Warning: Permanently added '2620:52:6:1161:dead:beef:cafe:c102' (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/10928561-fedora-rawhide-ppc64le --chroot fedora-rawhide-ppc64le Version: 1.9 PID: 3153 Logging PID: 3155 Task: {'allow_user_ssh': False, 'appstream': False, 'background': True, 'build_id': 10928561, 'buildroot_pkgs': ['fedora-clang-default-cc'], 'chroot': 'fedora-rawhide-ppc64le', '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-ppc64le/', '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-ppc64le/', '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-20260827/fedora-rawhide-ppc64le/', 'id': 'copr_fedora_llvm_team_llvm_snapshots_big_merge_20260827', 'module_hotfixes': True, 'name': 'Additional repo copr_fedora_llvm_team_llvm_snapshots_big_merge_20260827', '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': '10928561-fedora-rawhide-ppc64le', '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-730uyvce/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-730uyvce/htslib', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-730uyvce/htslib'... Running: git checkout 49f27db1f1a2a0ebbc1c4e903458121869bcfc42 -- cmd: ['git', 'checkout', '49f27db1f1a2a0ebbc1c4e903458121869bcfc42', '--'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-730uyvce/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 tail: /var/lib/copr-rpmbuild/main.log: file truncated cmd: ['dist-git-client', 'sources'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-730uyvce/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 10.36M 0 0 INFO: Reading stdout from command: md5sum htslib-1.24.tar.bz2 Running (timeout=90000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-730uyvce/htslib/htslib.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-730uyvce/htslib --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1788249070.975671 -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-730uyvce/htslib/htslib.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-730uyvce/htslib --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1788249070.975671 -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-730uyvce/htslib/htslib.spec) Config(fedora-rawhide-ppc64le) 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-ppc64le-bootstrap-1788249070.975671/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-ca136ccc-2e5f-4e9d-92d0-9ffdb5d6dccb INFO: Checking that 3fe53bf8ca59a4094215339357ece5803d87f9c5feaa623385033dadd5046c14 image matches host's architecture INFO: Copy content of container 3fe53bf8ca59a4094215339357ece5803d87f9c5feaa623385033dadd5046c14 to /var/lib/mock/fedora-rawhide-ppc64le-bootstrap-1788249070.975671/root INFO: mounting 3fe53bf8ca59a4094215339357ece5803d87f9c5feaa623385033dadd5046c14 with podman image mount INFO: image 3fe53bf8ca59a4094215339357ece5803d87f9c5feaa623385033dadd5046c14 as /var/lib/containers/storage/overlay/fc8d17b1b802f473774fc4159a035c59f6501542f841e390d4076b6a33ebe9a6/merged INFO: umounting image 3fe53bf8ca59a4094215339357ece5803d87f9c5feaa623385033dadd5046c14 (/var/lib/containers/storage/overlay/fc8d17b1b802f473774fc4159a035c59f6501542f841e390d4076b6a33ebe9a6/merged) with podman image umount INFO: Removing image mock-bootstrap-ca136ccc-2e5f-4e9d-92d0-9ffdb5d6dccb 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-ppc64le-1788249070.975671/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.ppc64le rpm-sequoia-1.10.2-5.fc45.ppc64le dnf5-5.4.3.0-2.fc46.ppc64le dnf5-plugins-5.4.3.0-2.fc46.ppc64le Start: installing minimal buildroot with dnf5 Updating and loading repositories: Additional repo copr_tstellar_fedora_c 100% | 110.0 B/s | 2.5 KiB | 00m23s Copr repository 100% | 131.1 KiB/s | 3.0 MiB | 00m23s Additional repo copr_fedora_llvm_team_ 100% | 1.1 KiB/s | 26.8 KiB | 00m24s fedora 100% | 78.6 KiB/s | 20.5 MiB | 04m27s >>> Downloading successful, but checksum doesn't match. Calculated: e7724453cb7cfb1400f8c4ec06af94c70c38acc7cb79484bc214ef90eab77dbdbc702ed6f80eb07693adb445498f39a011ce89176ce2b21705d13e8146debf75(sha512) e7724453cb7cfb1400f8c4ec06af94c70c38acc7cb79484bc214ef90eab77dbdbc702ed6f80eb07693adb445498f39a011ce89176ce2b21705d13e8146debf75(sha512) e7724453cb7cfb1400f8c4ec06af94c70c38acc7cb79484bc214ef90eab77dbdbc702ed6f80eb07693adb445498f39a011ce89176ce2b21705d13e8146debf75(sha512) Expected: 487018e38b0f3bfeb1b61a5f612fab4f805b0f12855cd9eb94c4e7e6afd4eed80035ddb514a17ac1c6e6b3a3c21a2c208a6707e3c148f4703a0bb8d295407763(sha512) e8ae023a2688be242c5ad65054b8b87db62c0563df824f0f97584b66fea35c85c670f26478651fd6732557e5d7ad91d7fd5636cc2aabdc7c683c8f894b3911f4(sha512) 47d4c0101494ea4972a9508dd7d03e4329e0ee24bd94b214a4f0eeb4af0bf01a1bce7e45b231e07f30af1fc4f11baa59c80c0727d769201227deb3ad4dfb5825(sha512) - https://dl.fedoraproject.org/pub/fedora-secondary/development/rawhide/Everything/ppc64le/os/repodata/repomd.xml >>> Downloading successful, but checksum doesn't match. Calculated: e7724453cb7cfb1400f8c4ec06af94c70c38acc7cb79484bc214ef90eab77dbdbc702ed6f80eb07693adb445498f39a011ce89176ce2b21705d13e8146debf75(sha512) e7724453cb7cfb1400f8c4ec06af94c70c38acc7cb79484bc214ef90eab77dbdbc702ed6f80eb07693adb445498f39a011ce89176ce2b21705d13e8146debf75(sha512) e7724453cb7cfb1400f8c4ec06af94c70c38acc7cb79484bc214ef90eab77dbdbc702ed6f80eb07693adb445498f39a011ce89176ce2b21705d13e8146debf75(sha512) Expected: 487018e38b0f3bfeb1b61a5f612fab4f805b0f12855cd9eb94c4e7e6afd4eed80035ddb514a17ac1c6e6b3a3c21a2c208a6707e3c148f4703a0bb8d295407763(sha512) e8ae023a2688be242c5ad65054b8b87db62c0563df824f0f97584b66fea35c85c670f26478651fd6732557e5d7ad91d7fd5636cc2aabdc7c683c8f894b3911f4(sha512) 47d4c0101494ea4972a9508dd7d03e4329e0ee24bd94b214a4f0eeb4af0bf01a1bce7e45b231e07f30af1fc4f11baa59c80c0727d769201227deb3ad4dfb5825(sha512) - https://dl.fedoraproject.org/pub/fedora-secondary/development/rawhide/Everything/ppc64le/os/repodata/repomd.xml >>> Status code: 404 for https://dl.fedoraproject.org/pub/fedora-secondary/development/rawhide/Everything/ppc64le/os/repodata/2e287673617d0c32abec5ed0cd3a696fcda0392de0dc32088405eb94a95e55ae-primary.xml.zck (IP: 10.16.163.51) - https://dl.fedoraproject.org/pub/fedora-secondary/development/rawhide/Everything/ppc64le/os/repodata/2e287673617d0c32abec5ed0cd3a696fcda0392de0dc32088405eb94a95e55ae-primary.xml.zck >>> Status code: 404 for https://dl.fedoraproject.org/pub/fedora-secondary/development/rawhide/Everything/ppc64le/os/repodata/2e287673617d0c32abec5ed0cd3a696fcda0392de0dc32088405eb94a95e55ae-primary.xml.zck (IP: 10.16.163.51) - https://dl.fedoraproject.org/pub/fedora-secondary/development/rawhide/Everything/ppc64le/os/repodata/2e287673617d0c32abec5ed0cd3a696fcda0392de0dc32088405eb94a95e55ae-primary.xml.zck >>> Curl error (28): Timeout was reached for https://muug.ca/mirror/fedora-secondary/development/rawhide/Everything/ppc64le/os/repodata/2e287673617d0c32abec5ed0cd3a696fcda0392de0dc32088405eb94a95e55ae-primary.xml.zck [Connection timed out after 30000 milliseconds] - https://muug.ca/mirror/fedora-secondary/development/rawhide/Everything/ppc64le/os/repodata/2e287673617d0c32abec5ed0cd3a696fcda0392de0dc32088405eb94a95e55ae-primary.xml.zck Repositories loaded. Package Arch Version Repository Size Installing group/module packages: bash ppc64le 0:5.3.15-2.fc46 copr_base 8.8 MiB bzip2 ppc64le 0:1.0.8-24.fc45 fedora 170.8 KiB coreutils ppc64le 0:9.11-6.fc45 fedora 9.6 MiB cpio ppc64le 0:2.15-10.fc45 copr_base 1.2 MiB diffutils ppc64le 0:3.12-6.fc45 fedora 1.7 MiB fedora-release-common noarch 0:46-0.1 fedora 4.6 KiB findutils ppc64le 1:4.11.0-2.fc45 fedora 2.1 MiB gawk ppc64le 0:5.4.1-1.fc45 fedora 3.2 MiB glibc-minimal-langpack ppc64le 0:2.44.9000-1.fc46 fedora 0.0 B grep ppc64le 0:3.12-4.fc45 fedora 1.0 MiB gzip ppc64le 0:1.14-4.fc45 copr_base 437.5 KiB info ppc64le 0:7.3-3.fc45 fedora 488.1 KiB patch ppc64le 0:2.8-5.fc45 fedora 262.3 KiB redhat-rpm-config noarch 0:344-5.fc45 fedora 184.2 KiB rpm-build ppc64le 0:6.1.0-1.fc46 fedora 679.8 KiB sed ppc64le 0:4.10-2.fc45 fedora 942.3 KiB shadow-utils ppc64le 2:4.20.0-1.fc45 fedora 4.8 MiB tar ppc64le 2:1.35-9.fc45 fedora 3.1 MiB unzip ppc64le 0:6.0-71.fc45 fedora 533.4 KiB util-linux ppc64le 0:2.42.2-3.fc45 fedora 7.0 MiB which ppc64le 0:2.25-2.fc46 copr_base 122.9 KiB xz ppc64le 1:5.8.3-2.fc46 copr_base 1.5 MiB Installing dependencies: R-srpm-macros noarch 0:1.3.7-3.fc45 fedora 3.5 KiB add-determinism ppc64le 0:0.7.3-3.fc45 fedora 2.3 MiB alternatives ppc64le 0:1.33-6.fc45 fedora 89.9 KiB ansible-srpm-macros noarch 0:1-22.fc45 fedora 35.7 KiB audit-libs ppc64le 0:4.2.1-2.fc45 fedora 550.2 KiB binutils ppc64le 0:2.47-1.fc45 fedora 33.7 MiB build-reproducibility-srpm-macros noarch 0:0.7.3-3.fc45 fedora 1.2 KiB bzip2-libs ppc64le 0:1.0.8-24.fc45 fedora 136.4 KiB ca-certificates noarch 0:2025.2.80_v9.0.304-9.fc45 fedora 2.6 MiB cmake-srpm-macros noarch 0:4.3.0-5.fc45 fedora 524.0 B coreutils-common ppc64le 0:9.11-6.fc45 fedora 10.9 MiB crypto-policies noarch 0:20260713-2.gitc42da77.fc45 fedora 134.3 KiB curl ppc64le 0:8.22.0~rc3-1.fc46 fedora 526.7 KiB cyrus-sasl-lib ppc64le 0:2.1.28-37.fc45 fedora 2.9 MiB debugedit ppc64le 0:5.3-3.fc45 fedora 384.4 KiB dwz ppc64le 0:0.17-3.fc45 fedora 386.6 KiB ed ppc64le 0:1.22.6-1.fc46 fedora 222.8 KiB efi-srpm-macros noarch 0:6-9.fc45 fedora 40.3 KiB elfutils ppc64le 0:0.196-1.fc46 fedora 3.4 MiB elfutils-debuginfod-client ppc64le 0:0.196-1.fc46 fedora 143.4 KiB elfutils-libelf ppc64le 0:0.196-1.fc46 fedora 1.5 MiB elfutils-libs ppc64le 0:0.196-1.fc46 fedora 874.5 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 ppc64le 0:5.47-3.fc45 fedora 141.0 KiB file-libs ppc64le 0:5.47-3.fc45 fedora 12.3 MiB filesystem ppc64le 0:3.18-59.fc45 fedora 112.0 B filesystem-srpm-macros noarch 0:3.18-59.fc45 fedora 38.2 KiB fips-provider ppc64le 0:1.5.2-3.fc45 fedora 4.7 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 ppc64le 0:17.2-4.fc45 fedora 16.3 MiB gdbm-libs ppc64le 1:1.23-12.fc45 copr_base 233.4 KiB ghc-srpm-macros noarch 0:1.10-2.fc45 fedora 792.0 B glibc ppc64le 0:2.44.9000-1.fc46 fedora 12.1 MiB glibc-common ppc64le 0:2.44.9000-1.fc46 fedora 1.5 MiB glibc-gconv-extra ppc64le 0:2.44.9000-1.fc46 fedora 18.5 MiB gmp ppc64le 1:6.3.0-6.fc45 fedora 786.1 KiB gnat-srpm-macros noarch 0:7-3.fc45 fedora 1.0 KiB gnome-srpm-macros noarch 0:1.0-2.fc45 fedora 3.5 KiB gnulib-l10n noarch 0:20241231-4.fc45 copr_base 655.0 KiB gnupg2 ppc64le 0:2.4.9-18.fc45 fedora 6.8 MiB gnupg2-dirmngr ppc64le 0:2.4.9-18.fc45 fedora 837.9 KiB gnupg2-gpg-agent ppc64le 0:2.4.9-18.fc45 fedora 974.1 KiB gnupg2-gpgconf ppc64le 0:2.4.9-18.fc45 fedora 321.5 KiB gnupg2-keyboxd ppc64le 0:2.4.9-18.fc45 fedora 233.1 KiB gnupg2-verify ppc64le 0:2.4.9-18.fc45 fedora 428.1 KiB gnutls ppc64le 0:3.8.13-3.fc45 fedora 4.1 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 ppc64le 0:1.6.2-12.fc45 copr_base 92.2 KiB jansson ppc64le 0:2.14-5.fc45 fedora 156.9 KiB java-srpm-macros noarch 0:1-9.fc45 fedora 870.0 B json-c ppc64le 0:0.18-9.fc45 copr_base 138.3 KiB kernel-srpm-macros noarch 0:1.0-30.fc45 fedora 1.9 KiB keyutils-libs ppc64le 0:1.6.3-8.fc45 copr_base 97.7 KiB krb5-libs ppc64le 0:1.22.2-9.fc45 fedora 3.0 MiB libacl ppc64le 0:2.4.0-2.fc45 fedora 67.6 KiB libarchive ppc64le 0:3.8.9-1.fc46 fedora 1.3 MiB libassuan ppc64le 0:2.5.7-6.fc45 copr_base 216.0 KiB libattr ppc64le 0:2.6.0-2.fc45 copr_base 67.8 KiB libblkid ppc64le 0:2.42.2-3.fc45 fedora 354.3 KiB libbrotli ppc64le 0:1.2.0-6.fc45 fedora 1.0 MiB libcap ppc64le 0:2.78-2.fc45 fedora 506.7 KiB libcap-ng ppc64le 0:0.9.5-1.fc46 fedora 160.2 KiB libcbor ppc64le 0:0.14.0-3.fc45 fedora 139.5 KiB libcom_err ppc64le 0:1.47.4-2.fc45 fedora 110.9 KiB libcurl ppc64le 0:8.22.0~rc3-1.fc46 fedora 1.3 MiB libeconf ppc64le 0:0.7.9-4.fc45 copr_base 80.9 KiB libevent ppc64le 0:2.1.12-19.fc45 copr_base 1.3 MiB libfdisk ppc64le 0:2.42.2-3.fc45 fedora 482.8 KiB libffi ppc64le 0:3.5.2-3.fc45 fedora 347.5 KiB libfido2 ppc64le 0:1.17.0-5.fc45 copr_base 345.1 KiB libfsverity ppc64le 0:1.7-4.fc45 fedora 68.0 KiB libgcc ppc64le 0:16.2.1-2.fc46 fedora 286.4 KiB libgcrypt ppc64le 0:1.12.3-1.fc46 fedora 1.6 MiB libgomp ppc64le 0:16.2.1-2.fc46 fedora 657.0 KiB libgpg-error ppc64le 0:1.61-2.fc45 copr_base 1.0 MiB libidn2 ppc64le 0:2.3.8-4.fc45 fedora 560.1 KiB libksba ppc64le 0:1.8.1-1.fc46 fedora 535.8 KiB liblastlog2 ppc64le 0:2.42.2-3.fc45 fedora 137.2 KiB libmount ppc64le 0:2.42.2-3.fc45 fedora 548.3 KiB libnghttp2 ppc64le 0:1.69.0-5.fc45 fedora 197.8 KiB libnghttp3 ppc64le 0:1.18.0-1.fc46 copr_base 207.7 KiB libpkgconf ppc64le 0:2.5.1-2.fc45 copr_base 133.7 KiB libpsl ppc64le 0:0.23.1-1.fc45 fedora 132.1 KiB librtas ppc64le 0:2.0.7-2.fc45 fedora 320.4 KiB libselinux ppc64le 0:3.11-4.fc45 fedora 329.1 KiB libselinux-utils ppc64le 0:3.11-4.fc45 fedora 1.3 MiB libsemanage ppc64le 0:3.11-3.fc45 fedora 423.9 KiB libsepol ppc64le 0:3.11-2.fc45 fedora 1.0 MiB libsmartcols ppc64le 0:2.42.2-3.fc45 fedora 289.4 KiB libssh ppc64le 0:0.12.2-1.fc45 fedora 913.5 KiB libssh-config noarch 0:0.12.2-1.fc45 fedora 277.0 B libstdc++ ppc64le 0:16.2.1-2.fc46 fedora 4.1 MiB libtasn1 ppc64le 0:4.21.0-2.fc45 copr_base 220.4 KiB libtool-ltdl ppc64le 0:2.5.4-11.fc45 fedora 93.8 KiB libunistring ppc64le 0:1.1-12.fc45 fedora 1.9 MiB libusb1 ppc64le 0:1.0.30-2.fc45 fedora 243.5 KiB libuuid ppc64le 0:2.42.2-3.fc45 fedora 69.2 KiB libverto ppc64le 0:0.3.2-13.fc45 fedora 69.0 KiB libxcrypt ppc64le 0:4.5.2-4.fc45 fedora 336.9 KiB libxml2 ppc64le 0:2.13.9-4.fc45 copr_base 2.3 MiB libzstd ppc64le 0:1.5.7-6.fc45 copr_base 1.0 MiB linkdupes ppc64le 0:0.7.3-3.fc45 fedora 838.4 KiB lua-libs ppc64le 0:5.5.1-2.fc46 fedora 393.9 KiB lua-srpm-macros noarch 0:1-18.fc45 fedora 1.3 KiB lz4-libs ppc64le 0:1.10.0-5.fc45 copr_base 260.8 KiB mpfr ppc64le 0:4.2.2-4.fc45 fedora 913.4 KiB ncurses-base noarch 0:6.6-3.fc45 fedora 329.7 KiB ncurses-libs ppc64le 0:6.6-3.fc45 fedora 1.5 MiB nettle ppc64le 0:4.0-5.fc45 fedora 965.1 KiB ngtcp2 ppc64le 0:1.22.1-3.fc45 fedora 405.1 KiB ngtcp2-crypto-ossl ppc64le 0:1.22.1-3.fc45 fedora 67.1 KiB npth ppc64le 0:1.8-5.fc45 fedora 93.0 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 ppc64le 0:2.6.14-1.fc46 fedora 892.8 KiB openssl-libs ppc64le 1:4.0.2-1.fc46 fedora 7.1 MiB p11-kit ppc64le 0:0.26.5-1.fc45 fedora 3.3 MiB p11-kit-trust ppc64le 0:0.26.5-1.fc45 fedora 594.0 KiB package-notes-srpm-macros noarch 0:0.20-2.fc45 fedora 1.6 KiB pam-libs ppc64le 0:1.7.2-4.fc45 copr_base 285.9 KiB pcre2 ppc64le 0:10.47-1.fc45.2 copr_base 905.1 KiB pcre2-syntax noarch 0:10.47-1.fc45.2 copr_base 281.9 KiB perl-srpm-macros noarch 0:1-65.fc45 fedora 861.0 B pkgconf ppc64le 0:2.5.1-2.fc45 copr_base 114.7 KiB pkgconf-m4 noarch 0:2.5.1-2.fc45 copr_base 14.3 KiB pkgconf-pkg-config ppc64le 0:2.5.1-2.fc45 copr_base 990.0 B policycoreutils ppc64le 0:3.11-2.fc45 fedora 1.5 MiB popt ppc64le 0:1.19-11.fc45 copr_base 144.4 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 ppc64le 0:8.3-6.fc45 fedora 627.4 KiB redhat-systemd-presets noarch 0:102-3.fc45 fedora 1.0 KiB redhat-systemd-presets-common noarch 0:102-3.fc45 fedora 16.9 KiB rpm ppc64le 0:6.1.0-1.fc46 fedora 4.2 MiB rpm-build-libs ppc64le 0:6.1.0-1.fc46 fedora 327.8 KiB rpm-libs ppc64le 0:6.1.0-1.fc46 fedora 1.4 MiB rpm-plugin-selinux ppc64le 0:6.1.0-1.fc46 fedora 67.8 KiB rpm-sequoia ppc64le 0:1.10.2-5.fc45 fedora 4.8 MiB rpm-sign-libs ppc64le 0:6.1.0-1.fc46 fedora 67.5 KiB rust-srpm-macros noarch 0:28.5-2.fc45 fedora 5.5 KiB selinux-policy noarch 0:45.15-1.fc46 fedora 32.1 KiB selinux-policy-targeted noarch 0:45.15-1.fc46 fedora 19.0 MiB setup noarch 0:2.15.1-2.fc45 fedora 725.6 KiB sqlite-libs ppc64le 0:3.53.4-1.fc45 fedora 2.0 MiB systemd-libs ppc64le 0:261.2-1.fc45 fedora 3.3 MiB systemd-standalone-sysusers ppc64le 0:261.2-1.fc45 fedora 1.1 MiB tpm2-tss ppc64le 0:4.2.0-1.fc45 copr_base 2.4 MiB tree-sitter-srpm-macros noarch 0:0.4.6-2.fc45 fedora 8.6 KiB util-linux-core ppc64le 0:2.42.2-3.fc45 fedora 2.6 MiB xxhash-libs ppc64le 0:0.8.3-5.fc45 fedora 85.5 KiB xz-libs ppc64le 1:5.8.3-2.fc46 copr_base 265.5 KiB zig-srpm-macros noarch 0:1-9.fc45 fedora 1.3 KiB zip ppc64le 0:3.0-46.fc45 fedora 889.2 KiB zlib-ng-compat ppc64le 0:2.3.3-6.fc45 fedora 197.3 KiB zstd ppc64le 0:1.5.7-6.fc45 copr_base 559.5 KiB Installing groups: Buildsystem building group Transaction Summary: Installing: 189 packages Total size of inbound packages is 76 MiB. Need to download 76 MiB. After this operation, 287 MiB extra will be used (install 287 MiB, remove 0 B). [ 1/189] fedora-release-common-0:46-0. 100% | 4.4 MiB/s | 18.2 KiB | 00m00s [ 2/189] glibc-minimal-langpack-0:2.44 100% | 20.8 MiB/s | 127.5 KiB | 00m00s [ 3/189] redhat-rpm-config-0:344-5.fc4 100% | 15.2 MiB/s | 77.7 KiB | 00m00s [ 4/189] rpm-build-0:6.1.0-1.fc46.ppc6 100% | 44.2 MiB/s | 180.9 KiB | 00m00s [ 5/189] unzip-0:6.0-71.fc45.ppc64le 100% | 28.3 MiB/s | 202.6 KiB | 00m00s [ 6/189] coreutils-0:9.11-6.fc45.ppc64 100% | 36.1 MiB/s | 1.3 MiB | 00m00s [ 7/189] tar-2:1.35-9.fc45.ppc64le 100% | 34.6 MiB/s | 886.6 KiB | 00m00s [ 8/189] bzip2-0:1.0.8-24.fc45.ppc64le 100% | 8.7 MiB/s | 53.3 KiB | 00m00s [ 9/189] diffutils-0:3.12-6.fc45.ppc64 100% | 66.1 MiB/s | 406.0 KiB | 00m00s [ 10/189] findutils-1:4.11.0-2.fc45.ppc 100% | 73.7 MiB/s | 603.7 KiB | 00m00s [ 11/189] gawk-0:5.4.1-1.fc45.ppc64le 100% | 86.1 MiB/s | 1.2 MiB | 00m00s [ 12/189] grep-0:3.12-4.fc45.ppc64le 100% | 60.3 MiB/s | 308.5 KiB | 00m00s [ 13/189] cpio-0:2.15-10.fc45.ppc64le 100% | 1.5 MiB/s | 302.1 KiB | 00m00s [ 14/189] info-0:7.3-3.fc45.ppc64le 100% | 28.9 MiB/s | 207.3 KiB | 00m00s [ 15/189] patch-0:2.8-5.fc45.ppc64le 100% | 24.0 MiB/s | 123.0 KiB | 00m00s [ 16/189] gzip-0:1.14-4.fc45.ppc64le 100% | 1.0 MiB/s | 176.6 KiB | 00m00s [ 17/189] sed-0:4.10-2.fc45.ppc64le 100% | 63.9 MiB/s | 327.4 KiB | 00m00s [ 18/189] shadow-utils-2:4.20.0-1.fc45. 100% | 71.5 MiB/s | 1.4 MiB | 00m00s [ 19/189] util-linux-0:2.42.2-3.fc45.pp 100% | 55.1 MiB/s | 1.3 MiB | 00m00s [ 20/189] bash-0:5.3.15-2.fc46.ppc64le 100% | 5.4 MiB/s | 1.9 MiB | 00m00s [ 21/189] which-0:2.25-2.fc46.ppc64le 100% | 363.6 KiB/s | 41.5 KiB | 00m00s [ 22/189] xz-1:5.8.3-2.fc46.ppc64le 100% | 4.9 MiB/s | 635.9 KiB | 00m00s [ 23/189] filesystem-0:3.18-59.fc45.ppc 100% | 43.2 MiB/s | 1.8 MiB | 00m00s [ 24/189] coreutils-common-0:9.11-6.fc4 100% | 38.0 MiB/s | 2.2 MiB | 00m00s [ 25/189] gmp-1:6.3.0-6.fc45.ppc64le 100% | 19.5 MiB/s | 319.9 KiB | 00m00s [ 26/189] libacl-0:2.4.0-2.fc45.ppc64le 100% | 9.5 MiB/s | 29.2 KiB | 00m00s [ 27/189] libcap-0:2.78-2.fc45.ppc64le 100% | 30.7 MiB/s | 94.4 KiB | 00m00s [ 28/189] systemd-libs-0:261.2-1.fc45.p 100% | 55.2 MiB/s | 961.2 KiB | 00m00s [ 29/189] glibc-0:2.44.9000-1.fc46.ppc6 100% | 41.9 MiB/s | 3.4 MiB | 00m00s [ 30/189] fedora-repos-0:46-0.3.noarch 100% | 455.2 KiB/s | 9.6 KiB | 00m00s [ 31/189] redhat-systemd-presets-0:102- 100% | 4.2 MiB/s | 8.5 KiB | 00m00s [ 32/189] openssl-libs-1:4.0.2-1.fc46.p 100% | 42.0 MiB/s | 2.4 MiB | 00m00s [ 33/189] R-srpm-macros-0:1.3.7-3.fc45. 100% | 857.6 KiB/s | 11.1 KiB | 00m00s [ 34/189] glibc-common-0:2.44.9000-1.fc 100% | 22.1 MiB/s | 429.4 KiB | 00m00s [ 35/189] ansible-srpm-macros-0:1-22.fc 100% | 4.8 MiB/s | 19.8 KiB | 00m00s [ 36/189] build-reproducibility-srpm-ma 100% | 2.6 MiB/s | 10.8 KiB | 00m00s [ 37/189] cmake-srpm-macros-0:4.3.0-5.f 100% | 3.4 MiB/s | 10.3 KiB | 00m00s [ 38/189] efi-srpm-macros-0:6-9.fc45.no 100% | 7.0 MiB/s | 21.4 KiB | 00m00s [ 39/189] dwz-0:0.17-3.fc45.ppc64le 100% | 35.8 MiB/s | 146.7 KiB | 00m00s [ 40/189] erlang-srpm-macros-0:0.3.11-2 100% | 4.9 MiB/s | 10.0 KiB | 00m00s [ 41/189] filesystem-srpm-macros-0:3.18 100% | 12.9 MiB/s | 26.4 KiB | 00m00s [ 42/189] forge-srpm-macros-0:0.4.0-5.f 100% | 9.6 MiB/s | 19.7 KiB | 00m00s [ 43/189] fonts-srpm-macros-1:5.0.0-4.f 100% | 8.8 MiB/s | 27.2 KiB | 00m00s [ 44/189] fpc-srpm-macros-0:1.3-17.fc45 100% | 2.5 MiB/s | 7.8 KiB | 00m00s [ 45/189] gap-srpm-macros-0:2-3.fc45.no 100% | 4.5 MiB/s | 9.3 KiB | 00m00s [ 46/189] ghc-srpm-macros-0:1.10-2.fc45 100% | 2.1 MiB/s | 8.5 KiB | 00m00s [ 47/189] gnome-srpm-macros-0:1.0-2.fc4 100% | 4.3 MiB/s | 8.8 KiB | 00m00s [ 48/189] gnat-srpm-macros-0:7-3.fc45.n 100% | 1.2 MiB/s | 8.6 KiB | 00m00s [ 49/189] go-srpm-macros-0:3.8.0-3.fc45 100% | 9.1 MiB/s | 27.8 KiB | 00m00s [ 50/189] java-srpm-macros-0:1-9.fc45.n 100% | 2.7 MiB/s | 8.3 KiB | 00m00s [ 51/189] kernel-srpm-macros-0:1.0-30.f 100% | 4.0 MiB/s | 8.3 KiB | 00m00s [ 52/189] ocaml-srpm-macros-0:11-4.fc45 100% | 4.4 MiB/s | 9.0 KiB | 00m00s [ 53/189] lua-srpm-macros-0:1-18.fc45.n 100% | 2.1 MiB/s | 8.7 KiB | 00m00s [ 54/189] openblas-srpm-macros-0:2-22.f 100% | 2.4 MiB/s | 7.5 KiB | 00m00s [ 55/189] package-notes-srpm-macros-0:0 100% | 3.4 MiB/s | 10.5 KiB | 00m00s [ 56/189] pyproject-srpm-macros-0:1.23. 100% | 7.6 MiB/s | 15.6 KiB | 00m00s [ 57/189] perl-srpm-macros-0:1-65.fc45. 100% | 2.0 MiB/s | 8.4 KiB | 00m00s [ 58/189] python-srpm-macros-0:3.15-2.f 100% | 7.8 MiB/s | 23.9 KiB | 00m00s [ 59/189] qt6-srpm-macros-0:6.11.2-1.fc 100% | 4.4 MiB/s | 9.1 KiB | 00m00s [ 60/189] qt5-srpm-macros-0:5.15.18-3.f 100% | 1.3 MiB/s | 8.1 KiB | 00m00s [ 61/189] rust-srpm-macros-0:28.5-2.fc4 100% | 5.6 MiB/s | 11.4 KiB | 00m00s [ 62/189] rpm-0:6.1.0-1.fc46.ppc64le 100% | 69.8 MiB/s | 572.0 KiB | 00m00s [ 63/189] tree-sitter-srpm-macros-0:0.4 100% | 2.7 MiB/s | 14.0 KiB | 00m00s [ 64/189] zig-srpm-macros-0:1-9.fc45.no 100% | 1.7 MiB/s | 8.8 KiB | 00m00s [ 65/189] zip-0:3.0-46.fc45.ppc64le 100% | 38.6 MiB/s | 276.7 KiB | 00m00s [ 66/189] elfutils-0:0.196-1.fc46.ppc64 100% | 46.8 MiB/s | 574.5 KiB | 00m00s [ 67/189] elfutils-libelf-0:0.196-1.fc4 100% | 47.9 MiB/s | 245.5 KiB | 00m00s [ 68/189] libgcc-0:16.2.1-2.fc46.ppc64l 100% | 37.8 MiB/s | 116.2 KiB | 00m00s [ 69/189] libstdc++-0:16.2.1-2.fc46.ppc 100% | 61.7 MiB/s | 1.1 MiB | 00m00s [ 70/189] rpm-build-libs-0:6.1.0-1.fc46 100% | 33.8 MiB/s | 138.4 KiB | 00m00s [ 71/189] binutils-0:2.47-1.fc45.ppc64l 100% | 83.1 MiB/s | 6.9 MiB | 00m00s [ 72/189] rpm-libs-0:6.1.0-1.fc46.ppc64 100% | 13.2 MiB/s | 526.2 KiB | 00m00s [ 73/189] mpfr-0:4.2.2-4.fc45.ppc64le 100% | 49.9 MiB/s | 357.4 KiB | 00m00s [ 74/189] audit-libs-0:4.2.1-2.fc45.ppc 100% | 38.6 MiB/s | 158.3 KiB | 00m00s [ 75/189] libsemanage-0:3.11-3.fc45.ppc 100% | 44.1 MiB/s | 135.4 KiB | 00m00s [ 76/189] libxcrypt-0:4.5.2-4.fc45.ppc6 100% | 27.3 MiB/s | 139.6 KiB | 00m00s [ 77/189] setup-0:2.15.1-2.fc45.noarch 100% | 25.7 MiB/s | 157.6 KiB | 00m00s [ 78/189] libblkid-0:2.42.2-3.fc45.ppc6 100% | 36.0 MiB/s | 147.5 KiB | 00m00s [ 79/189] libfdisk-0:2.42.2-3.fc45.ppc6 100% | 58.0 MiB/s | 178.2 KiB | 00m00s [ 80/189] liblastlog2-0:2.42.2-3.fc45.p 100% | 8.3 MiB/s | 25.5 KiB | 00m00s [ 81/189] libmount-0:2.42.2-3.fc45.ppc6 100% | 62.6 MiB/s | 192.4 KiB | 00m00s [ 82/189] librtas-0:2.0.7-2.fc45.ppc64l 100% | 21.1 MiB/s | 86.3 KiB | 00m00s [ 83/189] libuuid-0:2.42.2-3.fc45.ppc64 100% | 9.4 MiB/s | 28.8 KiB | 00m00s [ 84/189] libsmartcols-0:2.42.2-3.fc45. 100% | 18.4 MiB/s | 113.1 KiB | 00m00s [ 85/189] util-linux-core-0:2.42.2-3.fc 100% | 75.1 MiB/s | 615.1 KiB | 00m00s [ 86/189] glibc-gconv-extra-0:2.44.9000 100% | 103.9 MiB/s | 1.8 MiB | 00m00s [ 87/189] ca-certificates-0:2025.2.80_v 100% | 94.1 MiB/s | 963.4 KiB | 00m00s [ 88/189] crypto-policies-0:20260713-2. 100% | 47.6 MiB/s | 97.5 KiB | 00m00s [ 89/189] fips-provider-0:1.5.2-3.fc45. 100% | 58.3 MiB/s | 1.7 MiB | 00m00s [ 90/189] xz-libs-1:5.8.3-2.fc46.ppc64l 100% | 1.8 MiB/s | 127.6 KiB | 00m00s [ 91/189] fedora-gpg-keys-0:46-0.3.noar 100% | 46.8 MiB/s | 143.8 KiB | 00m00s [ 92/189] fedora-repos-rawhide-0:46-0.3 100% | 2.2 MiB/s | 9.0 KiB | 00m00s [ 93/189] redhat-systemd-presets-common 100% | 6.5 MiB/s | 13.2 KiB | 00m00s [ 94/189] add-determinism-0:0.7.3-3.fc4 100% | 77.6 MiB/s | 874.1 KiB | 00m00s [ 95/189] linkdupes-0:0.7.3-3.fc45.ppc6 100% | 29.8 MiB/s | 365.9 KiB | 00m00s [ 96/189] elfutils-debuginfod-client-0: 100% | 24.3 MiB/s | 49.7 KiB | 00m00s [ 97/189] elfutils-libs-0:0.196-1.fc46. 100% | 76.0 MiB/s | 311.5 KiB | 00m00s [ 98/189] libgomp-0:16.2.1-2.fc46.ppc64 100% | 80.1 MiB/s | 410.2 KiB | 00m00s [ 99/189] lua-libs-0:5.5.1-2.fc46.ppc64 100% | 51.5 MiB/s | 158.1 KiB | 00m00s [100/189] rpm-sign-libs-0:6.1.0-1.fc46. 100% | 13.4 MiB/s | 27.4 KiB | 00m00s [101/189] rpm-sequoia-0:1.10.2-5.fc45.p 100% | 95.4 MiB/s | 1.5 MiB | 00m00s [102/189] sqlite-libs-0:3.53.4-1.fc45.p 100% | 62.4 MiB/s | 895.2 KiB | 00m00s [103/189] libselinux-0:3.11-4.fc45.ppc6 100% | 37.2 MiB/s | 114.2 KiB | 00m00s [104/189] libsepol-0:3.11-2.fc45.ppc64l 100% | 74.3 MiB/s | 380.4 KiB | 00m00s [105/189] bzip2-libs-0:1.0.8-24.fc45.pp 100% | 24.1 MiB/s | 49.4 KiB | 00m00s [106/189] ncurses-libs-0:6.6-3.fc45.ppc 100% | 74.6 MiB/s | 381.8 KiB | 00m00s [107/189] ncurses-base-0:6.6-3.fc45.noa 100% | 28.7 MiB/s | 88.1 KiB | 00m00s [108/189] libcap-ng-0:0.9.5-1.fc46.ppc6 100% | 17.3 MiB/s | 35.5 KiB | 00m00s [109/189] pam-libs-0:1.7.2-4.fc45.ppc64 100% | 1.2 MiB/s | 58.1 KiB | 00m00s [110/189] readline-0:8.3-6.fc45.ppc64le 100% | 47.5 MiB/s | 243.0 KiB | 00m00s [111/189] zlib-ng-compat-0:2.3.3-6.fc45 100% | 29.1 MiB/s | 89.3 KiB | 00m00s [112/189] libeconf-0:0.7.9-4.fc45.ppc64 100% | 789.6 KiB/s | 37.9 KiB | 00m00s [113/189] gnupg2-0:2.4.9-18.fc45.ppc64l 100% | 76.8 MiB/s | 1.7 MiB | 00m00s [114/189] gpgverify-0:2.2-5.fc45.noarch 100% | 2.8 MiB/s | 11.3 KiB | 00m00s [115/189] gnupg2-dirmngr-0:2.4.9-18.fc4 100% | 43.7 MiB/s | 313.0 KiB | 00m00s [116/189] gnupg2-gpg-agent-0:2.4.9-18.f 100% | 42.4 MiB/s | 304.1 KiB | 00m00s [117/189] gnupg2-gpgconf-0:2.4.9-18.fc4 100% | 40.8 MiB/s | 125.3 KiB | 00m00s [118/189] gnupg2-keyboxd-0:2.4.9-18.fc4 100% | 33.4 MiB/s | 102.5 KiB | 00m00s [119/189] gnupg2-verify-0:2.4.9-18.fc45 100% | 44.9 MiB/s | 184.0 KiB | 00m00s [120/189] libgcrypt-0:1.12.3-1.fc46.ppc 100% | 67.7 MiB/s | 693.3 KiB | 00m00s [121/189] gnutls-0:3.8.13-3.fc45.ppc64l 100% | 80.9 MiB/s | 1.4 MiB | 00m00s [122/189] openldap-0:2.6.14-1.fc46.ppc6 100% | 56.5 MiB/s | 289.1 KiB | 00m00s [123/189] nettle-0:4.0-5.fc45.ppc64le 100% | 75.3 MiB/s | 462.5 KiB | 00m00s [124/189] cyrus-sasl-lib-0:2.1.28-37.fc 100% | 96.2 MiB/s | 886.5 KiB | 00m00s [125/189] libtool-ltdl-0:2.5.4-11.fc45. 100% | 19.2 MiB/s | 39.4 KiB | 00m00s [126/189] ima-evm-utils-libs-0:1.6.2-12 100% | 616.0 KiB/s | 29.6 KiB | 00m00s [127/189] libfsverity-0:1.7-4.fc45.ppc6 100% | 6.3 MiB/s | 19.3 KiB | 00m00s [128/189] popt-0:1.19-11.fc45.ppc64le 100% | 1.2 MiB/s | 60.7 KiB | 00m00s [129/189] libzstd-0:1.5.7-6.fc45.ppc64l 100% | 6.9 MiB/s | 380.7 KiB | 00m00s [130/189] debugedit-0:5.3-3.fc45.ppc64l 100% | 22.3 MiB/s | 91.3 KiB | 00m00s [131/189] libarchive-0:3.8.9-1.fc46.ppc 100% | 61.1 MiB/s | 500.3 KiB | 00m00s [132/189] pkgconf-pkg-config-0:2.5.1-2. 100% | 193.4 KiB/s | 9.3 KiB | 00m00s [133/189] zstd-0:1.5.7-6.fc45.ppc64le 100% | 3.5 MiB/s | 184.6 KiB | 00m00s [134/189] curl-0:8.22.0~rc3-1.fc46.ppc6 100% | 41.0 MiB/s | 251.8 KiB | 00m00s [135/189] ed-0:1.22.6-1.fc46.ppc64le 100% | 17.1 MiB/s | 87.5 KiB | 00m00s [136/189] libattr-0:2.6.0-2.fc45.ppc64l 100% | 370.7 KiB/s | 17.8 KiB | 00m00s [137/189] libevent-0:2.1.12-19.fc45.ppc 100% | 5.1 MiB/s | 273.7 KiB | 00m00s [138/189] pcre2-0:10.47-1.fc45.2.ppc64l 100% | 5.1 MiB/s | 273.0 KiB | 00m00s [139/189] libgpg-error-0:1.61-2.fc45.pp 100% | 4.7 MiB/s | 247.1 KiB | 00m00s [140/189] libxml2-0:2.13.9-4.fc45.ppc64 100% | 11.8 MiB/s | 735.4 KiB | 00m00s [141/189] lz4-libs-0:1.10.0-5.fc45.ppc6 100% | 1.9 MiB/s | 96.5 KiB | 00m00s [142/189] libidn2-0:2.3.8-4.fc45.ppc64l 100% | 43.1 MiB/s | 176.6 KiB | 00m00s [143/189] libtasn1-0:4.21.0-2.fc45.ppc6 100% | 1.6 MiB/s | 81.3 KiB | 00m00s [144/189] libunistring-0:1.1-12.fc45.pp 100% | 62.4 MiB/s | 574.7 KiB | 00m00s [145/189] p11-kit-0:0.26.5-1.fc45.ppc64 100% | 68.0 MiB/s | 556.8 KiB | 00m00s [146/189] p11-kit-trust-0:0.26.5-1.fc45 100% | 38.3 MiB/s | 156.9 KiB | 00m00s [147/189] libassuan-0:2.5.7-6.fc45.ppc6 100% | 1.4 MiB/s | 69.5 KiB | 00m00s [148/189] npth-0:1.8-5.fc45.ppc64le 100% | 8.1 MiB/s | 24.9 KiB | 00m00s [149/189] libksba-0:1.8.1-1.fc46.ppc64l 100% | 44.3 MiB/s | 181.3 KiB | 00m00s [150/189] tpm2-tss-0:4.2.0-1.fc45.ppc64 100% | 6.6 MiB/s | 364.7 KiB | 00m00s [151/189] json-c-0:0.18-9.fc45.ppc64le 100% | 1.0 MiB/s | 48.0 KiB | 00m00s [152/189] gdbm-libs-1:1.23-12.fc45.ppc6 100% | 1.3 MiB/s | 63.8 KiB | 00m00s [153/189] gnulib-l10n-0:20241231-4.fc45 100% | 2.9 MiB/s | 143.1 KiB | 00m00s [154/189] libffi-0:3.5.2-3.fc45.ppc64le 100% | 13.5 MiB/s | 41.6 KiB | 00m00s [155/189] alternatives-0:1.33-6.fc45.pp 100% | 20.2 MiB/s | 41.4 KiB | 00m00s [156/189] jansson-0:2.14-5.fc45.ppc64le 100% | 24.7 MiB/s | 50.5 KiB | 00m00s [157/189] libusb1-0:1.0.30-2.fc45.ppc64 100% | 28.2 MiB/s | 86.7 KiB | 00m00s [158/189] pkgconf-0:2.5.1-2.fc45.ppc64l 100% | 1.0 MiB/s | 50.2 KiB | 00m00s [159/189] pkgconf-m4-0:2.5.1-2.fc45.noa 100% | 277.7 KiB/s | 13.6 KiB | 00m00s [160/189] libpkgconf-0:2.5.1-2.fc45.ppc 100% | 881.3 KiB/s | 42.3 KiB | 00m00s [161/189] pcre2-syntax-0:10.47-1.fc45.2 100% | 3.2 MiB/s | 164.9 KiB | 00m00s [162/189] fedora-release-0:46-0.1.noarc 100% | 3.9 MiB/s | 11.9 KiB | 00m00s [163/189] systemd-standalone-sysusers-0 100% | 51.4 MiB/s | 421.2 KiB | 00m00s [164/189] gdb-minimal-0:17.2-4.fc45.ppc 100% | 85.3 MiB/s | 4.9 MiB | 00m00s [165/189] xxhash-libs-0:0.8.3-5.fc45.pp 100% | 9.2 MiB/s | 37.8 KiB | 00m00s [166/189] fedora-release-identity-basic 100% | 6.2 MiB/s | 12.7 KiB | 00m00s [167/189] libcurl-0:8.22.0~rc3-1.fc46.p 100% | 74.3 MiB/s | 532.8 KiB | 00m00s [168/189] libssh-0:0.12.2-1.fc45.ppc64l 100% | 62.2 MiB/s | 318.3 KiB | 00m00s [169/189] krb5-libs-0:1.22.2-9.fc45.ppc 100% | 93.2 MiB/s | 859.2 KiB | 00m00s [170/189] libpsl-0:0.23.1-1.fc45.ppc64l 100% | 33.4 MiB/s | 68.5 KiB | 00m00s [171/189] ngtcp2-0:1.22.1-3.fc45.ppc64l 100% | 54.8 MiB/s | 168.3 KiB | 00m00s [172/189] ngtcp2-crypto-ossl-0:1.22.1-3 100% | 13.3 MiB/s | 27.2 KiB | 00m00s [173/189] libssh-config-0:0.12.2-1.fc45 100% | 4.4 MiB/s | 8.9 KiB | 00m00s [174/189] libverto-0:0.3.2-13.fc45.ppc6 100% | 10.6 MiB/s | 21.7 KiB | 00m00s [175/189] publicsuffix-list-dafsa-0:202 100% | 19.9 MiB/s | 61.1 KiB | 00m00s [176/189] selinux-policy-targeted-0:45. 100% | 106.5 MiB/s | 6.8 MiB | 00m00s [177/189] selinux-policy-0:45.15-1.fc46 100% | 12.5 MiB/s | 38.5 KiB | 00m00s [178/189] rpm-plugin-selinux-0:6.1.0-1. 100% | 8.7 MiB/s | 17.8 KiB | 00m00s [179/189] policycoreutils-0:3.11-2.fc45 100% | 51.4 MiB/s | 263.0 KiB | 00m00s [180/189] libselinux-utils-0:3.11-4.fc4 100% | 62.2 MiB/s | 127.4 KiB | 00m00s [181/189] libfido2-0:1.17.0-5.fc45.ppc6 100% | 2.1 MiB/s | 107.3 KiB | 00m00s [182/189] libcbor-0:0.14.0-3.fc45.ppc64 100% | 12.3 MiB/s | 37.9 KiB | 00m00s [183/189] libbrotli-0:1.2.0-6.fc45.ppc6 100% | 54.8 MiB/s | 392.9 KiB | 00m00s [184/189] libnghttp2-0:1.69.0-5.fc45.pp 100% | 27.1 MiB/s | 83.2 KiB | 00m00s [185/189] file-libs-0:5.47-3.fc45.ppc64 100% | 503.7 KiB/s | 881.0 KiB | 00m02s >>> Status code: 404 for https://dl.fedoraproject.org/pub/fedora-secondary/development/rawhide/Everything/ppc64le/os/Packages/f/file-libs-5.47-3.fc45.ppc64le.rpm (IP: 10.16.163.49) - https://dl.fedoraproject.org/pub/fedora-secondary/development/rawhide/Everything/ppc64le/os/Packages/f/file-libs-5.47-3.fc45.ppc64le.rpm >>> Status code: 404 for https://dl.fedoraproject.org/pub/fedora-secondary/development/rawhide/Everything/ppc64le/os/Packages/f/file-libs-5.47-3.fc45.ppc64le.rpm (IP: 10.16.163.49) - https://dl.fedoraproject.org/pub/fedora-secondary/development/rawhide/Everything/ppc64le/os/Packages/f/file-libs-5.47-3.fc45.ppc64le.rpm [186/189] libnghttp3-0:1.18.0-1.fc46.pp 100% | 1.7 MiB/s | 85.4 KiB | 00m00s [187/189] libcom_err-0:1.47.4-2.fc45.pp 100% | 13.1 MiB/s | 26.8 KiB | 00m00s [188/189] keyutils-libs-0:1.6.3-8.fc45. 100% | 677.0 KiB/s | 31.8 KiB | 00m00s [189/189] file-0:5.47-3.fc45.ppc64le 100% | 1.5 KiB/s | 50.0 KiB | 00m34s >>> Status code: 404 for https://dl.fedoraproject.org/pub/fedora-secondary/development/rawhide/Everything/ppc64le/os/Packages/f/file-5.47-3.fc45.ppc64le.rpm (IP: 10.16.163.49) - https://dl.fedoraproject.org/pub/fedora-secondary/development/rawhide/Everything/ppc64le/os/Packages/f/file-5.47-3.fc45.ppc64le.rpm >>> Status code: 404 for https://dl.fedoraproject.org/pub/fedora-secondary/development/rawhide/Everything/ppc64le/os/Packages/f/file-5.47-3.fc45.ppc64le.rpm (IP: 10.16.163.49) - https://dl.fedoraproject.org/pub/fedora-secondary/development/rawhide/Everything/ppc64le/os/Packages/f/file-5.47-3.fc45.ppc64le.rpm -------------------------------------------------------------------------------- [189/189] Total 100% | 2.2 MiB/s | 76.0 MiB | 00m35s 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. [ 1/191] Verify package files 100% | 150.0 B/s | 189.0 B | 00m01s >>> Running %pretrans scriptlet: filesystem-0:3.18-59.fc45.ppc64le >>> Finished %pretrans scriptlet: filesystem-0:3.18-59.fc45.ppc64le >>> [RPM] /var/lib/mock/fedora-rawhide-ppc64le-1788249070.975671/root/var/cache/dnf/copr_base-bb8f6c99d12f7709/packages/bash-5.3.15-2.fc46.ppc64le.rpm: Header OpenPGP V4 RSA/SHA256 signature, key ID 5291f7fa5c4b3009: NOKEY >>> [RPM] failed to open /var/lib/mock/fedora-rawhide-ppc64le-1788249070.975671/root/etc/group for id/name lookup: No such file or directory [ 2/191] Prepare transaction 100% | 800.0 B/s | 189.0 B | 00m00s [ 3/191] Installing libgcc-0:16.2.1-2. 100% | 56.3 MiB/s | 288.1 KiB | 00m00s [ 4/191] Installing redhat-systemd-pre 100% | 1.4 MiB/s | 1.5 KiB | 00m00s [ 5/191] Installing redhat-systemd-pre 100% | 8.8 MiB/s | 18.1 KiB | 00m00s [ 6/191] Installing publicsuffix-list- 100% | 35.2 MiB/s | 72.0 KiB | 00m00s [ 7/191] Installing libssh-config-0:0. 100% | 796.9 KiB/s | 816.0 B | 00m00s [ 8/191] Installing fedora-release-ide 100% | 449.2 KiB/s | 920.0 B | 00m00s [ 9/191] Installing fedora-gpg-keys-0: 100% | 10.4 MiB/s | 181.7 KiB | 00m00s [ 10/191] Installing fedora-repos-rawhi 100% | 2.4 MiB/s | 2.5 KiB | 00m00s [ 11/191] Installing fedora-repos-0:46- 100% | 2.9 MiB/s | 5.9 KiB | 00m00s [ 12/191] Installing fedora-release-com 100% | 2.6 MiB/s | 8.0 KiB | 00m00s [ 13/191] Installing fedora-release-0:4 100% | 6.4 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. >>> [ 14/191] Installing setup-0:2.15.1-2.f 100% | 9.3 MiB/s | 731.3 KiB | 00m00s >>> [RPM] /etc/hosts created as /etc/hosts.rpmnew [ 15/191] Installing filesystem-0:3.18- 100% | 603.7 KiB/s | 253.6 KiB | 00m00s [ 16/191] Installing pcre2-syntax-0:10. 100% | 69.4 MiB/s | 284.3 KiB | 00m00s [ 17/191] Installing pkgconf-m4-0:2.5.1 100% | 14.4 MiB/s | 14.7 KiB | 00m00s [ 18/191] Installing gnulib-l10n-0:2024 100% | 49.7 MiB/s | 661.9 KiB | 00m00s [ 19/191] Installing coreutils-common-0 100% | 111.8 MiB/s | 11.0 MiB | 00m00s [ 20/191] Installing ncurses-base-0:6.6 100% | 17.3 MiB/s | 355.3 KiB | 00m00s [ 21/191] Installing glibc-common-0:2.4 100% | 20.7 MiB/s | 1.5 MiB | 00m00s [ 22/191] Installing glibc-gconv-extra- 100% | 99.4 MiB/s | 18.6 MiB | 00m00s [ 23/191] Installing glibc-0:2.44.9000- 100% | 68.6 MiB/s | 12.2 MiB | 00m00s [ 24/191] Installing ncurses-libs-0:6.6 100% | 93.4 MiB/s | 1.5 MiB | 00m00s [ 25/191] Installing bash-0:5.3.15-2.fc 100% | 71.6 MiB/s | 8.8 MiB | 00m00s [ 26/191] Installing glibc-minimal-lang 100% | 121.1 KiB/s | 124.0 B | 00m00s [ 27/191] Installing zlib-ng-compat-0:2 100% | 64.5 MiB/s | 198.1 KiB | 00m00s [ 28/191] Installing bzip2-libs-0:1.0.8 100% | 44.8 MiB/s | 137.5 KiB | 00m00s [ 29/191] Installing libgpg-error-0:1.6 100% | 15.8 MiB/s | 1.0 MiB | 00m00s [ 30/191] Installing libstdc++-0:16.2.1 100% | 120.8 MiB/s | 4.1 MiB | 00m00s [ 31/191] Installing libzstd-0:1.5.7-6. 100% | 102.8 MiB/s | 1.0 MiB | 00m00s [ 32/191] Installing elfutils-libelf-0: 100% | 117.0 MiB/s | 1.5 MiB | 00m00s [ 33/191] Installing libgcrypt-0:1.12.3 100% | 105.2 MiB/s | 1.6 MiB | 00m00s [ 34/191] Installing libassuan-0:2.5.7- 100% | 70.9 MiB/s | 217.8 KiB | 00m00s [ 35/191] Installing readline-0:8.3-6.f 100% | 87.8 MiB/s | 629.5 KiB | 00m00s [ 36/191] Installing gmp-1:6.3.0-6.fc45 100% | 96.2 MiB/s | 788.3 KiB | 00m00s [ 37/191] Installing libacl-0:2.4.0-2.f 100% | 33.4 MiB/s | 68.4 KiB | 00m00s [ 38/191] Installing systemd-libs-0:261 100% | 93.7 MiB/s | 3.3 MiB | 00m00s [ 39/191] Installing libuuid-0:2.42.2-3 100% | 34.3 MiB/s | 70.3 KiB | 00m00s [ 40/191] Installing xz-libs-1:5.8.3-2. 100% | 52.1 MiB/s | 266.6 KiB | 00m00s [ 41/191] Installing sqlite-libs-0:3.53 100% | 77.2 MiB/s | 2.0 MiB | 00m00s [ 42/191] Installing popt-0:1.19-11.fc4 100% | 10.5 MiB/s | 151.0 KiB | 00m00s [ 43/191] Installing npth-0:1.8-5.fc45. 100% | 23.0 MiB/s | 94.1 KiB | 00m00s [ 44/191] Installing elfutils-libs-0:0. 100% | 65.8 MiB/s | 876.4 KiB | 00m00s [ 45/191] Installing libblkid-0:2.42.2- 100% | 49.6 MiB/s | 355.5 KiB | 00m00s [ 46/191] Installing libsepol-0:3.11-2. 100% | 74.4 MiB/s | 1.0 MiB | 00m00s [ 47/191] Installing gnupg2-gpgconf-0:2 100% | 3.3 MiB/s | 323.6 KiB | 00m00s [ 48/191] Installing crypto-policies-0: 100% | 5.6 MiB/s | 159.5 KiB | 00m00s [ 49/191] Installing libxcrypt-0:4.5.2- 100% | 33.2 MiB/s | 339.6 KiB | 00m00s [ 50/191] Installing pcre2-0:10.47-1.fc 100% | 63.2 MiB/s | 906.5 KiB | 00m00s [ 51/191] Installing libselinux-0:3.11- 100% | 35.8 MiB/s | 330.4 KiB | 00m00s [ 52/191] Installing grep-0:3.12-4.fc45 100% | 11.0 MiB/s | 1.0 MiB | 00m00s [ 53/191] Installing sed-0:4.10-2.fc45. 100% | 13.5 MiB/s | 950.8 KiB | 00m00s [ 54/191] Installing findutils-1:4.11.0 100% | 27.8 MiB/s | 2.1 MiB | 00m00s [ 55/191] Installing libtasn1-0:4.21.0- 100% | 54.2 MiB/s | 222.2 KiB | 00m00s [ 56/191] Installing libunistring-0:1.1 100% | 98.5 MiB/s | 1.9 MiB | 00m00s [ 57/191] Installing libidn2-0:2.3.8-4. 100% | 42.5 MiB/s | 566.3 KiB | 00m00s [ 58/191] Installing xz-1:5.8.3-2.fc46. 100% | 17.7 MiB/s | 1.5 MiB | 00m00s [ 59/191] Installing libmount-0:2.42.2- 100% | 67.1 MiB/s | 549.3 KiB | 00m00s [ 60/191] Installing gnupg2-verify-0:2. 100% | 6.2 MiB/s | 429.5 KiB | 00m00s [ 61/191] Installing mpfr-0:4.2.2-4.fc4 100% | 63.8 MiB/s | 915.1 KiB | 00m00s [ 62/191] Installing gawk-0:5.4.1-1.fc4 100% | 34.5 MiB/s | 3.2 MiB | 00m00s [ 63/191] Installing dwz-0:0.17-3.fc45. 100% | 6.1 MiB/s | 388.0 KiB | 00m00s [ 64/191] Installing libksba-0:1.8.1-1. 100% | 75.1 MiB/s | 538.3 KiB | 00m00s [ 65/191] Installing unzip-0:6.0-71.fc4 100% | 8.9 MiB/s | 536.9 KiB | 00m00s [ 66/191] Installing file-libs-0:5.47-3 100% | 175.3 MiB/s | 12.3 MiB | 00m00s [ 67/191] Installing file-0:5.47-3.fc45 100% | 2.5 MiB/s | 142.5 KiB | 00m00s [ 68/191] Installing diffutils-0:3.12-6 100% | 23.1 MiB/s | 1.7 MiB | 00m00s [ 69/191] Installing libsmartcols-0:2.4 100% | 56.7 MiB/s | 290.5 KiB | 00m00s [ 70/191] Installing lua-libs-0:5.5.1-2 100% | 64.4 MiB/s | 395.4 KiB | 00m00s [ 71/191] Installing libcap-ng-0:0.9.5- 100% | 52.7 MiB/s | 162.0 KiB | 00m00s [ 72/191] Installing audit-libs-0:4.2.1 100% | 77.1 MiB/s | 552.8 KiB | 00m00s [ 73/191] Installing libsemanage-0:3.11 100% | 83.1 MiB/s | 425.6 KiB | 00m00s [ 74/191] Installing libeconf-0:0.7.9-4 100% | 26.9 MiB/s | 82.6 KiB | 00m00s [ 75/191] Installing pam-libs-0:1.7.2-4 100% | 70.4 MiB/s | 288.2 KiB | 00m00s [ 76/191] Installing libcap-0:2.78-2.fc 100% | 8.3 MiB/s | 511.9 KiB | 00m00s [ 77/191] Installing libattr-0:2.6.0-2. 100% | 22.4 MiB/s | 68.8 KiB | 00m00s [ 78/191] Installing json-c-0:0.18-9.fc 100% | 45.4 MiB/s | 139.6 KiB | 00m00s [ 79/191] Installing libffi-0:3.5.2-3.f 100% | 85.2 MiB/s | 348.9 KiB | 00m00s [ 80/191] Installing p11-kit-0:0.26.5-1 100% | 37.9 MiB/s | 3.3 MiB | 00m00s [ 81/191] Installing alternatives-0:1.3 100% | 1.7 MiB/s | 91.5 KiB | 00m00s [ 82/191] Installing p11-kit-trust-0:0. 100% | 8.7 MiB/s | 595.7 KiB | 00m00s [ 83/191] Installing ngtcp2-0:1.22.1-3. 100% | 66.2 MiB/s | 406.6 KiB | 00m00s [ 84/191] Installing liblastlog2-0:2.42 100% | 15.1 MiB/s | 139.3 KiB | 00m00s [ 85/191] Installing util-linux-core-0: 100% | 32.4 MiB/s | 2.7 MiB | 00m00s [ 86/191] Installing zip-0:3.0-46.fc45. 100% | 14.1 MiB/s | 893.1 KiB | 00m00s [ 87/191] Installing gnupg2-keyboxd-0:2 100% | 22.9 MiB/s | 234.4 KiB | 00m00s [ 88/191] Installing libpsl-0:0.23.1-1. 100% | 43.4 MiB/s | 133.2 KiB | 00m00s [ 89/191] Installing tar-2:1.35-9.fc45. 100% | 38.2 MiB/s | 3.1 MiB | 00m00s [ 90/191] Installing linkdupes-0:0.7.3- 100% | 13.4 MiB/s | 839.8 KiB | 00m00s [ 91/191] Installing libselinux-utils-0 100% | 20.2 MiB/s | 1.4 MiB | 00m00s [ 92/191] Installing libfdisk-0:2.42.2- 100% | 78.8 MiB/s | 483.9 KiB | 00m00s [ 93/191] Installing fips-provider-0:1. 100% | 126.8 MiB/s | 4.7 MiB | 00m00s [ 94/191] Installing openssl-libs-1:4.0 100% | 122.9 MiB/s | 7.1 MiB | 00m00s [ 95/191] Installing coreutils-0:9.11-6 100% | 68.9 MiB/s | 9.7 MiB | 00m00s [ 96/191] Installing ca-certificates-0: 100% | 646.7 KiB/s | 2.4 MiB | 00m04s [ 97/191] Installing gzip-0:1.14-4.fc45 100% | 7.0 MiB/s | 443.0 KiB | 00m00s [ 98/191] Installing rpm-sequoia-0:1.10 100% | 125.3 MiB/s | 4.8 MiB | 00m00s [ 99/191] Installing libfsverity-0:1.7- 100% | 33.7 MiB/s | 69.0 KiB | 00m00s [100/191] Installing libevent-0:2.1.12- 100% | 115.4 MiB/s | 1.3 MiB | 00m00s [101/191] Installing ngtcp2-crypto-ossl 100% | 33.2 MiB/s | 68.0 KiB | 00m00s [102/191] Installing libxml2-0:2.13.9-4 100% | 26.8 MiB/s | 2.3 MiB | 00m00s [103/191] Installing libusb1-0:1.0.30-2 100% | 13.3 MiB/s | 245.2 KiB | 00m00s >>> Running sysusers scriptlet: tpm2-tss-0:4.2.0-1.fc45.ppc64le >>> Finished sysusers scriptlet: tpm2-tss-0:4.2.0-1.fc45.ppc64le >>> Scriptlet output: >>> Creating group 'tss' with GID 59. >>> Creating user 'tss' (Account used for TPM access) with UID 59 and GID 59. >>> [104/191] Installing tpm2-tss-0:4.2.0-1 100% | 100.6 MiB/s | 2.4 MiB | 00m00s [105/191] Installing gnupg2-gpg-agent-0 100% | 12.2 MiB/s | 978.1 KiB | 00m00s [106/191] Installing ima-evm-utils-libs 100% | 30.4 MiB/s | 93.5 KiB | 00m00s [107/191] Installing nettle-0:4.0-5.fc4 100% | 94.6 MiB/s | 968.2 KiB | 00m00s [108/191] Installing gnutls-0:3.8.13-3. 100% | 118.5 MiB/s | 4.1 MiB | 00m00s [109/191] Installing zstd-0:1.5.7-6.fc4 100% | 8.9 MiB/s | 563.1 KiB | 00m00s [110/191] Installing bzip2-0:1.0.8-24.f 100% | 3.0 MiB/s | 175.4 KiB | 00m00s [111/191] Installing add-determinism-0: 100% | 30.8 MiB/s | 2.3 MiB | 00m00s [112/191] Installing filesystem-srpm-ma 100% | 19.0 MiB/s | 38.9 KiB | 00m00s [113/191] Installing ed-0:1.22.6-1.fc46 100% | 3.9 MiB/s | 225.1 KiB | 00m00s [114/191] Installing patch-0:2.8-5.fc45 100% | 4.4 MiB/s | 263.8 KiB | 00m00s [115/191] Installing cpio-0:2.15-10.fc4 100% | 17.4 MiB/s | 1.2 MiB | 00m00s [116/191] Installing librtas-0:2.0.7-2. 100% | 15.7 MiB/s | 322.5 KiB | 00m00s [117/191] Installing util-linux-0:2.42. 100% | 48.0 MiB/s | 7.1 MiB | 00m00s [118/191] Installing policycoreutils-0: 100% | 16.1 MiB/s | 1.5 MiB | 00m00s [119/191] Installing selinux-policy-0:4 100% | 1.0 MiB/s | 34.5 KiB | 00m00s [120/191] Installing selinux-policy-tar 100% | 49.3 MiB/s | 15.1 MiB | 00m00s [121/191] Installing build-reproducibil 100% | 757.8 KiB/s | 1.5 KiB | 00m00s [122/191] Installing libgomp-0:16.2.1-2 100% | 91.9 MiB/s | 658.4 KiB | 00m00s [123/191] Installing libtool-ltdl-0:2.5 100% | 46.3 MiB/s | 94.9 KiB | 00m00s [124/191] Installing lz4-libs-0:1.10.0- 100% | 63.9 MiB/s | 261.9 KiB | 00m00s [125/191] Installing libarchive-0:3.8.9 100% | 97.5 MiB/s | 1.3 MiB | 00m00s [126/191] Installing gdbm-libs-1:1.23-1 100% | 57.4 MiB/s | 235.1 KiB | 00m00s [127/191] Installing cyrus-sasl-lib-0:2 100% | 36.9 MiB/s | 2.9 MiB | 00m00s [128/191] Installing openldap-0:2.6.14- 100% | 73.0 MiB/s | 896.6 KiB | 00m00s [129/191] Installing gnupg2-dirmngr-0:2 100% | 11.7 MiB/s | 840.6 KiB | 00m00s [130/191] Installing gnupg2-0:2.4.9-18. 100% | 60.5 MiB/s | 6.8 MiB | 00m00s [131/191] Installing gpgverify-0:2.2-5. 100% | 4.6 MiB/s | 9.4 KiB | 00m00s [132/191] Installing jansson-0:2.14-5.f 100% | 51.5 MiB/s | 158.3 KiB | 00m00s [133/191] Installing libpkgconf-0:2.5.1 100% | 43.9 MiB/s | 134.9 KiB | 00m00s [134/191] Installing pkgconf-0:2.5.1-2. 100% | 2.0 MiB/s | 117.2 KiB | 00m00s [135/191] Installing pkgconf-pkg-config 100% | 32.2 KiB/s | 1.8 KiB | 00m00s [136/191] Installing systemd-standalone 100% | 16.1 MiB/s | 1.1 MiB | 00m00s [137/191] Installing rpm-libs-0:6.1.0-1 100% | 94.3 MiB/s | 1.4 MiB | 00m00s [138/191] Installing rpm-sign-libs-0:6. 100% | 33.4 MiB/s | 68.3 KiB | 00m00s [139/191] Installing rpm-build-libs-0:6 100% | 80.2 MiB/s | 328.7 KiB | 00m00s [140/191] Installing xxhash-libs-0:0.8. 100% | 42.4 MiB/s | 86.9 KiB | 00m00s [141/191] Installing libverto-0:0.3.2-1 100% | 34.6 MiB/s | 70.8 KiB | 00m00s [142/191] Installing libcbor-0:0.14.0-3 100% | 34.4 MiB/s | 140.9 KiB | 00m00s [143/191] Installing libfido2-0:1.17.0- 100% | 67.7 MiB/s | 346.7 KiB | 00m00s [144/191] Installing libbrotli-0:1.2.0- 100% | 92.2 MiB/s | 1.0 MiB | 00m00s [145/191] Installing libnghttp2-0:1.69. 100% | 64.8 MiB/s | 198.9 KiB | 00m00s [146/191] Installing libnghttp3-0:1.18. 100% | 34.0 MiB/s | 209.1 KiB | 00m00s [147/191] Installing keyutils-libs-0:1. 100% | 32.3 MiB/s | 99.1 KiB | 00m00s [148/191] Installing libcom_err-0:1.47. 100% | 36.5 MiB/s | 112.0 KiB | 00m00s [149/191] Installing krb5-libs-0:1.22.2 100% | 99.0 MiB/s | 3.0 MiB | 00m00s [150/191] Installing libssh-0:0.12.2-1. 100% | 89.4 MiB/s | 915.6 KiB | 00m00s [151/191] Installing libcurl-0:8.22.0~r 100% | 102.7 MiB/s | 1.3 MiB | 00m00s [152/191] Installing elfutils-debuginfo 100% | 2.5 MiB/s | 145.7 KiB | 00m00s [153/191] Installing binutils-0:2.47-1. 100% | 100.8 MiB/s | 33.8 MiB | 00m00s [154/191] Installing elfutils-0:0.196-1 100% | 42.1 MiB/s | 3.5 MiB | 00m00s [155/191] Installing gdb-minimal-0:17.2 100% | 89.0 MiB/s | 16.3 MiB | 00m00s [156/191] Installing debugedit-0:5.3-3. 100% | 6.4 MiB/s | 387.8 KiB | 00m00s [157/191] Installing curl-0:8.22.0~rc3- 100% | 6.7 MiB/s | 529.3 KiB | 00m00s [158/191] Installing rpm-0:6.1.0-1.fc46 100% | 24.4 MiB/s | 2.8 MiB | 00m00s [159/191] Installing cmake-srpm-macros- 100% | 785.2 KiB/s | 804.0 B | 00m00s [160/191] Installing efi-srpm-macros-0: 100% | 20.2 MiB/s | 41.3 KiB | 00m00s [161/191] Installing java-srpm-macros-0 100% | 1.1 MiB/s | 1.1 KiB | 00m00s [162/191] Installing lua-srpm-macros-0: 100% | 951.2 KiB/s | 1.9 KiB | 00m00s [163/191] Installing tree-sitter-srpm-m 100% | 4.7 MiB/s | 9.6 KiB | 00m00s [164/191] Installing zig-srpm-macros-0: 100% | 1.8 MiB/s | 1.9 KiB | 00m00s [165/191] Installing rust-srpm-macros-0 100% | 3.1 MiB/s | 6.4 KiB | 00m00s [166/191] Installing qt6-srpm-macros-0: 100% | 730.5 KiB/s | 748.0 B | 00m00s [167/191] Installing qt5-srpm-macros-0: 100% | 757.8 KiB/s | 776.0 B | 00m00s [168/191] Installing perl-srpm-macros-0 100% | 1.1 MiB/s | 1.1 KiB | 00m00s [169/191] Installing package-notes-srpm 100% | 2.0 MiB/s | 2.1 KiB | 00m00s [170/191] Installing openblas-srpm-macr 100% | 382.8 KiB/s | 392.0 B | 00m00s [171/191] Installing ocaml-srpm-macros- 100% | 85.8 KiB/s | 2.1 KiB | 00m00s [172/191] Installing kernel-srpm-macros 100% | 2.3 MiB/s | 2.3 KiB | 00m00s [173/191] Installing gnome-srpm-macros- 100% | 4.0 MiB/s | 4.1 KiB | 00m00s [174/191] Installing gnat-srpm-macros-0 100% | 1.2 MiB/s | 1.3 KiB | 00m00s [175/191] Installing ghc-srpm-macros-0: 100% | 1.0 MiB/s | 1.0 KiB | 00m00s [176/191] Installing gap-srpm-macros-0: 100% | 2.6 MiB/s | 2.7 KiB | 00m00s [177/191] Installing fpc-srpm-macros-0: 100% | 410.2 KiB/s | 420.0 B | 00m00s [178/191] Installing ansible-srpm-macro 100% | 11.8 MiB/s | 36.2 KiB | 00m00s [179/191] Installing redhat-rpm-config- 100% | 26.6 MiB/s | 190.4 KiB | 00m00s [180/191] Installing forge-srpm-macros- 100% | 19.7 MiB/s | 40.3 KiB | 00m00s [181/191] Installing rpm-build-0:6.1.0- 100% | 8.3 MiB/s | 689.8 KiB | 00m00s [182/191] Installing erlang-srpm-macros 100% | 1.2 MiB/s | 2.5 KiB | 00m00s [183/191] Installing pyproject-srpm-mac 100% | 3.9 MiB/s | 4.0 KiB | 00m00s [184/191] Installing fonts-srpm-macros- 100% | 27.8 MiB/s | 57.0 KiB | 00m00s [185/191] Installing go-srpm-macros-0:3 100% | 30.8 MiB/s | 63.0 KiB | 00m00s [186/191] Installing R-srpm-macros-0:1. 100% | 2.1 MiB/s | 4.4 KiB | 00m00s [187/191] Installing python-srpm-macros 100% | 17.2 MiB/s | 52.9 KiB | 00m00s [188/191] Installing rpm-plugin-selinux 100% | 22.4 MiB/s | 68.8 KiB | 00m00s [189/191] Installing which-0:2.25-2.fc4 100% | 2.0 MiB/s | 125.1 KiB | 00m00s [190/191] Installing shadow-utils-2:4.2 100% | 34.1 MiB/s | 4.9 MiB | 00m00s [191/191] Installing info-0:7.3-3.fc45. 100% | 30.5 KiB/s | 488.5 KiB | 00m16s Warning: skipped OpenPGP checks for 32 packages from repository: copr_base Complete! Updating and loading repositories: fedora 100% | 14.0 KiB/s | 5.8 KiB | 00m00s Additional repo copr_tstellar_fedora_c 100% | 5.1 KiB/s | 1.5 KiB | 00m00s Additional repo copr_fedora_llvm_team_ 100% | 5.6 KiB/s | 1.5 KiB | 00m00s Copr repository 100% | 5.6 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 0:13.28-1.fc45 fedora 99.7 KiB annobin-plugin-gcc ppc64le 0:13.28-1.fc45 fedora 785.3 KiB clang ppc64le 0:24.0.0~pre20260827.g325a853c12648a-28.fc46 copr_fedora_llvm_team_llvm_snapshots_big_merge_20260827 68.3 MiB clang-libs ppc64le 0:24.0.0~pre20260827.g325a853c12648a-28.fc46 copr_fedora_llvm_team_llvm_snapshots_big_merge_20260827 119.7 MiB clang-resource-filesystem ppc64le 0:24.0.0~pre20260827.g325a853c12648a-28.fc46 copr_fedora_llvm_team_llvm_snapshots_big_merge_20260827 15.3 KiB compiler-rt ppc64le 0:24.0.0~pre20260827.g325a853c12648a-28.fc46 copr_fedora_llvm_team_llvm_snapshots_big_merge_20260827 19.9 MiB cpp ppc64le 0:16.2.1-2.fc46 fedora 39.2 MiB expat ppc64le 0:2.8.1-2.fc45 copr_base 371.0 KiB gcc ppc64le 0:16.2.1-2.fc46 fedora 107.3 MiB gcc-c++ ppc64le 0:16.2.1-2.fc46 fedora 43.9 MiB gcc-plugin-annobin ppc64le 0:16.2.1-2.fc46 fedora 132.8 KiB glibc-devel ppc64le 0:2.44.9000-1.fc46 fedora 3.7 MiB kernel-headers ppc64le 0:7.2.0-61.fc46 fedora 7.0 MiB libasan ppc64le 0:16.2.1-2.fc46 fedora 2.2 MiB libatomic ppc64le 0:16.2.1-2.fc46 fedora 77.0 KiB libedit ppc64le 0:3.1-60.20260512cvs.fc45 copr_base 344.9 KiB libmpc ppc64le 0:1.4.1-2.fc45 fedora 281.6 KiB libomp ppc64le 0:24.0.0~pre20260827.g325a853c12648a-28.fc46 copr_fedora_llvm_team_llvm_snapshots_big_merge_20260827 3.6 MiB libstdc++-devel ppc64le 0:16.2.1-2.fc46 fedora 41.1 MiB libubsan ppc64le 0:16.2.1-2.fc46 fedora 668.9 KiB libxcrypt-devel ppc64le 0:4.5.2-4.fc45 fedora 31.0 KiB lld ppc64le 0:24.0.0~pre20260827.g325a853c12648a-28.fc46 copr_fedora_llvm_team_llvm_snapshots_big_merge_20260827 43.9 KiB lld-libs ppc64le 0:24.0.0~pre20260827.g325a853c12648a-28.fc46 copr_fedora_llvm_team_llvm_snapshots_big_merge_20260827 7.0 MiB llvm ppc64le 0:24.0.0~pre20260827.g325a853c12648a-28.fc46 copr_fedora_llvm_team_llvm_snapshots_big_merge_20260827 141.2 MiB llvm-filesystem ppc64le 0:24.0.0~pre20260827.g325a853c12648a-28.fc46 copr_fedora_llvm_team_llvm_snapshots_big_merge_20260827 0.0 B llvm-libs ppc64le 0:24.0.0~pre20260827.g325a853c12648a-28.fc46 copr_fedora_llvm_team_llvm_snapshots_big_merge_20260827 153.4 MiB make ppc64le 1:4.4.1-13.fc45 fedora 1.9 MiB mpdecimal ppc64le 0:4.0.1-4.fc45 fedora 281.1 KiB python-pip-wheel noarch 0:26.1.2-5.fc46 fedora 1.2 MiB python3 ppc64le 0:3.15.0~rc1-1.fc45 fedora 84.7 KiB python3-libs ppc64le 0:3.15.0~rc1-1.fc45 fedora 50.8 MiB tzdata noarch 0:2026c-1.fc45 fedora 1.2 MiB Transaction Summary: Installing: 33 packages Total size of inbound packages is 206 MiB. Need to download 206 MiB. After this operation, 816 MiB extra will be used (install 816 MiB, remove 0 B). [ 1/33] gcc-c++-0:16.2.1-2.fc46.ppc64le 100% | 110.4 MiB/s | 15.5 MiB | 00m00s [ 2/33] libstdc++-devel-0:16.2.1-2.fc46 100% | 115.2 MiB/s | 5.9 MiB | 00m00s [ 3/33] fedora-clang-default-cc-0:1-1.f 100% | 136.5 KiB/s | 7.4 KiB | 00m00s [ 4/33] clang-0:24.0.0~pre20260827.g325 100% | 16.0 MiB/s | 7.7 MiB | 00m00s [ 5/33] clang-libs-0:24.0.0~pre20260827 100% | 38.8 MiB/s | 29.0 MiB | 00m01s [ 6/33] gcc-0:16.2.1-2.fc46.ppc64le 100% | 74.3 MiB/s | 37.9 MiB | 00m01s [ 7/33] clang-resource-filesystem-0:24. 100% | 61.4 KiB/s | 18.1 KiB | 00m00s [ 8/33] llvm-libs-0:24.0.0~pre20260827. 100% | 29.6 MiB/s | 37.1 MiB | 00m01s [ 9/33] llvm-filesystem-0:24.0.0~pre202 100% | 38.7 KiB/s | 12.2 KiB | 00m00s [10/33] libasan-0:16.2.1-2.fc46.ppc64le 100% | 54.0 MiB/s | 553.5 KiB | 00m00s [11/33] glibc-devel-0:2.44.9000-1.fc46. 100% | 46.1 MiB/s | 708.4 KiB | 00m00s [12/33] libatomic-0:16.2.1-2.fc46.ppc64 100% | 10.7 MiB/s | 55.0 KiB | 00m00s [13/33] libubsan-0:16.2.1-2.fc46.ppc64l 100% | 68.1 MiB/s | 278.9 KiB | 00m00s [14/33] libxcrypt-devel-0:4.5.2-4.fc45. 100% | 14.8 MiB/s | 30.3 KiB | 00m00s [15/33] cpp-0:16.2.1-2.fc46.ppc64le 100% | 39.6 MiB/s | 12.8 MiB | 00m00s [16/33] lld-0:24.0.0~pre20260827.g325a8 100% | 253.6 KiB/s | 38.3 KiB | 00m00s [17/33] libomp-0:24.0.0~pre20260827.g32 100% | 5.8 MiB/s | 920.3 KiB | 00m00s [18/33] compiler-rt-0:24.0.0~pre2026082 100% | 9.9 MiB/s | 1.7 MiB | 00m00s [19/33] llvm-0:24.0.0~pre20260827.g325a 100% | 46.1 MiB/s | 37.2 MiB | 00m01s [20/33] libmpc-0:1.4.1-2.fc45.ppc64le 100% | 32.0 MiB/s | 98.3 KiB | 00m00s [21/33] make-1:4.4.1-13.fc45.ppc64le 100% | 97.9 MiB/s | 601.6 KiB | 00m00s [22/33] lld-libs-0:24.0.0~pre20260827.g 100% | 6.4 MiB/s | 1.8 MiB | 00m00s [23/33] python3-0:3.15.0~rc1-1.fc45.ppc 100% | 8.8 MiB/s | 27.1 KiB | 00m00s [24/33] python3-libs-0:3.15.0~rc1-1.fc4 100% | 120.3 MiB/s | 11.1 MiB | 00m00s [25/33] python-pip-wheel-0:26.1.2-5.fc4 100% | 97.9 MiB/s | 1.2 MiB | 00m00s [26/33] libedit-0:3.1-60.20260512cvs.fc 100% | 499.0 KiB/s | 114.8 KiB | 00m00s [27/33] mpdecimal-0:4.0.1-4.fc45.ppc64l 100% | 36.1 MiB/s | 110.9 KiB | 00m00s [28/33] tzdata-0:2026c-1.fc45.noarch 100% | 86.9 MiB/s | 712.0 KiB | 00m00s [29/33] annobin-plugin-gcc-0:13.28-1.fc 100% | 97.3 MiB/s | 697.4 KiB | 00m00s [30/33] gcc-plugin-annobin-0:16.2.1-2.f 100% | 29.9 MiB/s | 61.3 KiB | 00m00s [31/33] annobin-docs-0:13.28-1.fc45.noa 100% | 42.6 MiB/s | 87.3 KiB | 00m00s [32/33] expat-0:2.8.1-2.fc45.ppc64le 100% | 908.1 KiB/s | 131.7 KiB | 00m00s [33/33] kernel-headers-0:7.2.0-61.fc46. 100% | 58.3 KiB/s | 1.7 MiB | 00m30s >>> Status code: 404 for https://dl.fedoraproject.org/pub/fedora-secondary/development/rawhide/Everything/ppc64le/os/Packages/k/kernel-headers-7.2.0-61.fc46.ppc64le.rpm (IP: 10.16.163.85) - https://dl.fedoraproject.org/pub/fedora-secondary/development/rawhide/Everything/ppc64le/os/Packages/k/kernel-headers-7.2.0-61.fc46.ppc64le.rpm >>> Status code: 404 for https://dl.fedoraproject.org/pub/fedora-secondary/development/rawhide/Everything/ppc64le/os/Packages/k/kernel-headers-7.2.0-61.fc46.ppc64le.rpm (IP: 10.16.163.85) - https://dl.fedoraproject.org/pub/fedora-secondary/development/rawhide/Everything/ppc64le/os/Packages/k/kernel-headers-7.2.0-61.fc46.ppc64le.rpm >>> Curl error (28): Timeout was reached for https://muug.ca/mirror/fedora-secondary/development/rawhide/Everything/ppc64le/os/Packages/k/kernel-headers-7.2.0-61.fc46.ppc64le.rpm [Connection timed out after 30000 milliseconds] - https://muug.ca/mirror/fedora-secondary/development/rawhide/Everything/ppc64le/os/Packages/k/kernel-headers-7.2.0-61.fc46.ppc64le.rpm -------------------------------------------------------------------------------- [33/33] Total 100% | 6.4 MiB/s | 205.8 MiB | 00m32s Running transaction [ 1/35] Verify package files 100% | 9.0 B/s | 33.0 B | 00m04s [ 2/35] Prepare transaction 100% | 178.0 B/s | 33.0 B | 00m00s [ 3/35] Installing libmpc-0:1.4.1-2.fc4 100% | 39.5 MiB/s | 283.3 KiB | 00m00s [ 4/35] Installing clang-resource-files 100% | 2.3 MiB/s | 16.7 KiB | 00m00s [ 5/35] Installing libstdc++-devel-0:16 100% | 127.8 MiB/s | 41.3 MiB | 00m00s [ 6/35] Installing compiler-rt-0:24.0.0 100% | 156.7 MiB/s | 19.9 MiB | 00m00s [ 7/35] Installing cpp-0:16.2.1-2.fc46. 100% | 103.8 MiB/s | 39.2 MiB | 00m00s [ 8/35] Installing annobin-docs-0:13.28 100% | 7.6 MiB/s | 100.8 KiB | 00m00s [ 9/35] Installing tzdata-0:2026c-1.fc4 100% | 10.7 MiB/s | 1.5 MiB | 00m00s [10/35] Installing mpdecimal-0:4.0.1-4. 100% | 55.2 MiB/s | 282.7 KiB | 00m00s [11/35] Installing expat-0:2.8.1-2.fc45 100% | 5.9 MiB/s | 373.1 KiB | 00m00s [12/35] Installing python-pip-wheel-0:2 100% | 56.7 MiB/s | 1.2 MiB | 00m00s [13/35] Installing python3-libs-0:3.15. 100% | 92.9 MiB/s | 51.2 MiB | 00m01s [14/35] Installing python3-0:3.15.0~rc1 100% | 1.5 MiB/s | 86.4 KiB | 00m00s [15/35] Installing libedit-0:3.1-60.202 100% | 56.4 MiB/s | 346.6 KiB | 00m00s [16/35] Installing make-1:4.4.1-13.fc45 100% | 23.9 MiB/s | 1.9 MiB | 00m00s [17/35] Installing kernel-headers-0:7.2 100% | 52.6 MiB/s | 7.1 MiB | 00m00s [18/35] Installing glibc-devel-0:2.44.9 100% | 59.7 MiB/s | 3.8 MiB | 00m00s [19/35] Installing libxcrypt-devel-0:4. 100% | 10.8 MiB/s | 33.3 KiB | 00m00s [20/35] Installing libubsan-0:16.2.1-2. 100% | 93.4 MiB/s | 669.7 KiB | 00m00s [21/35] Installing libatomic-0:16.2.1-2 100% | 25.4 MiB/s | 78.2 KiB | 00m00s [22/35] Installing libasan-0:16.2.1-2.f 100% | 114.1 MiB/s | 2.2 MiB | 00m00s [23/35] Installing gcc-0:16.2.1-2.fc46. 100% | 120.9 MiB/s | 107.3 MiB | 00m01s [24/35] Installing gcc-c++-0:16.2.1-2.f 100% | 110.2 MiB/s | 44.0 MiB | 00m00s [25/35] Installing llvm-filesystem-0:24 100% | 531.2 KiB/s | 1.1 KiB | 00m00s [26/35] Installing llvm-libs-0:24.0.0~p 100% | 129.5 MiB/s | 153.4 MiB | 00m01s [27/35] Installing clang-libs-0:24.0.0~ 100% | 137.0 MiB/s | 119.7 MiB | 00m01s [28/35] Installing clang-0:24.0.0~pre20 100% | 149.4 MiB/s | 68.3 MiB | 00m00s [29/35] Installing llvm-0:24.0.0~pre202 100% | 126.0 MiB/s | 141.3 MiB | 00m01s [30/35] Installing libomp-0:24.0.0~pre2 100% | 121.7 MiB/s | 3.7 MiB | 00m00s [31/35] Installing lld-libs-0:24.0.0~pr 100% | 132.5 MiB/s | 7.0 MiB | 00m00s [32/35] Installing lld-0:24.0.0~pre2026 100% | 731.6 KiB/s | 46.8 KiB | 00m00s [33/35] Installing fedora-clang-default 100% | 140.6 KiB/s | 288.0 B | 00m00s [34/35] Installing annobin-plugin-gcc-0 100% | 28.5 MiB/s | 787.0 KiB | 00m00s [35/35] Installing gcc-plugin-annobin-0 100% | 399.0 KiB/s | 134.5 KiB | 00m00s Warning: skipped OpenPGP checks for 13 packages from repositories: copr_base, copr_fedora_llvm_team_llvm_snapshots_big_merge_20260827, 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.ppc64le alternatives-1.33-6.fc45.ppc64le annobin-docs-13.28-1.fc45.noarch annobin-plugin-gcc-13.28-1.fc45.ppc64le ansible-srpm-macros-1-22.fc45.noarch audit-libs-4.2.1-2.fc45.ppc64le bash-5.3.15-2.fc46.ppc64le binutils-2.47-1.fc45.ppc64le build-reproducibility-srpm-macros-0.7.3-3.fc45.noarch bzip2-1.0.8-24.fc45.ppc64le bzip2-libs-1.0.8-24.fc45.ppc64le ca-certificates-2025.2.80_v9.0.304-9.fc45.noarch clang-24.0.0~pre20260827.g325a853c12648a-28.fc46.ppc64le clang-libs-24.0.0~pre20260827.g325a853c12648a-28.fc46.ppc64le clang-resource-filesystem-24.0.0~pre20260827.g325a853c12648a-28.fc46.ppc64le cmake-srpm-macros-4.3.0-5.fc45.noarch compiler-rt-24.0.0~pre20260827.g325a853c12648a-28.fc46.ppc64le coreutils-9.11-6.fc45.ppc64le coreutils-common-9.11-6.fc45.ppc64le cpio-2.15-10.fc45.ppc64le cpp-16.2.1-2.fc46.ppc64le crypto-policies-20260713-2.gitc42da77.fc45.noarch curl-8.22.0~rc3-1.fc46.ppc64le cyrus-sasl-lib-2.1.28-37.fc45.ppc64le debugedit-5.3-3.fc45.ppc64le diffutils-3.12-6.fc45.ppc64le dwz-0.17-3.fc45.ppc64le ed-1.22.6-1.fc46.ppc64le efi-srpm-macros-6-9.fc45.noarch elfutils-0.196-1.fc46.ppc64le elfutils-debuginfod-client-0.196-1.fc46.ppc64le elfutils-libelf-0.196-1.fc46.ppc64le elfutils-libs-0.196-1.fc46.ppc64le erlang-srpm-macros-0.3.11-2.fc45.noarch expat-2.8.1-2.fc45.ppc64le 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-5.47-3.fc45.ppc64le file-libs-5.47-3.fc45.ppc64le filesystem-3.18-59.fc45.ppc64le filesystem-srpm-macros-3.18-59.fc45.noarch findutils-4.11.0-2.fc45.ppc64le fips-provider-1.5.2-3.fc45.ppc64le fonts-srpm-macros-5.0.0-4.fc45.noarch forge-srpm-macros-0.4.0-5.fc45.noarch fpc-srpm-macros-1.3-17.fc45.noarch gap-srpm-macros-2-3.fc45.noarch gawk-5.4.1-1.fc45.ppc64le gcc-16.2.1-2.fc46.ppc64le gcc-c++-16.2.1-2.fc46.ppc64le gcc-plugin-annobin-16.2.1-2.fc46.ppc64le gdb-minimal-17.2-4.fc45.ppc64le gdbm-libs-1.23-12.fc45.ppc64le ghc-srpm-macros-1.10-2.fc45.noarch glibc-2.44.9000-1.fc46.ppc64le glibc-common-2.44.9000-1.fc46.ppc64le glibc-devel-2.44.9000-1.fc46.ppc64le glibc-gconv-extra-2.44.9000-1.fc46.ppc64le glibc-minimal-langpack-2.44.9000-1.fc46.ppc64le gmp-6.3.0-6.fc45.ppc64le gnat-srpm-macros-7-3.fc45.noarch gnome-srpm-macros-1.0-2.fc45.noarch gnulib-l10n-20241231-4.fc45.noarch gnupg2-2.4.9-18.fc45.ppc64le gnupg2-dirmngr-2.4.9-18.fc45.ppc64le gnupg2-gpg-agent-2.4.9-18.fc45.ppc64le gnupg2-gpgconf-2.4.9-18.fc45.ppc64le gnupg2-keyboxd-2.4.9-18.fc45.ppc64le gnupg2-verify-2.4.9-18.fc45.ppc64le gnutls-3.8.13-3.fc45.ppc64le 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.ppc64le gzip-1.14-4.fc45.ppc64le ima-evm-utils-libs-1.6.2-12.fc45.ppc64le info-7.3-3.fc45.ppc64le jansson-2.14-5.fc45.ppc64le java-srpm-macros-1-9.fc45.noarch json-c-0.18-9.fc45.ppc64le kernel-headers-7.2.0-61.fc46.ppc64le kernel-srpm-macros-1.0-30.fc45.noarch keyutils-libs-1.6.3-8.fc45.ppc64le krb5-libs-1.22.2-9.fc45.ppc64le libacl-2.4.0-2.fc45.ppc64le libarchive-3.8.9-1.fc46.ppc64le libasan-16.2.1-2.fc46.ppc64le libassuan-2.5.7-6.fc45.ppc64le libatomic-16.2.1-2.fc46.ppc64le libattr-2.6.0-2.fc45.ppc64le libblkid-2.42.2-3.fc45.ppc64le libbrotli-1.2.0-6.fc45.ppc64le libcap-2.78-2.fc45.ppc64le libcap-ng-0.9.5-1.fc46.ppc64le libcbor-0.14.0-3.fc45.ppc64le libcom_err-1.47.4-2.fc45.ppc64le libcurl-8.22.0~rc3-1.fc46.ppc64le libeconf-0.7.9-4.fc45.ppc64le libedit-3.1-60.20260512cvs.fc45.ppc64le libevent-2.1.12-19.fc45.ppc64le libfdisk-2.42.2-3.fc45.ppc64le libffi-3.5.2-3.fc45.ppc64le libfido2-1.17.0-5.fc45.ppc64le libfsverity-1.7-4.fc45.ppc64le libgcc-16.2.1-2.fc46.ppc64le libgcrypt-1.12.3-1.fc46.ppc64le libgomp-16.2.1-2.fc46.ppc64le libgpg-error-1.61-2.fc45.ppc64le libidn2-2.3.8-4.fc45.ppc64le libksba-1.8.1-1.fc46.ppc64le liblastlog2-2.42.2-3.fc45.ppc64le libmount-2.42.2-3.fc45.ppc64le libmpc-1.4.1-2.fc45.ppc64le libnghttp2-1.69.0-5.fc45.ppc64le libnghttp3-1.18.0-1.fc46.ppc64le libomp-24.0.0~pre20260827.g325a853c12648a-28.fc46.ppc64le libpkgconf-2.5.1-2.fc45.ppc64le libpsl-0.23.1-1.fc45.ppc64le librtas-2.0.7-2.fc45.ppc64le libselinux-3.11-4.fc45.ppc64le libselinux-utils-3.11-4.fc45.ppc64le libsemanage-3.11-3.fc45.ppc64le libsepol-3.11-2.fc45.ppc64le libsmartcols-2.42.2-3.fc45.ppc64le libssh-0.12.2-1.fc45.ppc64le libssh-config-0.12.2-1.fc45.noarch libstdc++-16.2.1-2.fc46.ppc64le libstdc++-devel-16.2.1-2.fc46.ppc64le libtasn1-4.21.0-2.fc45.ppc64le libtool-ltdl-2.5.4-11.fc45.ppc64le libubsan-16.2.1-2.fc46.ppc64le libunistring-1.1-12.fc45.ppc64le libusb1-1.0.30-2.fc45.ppc64le libuuid-2.42.2-3.fc45.ppc64le libverto-0.3.2-13.fc45.ppc64le libxcrypt-4.5.2-4.fc45.ppc64le libxcrypt-devel-4.5.2-4.fc45.ppc64le libxml2-2.13.9-4.fc45.ppc64le libzstd-1.5.7-6.fc45.ppc64le linkdupes-0.7.3-3.fc45.ppc64le lld-24.0.0~pre20260827.g325a853c12648a-28.fc46.ppc64le lld-libs-24.0.0~pre20260827.g325a853c12648a-28.fc46.ppc64le llvm-24.0.0~pre20260827.g325a853c12648a-28.fc46.ppc64le llvm-filesystem-24.0.0~pre20260827.g325a853c12648a-28.fc46.ppc64le llvm-libs-24.0.0~pre20260827.g325a853c12648a-28.fc46.ppc64le lua-libs-5.5.1-2.fc46.ppc64le lua-srpm-macros-1-18.fc45.noarch lz4-libs-1.10.0-5.fc45.ppc64le make-4.4.1-13.fc45.ppc64le mpdecimal-4.0.1-4.fc45.ppc64le mpfr-4.2.2-4.fc45.ppc64le ncurses-base-6.6-3.fc45.noarch ncurses-libs-6.6-3.fc45.ppc64le nettle-4.0-5.fc45.ppc64le ngtcp2-1.22.1-3.fc45.ppc64le ngtcp2-crypto-ossl-1.22.1-3.fc45.ppc64le npth-1.8-5.fc45.ppc64le ocaml-srpm-macros-11-4.fc45.noarch openblas-srpm-macros-2-22.fc45.noarch openldap-2.6.14-1.fc46.ppc64le openssl-libs-4.0.2-1.fc46.ppc64le p11-kit-0.26.5-1.fc45.ppc64le p11-kit-trust-0.26.5-1.fc45.ppc64le package-notes-srpm-macros-0.20-2.fc45.noarch pam-libs-1.7.2-4.fc45.ppc64le patch-2.8-5.fc45.ppc64le pcre2-10.47-1.fc45.2.ppc64le pcre2-syntax-10.47-1.fc45.2.noarch perl-srpm-macros-1-65.fc45.noarch pkgconf-2.5.1-2.fc45.ppc64le pkgconf-m4-2.5.1-2.fc45.noarch pkgconf-pkg-config-2.5.1-2.fc45.ppc64le policycoreutils-3.11-2.fc45.ppc64le popt-1.19-11.fc45.ppc64le publicsuffix-list-dafsa-20260624-2.fc45.noarch pyproject-srpm-macros-1.23.2-1.fc45.noarch python-pip-wheel-26.1.2-5.fc46.noarch python-srpm-macros-3.15-2.fc45.noarch python3-3.15.0~rc1-1.fc45.ppc64le python3-libs-3.15.0~rc1-1.fc45.ppc64le qt5-srpm-macros-5.15.18-3.fc45.noarch qt6-srpm-macros-6.11.2-1.fc46.noarch readline-8.3-6.fc45.ppc64le redhat-rpm-config-344-5.fc45.noarch redhat-systemd-presets-102-3.fc45.noarch redhat-systemd-presets-common-102-3.fc45.noarch rpm-6.1.0-1.fc46.ppc64le rpm-build-6.1.0-1.fc46.ppc64le rpm-build-libs-6.1.0-1.fc46.ppc64le rpm-libs-6.1.0-1.fc46.ppc64le rpm-plugin-selinux-6.1.0-1.fc46.ppc64le rpm-sequoia-1.10.2-5.fc45.ppc64le rpm-sign-libs-6.1.0-1.fc46.ppc64le rust-srpm-macros-28.5-2.fc45.noarch sed-4.10-2.fc45.ppc64le selinux-policy-45.15-1.fc46.noarch selinux-policy-targeted-45.15-1.fc46.noarch setup-2.15.1-2.fc45.noarch shadow-utils-4.20.0-1.fc45.ppc64le sqlite-libs-3.53.4-1.fc45.ppc64le systemd-libs-261.2-1.fc45.ppc64le systemd-standalone-sysusers-261.2-1.fc45.ppc64le tar-1.35-9.fc45.ppc64le tpm2-tss-4.2.0-1.fc45.ppc64le tree-sitter-srpm-macros-0.4.6-2.fc45.noarch tzdata-2026c-1.fc45.noarch unzip-6.0-71.fc45.ppc64le util-linux-2.42.2-3.fc45.ppc64le util-linux-core-2.42.2-3.fc45.ppc64le which-2.25-2.fc46.ppc64le xxhash-libs-0.8.3-5.fc45.ppc64le xz-5.8.3-2.fc46.ppc64le xz-libs-5.8.3-2.fc46.ppc64le zig-srpm-macros-1-9.fc45.noarch zip-3.0-46.fc45.ppc64le zlib-ng-compat-2.3.3-6.fc45.ppc64le zstd-1.5.7-6.fc45.ppc64le Start: buildsrpm Start: rpmbuild -bs Building target platforms: ppc64le Building for target ppc64le 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-ppc64le-1788249070.975671/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-730uyvce/htslib/htslib.spec) Config(child) 7 minutes 40 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot INFO: Start(/var/lib/copr-rpmbuild/results/htslib-1.24-1.fc46.src.rpm) Config(fedora-rawhide-ppc64le) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-ppc64le-bootstrap-1788249070.975671/root. INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-ppc64le-bootstrap-1788249070.975671/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-ppc64le-1788249070.975671/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.ppc64le rpm-sequoia-1.10.2-5.fc45.ppc64le dnf5-5.4.3.0-2.fc46.ppc64le dnf5-plugins-5.4.3.0-2.fc46.ppc64le 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: ppc64le Building for target ppc64le setting SOURCE_DATE_EPOCH=1784246400 Wrote: /builddir/build/SRPMS/htslib-1.24-1.fc46.src.rpm Updating and loading repositories: fedora 100% | 15.3 KiB/s | 5.8 KiB | 00m00s Additional repo copr_tstellar_fedora_c 100% | 6.3 KiB/s | 1.5 KiB | 00m00s Additional repo copr_fedora_llvm_team_ 100% | 5.7 KiB/s | 1.5 KiB | 00m00s Copr repository 100% | 6.3 KiB/s | 1.5 KiB | 00m00s Repositories loaded. Package "gcc-16.2.1-2.fc46.ppc64le" is already installed. Package "make-1:4.4.1-13.fc45.ppc64le" is already installed. Package Arch Version Repository Size Installing: bzip2-devel ppc64le 0:1.0.8-24.fc45 fedora 309.8 KiB libcurl-devel ppc64le 0:8.22.0~rc3-1.fc46 fedora 1.4 MiB openssl-devel ppc64le 1:4.0.2-1.fc46 fedora 4.6 MiB perl-Data-Dumper ppc64le 0:2.192-528.fc45 fedora 135.2 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 ppc64le 4:5.44.0-527.fc45 fedora 175.7 KiB perl-lib ppc64le 0:0.65-527.fc45 fedora 8.5 KiB xz-devel ppc64le 1:5.8.3-2.fc46 copr_base 258.8 KiB zlib-ng-compat-devel ppc64le 0:2.3.3-6.fc45 fedora 107.0 KiB Installing dependencies: brotli ppc64le 0:1.2.0-6.fc45 fedora 69.4 KiB brotli-devel ppc64le 0:1.2.0-6.fc45 fedora 65.9 KiB cmake-filesystem ppc64le 0:4.3.0-5.fc45 fedora 0.0 B groff-base ppc64le 0:1.24.1-2.fc45 fedora 4.8 MiB keyutils-libs-devel ppc64le 0:1.6.3-8.fc45 copr_base 48.2 KiB krb5-devel ppc64le 0:1.22.2-9.fc45 fedora 709.9 KiB libcom_err-devel ppc64le 0:1.47.4-2.fc45 fedora 16.7 KiB libidn2-devel ppc64le 0:2.3.8-4.fc45 fedora 152.1 KiB libkadm5 ppc64le 0:1.22.2-9.fc45 fedora 329.6 KiB libnghttp2-devel ppc64le 0:1.69.0-5.fc45 fedora 288.0 KiB libnghttp3-devel ppc64le 0:1.18.0-1.fc46 copr_base 119.4 KiB libpsl-devel ppc64le 0:0.23.1-1.fc45 fedora 111.5 KiB libselinux-devel ppc64le 0:3.11-4.fc45 fedora 121.9 KiB libsepol-devel ppc64le 0:3.11-2.fc45 fedora 120.7 KiB libssh-devel ppc64le 0:0.12.2-1.fc45 fedora 204.2 KiB libverto-devel ppc64le 0:0.3.2-13.fc45 fedora 25.7 KiB libzstd-devel ppc64le 0:1.5.7-6.fc45 copr_base 217.6 KiB ncurses ppc64le 0:6.6-3.fc45 fedora 958.6 KiB ngtcp2-crypto-ossl-devel ppc64le 0:1.22.1-3.fc45 fedora 7.5 KiB ngtcp2-devel ppc64le 0:1.22.1-3.fc45 fedora 262.8 KiB pcre2-devel ppc64le 0:10.47-1.fc45.2 copr_base 2.1 MiB pcre2-utf16 ppc64le 0:10.47-1.fc45.2 copr_base 774.4 KiB pcre2-utf32 ppc64le 0:10.47-1.fc45.2 copr_base 774.2 KiB perl-AutoLoader noarch 0:5.74-527.fc45 fedora 20.6 KiB perl-B ppc64le 0:1.92-527.fc45 fedora 557.4 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 ppc64le 0:2.59-527.fc45 fedora 103.2 KiB perl-DynaLoader ppc64le 0:1.57-527.fc45 fedora 32.1 KiB perl-Encode ppc64le 4:3.24-527.fc45 fedora 4.8 MiB perl-Errno ppc64le 0:1.39-527.fc45 fedora 8.4 KiB perl-Exporter noarch 0:5.79-527.fc45 fedora 54.2 KiB perl-Fcntl ppc64le 0:1.20-527.fc45 fedora 92.3 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 ppc64le 0:1.56-527.fc45 fedora 191.0 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 ppc64le 0:3.16-527.fc45 fedora 93.5 KiB perl-Net-SSLeay ppc64le 0:1.96-5.fc45 fedora 1.5 MiB perl-POSIX ppc64le 0:2.26-527.fc45 fedora 326.1 KiB perl-PathTools ppc64le 0:3.95-527.fc45 fedora 223.8 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 ppc64le 5:1.70-527.fc45 fedora 152.5 KiB perl-SelectSaver noarch 0:1.03-527.fc45 fedora 2.1 KiB perl-Socket ppc64le 4:2.043-1.fc46 fedora 145.4 KiB perl-Storable ppc64le 1:3.41-527.fc45 fedora 242.8 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 ppc64le 4:1.9780-527.fc45 fedora 151.3 KiB perl-Time-Local noarch 2:1.350-527.fc45 fedora 69.0 KiB perl-URI noarch 0:5.36-1.fc46 fedora 275.3 KiB perl-Unicode-Normalize ppc64le 0:1.32-527.fc45 fedora 524.3 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 ppc64le 4:5.44.0-527.fc45 fedora 12.8 MiB perl-locale noarch 0:1.13-527.fc45 fedora 6.1 KiB perl-mro ppc64le 0:1.30-527.fc45 fedora 81.1 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 1:6.1.0-2.fc45 fedora 324.7 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 15 MiB. After this operation, 45 MiB extra will be used (install 45 MiB, remove 0 B). [ 1/90] perl-Data-Dumper-0:2.192-528.fc 100% | 7.1 MiB/s | 58.2 KiB | 00m00s [ 2/90] perl-Getopt-Long-1:2.58-527.fc4 100% | 10.3 MiB/s | 63.2 KiB | 00m00s [ 3/90] bzip2-devel-0:1.0.8-24.fc45.ppc 100% | 34.7 MiB/s | 213.5 KiB | 00m00s [ 4/90] perl-FindBin-0:1.54-527.fc45.no 100% | 4.5 MiB/s | 13.9 KiB | 00m00s [ 5/90] perl-lib-0:0.65-527.fc45.ppc64l 100% | 7.1 MiB/s | 14.5 KiB | 00m00s [ 6/90] perl-interpreter-4:5.44.0-527.f 100% | 17.8 MiB/s | 72.7 KiB | 00m00s [ 7/90] zlib-ng-compat-devel-0:2.3.3-6. 100% | 18.4 MiB/s | 37.7 KiB | 00m00s [ 8/90] libcurl-devel-0:8.22.0~rc3-1.fc 100% | 61.4 MiB/s | 1.0 MiB | 00m00s [ 9/90] perl-Carp-0:1.54-527.fc45.noarc 100% | 5.6 MiB/s | 28.6 KiB | 00m00s [10/90] perl-Exporter-0:5.79-527.fc45.n 100% | 14.9 MiB/s | 30.6 KiB | 00m00s [11/90] perl-Scalar-List-Utils-5:1.70-5 100% | 37.9 MiB/s | 77.6 KiB | 00m00s [12/90] perl-constant-0:1.33-528.fc45.n 100% | 22.2 MiB/s | 22.7 KiB | 00m00s [13/90] perl-Pod-Usage-4:2.05-527.fc45. 100% | 13.1 MiB/s | 40.4 KiB | 00m00s [14/90] perl-Text-ParseWords-0:3.31-527 100% | 7.9 MiB/s | 16.2 KiB | 00m00s [15/90] krb5-devel-0:1.22.2-9.fc45.ppc6 100% | 46.6 MiB/s | 143.2 KiB | 00m00s [16/90] ngtcp2-crypto-ossl-devel-0:1.22 100% | 11.2 MiB/s | 11.5 KiB | 00m00s [17/90] cmake-filesystem-0:4.3.0-5.fc45 100% | 14.5 MiB/s | 14.8 KiB | 00m00s [18/90] perl-libs-4:5.44.0-527.fc45.ppc 100% | 80.5 MiB/s | 2.7 MiB | 00m00s [19/90] perl-Pod-Perldoc-0:3.28.01-527. 100% | 27.6 MiB/s | 84.7 KiB | 00m00s [20/90] perl-podlators-1:6.1.0-2.fc45.n 100% | 42.9 MiB/s | 131.6 KiB | 00m00s [21/90] perl-Encode-4:3.24-527.fc45.ppc 100% | 33.8 MiB/s | 1.0 MiB | 00m00s [22/90] libkadm5-0:1.22.2-9.fc45.ppc64l 100% | 11.9 MiB/s | 85.6 KiB | 00m00s [23/90] libverto-devel-0:0.3.2-13.fc45. 100% | 13.8 MiB/s | 14.2 KiB | 00m00s [24/90] ngtcp2-devel-0:1.22.1-3.fc45.pp 100% | 23.7 MiB/s | 48.5 KiB | 00m00s [25/90] perl-MIME-Base64-0:3.16-527.fc4 100% | 14.9 MiB/s | 30.5 KiB | 00m00s [26/90] perl-parent-1:0.244-527.fc45.no 100% | 14.4 MiB/s | 14.7 KiB | 00m00s [27/90] perl-Storable-1:3.41-527.fc45.p 100% | 33.3 MiB/s | 102.2 KiB | 00m00s [28/90] perl-Fcntl-0:1.20-527.fc45.ppc6 100% | 29.1 MiB/s | 29.8 KiB | 00m00s [29/90] perl-File-Temp-1:0.231.200-527. 100% | 28.9 MiB/s | 59.3 KiB | 00m00s [30/90] perl-HTTP-Tiny-0:0.096-528.fc45 100% | 28.5 MiB/s | 58.4 KiB | 00m00s [31/90] perl-IO-0:1.56-527.fc45.ppc64le 100% | 40.7 MiB/s | 83.4 KiB | 00m00s [32/90] perl-PathTools-0:3.95-527.fc45. 100% | 43.1 MiB/s | 88.4 KiB | 00m00s [33/90] perl-Pod-Simple-1:3.48-527.fc45 100% | 54.2 MiB/s | 222.0 KiB | 00m00s [34/90] perl-POSIX-0:2.26-527.fc45.ppc6 100% | 56.9 MiB/s | 116.6 KiB | 00m00s [35/90] perl-Term-ANSIColor-0:5.01-527. 100% | 46.2 MiB/s | 47.3 KiB | 00m00s [36/90] perl-Term-Cap-0:1.18-527.fc45.n 100% | 21.2 MiB/s | 21.7 KiB | 00m00s [37/90] perl-Errno-0:1.39-527.fc45.ppc6 100% | 14.2 MiB/s | 14.6 KiB | 00m00s [38/90] perl-B-0:1.92-527.fc45.ppc64le 100% | 60.2 MiB/s | 184.9 KiB | 00m00s [39/90] perl-File-Path-0:2.18-527.fc45. 100% | 34.0 MiB/s | 34.8 KiB | 00m00s [40/90] perl-IO-Socket-SSL-0:2.099-2.fc 100% | 57.7 MiB/s | 236.2 KiB | 00m00s [41/90] perl-Net-SSLeay-0:1.96-5.fc45.p 100% | 54.4 MiB/s | 390.1 KiB | 00m00s [42/90] perl-Socket-4:2.043-1.fc46.ppc6 100% | 18.3 MiB/s | 56.2 KiB | 00m00s [43/90] perl-Time-HiRes-4:1.9780-527.fc 100% | 28.1 MiB/s | 57.5 KiB | 00m00s [44/90] perl-Time-Local-2:1.350-527.fc4 100% | 16.7 MiB/s | 34.2 KiB | 00m00s [45/90] perl-Pod-Escapes-1:1.07-527.fc4 100% | 9.5 MiB/s | 19.6 KiB | 00m00s [46/90] perl-Text-Tabs+Wrap-0:2024.001- 100% | 21.0 MiB/s | 21.5 KiB | 00m00s [47/90] perl-IO-Socket-IP-0:0.44-527.fc 100% | 20.5 MiB/s | 42.0 KiB | 00m00s [48/90] perl-MIME-Base32-0:1.303-26.fc4 100% | 10.0 MiB/s | 20.4 KiB | 00m00s [49/90] perl-URI-0:5.36-1.fc46.noarch 100% | 49.1 MiB/s | 150.9 KiB | 00m00s [50/90] perl-Unicode-Normalize-0:1.32-5 100% | 36.1 MiB/s | 73.9 KiB | 00m00s [51/90] perl-libnet-0:3.15-528.fc45.noa 100% | 62.7 MiB/s | 128.3 KiB | 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pcre2-utf32-0:10.47-1.fc45.2.pp 100% | 2.0 MiB/s | 244.2 KiB | 00m00s -------------------------------------------------------------------------------- [90/90] Total 100% | 31.3 MiB/s | 15.2 MiB | 00m00s Running transaction [ 1/92] Verify package files 100% | 350.0 B/s | 90.0 B | 00m00s [ 2/92] Prepare transaction 100% | 333.0 B/s | 90.0 B | 00m00s [ 3/92] Installing cmake-filesystem-0:4 100% | 1.3 MiB/s | 9.4 KiB | 00m00s [ 4/92] Installing libidn2-devel-0:2.3. 100% | 5.2 MiB/s | 159.8 KiB | 00m00s [ 5/92] Installing openssl-devel-1:4.0. 100% | 16.5 MiB/s | 5.6 MiB | 00m00s [ 6/92] Installing ngtcp2-devel-0:1.22. 100% | 64.5 MiB/s | 264.1 KiB | 00m00s [ 7/92] Installing ngtcp2-crypto-ossl-d 100% | 7.9 MiB/s | 8.1 KiB | 00m00s [ 8/92] Installing zlib-ng-compat-devel 100% | 53.0 MiB/s | 108.6 KiB | 00m00s [ 9/92] Installing libzstd-devel-0:1.5. 100% | 71.3 MiB/s | 219.1 KiB | 00m00s [10/92] Installing pcre2-utf32-0:10.47- 100% | 108.1 MiB/s | 775.1 KiB | 00m00s [11/92] Installing 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Building target platforms: ppc64le Building for target ppc64le setting SOURCE_DATE_EPOCH=1784246400 Wrote: /builddir/build/SRPMS/htslib-1.24-1.fc46.src.rpm Updating and loading repositories: fedora 100% | 13.9 KiB/s | 5.8 KiB | 00m00s Additional repo copr_tstellar_fedora_c 100% | 4.9 KiB/s | 1.5 KiB | 00m00s Additional repo copr_fedora_llvm_team_ 100% | 5.4 KiB/s | 1.5 KiB | 00m00s Copr repository 100% | 5.4 KiB/s | 1.5 KiB | 00m00s Repositories loaded. Package "bzip2-devel-1.0.8-24.fc45.ppc64le" is already installed. Package "gcc-16.2.1-2.fc46.ppc64le" is already installed. Package "libcurl-devel-8.22.0~rc3-1.fc46.ppc64le" is already installed. Package "make-1:4.4.1-13.fc45.ppc64le" is already installed. Package "openssl-devel-1:4.0.2-1.fc46.ppc64le" is already installed. Package "perl-Data-Dumper-2.192-528.fc45.ppc64le" 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.ppc64le" is already installed. Package "perl-interpreter-4:5.44.0-527.fc45.ppc64le" is already installed. Package "xz-devel-1:5.8.3-2.fc46.ppc64le" is already installed. Package "zlib-ng-compat-devel-2.3.3-6.fc45.ppc64le" 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: ppc64le Building for target ppc64le setting SOURCE_DATE_EPOCH=1784246400 Executing(mkbuilddir): /bin/sh -e /var/tmp/rpm-tmp.JbNjH3 Creating(rpmbuild.env): /builddir/build/BUILD/htslib-1.24-build/rpmbuild.env RPM_SOURCE_DIR="/builddir/build/SOURCES" RPM_BUILD_DIR="/builddir/build/BUILD/htslib-1.24-build" RPM_OPT_FLAGS="-O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection" 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="ppc64le" RPM_OS="linux" RPM_BUILD_NCPUS="5" 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.RAswEl + 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.EnC3Qg + umask 022 + cd /builddir/build/BUILD/htslib-1.24-build + CFLAGS='-O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CFLAGS + CXXFLAGS='-O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CXXFLAGS + FFLAGS='-O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=clang + export CC + CXX=clang++ + export CXX + cd htslib-1.24 + CFLAGS='-O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CFLAGS + CXXFLAGS='-O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CXXFLAGS + FFLAGS='-O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none --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 $(dirname ./configure) -name config.guess -o -name config.sub) ++ basename ./config.sub + '[' -f /usr/lib/rpm/redhat/config.sub ']' + /usr/bin/rm -f ./config.sub ++ basename ./config.sub + /usr/bin/cp -fv /usr/lib/rpm/redhat/config.sub ./config.sub '/usr/lib/rpm/redhat/config.sub' -> './config.sub' + '[' 1 = 1 ']' + '[' x '!=' 'x-Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg' ']' ++ find . -name ltmain.sh ++ grep -q runstatedir=DIR ./configure ++ echo --runstatedir=/run + ./configure --build=ppc64le-redhat-linux --host=ppc64le-redhat-linux --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/bin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/libexec --localstatedir=/var --runstatedir=/run --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info 'CFLAGS=-O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection' 'LDFLAGS=-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 ' --prefix=/usr --libdir=/usr/lib64 --enable-plugins '--with-plugin-path=/usr/local/libexec/htslib:$(plugindir)' --enable-gcs --enable-libcurl --enable-s3 configure: WARNING: unrecognized options: --disable-dependency-tracking checking for ppc64le-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 ppc64le-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 ppc64le-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 ppc64le-redhat-linux... plain .so checking whether the linker supports versioned symbols... yes checking whether the compiler accepts -fvisibility=hidden... yes checking build system type... powerpc64le-redhat-linux-gnu checking host system type... powerpc64le-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... no checking whether the compiler accepts -fno-delete-null-pointer-checks... yes checking whether the compiler accepts -Wl,-z,noexecstack... yes checking whether the compiler accepts -Wl,-z,relro... yes checking whether the compiler accepts -Wl,-z,now... yes checking whether the compiler accepts -Wl,--as-needed... yes checking whether the compiler accepts -Wl,--no-copy-dt-needed-entries... yes checking whether the compiler accepts -Wl,-z,nodlopen... yes checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating htslib.pc.tmp config.status: creating config.h config.status: linking htscodecs_bundled.mk to htscodecs.mk configure: WARNING: unrecognized options: --disable-dependency-tracking + /usr/bin/make -O -j5 V=1 VERBOSE=1 clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o kfunc.o kfunc.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o errmod.o errmod.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o kstring.o kstring.c kstring.c:468:10: warning: returning 'const void *' from a function with result type 'void *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] 468 | return memchr(str, pat[0], n); | ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/string.h:122:3: note: expanded from macro 'memchr' 122 | __glibc_const_generic (S, const void *, memchr (S, C, N)) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/sys/cdefs.h:847:3: note: expanded from macro '__glibc_const_generic' 847 | _Generic (0 ? (PTR) : (void *) 1, \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 848 | const void *: (CTYPE) (CALL), \ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 849 | default: CALL) | ~~~~~~~~~~~~~~ 1 warning generated. clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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. echo '#define HTS_VERSION_TEXT "1.24"' > version.h printf '#define HTS_CC "%s"\n#define HTS_CPPFLAGS "%s"\n#define HTS_CFLAGS "%s"\n#define HTS_LDFLAGS "%s"\n#define HTS_LIBS "%s"\n' \ 'clang -std=gnu23' \ '' \ '-O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden' \ '-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic' \ '-llzma -lbz2 -lz -lm ' > config_vars.h clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o bcf_sr_sort.o bcf_sr_sort.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o hts_os.o hts_os.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o bgzf.o bgzf.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o hfile.o hfile.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o md5.o md5.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o hts_expr.o hts_expr.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o multipart.o multipart.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o probaln.o probaln.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o region.o region.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o realn.o realn.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o simd.o simd.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o regidx.o regidx.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o sam_mods.o sam_mods.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o header.o header.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o vcf_sweep.o vcf_sweep.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o textutils.o textutils.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o thread_pool.o thread_pool.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o tbx.o tbx.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o synced_bcf_reader.o synced_bcf_reader.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/cram_codecs.o cram/cram_codecs.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o vcfutils.o vcfutils.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/cram_decode.o cram/cram_decode.c cram/cram_decode.c:1234:31: warning: initializing 'char *' with an expression of type 'const void *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] 1234 | char *N = memchr(refp, 'N', frag_len); | ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1 warning generated. clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/cram_external.o cram/cram_external.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/cram_index.o cram/cram_index.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/cram_stats.o cram/cram_stats.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o sam.o sam.c sam.c:5222:15: warning: assigning to 'char *' from 'const char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] 5222 | if ((opts = strchr(format, ','))) { | ^ ~~~~~~~~~~~~~~~~~~~ 1 warning generated. clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/mFILE.o cram/mFILE.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/open_trace_file.o cram/open_trace_file.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/string_alloc.o cram/string_alloc.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/cram_encode.o cram/cram_encode.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/cram_io.o cram/cram_io.c cram/cram_io.c:2323:11: warning: initializing 'char *' with an expression of type 'const char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] 2323 | char *fn_delim = strstr(fn, HTS_IDX_DELIM); | ^ ~~~~~~~~~~~~~~~~~~~~~~~~~ cram/cram_io.c:5070:29: warning: assigning to 'char *' from 'const char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] 5070 | fd->prefix = strdup((cp = strrchr(filename, '/')) ? cp+1 : filename); | ^ ~~~~~~~~~~~~~~~~~~~~~~ 2 warnings generated. clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr_neon.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o vcf.o vcf.c vcf.c:168:17: warning: assigning to 'char *' from 'const char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] 168 | if (!(major = strstr(version, vcf))) { //bad format | ^ ~~~~~~~~~~~~~~~~~~~~ 1 warning generated. clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c htscodecs/htscodecs/rANS_static4x16pr.c:807:12: warning: variable 'rans_cpu' set but not used [-Wunused-but-set-global] 807 | static int rans_cpu = 0xFFFF; // all | ^ 1 warning generated. clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/utils.o htscodecs/htscodecs/utils.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static32x16pr.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o kfunc.pico kfunc.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -DPLUGINPATH=\"/usr/local/libexec/htslib:/usr/libexec/htslib\" -c -o plugin.o plugin.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o errmod.pico errmod.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o kstring.pico kstring.c kstring.c:468:10: warning: returning 'const void *' from a function with result type 'void *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] 468 | return memchr(str, pat[0], n); | ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/string.h:122:3: note: expanded from macro 'memchr' 122 | __glibc_const_generic (S, const void *, memchr (S, C, N)) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/sys/cdefs.h:847:3: note: expanded from macro '__glibc_const_generic' 847 | _Generic (0 ? (PTR) : (void *) 1, \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 848 | const void *: (CTYPE) (CALL), \ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 849 | default: CALL) | ~~~~~~~~~~~~~~ 1 warning generated. clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o faidx.pico faidx.c faidx.c:1067:15: warning: initializing 'char *' with an expression of type 'const char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] 1067 | char *fai_tmp = strstr(fa, HTS_IDX_DELIM); | ^ ~~~~~~~~~~~~~~~~~~~~~~~~~ 1 warning generated. clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o bcf_sr_sort.pico bcf_sr_sort.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o bgzf.pico bgzf.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o hts_os.pico hts_os.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o hfile.pico hfile.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o md5.pico md5.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o multipart.pico multipart.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o hts_expr.pico hts_expr.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o probaln.pico probaln.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o realn.pico realn.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o region.pico region.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o header.pico header.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o simd.pico simd.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o regidx.pico regidx.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o vcf_sweep.pico vcf_sweep.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o sam_mods.pico sam_mods.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o textutils.pico textutils.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o tbx.pico tbx.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o thread_pool.pico thread_pool.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o synced_bcf_reader.pico synced_bcf_reader.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o hts.pico hts.c hts.c:942:25: warning: initializing 'char *' with an expression of type 'const char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] 942 | char *rmme = NULL, *fnidx = strstr(fn, HTS_IDX_DELIM); | ^ ~~~~~~~~~~~~~~~~~~~~~~~~~ hts.c:1478:13: warning: assigning to 'char *' from 'const char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] 1478 | if ((cp = strchr(mode, ','))) { | ^ ~~~~~~~~~~~~~~~~~ hts.c:4929:11: warning: initializing 'char *' with an expression of type 'const char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] 4929 | char *fnidx = strstr(fn, HTS_IDX_DELIM); | ^ ~~~~~~~~~~~~~~~~~~~~~~~~~ 3 warnings generated. clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o cram/cram_codecs.pico cram/cram_codecs.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o vcfutils.pico vcfutils.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o cram/cram_external.pico cram/cram_external.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o cram/cram_decode.pico cram/cram_decode.c cram/cram_decode.c:1234:31: warning: initializing 'char *' with an expression of type 'const void *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] 1234 | char *N = memchr(refp, 'N', frag_len); | ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1 warning generated. clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o cram/cram_index.pico cram/cram_index.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o sam.pico sam.c sam.c:5222:15: warning: assigning to 'char *' from 'const char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] 5222 | if ((opts = strchr(format, ','))) { | ^ ~~~~~~~~~~~~~~~~~~~ 1 warning generated. clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o cram/cram_stats.pico cram/cram_stats.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o cram/mFILE.pico cram/mFILE.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o cram/open_trace_file.pico cram/open_trace_file.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o cram/pooled_alloc.pico cram/pooled_alloc.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o cram/string_alloc.pico cram/string_alloc.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o cram/cram_encode.pico cram/cram_encode.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/htscodecs.pico htscodecs/htscodecs/htscodecs.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o cram/cram_io.pico cram/cram_io.c cram/cram_io.c:2323:11: warning: initializing 'char *' with an expression of type 'const char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] 2323 | char *fn_delim = strstr(fn, HTS_IDX_DELIM); | ^ ~~~~~~~~~~~~~~~~~~~~~~~~~ cram/cram_io.c:5070:29: warning: assigning to 'char *' from 'const char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] 5070 | fd->prefix = strdup((cp = strrchr(filename, '/')) ? cp+1 : filename); | ^ ~~~~~~~~~~~~~~~~~~~~~~ 2 warnings generated. clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/pack.pico htscodecs/htscodecs/pack.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o vcf.pico vcf.c vcf.c:168:17: warning: assigning to 'char *' from 'const char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] 168 | if (!(major = strstr(version, vcf))) { //bad format | ^ ~~~~~~~~~~~~~~~~~~~~ 1 warning generated. clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr_neon.pico htscodecs/htscodecs/rANS_static32x16pr_neon.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/arith_dynamic.pico htscodecs/htscodecs/arith_dynamic.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rle.pico htscodecs/htscodecs/rle.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rANS_static.pico htscodecs/htscodecs/rANS_static.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/utils.pico htscodecs/htscodecs/utils.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rANS_static4x16pr.pico htscodecs/htscodecs/rANS_static4x16pr.c htscodecs/htscodecs/rANS_static4x16pr.c:807:12: warning: variable 'rans_cpu' set but not used [-Wunused-but-set-global] 807 | static int rans_cpu = 0xFFFF; // all | ^ 1 warning generated. clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/fqzcomp_qual.pico htscodecs/htscodecs/fqzcomp_qual.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -DPLUGINPATH=\"/usr/local/libexec/htslib:/usr/libexec/htslib\" -fpic -c -o plugin.pico plugin.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr.pico htscodecs/htscodecs/rANS_static32x16pr.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/tokenise_name3.pico htscodecs/htscodecs/tokenise_name3.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o htsfile.o htsfile.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o hfile_gcs.pico hfile_gcs.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o bgzip.o bgzip.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o tabix.o tabix.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o annot-tsv.o annot-tsv.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/fieldarith.o test/fieldarith.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/hts_endian.o test/hts_endian.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/pileup.o test/pileup.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/hfile.o test/hfile.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/plugins-dlhts.o test/plugins-dlhts.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/pileup_mod.o test/pileup_mod.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_alloc.o test/test_alloc.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o hfile_libcurl.pico hfile_libcurl.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_faidx.o test/test_faidx.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_kfunc.o test/test_kfunc.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_bgzf.o test/test_bgzf.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_expr.o test/test_expr.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_mod.o test/test_mod.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/sam.o test/sam.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_khash.o test/test_khash.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_realn.o test/test_realn.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o hfile_s3.pico hfile_s3.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_nibbles.o test/test_nibbles.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_time_funcs.o test/test_time_funcs.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test-regidx.o test/test-regidx.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_str2int.o test/test_str2int.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_index.o test/test_index.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_view.o test/test_view.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_kstring.o test/test_kstring.c In file included from test/test_kstring.c:38: test/../kstring.c:468:10: warning: returning 'const void *' from a function with result type 'void *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] 468 | return memchr(str, pat[0], n); | ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/string.h:122:3: note: expanded from macro 'memchr' 122 | __glibc_const_generic (S, const void *, memchr (S, C, N)) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/sys/cdefs.h:847:3: note: expanded from macro '__glibc_const_generic' 847 | _Generic (0 ? (PTR) : (void *) 1, \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 848 | const void *: (CTYPE) (CALL), \ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 849 | default: CALL) | ~~~~~~~~~~~~~~ 1 warning generated. clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/fuzz/hts_open_fuzzer.o test/fuzz/hts_open_fuzzer.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test-bcf-translate.o test/test-bcf-translate.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test-bcf-sr.o test/test-bcf-sr.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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 clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test-parse-reg.o test/test-parse-reg.c sed -e "s#@-includedir@#`pwd`#g;s#@-libdir@#`pwd`#g" htslib.pc.tmp > htslib-uninstalled.pc clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fno-delete-null-pointer-checks -I. -c -o ref_cache/cmsg_wrap.o ref_cache/cmsg_wrap.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test-vcf-api.o test/test-vcf-api.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_hfile_libcurl.o test/test_hfile_libcurl.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fno-delete-null-pointer-checks -I. -c -o ref_cache/listener.o ref_cache/listener.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fno-delete-null-pointer-checks -I. -c -o ref_cache/misc.o ref_cache/misc.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fno-delete-null-pointer-checks -I. -c -o ref_cache/log_files.o ref_cache/log_files.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fno-delete-null-pointer-checks -I. -c -o ref_cache/http_parser.o ref_cache/http_parser.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fno-delete-null-pointer-checks -I. -c -o ref_cache/poll_wrap_poll.o ref_cache/poll_wrap_poll.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fno-delete-null-pointer-checks -I. -c -o ref_cache/poll_wrap_epoll.o ref_cache/poll_wrap_epoll.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fno-delete-null-pointer-checks -I. -c -o ref_cache/ping.o ref_cache/ping.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fno-delete-null-pointer-checks -I. -c -o ref_cache/sendfile_wrap.o ref_cache/sendfile_wrap.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fno-delete-null-pointer-checks -I. -c -o ref_cache/ref_files.o ref_cache/ref_files.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fno-delete-null-pointer-checks -I. -c -o ref_cache/request_handler.o ref_cache/request_handler.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fno-delete-null-pointer-checks -I. -c -o ref_cache/main.o ref_cache/main.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fno-delete-null-pointer-checks -I. -c -o ref_cache/transaction.o ref_cache/transaction.c clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fno-delete-null-pointer-checks -I. -c -o ref_cache/server.o ref_cache/server.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 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 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -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/test_time_funcs test/test_time_funcs.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 -Wl,-z,noexecstack -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-copy-dt-needed-entries -Wl,-z,nodlopen -o ref_cache/ref-cache ref_cache/cmsg_wrap.o ref_cache/http_parser.o ref_cache/listener.o ref_cache/log_files.o ref_cache/main.o ref_cache/misc.o ref_cache/ping.o ref_cache/poll_wrap_epoll.o ref_cache/poll_wrap_poll.o ref_cache/ref_files.o ref_cache/request_handler.o ref_cache/sendfile_wrap.o ref_cache/server.o ref_cache/transaction.o ref_cache/upstream.o cram/pooled_alloc.o md5.o -lcurl clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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 bgzip bgzip.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 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 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/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/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_khash test/test_khash.o libhts.a -llzma -lbz2 -lz -lm -lpthread clang -std=gnu23 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o test/test_bgzf test/test_bgzf.o libhts.a -llzma -lbz2 -lz -lm -lpthread clang -std=gnu23 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o test/test_expr test/test_expr.o libhts.a -llzma -lbz2 -lz -lm -lpthread clang -std=gnu23 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o test/test_faidx test/test_faidx.o libhts.a -llzma -lbz2 -lz -lm -lpthread clang -std=gnu23 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o test/test_mod test/test_mod.o libhts.a -llzma -lbz2 -lz -lm -lpthread clang -std=gnu23 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o test/test_nibbles test/test_nibbles.o libhts.a -llzma -lbz2 -lz -lm -lpthread clang -std=gnu23 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o test/test_realn test/test_realn.o libhts.a -llzma -lbz2 -lz -lm -lpthread clang -std=gnu23 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o test/test-regidx test/test-regidx.o libhts.a -llzma -lbz2 -lz -lm -lpthread clang -std=gnu23 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o test/test_str2int test/test_str2int.o libhts.a -llzma -lbz2 -lz -lm -lpthread clang -std=gnu23 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o test/test_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_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-vcf-api test/test-vcf-api.o libhts.a -llzma -lbz2 -lz -lm -lpthread clang -std=gnu23 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -llzma -lbz2 -lz -lm -lpthread clang -std=gnu23 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -llzma -lbz2 -lz -lm -lpthread clang -std=gnu23 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o test/test-parse-reg test/test-parse-reg.o libhts.a -llzma -lbz2 -lz -lm -lpthread clang -std=gnu23 -shared -Wl,-E -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o hfile_libcurl.so hfile_libcurl.pico libhts.so -llzma -lbz2 -lz -lm -lcurl -lpthread clang -std=gnu23 -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 -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_s3.so hfile_s3.pico libhts.so -llzma -lbz2 -lz -lm -lcrypto -lcurl -lpthread clang -std=gnu23 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o test/test_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.gls2ib + umask 022 + cd /builddir/build/BUILD/htslib-1.24-build + '[' /builddir/build/BUILD/htslib-1.24-build/BUILDROOT '!=' / ']' + rm -rf /builddir/build/BUILD/htslib-1.24-build/BUILDROOT ++ dirname /builddir/build/BUILD/htslib-1.24-build/BUILDROOT + mkdir -p /builddir/build/BUILD/htslib-1.24-build + mkdir /builddir/build/BUILD/htslib-1.24-build/BUILDROOT + CFLAGS='-O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CFLAGS + CXXFLAGS='-O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CXXFLAGS + FFLAGS='-O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none --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 ~/build/BUILD/htslib-1.24-build/BUILDROOT/usr/lib64 ~/build/BUILD/htslib-1.24-build/htslib-1.24 + pushd /builddir/build/BUILD/htslib-1.24-build/BUILDROOT//usr/lib64 + chmod 755 libhts.so.1.24 ~/build/BUILD/htslib-1.24-build/htslib-1.24 + popd + 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 -j5 --strict-build-id -m -i --build-id-seed 1.24-1.fc46 --unique-debug-suffix -1.24-1.fc46.ppc64le --unique-debug-src-base htslib-1.24-1.fc46.ppc64le --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.ppc64le.debug: Unknown debugging section .debug_addr dwz: ./usr/bin/bgzip-1.24-1.fc46.ppc64le.debug: Unknown debugging section .debug_addr dwz: ./usr/bin/htsfile-1.24-1.fc46.ppc64le.debug: Unknown debugging section .debug_addr dwz: ./usr/bin/ref-cache-1.24-1.fc46.ppc64le.debug: Unknown debugging section .debug_addr dwz: ./usr/bin/tabix-1.24-1.fc46.ppc64le.debug: Unknown debugging section .debug_addr dwz: ./usr/lib64/libhts.so.1.24-1.24-1.fc46.ppc64le.debug: Unknown debugging section .debug_addr dwz: ./usr/libexec/htslib/hfile_gcs.so-1.24-1.fc46.ppc64le.debug: Unknown debugging section .debug_addr dwz: ./usr/libexec/htslib/hfile_libcurl.so-1.24-1.fc46.ppc64le.debug: Unknown debugging section .debug_addr dwz: ./usr/libexec/htslib/hfile_s3.so-1.24-1.fc46.ppc64le.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.ppc64le 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 -j5 + /usr/lib/rpm/redhat/brp-python-hardlink + /usr/bin/add-det --brp -j5 /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.5RFR3u + umask 022 + cd /builddir/build/BUILD/htslib-1.24-build + CFLAGS='-O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CFLAGS + CXXFLAGS='-O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CXXFLAGS + FFLAGS='-O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=clang + export CC + CXX=clang++ + export CXX + cd htslib-1.24 + make test sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' htslib.pc.tmp > htslib_static.mk sed -e "s#@-includedir@#`pwd`#g;s#@-libdir@#`pwd`#g" htslib.pc.tmp > htslib-uninstalled.pc clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -Ihtscodecs -c -o htscodecs/tests/rANS_static_test.o htscodecs/tests/rANS_static_test.c clang -std=gnu23 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o htscodecs/tests/rans4x8 htscodecs/tests/rANS_static_test.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o -llzma -lbz2 -lz -lm -lm -lpthread cd htscodecs/tests && srcdir=. && export srcdir && ./rans4x8.test Testing rans4x8 -r -o0 on ./dat/q4 11674 Testing rans4x8 -r -o1 on ./dat/q4 10870 Testing rans4x8 -r -o0 on ./dat/q40+dir 50258 Testing rans4x8 -r -o1 on ./dat/q40+dir 50537 Testing rans4x8 -r -o0 on ./dat/q8 33099 Testing rans4x8 -r -o1 on ./dat/q8 31428 Testing rans4x8 -r -o0 on ./dat/qvar 32997 Testing rans4x8 -r -o1 on ./dat/qvar 32832 clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -Ihtscodecs -c -o htscodecs/tests/rANS_static4x16pr_test.o htscodecs/tests/rANS_static4x16pr_test.c clang -std=gnu23 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o htscodecs/tests/rans4x16pr htscodecs/tests/rANS_static4x16pr_test.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o -llzma -lbz2 -lz -lm -lm -lpthread cd htscodecs/tests && srcdir=. && export srcdir && ./rans4x16.test Testing rans4x16 -r -o0 on ./dat/q4 11660 Testing rans4x16 -r -o1 on ./dat/q4 10848 Testing rans4x16 -r -o64 on ./dat/q4 12878 Testing rans4x16 -r -o65 on ./dat/q4 10672 Testing rans4x16 -r -o128 on ./dat/q4 10902 Testing rans4x16 -r -o129 on ./dat/q4 10890 Testing rans4x16 -r -o192 on ./dat/q4 11225 Testing rans4x16 -r -o193 on ./dat/q4 10825 Testing rans4x16 -r -o8 on ./dat/q4 11731 Testing rans4x16 -r -o9 on ./dat/q4 11111 Testing rans4x16 -r -o4 on ./dat/q4 11746 11746 11746 11746 Testing rans4x16 -r -o5 on ./dat/q4 10932 10932 10932 10932 Testing rans4x16 -r -o0 on ./dat/q40+dir 50247 Testing rans4x16 -r -o1 on ./dat/q40+dir 49449 Testing rans4x16 -r -o8 on ./dat/q40+dir 50072 Testing rans4x16 -r -o9 on ./dat/q40+dir 50072 Testing rans4x16 -r -o4 on ./dat/q40+dir 50331 50331 50331 50331 Testing rans4x16 -r -o5 on ./dat/q40+dir 49537 49537 49537 49537 Testing rans4x16 -r -o0 on ./dat/q8 33088 Testing rans4x16 -r -o1 on ./dat/q8 31372 Testing rans4x16 -r -o64 on ./dat/q8 33458 Testing rans4x16 -r -o65 on ./dat/q8 31025 Testing rans4x16 -r -o128 on ./dat/q8 32237 Testing rans4x16 -r -o129 on ./dat/q8 31258 Testing rans4x16 -r -o192 on ./dat/q8 32024 Testing rans4x16 -r -o193 on ./dat/q8 31146 Testing rans4x16 -r -o4 on ./dat/q8 33176 33176 33176 33176 Testing rans4x16 -r -o5 on ./dat/q8 31458 31458 31458 31458 Testing rans4x16 -r -o69 on ./dat/qsimd 35 Testing rans4x16 -r -o4 on ./dat/qsimd 219 219 219 219 Testing rans4x16 -r -o5 on ./dat/qsimd 151 151 151 151 Testing rans4x16 -r -o0 on ./dat/qvar 32987 Testing rans4x16 -r -o1 on ./dat/qvar 32261 Testing rans4x16 -r -o32 on ./dat/qvar 62345 Testing rans4x16 -r -o4 on ./dat/qvar 33073 33073 33073 33073 Testing rans4x16 -r -o5 on ./dat/qvar 32353 32353 32353 32353 clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -Ihtscodecs -c -o htscodecs/tests/arith_dynamic_test.o htscodecs/tests/arith_dynamic_test.c clang -std=gnu23 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o htscodecs/tests/arith_dynamic htscodecs/tests/arith_dynamic_test.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o -llzma -lbz2 -lz -lm -lm -lpthread cd htscodecs/tests && srcdir=. && export srcdir && ./arith.test Testing arith_dynamic -r -o0 on ./dat/q4 11615 Testing arith_dynamic -r -o1 on ./dat/q4 10831 Testing arith_dynamic -r -o64 on ./dat/q4 13360 Testing arith_dynamic -r -o65 on ./dat/q4 10484 Testing arith_dynamic -r -o128 on ./dat/q4 10774 Testing arith_dynamic -r -o129 on ./dat/q4 10329 Testing arith_dynamic -r -o192 on ./dat/q4 11095 Testing arith_dynamic -r -o193 on ./dat/q4 10283 Testing arith_dynamic -r -o8 on ./dat/q4 11448 Testing arith_dynamic -r -o9 on ./dat/q4 11083 Testing arith_dynamic -r -o0 on ./dat/q40+dir 49949 Testing arith_dynamic -r -o1 on ./dat/q40+dir 49034 Testing arith_dynamic -r -o64 on ./dat/q40+dir 51242 Testing arith_dynamic -r -o65 on ./dat/q40+dir 49061 Testing arith_dynamic -r -o8 on ./dat/q40+dir 49820 Testing arith_dynamic -r -o9 on ./dat/q40+dir 49448 Testing arith_dynamic -r -o0 on ./dat/q8 32752 Testing arith_dynamic -r -o1 on ./dat/q8 31331 Testing arith_dynamic -r -o64 on ./dat/q8 35211 Testing arith_dynamic -r -o65 on ./dat/q8 30907 Testing arith_dynamic -r -o128 on ./dat/q8 32063 Testing arith_dynamic -r -o129 on ./dat/q8 31084 Testing arith_dynamic -r -o192 on ./dat/q8 32267 Testing arith_dynamic -r -o193 on ./dat/q8 30931 Testing arith_dynamic -r -o0 on ./dat/qvar 32597 Testing arith_dynamic -r -o1 on ./dat/qvar 31982 Testing arith_dynamic -r -o32 on ./dat/qvar 62345 Testing arith_dynamic -r -o64 on ./dat/qvar 33237 Testing arith_dynamic -r -o65 on ./dat/qvar 31993 Testing arith_dynamic -r -o1 on ./dat/u32 27005 Testing arith_dynamic -r -o65 on ./dat/u32 23864 Testing arith_dynamic -r -o9 on ./dat/u32 24811 Testing arith_dynamic -r -o4 on ./dat/u32 20849 clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -Ihtscodecs -c -o htscodecs/tests/tokenise_name3_test.o htscodecs/tests/tokenise_name3_test.c clang -std=gnu23 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o htscodecs/tests/tokenise_name3 htscodecs/tests/tokenise_name3_test.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o -llzma -lbz2 -lz -lm -lm -lpthread cd htscodecs/tests && srcdir=. && export srcdir && ./tok3.test Testing tokenise_name3 -r -1 on ./names/01.names 2708 Testing tokenise_name3 -r -3 on ./names/01.names 2429 Testing tokenise_name3 -r -5 on ./names/01.names 2264 Testing tokenise_name3 -r -7 on ./names/01.names 2264 Testing tokenise_name3 -r -9 on ./names/01.names 2234 Testing tokenise_name3 -r -11 on ./names/01.names 2449 Testing tokenise_name3 -r -13 on ./names/01.names 2085 Testing tokenise_name3 -r -15 on ./names/01.names 2071 Testing tokenise_name3 -r -17 on ./names/01.names 2070 Testing tokenise_name3 -r -19 on ./names/01.names 2051 Testing tokenise_name3 -r -1 on ./names/02.names 5390 Testing tokenise_name3 -r -3 on ./names/02.names 4955 Testing tokenise_name3 -r -5 on ./names/02.names 4923 Testing tokenise_name3 -r -7 on ./names/02.names 4923 Testing tokenise_name3 -r -9 on ./names/02.names 4918 Testing tokenise_name3 -r -11 on ./names/02.names 4838 Testing tokenise_name3 -r -13 on ./names/02.names 4757 Testing tokenise_name3 -r -15 on ./names/02.names 4743 Testing tokenise_name3 -r -17 on ./names/02.names 4716 Testing tokenise_name3 -r -19 on ./names/02.names 4700 Testing tokenise_name3 -r -1 on ./names/03.names 8854 Testing tokenise_name3 -r -3 on ./names/03.names 7782 Testing tokenise_name3 -r -5 on ./names/03.names 7771 Testing tokenise_name3 -r -7 on ./names/03.names 7771 Testing tokenise_name3 -r -9 on ./names/03.names 7521 Testing tokenise_name3 -r -11 on ./names/03.names 7395 Testing tokenise_name3 -r -13 on ./names/03.names 7252 Testing tokenise_name3 -r -15 on ./names/03.names 7252 Testing tokenise_name3 -r -17 on ./names/03.names 7225 Testing tokenise_name3 -r -19 on ./names/03.names 7075 Testing tokenise_name3 -r -1 on ./names/05.names 3787 Testing tokenise_name3 -r -3 on ./names/05.names 3564 Testing tokenise_name3 -r -5 on ./names/05.names 3536 Testing tokenise_name3 -r -7 on ./names/05.names 3536 Testing tokenise_name3 -r -9 on ./names/05.names 3534 Testing tokenise_name3 -r -11 on ./names/05.names 3411 Testing tokenise_name3 -r -13 on ./names/05.names 3397 Testing tokenise_name3 -r -15 on ./names/05.names 3383 Testing tokenise_name3 -r -17 on ./names/05.names 3383 Testing tokenise_name3 -r -19 on ./names/05.names 3377 Testing tokenise_name3 -r -1 on ./names/08.names 5579 Testing tokenise_name3 -r -3 on ./names/08.names 5274 Testing tokenise_name3 -r -5 on ./names/08.names 5246 Testing tokenise_name3 -r -7 on ./names/08.names 5213 Testing tokenise_name3 -r -9 on ./names/08.names 5160 Testing tokenise_name3 -r -11 on ./names/08.names 4915 Testing tokenise_name3 -r -13 on ./names/08.names 4901 Testing tokenise_name3 -r -15 on ./names/08.names 4887 Testing tokenise_name3 -r -17 on ./names/08.names 4844 Testing tokenise_name3 -r -19 on ./names/08.names 4805 Testing tokenise_name3 -r -1 on ./names/09.names 3740 Testing tokenise_name3 -r -3 on ./names/09.names 3539 Testing tokenise_name3 -r -5 on ./names/09.names 3539 Testing tokenise_name3 -r -7 on ./names/09.names 3528 Testing tokenise_name3 -r -9 on ./names/09.names 3493 Testing tokenise_name3 -r -11 on ./names/09.names 3431 Testing tokenise_name3 -r -13 on ./names/09.names 3394 Testing tokenise_name3 -r -15 on ./names/09.names 3394 Testing tokenise_name3 -r -17 on ./names/09.names 3386 Testing tokenise_name3 -r -19 on ./names/09.names 3366 Testing tokenise_name3 -r -1 on ./names/10.names 5210 Testing tokenise_name3 -r -3 on ./names/10.names 4782 Testing tokenise_name3 -r -5 on ./names/10.names 4752 Testing tokenise_name3 -r -7 on ./names/10.names 4752 Testing tokenise_name3 -r -9 on ./names/10.names 4744 Testing tokenise_name3 -r -11 on ./names/10.names 4566 Testing tokenise_name3 -r -13 on ./names/10.names 4520 Testing tokenise_name3 -r -15 on ./names/10.names 4506 Testing tokenise_name3 -r -17 on ./names/10.names 4494 Testing tokenise_name3 -r -19 on ./names/10.names 4476 Testing tokenise_name3 -r -1 on ./names/20.names 1783 Testing tokenise_name3 -r -3 on ./names/20.names 1668 Testing tokenise_name3 -r -5 on ./names/20.names 1640 Testing tokenise_name3 -r -7 on ./names/20.names 1640 Testing tokenise_name3 -r -9 on ./names/20.names 1632 Testing tokenise_name3 -r -11 on ./names/20.names 1645 Testing tokenise_name3 -r -13 on ./names/20.names 1625 Testing tokenise_name3 -r -15 on ./names/20.names 1611 Testing tokenise_name3 -r -17 on ./names/20.names 1609 Testing tokenise_name3 -r -19 on ./names/20.names 1600 Testing tokenise_name3 -r -1 on ./names/nv.names 5273 Testing tokenise_name3 -r -3 on ./names/nv.names 4968 Testing tokenise_name3 -r -5 on ./names/nv.names 4941 Testing tokenise_name3 -r -7 on ./names/nv.names 4941 Testing tokenise_name3 -r -9 on ./names/nv.names 4937 Testing tokenise_name3 -r -11 on ./names/nv.names 4864 Testing tokenise_name3 -r -13 on ./names/nv.names 4785 Testing tokenise_name3 -r -15 on ./names/nv.names 4772 Testing tokenise_name3 -r -17 on ./names/nv.names 4772 Testing tokenise_name3 -r -19 on ./names/nv.names 4767 Testing tokenise_name3 -r -1 on ./names/nv2.names 1060 Testing tokenise_name3 -r -3 on ./names/nv2.names 891 Testing tokenise_name3 -r -5 on ./names/nv2.names 863 Testing tokenise_name3 -r -7 on ./names/nv2.names 863 Testing tokenise_name3 -r -9 on ./names/nv2.names 855 Testing tokenise_name3 -r -11 on ./names/nv2.names 836 Testing tokenise_name3 -r -13 on ./names/nv2.names 799 Testing tokenise_name3 -r -15 on ./names/nv2.names 785 Testing tokenise_name3 -r -17 on ./names/nv2.names 779 Testing tokenise_name3 -r -19 on ./names/nv2.names 767 Testing tokenise_name3 -r -1 on ./names/rr.names 6605 Testing tokenise_name3 -r -3 on ./names/rr.names 6237 Testing tokenise_name3 -r -5 on ./names/rr.names 6237 Testing tokenise_name3 -r -7 on ./names/rr.names 6237 Testing tokenise_name3 -r -9 on ./names/rr.names 6230 Testing tokenise_name3 -r -11 on ./names/rr.names 6151 Testing tokenise_name3 -r -13 on ./names/rr.names 6025 Testing tokenise_name3 -r -15 on ./names/rr.names 6025 Testing tokenise_name3 -r -17 on ./names/rr.names 6023 Testing tokenise_name3 -r -19 on ./names/rr.names 5973 clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -Ihtscodecs -c -o htscodecs/tests/fqzcomp_qual_test.o htscodecs/tests/fqzcomp_qual_test.c clang -std=gnu23 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now --config=/usr/lib/rpm/redhat/redhat-hardened-clang-ld.cfg -flto=thin -ffat-lto-objects -Wl,--build-id=sha1 -fvisibility=hidden -rdynamic -o htscodecs/tests/fqzcomp_qual htscodecs/tests/fqzcomp_qual_test.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o -llzma -lbz2 -lz -lm -lm -lpthread cd htscodecs/tests && srcdir=. && export srcdir && ./fqzcomp.test clang -std=gnu23 -O2 -flto=thin -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS --config=/usr/lib/rpm/redhat/redhat-hardened-clang.cfg -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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/VOgdqi3YHK/index.bam.csi /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.sam > /tmp/VOgdqi3YHK/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -c /tmp/VOgdqi3YHK/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/VOgdqi3YHK/index.bam.bai /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.sam > /tmp/VOgdqi3YHK/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -b /tmp/VOgdqi3YHK/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/VOgdqi3YHK/index.sam.gz.csi /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.sam > /tmp/VOgdqi3YHK/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -c /tmp/VOgdqi3YHK/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/VOgdqi3YHK/index.sam.gz.bai /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.sam > /tmp/VOgdqi3YHK/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -b /tmp/VOgdqi3YHK/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/VOgdqi3YHK/index.sam.gz.csi /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index_dos.sam > /tmp/VOgdqi3YHK/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -c /tmp/VOgdqi3YHK/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/VOgdqi3YHK/index.sam.gz.bai /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index_dos.sam > /tmp/VOgdqi3YHK/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -b /tmp/VOgdqi3YHK/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view -l 0 -C -x /tmp/VOgdqi3YHK/index.cram.crai /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.sam > /tmp/VOgdqi3YHK/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index /tmp/VOgdqi3YHK/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view -p /tmp/VOgdqi3YHK/index3_rgn.sam /tmp/VOgdqi3YHK/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/VOgdqi3YHK/index3_rgnm.sam /tmp/VOgdqi3YHK/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/VOgdqi3YHK/index.bcf.csi /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.vcf > /tmp/VOgdqi3YHK/index.bcf .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -c /tmp/VOgdqi3YHK/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/VOgdqi3YHK/index.vcf.gz.csi /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.vcf > /tmp/VOgdqi3YHK/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -c /tmp/VOgdqi3YHK/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/VOgdqi3YHK/index.vcf.gz.tbi /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.vcf > /tmp/VOgdqi3YHK/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -t /tmp/VOgdqi3YHK/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/tabix /tmp/VOgdqi3YHK/index.vcf.gz##idx##/tmp/VOgdqi3YHK/index.vcf.gz.tbi 1:10000060-10000060 .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view /tmp/VOgdqi3YHK/index2.bam 1:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view /tmp/VOgdqi3YHK/index2.bam 1:2000000-2000000 .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view /tmp/VOgdqi3YHK/index2.bam 2:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view /tmp/VOgdqi3YHK/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/VOgdqi3YHK/index.bam.csi /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.sam > /tmp/VOgdqi3YHK/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -c /tmp/VOgdqi3YHK/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/VOgdqi3YHK/index.bam.bai /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.sam > /tmp/VOgdqi3YHK/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -b /tmp/VOgdqi3YHK/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/VOgdqi3YHK/index.sam.gz.csi /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.sam > /tmp/VOgdqi3YHK/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -c /tmp/VOgdqi3YHK/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/VOgdqi3YHK/index.sam.gz.bai /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.sam > /tmp/VOgdqi3YHK/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -b /tmp/VOgdqi3YHK/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/VOgdqi3YHK/index.sam.gz.csi /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index_dos.sam > /tmp/VOgdqi3YHK/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -c /tmp/VOgdqi3YHK/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/VOgdqi3YHK/index.sam.gz.bai /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index_dos.sam > /tmp/VOgdqi3YHK/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -b /tmp/VOgdqi3YHK/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/VOgdqi3YHK/index.cram.crai /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.sam > /tmp/VOgdqi3YHK/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index /tmp/VOgdqi3YHK/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view -@4 -p /tmp/VOgdqi3YHK/index3_rgn.sam /tmp/VOgdqi3YHK/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/VOgdqi3YHK/index3_rgnm.sam /tmp/VOgdqi3YHK/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/VOgdqi3YHK/index.bcf.csi /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.vcf > /tmp/VOgdqi3YHK/index.bcf .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -c /tmp/VOgdqi3YHK/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/VOgdqi3YHK/index.vcf.gz.csi /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.vcf > /tmp/VOgdqi3YHK/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -c /tmp/VOgdqi3YHK/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/VOgdqi3YHK/index.vcf.gz.tbi /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.vcf > /tmp/VOgdqi3YHK/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -t /tmp/VOgdqi3YHK/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/tabix /tmp/VOgdqi3YHK/index.vcf.gz##idx##/tmp/VOgdqi3YHK/index.vcf.gz.tbi 1:10000060-10000060 .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view /tmp/VOgdqi3YHK/index2.bam 1:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view /tmp/VOgdqi3YHK/index2.bam 1:2000000-2000000 .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view /tmp/VOgdqi3YHK/index2.bam 2:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view /tmp/VOgdqi3YHK/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/VOgdqi3YHK/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/VOgdqi3YHK/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/VOgdqi3YHK -s 74452500 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr.pl -t /tmp/VOgdqi3YHK -s 34270147 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr.pl -t /tmp/VOgdqi3YHK -s 11108528 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr.pl -t /tmp/VOgdqi3YHK -s 42233895 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr.pl -t /tmp/VOgdqi3YHK -s 8111117 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr.pl -t /tmp/VOgdqi3YHK -s 85644070 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr.pl -t /tmp/VOgdqi3YHK -s 49879942 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr.pl -t /tmp/VOgdqi3YHK -s 47881429 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr.pl -t /tmp/VOgdqi3YHK -s 69081244 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr.pl -t /tmp/VOgdqi3YHK -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/VOgdqi3YHK/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/VOgdqi3YHK/no_index_2.out 2> /tmp/VOgdqi3YHK/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/VOgdqi3YHK/no_index_3.out 2> /tmp/VOgdqi3YHK/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/VOgdqi3YHK/no_index_4.out 2> /tmp/VOgdqi3YHK/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/VOgdqi3YHK/weird-chr-names.vcf.bcf -x /tmp/VOgdqi3YHK/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/VOgdqi3YHK/range_test_1.out.vcf -r '1' --args /tmp/VOgdqi3YHK/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/VOgdqi3YHK/range_test_2.out.vcf -r '1:1-2' --args /tmp/VOgdqi3YHK/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/VOgdqi3YHK/range_test_3.out.vcf -r '1:1,1:2' --args /tmp/VOgdqi3YHK/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/VOgdqi3YHK/range_test_4.out.vcf -r '1:1-1' --args /tmp/VOgdqi3YHK/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/VOgdqi3YHK/range_test_5.out.vcf -r '{1:1}' --args /tmp/VOgdqi3YHK/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/VOgdqi3YHK/range_test_6.out.vcf -r '{1:1}:1-2' --args /tmp/VOgdqi3YHK/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/VOgdqi3YHK/range_test_7.out.vcf -r '{1:1}:1,{1:1}:2' --args /tmp/VOgdqi3YHK/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/VOgdqi3YHK/range_test_8.out.vcf -r '{1:1}:1-1' --args /tmp/VOgdqi3YHK/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/VOgdqi3YHK/range_test_9.out.vcf -r '{1:1-1}' --args /tmp/VOgdqi3YHK/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/VOgdqi3YHK/range_test_10.out.vcf -r '{1:1-1}:1-2' --args /tmp/VOgdqi3YHK/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/VOgdqi3YHK/range_test_11.out.vcf -r '{1:1-1}:1,{1:1-1}:2' --args /tmp/VOgdqi3YHK/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/VOgdqi3YHK/range_test_12.out.vcf -r '{1:1-1}:1-1' --args /tmp/VOgdqi3YHK/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/VOgdqi3YHK/range_test_13.out.vcf -r '{1:1-1}-2' --args /tmp/VOgdqi3YHK/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/VOgdqi3YHK/range_test_14.out.vcf -t '1' --args /tmp/VOgdqi3YHK/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/VOgdqi3YHK/range_test_15.out.vcf -t '1:1-2' --args /tmp/VOgdqi3YHK/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/VOgdqi3YHK/range_test_16.out.vcf -t '1:1,1:2' --args /tmp/VOgdqi3YHK/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/VOgdqi3YHK/range_test_17.out.vcf -t '1:1-1' --args /tmp/VOgdqi3YHK/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/VOgdqi3YHK/range_test_18.out.vcf -t '{1:1}' --args /tmp/VOgdqi3YHK/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/VOgdqi3YHK/range_test_19.out.vcf -t '{1:1}:1-2' --args /tmp/VOgdqi3YHK/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/VOgdqi3YHK/range_test_20.out.vcf -t '{1:1}:1,{1:1}:2' --args /tmp/VOgdqi3YHK/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/VOgdqi3YHK/range_test_21.out.vcf -t '{1:1}:1-1' --args /tmp/VOgdqi3YHK/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/VOgdqi3YHK/range_test_22.out.vcf -t '{1:1-1}' --args /tmp/VOgdqi3YHK/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/VOgdqi3YHK/range_test_23.out.vcf -t '{1:1-1}:1-2' --args /tmp/VOgdqi3YHK/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/VOgdqi3YHK/range_test_24.out.vcf -t '{1:1-1}:1,{1:1-1}:2' --args /tmp/VOgdqi3YHK/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/VOgdqi3YHK/range_test_25.out.vcf -t '{1:1-1}:1-1' --args /tmp/VOgdqi3YHK/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/VOgdqi3YHK/range_test_26.out.vcf -t '{1:1-1}-2' --args /tmp/VOgdqi3YHK/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/VOgdqi3YHK/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/VOgdqi3YHK/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/VOgdqi3YHK/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.ppc64le Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.WwCGFP + 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.VfUwjn + 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(ppc-64) = 1.24-1.fc46 libhts.so.3()(64bit) libhts.so.3(HTSLIB_1.0)(64bit) libhts.so.3(HTSLIB_1.1)(64bit) libhts.so.3(HTSLIB_1.10)(64bit) libhts.so.3(HTSLIB_1.11)(64bit) libhts.so.3(HTSLIB_1.12)(64bit) libhts.so.3(HTSLIB_1.13)(64bit) libhts.so.3(HTSLIB_1.14)(64bit) libhts.so.3(HTSLIB_1.15)(64bit) libhts.so.3(HTSLIB_1.16)(64bit) libhts.so.3(HTSLIB_1.17)(64bit) libhts.so.3(HTSLIB_1.18)(64bit) libhts.so.3(HTSLIB_1.2.1)(64bit) libhts.so.3(HTSLIB_1.20)(64bit) libhts.so.3(HTSLIB_1.21)(64bit) libhts.so.3(HTSLIB_1.22)(64bit) libhts.so.3(HTSLIB_1.23)(64bit) libhts.so.3(HTSLIB_1.24)(64bit) libhts.so.3(HTSLIB_1.3)(64bit) libhts.so.3(HTSLIB_1.4)(64bit) libhts.so.3(HTSLIB_1.5)(64bit) libhts.so.3(HTSLIB_1.6)(64bit) libhts.so.3(HTSLIB_1.7)(64bit) libhts.so.3(HTSLIB_1.9)(64bit) Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: libbz2.so.1()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.17)(64bit) libc.so.6(GLIBC_2.32)(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.ppc64le Provides: htslib-devel = 1.24-1.fc46 htslib-devel(ppc-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.ppc64le Provides: htslib-tools = 1.24-1.fc46 htslib-tools(ppc-64) = 1.24-1.fc46 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: libbz2.so.1()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.17)(64bit) libc.so.6(GLIBC_2.32)(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.ppc64le Provides: htslib-debugsource = 1.24-1.fc46 htslib-debugsource(ppc-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.ppc64le Provides: debuginfo(build-id) = 63dffbc4e06697c66ae22a9bef9526f42186f09b debuginfo(build-id) = a8ad9c0b330cf5b3fe0224827cea225bff072a8a debuginfo(build-id) = b89ac5d14bd0abdb97a162045d2d405b837ec164 debuginfo(build-id) = d4e97c3c388e29573b7d363b3995ac9fa7882c6c htslib-debuginfo = 1.24-1.fc46 htslib-debuginfo(ppc-64) = 1.24-1.fc46 libhts.so.1.24-1.24-1.fc46.ppc64le.debug()(64bit) Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: htslib-debugsource(ppc-64) = 1.24-1.fc46 Processing files: htslib-tools-debuginfo-1.24-1.fc46.ppc64le Provides: debuginfo(build-id) = 1f849ea36e9f7a3cfc66dff2a5c5cf9ec7c19902 debuginfo(build-id) = 3d8f04520dcbfc40d891ac36df8af483e2785cb1 debuginfo(build-id) = 772795052f20f7c8731774a1a0ca082e0be2b92a debuginfo(build-id) = ae033b280f9cd9fee8ae0baab4c9dccc05e4ef25 debuginfo(build-id) = d638129186219b969352556bc876ee1627b1a45b htslib-tools-debuginfo = 1.24-1.fc46 htslib-tools-debuginfo(ppc-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(ppc-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-1.24-1.fc46.ppc64le.rpm Wrote: /builddir/build/RPMS/htslib-devel-1.24-1.fc46.ppc64le.rpm Wrote: /builddir/build/RPMS/htslib-debuginfo-1.24-1.fc46.ppc64le.rpm Wrote: /builddir/build/RPMS/htslib-tools-1.24-1.fc46.ppc64le.rpm Wrote: /builddir/build/RPMS/htslib-debugsource-1.24-1.fc46.ppc64le.rpm Wrote: /builddir/build/RPMS/htslib-tools-debuginfo-1.24-1.fc46.ppc64le.rpm Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.fALjPt + 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-ppc64le-1788249070.975671/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) 3 minutes 39 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-debugsource", "epoch": null, "version": "1.24", "release": "1.fc46", "arch": "ppc64le" }, { "name": "htslib-devel", "epoch": null, "version": "1.24", "release": "1.fc46", "arch": "ppc64le" }, { "name": "htslib", "epoch": null, "version": "1.24", "release": "1.fc46", "arch": "ppc64le" }, { "name": "htslib-tools-debuginfo", "epoch": null, "version": "1.24", "release": "1.fc46", "arch": "ppc64le" }, { "name": "htslib-tools", "epoch": null, "version": "1.24", "release": "1.fc46", "arch": "ppc64le" }, { "name": "htslib", "epoch": null, "version": "1.24", "release": "1.fc46", "arch": "src" }, { "name": "htslib-debuginfo", "epoch": null, "version": "1.24", "release": "1.fc46", "arch": "ppc64le" } ] } RPMResults finished