Warning: Permanently added '54.198.67.208' (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-aarch64 --chroot fedora-rawhide-aarch64 Version: 1.10 PID: 24484 Logging PID: 24486 Task: {'allow_user_ssh': False, 'appstream': False, 'background': True, 'build_id': 11058182, 'buildroot_pkgs': ['fedora-clang-default-cc'], 'chroot': 'fedora-rawhide-aarch64', '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-aarch64/', '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-aarch64/', '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-aarch64/', '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-aarch64', 'timeout': 90000, 'uses_devel_repo': False, 'with_opts': ['toolchain_clang', 'clang_lto'], 'without_opts': []} Running: git clone https://copr-dist-git.fedorainfracloud.org/git/@fedora-llvm-team/clang-monthly-fedora-rebuild/htslib /var/lib/copr-rpmbuild/workspace/workdir-zcymtufs/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-zcymtufs/htslib', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-zcymtufs/htslib'... Running: git checkout 49f27db1f1a2a0ebbc1c4e903458121869bcfc42 -- cmd: ['git', 'checkout', '49f27db1f1a2a0ebbc1c4e903458121869bcfc42', '--'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-zcymtufs/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-zcymtufs/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 15.88M 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-zcymtufs/htslib/htslib.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-zcymtufs/htslib --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1790841033.072590 -r /var/lib/copr-rpmbuild/results/configs/child.cfg --with toolchain_clang --with 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-zcymtufs/htslib/htslib.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-zcymtufs/htslib --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1790841033.072590 -r /var/lib/copr-rpmbuild/results/configs/child.cfg --with toolchain_clang --with 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-zcymtufs/htslib/htslib.spec) Config(fedora-rawhide-aarch64) 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-aarch64-bootstrap-1790841033.072590/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-cfc452c5-c032-4a08-b485-2d60a8df72f0 INFO: Checking that d2403bcc646e70a420d1d00a003e45afe49a61b25a1f37f4ab6e85af91f467f2 image matches host's architecture INFO: Copy content of container d2403bcc646e70a420d1d00a003e45afe49a61b25a1f37f4ab6e85af91f467f2 to /var/lib/mock/fedora-rawhide-aarch64-bootstrap-1790841033.072590/root INFO: mounting d2403bcc646e70a420d1d00a003e45afe49a61b25a1f37f4ab6e85af91f467f2 with podman image mount INFO: image d2403bcc646e70a420d1d00a003e45afe49a61b25a1f37f4ab6e85af91f467f2 as /var/lib/containers/storage/overlay/c60d587f9d95b0b26d69a2d072908cc9f6775b5c5fe732ffc06a4094f83606ae/merged INFO: umounting image d2403bcc646e70a420d1d00a003e45afe49a61b25a1f37f4ab6e85af91f467f2 (/var/lib/containers/storage/overlay/c60d587f9d95b0b26d69a2d072908cc9f6775b5c5fe732ffc06a4094f83606ae/merged) with podman image umount INFO: Removing image mock-bootstrap-cfc452c5-c032-4a08-b485-2d60a8df72f0 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-aarch64-1790841033.072590/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.aarch64 rpm-sequoia-1.10.3-1.fc46.aarch64 dnf5-5.4.6.0-1.fc46.aarch64 dnf5-plugins-5.4.6.0-1.fc46.aarch64 Start: installing minimal buildroot with dnf5 Updating and loading repositories: fedora 100% | 61.7 KiB/s | 10.2 KiB | 00m00s Additional repo copr_tstellar_fedora_c 100% | 12.5 KiB/s | 1.5 KiB | 00m00s Additional repo copr_fedora_llvm_team_ 100% | 12.4 KiB/s | 1.5 KiB | 00m00s Copr repository 100% | 12.6 KiB/s | 1.5 KiB | 00m00s Repositories loaded. Package Arch Version Repository Size Installing group/module packages: bash aarch64 0:5.3.15-2.fc46 copr_base 8.5 MiB bzip2 aarch64 0:1.0.8-24.fc46 copr_base 170.8 KiB coreutils aarch64 0:9.12-1.fc46 fedora 8.6 MiB cpio aarch64 0:2.15-10.fc46 copr_base 1.2 MiB diffutils aarch64 0:3.12-6.fc45 fedora 1.6 MiB fedora-release-common noarch 0:46-0.1 fedora 4.6 KiB findutils aarch64 1:4.11.0-2.fc46 copr_base 2.1 MiB gawk aarch64 0:5.4.1-1.fc46 copr_base 2.9 MiB glibc-minimal-langpack aarch64 0:2.44.9000-4.fc46 fedora 0.0 B grep aarch64 0:3.12-4.fc45 fedora 1.0 MiB gzip aarch64 0:1.14-4.fc46 copr_base 437.6 KiB info aarch64 0:7.3-3.fc46 copr_base 423.7 KiB patch aarch64 0:2.8-6.fc46 fedora 262.4 KiB redhat-rpm-config noarch 0:345-4.fc46 fedora 184.2 KiB rpm-build aarch64 0:6.1.0-1.fc46 fedora 616.1 KiB sed aarch64 0:4.10-2.fc45 fedora 878.4 KiB shadow-utils aarch64 2:4.20.0-1.fc46 copr_base 4.4 MiB tar aarch64 2:1.35-9.fc45 fedora 3.0 MiB unzip aarch64 0:6.0-71.fc45 fedora 469.9 KiB util-linux aarch64 0:2.42.4-2.fc46 fedora 6.9 MiB which aarch64 0:2.25-2.fc46 copr_base 123.1 KiB xz aarch64 1:5.8.4-1.fc46 fedora 1.5 MiB Installing dependencies: R-srpm-macros noarch 0:1.3.7-3.fc45 fedora 3.5 KiB add-determinism aarch64 0:0.7.3-3.fc45 fedora 1.9 MiB alternatives aarch64 0:1.33-6.fc46 copr_base 89.9 KiB ansible-srpm-macros noarch 0:1-22.fc45 fedora 35.7 KiB audit-libs aarch64 0:4.2.1-2.fc45 fedora 486.7 KiB binutils aarch64 0:2.47.50-12.fc46 fedora 27.2 MiB build-reproducibility-srpm-macros noarch 0:0.7.3-3.fc45 fedora 1.2 KiB bzip2-libs aarch64 0:1.0.8-24.fc46 copr_base 136.4 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 aarch64 0:9.12-1.fc46 fedora 11.5 MiB crypto-policies noarch 0:20260713-2.gitc42da77.fc45 fedora 134.3 KiB curl aarch64 0:8.23.0~rc2-1.fc46 fedora 525.6 KiB cyrus-sasl-lib aarch64 0:2.1.28-37.fc45 fedora 2.4 MiB debugedit aarch64 0:5.3-3.fc46 copr_base 320.5 KiB dwz aarch64 0:0.17-3.fc45 fedora 322.7 KiB ed aarch64 0:1.22.6-1.fc46 copr_base 223.0 KiB efi-srpm-macros noarch 0:6-9.fc45 fedora 40.3 KiB elfutils aarch64 0:0.196-1.fc46 fedora 3.8 MiB elfutils-debuginfod-client aarch64 0:0.196-1.fc46 fedora 144.0 KiB elfutils-libelf aarch64 0:0.196-1.fc46 fedora 1.5 MiB elfutils-libs aarch64 0:0.196-1.fc46 fedora 746.6 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 aarch64 0:5.48-3.fc46 fedora 141.9 KiB file-libs aarch64 0:5.48-3.fc46 fedora 12.4 MiB filesystem aarch64 0:3.18-59.fc45 fedora 112.0 B filesystem-srpm-macros noarch 0:3.18-59.fc45 fedora 38.2 KiB fips-provider aarch64 0:1.5.3-1.fc46 fedora 3.8 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 aarch64 0:17.2-6.fc46 fedora 13.5 MiB gdbm-libs aarch64 1:1.23-12.fc46 copr_base 233.9 KiB ghc-srpm-macros noarch 0:1.10-2.fc45 fedora 792.0 B glibc aarch64 0:2.44.9000-4.fc46 fedora 6.6 MiB glibc-common aarch64 0:2.44.9000-4.fc46 fedora 1.3 MiB glibc-gconv-extra aarch64 0:2.44.9000-4.fc46 fedora 18.6 MiB gmp aarch64 1:6.3.0-6.fc45 fedora 657.9 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 aarch64 0:2.4.9-18.fc46 copr_base 6.6 MiB gnupg2-dirmngr aarch64 0:2.4.9-18.fc46 copr_base 712.4 KiB gnupg2-gpg-agent aarch64 0:2.4.9-18.fc46 copr_base 850.4 KiB gnupg2-gpgconf aarch64 0:2.4.9-18.fc46 copr_base 323.1 KiB gnupg2-keyboxd aarch64 0:2.4.9-18.fc46 copr_base 234.4 KiB gnupg2-verify aarch64 0:2.4.9-18.fc46 copr_base 431.3 KiB gnutls aarch64 0:3.8.13-5.fc46 fedora 3.7 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 aarch64 0:1.6.2-12.fc46 copr_base 92.5 KiB jansson aarch64 0:2.14-5.fc46 copr_base 157.2 KiB java-srpm-macros noarch 0:1-9.fc45 fedora 870.0 B json-c aarch64 0:0.18-9.fc46 copr_base 138.5 KiB kernel-srpm-macros noarch 0:1.0-30.fc45 fedora 1.9 KiB keyutils-libs aarch64 0:1.6.3-8.fc46 copr_base 98.1 KiB krb5-libs aarch64 0:1.22.2-9.fc45 fedora 2.5 MiB libacl aarch64 0:2.4.0-2.fc45 fedora 67.9 KiB libarchive aarch64 0:3.8.9-2.fc46 fedora 975.7 KiB libassuan aarch64 0:2.5.7-6.fc46 copr_base 216.1 KiB libattr aarch64 0:2.6.0-2.fc46 copr_base 68.2 KiB libblkid aarch64 0:2.42.4-2.fc46 fedora 290.3 KiB libbrotli aarch64 0:1.2.0-6.fc46 copr_base 909.0 KiB libcap aarch64 0:2.78-2.fc45 fedora 508.4 KiB libcap-ng aarch64 0:0.9.6-1.fc46 fedora 160.9 KiB libcbor aarch64 0:0.14.0-3.fc45 fedora 139.6 KiB libcom_err aarch64 0:1.47.4-2.fc46 copr_base 110.9 KiB libcurl aarch64 0:8.23.0~rc2-1.fc46 fedora 1.0 MiB libeconf aarch64 0:0.7.9-4.fc46 copr_base 81.1 KiB libevent aarch64 0:2.1.13-1.fc46 fedora 1.1 MiB libfdisk aarch64 0:2.42.4-2.fc46 fedora 418.8 KiB libffi aarch64 0:3.8.0-1.fc46 fedora 159.6 KiB libfido2 aarch64 0:1.17.0-5.fc46 copr_base 281.5 KiB libfsverity aarch64 0:1.7-4.fc45 fedora 68.4 KiB libgcc aarch64 0:16.2.1-2.fc46.1 fedora 222.3 KiB libgcrypt aarch64 0:1.12.4-1.fc46 fedora 1.2 MiB libgomp aarch64 0:16.2.1-2.fc46.1 fedora 592.9 KiB libgpg-error aarch64 0:1.61-2.fc46 copr_base 998.4 KiB libidn2 aarch64 0:2.3.8-4.fc46 copr_base 560.4 KiB libksba aarch64 0:1.8.1-1.fc46 copr_base 473.0 KiB liblastlog2 aarch64 0:2.42.4-2.fc46 fedora 137.8 KiB libmount aarch64 0:2.42.4-2.fc46 fedora 420.4 KiB libnghttp2 aarch64 0:1.69.0-6.fc46 fedora 197.9 KiB libnghttp3 aarch64 0:1.18.0-1.fc46 copr_base 207.7 KiB libpfm aarch64 0:4.13.0-23.fc45 fedora 252.0 KiB libpkgconf aarch64 0:2.5.1-2.fc46 copr_base 133.9 KiB libpsl aarch64 0:0.23.3-1.fc46 fedora 132.5 KiB libselinux aarch64 0:3.11-5.fc46 fedora 265.2 KiB libselinux-utils aarch64 0:3.11-5.fc46 fedora 1.3 MiB libsemanage aarch64 0:3.11-4.fc46 fedora 360.3 KiB libsepol aarch64 0:3.11-2.fc46 copr_base 940.5 KiB libsmartcols aarch64 0:2.42.4-2.fc46 fedora 224.4 KiB libssh aarch64 0:0.12.2-1.fc45 fedora 721.4 KiB libssh-config noarch 0:0.12.2-1.fc45 fedora 277.0 B libstdc++ aarch64 0:16.2.1-2.fc46.1 fedora 3.0 MiB libtasn1 aarch64 0:4.21.0-2.fc46 copr_base 220.7 KiB libtool-ltdl aarch64 0:2.6.2-1.fc46 fedora 93.9 KiB libunistring aarch64 0:1.1-12.fc46 copr_base 1.7 MiB libusb1 aarch64 0:1.0.30-2.fc45 fedora 179.7 KiB libuuid aarch64 0:2.42.4-2.fc46 fedora 69.3 KiB libverto aarch64 0:0.3.2-13.fc45 fedora 69.3 KiB libxcrypt aarch64 0:4.5.2-4.fc45 fedora 273.2 KiB libxml2 aarch64 0:2.15.4-1.fc46 fedora 1.7 MiB libzstd aarch64 0:1.5.7-6.fc46 copr_base 795.4 KiB linkdupes aarch64 0:0.7.3-3.fc45 fedora 711.0 KiB lua-libs aarch64 0:5.5.1-2.fc46 fedora 330.0 KiB lua-srpm-macros noarch 0:1-18.fc45 fedora 1.3 KiB lz4-libs aarch64 0:1.10.0-5.fc46 copr_base 197.1 KiB meson-srpm-macros noarch 0:1.12.1-2.fc46 fedora 1.7 KiB mpfr aarch64 0:4.2.2-4.fc45 fedora 755.4 KiB ncurses-base noarch 0:6.6-3.fc46 copr_base 329.7 KiB ncurses-libs aarch64 0:6.6-3.fc46 copr_base 1.3 MiB nettle aarch64 0:4.0-5.fc45 fedora 836.7 KiB ngtcp2 aarch64 0:1.22.1-3.fc45 fedora 341.1 KiB ngtcp2-crypto-ossl aarch64 0:1.22.1-3.fc45 fedora 67.5 KiB npth aarch64 0:1.8-5.fc46 copr_base 93.4 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 aarch64 0:2.6.14-1.fc46 fedora 765.1 KiB openssl-libs aarch64 1:4.0.3-1.fc46 fedora 5.8 MiB p11-kit aarch64 0:0.26.5-1.fc46 copr_base 2.8 MiB p11-kit-trust aarch64 0:0.26.5-1.fc46 copr_base 596.1 KiB package-notes-srpm-macros noarch 0:0.20-2.fc45 fedora 1.6 KiB pam-libs aarch64 0:1.7.2-4.fc46 copr_base 222.7 KiB pcre2 aarch64 0:10.47-1.fc46.2 copr_base 841.7 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 aarch64 0:2.5.1-2.fc46 copr_base 114.8 KiB pkgconf-m4 noarch 0:2.5.1-2.fc46 copr_base 14.3 KiB pkgconf-pkg-config aarch64 0:2.5.1-2.fc46 copr_base 990.0 B policycoreutils aarch64 0:3.11-2.fc46 copr_base 1.5 MiB popt aarch64 0:1.19-11.fc46 copr_base 144.5 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 aarch64 0:8.3-6.fc46 copr_base 563.6 KiB redhat-systemd-presets noarch 0:102-3.fc45 fedora 1.0 KiB redhat-systemd-presets-common noarch 0:102-3.fc45 fedora 16.9 KiB rpm aarch64 0:6.1.0-1.fc46 fedora 3.3 MiB rpm-build-libs aarch64 0:6.1.0-1.fc46 fedora 264.0 KiB rpm-libs aarch64 0:6.1.0-1.fc46 fedora 1.1 MiB rpm-plugin-selinux aarch64 0:6.1.0-1.fc46 fedora 67.9 KiB rpm-sequoia aarch64 0:1.10.3-1.fc46 fedora 2.3 MiB rpm-sign-libs aarch64 0:6.1.0-1.fc46 fedora 67.7 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 aarch64 0:3.53.4-1.fc45 fedora 1.6 MiB systemd-libs aarch64 0:262-3.fc46 fedora 2.8 MiB systemd-standalone-sysusers aarch64 0:262-3.fc46 fedora 979.3 KiB tpm2-tss aarch64 0:4.2.0-1.fc46 copr_base 2.3 MiB tree-sitter-srpm-macros noarch 0:0.4.6-2.fc45 fedora 8.6 KiB util-linux-core aarch64 0:2.42.4-2.fc46 fedora 2.5 MiB xxhash-libs aarch64 0:0.8.4-1.fc46 fedora 85.8 KiB xz-libs aarch64 1:5.8.4-1.fc46 fedora 265.5 KiB zig-srpm-macros noarch 0:1-9.fc45 fedora 1.3 KiB zip aarch64 0:3.0-46.fc45 fedora 762.2 KiB zlib-ng-compat aarch64 0:2.3.3-6.fc46 copr_base 133.2 KiB zstd aarch64 0:1.5.7-6.fc46 copr_base 559.9 KiB Installing groups: Buildsystem building group Transaction Summary: Installing: 190 packages Total size of inbound packages is 68 MiB. Need to download 0 B. After this operation, 254 MiB extra will be used (install 254 MiB, remove 0 B). [ 1/190] tar-2:1.35-9.fc45.aarch64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 2/190] redhat-rpm-config-0:345-4.fc4 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 3/190] rpm-build-0:6.1.0-1.fc46.aarc 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 4/190] unzip-0:6.0-71.fc45.aarch64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 5/190] fedora-release-common-0:46-0. 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 6/190] glibc-minimal-langpack-0:2.44 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 7/190] bzip2-0:1.0.8-24.fc46.aarch64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 8/190] cpio-0:2.15-10.fc46.aarch64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 9/190] which-0:2.25-2.fc46.aarch64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 10/190] bash-0:5.3.15-2.fc46.aarch64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 11/190] coreutils-0:9.12-1.fc46.aarch 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 12/190] grep-0:3.12-4.fc45.aarch64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 13/190] patch-0:2.8-6.fc46.aarch64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 14/190] sed-0:4.10-2.fc45.aarch64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 15/190] shadow-utils-2:4.20.0-1.fc46. 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 16/190] util-linux-0:2.42.4-2.fc46.aa 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 17/190] diffutils-0:3.12-6.fc45.aarch 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 18/190] findutils-1:4.11.0-2.fc46.aar 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 19/190] gawk-0:5.4.1-1.fc46.aarch64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 20/190] gzip-0:1.14-4.fc46.aarch64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 21/190] info-0:7.3-3.fc46.aarch64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 22/190] xz-1:5.8.4-1.fc46.aarch64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 23/190] glibc-0:2.44.9000-4.fc46.aarc 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 24/190] libacl-0:2.4.0-2.fc45.aarch64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 25/190] R-srpm-macros-0:1.3.7-3.fc45. 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 26/190] ansible-srpm-macros-0:1-22.fc 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 27/190] build-reproducibility-srpm-ma 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 28/190] cmake-srpm-macros-0:4.3.0-5.f 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 29/190] dwz-0:0.17-3.fc45.aarch64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 30/190] efi-srpm-macros-0:6-9.fc45.no 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 31/190] erlang-srpm-macros-0:0.3.11-2 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 32/190] file-0:5.48-3.fc46.aarch64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 33/190] filesystem-srpm-macros-0:3.18 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 34/190] fonts-srpm-macros-1:5.0.0-4.f 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 35/190] forge-srpm-macros-0:0.4.0-5.f 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 36/190] fpc-srpm-macros-0:1.3-17.fc45 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 37/190] gap-srpm-macros-0:2-3.fc45.no 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 38/190] ghc-srpm-macros-0:1.10-2.fc45 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 39/190] gnat-srpm-macros-0:7-3.fc45.n 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 40/190] gnome-srpm-macros-0:1.0-2.fc4 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 41/190] go-srpm-macros-0:3.8.0-3.fc45 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 42/190] java-srpm-macros-0:1-9.fc45.n 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 43/190] kernel-srpm-macros-0:1.0-30.f 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 44/190] lua-srpm-macros-0:1-18.fc45.n 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 45/190] meson-srpm-macros-0:1.12.1-2. 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 46/190] ocaml-srpm-macros-0:11-4.fc45 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 47/190] openblas-srpm-macros-0:2-22.f 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 48/190] package-notes-srpm-macros-0:0 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 49/190] perl-srpm-macros-0:1-65.fc45. 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 50/190] pyproject-srpm-macros-0:1.23. 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 51/190] python-srpm-macros-0:3.15-2.f 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 52/190] qt5-srpm-macros-0:5.15.18-3.f 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 53/190] qt6-srpm-macros-0:6.11.2-1.fc 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 54/190] rpm-0:6.1.0-1.fc46.aarch64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 55/190] rust-srpm-macros-0:28.5-2.fc4 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 56/190] tree-sitter-srpm-macros-0:0.4 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 57/190] zig-srpm-macros-0:1-9.fc45.no 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 58/190] zip-0:3.0-46.fc45.aarch64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 59/190] binutils-0:2.47.50-12.fc46.aa 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 60/190] elfutils-0:0.196-1.fc46.aarch 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 61/190] elfutils-libelf-0:0.196-1.fc4 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 62/190] libgcc-0:16.2.1-2.fc46.1.aarc 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 63/190] libstdc++-0:16.2.1-2.fc46.1.a 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 64/190] rpm-build-libs-0:6.1.0-1.fc46 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 65/190] rpm-libs-0:6.1.0-1.fc46.aarch 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 66/190] fedora-repos-0:46-0.3.noarch 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 67/190] redhat-systemd-presets-0:102- 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 68/190] glibc-common-0:2.44.9000-4.fc 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 69/190] filesystem-0:3.18-59.fc45.aar 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 70/190] coreutils-common-0:9.12-1.fc4 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 71/190] gmp-1:6.3.0-6.fc45.aarch64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 72/190] libcap-0:2.78-2.fc45.aarch64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 73/190] openssl-libs-1:4.0.3-1.fc46.a 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 74/190] systemd-libs-0:262-3.fc46.aar 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 75/190] audit-libs-0:4.2.1-2.fc45.aar 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 76/190] libsemanage-0:3.11-4.fc46.aar 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 77/190] libxcrypt-0:4.5.2-4.fc45.aarc 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 78/190] setup-0:2.15.1-2.fc45.noarch 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 79/190] libblkid-0:2.42.4-2.fc46.aarc 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 80/190] libfdisk-0:2.42.4-2.fc46.aarc 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 81/190] liblastlog2-0:2.42.4-2.fc46.a 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 82/190] libmount-0:2.42.4-2.fc46.aarc 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 83/190] libsmartcols-0:2.42.4-2.fc46. 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 84/190] libuuid-0:2.42.4-2.fc46.aarch 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 85/190] util-linux-core-0:2.42.4-2.fc 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 86/190] xz-libs-1:5.8.4-1.fc46.aarch6 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 87/190] glibc-gconv-extra-0:2.44.9000 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 88/190] add-determinism-0:0.7.3-3.fc4 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 89/190] linkdupes-0:0.7.3-3.fc45.aarc 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 90/190] file-libs-0:5.48-3.fc46.aarch 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 91/190] elfutils-debuginfod-client-0: 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 92/190] elfutils-libs-0:0.196-1.fc46. 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 93/190] libpfm-0:4.13.0-23.fc45.aarch 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 94/190] libgomp-0:16.2.1-2.fc46.1.aar 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 95/190] lua-libs-0:5.5.1-2.fc46.aarch 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 96/190] rpm-sign-libs-0:6.1.0-1.fc46. 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 97/190] fedora-gpg-keys-0:46-0.3.noar 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 98/190] fedora-repos-rawhide-0:46-0.3 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 99/190] redhat-systemd-presets-common 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [100/190] ca-certificates-0:2026.2.90_v 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [101/190] crypto-policies-0:20260713-2. 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [102/190] fips-provider-0:1.5.3-1.fc46. 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [103/190] libselinux-0:3.11-5.fc46.aarc 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [104/190] libeconf-0:0.7.9-4.fc46.aarch 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [105/190] pam-libs-0:1.7.2-4.fc46.aarch 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [106/190] ncurses-libs-0:6.6-3.fc46.aar 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [107/190] ncurses-base-0:6.6-3.fc46.noa 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [108/190] mpfr-0:4.2.2-4.fc45.aarch64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [109/190] readline-0:8.3-6.fc46.aarch64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [110/190] bzip2-libs-0:1.0.8-24.fc46.aa 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [111/190] libcap-ng-0:0.9.6-1.fc46.aarc 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [112/190] zlib-ng-compat-0:2.3.3-6.fc46 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [113/190] gnupg2-0:2.4.9-18.fc46.aarch6 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [114/190] gpgverify-0:2.2-5.fc45.noarch 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [115/190] libgcrypt-0:1.12.4-1.fc46.aar 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [116/190] gnupg2-dirmngr-0:2.4.9-18.fc4 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [117/190] gnupg2-gpg-agent-0:2.4.9-18.f 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [118/190] gnupg2-gpgconf-0:2.4.9-18.fc4 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [119/190] gnupg2-keyboxd-0:2.4.9-18.fc4 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [120/190] gnupg2-verify-0:2.4.9-18.fc46 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [121/190] gnutls-0:3.8.13-5.fc46.aarch6 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [122/190] openldap-0:2.6.14-1.fc46.aarc 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [123/190] nettle-0:4.0-5.fc45.aarch64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [124/190] cyrus-sasl-lib-0:2.1.28-37.fc 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [125/190] libtool-ltdl-0:2.6.2-1.fc46.a 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [126/190] ima-evm-utils-libs-0:1.6.2-12 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [127/190] libfsverity-0:1.7-4.fc45.aarc 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [128/190] popt-0:1.19-11.fc46.aarch64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [129/190] libzstd-0:1.5.7-6.fc46.aarch6 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [130/190] rpm-sequoia-0:1.10.3-1.fc46.a 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [131/190] sqlite-libs-0:3.53.4-1.fc45.a 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [132/190] debugedit-0:5.3-3.fc46.aarch6 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [133/190] libarchive-0:3.8.9-2.fc46.aar 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [134/190] libxml2-0:2.15.4-1.fc46.aarch 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [135/190] pkgconf-pkg-config-0:2.5.1-2. 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [136/190] pkgconf-0:2.5.1-2.fc46.aarch6 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [137/190] pkgconf-m4-0:2.5.1-2.fc46.noa 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [138/190] libpkgconf-0:2.5.1-2.fc46.aar 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [139/190] zstd-0:1.5.7-6.fc46.aarch64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [140/190] curl-0:8.23.0~rc2-1.fc46.aarc 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [141/190] ed-0:1.22.6-1.fc46.aarch64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [142/190] libattr-0:2.6.0-2.fc46.aarch6 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [143/190] libevent-0:2.1.13-1.fc46.aarc 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [144/190] libsepol-0:3.11-2.fc46.aarch6 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [145/190] pcre2-0:10.47-1.fc46.2.aarch6 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [146/190] pcre2-syntax-0:10.47-1.fc46.2 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [147/190] libgpg-error-0:1.61-2.fc46.aa 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [148/190] lz4-libs-0:1.10.0-5.fc46.aarc 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [149/190] libidn2-0:2.3.8-4.fc46.aarch6 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [150/190] libtasn1-0:4.21.0-2.fc46.aarc 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [151/190] libunistring-0:1.1-12.fc46.aa 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [152/190] p11-kit-0:0.26.5-1.fc46.aarch 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [153/190] p11-kit-trust-0:0.26.5-1.fc46 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [154/190] json-c-0:0.18-9.fc46.aarch64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [155/190] gdbm-libs-1:1.23-12.fc46.aarc 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [156/190] gnulib-l10n-0:20241231-4.fc46 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [157/190] libffi-0:3.8.0-1.fc46.aarch64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [158/190] alternatives-0:1.33-6.fc46.aa 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [159/190] jansson-0:2.14-5.fc46.aarch64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [160/190] tpm2-tss-0:4.2.0-1.fc46.aarch 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [161/190] libassuan-0:2.5.7-6.fc46.aarc 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [162/190] npth-0:1.8-5.fc46.aarch64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [163/190] libksba-0:1.8.1-1.fc46.aarch6 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [164/190] libusb1-0:1.0.30-2.fc45.aarch 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [165/190] fedora-release-0:46-0.1.noarc 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [166/190] systemd-standalone-sysusers-0 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [167/190] gdb-minimal-0:17.2-6.fc46.aar 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [168/190] xxhash-libs-0:0.8.4-1.fc46.aa 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [169/190] fedora-release-identity-basic 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [170/190] libcurl-0:8.23.0~rc2-1.fc46.a 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [171/190] krb5-libs-0:1.22.2-9.fc45.aar 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [172/190] libpsl-0:0.23.3-1.fc46.aarch6 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [173/190] libssh-0:0.12.2-1.fc45.aarch6 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [174/190] ngtcp2-0:1.22.1-3.fc45.aarch6 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [175/190] ngtcp2-crypto-ossl-0:1.22.1-3 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [176/190] libverto-0:0.3.2-13.fc45.aarc 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [177/190] publicsuffix-list-dafsa-0:202 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [178/190] libssh-config-0:0.12.2-1.fc45 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [179/190] selinux-policy-targeted-0:45. 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [180/190] selinux-policy-0:45.20-1.fc46 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [181/190] rpm-plugin-selinux-0:6.1.0-1. 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [182/190] policycoreutils-0:3.11-2.fc46 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [183/190] libselinux-utils-0:3.11-5.fc4 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [184/190] libfido2-0:1.17.0-5.fc46.aarc 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [185/190] libcbor-0:0.14.0-3.fc45.aarch 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [186/190] libbrotli-0:1.2.0-6.fc46.aarc 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [187/190] libnghttp2-0:1.69.0-6.fc46.aa 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [188/190] libnghttp3-0:1.18.0-1.fc46.aa 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [189/190] keyutils-libs-0:1.6.3-8.fc46. 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [190/190] libcom_err-0:1.47.4-2.fc46.aa 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [190/190] Total 100% | 0.0 B/s | 0.0 B | 00m00s Running transaction Importing OpenPGP key 0x91211FCE: UserID : "Fedora (46) " Fingerprint: D924B10D3E810DABDD8B56B596E7E91491211FCE From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-46-primary The key was successfully imported. Importing OpenPGP key 0x91211FCE: UserID : "Fedora (46) " Fingerprint: D924B10D3E810DABDD8B56B596E7E91491211FCE From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-46-primary The key was successfully imported. Importing OpenPGP key 0xF577861E: UserID : "Fedora (45) " Fingerprint: 4F50A6114CD5C6976A7F1179655A4B02F577861E From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-45-primary The key was successfully imported. Importing OpenPGP key 0x9488FB64: UserID : "Fedora (47) " Fingerprint: B2E766FA50CA6FA2D5ED06FC09D879E09488FB64 From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-47-primary The key was successfully imported. [ 1/192] Verify package files 100% | 725.0 B/s | 190.0 B | 00m00s >>> Running %pretrans scriptlet: filesystem-0:3.18-59.fc45.aarch64 >>> Finished %pretrans scriptlet: filesystem-0:3.18-59.fc45.aarch64 >>> [RPM] /var/lib/mock/fedora-rawhide-aarch64-1790841033.072590/root/var/cache/dnf/copr_base-40e073fdd9fcc57e/packages/bzip2-1.0.8-24.fc46.aarch64.rpm: Header OpenPGP V4 RSA/SHA256 signature, key ID 5291f7fa5c4b3009: NOKEY >>> [RPM] failed to open /var/lib/mock/fedora-rawhide-aarch64-1790841033.072590/root/etc/group for id/name lookup: No such file or directory [ 2/192] Prepare transaction 100% | 2.3 KiB/s | 190.0 B | 00m00s [ 3/192] Installing libgcc-0:16.2.1-2. 100% | 109.4 MiB/s | 224.0 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% | 898.4 KiB/s | 920.0 B | 00m00s [ 9/192] Installing fedora-gpg-keys-0: 100% | 29.6 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% | 24.2 KiB/s | 124.0 B | 00m00s >>> Running sysusers scriptlet: setup-0:2.15.1-2.fc45.noarch >>> Finished sysusers scriptlet: setup-0:2.15.1-2.fc45.noarch >>> Scriptlet output: >>> Creating group 'adm' with GID 4. >>> Creating group 'audio' with GID 63. >>> Creating group 'cdrom' with GID 11. >>> Creating group 'clock' with GID 103. >>> Creating group 'dialout' with GID 18. >>> Creating group 'disk' with GID 6. >>> Creating group 'floppy' with GID 19. >>> Creating group 'ftp' with GID 50. >>> Creating group 'games' with GID 20. >>> Creating group 'input' with GID 104. >>> Creating group 'kmem' with GID 9. >>> Creating group 'kvm' with GID 36. >>> Creating group 'lock' with GID 54. >>> Creating group 'lp' with GID 7. >>> Creating group 'mail' with GID 12. >>> Creating group 'man' with GID 15. >>> Creating group 'mem' with GID 8. >>> Creating group 'nobody' with GID 65534. >>> Creating group 'render' with GID 105. >>> Creating group 'root' with GID 0. >>> Creating group 'sgx' with GID 106. >>> Creating group 'sys' with GID 3. >>> Creating group 'tape' with GID 33. >>> Creating group 'tty' with GID 5. >>> Creating group 'users' with GID 100. >>> Creating group 'utmp' with GID 22. >>> Creating group 'video' with GID 39. >>> Creating group 'wheel' with GID 10. >>> Creating user 'adm' (adm) with UID 3 and GID 4. >>> Creating group 'bin' with GID 1. >>> Creating user 'bin' (bin) with UID 1 and GID 1. >>> Creating group 'daemon' with GID 2. >>> Creating user 'daemon' (daemon) with UID 2 and GID 2. >>> Creating user 'ftp' (FTP User) with UID 14 and GID 50. >>> Creating user 'games' (games) with UID 12 and GID 100. >>> Creating user 'halt' (halt) with UID 7 and GID 0. >>> Creating user 'lp' (lp) with UID 4 and GID 7. >>> Creating user 'mail' (mail) with UID 8 and GID 12. >>> Creating user 'nobody' (Kernel Overflow User) with UID 65534 and GID 65534. >>> Creating user 'operator' (operator) with UID 11 and GID 0. >>> Creating user 'root' (Super User) with UID 0 and GID 0. >>> Creating user 'shutdown' (shutdown) with UID 6 and GID 0. >>> Creating user 'sync' (sync) with UID 5 and GID 0. >>> [ 14/192] Installing setup-0:2.15.1-2.f 100% | 29.8 MiB/s | 731.3 KiB | 00m00s >>> [RPM] /etc/hosts created as /etc/hosts.rpmnew [ 15/192] Installing filesystem-0:3.18- 100% | 1.8 MiB/s | 253.6 KiB | 00m00s [ 16/192] Installing gnulib-l10n-0:2024 100% | 129.3 MiB/s | 661.9 KiB | 00m00s [ 17/192] Installing coreutils-common-0 100% | 340.0 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% | 14.4 MiB/s | 14.7 KiB | 00m00s [ 20/192] Installing ncurses-base-0:6.6 100% | 49.6 MiB/s | 355.3 KiB | 00m00s [ 21/192] Installing glibc-common-0:2.4 100% | 47.6 MiB/s | 1.3 MiB | 00m00s [ 22/192] Installing glibc-gconv-extra- 100% | 397.5 MiB/s | 18.7 MiB | 00m00s [ 23/192] Installing glibc-0:2.44.9000- 100% | 137.3 MiB/s | 6.6 MiB | 00m00s [ 24/192] Installing ncurses-libs-0:6.6 100% | 261.3 MiB/s | 1.3 MiB | 00m00s [ 25/192] Installing bash-0:5.3.15-2.fc 100% | 193.0 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% | 130.9 MiB/s | 134.0 KiB | 00m00s [ 28/192] Installing bzip2-libs-0:1.0.8 100% | 134.3 MiB/s | 137.5 KiB | 00m00s [ 29/192] Installing libgpg-error-0:1.6 100% | 37.7 MiB/s | 1.0 MiB | 00m00s [ 30/192] Installing readline-0:8.3-6.f 100% | 184.2 MiB/s | 565.8 KiB | 00m00s [ 31/192] Installing libstdc++-0:16.2.1 100% | 330.2 MiB/s | 3.0 MiB | 00m00s [ 32/192] Installing libzstd-0:1.5.7-6. 100% | 259.3 MiB/s | 796.7 KiB | 00m00s [ 33/192] Installing elfutils-libelf-0: 100% | 364.6 MiB/s | 1.5 MiB | 00m00s [ 34/192] Installing libgcrypt-0:1.12.4 100% | 300.9 MiB/s | 1.2 MiB | 00m00s [ 35/192] Installing libassuan-0:2.5.7- 100% | 212.8 MiB/s | 217.9 KiB | 00m00s [ 36/192] Installing libacl-0:2.4.0-2.f 100% | 67.1 MiB/s | 68.8 KiB | 00m00s [ 37/192] Installing gmp-1:6.3.0-6.fc45 100% | 214.9 MiB/s | 660.1 KiB | 00m00s [ 38/192] Installing systemd-libs-0:262 100% | 309.0 MiB/s | 2.8 MiB | 00m00s [ 39/192] Installing libuuid-0:2.42.4-2 100% | 68.8 MiB/s | 70.4 KiB | 00m00s [ 40/192] Installing xz-libs-1:5.8.4-1. 100% | 260.3 MiB/s | 266.6 KiB | 00m00s [ 41/192] Installing popt-0:1.19-11.fc4 100% | 49.2 MiB/s | 151.2 KiB | 00m00s [ 42/192] Installing sqlite-libs-0:3.53 100% | 261.4 MiB/s | 1.6 MiB | 00m00s [ 43/192] Installing npth-0:1.8-5.fc46. 100% | 92.3 MiB/s | 94.5 KiB | 00m00s [ 44/192] Installing elfutils-libs-0:0. 100% | 243.7 MiB/s | 748.5 KiB | 00m00s [ 45/192] Installing libblkid-0:2.42.4- 100% | 284.5 MiB/s | 291.3 KiB | 00m00s [ 46/192] Installing libsepol-0:3.11-2. 100% | 306.5 MiB/s | 941.5 KiB | 00m00s [ 47/192] Installing gnupg2-gpgconf-0:2 100% | 11.8 MiB/s | 325.2 KiB | 00m00s [ 48/192] Installing crypto-policies-0: 100% | 22.3 MiB/s | 159.5 KiB | 00m00s [ 49/192] Installing libxcrypt-0:4.5.2- 100% | 134.7 MiB/s | 275.9 KiB | 00m00s [ 50/192] Installing pcre2-0:10.47-1.fc 100% | 274.5 MiB/s | 843.1 KiB | 00m00s [ 51/192] Installing libselinux-0:3.11- 100% | 130.1 MiB/s | 266.5 KiB | 00m00s [ 52/192] Installing grep-0:3.12-4.fc45 100% | 37.1 MiB/s | 1.0 MiB | 00m00s [ 53/192] Installing sed-0:4.10-2.fc45. 100% | 32.1 MiB/s | 886.9 KiB | 00m00s [ 54/192] Installing findutils-1:4.11.0 100% | 71.7 MiB/s | 2.1 MiB | 00m00s [ 55/192] Installing libtasn1-0:4.21.0- 100% | 217.3 MiB/s | 222.5 KiB | 00m00s [ 56/192] Installing libunistring-0:1.1 100% | 291.0 MiB/s | 1.7 MiB | 00m00s [ 57/192] Installing libidn2-0:2.3.8-4. 100% | 138.3 MiB/s | 566.5 KiB | 00m00s [ 58/192] Installing json-c-0:0.18-9.fc 100% | 136.5 MiB/s | 139.8 KiB | 00m00s [ 59/192] Installing xz-1:5.8.4-1.fc46. 100% | 50.1 MiB/s | 1.5 MiB | 00m00s [ 60/192] Installing libmount-0:2.42.4- 100% | 205.8 MiB/s | 421.5 KiB | 00m00s [ 61/192] Installing gnupg2-verify-0:2. 100% | 18.4 MiB/s | 432.6 KiB | 00m00s [ 62/192] Installing mpfr-0:4.2.2-4.fc4 100% | 246.4 MiB/s | 757.1 KiB | 00m00s [ 63/192] Installing gawk-0:5.4.1-1.fc4 100% | 97.5 MiB/s | 2.9 MiB | 00m00s [ 64/192] Installing dwz-0:0.17-3.fc45. 100% | 13.8 MiB/s | 324.0 KiB | 00m00s [ 65/192] Installing libksba-0:1.8.1-1. 100% | 232.2 MiB/s | 475.5 KiB | 00m00s [ 66/192] Installing unzip-0:6.0-71.fc4 100% | 20.1 MiB/s | 473.4 KiB | 00m00s [ 67/192] Installing file-libs-0:5.48-3 100% | 618.0 MiB/s | 12.4 MiB | 00m00s [ 68/192] Installing file-0:5.48-3.fc46 100% | 6.1 MiB/s | 143.4 KiB | 00m00s [ 69/192] Installing diffutils-0:3.12-6 100% | 56.0 MiB/s | 1.6 MiB | 00m00s [ 70/192] Installing libsmartcols-0:2.4 100% | 220.1 MiB/s | 225.4 KiB | 00m00s [ 71/192] Installing lua-libs-0:5.5.1-2 100% | 161.9 MiB/s | 331.5 KiB | 00m00s [ 72/192] Installing libeconf-0:0.7.9-4 100% | 80.8 MiB/s | 82.7 KiB | 00m00s [ 73/192] Installing libcap-ng-0:0.9.6- 100% | 159.0 MiB/s | 162.8 KiB | 00m00s [ 74/192] Installing audit-libs-0:4.2.1 100% | 238.9 MiB/s | 489.3 KiB | 00m00s [ 75/192] Installing pam-libs-0:1.7.2-4 100% | 219.8 MiB/s | 225.1 KiB | 00m00s [ 76/192] Installing libcap-0:2.78-2.fc 100% | 20.9 MiB/s | 513.5 KiB | 00m00s [ 77/192] Installing libsemanage-0:3.11 100% | 176.8 MiB/s | 362.0 KiB | 00m00s [ 78/192] Installing libattr-0:2.6.0-2. 100% | 67.5 MiB/s | 69.1 KiB | 00m00s [ 79/192] Installing libffi-0:3.8.0-1.f 100% | 157.2 MiB/s | 161.0 KiB | 00m00s [ 80/192] Installing p11-kit-0:0.26.5-1 100% | 83.8 MiB/s | 2.9 MiB | 00m00s [ 81/192] Installing alternatives-0:1.3 100% | 4.1 MiB/s | 91.5 KiB | 00m00s [ 82/192] Installing p11-kit-trust-0:0. 100% | 20.9 MiB/s | 597.9 KiB | 00m00s [ 83/192] Installing ngtcp2-0:1.22.1-3. 100% | 167.3 MiB/s | 342.7 KiB | 00m00s [ 84/192] Installing liblastlog2-0:2.42 100% | 34.1 MiB/s | 139.8 KiB | 00m00s [ 85/192] Installing util-linux-core-0: 100% | 79.2 MiB/s | 2.5 MiB | 00m00s [ 86/192] Installing zip-0:3.0-46.fc45. 100% | 31.2 MiB/s | 766.1 KiB | 00m00s [ 87/192] Installing gnupg2-keyboxd-0:2 100% | 57.5 MiB/s | 235.5 KiB | 00m00s [ 88/192] Installing libpsl-0:0.23.3-1. 100% | 130.4 MiB/s | 133.6 KiB | 00m00s [ 89/192] Installing tar-2:1.35-9.fc45. 100% | 91.1 MiB/s | 3.0 MiB | 00m00s [ 90/192] Installing linkdupes-0:0.7.3- 100% | 27.8 MiB/s | 712.4 KiB | 00m00s [ 91/192] Installing libselinux-utils-0 100% | 52.2 MiB/s | 1.4 MiB | 00m00s [ 92/192] Installing libfdisk-0:2.42.4- 100% | 205.0 MiB/s | 419.9 KiB | 00m00s [ 93/192] Installing fips-provider-0:1. 100% | 344.5 MiB/s | 3.8 MiB | 00m00s [ 94/192] Installing openssl-libs-1:4.0 100% | 322.9 MiB/s | 5.8 MiB | 00m00s [ 95/192] Installing coreutils-0:9.12-1 100% | 175.6 MiB/s | 8.6 MiB | 00m00s [ 96/192] Installing ca-certificates-0: 100% | 1.6 MiB/s | 2.5 MiB | 00m02s [ 97/192] Installing util-linux-0:2.42. 100% | 129.8 MiB/s | 7.0 MiB | 00m00s [ 98/192] Installing policycoreutils-0: 100% | 40.2 MiB/s | 1.5 MiB | 00m00s [ 99/192] Installing selinux-policy-0:4 100% | 2.0 MiB/s | 34.5 KiB | 00m00s [100/192] Installing selinux-policy-tar 100% | 145.7 MiB/s | 15.2 MiB | 00m00s [101/192] Installing gzip-0:1.14-4.fc46 100% | 17.3 MiB/s | 443.2 KiB | 00m00s [102/192] Installing libfsverity-0:1.7- 100% | 67.8 MiB/s | 69.4 KiB | 00m00s [103/192] Installing rpm-sequoia-0:1.10 100% | 286.5 MiB/s | 2.3 MiB | 00m00s [104/192] Installing libevent-0:2.1.13- 100% | 271.7 MiB/s | 1.1 MiB | 00m00s [105/192] Installing ngtcp2-crypto-ossl 100% | 66.7 MiB/s | 68.3 KiB | 00m00s [106/192] Installing libusb1-0:1.0.30-2 100% | 16.1 MiB/s | 181.4 KiB | 00m00s >>> Running sysusers scriptlet: tpm2-tss-0:4.2.0-1.fc46.aarch64 >>> Finished sysusers scriptlet: tpm2-tss-0:4.2.0-1.fc46.aarch64 >>> 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% | 286.7 MiB/s | 2.3 MiB | 00m00s [108/192] Installing gnupg2-gpg-agent-0 100% | 28.8 MiB/s | 854.4 KiB | 00m00s [109/192] Installing ima-evm-utils-libs 100% | 91.6 MiB/s | 93.8 KiB | 00m00s [110/192] Installing nettle-0:4.0-5.fc4 100% | 205.0 MiB/s | 839.8 KiB | 00m00s [111/192] Installing gnutls-0:3.8.13-5. 100% | 309.1 MiB/s | 3.7 MiB | 00m00s [112/192] Installing zstd-0:1.5.7-6.fc4 100% | 22.0 MiB/s | 563.5 KiB | 00m00s [113/192] Installing libxml2-0:2.15.4-1 100% | 61.5 MiB/s | 1.7 MiB | 00m00s [114/192] Installing bzip2-0:1.0.8-24.f 100% | 7.4 MiB/s | 175.3 KiB | 00m00s [115/192] Installing add-determinism-0: 100% | 68.0 MiB/s | 1.9 MiB | 00m00s [116/192] Installing build-reproducibil 100% | 0.0 B/s | 1.5 KiB | 00m00s [117/192] Installing filesystem-srpm-ma 100% | 38.0 MiB/s | 38.9 KiB | 00m00s [118/192] Installing ed-0:1.22.6-1.fc46 100% | 9.6 MiB/s | 225.3 KiB | 00m00s [119/192] Installing patch-0:2.8-6.fc46 100% | 11.2 MiB/s | 263.9 KiB | 00m00s [120/192] Installing cpio-0:2.15-10.fc4 100% | 42.9 MiB/s | 1.2 MiB | 00m00s [121/192] Installing libpfm-0:4.13.0-23 100% | 247.4 MiB/s | 253.3 KiB | 00m00s [122/192] Installing libgomp-0:16.2.1-2 100% | 290.2 MiB/s | 594.3 KiB | 00m00s [123/192] Installing libtool-ltdl-0:2.6 100% | 92.8 MiB/s | 95.0 KiB | 00m00s [124/192] Installing libpkgconf-0:2.5.1 100% | 131.9 MiB/s | 135.0 KiB | 00m00s [125/192] Installing pkgconf-0:2.5.1-2. 100% | 5.2 MiB/s | 117.4 KiB | 00m00s [126/192] Installing pkgconf-pkg-config 100% | 80.6 KiB/s | 1.8 KiB | 00m00s [127/192] Installing lz4-libs-0:1.10.0- 100% | 193.6 MiB/s | 198.2 KiB | 00m00s [128/192] Installing libarchive-0:3.8.9 100% | 238.7 MiB/s | 977.6 KiB | 00m00s [129/192] Installing gdbm-libs-1:1.23-1 100% | 230.0 MiB/s | 235.6 KiB | 00m00s [130/192] Installing cyrus-sasl-lib-0:2 100% | 83.3 MiB/s | 2.4 MiB | 00m00s [131/192] Installing openldap-0:2.6.14- 100% | 187.7 MiB/s | 768.9 KiB | 00m00s [132/192] Installing gnupg2-dirmngr-0:2 100% | 24.9 MiB/s | 715.1 KiB | 00m00s [133/192] Installing gnupg2-0:2.4.9-18. 100% | 154.6 MiB/s | 6.6 MiB | 00m00s [134/192] Installing gpgverify-0:2.2-5. 100% | 9.2 MiB/s | 9.4 KiB | 00m00s [135/192] Installing jansson-0:2.14-5.f 100% | 154.9 MiB/s | 158.6 KiB | 00m00s [136/192] Installing systemd-standalone 100% | 38.3 MiB/s | 979.9 KiB | 00m00s [137/192] Installing rpm-libs-0:6.1.0-1 100% | 275.1 MiB/s | 1.1 MiB | 00m00s [138/192] Installing rpm-sign-libs-0:6. 100% | 66.9 MiB/s | 68.5 KiB | 00m00s [139/192] Installing rpm-build-libs-0:6 100% | 258.6 MiB/s | 264.9 KiB | 00m00s [140/192] Installing xxhash-libs-0:0.8. 100% | 85.1 MiB/s | 87.2 KiB | 00m00s [141/192] Installing libverto-0:0.3.2-1 100% | 69.5 MiB/s | 71.1 KiB | 00m00s [142/192] Installing libcbor-0:0.14.0-3 100% | 137.7 MiB/s | 141.0 KiB | 00m00s [143/192] Installing libfido2-0:1.17.0- 100% | 276.4 MiB/s | 283.1 KiB | 00m00s [144/192] Installing libbrotli-0:1.2.0- 100% | 222.5 MiB/s | 911.3 KiB | 00m00s [145/192] Installing libnghttp2-0:1.69. 100% | 194.4 MiB/s | 199.0 KiB | 00m00s [146/192] Installing libnghttp3-0:1.18. 100% | 204.2 MiB/s | 209.1 KiB | 00m00s [147/192] Installing keyutils-libs-0:1. 100% | 97.2 MiB/s | 99.5 KiB | 00m00s [148/192] Installing libcom_err-0:1.47. 100% | 109.4 MiB/s | 112.0 KiB | 00m00s [149/192] Installing krb5-libs-0:1.22.2 100% | 253.4 MiB/s | 2.5 MiB | 00m00s [150/192] Installing libssh-0:0.12.2-1. 100% | 235.5 MiB/s | 723.4 KiB | 00m00s [151/192] Installing libcurl-0:8.23.0~r 100% | 255.7 MiB/s | 1.0 MiB | 00m00s [152/192] Installing elfutils-debuginfo 100% | 6.0 MiB/s | 146.3 KiB | 00m00s [153/192] Installing binutils-0:2.47.50 100% | 283.7 MiB/s | 27.2 MiB | 00m00s [154/192] Installing elfutils-0:0.196-1 100% | 114.5 MiB/s | 3.8 MiB | 00m00s [155/192] Installing gdb-minimal-0:17.2 100% | 225.6 MiB/s | 13.5 MiB | 00m00s [156/192] Installing debugedit-0:5.3-3. 100% | 13.2 MiB/s | 323.8 KiB | 00m00s [157/192] Installing curl-0:8.23.0~rc2- 100% | 16.6 MiB/s | 528.3 KiB | 00m00s [158/192] Installing rpm-0:6.1.0-1.fc46 100% | 61.2 MiB/s | 2.8 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% | 0.0 B/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% | 9.4 MiB/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% | 357.4 KiB/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 rpm-build-0:6.1.0- 100% | 23.5 MiB/s | 626.1 KiB | 00m00s [181/192] Installing erlang-srpm-macros 100% | 0.0 B/s | 2.5 KiB | 00m00s [182/192] Installing pyproject-srpm-mac 100% | 3.9 MiB/s | 4.0 KiB | 00m00s [183/192] Installing redhat-rpm-config- 100% | 93.0 MiB/s | 190.4 KiB | 00m00s [184/192] Installing forge-srpm-macros- 100% | 39.3 MiB/s | 40.3 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% | 67.3 MiB/s | 68.9 KiB | 00m00s [190/192] Installing which-0:2.25-2.fc4 100% | 5.1 MiB/s | 125.3 KiB | 00m00s [191/192] Installing shadow-utils-2:4.2 100% | 97.9 MiB/s | 4.5 MiB | 00m00s [192/192] Installing info-0:7.3-3.fc46. 100% | 52.7 KiB/s | 424.1 KiB | 00m08s Warning: skipped OpenPGP checks for 58 packages from repository: copr_base Complete! Updating and loading repositories: fedora 100% | 61.7 KiB/s | 10.2 KiB | 00m00s Additional repo copr_tstellar_fedora_c 100% | 12.1 KiB/s | 1.5 KiB | 00m00s Additional repo copr_fedora_llvm_team_ 100% | 12.0 KiB/s | 1.5 KiB | 00m00s Copr repository 100% | 12.3 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 aarch64 0:13.32-1.fc46 fedora 736.6 KiB clang aarch64 0:24.0.0~pre20260928.g6909c17f146832-6.fc46 copr_fedora_llvm_team_llvm_snapshots_big_merge_20260928 70.9 MiB clang-libs aarch64 0:24.0.0~pre20260928.g6909c17f146832-6.fc46 copr_fedora_llvm_team_llvm_snapshots_big_merge_20260928 107.1 MiB clang-resource-filesystem aarch64 0:24.0.0~pre20260928.g6909c17f146832-6.fc46 copr_fedora_llvm_team_llvm_snapshots_big_merge_20260928 15.3 KiB compiler-rt aarch64 0:24.0.0~pre20260928.g6909c17f146832-6.fc46 copr_fedora_llvm_team_llvm_snapshots_big_merge_20260928 35.6 MiB cpp aarch64 0:16.2.1-2.fc46.1 fedora 40.8 MiB expat aarch64 0:2.8.3-1.fc46 copr_base 378.2 KiB gcc aarch64 0:16.2.1-2.fc46.1 fedora 112.5 MiB gcc-c++ aarch64 0:16.2.1-2.fc46.1 fedora 44.8 MiB gcc-plugin-annobin aarch64 0:16.2.1-2.fc46.1 fedora 69.1 KiB glibc-devel aarch64 0:2.44.9000-4.fc46 fedora 2.3 MiB kernel-headers aarch64 0:7.3.0-0.rc5.45.fc46 fedora 6.9 MiB libasan aarch64 0:16.2.1-2.fc46.1 fedora 1.5 MiB libatomic aarch64 0:16.2.1-2.fc46.1 fedora 77.7 KiB libedit aarch64 0:3.1-60.20260512cvs.fc46 copr_base 281.0 KiB libmpc aarch64 0:1.4.1-2.fc46 copr_base 216.8 KiB libomp aarch64 0:24.0.0~pre20260928.g6909c17f146832-6.fc46 copr_fedora_llvm_team_llvm_snapshots_big_merge_20260928 2.9 MiB libstdc++-devel aarch64 0:16.2.1-2.fc46.1 fedora 40.4 MiB libubsan aarch64 0:16.2.1-2.fc46.1 fedora 475.9 KiB libxcrypt-devel aarch64 0:4.5.2-4.fc45 fedora 31.0 KiB lld aarch64 0:24.0.0~pre20260928.g6909c17f146832-6.fc46 copr_fedora_llvm_team_llvm_snapshots_big_merge_20260928 43.2 KiB lld-libs aarch64 0:24.0.0~pre20260928.g6909c17f146832-6.fc46 copr_fedora_llvm_team_llvm_snapshots_big_merge_20260928 5.9 MiB llvm aarch64 0:24.0.0~pre20260928.g6909c17f146832-6.fc46 copr_fedora_llvm_team_llvm_snapshots_big_merge_20260928 129.9 MiB llvm-filesystem aarch64 0:24.0.0~pre20260928.g6909c17f146832-6.fc46 copr_fedora_llvm_team_llvm_snapshots_big_merge_20260928 0.0 B llvm-libs aarch64 0:24.0.0~pre20260928.g6909c17f146832-6.fc46 copr_fedora_llvm_team_llvm_snapshots_big_merge_20260928 144.6 MiB make aarch64 1:4.4.1-13.fc46 copr_base 1.8 MiB mpdecimal aarch64 0:4.0.1-4.fc46 copr_base 281.1 KiB python-pip-wheel noarch 0:26.2.1-1.fc46 fedora 1.3 MiB python3 aarch64 0:3.15.0~rc2-1.fc46 fedora 84.8 KiB python3-libs aarch64 0:3.15.0~rc2-1.fc46 fedora 49.8 MiB tzdata noarch 0:2026c-2.fc46 fedora 1.2 MiB Transaction Summary: Installing: 33 packages Total size of inbound packages is 205 MiB. Need to download 0 B. After this operation, 803 MiB extra will be used (install 803 MiB, remove 0 B). [ 1/33] fedora-clang-default-cc-0:1-1.f 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 2/33] clang-0:24.0.0~pre20260928.g690 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 3/33] gcc-c++-0:16.2.1-2.fc46.1.aarch 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 4/33] libstdc++-devel-0:16.2.1-2.fc46 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 5/33] clang-libs-0:24.0.0~pre20260928 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 6/33] llvm-libs-0:24.0.0~pre20260928. 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 7/33] gcc-0:16.2.1-2.fc46.1.aarch64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 8/33] clang-resource-filesystem-0:24. 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 9/33] llvm-filesystem-0:24.0.0~pre202 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [10/33] cpp-0:16.2.1-2.fc46.1.aarch64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [11/33] glibc-devel-0:2.44.9000-4.fc46. 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [12/33] libasan-0:16.2.1-2.fc46.1.aarch 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [13/33] libatomic-0:16.2.1-2.fc46.1.aar 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [14/33] libubsan-0:16.2.1-2.fc46.1.aarc 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [15/33] kernel-headers-0:7.3.0-0.rc5.45 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [16/33] libxcrypt-devel-0:4.5.2-4.fc45. 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [17/33] llvm-0:24.0.0~pre20260928.g6909 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [18/33] lld-0:24.0.0~pre20260928.g6909c 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [19/33] libomp-0:24.0.0~pre20260928.g69 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [20/33] compiler-rt-0:24.0.0~pre2026092 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [21/33] python3-0:3.15.0~rc2-1.fc46.aar 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [22/33] lld-libs-0:24.0.0~pre20260928.g 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [23/33] python3-libs-0:3.15.0~rc2-1.fc4 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [24/33] python-pip-wheel-0:26.2.1-1.fc4 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [25/33] expat-0:2.8.3-1.fc46.aarch64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [26/33] mpdecimal-0:4.0.1-4.fc46.aarch6 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [27/33] tzdata-0:2026c-2.fc46.noarch 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [28/33] libmpc-0:1.4.1-2.fc46.aarch64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [29/33] make-1:4.4.1-13.fc46.aarch64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [30/33] libedit-0:3.1-60.20260512cvs.fc 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [31/33] annobin-plugin-gcc-0:13.32-1.fc 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [32/33] gcc-plugin-annobin-0:16.2.1-2.f 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [33/33] annobin-docs-0:13.32-1.fc46.noa 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [33/33] Total 100% | 0.0 B/s | 0.0 B | 00m00s Running transaction [ 1/35] Verify package files 100% | 46.0 B/s | 33.0 B | 00m01s [ 2/35] Prepare transaction 100% | 532.0 B/s | 33.0 B | 00m00s [ 3/35] Installing libmpc-0:1.4.1-2.fc4 100% | 106.7 MiB/s | 218.5 KiB | 00m00s [ 4/35] Installing clang-resource-files 100% | 5.4 MiB/s | 16.7 KiB | 00m00s [ 5/35] Installing libstdc++-devel-0:16 100% | 405.2 MiB/s | 40.5 MiB | 00m00s [ 6/35] Installing cpp-0:16.2.1-2.fc46. 100% | 297.7 MiB/s | 40.8 MiB | 00m00s [ 7/35] Installing annobin-docs-0:13.32 100% | 98.5 MiB/s | 100.8 KiB | 00m00s [ 8/35] Installing libedit-0:3.1-60.202 100% | 138.0 MiB/s | 282.6 KiB | 00m00s [ 9/35] Installing make-1:4.4.1-13.fc46 100% | 54.4 MiB/s | 1.8 MiB | 00m00s [10/35] Installing tzdata-0:2026c-2.fc4 100% | 30.7 MiB/s | 1.5 MiB | 00m00s [11/35] Installing mpdecimal-0:4.0.1-4. 100% | 138.0 MiB/s | 282.6 KiB | 00m00s [12/35] Installing expat-0:2.8.3-1.fc46 100% | 15.5 MiB/s | 380.3 KiB | 00m00s [13/35] Installing python-pip-wheel-0:2 100% | 158.5 MiB/s | 1.3 MiB | 00m00s [14/35] Installing python3-libs-0:3.15. 100% | 285.4 MiB/s | 50.2 MiB | 00m00s [15/35] Installing python3-0:3.15.0~rc2 100% | 3.7 MiB/s | 86.5 KiB | 00m00s [16/35] Installing compiler-rt-0:24.0.0 100% | 574.2 MiB/s | 35.6 MiB | 00m00s [17/35] Installing kernel-headers-0:7.3 100% | 150.9 MiB/s | 7.1 MiB | 00m00s [18/35] Installing glibc-devel-0:2.44.9 100% | 124.8 MiB/s | 2.4 MiB | 00m00s [19/35] Installing libxcrypt-devel-0:4. 100% | 32.5 MiB/s | 33.3 KiB | 00m00s [20/35] Installing libubsan-0:16.2.1-2. 100% | 232.8 MiB/s | 476.7 KiB | 00m00s [21/35] Installing libatomic-0:16.2.1-2 100% | 77.0 MiB/s | 78.8 KiB | 00m00s [22/35] Installing libasan-0:16.2.1-2.f 100% | 308.3 MiB/s | 1.5 MiB | 00m00s [23/35] Installing gcc-0:16.2.1-2.fc46. 100% | 352.8 MiB/s | 112.5 MiB | 00m00s [24/35] Installing gcc-c++-0:16.2.1-2.f 100% | 302.8 MiB/s | 44.8 MiB | 00m00s [25/35] Installing llvm-filesystem-0:24 100% | 1.0 MiB/s | 1.1 KiB | 00m00s [26/35] Installing llvm-libs-0:24.0.0~p 100% | 406.1 MiB/s | 144.6 MiB | 00m00s [27/35] Installing clang-libs-0:24.0.0~ 100% | 399.9 MiB/s | 107.2 MiB | 00m00s [28/35] Installing clang-0:24.0.0~pre20 100% | 514.0 MiB/s | 70.9 MiB | 00m00s [29/35] Installing llvm-0:24.0.0~pre202 100% | 357.0 MiB/s | 129.9 MiB | 00m00s [30/35] Installing libomp-0:24.0.0~pre2 100% | 326.1 MiB/s | 2.9 MiB | 00m00s [31/35] Installing lld-libs-0:24.0.0~pr 100% | 367.3 MiB/s | 5.9 MiB | 00m00s [32/35] Installing lld-0:24.0.0~pre2026 100% | 1.6 MiB/s | 46.2 KiB | 00m00s [33/35] Installing fedora-clang-default 100% | 0.0 B/s | 288.0 B | 00m00s [34/35] Installing annobin-plugin-gcc-0 100% | 55.5 MiB/s | 738.3 KiB | 00m00s [35/35] Installing gcc-plugin-annobin-0 100% | 548.4 KiB/s | 70.7 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.aarch64 alternatives-1.33-6.fc46.aarch64 annobin-docs-13.32-1.fc46.noarch annobin-plugin-gcc-13.32-1.fc46.aarch64 ansible-srpm-macros-1-22.fc45.noarch audit-libs-4.2.1-2.fc45.aarch64 bash-5.3.15-2.fc46.aarch64 binutils-2.47.50-12.fc46.aarch64 build-reproducibility-srpm-macros-0.7.3-3.fc45.noarch bzip2-1.0.8-24.fc46.aarch64 bzip2-libs-1.0.8-24.fc46.aarch64 ca-certificates-2026.2.90_v9.0.317-1.fc46.noarch clang-24.0.0~pre20260928.g6909c17f146832-6.fc46.aarch64 clang-libs-24.0.0~pre20260928.g6909c17f146832-6.fc46.aarch64 clang-resource-filesystem-24.0.0~pre20260928.g6909c17f146832-6.fc46.aarch64 cmake-srpm-macros-4.3.0-5.fc45.noarch compiler-rt-24.0.0~pre20260928.g6909c17f146832-6.fc46.aarch64 coreutils-9.12-1.fc46.aarch64 coreutils-common-9.12-1.fc46.aarch64 cpio-2.15-10.fc46.aarch64 cpp-16.2.1-2.fc46.1.aarch64 crypto-policies-20260713-2.gitc42da77.fc45.noarch curl-8.23.0~rc2-1.fc46.aarch64 cyrus-sasl-lib-2.1.28-37.fc45.aarch64 debugedit-5.3-3.fc46.aarch64 diffutils-3.12-6.fc45.aarch64 dwz-0.17-3.fc45.aarch64 ed-1.22.6-1.fc46.aarch64 efi-srpm-macros-6-9.fc45.noarch elfutils-0.196-1.fc46.aarch64 elfutils-debuginfod-client-0.196-1.fc46.aarch64 elfutils-libelf-0.196-1.fc46.aarch64 elfutils-libs-0.196-1.fc46.aarch64 erlang-srpm-macros-0.3.11-2.fc45.noarch expat-2.8.3-1.fc46.aarch64 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.aarch64 file-libs-5.48-3.fc46.aarch64 filesystem-3.18-59.fc45.aarch64 filesystem-srpm-macros-3.18-59.fc45.noarch findutils-4.11.0-2.fc46.aarch64 fips-provider-1.5.3-1.fc46.aarch64 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.aarch64 gcc-16.2.1-2.fc46.1.aarch64 gcc-c++-16.2.1-2.fc46.1.aarch64 gcc-plugin-annobin-16.2.1-2.fc46.1.aarch64 gdb-minimal-17.2-6.fc46.aarch64 gdbm-libs-1.23-12.fc46.aarch64 ghc-srpm-macros-1.10-2.fc45.noarch glibc-2.44.9000-4.fc46.aarch64 glibc-common-2.44.9000-4.fc46.aarch64 glibc-devel-2.44.9000-4.fc46.aarch64 glibc-gconv-extra-2.44.9000-4.fc46.aarch64 glibc-minimal-langpack-2.44.9000-4.fc46.aarch64 gmp-6.3.0-6.fc45.aarch64 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.aarch64 gnupg2-dirmngr-2.4.9-18.fc46.aarch64 gnupg2-gpg-agent-2.4.9-18.fc46.aarch64 gnupg2-gpgconf-2.4.9-18.fc46.aarch64 gnupg2-keyboxd-2.4.9-18.fc46.aarch64 gnupg2-verify-2.4.9-18.fc46.aarch64 gnutls-3.8.13-5.fc46.aarch64 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.aarch64 gzip-1.14-4.fc46.aarch64 ima-evm-utils-libs-1.6.2-12.fc46.aarch64 info-7.3-3.fc46.aarch64 jansson-2.14-5.fc46.aarch64 java-srpm-macros-1-9.fc45.noarch json-c-0.18-9.fc46.aarch64 kernel-headers-7.3.0-0.rc5.45.fc46.aarch64 kernel-srpm-macros-1.0-30.fc45.noarch keyutils-libs-1.6.3-8.fc46.aarch64 krb5-libs-1.22.2-9.fc45.aarch64 libacl-2.4.0-2.fc45.aarch64 libarchive-3.8.9-2.fc46.aarch64 libasan-16.2.1-2.fc46.1.aarch64 libassuan-2.5.7-6.fc46.aarch64 libatomic-16.2.1-2.fc46.1.aarch64 libattr-2.6.0-2.fc46.aarch64 libblkid-2.42.4-2.fc46.aarch64 libbrotli-1.2.0-6.fc46.aarch64 libcap-2.78-2.fc45.aarch64 libcap-ng-0.9.6-1.fc46.aarch64 libcbor-0.14.0-3.fc45.aarch64 libcom_err-1.47.4-2.fc46.aarch64 libcurl-8.23.0~rc2-1.fc46.aarch64 libeconf-0.7.9-4.fc46.aarch64 libedit-3.1-60.20260512cvs.fc46.aarch64 libevent-2.1.13-1.fc46.aarch64 libfdisk-2.42.4-2.fc46.aarch64 libffi-3.8.0-1.fc46.aarch64 libfido2-1.17.0-5.fc46.aarch64 libfsverity-1.7-4.fc45.aarch64 libgcc-16.2.1-2.fc46.1.aarch64 libgcrypt-1.12.4-1.fc46.aarch64 libgomp-16.2.1-2.fc46.1.aarch64 libgpg-error-1.61-2.fc46.aarch64 libidn2-2.3.8-4.fc46.aarch64 libksba-1.8.1-1.fc46.aarch64 liblastlog2-2.42.4-2.fc46.aarch64 libmount-2.42.4-2.fc46.aarch64 libmpc-1.4.1-2.fc46.aarch64 libnghttp2-1.69.0-6.fc46.aarch64 libnghttp3-1.18.0-1.fc46.aarch64 libomp-24.0.0~pre20260928.g6909c17f146832-6.fc46.aarch64 libpfm-4.13.0-23.fc45.aarch64 libpkgconf-2.5.1-2.fc46.aarch64 libpsl-0.23.3-1.fc46.aarch64 libselinux-3.11-5.fc46.aarch64 libselinux-utils-3.11-5.fc46.aarch64 libsemanage-3.11-4.fc46.aarch64 libsepol-3.11-2.fc46.aarch64 libsmartcols-2.42.4-2.fc46.aarch64 libssh-0.12.2-1.fc45.aarch64 libssh-config-0.12.2-1.fc45.noarch libstdc++-16.2.1-2.fc46.1.aarch64 libstdc++-devel-16.2.1-2.fc46.1.aarch64 libtasn1-4.21.0-2.fc46.aarch64 libtool-ltdl-2.6.2-1.fc46.aarch64 libubsan-16.2.1-2.fc46.1.aarch64 libunistring-1.1-12.fc46.aarch64 libusb1-1.0.30-2.fc45.aarch64 libuuid-2.42.4-2.fc46.aarch64 libverto-0.3.2-13.fc45.aarch64 libxcrypt-4.5.2-4.fc45.aarch64 libxcrypt-devel-4.5.2-4.fc45.aarch64 libxml2-2.15.4-1.fc46.aarch64 libzstd-1.5.7-6.fc46.aarch64 linkdupes-0.7.3-3.fc45.aarch64 lld-24.0.0~pre20260928.g6909c17f146832-6.fc46.aarch64 lld-libs-24.0.0~pre20260928.g6909c17f146832-6.fc46.aarch64 llvm-24.0.0~pre20260928.g6909c17f146832-6.fc46.aarch64 llvm-filesystem-24.0.0~pre20260928.g6909c17f146832-6.fc46.aarch64 llvm-libs-24.0.0~pre20260928.g6909c17f146832-6.fc46.aarch64 lua-libs-5.5.1-2.fc46.aarch64 lua-srpm-macros-1-18.fc45.noarch lz4-libs-1.10.0-5.fc46.aarch64 make-4.4.1-13.fc46.aarch64 meson-srpm-macros-1.12.1-2.fc46.noarch mpdecimal-4.0.1-4.fc46.aarch64 mpfr-4.2.2-4.fc45.aarch64 ncurses-base-6.6-3.fc46.noarch ncurses-libs-6.6-3.fc46.aarch64 nettle-4.0-5.fc45.aarch64 ngtcp2-1.22.1-3.fc45.aarch64 ngtcp2-crypto-ossl-1.22.1-3.fc45.aarch64 npth-1.8-5.fc46.aarch64 ocaml-srpm-macros-11-4.fc45.noarch openblas-srpm-macros-2-22.fc45.noarch openldap-2.6.14-1.fc46.aarch64 openssl-libs-4.0.3-1.fc46.aarch64 p11-kit-0.26.5-1.fc46.aarch64 p11-kit-trust-0.26.5-1.fc46.aarch64 package-notes-srpm-macros-0.20-2.fc45.noarch pam-libs-1.7.2-4.fc46.aarch64 patch-2.8-6.fc46.aarch64 pcre2-10.47-1.fc46.2.aarch64 pcre2-syntax-10.47-1.fc46.2.noarch perl-srpm-macros-1-65.fc45.noarch pkgconf-2.5.1-2.fc46.aarch64 pkgconf-m4-2.5.1-2.fc46.noarch pkgconf-pkg-config-2.5.1-2.fc46.aarch64 policycoreutils-3.11-2.fc46.aarch64 popt-1.19-11.fc46.aarch64 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.aarch64 python3-libs-3.15.0~rc2-1.fc46.aarch64 qt5-srpm-macros-5.15.18-3.fc45.noarch qt6-srpm-macros-6.11.2-1.fc46.noarch readline-8.3-6.fc46.aarch64 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.aarch64 rpm-build-6.1.0-1.fc46.aarch64 rpm-build-libs-6.1.0-1.fc46.aarch64 rpm-libs-6.1.0-1.fc46.aarch64 rpm-plugin-selinux-6.1.0-1.fc46.aarch64 rpm-sequoia-1.10.3-1.fc46.aarch64 rpm-sign-libs-6.1.0-1.fc46.aarch64 rust-srpm-macros-28.5-2.fc45.noarch sed-4.10-2.fc45.aarch64 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.aarch64 sqlite-libs-3.53.4-1.fc45.aarch64 systemd-libs-262-3.fc46.aarch64 systemd-standalone-sysusers-262-3.fc46.aarch64 tar-1.35-9.fc45.aarch64 tpm2-tss-4.2.0-1.fc46.aarch64 tree-sitter-srpm-macros-0.4.6-2.fc45.noarch tzdata-2026c-2.fc46.noarch unzip-6.0-71.fc45.aarch64 util-linux-2.42.4-2.fc46.aarch64 util-linux-core-2.42.4-2.fc46.aarch64 which-2.25-2.fc46.aarch64 xxhash-libs-0.8.4-1.fc46.aarch64 xz-5.8.4-1.fc46.aarch64 xz-libs-5.8.4-1.fc46.aarch64 zig-srpm-macros-1-9.fc45.noarch zip-3.0-46.fc45.aarch64 zlib-ng-compat-2.3.3-6.fc46.aarch64 zstd-1.5.7-6.fc46.aarch64 Start: buildsrpm Start: rpmbuild -bs Building target platforms: aarch64 Building for target aarch64 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-aarch64-1790841033.072590/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-zcymtufs/htslib/htslib.spec) Config(child) 0 minutes 29 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-aarch64) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-aarch64-bootstrap-1790841033.072590/root. INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-aarch64-bootstrap-1790841033.072590/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-aarch64-1790841033.072590/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.aarch64 rpm-sequoia-1.10.3-1.fc46.aarch64 dnf5-5.4.6.0-1.fc46.aarch64 dnf5-plugins-5.4.6.0-1.fc46.aarch64 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: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1784246400 Wrote: /builddir/build/SRPMS/htslib-1.24-1.fc46.src.rpm Updating and loading repositories: fedora 100% | 55.6 KiB/s | 10.2 KiB | 00m00s Additional repo copr_tstellar_fedora_c 100% | 10.4 KiB/s | 1.5 KiB | 00m00s Additional repo copr_fedora_llvm_team_ 100% | 10.4 KiB/s | 1.5 KiB | 00m00s Copr repository 100% | 10.5 KiB/s | 1.5 KiB | 00m00s Repositories loaded. Package "gcc-16.2.1-2.fc46.1.aarch64" is already installed. Package "make-1:4.4.1-13.fc46.aarch64" is already installed. Package Arch Version Repository Size Installing: bzip2-devel aarch64 0:1.0.8-24.fc46 copr_base 309.8 KiB libcurl-devel aarch64 0:8.23.0~rc2-1.fc46 fedora 1.4 MiB openssl-devel aarch64 1:4.0.3-1.fc46 fedora 4.6 MiB perl-Data-Dumper aarch64 0:2.192-528.fc45 fedora 135.5 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 aarch64 4:5.44.0-527.fc45 fedora 175.8 KiB perl-lib aarch64 0:0.65-527.fc45 fedora 8.5 KiB xz-devel aarch64 1:5.8.4-1.fc46 fedora 258.8 KiB zlib-ng-compat-devel aarch64 0:2.3.3-6.fc46 copr_base 107.0 KiB Installing dependencies: brotli aarch64 0:1.2.0-6.fc46 copr_base 69.3 KiB brotli-devel aarch64 0:1.2.0-6.fc46 copr_base 65.9 KiB cmake-filesystem aarch64 0:4.3.0-5.fc45 fedora 0.0 B groff-base aarch64 0:1.24.1-2.fc46 copr_base 4.7 MiB keyutils-libs-devel aarch64 0:1.6.3-8.fc46 copr_base 48.2 KiB krb5-devel aarch64 0:1.22.2-9.fc45 fedora 709.9 KiB libcom_err-devel aarch64 0:1.47.4-2.fc46 copr_base 16.7 KiB libidn2-devel aarch64 0:2.3.8-4.fc46 copr_base 152.1 KiB libkadm5 aarch64 0:1.22.2-9.fc45 fedora 266.0 KiB libnghttp2-devel aarch64 0:1.69.0-6.fc46 fedora 288.0 KiB libnghttp3-devel aarch64 0:1.18.0-1.fc46 copr_base 119.4 KiB libpsl-devel aarch64 0:0.23.3-1.fc46 fedora 111.5 KiB libselinux-devel aarch64 0:3.11-5.fc46 fedora 121.9 KiB libsepol-devel aarch64 0:3.11-2.fc46 copr_base 120.7 KiB libssh-devel aarch64 0:0.12.2-1.fc45 fedora 204.2 KiB libverto-devel aarch64 0:0.3.2-13.fc45 fedora 25.7 KiB libzstd-devel aarch64 0:1.5.7-6.fc46 copr_base 217.6 KiB ncurses aarch64 0:6.6-3.fc46 copr_base 895.2 KiB ngtcp2-crypto-ossl-devel aarch64 0:1.22.1-3.fc45 fedora 7.5 KiB ngtcp2-devel aarch64 0:1.22.1-3.fc45 fedora 262.8 KiB pcre2-devel aarch64 0:10.47-1.fc46.2 copr_base 2.1 MiB pcre2-utf16 aarch64 0:10.47-1.fc46.2 copr_base 710.5 KiB pcre2-utf32 aarch64 0:10.47-1.fc46.2 copr_base 710.4 KiB perl-AutoLoader noarch 0:5.74-527.fc45 fedora 20.6 KiB perl-B aarch64 0:1.92-527.fc45 fedora 557.5 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 aarch64 0:2.59-527.fc45 fedora 103.6 KiB perl-DynaLoader aarch64 0:1.57-527.fc45 fedora 32.1 KiB perl-Encode aarch64 4:3.24-527.fc45 fedora 4.8 MiB perl-Errno aarch64 0:1.39-527.fc45 fedora 8.4 KiB perl-Exporter noarch 0:5.79-527.fc45 fedora 54.2 KiB perl-Fcntl aarch64 0:1.20-527.fc45 fedora 92.7 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 aarch64 0:1.56-527.fc45 fedora 191.3 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 aarch64 0:3.16-527.fc45 fedora 93.9 KiB perl-Net-SSLeay aarch64 0:1.96-5.fc45 fedora 1.4 MiB perl-POSIX aarch64 0:2.26-527.fc45 fedora 261.4 KiB perl-PathTools aarch64 0:3.95-527.fc45 fedora 224.0 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 aarch64 5:1.70-527.fc45 fedora 152.9 KiB perl-SelectSaver noarch 0:1.03-527.fc45 fedora 2.1 KiB perl-Socket aarch64 4:2.043-1.fc46 fedora 145.8 KiB perl-Storable aarch64 1:3.41-527.fc45 fedora 242.9 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 aarch64 4:1.9780-527.fc45 fedora 151.7 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 aarch64 0:1.32-527.fc45 fedora 524.5 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 aarch64 4:5.44.0-527.fc45 fedora 12.0 MiB perl-locale noarch 0:1.13-527.fc45 fedora 6.1 KiB perl-mro aarch64 0:1.30-527.fc45 fedora 81.5 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, 44 MiB extra will be used (install 44 MiB, remove 0 B). [ 1/90] perl-Data-Dumper-0:2.192-528.fc 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 2/90] perl-Getopt-Long-1:2.58-527.fc4 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 3/90] perl-interpreter-4:5.44.0-527.f 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 4/90] perl-Carp-0:1.54-527.fc45.noarc 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 5/90] perl-Exporter-0:5.79-527.fc45.n 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 6/90] perl-Scalar-List-Utils-5:1.70-5 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 7/90] perl-constant-0:1.33-528.fc45.n 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 8/90] perl-libs-4:5.44.0-527.fc45.aar 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 9/90] perl-Pod-Usage-4:2.05-527.fc45. 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [10/90] perl-Text-ParseWords-0:3.31-527 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [11/90] perl-Encode-4:3.24-527.fc45.aar 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [12/90] perl-Pod-Perldoc-0:3.28.01-527. 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [13/90] perl-podlators-1:6.1.1-1.fc46.n 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [14/90] perl-MIME-Base64-0:3.16-527.fc4 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [15/90] perl-Storable-1:3.41-527.fc45.a 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [16/90] perl-parent-1:0.244-527.fc45.no 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [17/90] perl-Fcntl-0:1.20-527.fc45.aarc 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [18/90] perl-File-Temp-1:0.231.200-527. 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [19/90] perl-HTTP-Tiny-0:0.096-528.fc45 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [20/90] perl-IO-0:1.56-527.fc45.aarch64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [21/90] perl-PathTools-0:3.95-527.fc45. 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [22/90] perl-Pod-Simple-1:3.48-527.fc45 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [23/90] perl-POSIX-0:2.26-527.fc45.aarc 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [24/90] perl-Term-ANSIColor-0:5.01-527. 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [25/90] perl-Term-Cap-0:1.18-527.fc45.n 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [26/90] perl-B-0:1.92-527.fc45.aarch64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [27/90] perl-Errno-0:1.39-527.fc45.aarc 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [28/90] perl-File-Path-0:2.18-527.fc45. 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [29/90] perl-IO-Socket-SSL-0:2.099-2.fc 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [30/90] perl-Net-SSLeay-0:1.96-5.fc45.a 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [31/90] perl-Socket-4:2.043-1.fc46.aarc 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [32/90] perl-Time-HiRes-4:1.9780-527.fc 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [33/90] perl-Time-Local-2:1.350-527.fc4 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [34/90] perl-Pod-Escapes-1:1.07-527.fc4 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [35/90] perl-Text-Tabs+Wrap-0:2024.001- 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [36/90] perl-IO-Socket-IP-0:0.44-527.fc 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [37/90] perl-URI-0:5.37-1.fc46.noarch 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [38/90] perl-MIME-Base32-0:1.303-26.fc4 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [39/90] perl-Unicode-Normalize-0:1.32-5 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [40/90] perl-libnet-0:3.15-528.fc45.noa 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [41/90] perl-Digest-MD5-0:2.59-527.fc45 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [42/90] perl-Digest-0:1.20-527.fc45.noa 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [43/90] perl-File-Basename-0:2.86-527.f 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [44/90] perl-DynaLoader-0:1.57-527.fc45 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [45/90] perl-FileHandle-0:2.05-527.fc45 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [46/90] perl-Symbol-0:1.09-527.fc45.noa 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [47/90] perl-base-0:2.27-527.fc45.noarc 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [48/90] perl-overload-0:1.40-527.fc45.n 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [49/90] perl-mro-0:1.30-527.fc45.aarch6 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [50/90] ncurses-0:6.6-3.fc46.aarch64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [51/90] perl-vars-0:1.05-527.fc45.noarc 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [52/90] perl-if-0:0.61.000-527.fc45.noa 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [53/90] groff-base-0:1.24.1-2.fc46.aarc 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [54/90] perl-IPC-Open3-0:1.24-527.fc45. 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [55/90] perl-locale-0:1.13-527.fc45.noa 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [56/90] perl-AutoLoader-0:5.74-527.fc45 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [57/90] perl-File-stat-0:1.15-527.fc45. 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [58/90] perl-SelectSaver-0:1.03-527.fc4 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [59/90] perl-Class-Struct-0:0.68-527.fc 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [60/90] perl-Getopt-Std-0:1.15-527.fc45 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [61/90] perl-overloading-0:0.03-527.fc4 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [62/90] bzip2-devel-0:1.0.8-24.fc46.aar 100% | 41.7 MiB/s | 213.4 KiB | 00m00s [63/90] perl-FindBin-0:1.54-527.fc45.no 100% | 6.8 MiB/s | 13.9 KiB | 00m00s [64/90] xz-devel-1:5.8.4-1.fc46.aarch64 100% | 12.9 MiB/s | 66.2 KiB | 00m00s [65/90] perl-lib-0:0.65-527.fc45.aarch6 100% | 2.0 MiB/s | 14.6 KiB | 00m00s [66/90] libcurl-devel-0:8.23.0~rc2-1.fc 100% | 98.5 MiB/s | 1.0 MiB | 00m00s [67/90] zlib-ng-compat-devel-0:2.3.3-6. 100% | 18.4 MiB/s | 37.7 KiB | 00m00s [68/90] krb5-devel-0:1.22.2-9.fc45.aarc 100% | 46.6 MiB/s | 143.2 KiB | 00m00s [69/90] libssh-devel-0:0.12.2-1.fc45.aa 100% | 23.1 MiB/s | 47.2 KiB | 00m00s [70/90] cmake-filesystem-0:4.3.0-5.fc45 100% | 7.3 MiB/s | 14.9 KiB | 00m00s [71/90] ngtcp2-crypto-ossl-devel-0:1.22 100% | 3.7 MiB/s | 11.5 KiB | 00m00s [72/90] libkadm5-0:1.22.2-9.fc45.aarch6 100% | 38.3 MiB/s | 78.4 KiB | 00m00s [73/90] libverto-devel-0:0.3.2-13.fc45. 100% | 6.9 MiB/s | 14.2 KiB | 00m00s [74/90] ngtcp2-devel-0:1.22.1-3.fc45.aa 100% | 23.7 MiB/s | 48.6 KiB | 00m00s [75/90] brotli-devel-0:1.2.0-6.fc46.aar 100% | 16.8 MiB/s | 34.4 KiB | 00m00s [76/90] brotli-0:1.2.0-6.fc46.aarch64 100% | 11.1 MiB/s | 22.7 KiB | 00m00s [77/90] libidn2-devel-0:2.3.8-4.fc46.aa 100% | 28.5 MiB/s | 58.4 KiB | 00m00s [78/90] libnghttp2-devel-0:1.69.0-6.fc4 100% | 17.7 MiB/s | 54.2 KiB | 00m00s [79/90] libnghttp3-devel-0:1.18.0-1.fc4 100% | 13.5 MiB/s | 27.7 KiB | 00m00s [80/90] libpsl-devel-0:0.23.3-1.fc46.aa 100% | 11.0 MiB/s | 33.7 KiB | 00m00s [81/90] publicsuffix-list-0:20260624-2. 100% | 22.7 MiB/s | 92.8 KiB | 00m00s [82/90] libzstd-devel-0:1.5.7-6.fc46.aa 100% | 27.4 MiB/s | 56.1 KiB | 00m00s [83/90] openssl-devel-1:4.0.3-1.fc46.aa 100% | 186.7 MiB/s | 3.2 MiB | 00m00s [84/90] keyutils-libs-devel-0:1.6.3-8.f 100% | 14.0 MiB/s | 57.3 KiB | 00m00s [85/90] libcom_err-devel-0:1.47.4-2.fc4 100% | 5.3 MiB/s | 16.3 KiB | 00m00s [86/90] libselinux-devel-0:3.11-5.fc46. 100% | 78.4 MiB/s | 160.6 KiB | 00m00s [87/90] libsepol-devel-0:3.11-2.fc46.aa 100% | 19.6 MiB/s | 40.2 KiB | 00m00s [88/90] pcre2-devel-0:10.47-1.fc46.2.aa 100% | 85.8 MiB/s | 527.3 KiB | 00m00s [89/90] pcre2-utf16-0:10.47-1.fc46.2.aa 100% | 45.7 MiB/s | 234.1 KiB | 00m00s [90/90] pcre2-utf32-0:10.47-1.fc46.2.aa 100% | 44.0 MiB/s | 225.4 KiB | 00m00s -------------------------------------------------------------------------------- [90/90] Total 100% | 97.7 MiB/s | 6.4 MiB | 00m00s Running transaction [ 1/92] Verify package files 100% | 1.5 KiB/s | 90.0 B | 00m00s [ 2/92] Prepare transaction 100% | 967.0 B/s | 90.0 B | 00m00s [ 3/92] Installing cmake-filesystem-0:4 100% | 4.6 MiB/s | 9.4 KiB | 00m00s [ 4/92] Installing libidn2-devel-0:2.3. 100% | 14.2 MiB/s | 159.8 KiB | 00m00s [ 5/92] Installing openssl-devel-1:4.0. 100% | 47.8 MiB/s | 5.6 MiB | 00m00s [ 6/92] Installing ngtcp2-devel-0:1.22. 100% | 257.9 MiB/s | 264.1 KiB | 00m00s [ 7/92] Installing ngtcp2-crypto-ossl-d 100% | 0.0 B/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% | 347.3 MiB/s | 711.3 KiB | 00m00s [11/92] Installing pcre2-utf16-0:10.47- 100% | 231.6 MiB/s | 711.4 KiB | 00m00s [12/92] Installing pcre2-devel-0:10.47- 100% | 64.2 MiB/s | 2.1 MiB | 00m00s [13/92] Installing libsepol-devel-0:3.1 100% | 41.7 MiB/s | 128.2 KiB | 00m00s [14/92] Installing libselinux-devel-0:3 100% | 30.6 MiB/s | 156.6 KiB | 00m00s [15/92] Installing libcom_err-devel-0:1 100% | 794.5 KiB/s | 18.3 KiB | 00m00s [16/92] Installing keyutils-libs-devel- 100% | 27.0 MiB/s | 55.2 KiB | 00m00s [17/92] Installing publicsuffix-list-0: 100% | 338.8 MiB/s | 346.9 KiB | 00m00s [18/92] Installing libpsl-devel-0:0.23. 100% | 112.1 MiB/s | 114.8 KiB | 00m00s [19/92] Installing libnghttp3-devel-0:1 100% | 117.4 MiB/s | 120.2 KiB | 00m00s [20/92] Installing libnghttp2-devel-0:1 100% | 282.3 MiB/s | 289.1 KiB | 00m00s [21/92] Installing brotli-0:1.2.0-6.fc4 100% | 3.0 MiB/s | 70.1 KiB | 00m00s [22/92] Installing brotli-devel-0:1.2.0 100% | 9.5 MiB/s | 68.4 KiB | 00m00s [23/92] Installing groff-base-0:1.24.1- 100% | 101.2 MiB/s | 4.8 MiB | 00m00s [24/92] Installing ncurses-0:6.6-3.fc46 100% | 33.9 MiB/s | 901.8 KiB | 00m00s [25/92] Installing perl-Digest-0:1.20-5 100% | 36.1 MiB/s | 37.0 KiB | 00m00s [26/92] Installing perl-FileHandle-0:2. 100% | 0.0 B/s | 9.8 KiB | 00m00s [27/92] Installing perl-B-0:1.92-527.fc 100% | 182.6 MiB/s | 560.9 KiB | 00m00s [28/92] Installing perl-Digest-MD5-0:2. 100% | 103.0 MiB/s | 105.5 KiB | 00m00s [29/92] Installing perl-Data-Dumper-0:2 100% | 134.2 MiB/s | 137.4 KiB | 00m00s [30/92] Installing perl-libnet-0:3.15-5 100% | 143.4 MiB/s | 293.8 KiB | 00m00s [31/92] Installing perl-Unicode-Normali 100% | 257.2 MiB/s | 526.8 KiB | 00m00s [32/92] Installing perl-MIME-Base32-0:1 100% | 31.4 MiB/s | 32.2 KiB | 00m00s [33/92] Installing perl-URI-0:5.37-1.fc 100% | 70.6 MiB/s | 289.2 KiB | 00m00s [34/92] Installing perl-IO-Socket-IP-0: 100% | 99.9 MiB/s | 102.3 KiB | 00m00s [35/92] Installing perl-AutoLoader-0:5. 100% | 0.0 B/s | 21.0 KiB | 00m00s [36/92] Installing perl-IO-Socket-SSL-0 100% | 238.0 MiB/s | 731.0 KiB | 00m00s [37/92] Installing perl-Net-SSLeay-0:1. 100% | 206.0 MiB/s | 1.4 MiB | 00m00s [38/92] Installing perl-locale-0:1.13-5 100% | 0.0 B/s | 6.5 KiB | 00m00s [39/92] Installing perl-if-0:0.61.000-5 100% | 0.0 B/s | 6.2 KiB | 00m00s [40/92] Installing perl-Pod-Escapes-1:1 100% | 25.3 MiB/s | 25.9 KiB | 00m00s [41/92] Installing perl-File-Path-0:2.1 100% | 62.9 MiB/s | 64.4 KiB | 00m00s [42/92] Installing perl-Text-Tabs+Wrap- 100% | 23.3 MiB/s | 23.9 KiB | 00m00s [43/92] Installing perl-Time-Local-2:1. 100% | 68.9 MiB/s | 70.6 KiB | 00m00s [44/92] Installing perl-Time-HiRes-4:1. 100% | 150.1 MiB/s | 153.7 KiB | 00m00s [45/92] Installing perl-HTTP-Tiny-0:0.0 100% | 160.6 MiB/s | 164.5 KiB | 00m00s [46/92] Installing perl-Pod-Simple-1:3. 100% | 187.1 MiB/s | 574.8 KiB | 00m00s [47/92] Installing perl-IPC-Open3-0:1.2 100% | 0.0 B/s | 28.5 KiB | 00m00s [48/92] Installing perl-File-Temp-1:0.2 100% | 161.6 MiB/s | 165.5 KiB | 00m00s [49/92] Installing perl-Class-Struct-0: 100% | 0.0 B/s | 25.9 KiB | 00m00s [50/92] Installing perl-POSIX-0:2.26-52 100% | 256.5 MiB/s | 262.7 KiB | 00m00s [51/92] Installing perl-Term-Cap-0:1.18 100% | 29.8 MiB/s | 30.6 KiB | 00m00s [52/92] Installing perl-Term-ANSIColor- 100% | 96.8 MiB/s | 99.1 KiB | 00m00s [53/92] Installing perl-Pod-Perldoc-0:3 100% | 6.9 MiB/s | 169.4 KiB | 00m00s [54/92] Installing perl-podlators-1:6.1 100% | 12.9 MiB/s | 331.1 KiB | 00m00s [55/92] Installing perl-File-stat-0:1.1 100% | 13.9 MiB/s | 14.2 KiB | 00m00s [56/92] Installing perl-SelectSaver-0:1 100% | 0.0 B/s | 2.5 KiB | 00m00s [57/92] Installing perl-Symbol-0:1.09-5 100% | 0.0 B/s | 7.3 KiB | 00m00s [58/92] Installing perl-Socket-4:2.043- 100% | 144.4 MiB/s | 147.8 KiB | 00m00s [59/92] Installing perl-Pod-Usage-4:2.0 100% | 3.7 MiB/s | 87.8 KiB | 00m00s [60/92] Installing perl-overloading-0:0 100% | 5.4 MiB/s | 5.5 KiB | 00m00s [61/92] Installing perl-IO-0:1.56-527.f 100% | 95.5 MiB/s | 195.6 KiB | 00m00s [62/92] Installing perl-mro-0:1.30-527. 100% | 80.7 MiB/s | 82.6 KiB | 00m00s [63/92] Installing perl-base-0:2.27-527 100% | 0.0 B/s | 13.0 KiB | 00m00s [64/92] Installing perl-Fcntl-0:1.20-52 100% | 91.6 MiB/s | 93.8 KiB | 00m00s [65/92] Installing perl-Text-ParseWords 100% | 14.2 MiB/s | 14.6 KiB | 00m00s [66/92] Installing perl-Getopt-Long-1:2 100% | 143.8 MiB/s | 147.2 KiB | 00m00s [67/92] Installing perl-overload-0:1.40 100% | 0.0 B/s | 72.0 KiB | 00m00s [68/92] Installing perl-Storable-1:3.41 100% | 238.8 MiB/s | 244.5 KiB | 00m00s [69/92] Installing perl-Getopt-Std-0:1. 100% | 0.0 B/s | 13.0 KiB | 00m00s [70/92] Installing perl-vars-0:1.05-527 100% | 0.0 B/s | 4.3 KiB | 00m00s [71/92] Installing perl-File-Basename-0 100% | 0.0 B/s | 14.6 KiB | 00m00s [72/92] Installing perl-Errno-0:1.39-52 100% | 0.0 B/s | 8.8 KiB | 00m00s [73/92] Installing perl-parent-1:0.244- 100% | 0.0 B/s | 11.0 KiB | 00m00s [74/92] Installing perl-MIME-Base64-0:3 100% | 93.9 MiB/s | 96.1 KiB | 00m00s [75/92] Installing perl-constant-0:1.33 100% | 26.8 MiB/s | 27.4 KiB | 00m00s [76/92] Installing perl-Scalar-List-Uti 100% | 76.5 MiB/s | 156.6 KiB | 00m00s [77/92] Installing perl-Encode-4:3.24-5 100% | 134.5 MiB/s | 4.8 MiB | 00m00s [78/92] Installing perl-DynaLoader-0:1. 100% | 31.7 MiB/s | 32.5 KiB | 00m00s [79/92] Installing perl-PathTools-0:3.9 100% | 111.6 MiB/s | 228.6 KiB | 00m00s [80/92] Installing perl-Exporter-0:5.79 100% | 54.2 MiB/s | 55.5 KiB | 00m00s [81/92] Installing perl-Carp-0:1.54-527 100% | 23.3 MiB/s | 47.7 KiB | 00m00s [82/92] Installing perl-libs-4:5.44.0-5 100% | 225.3 MiB/s | 12.2 MiB | 00m00s [83/92] Installing perl-interpreter-4:5 100% | 7.2 MiB/s | 177.5 KiB | 00m00s [84/92] Installing libverto-devel-0:0.3 100% | 25.7 MiB/s | 26.4 KiB | 00m00s [85/92] Installing libkadm5-0:1.22.2-9. 100% | 130.8 MiB/s | 267.8 KiB | 00m00s [86/92] Installing krb5-devel-0:1.22.2- 100% | 26.0 MiB/s | 719.2 KiB | 00m00s [87/92] Installing libssh-devel-0:0.12. 100% | 67.3 MiB/s | 206.9 KiB | 00m00s [88/92] Installing libcurl-devel-0:8.23 100% | 34.5 MiB/s | 1.5 MiB | 00m00s [89/92] Installing perl-FindBin-0:1.54- 100% | 0.0 B/s | 7.2 KiB | 00m00s [90/92] Installing perl-lib-0:0.65-527. 100% | 0.0 B/s | 8.9 KiB | 00m00s [91/92] Installing xz-devel-1:5.8.4-1.f 100% | 128.2 MiB/s | 262.6 KiB | 00m00s [92/92] Installing bzip2-devel-0:1.0.8- 100% | 6.6 MiB/s | 310.7 KiB | 00m00s Warning: skipped OpenPGP checks for 15 packages from repository: copr_base Complete! Building target platforms: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1784246400 Wrote: /builddir/build/SRPMS/htslib-1.24-1.fc46.src.rpm Updating and loading repositories: fedora 100% | 61.3 KiB/s | 10.2 KiB | 00m00s Additional repo copr_tstellar_fedora_c 100% | 11.8 KiB/s | 1.5 KiB | 00m00s Additional repo copr_fedora_llvm_team_ 100% | 12.0 KiB/s | 1.5 KiB | 00m00s Copr repository 100% | 11.8 KiB/s | 1.5 KiB | 00m00s Repositories loaded. Package "bzip2-devel-1.0.8-24.fc46.aarch64" is already installed. Package "gcc-16.2.1-2.fc46.1.aarch64" is already installed. Package "libcurl-devel-8.23.0~rc2-1.fc46.aarch64" is already installed. Package "make-1:4.4.1-13.fc46.aarch64" is already installed. Package "openssl-devel-1:4.0.3-1.fc46.aarch64" is already installed. Package "perl-Data-Dumper-2.192-528.fc45.aarch64" 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.aarch64" is already installed. Package "perl-interpreter-4:5.44.0-527.fc45.aarch64" is already installed. Package "xz-devel-1:5.8.4-1.fc46.aarch64" is already installed. Package "zlib-ng-compat-devel-2.3.3-6.fc46.aarch64" is already installed. Nothing to do. Finish: build setup for htslib-1.24-1.fc46.src.rpm Start: rpmbuild htslib-1.24-1.fc46.src.rpm Building target platforms: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1784246400 Executing(mkbuilddir): /bin/sh -e /var/tmp/rpm-tmp.EijmiH 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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="aarch64" 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.tmfhwS + 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.fLdXG1 + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 $(dirname ./configure) -name config.guess -o -name config.sub) ++ basename ./config.sub + '[' -f /usr/lib/rpm/redhat/config.sub ']' + /usr/bin/rm -f ./config.sub ++ basename ./config.sub + /usr/bin/cp -fv /usr/lib/rpm/redhat/config.sub ./config.sub '/usr/lib/rpm/redhat/config.sub' -> './config.sub' + '[' 1 = 1 ']' + '[' x '!=' 'x-Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg' ']' ++ find . -name ltmain.sh ++ grep -q runstatedir=DIR ./configure ++ echo --runstatedir=/run + ./configure --build=aarch64-redhat-linux --host=aarch64-redhat-linux --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/bin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/libexec --localstatedir=/var --runstatedir=/run --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info 'CFLAGS=-O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer' 'LDFLAGS=-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 ' --prefix=/usr --libdir=/usr/lib64 --enable-plugins '--with-plugin-path=/usr/local/libexec/htslib:$(plugindir)' --enable-gcs --enable-libcurl --enable-s3 configure: WARNING: unrecognized options: --disable-dependency-tracking checking for aarch64-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 aarch64-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... no checking whether __cpuid_count is declared... no checking for x86intrin.h... no checking for aarch64-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 aarch64-redhat-linux... plain .so checking whether the linker supports versioned symbols... yes checking whether the compiler accepts -fvisibility=hidden... yes checking build system type... aarch64-redhat-linux-gnu checking host system type... aarch64-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... no checking whether the compiler accepts -mbranch-protection=standard... yes 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -mbranch-protection=standard -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -mbranch-protection=standard -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -mbranch-protection=standard -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -mbranch-protection=standard -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -mbranch-protection=standard -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -mbranch-protection=standard -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -mbranch-protection=standard -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -mbranch-protection=standard -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -mbranch-protection=standard -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -mbranch-protection=standard -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -mbranch-protection=standard -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -mbranch-protection=standard -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -mbranch-protection=standard -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -mbranch-protection=standard -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -mbranch-protection=standard -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -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 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,-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 -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_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 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 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/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 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_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_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_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_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_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_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-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-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-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-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-parse-reg test/test-parse-reg.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_introspection test/test_introspection.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_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.0VLt8b + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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.aarch64 --unique-debug-src-base htslib-1.24-1.fc46.aarch64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 --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.aarch64.debug: Unknown debugging section .debug_addr dwz: ./usr/bin/bgzip-1.24-1.fc46.aarch64.debug: Unknown debugging section .debug_addr dwz: ./usr/bin/htsfile-1.24-1.fc46.aarch64.debug: Unknown debugging section .debug_addr dwz: ./usr/bin/ref-cache-1.24-1.fc46.aarch64.debug: Unknown debugging section .debug_addr dwz: ./usr/bin/tabix-1.24-1.fc46.aarch64.debug: Unknown debugging section .debug_addr dwz: ./usr/lib64/libhts.so.1.24-1.24-1.fc46.aarch64.debug: Unknown debugging section .debug_addr dwz: ./usr/libexec/htslib/hfile_gcs.so-1.24-1.fc46.aarch64.debug: Unknown debugging section .debug_addr dwz: ./usr/libexec/htslib/hfile_libcurl.so-1.24-1.fc46.aarch64.debug: Unknown debugging section .debug_addr dwz: ./usr/libexec/htslib/hfile_s3.so-1.24-1.fc46.aarch64.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.aarch64 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 205 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 205 files, considered 203 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.rVn8Wy + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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/guhrcJezR2/index.bam.csi /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.sam > /tmp/guhrcJezR2/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -c /tmp/guhrcJezR2/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/guhrcJezR2/index.bam.bai /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.sam > /tmp/guhrcJezR2/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -b /tmp/guhrcJezR2/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/guhrcJezR2/index.sam.gz.csi /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.sam > /tmp/guhrcJezR2/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -c /tmp/guhrcJezR2/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/guhrcJezR2/index.sam.gz.bai /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.sam > /tmp/guhrcJezR2/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -b /tmp/guhrcJezR2/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/guhrcJezR2/index.sam.gz.csi /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index_dos.sam > /tmp/guhrcJezR2/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -c /tmp/guhrcJezR2/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/guhrcJezR2/index.sam.gz.bai /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index_dos.sam > /tmp/guhrcJezR2/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -b /tmp/guhrcJezR2/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view -l 0 -C -x /tmp/guhrcJezR2/index.cram.crai /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.sam > /tmp/guhrcJezR2/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index /tmp/guhrcJezR2/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view -p /tmp/guhrcJezR2/index3_rgn.sam /tmp/guhrcJezR2/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/guhrcJezR2/index3_rgnm.sam /tmp/guhrcJezR2/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/guhrcJezR2/index.bcf.csi /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.vcf > /tmp/guhrcJezR2/index.bcf .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -c /tmp/guhrcJezR2/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/guhrcJezR2/index.vcf.gz.csi /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.vcf > /tmp/guhrcJezR2/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -c /tmp/guhrcJezR2/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/guhrcJezR2/index.vcf.gz.tbi /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.vcf > /tmp/guhrcJezR2/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -t /tmp/guhrcJezR2/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/tabix /tmp/guhrcJezR2/index.vcf.gz##idx##/tmp/guhrcJezR2/index.vcf.gz.tbi 1:10000060-10000060 .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view /tmp/guhrcJezR2/index2.bam 1:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view /tmp/guhrcJezR2/index2.bam 1:2000000-2000000 .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view /tmp/guhrcJezR2/index2.bam 2:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view /tmp/guhrcJezR2/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/guhrcJezR2/index.bam.csi /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.sam > /tmp/guhrcJezR2/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -c /tmp/guhrcJezR2/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/guhrcJezR2/index.bam.bai /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.sam > /tmp/guhrcJezR2/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -b /tmp/guhrcJezR2/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/guhrcJezR2/index.sam.gz.csi /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.sam > /tmp/guhrcJezR2/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -c /tmp/guhrcJezR2/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/guhrcJezR2/index.sam.gz.bai /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.sam > /tmp/guhrcJezR2/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -b /tmp/guhrcJezR2/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/guhrcJezR2/index.sam.gz.csi /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index_dos.sam > /tmp/guhrcJezR2/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -c /tmp/guhrcJezR2/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/guhrcJezR2/index.sam.gz.bai /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index_dos.sam > /tmp/guhrcJezR2/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -b /tmp/guhrcJezR2/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/guhrcJezR2/index.cram.crai /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.sam > /tmp/guhrcJezR2/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index /tmp/guhrcJezR2/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view -@4 -p /tmp/guhrcJezR2/index3_rgn.sam /tmp/guhrcJezR2/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/guhrcJezR2/index3_rgnm.sam /tmp/guhrcJezR2/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/guhrcJezR2/index.bcf.csi /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.vcf > /tmp/guhrcJezR2/index.bcf .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -c /tmp/guhrcJezR2/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/guhrcJezR2/index.vcf.gz.csi /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.vcf > /tmp/guhrcJezR2/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -c /tmp/guhrcJezR2/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/guhrcJezR2/index.vcf.gz.tbi /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.vcf > /tmp/guhrcJezR2/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -t /tmp/guhrcJezR2/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/tabix /tmp/guhrcJezR2/index.vcf.gz##idx##/tmp/guhrcJezR2/index.vcf.gz.tbi 1:10000060-10000060 .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view /tmp/guhrcJezR2/index2.bam 1:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view /tmp/guhrcJezR2/index2.bam 1:2000000-2000000 .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view /tmp/guhrcJezR2/index2.bam 2:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view /tmp/guhrcJezR2/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/guhrcJezR2/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/guhrcJezR2/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/guhrcJezR2 -s 74452500 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr.pl -t /tmp/guhrcJezR2 -s 34270147 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr.pl -t /tmp/guhrcJezR2 -s 11108528 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr.pl -t /tmp/guhrcJezR2 -s 42233895 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr.pl -t /tmp/guhrcJezR2 -s 8111117 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr.pl -t /tmp/guhrcJezR2 -s 85644070 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr.pl -t /tmp/guhrcJezR2 -s 49879942 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr.pl -t /tmp/guhrcJezR2 -s 47881429 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr.pl -t /tmp/guhrcJezR2 -s 69081244 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr.pl -t /tmp/guhrcJezR2 -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/guhrcJezR2/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/guhrcJezR2/no_index_2.out 2> /tmp/guhrcJezR2/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/guhrcJezR2/no_index_3.out 2> /tmp/guhrcJezR2/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/guhrcJezR2/no_index_4.out 2> /tmp/guhrcJezR2/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/guhrcJezR2/weird-chr-names.vcf.bcf -x /tmp/guhrcJezR2/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/guhrcJezR2/range_test_1.out.vcf -r '1' --args /tmp/guhrcJezR2/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/guhrcJezR2/range_test_2.out.vcf -r '1:1-2' --args /tmp/guhrcJezR2/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/guhrcJezR2/range_test_3.out.vcf -r '1:1,1:2' --args /tmp/guhrcJezR2/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/guhrcJezR2/range_test_4.out.vcf -r '1:1-1' --args /tmp/guhrcJezR2/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/guhrcJezR2/range_test_5.out.vcf -r '{1:1}' --args /tmp/guhrcJezR2/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/guhrcJezR2/range_test_6.out.vcf -r '{1:1}:1-2' --args /tmp/guhrcJezR2/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/guhrcJezR2/range_test_7.out.vcf -r '{1:1}:1,{1:1}:2' --args /tmp/guhrcJezR2/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/guhrcJezR2/range_test_8.out.vcf -r '{1:1}:1-1' --args /tmp/guhrcJezR2/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/guhrcJezR2/range_test_9.out.vcf -r '{1:1-1}' --args /tmp/guhrcJezR2/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/guhrcJezR2/range_test_10.out.vcf -r '{1:1-1}:1-2' --args /tmp/guhrcJezR2/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/guhrcJezR2/range_test_11.out.vcf -r '{1:1-1}:1,{1:1-1}:2' --args /tmp/guhrcJezR2/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/guhrcJezR2/range_test_12.out.vcf -r '{1:1-1}:1-1' --args /tmp/guhrcJezR2/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/guhrcJezR2/range_test_13.out.vcf -r '{1:1-1}-2' --args /tmp/guhrcJezR2/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/guhrcJezR2/range_test_14.out.vcf -t '1' --args /tmp/guhrcJezR2/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/guhrcJezR2/range_test_15.out.vcf -t '1:1-2' --args /tmp/guhrcJezR2/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/guhrcJezR2/range_test_16.out.vcf -t '1:1,1:2' --args /tmp/guhrcJezR2/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/guhrcJezR2/range_test_17.out.vcf -t '1:1-1' --args /tmp/guhrcJezR2/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/guhrcJezR2/range_test_18.out.vcf -t '{1:1}' --args /tmp/guhrcJezR2/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/guhrcJezR2/range_test_19.out.vcf -t '{1:1}:1-2' --args /tmp/guhrcJezR2/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/guhrcJezR2/range_test_20.out.vcf -t '{1:1}:1,{1:1}:2' --args /tmp/guhrcJezR2/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/guhrcJezR2/range_test_21.out.vcf -t '{1:1}:1-1' --args /tmp/guhrcJezR2/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/guhrcJezR2/range_test_22.out.vcf -t '{1:1-1}' --args /tmp/guhrcJezR2/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/guhrcJezR2/range_test_23.out.vcf -t '{1:1-1}:1-2' --args /tmp/guhrcJezR2/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/guhrcJezR2/range_test_24.out.vcf -t '{1:1-1}:1,{1:1-1}:2' --args /tmp/guhrcJezR2/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/guhrcJezR2/range_test_25.out.vcf -t '{1:1-1}:1-1' --args /tmp/guhrcJezR2/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/guhrcJezR2/range_test_26.out.vcf -t '{1:1-1}-2' --args /tmp/guhrcJezR2/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/guhrcJezR2/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/guhrcJezR2/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/guhrcJezR2/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.aarch64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.ju2kEA + 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.gpaWfM + 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(aarch-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: ld-linux-aarch64.so.1()(64bit) ld-linux-aarch64.so.1(GLIBC_2.17)(64bit) libbz2.so.1()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.17)(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_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_2.17)(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.aarch64 Provides: htslib-devel = 1.24-1.fc46 htslib-devel(aarch-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.aarch64 Provides: htslib-tools = 1.24-1.fc46 htslib-tools(aarch-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: ld-linux-aarch64.so.1()(64bit) ld-linux-aarch64.so.1(GLIBC_2.17)(64bit) libbz2.so.1()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.17)(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_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_2.17)(64bit) libm.so.6(GLIBC_2.29)(64bit) libz.so.1()(64bit) rtld(GNU_HASH) Processing files: htslib-debugsource-1.24-1.fc46.aarch64 Provides: htslib-debugsource = 1.24-1.fc46 htslib-debugsource(aarch-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.aarch64 Provides: debuginfo(build-id) = 3af9d0473d430e85ee3a1e0bd261bb0679de74a8 debuginfo(build-id) = 409e81e6311ef209bc77b85088d307043981699e debuginfo(build-id) = 99a64a82b9bec118c4009d2887e8d3b381efa81f debuginfo(build-id) = f1be8437cc7049f21eef55f674462d12f8c4d575 htslib-debuginfo = 1.24-1.fc46 htslib-debuginfo(aarch-64) = 1.24-1.fc46 libhts.so.1.24-1.24-1.fc46.aarch64.debug()(64bit) Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: htslib-debugsource(aarch-64) = 1.24-1.fc46 Processing files: htslib-tools-debuginfo-1.24-1.fc46.aarch64 Provides: debuginfo(build-id) = 031d049b6eee1558196660dad81d961216ed90a9 debuginfo(build-id) = 2335db63a0e971c69abdb23fdbed76dd909599e1 debuginfo(build-id) = 2fe34a9280d9500ce1a176950c97006981bc75ed debuginfo(build-id) = ad150d055e55b6d0c126c55eb1b78dc5fa38aff9 debuginfo(build-id) = b3b5e3c0ce65ef60f2980b97aa0565480513df5d htslib-tools-debuginfo = 1.24-1.fc46 htslib-tools-debuginfo(aarch-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(aarch-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.aarch64.rpm Wrote: /builddir/build/RPMS/htslib-tools-1.24-1.fc46.aarch64.rpm Wrote: /builddir/build/RPMS/htslib-1.24-1.fc46.aarch64.rpm Wrote: /builddir/build/RPMS/htslib-devel-1.24-1.fc46.aarch64.rpm Wrote: /builddir/build/RPMS/htslib-debugsource-1.24-1.fc46.aarch64.rpm Wrote: /builddir/build/RPMS/htslib-tools-debuginfo-1.24-1.fc46.aarch64.rpm Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.r034Pe + 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-aarch64-1790841033.072590/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 4 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": "aarch64" }, { "name": "htslib-debuginfo", "epoch": null, "version": "1.24", "release": "1.fc46", "arch": "aarch64" }, { "name": "htslib-tools-debuginfo", "epoch": null, "version": "1.24", "release": "1.fc46", "arch": "aarch64" }, { "name": "htslib", "epoch": null, "version": "1.24", "release": "1.fc46", "arch": "src" }, { "name": "htslib", "epoch": null, "version": "1.24", "release": "1.fc46", "arch": "aarch64" }, { "name": "htslib-debugsource", "epoch": null, "version": "1.24", "release": "1.fc46", "arch": "aarch64" }, { "name": "htslib-devel", "epoch": null, "version": "1.24", "release": "1.fc46", "arch": "aarch64" } ] } RPMResults finished