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.1.txt -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.1.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -f smpl:overlap --allow-dups --max-annots 2 -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.1.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -f smpl:overlap --allow-dups --max-annots 2 -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.2.txt -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.2.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.2.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.2.txt -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.2.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.2.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,3:1,2,3 -f 4,value:5,value -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.2.txt -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.2.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,3:1,2,3 -f 4,value:5,value -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.2.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,3:1,2,3 -f 4,value:5,value -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.2.txt -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.2.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.2.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -a nbp,frac -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.2.txt -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.2.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -a nbp,frac -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.2.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -a nbp,frac -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups --max-annots 2 -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.2.txt -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.2.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups --max-annots 2 -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.2.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups --max-annots 2 -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -f smpl:overlap -a nbp,frac -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.3.txt -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.3.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.3.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -f smpl:overlap -a nbp,frac -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.3.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.3.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -f smpl:overlap -a nbp,frac -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.3.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 2,3,4:2,3,4 -m 1:1 -f 1:1 -a nbp,frac -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.4.txt -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.4.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.4.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 2,3,4:2,3,4 -m 1:1 -f 1:1 -a nbp,frac -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.4.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.4.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 2,3,4:2,3,4 -m 1:1 -f 1:1 -a nbp,frac -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.4.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 2,3,4:2,3,4 -a nbp,frac -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.5.txt -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.5.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.5.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 2,3,4:2,3,4 -a nbp,frac -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.5.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.5.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 2,3,4:2,3,4 -a nbp,frac -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.5.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,2:1,2,2 -a nbp -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.6.txt -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.6.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.6.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,2:1,2,2 -a nbp -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.6.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.6.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,2:1,2,2 -a nbp -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.6.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,2:1,2,2 -f overlap -H -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.7.txt -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.7.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.7.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,2:1,2,2 -f overlap -H -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.7.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.7.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,2:1,2,2 -f overlap -H -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.7.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c chr,beg,end:chr,start,end -m sample -f is_tp -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.8.txt -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.8.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.8.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c chr,beg,end:chr,start,end -m sample -f is_tp -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.8.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.8.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c chr,beg,end:chr,start,end -m sample -f is_tp -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.8.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,3:chr,beg,end -a nbp,frac,cnt -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.9.txt -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.9.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.9.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,3:chr,beg,end -a nbp,frac,cnt -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.9.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.9.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,3:chr,beg,end -a nbp,frac,cnt -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.9.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -f smpl -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.10.txt -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.10.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -f smpl -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.10.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -f smpl -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.10.txt -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.10.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.10.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -x -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.10.txt -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.10.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -x -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.10.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -x -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -m smpl -f smpl -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.10.txt -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.10.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -m smpl -f smpl -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.10.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -m smpl -f smpl -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -m smpl -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.10.txt -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.10.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -m smpl -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.10.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -m smpl -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -m smpl -x -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.10.txt -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.10.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -m smpl -x -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.10.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -m smpl -x -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.11.txt -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.11.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.11.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -II -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.11.txt -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.11.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -II -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.11.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -II -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:-1 -II -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.11.txt -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.11.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:-1 -II -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.11.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:-1 -II -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.11.txt -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.11.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.11.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.11.txt -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.11.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.11.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -I -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.11.txt -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.11.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -I -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.11.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -I -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -I -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.11.txt -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.11.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -I -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.11.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -I -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d , -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.12.txt -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.12.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.12.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d , -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.12.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.12.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d , -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.12.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d $',:\t' -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.12.txt -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.11.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d $',:\t' -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.12.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.12.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d $',:\t' -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,3 -f 4:5 -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.13.txt -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,3 -f 4:5 -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,3 -f 4:5 -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.13.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.13.txt -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.13.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -r -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.13.txt -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -r -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -r -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.13.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,3 -f 4:5 -O 0.5,0.5 -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.13.txt -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,3 -f 4:5 -O 0.5,0.5 -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,3 -f 4:5 -O 0.5,0.5 -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.13.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,3 -f 4:5 -O 0,1 -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.13.txt -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,3 -f 4:5 -O 0,1 -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,3 -f 4:5 -O 0,1 -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.13.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,3 -f 4:5 -O 1,0 -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.13.txt -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,3 -f 4:5 -O 1,0 -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,3 -f 4:5 -O 1,0 -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.13.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,3 -C 11:11 -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.14.txt -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.14.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.14.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,3 -C 11:11 -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.14.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.14.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,3 -C 11:11 -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.14.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,3 -C 01:01 -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.14.txt -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.14.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.14.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,3 -C 01:01 -s /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.14.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/src.14.txt | /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/annot-tsv -c 1,2,3 -C 01:01 -t /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/annot-tsv/dst.14.txt .. ok ref-cache: ./test_view -C -p ref_cache/ce_m5.sam.tmp.cram ref_cache/ce_m5.sam ./test_view -p ref_cache/ce_m5.sam.tmp.cram.sam ref_cache/ce_m5.sam.tmp.cram ./compare_sam.pl --nomd ref_cache/ce_m5.sam ref_cache/ce_m5.sam.tmp.cram.sam ./test_view -p ref_cache/ce_m5.sam.tmp.cram.2.sam ref_cache/ce_m5.sam.tmp.cram ./compare_sam.pl --nomd ref_cache/ce_m5.sam ref_cache/ce_m5.sam.tmp.cram.2.sam ./test_view -p ref_cache/ce_m5.sam.tmp.cram.3.sam ref_cache/ce_m5.sam.tmp.cram ./compare_sam.pl --nomd ref_cache/ce_m5.sam ref_cache/ce_m5.sam.tmp.cram.3.sam .. ok Number of tests: total .. 358 passed .. 358 failed .. 0 if test "xhfile_libcurl.so hfile_gcs.so hfile_s3.so" != "x"; then \ HTS_PATH=. ./test/with-shlib.sh test/test_hfile_libcurl ; \ else \ test/test_hfile_libcurl ; \ fi test_hfile_libcurl: PASS: Normal transfer [W::libcurl_open] Retrying open (attempt 1/3) [W::libcurl_open] Retrying open (attempt 2/3) PASS: 503 retry succeeds [W::libcurl_open] Retrying open (attempt 1/3) [W::libcurl_open] Retrying open (attempt 2/3) PASS: 429 retry succeeds [W::retry_reconnect] Retrying connection (attempt 1/5) at offset 8192 [W::retry_reconnect] Retrying connection (attempt 1/5) at offset 12288 PASS: Connection drop retry PASS: 404 not retried [W::libcurl_open] Retrying open (attempt 1/2) [W::libcurl_open] Retrying open (attempt 2/2) PASS: Retry exhaustion PASS: Retry disabled All tests passed. + RPM_EC=0 ++ jobs -p + exit 0 Processing files: htslib-1.24-1.fc46.x86_64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.8vTmrC + umask 022 + cd /builddir/build/BUILD/htslib-1.24-build + cd htslib-1.24 + DOCDIR=/builddir/build/BUILD/htslib-1.24-build/BUILDROOT/usr/share/doc/htslib + export LC_ALL=C.UTF-8 + LC_ALL=C.UTF-8 + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILD/htslib-1.24-build/BUILDROOT/usr/share/doc/htslib + cp -pr /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/NEWS /builddir/build/BUILD/htslib-1.24-build/BUILDROOT/usr/share/doc/htslib + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.j0wFJA + umask 022 + cd /builddir/build/BUILD/htslib-1.24-build + cd htslib-1.24 + LICENSEDIR=/builddir/build/BUILD/htslib-1.24-build/BUILDROOT/usr/share/licenses/htslib + export LC_ALL=C.UTF-8 + LC_ALL=C.UTF-8 + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILD/htslib-1.24-build/BUILDROOT/usr/share/licenses/htslib + cp -pr /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/LICENSE /builddir/build/BUILD/htslib-1.24-build/BUILDROOT/usr/share/licenses/htslib + RPM_EC=0 ++ jobs -p + exit 0 Provides: htslib = 1.24-1.fc46 htslib(x86-64) = 1.24-1.fc46 libhts.so.3()(64bit) libhts.so.3(HTSLIB_1.0)(64bit) libhts.so.3(HTSLIB_1.1)(64bit) libhts.so.3(HTSLIB_1.10)(64bit) libhts.so.3(HTSLIB_1.11)(64bit) libhts.so.3(HTSLIB_1.12)(64bit) libhts.so.3(HTSLIB_1.13)(64bit) libhts.so.3(HTSLIB_1.14)(64bit) libhts.so.3(HTSLIB_1.15)(64bit) libhts.so.3(HTSLIB_1.16)(64bit) libhts.so.3(HTSLIB_1.17)(64bit) libhts.so.3(HTSLIB_1.18)(64bit) libhts.so.3(HTSLIB_1.2.1)(64bit) libhts.so.3(HTSLIB_1.20)(64bit) libhts.so.3(HTSLIB_1.21)(64bit) libhts.so.3(HTSLIB_1.22)(64bit) libhts.so.3(HTSLIB_1.23)(64bit) libhts.so.3(HTSLIB_1.24)(64bit) libhts.so.3(HTSLIB_1.3)(64bit) libhts.so.3(HTSLIB_1.4)(64bit) libhts.so.3(HTSLIB_1.5)(64bit) libhts.so.3(HTSLIB_1.6)(64bit) libhts.so.3(HTSLIB_1.7)(64bit) libhts.so.3(HTSLIB_1.9)(64bit) Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: libbz2.so.1()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(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) libc.so.6(GLIBC_ABI_DT_RELR)(64bit) libcrypto.so.4()(64bit) libcrypto.so.4(OPENSSL_4.0.0)(64bit) libcurl.so.4()(64bit) libhts.so.3()(64bit) libhts.so.3(HTSLIB_1.0)(64bit) libhts.so.3(HTSLIB_1.24)(64bit) libhts.so.3(HTSLIB_1.3)(64bit) libhts.so.3(HTSLIB_1.4)(64bit) libhts.so.3(HTSLIB_1.5)(64bit) libhts.so.3(HTSLIB_1.7)(64bit) liblzma.so.5()(64bit) liblzma.so.5(XZ_5.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.23)(64bit) libm.so.6(GLIBC_2.29)(64bit) libz.so.1()(64bit) rtld(GNU_HASH) Processing files: htslib-devel-1.24-1.fc46.x86_64 Provides: htslib-devel = 1.24-1.fc46 htslib-devel(x86-64) = 1.24-1.fc46 pkgconfig(htslib) = 1.24 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: /usr/bin/pkg-config libhts.so.3()(64bit) Processing files: htslib-tools-1.24-1.fc46.x86_64 Provides: htslib-tools = 1.24-1.fc46 htslib-tools(x86-64) = 1.24-1.fc46 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: libbz2.so.1()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(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) libc.so.6(GLIBC_2.7)(64bit) libc.so.6(GLIBC_ABI_DT_RELR)(64bit) libcurl.so.4()(64bit) liblzma.so.5()(64bit) liblzma.so.5(XZ_5.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.29)(64bit) libz.so.1()(64bit) rtld(GNU_HASH) Processing files: htslib-debugsource-1.24-1.fc46.x86_64 Provides: htslib-debugsource = 1.24-1.fc46 htslib-debugsource(x86-64) = 1.24-1.fc46 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: htslib-debuginfo-1.24-1.fc46.x86_64 Provides: debuginfo(build-id) = 6a317946ca50ec35547a34db37b3e1d4bd136564 debuginfo(build-id) = a439a9e2c31b1a42d2cbc93622735d61128c6e22 debuginfo(build-id) = dc27066cd8f616392113e67683c8111f737bd693 debuginfo(build-id) = e8ff38f071e4eec97966a2c33f18ca1210ff23cf htslib-debuginfo = 1.24-1.fc46 htslib-debuginfo(x86-64) = 1.24-1.fc46 libhts.so.1.24-1.24-1.fc46.x86_64.debug()(64bit) Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: htslib-debugsource(x86-64) = 1.24-1.fc46 Processing files: htslib-tools-debuginfo-1.24-1.fc46.x86_64 Provides: debuginfo(build-id) = 0b8d7ae0ae4f5a37aa8c68be41cb27605af9a1ba debuginfo(build-id) = 3b5d5f19bd62b49bb68a064432f3db6591c2cb47 debuginfo(build-id) = 789e924271481988f041bbe2da2806d297d1fd8d debuginfo(build-id) = 7d128639866f461a145288e7a8b4accdf772cbee debuginfo(build-id) = cf6acc0d5fc4b0b52f77eaf81817cb89010787da htslib-tools-debuginfo = 1.24-1.fc46 htslib-tools-debuginfo(x86-64) = 1.24-1.fc46 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: htslib-debugsource(x86-64) = 1.24-1.fc46 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILD/htslib-1.24-build/BUILDROOT Wrote: /builddir/build/RPMS/htslib-debuginfo-1.24-1.fc46.x86_64.rpm Wrote: /builddir/build/RPMS/htslib-1.24-1.fc46.x86_64.rpm Wrote: /builddir/build/RPMS/htslib-tools-1.24-1.fc46.x86_64.rpm Wrote: /builddir/build/RPMS/htslib-debugsource-1.24-1.fc46.x86_64.rpm Wrote: /builddir/build/RPMS/htslib-devel-1.24-1.fc46.x86_64.rpm Wrote: /builddir/build/RPMS/htslib-tools-debuginfo-1.24-1.fc46.x86_64.rpm Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.yZvBWC + umask 022 + cd /builddir/build/BUILD/htslib-1.24-build + test -d /builddir/build/BUILD/htslib-1.24-build + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w /builddir/build/BUILD/htslib-1.24-build + rm -rf /builddir/build/BUILD/htslib-1.24-build + RPM_EC=0 ++ jobs -p + exit 0 Finish: rpmbuild htslib-1.24-1.fc46.src.rpm Finish: build phase for htslib-1.24-1.fc46.src.rpm INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-x86_64-1790841053.256992/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/htslib-1.24-1.fc46.src.rpm) Config(child) 2 minutes 59 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": "htslib-tools", "epoch": null, "version": "1.24", "release": "1.fc46", "arch": "x86_64" }, { "name": "htslib", "epoch": null, "version": "1.24", "release": "1.fc46", "arch": "x86_64" }, { "name": "htslib", "epoch": null, "version": "1.24", "release": "1.fc46", "arch": "src" }, { "name": "htslib-debuginfo", "epoch": null, "version": "1.24", "release": "1.fc46", "arch": "x86_64" }, { "name": "htslib-debugsource", "epoch": null, "version": "1.24", "release": "1.fc46", "arch": "x86_64" }, { "name": "htslib-tools-debuginfo", "epoch": null, "version": "1.24", "release": "1.fc46", "arch": "x86_64" }, { "name": "htslib-devel", "epoch": null, "version": "1.24", "release": "1.fc46", "arch": "x86_64" } ] } RPMResults finished