Warning: Permanently added '13.121.85.98' (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/11056539-fedora-rawhide-s390x --chroot fedora-rawhide-s390x Version: 1.10 PID: 4976 Logging PID: 4978 Task: {'allow_user_ssh': False, 'appstream': False, 'background': False, 'build_id': 11056539, 'buildroot_pkgs': [], 'chroot': 'fedora-rawhide-s390x', 'enable_net': False, 'fedora_review': False, 'git_hash': '71e306aa0b6f916b8c2cb70aaecb597c76fcf13b', 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/jjames/HTS/htslib', 'isolation': 'default', 'memory_reqs': 2048, 'package_name': 'htslib', 'package_version': '1.24-2', 'project_dirname': 'HTS', 'project_name': 'HTS', 'project_owner': 'jjames', 'repo_priority': None, 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/jjames/HTS/fedora-rawhide-s390x/', 'id': 'copr_base', 'name': 'Copr repository', 'priority': None, 'repo_gpgcheck': False}], 'sandbox': 'jjames/HTS--jjames', 'source_json': {}, 'source_type': None, 'ssh_public_keys': None, 'storage': 1, 'submitter': 'jjames', 'tags': [], 'task_id': '11056539-fedora-rawhide-s390x', 'timeout': 18000, 'uses_devel_repo': False, 'with_opts': [], 'without_opts': []} Running: git clone https://copr-dist-git.fedorainfracloud.org/git/jjames/HTS/htslib /var/lib/copr-rpmbuild/workspace/workdir-g9haodi1/htslib --depth 500 --no-single-branch --recursive cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/jjames/HTS/htslib', '/var/lib/copr-rpmbuild/workspace/workdir-g9haodi1/htslib', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-g9haodi1/htslib'... Running: git checkout 71e306aa0b6f916b8c2cb70aaecb597c76fcf13b -- cmd: ['git', 'checkout', '71e306aa0b6f916b8c2cb70aaecb597c76fcf13b', '--'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-g9haodi1/htslib rc: 0 stdout: stderr: Note: switching to '71e306aa0b6f916b8c2cb70aaecb597c76fcf13b'. 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 71e306a automatic import of htslib Running: dist-git-client sources cmd: ['dist-git-client', 'sources'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-g9haodi1/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/jjames/HTS/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 4.20M 0 00:01 00:01 1.46M INFO: Reading stdout from command: md5sum htslib-1.24.tar.bz2 tail: /var/lib/copr-rpmbuild/main.log: file truncated Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-g9haodi1/htslib/htslib.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-g9haodi1/htslib --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1790798737.214009 -r /var/lib/copr-rpmbuild/results/configs/child.cfg 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-g9haodi1/htslib/htslib.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-g9haodi1/htslib --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1790798737.214009 -r /var/lib/copr-rpmbuild/results/configs/child.cfg Start(bootstrap): init plugins INFO: tmpfs initialized INFO: selinux enabled INFO: chroot_scan: initialized INFO: compress_logs: initialized Finish(bootstrap): init plugins Start: init plugins INFO: tmpfs initialized INFO: selinux enabled INFO: chroot_scan: initialized INFO: compress_logs: initialized Finish: init plugins INFO: Signal handler active Start: run INFO: Start(/var/lib/copr-rpmbuild/workspace/workdir-g9haodi1/htslib/htslib.spec) Config(fedora-rawhide-s390x) 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-s390x-bootstrap-1790798737.214009/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-58ce7db7-8fa6-487c-a684-4faedd75e412 INFO: Checking that 0b7f0e01e843e61ebd7d5c58ff1954422b525ff6e47aba27fbb047d81a29127d image matches host's architecture INFO: Copy content of container 0b7f0e01e843e61ebd7d5c58ff1954422b525ff6e47aba27fbb047d81a29127d to /var/lib/mock/fedora-rawhide-s390x-bootstrap-1790798737.214009/root INFO: mounting 0b7f0e01e843e61ebd7d5c58ff1954422b525ff6e47aba27fbb047d81a29127d with podman image mount INFO: image 0b7f0e01e843e61ebd7d5c58ff1954422b525ff6e47aba27fbb047d81a29127d as /var/lib/containers/storage/overlay/8d2e4c4ac9d6eecdcc527b6c1adea79e0b5648e4a5673963c6b860d9cc542537/merged INFO: umounting image 0b7f0e01e843e61ebd7d5c58ff1954422b525ff6e47aba27fbb047d81a29127d (/var/lib/containers/storage/overlay/8d2e4c4ac9d6eecdcc527b6c1adea79e0b5648e4a5673963c6b860d9cc542537/merged) with podman image umount INFO: Removing image mock-bootstrap-58ce7db7-8fa6-487c-a684-4faedd75e412 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-s390x-1790798737.214009/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.s390x rpm-sequoia-1.10.3-1.fc46.s390x dnf5-5.4.6.0-1.fc46.s390x dnf5-plugins-5.4.6.0-1.fc46.s390x Start: installing minimal buildroot with dnf5 Updating and loading repositories: Copr repository 100% | 1.8 KiB/s | 3.2 KiB | 00m02s fedora 100% | 2.9 MiB/s | 19.7 MiB | 00m07s Repositories loaded. Package Arch Version Repository Size Installing group/module packages: bash s390x 0:5.3.15-2.fc45 fedora 8.6 MiB bzip2 s390x 0:1.0.8-24.fc45 fedora 86.6 KiB coreutils s390x 0:9.12-1.fc46 fedora 6.5 MiB cpio s390x 0:2.15-10.fc45 fedora 1.1 MiB diffutils s390x 0:3.12-6.fc45 fedora 1.6 MiB fedora-release-common noarch 0:46-0.1 fedora 4.6 KiB findutils s390x 1:4.11.0-2.fc45 fedora 2.0 MiB gawk s390x 0:5.4.1-1.fc45 fedora 2.2 MiB glibc-minimal-langpack s390x 0:2.44.9000-2.fc46 fedora 0.0 B grep s390x 0:3.12-4.fc45 fedora 1.0 MiB gzip s390x 0:1.14-4.fc45 fedora 397.2 KiB info s390x 0:7.3-3.fc45 fedora 403.7 KiB patch s390x 0:2.8-5.fc45 fedora 238.1 KiB redhat-rpm-config noarch 0:345-4.fc46 fedora 184.2 KiB rpm-build s390x 0:6.1.0-1.fc46 fedora 302.1 KiB sed s390x 0:4.10-2.fc45 fedora 870.1 KiB shadow-utils s390x 2:4.20.0-1.fc45 fedora 3.9 MiB tar s390x 2:1.35-9.fc45 fedora 3.0 MiB unzip s390x 0:6.0-71.fc45 fedora 440.9 KiB util-linux s390x 0:2.42.4-2.fc46 fedora 3.5 MiB which s390x 0:2.25-2.fc45 fedora 83.3 KiB xz s390x 1:5.8.4-1.fc46 fedora 1.4 MiB Installing dependencies: R-srpm-macros noarch 0:1.3.7-3.fc45 fedora 3.5 KiB add-determinism s390x 0:0.7.3-3.fc45 fedora 2.3 MiB alternatives s390x 0:1.33-6.fc45 fedora 61.8 KiB ansible-srpm-macros noarch 0:1-22.fc45 fedora 35.7 KiB audit-libs s390x 0:4.2.1-2.fc45 fedora 397.8 KiB binutils s390x 0:2.47.50-11.fc46 fedora 25.0 MiB build-reproducibility-srpm-macros noarch 0:0.7.3-3.fc45 fedora 1.2 KiB bzip2-libs s390x 0:1.0.8-24.fc45 fedora 84.3 KiB ca-certificates noarch 0:2026.2.90_v9.0.317-1.fc46 fedora 2.6 MiB cmake-srpm-macros noarch 0:4.3.0-5.fc45 fedora 524.0 B coreutils-common s390x 0:9.12-1.fc46 fedora 11.5 MiB crypto-policies noarch 0:20260713-2.gitc42da77.fc45 fedora 134.3 KiB curl s390x 0:8.23.0~rc2-1.fc46 fedora 509.3 KiB cyrus-sasl-lib s390x 0:2.1.28-37.fc45 fedora 2.4 MiB debugedit s390x 0:5.3-3.fc45 fedora 224.1 KiB dwz s390x 0:0.17-3.fc45 fedora 310.4 KiB ed s390x 0:1.22.6-1.fc46 fedora 150.6 KiB efi-srpm-macros noarch 0:6-9.fc45 fedora 40.3 KiB elfutils s390x 0:0.196-1.fc46 fedora 3.0 MiB elfutils-debuginfod-client s390x 0:0.196-1.fc46 fedora 75.4 KiB elfutils-libelf s390x 0:0.196-1.fc46 fedora 1.4 MiB elfutils-libs s390x 0:0.196-1.fc46 fedora 786.2 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 s390x 0:5.48-3.fc46 fedora 101.6 KiB file-libs s390x 0:5.48-3.fc46 fedora 12.3 MiB filesystem s390x 0:3.18-59.fc45 fedora 112.0 B filesystem-srpm-macros noarch 0:3.18-59.fc45 fedora 38.2 KiB fips-provider s390x 0:1.5.3-1.fc46 fedora 4.1 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 s390x 0:17.2-6.fc46 fedora 15.9 MiB gdbm-libs s390x 1:1.23-12.fc45 fedora 125.2 KiB ghc-srpm-macros noarch 0:1.10-2.fc45 fedora 792.0 B glibc s390x 0:2.44.9000-2.fc46 fedora 5.5 MiB glibc-common s390x 0:2.44.9000-2.fc46 fedora 1.1 MiB glibc-gconv-extra s390x 0:2.44.9000-2.fc46 fedora 6.8 MiB gmp s390x 1:6.3.0-6.fc45 fedora 769.7 KiB gnat-srpm-macros noarch 0:7-3.fc45 fedora 1.0 KiB gnome-srpm-macros noarch 0:1.0-2.fc45 fedora 3.5 KiB gnulib-l10n noarch 0:20241231-4.fc45 fedora 655.0 KiB gnupg2 s390x 0:2.4.9-18.fc45 fedora 6.6 MiB gnupg2-dirmngr s390x 0:2.4.9-18.fc45 fedora 657.2 KiB gnupg2-gpg-agent s390x 0:2.4.9-18.fc45 fedora 717.4 KiB gnupg2-gpgconf s390x 0:2.4.9-18.fc45 fedora 269.1 KiB gnupg2-keyboxd s390x 0:2.4.9-18.fc45 fedora 213.0 KiB gnupg2-verify s390x 0:2.4.9-18.fc45 fedora 364.0 KiB gnutls s390x 0:3.8.13-5.fc46 fedora 3.7 MiB go-srpm-macros noarch 0:3.8.0-3.fc45 fedora 61.9 KiB gpgverify noarch 0:2.2-5.fc45 fedora 8.7 KiB ima-evm-utils-libs s390x 0:1.6.2-12.fc45 fedora 56.3 KiB jansson s390x 0:2.14-5.fc45 fedora 88.7 KiB java-srpm-macros noarch 0:1-9.fc45 fedora 870.0 B json-c s390x 0:0.18-9.fc45 fedora 82.3 KiB kernel-srpm-macros noarch 0:1.0-30.fc45 fedora 1.9 KiB keyutils-libs s390x 0:1.6.3-8.fc45 fedora 49.9 KiB krb5-libs s390x 0:1.22.2-9.fc45 fedora 2.5 MiB libacl s390x 0:2.4.0-2.fc45 fedora 43.6 KiB libarchive s390x 0:3.8.9-2.fc46 fedora 1.0 MiB libassuan s390x 0:2.5.7-6.fc45 fedora 163.6 KiB libattr s390x 0:2.6.0-2.fc45 fedora 24.1 KiB libblkid s390x 0:2.42.4-2.fc46 fedora 290.1 KiB libbrotli s390x 0:1.2.0-6.fc45 fedora 912.3 KiB libcap s390x 0:2.78-2.fc45 fedora 210.1 KiB libcap-ng s390x 0:0.9.6-1.fc46 fedora 64.3 KiB libcbor s390x 0:0.14.0-3.fc45 fedora 83.3 KiB libcom_err s390x 0:1.47.4-2.fc45 fedora 58.8 KiB libcurl s390x 0:8.23.0~rc2-1.fc46 fedora 1.1 MiB libeconf s390x 0:0.7.9-4.fc45 fedora 64.6 KiB libevent s390x 0:2.1.13-1.fc46 fedora 991.6 KiB libfdisk s390x 0:2.42.4-2.fc46 fedora 394.6 KiB libffi s390x 0:3.8.0-1.fc46 fedora 83.1 KiB libfido2 s390x 0:1.17.0-5.fc45 fedora 252.5 KiB libfsverity s390x 0:1.7-4.fc45 fedora 24.1 KiB libgcc s390x 0:16.2.1-2.fc46.1 fedora 213.6 KiB libgcrypt s390x 0:1.12.4-1.fc46 fedora 1.3 MiB libgomp s390x 0:16.2.1-2.fc46.1 fedora 576.9 KiB libgpg-error s390x 0:1.61-2.fc45 fedora 957.4 KiB libidn2 s390x 0:2.3.8-4.fc45 fedora 560.2 KiB libksba s390x 0:1.8.1-1.fc46 fedora 427.6 KiB liblastlog2 s390x 0:2.42.4-2.fc46 fedora 33.2 KiB libmount s390x 0:2.42.4-2.fc46 fedora 408.1 KiB libnghttp2 s390x 0:1.69.0-6.fc46 fedora 173.7 KiB libnghttp3 s390x 0:1.18.0-1.fc45 fedora 154.5 KiB libpkgconf s390x 0:2.5.1-2.fc45 fedora 93.7 KiB libpsl s390x 0:0.23.3-1.fc46 fedora 80.2 KiB libselinux s390x 0:3.11-5.fc46 fedora 217.0 KiB libselinux-utils s390x 0:3.11-5.fc46 fedora 269.5 KiB libsemanage s390x 0:3.11-4.fc46 fedora 320.1 KiB libsepol s390x 0:3.11-2.fc45 fedora 861.7 KiB libsmartcols s390x 0:2.42.4-2.fc46 fedora 196.1 KiB libssh s390x 0:0.12.2-1.fc45 fedora 709.1 KiB libssh-config noarch 0:0.12.2-1.fc45 fedora 277.0 B libstdc++ s390x 0:16.2.1-2.fc46.1 fedora 3.4 MiB libtasn1 s390x 0:4.21.0-2.fc45 fedora 184.4 KiB libtool-ltdl s390x 0:2.6.2-1.fc46 fedora 69.6 KiB libunistring s390x 0:1.1-12.fc45 fedora 1.8 MiB libusb1 s390x 0:1.0.30-2.fc45 fedora 175.4 KiB libuuid s390x 0:2.42.4-2.fc46 fedora 33.0 KiB libverto s390x 0:0.3.2-13.fc45 fedora 25.0 KiB libxcrypt s390x 0:4.5.2-4.fc45 fedora 289.0 KiB libxml2 s390x 0:2.15.4-1.fc46 fedora 1.7 MiB libzstd s390x 0:1.5.7-6.fc45 fedora 1.0 MiB linkdupes s390x 0:0.7.3-3.fc45 fedora 905.1 KiB lua-libs s390x 0:5.5.1-2.fc46 fedora 341.8 KiB lua-srpm-macros noarch 0:1-18.fc45 fedora 1.3 KiB lz4-libs s390x 0:1.10.0-5.fc45 fedora 197.1 KiB meson-srpm-macros noarch 0:1.12.1-2.fc46 fedora 1.7 KiB mpfr s390x 0:4.2.2-4.fc45 fedora 695.3 KiB ncurses-base noarch 0:6.6-3.fc45 fedora 329.7 KiB ncurses-libs s390x 0:6.6-3.fc45 fedora 1.0 MiB nettle s390x 0:4.0-5.fc45 fedora 849.1 KiB ngtcp2 s390x 0:1.22.1-3.fc45 fedora 316.9 KiB ngtcp2-crypto-ossl s390x 0:1.22.1-3.fc45 fedora 47.2 KiB npth s390x 0:1.8-5.fc45 fedora 45.1 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 s390x 0:2.6.14-1.fc46 fedora 676.3 KiB openssl-libs s390x 1:4.0.2-3.fc46 fedora 6.0 MiB p11-kit s390x 0:0.26.5-1.fc45 fedora 3.0 MiB p11-kit-trust s390x 0:0.26.5-1.fc45 fedora 573.6 KiB package-notes-srpm-macros noarch 0:0.20-2.fc45 fedora 1.6 KiB pam-libs s390x 0:1.7.2-4.fc45 fedora 121.8 KiB pcre2 s390x 0:10.47-1.fc45.2 fedora 725.9 KiB pcre2-syntax noarch 0:10.47-1.fc45.2 fedora 281.9 KiB perl-srpm-macros noarch 0:1-65.fc45 fedora 861.0 B pkgconf s390x 0:2.5.1-2.fc45 fedora 92.5 KiB pkgconf-m4 noarch 0:2.5.1-2.fc45 fedora 14.3 KiB pkgconf-pkg-config s390x 0:2.5.1-2.fc45 fedora 988.0 B policycoreutils s390x 0:3.11-2.fc45 fedora 866.1 KiB popt s390x 0:1.19-11.fc45 fedora 140.4 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 s390x 0:8.3-6.fc45 fedora 571.1 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 s390x 0:6.1.0-1.fc46 fedora 3.1 MiB rpm-build-libs s390x 0:6.1.0-1.fc46 fedora 283.7 KiB rpm-libs s390x 0:6.1.0-1.fc46 fedora 1.1 MiB rpm-plugin-selinux s390x 0:6.1.0-1.fc46 fedora 11.6 KiB rpm-sequoia s390x 0:1.10.3-1.fc46 fedora 2.6 MiB rpm-sign-libs s390x 0:6.1.0-1.fc46 fedora 35.4 KiB rust-srpm-macros noarch 0:28.5-2.fc45 fedora 5.5 KiB selinux-policy noarch 0:45.19-1.fc46 fedora 32.1 KiB selinux-policy-targeted noarch 0:45.19-1.fc46 fedora 19.0 MiB setup noarch 0:2.15.1-2.fc45 fedora 725.6 KiB sqlite-libs s390x 0:3.53.4-1.fc45 fedora 1.7 MiB systemd-libs s390x 0:262-1.fc46 fedora 2.7 MiB systemd-standalone-sysusers s390x 0:262-1.fc46 fedora 979.1 KiB tpm2-tss s390x 0:4.2.0-1.fc45 fedora 1.6 MiB tree-sitter-srpm-macros noarch 0:0.4.6-2.fc45 fedora 8.6 KiB util-linux-core s390x 0:2.42.4-2.fc46 fedora 1.5 MiB xxhash-libs s390x 0:0.8.4-1.fc46 fedora 61.5 KiB xz-libs s390x 1:5.8.4-1.fc46 fedora 221.2 KiB zig-srpm-macros noarch 0:1-9.fc45 fedora 1.3 KiB zip s390x 0:3.0-46.fc45 fedora 729.1 KiB zlib-ng-compat s390x 0:2.3.3-6.fc45 fedora 125.1 KiB zstd s390x 0:1.5.7-6.fc45 fedora 509.6 KiB Installing groups: Buildsystem building group Transaction Summary: Installing: 189 packages Total size of inbound packages is 70 MiB. Need to download 70 MiB. After this operation, 228 MiB extra will be used (install 228 MiB, remove 0 B). [ 1/189] bzip2-0:1.0.8-24.fc45.s390x 100% | 75.2 KiB/s | 52.8 KiB | 00m01s [ 2/189] bash-0:5.3.15-2.fc45.s390x 100% | 1.3 MiB/s | 1.9 MiB | 00m01s [ 3/189] diffutils-0:3.12-6.fc45.s390x 100% | 2.1 MiB/s | 404.8 KiB | 00m00s [ 4/189] fedora-release-common-0:46-0. 100% | 110.4 KiB/s | 18.2 KiB | 00m00s [ 5/189] cpio-0:2.15-10.fc45.s390x 100% | 275.1 KiB/s | 296.8 KiB | 00m01s [ 6/189] coreutils-0:9.12-1.fc46.s390x 100% | 731.3 KiB/s | 1.3 MiB | 00m02s [ 7/189] findutils-1:4.11.0-2.fc45.s39 100% | 2.7 MiB/s | 572.8 KiB | 00m00s [ 8/189] glibc-minimal-langpack-0:2.44 100% | 508.5 KiB/s | 127.6 KiB | 00m00s [ 9/189] grep-0:3.12-4.fc45.s390x 100% | 1.5 MiB/s | 303.7 KiB | 00m00s [ 10/189] info-0:7.3-3.fc45.s390x 100% | 1.1 MiB/s | 197.3 KiB | 00m00s [ 11/189] gzip-0:1.14-4.fc45.s390x 100% | 792.8 KiB/s | 179.2 KiB | 00m00s [ 12/189] patch-0:2.8-5.fc45.s390x 100% | 682.8 KiB/s | 120.2 KiB | 00m00s [ 13/189] redhat-rpm-config-0:345-4.fc4 100% | 400.7 KiB/s | 78.1 KiB | 00m00s [ 14/189] 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00m00s [155/189] libusb1-0:1.0.30-2.fc45.s390x 100% | 496.6 KiB/s | 79.5 KiB | 00m00s [156/189] libidn2-0:2.3.8-4.fc45.s390x 100% | 1.0 MiB/s | 176.5 KiB | 00m00s [157/189] libksba-0:1.8.1-1.fc46.s390x 100% | 330.9 KiB/s | 167.4 KiB | 00m01s [158/189] libunistring-0:1.1-12.fc45.s3 100% | 2.9 MiB/s | 556.3 KiB | 00m00s [159/189] nettle-0:4.0-5.fc45.s390x 100% | 2.4 MiB/s | 458.6 KiB | 00m00s [160/189] libevent-0:2.1.13-1.fc46.s390 100% | 1.6 MiB/s | 283.6 KiB | 00m00s [161/189] libtool-ltdl-0:2.6.2-1.fc46.s 100% | 228.1 KiB/s | 36.7 KiB | 00m00s [162/189] gdbm-libs-1:1.23-12.fc45.s390 100% | 353.7 KiB/s | 57.7 KiB | 00m00s [163/189] fedora-release-0:46-0.1.noarc 100% | 73.9 KiB/s | 11.9 KiB | 00m00s [164/189] systemd-standalone-sysusers-0 100% | 2.2 MiB/s | 424.0 KiB | 00m00s [165/189] xxhash-libs-0:0.8.4-1.fc46.s3 100% | 232.2 KiB/s | 36.7 KiB | 00m00s [166/189] gdb-minimal-0:17.2-6.fc46.s39 100% | 10.5 MiB/s | 4.8 MiB | 00m00s [167/189] fedora-release-identity-basic 100% | 80.6 KiB/s | 12.7 KiB | 00m00s [168/189] libcurl-0:8.23.0~rc2-1.fc46.s 100% | 2.7 MiB/s | 489.8 KiB | 00m00s [169/189] krb5-libs-0:1.22.2-9.fc45.s39 100% | 3.7 MiB/s | 792.9 KiB | 00m00s [170/189] libbrotli-0:1.2.0-6.fc45.s390 100% | 2.1 MiB/s | 379.3 KiB | 00m00s [171/189] cyrus-sasl-lib-0:2.1.28-37.fc 100% | 673.8 KiB/s | 813.3 KiB | 00m01s [172/189] libnghttp2-0:1.69.0-6.fc46.s3 100% | 464.1 KiB/s | 77.0 KiB | 00m00s [173/189] libnghttp3-0:1.18.0-1.fc45.s3 100% | 449.9 KiB/s | 71.5 KiB | 00m00s [174/189] libssh-0:0.12.2-1.fc45.s390x 100% | 1.6 MiB/s | 279.1 KiB | 00m00s [175/189] libpsl-0:0.23.3-1.fc46.s390x 100% | 268.6 KiB/s | 67.7 KiB | 00m00s [176/189] ngtcp2-0:1.22.1-3.fc45.s390x 100% | 946.2 KiB/s | 152.3 KiB | 00m00s [177/189] ngtcp2-crypto-ossl-0:1.22.1-3 100% | 150.9 KiB/s | 25.8 KiB | 00m00s [178/189] libcom_err-0:1.47.4-2.fc45.s3 100% | 160.4 KiB/s | 26.5 KiB | 00m00s [179/189] keyutils-libs-0:1.6.3-8.fc45. 100% | 151.2 KiB/s | 31.2 KiB | 00m00s [180/189] libverto-0:0.3.2-13.fc45.s390 100% | 119.5 KiB/s | 20.4 KiB | 00m00s [181/189] publicsuffix-list-dafsa-0:202 100% | 355.0 KiB/s | 61.1 KiB | 00m00s [182/189] libssh-config-0:0.12.2-1.fc45 100% | 55.2 KiB/s | 8.9 KiB | 00m00s [183/189] libfido2-0:1.17.0-5.fc45.s390 100% | 333.0 KiB/s | 96.6 KiB | 00m00s [184/189] libcbor-0:0.14.0-3.fc45.s390x 100% | 205.6 KiB/s | 35.8 KiB | 00m00s [185/189] selinux-policy-0:45.19-1.fc46 100% | 205.0 KiB/s | 41.0 KiB | 00m00s [186/189] libselinux-utils-0:3.11-5.fc4 100% | 643.0 KiB/s | 123.5 KiB | 00m00s [187/189] policycoreutils-0:3.11-2.fc45 100% | 532.6 KiB/s | 262.6 KiB | 00m00s [188/189] selinux-policy-targeted-0:45. 100% | 11.5 MiB/s | 6.8 MiB | 00m01s [189/189] rpm-plugin-selinux-0:6.1.0-1. 100% | 101.2 KiB/s | 17.5 KiB | 00m00s -------------------------------------------------------------------------------- [189/189] Total 100% | 3.2 MiB/s | 70.4 MiB | 00m22s 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% | 1.0 KiB/s | 189.0 B | 00m00s >>> Running %pretrans scriptlet: filesystem-0:3.18-59.fc45.s390x >>> Finished %pretrans scriptlet: filesystem-0:3.18-59.fc45.s390x >>> [RPM] failed to open /var/lib/mock/fedora-rawhide-s390x-1790798737.214009/root/etc/group for id/name lookup: No such file or directory [ 2/191] Prepare transaction 100% | 2.2 KiB/s | 189.0 B | 00m00s [ 3/191] Installing libgcc-0:16.2.1-2. 100% | 210.3 MiB/s | 215.3 KiB | 00m00s [ 4/191] Installing redhat-systemd-pre 100% | 0.0 B/s | 1.5 KiB | 00m00s [ 5/191] Installing redhat-systemd-pre 100% | 0.0 B/s | 18.1 KiB | 00m00s [ 6/191] Installing libssh-config-0:0. 100% | 0.0 B/s | 816.0 B | 00m00s [ 7/191] Installing publicsuffix-list- 100% | 0.0 B/s | 72.0 KiB | 00m00s [ 8/191] Installing fedora-release-ide 100% | 898.4 KiB/s | 920.0 B | 00m00s [ 9/191] Installing fedora-gpg-keys-0: 100% | 35.5 MiB/s | 181.7 KiB | 00m00s [ 10/191] Installing fedora-repos-rawhi 100% | 0.0 B/s | 2.5 KiB | 00m00s [ 11/191] Installing fedora-repos-0:46- 100% | 0.0 B/s | 5.9 KiB | 00m00s [ 12/191] Installing fedora-release-com 100% | 7.8 MiB/s | 8.0 KiB | 00m00s [ 13/191] Installing fedora-release-0:4 100% | 15.1 KiB/s | 124.0 B | 00m00s >>> Running sysusers scriptlet: setup-0:2.15.1-2.fc45.noarch >>> Finished sysusers scriptlet: setup-0:2.15.1-2.fc45.noarch >>> Scriptlet output: >>> Creating group 'adm' with GID 4. >>> Creating group 'audio' with GID 63. >>> Creating group 'cdrom' with GID 11. >>> Creating group 'clock' with GID 103. >>> Creating group 'dialout' with GID 18. >>> Creating group 'disk' with GID 6. >>> Creating group 'floppy' with GID 19. >>> Creating group 'ftp' with GID 50. >>> Creating group 'games' with GID 20. >>> Creating group 'input' with GID 104. >>> Creating group 'kmem' with GID 9. >>> Creating group 'kvm' with GID 36. >>> Creating group 'lock' with GID 54. >>> Creating group 'lp' with GID 7. >>> Creating group 'mail' with GID 12. >>> Creating group 'man' with GID 15. >>> Creating group 'mem' with GID 8. >>> Creating group 'nobody' with GID 65534. >>> Creating group 'render' with GID 105. >>> Creating group 'root' with GID 0. >>> Creating group 'sgx' with GID 106. >>> Creating group 'sys' with GID 3. >>> Creating group 'tape' with GID 33. >>> Creating group 'tty' with GID 5. >>> Creating group 'users' with GID 100. >>> Creating group 'utmp' with GID 22. >>> Creating group 'video' with GID 39. >>> Creating group 'wheel' with GID 10. >>> Creating user 'adm' (adm) with UID 3 and GID 4. >>> Creating group 'bin' with GID 1. >>> Creating user 'bin' (bin) with UID 1 and GID 1. >>> Creating group 'daemon' with GID 2. >>> Creating user 'daemon' (daemon) with UID 2 and GID 2. >>> Creating user 'ftp' (FTP User) with UID 14 and GID 50. >>> Creating user 'games' (games) with UID 12 and GID 100. >>> Creating user 'halt' (halt) with UID 7 and GID 0. >>> Creating user 'lp' (lp) with UID 4 and GID 7. >>> Creating user 'mail' (mail) with UID 8 and GID 12. >>> Creating user 'nobody' (Kernel Overflow User) with UID 65534 and GID 65534. >>> Creating user 'operator' (operator) with UID 11 and GID 0. >>> Creating user 'root' (Super User) with UID 0 and GID 0. >>> Creating user 'shutdown' (shutdown) with UID 6 and GID 0. >>> Creating user 'sync' (sync) with UID 5 and GID 0. >>> [ 14/191] Installing setup-0:2.15.1-2.f 100% | 28.6 MiB/s | 731.3 KiB | 00m00s >>> [RPM] /etc/hosts created as /etc/hosts.rpmnew [ 15/191] Installing filesystem-0:3.18- 100% | 2.0 MiB/s | 253.6 KiB | 00m00s [ 16/191] Installing pkgconf-m4-0:2.5.1 100% | 0.0 B/s | 14.7 KiB | 00m00s [ 17/191] Installing pcre2-syntax-0:10. 100% | 277.7 MiB/s | 284.3 KiB | 00m00s [ 18/191] Installing gnulib-l10n-0:2024 100% | 161.6 MiB/s | 661.9 KiB | 00m00s [ 19/191] Installing coreutils-common-0 100% | 275.3 MiB/s | 11.6 MiB | 00m00s [ 20/191] Installing ncurses-base-0:6.6 100% | 69.4 MiB/s | 355.3 KiB | 00m00s [ 21/191] Installing bash-0:5.3.15-2.fc 100% | 187.6 MiB/s | 8.6 MiB | 00m00s [ 22/191] Installing glibc-common-0:2.4 100% | 43.5 MiB/s | 1.1 MiB | 00m00s [ 23/191] Installing glibc-gconv-extra- 100% | 214.6 MiB/s | 6.9 MiB | 00m00s [ 24/191] Installing glibc-0:2.44.9000- 100% | 110.5 MiB/s | 5.5 MiB | 00m00s [ 25/191] Installing ncurses-libs-0:6.6 100% | 201.7 MiB/s | 1.0 MiB | 00m00s [ 26/191] Installing glibc-minimal-lang 100% | 0.0 B/s | 124.0 B | 00m00s [ 27/191] Installing zlib-ng-compat-0:2 100% | 123.0 MiB/s | 125.9 KiB | 00m00s [ 28/191] Installing bzip2-libs-0:1.0.8 100% | 83.4 MiB/s | 85.4 KiB | 00m00s [ 29/191] Installing libgpg-error-0:1.6 100% | 42.8 MiB/s | 963.3 KiB | 00m00s [ 30/191] Installing readline-0:8.3-6.f 100% | 186.6 MiB/s | 573.2 KiB | 00m00s [ 31/191] Installing libstdc++-0:16.2.1 100% | 259.3 MiB/s | 3.4 MiB | 00m00s [ 32/191] Installing libzstd-0:1.5.7-6. 100% | 251.3 MiB/s | 1.0 MiB | 00m00s [ 33/191] Installing elfutils-libelf-0: 100% | 290.1 MiB/s | 1.5 MiB | 00m00s [ 34/191] Installing libassuan-0:2.5.7- 100% | 161.5 MiB/s | 165.4 KiB | 00m00s [ 35/191] Installing libgcrypt-0:1.12.4 100% | 217.4 MiB/s | 1.3 MiB | 00m00s [ 36/191] Installing gmp-1:6.3.0-6.fc45 100% | 251.3 MiB/s | 772.0 KiB | 00m00s [ 37/191] Installing libacl-0:2.4.0-2.f 100% | 43.4 MiB/s | 44.5 KiB | 00m00s [ 38/191] Installing systemd-libs-0:262 100% | 249.8 MiB/s | 2.7 MiB | 00m00s [ 39/191] Installing libuuid-0:2.42.4-2 100% | 33.3 MiB/s | 34.1 KiB | 00m00s [ 40/191] Installing popt-0:1.19-11.fc4 100% | 71.8 MiB/s | 147.0 KiB | 00m00s [ 41/191] Installing xz-libs-1:5.8.4-1. 100% | 217.1 MiB/s | 222.3 KiB | 00m00s [ 42/191] Installing sqlite-libs-0:3.53 100% | 245.8 MiB/s | 1.7 MiB | 00m00s [ 43/191] Installing npth-0:1.8-5.fc45. 100% | 45.1 MiB/s | 46.2 KiB | 00m00s [ 44/191] Installing elfutils-libs-0:0. 100% | 192.4 MiB/s | 788.1 KiB | 00m00s [ 45/191] Installing libblkid-0:2.42.4- 100% | 142.1 MiB/s | 291.1 KiB | 00m00s [ 46/191] Installing libsepol-0:3.11-2. 100% | 210.6 MiB/s | 862.7 KiB | 00m00s [ 47/191] Installing gnupg2-gpgconf-0:2 100% | 13.2 MiB/s | 271.2 KiB | 00m00s [ 48/191] Installing pcre2-0:10.47-1.fc 100% | 236.8 MiB/s | 727.3 KiB | 00m00s [ 49/191] Installing libselinux-0:3.11- 100% | 106.6 MiB/s | 218.2 KiB | 00m00s [ 50/191] Installing grep-0:3.12-4.fc45 100% | 42.2 MiB/s | 1.0 MiB | 00m00s [ 51/191] Installing sed-0:4.10-2.fc45. 100% | 37.3 MiB/s | 878.6 KiB | 00m00s [ 52/191] Installing findutils-1:4.11.0 100% | 76.0 MiB/s | 2.0 MiB | 00m00s [ 53/191] Installing libxcrypt-0:4.5.2- 100% | 142.4 MiB/s | 291.7 KiB | 00m00s [ 54/191] Installing libtasn1-0:4.21.0- 100% | 181.9 MiB/s | 186.2 KiB | 00m00s [ 55/191] Installing libunistring-0:1.1 100% | 252.2 MiB/s | 1.8 MiB | 00m00s [ 56/191] Installing libidn2-0:2.3.8-4. 100% | 50.3 MiB/s | 566.3 KiB | 00m00s [ 57/191] Installing crypto-policies-0: 100% | 31.2 MiB/s | 159.5 KiB | 00m00s [ 58/191] Installing xz-1:5.8.4-1.fc46. 100% | 50.9 MiB/s | 1.4 MiB | 00m00s [ 59/191] Installing libmount-0:2.42.4- 100% | 199.8 MiB/s | 409.1 KiB | 00m00s [ 60/191] Installing gnupg2-verify-0:2. 100% | 17.8 MiB/s | 365.4 KiB | 00m00s [ 61/191] Installing mpfr-0:4.2.2-4.fc4 100% | 170.2 MiB/s | 697.0 KiB | 00m00s [ 62/191] Installing gawk-0:5.4.1-1.fc4 100% | 83.0 MiB/s | 2.2 MiB | 00m00s [ 63/191] Installing dwz-0:0.17-3.fc45. 100% | 15.2 MiB/s | 311.8 KiB | 00m00s [ 64/191] Installing libksba-0:1.8.1-1. 100% | 210.0 MiB/s | 430.2 KiB | 00m00s [ 65/191] Installing unzip-0:6.0-71.fc4 100% | 20.7 MiB/s | 444.5 KiB | 00m00s [ 66/191] Installing file-libs-0:5.48-3 100% | 457.2 MiB/s | 12.3 MiB | 00m00s [ 67/191] Installing file-0:5.48-3.fc46 100% | 5.3 MiB/s | 103.1 KiB | 00m00s [ 68/191] Installing diffutils-0:3.12-6 100% | 63.5 MiB/s | 1.6 MiB | 00m00s [ 69/191] Installing libattr-0:2.6.0-2. 100% | 0.0 B/s | 25.0 KiB | 00m00s [ 70/191] Installing libeconf-0:0.7.9-4 100% | 64.7 MiB/s | 66.2 KiB | 00m00s [ 71/191] Installing libcap-ng-0:0.9.6- 100% | 64.6 MiB/s | 66.2 KiB | 00m00s [ 72/191] Installing audit-libs-0:4.2.1 100% | 195.5 MiB/s | 400.4 KiB | 00m00s [ 73/191] Installing pam-libs-0:1.7.2-4 100% | 121.3 MiB/s | 124.2 KiB | 00m00s [ 74/191] Installing libcap-0:2.78-2.fc 100% | 10.5 MiB/s | 215.2 KiB | 00m00s [ 75/191] Installing libsemanage-0:3.11 100% | 157.2 MiB/s | 321.9 KiB | 00m00s [ 76/191] Installing libsmartcols-0:2.4 100% | 192.7 MiB/s | 197.3 KiB | 00m00s [ 77/191] Installing alternatives-0:1.3 100% | 3.3 MiB/s | 63.4 KiB | 00m00s [ 78/191] Installing lua-libs-0:5.5.1-2 100% | 167.6 MiB/s | 343.3 KiB | 00m00s [ 79/191] Installing libffi-0:3.8.0-1.f 100% | 82.5 MiB/s | 84.5 KiB | 00m00s [ 80/191] Installing p11-kit-0:0.26.5-1 100% | 95.8 MiB/s | 3.0 MiB | 00m00s [ 81/191] Installing p11-kit-trust-0:0. 100% | 20.1 MiB/s | 575.3 KiB | 00m00s [ 82/191] Installing json-c-0:0.18-9.fc 100% | 81.6 MiB/s | 83.5 KiB | 00m00s [ 83/191] Installing ngtcp2-0:1.22.1-3. 100% | 155.5 MiB/s | 318.4 KiB | 00m00s [ 84/191] Installing util-linux-core-0: 100% | 52.8 MiB/s | 1.5 MiB | 00m00s [ 85/191] Installing liblastlog2-0:2.42 100% | 6.9 MiB/s | 35.3 KiB | 00m00s [ 86/191] Installing zip-0:3.0-46.fc45. 100% | 29.8 MiB/s | 733.0 KiB | 00m00s [ 87/191] Installing gnupg2-keyboxd-0:2 100% | 41.8 MiB/s | 214.2 KiB | 00m00s [ 88/191] Installing libpsl-0:0.23.3-1. 100% | 79.4 MiB/s | 81.3 KiB | 00m00s [ 89/191] Installing tar-2:1.35-9.fc45. 100% | 94.4 MiB/s | 3.0 MiB | 00m00s [ 90/191] Installing linkdupes-0:0.7.3- 100% | 40.2 MiB/s | 906.5 KiB | 00m00s [ 91/191] Installing libselinux-utils-0 100% | 13.2 MiB/s | 283.7 KiB | 00m00s [ 92/191] Installing libfdisk-0:2.42.4- 100% | 193.2 MiB/s | 395.7 KiB | 00m00s [ 93/191] Installing fips-provider-0:1. 100% | 253.6 MiB/s | 4.1 MiB | 00m00s [ 94/191] Installing openssl-libs-1:4.0 100% | 259.4 MiB/s | 6.0 MiB | 00m00s [ 95/191] Installing coreutils-0:9.12-1 100% | 139.5 MiB/s | 6.6 MiB | 00m00s [ 96/191] Installing ca-certificates-0: 100% | 1.6 MiB/s | 2.5 MiB | 00m02s [ 97/191] Installing gzip-0:1.14-4.fc45 100% | 15.7 MiB/s | 402.7 KiB | 00m00s [ 98/191] Installing util-linux-0:2.42. 100% | 68.8 MiB/s | 3.6 MiB | 00m00s [ 99/191] Installing policycoreutils-0: 100% | 25.7 MiB/s | 894.4 KiB | 00m00s [100/191] Installing selinux-policy-0:4 100% | 1.5 MiB/s | 34.5 KiB | 00m00s [101/191] Installing selinux-policy-tar 100% | 162.9 MiB/s | 15.1 MiB | 00m00s [102/191] Installing rpm-sequoia-0:1.10 100% | 216.5 MiB/s | 2.6 MiB | 00m00s [103/191] Installing libfsverity-0:1.7- 100% | 24.5 MiB/s | 25.1 KiB | 00m00s [104/191] Installing libevent-0:2.1.13- 100% | 243.0 MiB/s | 995.2 KiB | 00m00s [105/191] Installing ngtcp2-crypto-ossl 100% | 0.0 B/s | 48.1 KiB | 00m00s [106/191] Installing libusb1-0:1.0.30-2 100% | 12.4 MiB/s | 177.1 KiB | 00m00s >>> Running sysusers scriptlet: tpm2-tss-0:4.2.0-1.fc45.s390x >>> Finished sysusers scriptlet: tpm2-tss-0:4.2.0-1.fc45.s390x >>> Scriptlet output: >>> Creating group 'tss' with GID 59. >>> Creating user 'tss' (Account used for TPM access) with UID 59 and GID 59. >>> [107/191] Installing tpm2-tss-0:4.2.0-1 100% | 207.0 MiB/s | 1.7 MiB | 00m00s [108/191] Installing ima-evm-utils-libs 100% | 56.3 MiB/s | 57.6 KiB | 00m00s [109/191] Installing gnupg2-gpg-agent-0 100% | 23.5 MiB/s | 721.1 KiB | 00m00s [110/191] Installing nettle-0:4.0-5.fc4 100% | 208.1 MiB/s | 852.2 KiB | 00m00s [111/191] Installing gnutls-0:3.8.13-5. 100% | 245.7 MiB/s | 3.7 MiB | 00m00s [112/191] Installing zstd-0:1.5.7-6.fc4 100% | 23.9 MiB/s | 513.2 KiB | 00m00s [113/191] Installing libxml2-0:2.15.4-1 100% | 65.9 MiB/s | 1.7 MiB | 00m00s [114/191] Installing bzip2-0:1.0.8-24.f 100% | 4.7 MiB/s | 91.1 KiB | 00m00s [115/191] Installing add-determinism-0: 100% | 83.7 MiB/s | 2.3 MiB | 00m00s [116/191] Installing build-reproducibil 100% | 0.0 B/s | 1.5 KiB | 00m00s [117/191] Installing cpio-0:2.15-10.fc4 100% | 48.5 MiB/s | 1.1 MiB | 00m00s [118/191] Installing ed-0:1.22.6-1.fc46 100% | 7.9 MiB/s | 152.9 KiB | 00m00s [119/191] Installing patch-0:2.8-5.fc45 100% | 11.7 MiB/s | 239.6 KiB | 00m00s [120/191] Installing jansson-0:2.14-5.f 100% | 88.0 MiB/s | 90.1 KiB | 00m00s [121/191] Installing lz4-libs-0:1.10.0- 100% | 193.5 MiB/s | 198.1 KiB | 00m00s [122/191] Installing libarchive-0:3.8.9 100% | 206.6 MiB/s | 1.0 MiB | 00m00s [123/191] Installing libgomp-0:16.2.1-2 100% | 188.2 MiB/s | 578.3 KiB | 00m00s [124/191] Installing libpkgconf-0:2.5.1 100% | 92.6 MiB/s | 94.9 KiB | 00m00s [125/191] Installing pkgconf-0:2.5.1-2. 100% | 4.9 MiB/s | 95.0 KiB | 00m00s [126/191] Installing pkgconf-pkg-config 100% | 98.5 KiB/s | 1.8 KiB | 00m00s [127/191] Installing libtool-ltdl-0:2.6 100% | 69.1 MiB/s | 70.7 KiB | 00m00s [128/191] Installing gdbm-libs-1:1.23-1 100% | 123.9 MiB/s | 126.9 KiB | 00m00s [129/191] Installing cyrus-sasl-lib-0:2 100% | 84.2 MiB/s | 2.4 MiB | 00m00s [130/191] Installing openldap-0:2.6.14- 100% | 166.0 MiB/s | 680.1 KiB | 00m00s [131/191] Installing gnupg2-dirmngr-0:2 100% | 22.2 MiB/s | 659.9 KiB | 00m00s [132/191] Installing gnupg2-0:2.4.9-18. 100% | 146.1 MiB/s | 6.6 MiB | 00m00s [133/191] Installing gpgverify-0:2.2-5. 100% | 0.0 B/s | 9.4 KiB | 00m00s [134/191] Installing systemd-standalone 100% | 41.6 MiB/s | 979.8 KiB | 00m00s [135/191] Installing rpm-libs-0:6.1.0-1 100% | 188.6 MiB/s | 1.1 MiB | 00m00s [136/191] Installing rpm-sign-libs-0:6. 100% | 0.0 B/s | 36.2 KiB | 00m00s [137/191] Installing rpm-build-libs-0:6 100% | 138.9 MiB/s | 284.6 KiB | 00m00s [138/191] Installing xxhash-libs-0:0.8. 100% | 61.4 MiB/s | 62.9 KiB | 00m00s [139/191] Installing libbrotli-0:1.2.0- 100% | 223.3 MiB/s | 914.6 KiB | 00m00s [140/191] Installing libnghttp2-0:1.69. 100% | 170.7 MiB/s | 174.8 KiB | 00m00s [141/191] Installing libnghttp3-0:1.18. 100% | 152.3 MiB/s | 155.9 KiB | 00m00s [142/191] Installing keyutils-libs-0:1. 100% | 50.2 MiB/s | 51.4 KiB | 00m00s [143/191] Installing libcom_err-0:1.47. 100% | 0.0 B/s | 59.9 KiB | 00m00s [144/191] Installing libverto-0:0.3.2-1 100% | 26.2 MiB/s | 26.8 KiB | 00m00s [145/191] Installing krb5-libs-0:1.22.2 100% | 225.5 MiB/s | 2.5 MiB | 00m00s [146/191] Installing libcbor-0:0.14.0-3 100% | 82.7 MiB/s | 84.7 KiB | 00m00s [147/191] Installing libfido2-0:1.17.0- 100% | 124.0 MiB/s | 254.0 KiB | 00m00s [148/191] Installing libssh-0:0.12.2-1. 100% | 173.6 MiB/s | 711.2 KiB | 00m00s [149/191] Installing libcurl-0:8.23.0~r 100% | 220.9 MiB/s | 1.1 MiB | 00m00s [150/191] Installing elfutils-debuginfo 100% | 3.8 MiB/s | 77.7 KiB | 00m00s [151/191] Installing binutils-0:2.47.50 100% | 231.5 MiB/s | 25.0 MiB | 00m00s [152/191] Installing elfutils-0:0.196-1 100% | 97.4 MiB/s | 3.0 MiB | 00m00s [153/191] Installing gdb-minimal-0:17.2 100% | 207.0 MiB/s | 15.9 MiB | 00m00s [154/191] Installing debugedit-0:5.3-3. 100% | 11.1 MiB/s | 227.4 KiB | 00m00s [155/191] Installing curl-0:8.23.0~rc2- 100% | 17.2 MiB/s | 511.9 KiB | 00m00s [156/191] Installing rpm-0:6.1.0-1.fc46 100% | 56.9 MiB/s | 2.5 MiB | 00m00s [157/191] Installing cmake-srpm-macros- 100% | 0.0 B/s | 804.0 B | 00m00s [158/191] Installing efi-srpm-macros-0: 100% | 40.3 MiB/s | 41.3 KiB | 00m00s [159/191] Installing java-srpm-macros-0 100% | 0.0 B/s | 1.1 KiB | 00m00s [160/191] Installing lua-srpm-macros-0: 100% | 0.0 B/s | 1.9 KiB | 00m00s [161/191] Installing tree-sitter-srpm-m 100% | 0.0 B/s | 9.6 KiB | 00m00s [162/191] Installing zig-srpm-macros-0: 100% | 0.0 B/s | 1.9 KiB | 00m00s [163/191] Installing filesystem-srpm-ma 100% | 0.0 B/s | 38.9 KiB | 00m00s [164/191] Installing rust-srpm-macros-0 100% | 0.0 B/s | 6.4 KiB | 00m00s [165/191] Installing qt6-srpm-macros-0: 100% | 0.0 B/s | 748.0 B | 00m00s [166/191] Installing qt5-srpm-macros-0: 100% | 84.2 KiB/s | 776.0 B | 00m00s [167/191] Installing perl-srpm-macros-0 100% | 0.0 B/s | 1.1 KiB | 00m00s [168/191] Installing package-notes-srpm 100% | 2.0 MiB/s | 2.1 KiB | 00m00s [169/191] Installing openblas-srpm-macr 100% | 0.0 B/s | 392.0 B | 00m00s [170/191] Installing ocaml-srpm-macros- 100% | 0.0 B/s | 2.1 KiB | 00m00s [171/191] Installing meson-srpm-macros- 100% | 0.0 B/s | 1.9 KiB | 00m00s [172/191] Installing kernel-srpm-macros 100% | 2.3 MiB/s | 2.3 KiB | 00m00s [173/191] Installing gnome-srpm-macros- 100% | 0.0 B/s | 4.1 KiB | 00m00s [174/191] Installing gnat-srpm-macros-0 100% | 0.0 B/s | 1.3 KiB | 00m00s [175/191] Installing ghc-srpm-macros-0: 100% | 0.0 B/s | 1.0 KiB | 00m00s [176/191] Installing gap-srpm-macros-0: 100% | 0.0 B/s | 2.7 KiB | 00m00s [177/191] Installing fpc-srpm-macros-0: 100% | 0.0 B/s | 420.0 B | 00m00s [178/191] Installing ansible-srpm-macro 100% | 35.4 MiB/s | 36.2 KiB | 00m00s [179/191] Installing redhat-rpm-config- 100% | 93.0 MiB/s | 190.4 KiB | 00m00s [180/191] Installing forge-srpm-macros- 100% | 39.3 MiB/s | 40.3 KiB | 00m00s [181/191] Installing rpm-build-0:6.1.0- 100% | 12.7 MiB/s | 312.1 KiB | 00m00s [182/191] Installing erlang-srpm-macros 100% | 0.0 B/s | 2.5 KiB | 00m00s [183/191] Installing pyproject-srpm-mac 100% | 0.0 B/s | 4.0 KiB | 00m00s [184/191] Installing fonts-srpm-macros- 100% | 55.7 MiB/s | 57.0 KiB | 00m00s [185/191] Installing go-srpm-macros-0:3 100% | 61.6 MiB/s | 63.0 KiB | 00m00s [186/191] Installing R-srpm-macros-0:1. 100% | 0.0 B/s | 4.4 KiB | 00m00s [187/191] Installing python-srpm-macros 100% | 0.0 B/s | 52.9 KiB | 00m00s [188/191] Installing rpm-plugin-selinux 100% | 0.0 B/s | 12.6 KiB | 00m00s [189/191] Installing which-0:2.25-2.fc4 100% | 4.0 MiB/s | 85.5 KiB | 00m00s [190/191] Installing shadow-utils-2:4.2 100% | 96.9 MiB/s | 4.0 MiB | 00m00s [191/191] Installing info-0:7.3-3.fc45. 100% | 50.5 KiB/s | 404.1 KiB | 00m08s 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.s390x alternatives-1.33-6.fc45.s390x ansible-srpm-macros-1-22.fc45.noarch audit-libs-4.2.1-2.fc45.s390x bash-5.3.15-2.fc45.s390x binutils-2.47.50-11.fc46.s390x build-reproducibility-srpm-macros-0.7.3-3.fc45.noarch bzip2-1.0.8-24.fc45.s390x bzip2-libs-1.0.8-24.fc45.s390x ca-certificates-2026.2.90_v9.0.317-1.fc46.noarch cmake-srpm-macros-4.3.0-5.fc45.noarch coreutils-9.12-1.fc46.s390x coreutils-common-9.12-1.fc46.s390x cpio-2.15-10.fc45.s390x crypto-policies-20260713-2.gitc42da77.fc45.noarch curl-8.23.0~rc2-1.fc46.s390x cyrus-sasl-lib-2.1.28-37.fc45.s390x debugedit-5.3-3.fc45.s390x diffutils-3.12-6.fc45.s390x dwz-0.17-3.fc45.s390x ed-1.22.6-1.fc46.s390x efi-srpm-macros-6-9.fc45.noarch elfutils-0.196-1.fc46.s390x elfutils-debuginfod-client-0.196-1.fc46.s390x elfutils-libelf-0.196-1.fc46.s390x elfutils-libs-0.196-1.fc46.s390x erlang-srpm-macros-0.3.11-2.fc45.noarch fedora-gpg-keys-46-0.3.noarch fedora-release-46-0.1.noarch fedora-release-common-46-0.1.noarch fedora-release-identity-basic-46-0.1.noarch fedora-repos-46-0.3.noarch fedora-repos-rawhide-46-0.3.noarch file-5.48-3.fc46.s390x file-libs-5.48-3.fc46.s390x filesystem-3.18-59.fc45.s390x filesystem-srpm-macros-3.18-59.fc45.noarch findutils-4.11.0-2.fc45.s390x fips-provider-1.5.3-1.fc46.s390x 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.s390x gdb-minimal-17.2-6.fc46.s390x gdbm-libs-1.23-12.fc45.s390x ghc-srpm-macros-1.10-2.fc45.noarch glibc-2.44.9000-2.fc46.s390x glibc-common-2.44.9000-2.fc46.s390x glibc-gconv-extra-2.44.9000-2.fc46.s390x glibc-minimal-langpack-2.44.9000-2.fc46.s390x gmp-6.3.0-6.fc45.s390x 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.s390x gnupg2-dirmngr-2.4.9-18.fc45.s390x gnupg2-gpg-agent-2.4.9-18.fc45.s390x gnupg2-gpgconf-2.4.9-18.fc45.s390x gnupg2-keyboxd-2.4.9-18.fc45.s390x gnupg2-verify-2.4.9-18.fc45.s390x gnutls-3.8.13-5.fc46.s390x 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.s390x gzip-1.14-4.fc45.s390x ima-evm-utils-libs-1.6.2-12.fc45.s390x info-7.3-3.fc45.s390x jansson-2.14-5.fc45.s390x java-srpm-macros-1-9.fc45.noarch json-c-0.18-9.fc45.s390x kernel-srpm-macros-1.0-30.fc45.noarch keyutils-libs-1.6.3-8.fc45.s390x krb5-libs-1.22.2-9.fc45.s390x libacl-2.4.0-2.fc45.s390x libarchive-3.8.9-2.fc46.s390x libassuan-2.5.7-6.fc45.s390x libattr-2.6.0-2.fc45.s390x libblkid-2.42.4-2.fc46.s390x libbrotli-1.2.0-6.fc45.s390x libcap-2.78-2.fc45.s390x libcap-ng-0.9.6-1.fc46.s390x libcbor-0.14.0-3.fc45.s390x libcom_err-1.47.4-2.fc45.s390x libcurl-8.23.0~rc2-1.fc46.s390x libeconf-0.7.9-4.fc45.s390x libevent-2.1.13-1.fc46.s390x libfdisk-2.42.4-2.fc46.s390x libffi-3.8.0-1.fc46.s390x libfido2-1.17.0-5.fc45.s390x libfsverity-1.7-4.fc45.s390x libgcc-16.2.1-2.fc46.1.s390x libgcrypt-1.12.4-1.fc46.s390x libgomp-16.2.1-2.fc46.1.s390x libgpg-error-1.61-2.fc45.s390x libidn2-2.3.8-4.fc45.s390x libksba-1.8.1-1.fc46.s390x liblastlog2-2.42.4-2.fc46.s390x libmount-2.42.4-2.fc46.s390x libnghttp2-1.69.0-6.fc46.s390x libnghttp3-1.18.0-1.fc45.s390x libpkgconf-2.5.1-2.fc45.s390x libpsl-0.23.3-1.fc46.s390x libselinux-3.11-5.fc46.s390x libselinux-utils-3.11-5.fc46.s390x libsemanage-3.11-4.fc46.s390x libsepol-3.11-2.fc45.s390x libsmartcols-2.42.4-2.fc46.s390x libssh-0.12.2-1.fc45.s390x libssh-config-0.12.2-1.fc45.noarch libstdc++-16.2.1-2.fc46.1.s390x libtasn1-4.21.0-2.fc45.s390x libtool-ltdl-2.6.2-1.fc46.s390x libunistring-1.1-12.fc45.s390x libusb1-1.0.30-2.fc45.s390x libuuid-2.42.4-2.fc46.s390x libverto-0.3.2-13.fc45.s390x libxcrypt-4.5.2-4.fc45.s390x libxml2-2.15.4-1.fc46.s390x libzstd-1.5.7-6.fc45.s390x linkdupes-0.7.3-3.fc45.s390x lua-libs-5.5.1-2.fc46.s390x lua-srpm-macros-1-18.fc45.noarch lz4-libs-1.10.0-5.fc45.s390x meson-srpm-macros-1.12.1-2.fc46.noarch mpfr-4.2.2-4.fc45.s390x ncurses-base-6.6-3.fc45.noarch ncurses-libs-6.6-3.fc45.s390x nettle-4.0-5.fc45.s390x ngtcp2-1.22.1-3.fc45.s390x ngtcp2-crypto-ossl-1.22.1-3.fc45.s390x npth-1.8-5.fc45.s390x ocaml-srpm-macros-11-4.fc45.noarch openblas-srpm-macros-2-22.fc45.noarch openldap-2.6.14-1.fc46.s390x openssl-libs-4.0.2-3.fc46.s390x p11-kit-0.26.5-1.fc45.s390x p11-kit-trust-0.26.5-1.fc45.s390x package-notes-srpm-macros-0.20-2.fc45.noarch pam-libs-1.7.2-4.fc45.s390x patch-2.8-5.fc45.s390x pcre2-10.47-1.fc45.2.s390x pcre2-syntax-10.47-1.fc45.2.noarch perl-srpm-macros-1-65.fc45.noarch pkgconf-2.5.1-2.fc45.s390x pkgconf-m4-2.5.1-2.fc45.noarch pkgconf-pkg-config-2.5.1-2.fc45.s390x policycoreutils-3.11-2.fc45.s390x popt-1.19-11.fc45.s390x publicsuffix-list-dafsa-20260624-2.fc45.noarch pyproject-srpm-macros-1.23.2-1.fc45.noarch python-srpm-macros-3.15-2.fc45.noarch qt5-srpm-macros-5.15.18-3.fc45.noarch qt6-srpm-macros-6.11.2-1.fc46.noarch readline-8.3-6.fc45.s390x redhat-rpm-config-345-4.fc46.noarch redhat-systemd-presets-102-3.fc45.noarch redhat-systemd-presets-common-102-3.fc45.noarch rpm-6.1.0-1.fc46.s390x rpm-build-6.1.0-1.fc46.s390x rpm-build-libs-6.1.0-1.fc46.s390x rpm-libs-6.1.0-1.fc46.s390x rpm-plugin-selinux-6.1.0-1.fc46.s390x rpm-sequoia-1.10.3-1.fc46.s390x rpm-sign-libs-6.1.0-1.fc46.s390x rust-srpm-macros-28.5-2.fc45.noarch sed-4.10-2.fc45.s390x selinux-policy-45.19-1.fc46.noarch selinux-policy-targeted-45.19-1.fc46.noarch setup-2.15.1-2.fc45.noarch shadow-utils-4.20.0-1.fc45.s390x sqlite-libs-3.53.4-1.fc45.s390x systemd-libs-262-1.fc46.s390x systemd-standalone-sysusers-262-1.fc46.s390x tar-1.35-9.fc45.s390x tpm2-tss-4.2.0-1.fc45.s390x tree-sitter-srpm-macros-0.4.6-2.fc45.noarch unzip-6.0-71.fc45.s390x util-linux-2.42.4-2.fc46.s390x util-linux-core-2.42.4-2.fc46.s390x which-2.25-2.fc45.s390x xxhash-libs-0.8.4-1.fc46.s390x xz-5.8.4-1.fc46.s390x xz-libs-5.8.4-1.fc46.s390x zig-srpm-macros-1-9.fc45.noarch zip-3.0-46.fc45.s390x zlib-ng-compat-2.3.3-6.fc45.s390x zstd-1.5.7-6.fc45.s390x Start: buildsrpm Start: rpmbuild -bs Building target platforms: s390x Building for target s390x setting SOURCE_DATE_EPOCH=1790726400 Wrote: /builddir/build/SRPMS/htslib-1.24-2.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-s390x-1790798737.214009/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-g9haodi1/htslib/htslib.spec) Config(child) 1 minutes 2 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-1.24-2.fc46.src.rpm) Config(fedora-rawhide-s390x) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-s390x-bootstrap-1790798737.214009/root. INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-s390x-bootstrap-1790798737.214009/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-s390x-1790798737.214009/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.s390x rpm-sequoia-1.10.3-1.fc46.s390x dnf5-5.4.6.0-1.fc46.s390x dnf5-plugins-5.4.6.0-1.fc46.s390x Finish: chroot init Start: build phase for htslib-1.24-2.fc46.src.rpm Start: build setup for htslib-1.24-2.fc46.src.rpm Building target platforms: s390x Building for target s390x setting SOURCE_DATE_EPOCH=1790726400 Wrote: /builddir/build/SRPMS/htslib-1.24-2.fc46.src.rpm Updating and loading repositories: fedora 100% | 4.8 KiB/s | 4.2 KiB | 00m01s Copr repository 100% | 2.0 KiB/s | 1.5 KiB | 00m01s Repositories loaded. Package Arch Version Repository Size Installing: bzip2-devel s390x 0:1.0.8-24.fc45 fedora 309.8 KiB gcc s390x 0:16.2.1-2.fc46.1 fedora 88.6 MiB htscodecs-devel s390x 0:1.6.7-1.fc46 copr_base 38.5 KiB libcurl-devel s390x 0:8.23.0~rc2-1.fc46 fedora 1.4 MiB libdeflate-devel s390x 0:1.26-1.fc46 fedora 26.0 KiB make s390x 1:4.4.1-13.fc45 fedora 1.9 MiB openssl-devel s390x 1:4.0.2-3.fc46 fedora 4.6 MiB perl-Data-Dumper s390x 0:2.192-528.fc45 fedora 111.2 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 s390x 4:5.44.0-527.fc45 fedora 119.5 KiB perl-lib s390x 0:0.65-527.fc45 fedora 8.5 KiB xz-devel s390x 1:5.8.4-1.fc46 fedora 258.8 KiB zlib-ng-compat-devel s390x 0:2.3.3-6.fc45 fedora 107.0 KiB Installing dependencies: annobin-docs noarch 0:13.31-1.fc46 fedora 99.7 KiB annobin-plugin-gcc s390x 0:13.31-1.fc46 fedora 715.8 KiB brotli s390x 0:1.2.0-6.fc45 fedora 33.2 KiB brotli-devel s390x 0:1.2.0-6.fc45 fedora 65.9 KiB cmake-filesystem s390x 0:4.3.0-5.fc45 fedora 0.0 B cpp s390x 0:16.2.1-2.fc46.1 fedora 30.6 MiB gcc-plugin-annobin s390x 0:16.2.1-2.fc46.1 fedora 56.7 KiB glibc-devel s390x 0:2.44.9000-2.fc46 fedora 3.7 MiB groff-base s390x 0:1.24.1-2.fc45 fedora 4.6 MiB htscodecs s390x 0:1.6.7-1.fc46 copr_base 205.1 KiB kernel-headers s390x 0:7.3.0-0.rc5.45.fc46 fedora 7.0 MiB keyutils-libs-devel s390x 0:1.6.3-8.fc45 fedora 48.2 KiB krb5-devel s390x 0:1.22.2-9.fc45 fedora 709.9 KiB libasan s390x 0:16.2.1-2.fc46.1 fedora 1.9 MiB libatomic s390x 0:16.2.1-2.fc46.1 fedora 37.2 KiB libcom_err-devel s390x 0:1.47.4-2.fc45 fedora 16.7 KiB libdeflate s390x 0:1.26-1.fc46 fedora 107.4 KiB libidn2-devel s390x 0:2.3.8-4.fc45 fedora 152.1 KiB libkadm5 s390x 0:1.22.2-9.fc45 fedora 225.5 KiB libmpc s390x 0:1.4.1-2.fc45 fedora 164.5 KiB libnghttp2-devel s390x 0:1.69.0-6.fc46 fedora 288.0 KiB libnghttp3-devel s390x 0:1.18.0-1.fc45 fedora 119.4 KiB libpsl-devel s390x 0:0.23.3-1.fc46 fedora 111.5 KiB libselinux-devel s390x 0:3.11-5.fc46 fedora 121.9 KiB libsepol-devel s390x 0:3.11-2.fc45 fedora 120.7 KiB libssh-devel s390x 0:0.12.2-1.fc45 fedora 204.2 KiB libubsan s390x 0:16.2.1-2.fc46.1 fedora 499.8 KiB libverto-devel s390x 0:0.3.2-13.fc45 fedora 25.7 KiB libxcrypt-devel s390x 0:4.5.2-4.fc45 fedora 31.0 KiB libzstd-devel s390x 0:1.5.7-6.fc45 fedora 217.6 KiB ncurses s390x 0:6.6-3.fc45 fedora 621.7 KiB ngtcp2-crypto-ossl-devel s390x 0:1.22.1-3.fc45 fedora 7.5 KiB ngtcp2-devel s390x 0:1.22.1-3.fc45 fedora 262.8 KiB pcre2-devel s390x 0:10.47-1.fc45.2 fedora 2.1 MiB pcre2-utf16 s390x 0:10.47-1.fc45.2 fedora 674.8 KiB pcre2-utf32 s390x 0:10.47-1.fc45.2 fedora 642.7 KiB perl-AutoLoader noarch 0:5.74-527.fc45 fedora 20.6 KiB perl-B s390x 0:1.92-527.fc45 fedora 529.3 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 s390x 0:2.59-527.fc45 fedora 55.3 KiB perl-DynaLoader s390x 0:1.57-527.fc45 fedora 32.1 KiB perl-Encode s390x 4:3.24-527.fc45 fedora 9.6 MiB perl-Errno s390x 0:1.39-527.fc45 fedora 8.4 KiB perl-Exporter noarch 0:5.79-527.fc45 fedora 54.2 KiB perl-Fcntl s390x 0:1.20-527.fc45 fedora 48.4 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 s390x 0:1.56-527.fc45 fedora 147.0 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 s390x 0:3.16-527.fc45 fedora 45.6 KiB perl-Net-SSLeay s390x 0:1.96-5.fc45 fedora 1.4 MiB perl-POSIX s390x 0:2.26-527.fc45 fedora 241.1 KiB perl-PathTools s390x 0:3.95-527.fc45 fedora 175.7 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 s390x 5:1.70-527.fc45 fedora 144.5 KiB perl-SelectSaver noarch 0:1.03-527.fc45 fedora 2.1 KiB perl-Socket s390x 4:2.043-1.fc46 fedora 125.5 KiB perl-Storable s390x 1:3.41-527.fc45 fedora 226.6 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 s390x 4:1.9780-527.fc45 fedora 115.4 KiB perl-Time-Local noarch 2:1.350-527.fc45 fedora 69.0 KiB perl-URI noarch 0:5.37-1.fc46 fedora 275.5 KiB perl-Unicode-Normalize s390x 0:1.32-527.fc45 fedora 672.2 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 s390x 4:5.44.0-527.fc45 fedora 12.3 MiB perl-locale noarch 0:1.13-527.fc45 fedora 6.1 KiB perl-mro s390x 0:1.30-527.fc45 fedora 41.2 KiB perl-overload noarch 0:1.40-527.fc45 fedora 71.6 KiB perl-overloading noarch 0:0.03-527.fc45 fedora 4.8 KiB perl-parent noarch 1:0.244-527.fc45 fedora 10.3 KiB perl-podlators noarch 1:6.1.1-1.fc46 fedora 327.2 KiB perl-vars noarch 0:1.05-527.fc45 fedora 3.9 KiB publicsuffix-list noarch 0:20260624-2.fc45 fedora 345.9 KiB Transaction Summary: Installing: 107 packages Total size of inbound packages is 68 MiB. Need to download 68 MiB. After this operation, 183 MiB extra will be used (install 183 MiB, remove 0 B). [ 1/107] htscodecs-devel-0:1.6.7-1.fc4 100% | 16.3 KiB/s | 15.2 KiB | 00m01s [ 2/107] bzip2-devel-0:1.0.8-24.fc45.s 100% | 188.6 KiB/s | 213.5 KiB | 00m01s [ 3/107] libdeflate-devel-0:1.26-1.fc4 100% | 85.8 KiB/s | 16.0 KiB | 00m00s [ 4/107] make-1:4.4.1-13.fc45.s390x 100% | 943.5 KiB/s | 604.8 KiB | 00m01s [ 5/107] perl-Data-Dumper-0:2.192-528. 100% | 243.4 KiB/s | 57.4 KiB | 00m00s [ 6/107] perl-FindBin-0:1.54-527.fc45. 100% | 61.3 KiB/s | 13.9 KiB | 00m00s [ 7/107] perl-Getopt-Long-1:2.58-527.f 100% | 252.8 KiB/s | 63.2 KiB | 00m00s [ 8/107] libcurl-devel-0:8.23.0~rc2-1. 100% | 522.3 KiB/s | 1.0 MiB | 00m02s [ 9/107] perl-lib-0:0.65-527.fc45.s390 100% | 59.0 KiB/s | 14.5 KiB | 00m00s [ 10/107] xz-devel-1:5.8.4-1.fc46.s390x 100% | 325.8 KiB/s | 66.1 KiB | 00m00s [ 11/107] perl-interpreter-4:5.44.0-527 100% | 261.5 KiB/s | 72.4 KiB | 00m00s [ 12/107] zlib-ng-compat-devel-0:2.3.3- 100% | 188.7 KiB/s | 37.7 KiB | 00m00s [ 13/107] glibc-devel-0:2.44.9000-2.fc4 100% | 2.0 MiB/s | 706.4 KiB | 00m00s [ 14/107] gcc-0:16.2.1-2.fc46.1.s390x 100% | 9.1 MiB/s | 35.2 MiB | 00m04s [ 15/107] libasan-0:16.2.1-2.fc46.1.s39 100% | 2.1 MiB/s | 563.2 KiB | 00m00s [ 16/107] libatomic-0:16.2.1-2.fc46.1.s 100% | 285.4 KiB/s | 53.7 KiB | 00m00s [ 17/107] libmpc-0:1.4.1-2.fc45.s390x 100% | 346.8 KiB/s | 75.3 KiB | 00m00s [ 18/107] libubsan-0:16.2.1-2.fc46.1.s3 100% | 1.1 MiB/s | 241.9 KiB | 00m00s [ 19/107] brotli-devel-0:1.2.0-6.fc45.s 100% | 179.5 KiB/s | 34.5 KiB | 00m00s [ 20/107] cpp-0:16.2.1-2.fc46.1.s390x 100% | 8.9 MiB/s | 11.5 MiB | 00m01s [ 21/107] krb5-devel-0:1.22.2-9.fc45.s3 100% | 773.8 KiB/s | 143.1 KiB | 00m00s [ 22/107] libidn2-devel-0:2.3.8-4.fc45. 100% | 401.6 KiB/s | 65.9 KiB | 00m00s [ 23/107] libnghttp2-devel-0:1.69.0-6.f 100% | 311.3 KiB/s | 54.2 KiB | 00m00s [ 24/107] libnghttp3-devel-0:1.18.0-1.f 100% | 163.3 KiB/s | 27.8 KiB | 00m00s [ 25/107] htscodecs-0:1.6.7-1.fc46.s390 100% | 146.3 KiB/s | 110.9 KiB | 00m01s [ 26/107] libpsl-devel-0:0.23.3-1.fc46. 100% | 187.7 KiB/s | 33.6 KiB | 00m00s [ 27/107] libssh-devel-0:0.12.2-1.fc45. 100% | 262.1 KiB/s | 47.2 KiB | 00m00s [ 28/107] libzstd-devel-0:1.5.7-6.fc45. 100% | 313.8 KiB/s | 56.2 KiB | 00m00s [ 29/107] ngtcp2-crypto-ossl-devel-0:1. 100% | 72.9 KiB/s | 11.4 KiB | 00m00s [ 30/107] ngtcp2-devel-0:1.22.1-3.fc45. 100% | 301.2 KiB/s | 48.5 KiB | 00m00s [ 31/107] cmake-filesystem-0:4.3.0-5.fc 100% | 78.3 KiB/s | 14.8 KiB | 00m00s [ 32/107] perl-B-0:1.92-527.fc45.s390x 100% | 863.1 KiB/s | 183.8 KiB | 00m00s [ 33/107] libdeflate-0:1.26-1.fc46.s390 100% | 268.8 KiB/s | 62.9 KiB | 00m00s [ 34/107] perl-Carp-0:1.54-527.fc45.noa 100% | 154.4 KiB/s | 28.6 KiB | 00m00s [ 35/107] perl-Exporter-0:5.79-527.fc45 100% | 182.2 KiB/s | 30.6 KiB | 00m00s [ 36/107] perl-Scalar-List-Utils-5:1.70 100% | 432.3 KiB/s | 75.7 KiB | 00m00s [ 37/107] perl-constant-0:1.33-528.fc45 100% | 115.4 KiB/s | 22.7 KiB | 00m00s [ 38/107] perl-File-Basename-0:2.86-527 100% | 81.8 KiB/s | 16.8 KiB | 00m00s [ 39/107] perl-PathTools-0:3.95-527.fc4 100% | 436.5 KiB/s | 87.7 KiB | 00m00s [ 40/107] perl-libs-4:5.44.0-527.fc45.s 100% | 8.6 MiB/s | 2.7 MiB | 00m00s [ 41/107] perl-Pod-Usage-4:2.05-527.fc4 100% | 204.0 KiB/s | 40.4 KiB | 00m00s [ 42/107] perl-base-0:2.27-527.fc45.noa 100% | 85.5 KiB/s | 15.9 KiB | 00m00s [ 43/107] perl-Text-ParseWords-0:3.31-5 100% | 77.1 KiB/s | 16.2 KiB | 00m00s [ 44/107] perl-overload-0:1.40-527.fc45 100% | 216.5 KiB/s | 45.2 KiB | 00m00s [ 45/107] libxcrypt-devel-0:4.5.2-4.fc4 100% | 139.2 KiB/s | 30.3 KiB | 00m00s [ 46/107] kernel-headers-0:7.3.0-0.rc5. 100% | 6.2 MiB/s | 1.8 MiB | 00m00s [ 47/107] brotli-0:1.2.0-6.fc45.s390x 100% | 107.6 KiB/s | 24.4 KiB | 00m00s [ 48/107] keyutils-libs-devel-0:1.6.3-8 100% | 318.9 KiB/s | 63.1 KiB | 00m00s [ 49/107] libcom_err-devel-0:1.47.4-2.f 100% | 67.7 KiB/s | 16.4 KiB | 00m00s [ 50/107] libselinux-devel-0:3.11-5.fc4 100% | 802.8 KiB/s | 160.6 KiB | 00m00s [ 51/107] libkadm5-0:1.22.2-9.fc45.s390 100% | 272.3 KiB/s | 78.7 KiB | 00m00s [ 52/107] libverto-devel-0:0.3.2-13.fc4 100% | 58.3 KiB/s | 14.2 KiB | 00m00s [ 53/107] publicsuffix-list-0:20260624- 100% | 576.5 KiB/s | 92.8 KiB | 00m00s [ 54/107] perl-if-0:0.61.000-527.fc45.n 100% | 56.3 KiB/s | 13.7 KiB | 00m00s [ 55/107] perl-DynaLoader-0:1.57-527.fc 100% | 143.0 KiB/s | 25.6 KiB | 00m00s [ 56/107] perl-overloading-0:0.03-527.f 100% | 47.3 KiB/s | 12.5 KiB | 00m00s [ 57/107] perl-Errno-0:1.39-527.fc45.s3 100% | 79.9 KiB/s | 14.5 KiB | 00m00s [ 58/107] perl-Pod-Perldoc-0:3.28.01-52 100% | 519.6 KiB/s | 84.7 KiB | 00m00s [ 59/107] perl-podlators-1:6.1.1-1.fc46 100% | 692.9 KiB/s | 132.4 KiB | 00m00s [ 60/107] perl-Encode-4:3.24-527.fc45.s 100% | 3.6 MiB/s | 1.7 MiB | 00m00s [ 61/107] perl-mro-0:1.30-527.fc45.s390 100% | 156.8 KiB/s | 29.3 KiB | 00m00s [ 62/107] libsepol-devel-0:3.11-2.fc45. 100% | 252.5 KiB/s | 48.2 KiB | 00m00s [ 63/107] pcre2-devel-0:10.47-1.fc45.2. 100% | 2.7 MiB/s | 560.4 KiB | 00m00s [ 64/107] perl-vars-0:1.05-527.fc45.noa 100% | 74.1 KiB/s | 12.7 KiB | 00m00s [ 65/107] perl-Getopt-Std-0:1.15-527.fc 100% | 93.6 KiB/s | 15.4 KiB | 00m00s [ 66/107] perl-MIME-Base64-0:3.16-527.f 100% | 186.3 KiB/s | 30.0 KiB | 00m00s [ 67/107] perl-Storable-1:3.41-527.fc45 100% | 590.4 KiB/s | 99.8 KiB | 00m00s [ 68/107] perl-parent-1:0.244-527.fc45. 100% | 82.3 KiB/s | 14.7 KiB | 00m00s [ 69/107] perl-Fcntl-0:1.20-527.fc45.s3 100% | 168.6 KiB/s | 29.5 KiB | 00m00s [ 70/107] groff-base-0:1.24.1-2.fc45.s3 100% | 5.0 MiB/s | 1.3 MiB | 00m00s [ 71/107] perl-HTTP-Tiny-0:0.096-528.fc 100% | 362.4 KiB/s | 58.4 KiB | 00m00s [ 72/107] perl-File-Temp-1:0.231.200-52 100% | 304.0 KiB/s | 59.3 KiB | 00m00s [ 73/107] perl-IO-0:1.56-527.fc45.s390x 100% | 514.4 KiB/s | 82.8 KiB | 00m00s [ 74/107] perl-IPC-Open3-0:1.24-527.fc4 100% | 148.3 KiB/s | 23.7 KiB | 00m00s [ 75/107] perl-Pod-Simple-1:3.48-527.fc 100% | 1.3 MiB/s | 222.0 KiB | 00m00s [ 76/107] perl-Symbol-0:1.09-527.fc45.n 100% | 89.0 KiB/s | 13.9 KiB | 00m00s [ 77/107] perl-POSIX-0:2.26-527.fc45.s3 100% | 602.4 KiB/s | 97.6 KiB | 00m00s [ 78/107] perl-Term-ANSIColor-0:5.01-52 100% | 247.8 KiB/s | 47.3 KiB | 00m00s [ 79/107] perl-Term-Cap-0:1.18-527.fc45 100% | 138.3 KiB/s | 21.7 KiB | 00m00s [ 80/107] pcre2-utf16-0:10.47-1.fc45.2. 100% | 1.6 MiB/s | 269.1 KiB | 00m00s [ 81/107] perl-File-Path-0:2.18-527.fc4 100% | 220.5 KiB/s | 34.8 KiB | 00m00s [ 82/107] pcre2-utf32-0:10.47-1.fc45.2. 100% | 1.4 MiB/s | 256.8 KiB | 00m00s [ 83/107] perl-IO-Socket-SSL-0:2.099-2. 100% | 1.4 MiB/s | 236.2 KiB | 00m00s [ 84/107] perl-Socket-4:2.043-1.fc46.s3 100% | 336.1 KiB/s | 56.1 KiB | 00m00s [ 85/107] perl-Net-SSLeay-0:1.96-5.fc45 100% | 2.1 MiB/s | 392.6 KiB | 00m00s [ 86/107] perl-Time-HiRes-4:1.9780-527. 100% | 352.6 KiB/s | 56.8 KiB | 00m00s [ 87/107] perl-File-stat-0:1.15-527.fc4 100% | 109.5 KiB/s | 17.2 KiB | 00m00s [ 88/107] perl-Time-Local-2:1.350-527.f 100% | 199.0 KiB/s | 34.2 KiB | 00m00s [ 89/107] perl-SelectSaver-0:1.03-527.f 100% | 70.9 KiB/s | 11.3 KiB | 00m00s [ 90/107] perl-Pod-Escapes-1:1.07-527.f 100% | 123.8 KiB/s | 19.6 KiB | 00m00s [ 91/107] perl-Text-Tabs+Wrap-0:2024.00 100% | 120.4 KiB/s | 21.5 KiB | 00m00s [ 92/107] perl-locale-0:1.13-527.fc45.n 100% | 81.9 KiB/s | 13.2 KiB | 00m00s [ 93/107] ncurses-0:6.6-3.fc45.s390x 100% | 2.3 MiB/s | 438.7 KiB | 00m00s [ 94/107] perl-IO-Socket-IP-0:0.44-527. 100% | 238.8 KiB/s | 42.0 KiB | 00m00s [ 95/107] perl-URI-0:5.37-1.fc46.noarch 100% | 915.2 KiB/s | 151.0 KiB | 00m00s [ 96/107] perl-AutoLoader-0:5.74-527.fc 100% | 123.1 KiB/s | 20.9 KiB | 00m00s [ 97/107] perl-Class-Struct-0:0.68-527. 100% | 119.5 KiB/s | 21.8 KiB | 00m00s [ 98/107] perl-MIME-Base32-0:1.303-26.f 100% | 117.5 KiB/s | 20.4 KiB | 00m00s [ 99/107] perl-Unicode-Normalize-0:1.32 100% | 564.9 KiB/s | 92.1 KiB | 00m00s [100/107] perl-libnet-0:3.15-528.fc45.n 100% | 697.4 KiB/s | 128.3 KiB | 00m00s [101/107] perl-Digest-MD5-0:2.59-527.fc 100% | 175.1 KiB/s | 35.0 KiB | 00m00s [102/107] perl-FileHandle-0:2.05-527.fc 100% | 74.1 KiB/s | 15.2 KiB | 00m00s [103/107] perl-Digest-0:1.20-527.fc45.n 100% | 134.6 KiB/s | 24.8 KiB | 00m00s [104/107] gcc-plugin-annobin-0:16.2.1-2 100% | 351.4 KiB/s | 58.7 KiB | 00m00s [105/107] openssl-devel-1:4.0.2-3.fc46. 100% | 9.7 MiB/s | 3.2 MiB | 00m00s [106/107] annobin-plugin-gcc-0:13.31-1. 100% | 2.7 MiB/s | 700.7 KiB | 00m00s [107/107] annobin-docs-0:13.31-1.fc46.n 100% | 450.7 KiB/s | 87.0 KiB | 00m00s -------------------------------------------------------------------------------- [107/107] Total 100% | 6.5 MiB/s | 67.6 MiB | 00m10s Running transaction [ 1/109] Verify package files 100% | 681.0 B/s | 107.0 B | 00m00s [ 2/109] Prepare transaction 100% | 1.1 KiB/s | 107.0 B | 00m00s [ 3/109] Installing cmake-filesystem-0 100% | 851.6 KiB/s | 9.4 KiB | 00m00s [ 4/109] Installing openssl-devel-1:4. 100% | 56.8 MiB/s | 5.6 MiB | 00m00s [ 5/109] Installing ngtcp2-devel-0:1.2 100% | 257.9 MiB/s | 264.1 KiB | 00m00s [ 6/109] Installing libidn2-devel-0:2. 100% | 78.0 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perl-Digest-MD5-0: 100% | 55.8 MiB/s | 57.2 KiB | 00m00s [ 20/109] Installing perl-FileHandle-0: 100% | 0.0 B/s | 9.8 KiB | 00m00s [ 21/109] Installing perl-B-0:1.92-527. 100% | 260.1 MiB/s | 532.6 KiB | 00m00s [ 22/109] Installing perl-Data-Dumper-0 100% | 110.5 MiB/s | 113.1 KiB | 00m00s [ 23/109] Installing perl-libnet-0:3.15 100% | 143.4 MiB/s | 293.8 KiB | 00m00s [ 24/109] Installing perl-Unicode-Norma 100% | 329.3 MiB/s | 674.5 KiB | 00m00s [ 25/109] Installing perl-MIME-Base32-0 100% | 31.4 MiB/s | 32.2 KiB | 00m00s [ 26/109] Installing perl-URI-0:5.37-1. 100% | 94.2 MiB/s | 289.2 KiB | 00m00s [ 27/109] Installing perl-IO-Socket-IP- 100% | 99.9 MiB/s | 102.3 KiB | 00m00s [ 28/109] Installing perl-AutoLoader-0: 100% | 0.0 B/s | 21.0 KiB | 00m00s [ 29/109] Installing perl-IO-Socket-SSL 100% | 238.0 MiB/s | 731.0 KiB | 00m00s [ 30/109] Installing perl-Net-SSLeay-0: 100% | 239.0 MiB/s | 1.4 MiB | 00m00s [ 31/109] Installing perl-locale-0:1.13 100% | 0.0 B/s | 6.5 KiB | 00m00s [ 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[ 45/109] Installing perl-Term-ANSIColo 100% | 96.8 MiB/s | 99.1 KiB | 00m00s [ 46/109] Installing perl-Pod-Perldoc-0 100% | 8.3 MiB/s | 169.4 KiB | 00m00s [ 47/109] Installing perl-podlators-1:6 100% | 16.2 MiB/s | 331.1 KiB | 00m00s [ 48/109] Installing perl-File-stat-0:1 100% | 0.0 B/s | 14.2 KiB | 00m00s [ 49/109] Installing perl-SelectSaver-0 100% | 0.0 B/s | 2.5 KiB | 00m00s [ 50/109] Installing perl-Socket-4:2.04 100% | 124.6 MiB/s | 127.5 KiB | 00m00s [ 51/109] Installing perl-Symbol-0:1.09 100% | 0.0 B/s | 7.3 KiB | 00m00s [ 52/109] Installing perl-Pod-Usage-4:2 100% | 4.5 MiB/s | 87.8 KiB | 00m00s [ 53/109] Installing perl-IO-0:1.56-527 100% | 147.8 MiB/s | 151.3 KiB | 00m00s [ 54/109] Installing perl-Fcntl-0:1.20- 100% | 0.0 B/s | 49.5 KiB | 00m00s [ 55/109] Installing perl-mro-0:1.30-52 100% | 41.3 MiB/s | 42.3 KiB | 00m00s [ 56/109] Installing perl-overloading-0 100% | 0.0 B/s | 5.5 KiB | 00m00s [ 57/109] Installing perl-base-0:2.27-5 100% | 0.0 B/s | 13.0 KiB | 00m00s [ 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Installing perl-DynaLoader-0: 100% | 0.0 B/s | 32.5 KiB | 00m00s [ 72/109] Installing perl-PathTools-0:3 100% | 176.1 MiB/s | 180.3 KiB | 00m00s [ 73/109] Installing perl-Exporter-0:5. 100% | 54.2 MiB/s | 55.5 KiB | 00m00s [ 74/109] Installing perl-Carp-0:1.54-5 100% | 15.5 MiB/s | 47.7 KiB | 00m00s [ 75/109] Installing perl-libs-4:5.44.0 100% | 247.6 MiB/s | 12.4 MiB | 00m00s [ 76/109] Installing perl-interpreter-4 100% | 6.2 MiB/s | 121.2 KiB | 00m00s [ 77/109] Installing libsepol-devel-0:3 100% | 62.6 MiB/s | 128.2 KiB | 00m00s [ 78/109] Installing libselinux-devel-0 100% | 38.2 MiB/s | 156.6 KiB | 00m00s [ 79/109] Installing publicsuffix-list- 100% | 338.8 MiB/s | 346.9 KiB | 00m00s [ 80/109] Installing libpsl-devel-0:0.2 100% | 112.1 MiB/s | 114.8 KiB | 00m00s [ 81/109] Installing libverto-devel-0:0 100% | 0.0 B/s | 26.4 KiB | 00m00s [ 82/109] Installing libkadm5-0:1.22.2- 100% | 222.2 MiB/s | 227.5 KiB | 00m00s [ 83/109] Installing libcom_err-devel-0 100% | 961.8 KiB/s | 18.3 KiB 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| 244.4 MiB/s | 500.6 KiB | 00m00s [ 97/109] Installing libatomic-0:16.2.1 100% | 37.4 MiB/s | 38.3 KiB | 00m00s [ 98/109] Installing libasan-0:16.2.1-2 100% | 311.7 MiB/s | 1.9 MiB | 00m00s [ 99/109] Installing make-1:4.4.1-13.fc 100% | 71.5 MiB/s | 1.9 MiB | 00m00s [100/109] Installing gcc-0:16.2.1-2.fc4 100% | 283.2 MiB/s | 88.7 MiB | 00m00s [101/109] Installing annobin-plugin-gcc 100% | 53.9 MiB/s | 717.4 KiB | 00m00s [102/109] Installing gcc-plugin-annobin 100% | 4.7 MiB/s | 58.4 KiB | 00m00s [103/109] Installing htscodecs-devel-0: 100% | 13.1 MiB/s | 40.2 KiB | 00m00s [104/109] Installing libcurl-devel-0:8. 100% | 39.1 MiB/s | 1.5 MiB | 00m00s [105/109] Installing libdeflate-devel-0 100% | 0.0 B/s | 27.3 KiB | 00m00s [106/109] Installing perl-FindBin-0:1.5 100% | 0.0 B/s | 7.2 KiB | 00m00s [107/109] Installing perl-lib-0:0.65-52 100% | 0.0 B/s | 8.9 KiB | 00m00s [108/109] Installing xz-devel-1:5.8.4-1 100% | 128.2 MiB/s | 262.6 KiB | 00m00s [109/109] Installing bzip2-devel-0:1.0. 100% | 2.2 MiB/s | 310.7 KiB | 00m00s Warning: skipped OpenPGP checks for 2 packages from repository: copr_base Complete! Building target platforms: s390x Building for target s390x setting SOURCE_DATE_EPOCH=1790726400 Wrote: /builddir/build/SRPMS/htslib-1.24-2.fc46.src.rpm Updating and loading repositories: fedora 100% | 5.0 KiB/s | 4.2 KiB | 00m01s Copr repository 100% | 2.0 KiB/s | 1.5 KiB | 00m01s Repositories loaded. Package "bzip2-devel-1.0.8-24.fc45.s390x" is already installed. Package "gcc-16.2.1-2.fc46.1.s390x" is already installed. Package "htscodecs-devel-1.6.7-1.fc46.s390x" is already installed. Package "libcurl-devel-8.23.0~rc2-1.fc46.s390x" is already installed. Package "libdeflate-devel-1.26-1.fc46.s390x" is already installed. Package "make-1:4.4.1-13.fc45.s390x" is already installed. Package "openssl-devel-1:4.0.2-3.fc46.s390x" is already installed. Package "perl-Data-Dumper-2.192-528.fc45.s390x" 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.s390x" is already installed. Package "perl-interpreter-4:5.44.0-527.fc45.s390x" is already installed. Package "xz-devel-1:5.8.4-1.fc46.s390x" is already installed. Package "zlib-ng-compat-devel-2.3.3-6.fc45.s390x" is already installed. Nothing to do. Finish: build setup for htslib-1.24-2.fc46.src.rpm Start: rpmbuild htslib-1.24-2.fc46.src.rpm Building target platforms: s390x Building for target s390x setting SOURCE_DATE_EPOCH=1790726400 Executing(mkbuilddir): /bin/sh -e /var/tmp/rpm-tmp.pXZ6Au 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=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection" RPM_LD_FLAGS="-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes " RPM_ARCH="s390x" RPM_OS="linux" RPM_BUILD_NCPUS="2" 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="2.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.V4XJKT + 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 . + /usr/bin/rpmuncompress /builddir/build/SOURCES/htslib-tool-link.patch + /usr/bin/patch -p1 -s --fuzz=0 --no-backup-if-mismatch -f + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.uqYjAQ + umask 022 + cd /builddir/build/BUILD/htslib-1.24-build + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -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 -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd htslib-1.24 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -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 -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + '[' '-flto=auto -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 $(dirname ./configure) -name config.guess -o -name config.sub) ++ basename ./config.sub + '[' -f /usr/lib/rpm/redhat/config.sub ']' + /usr/bin/rm -f ./config.sub ++ basename ./config.sub + /usr/bin/cp -fv /usr/lib/rpm/redhat/config.sub ./config.sub '/usr/lib/rpm/redhat/config.sub' -> './config.sub' + '[' 1 = 1 ']' + '[' x '!=' 'x-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors' ']' ++ find . -name ltmain.sh ++ grep -q runstatedir=DIR ./configure ++ echo --runstatedir=/run + ./configure --build=s390x-redhat-linux --host=s390x-redhat-linux --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/bin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/libexec --localstatedir=/var --runstatedir=/run --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info --prefix=/usr --libdir=/usr/lib64 --enable-plugins '--with-plugin-path=/usr/local/libexec/htslib:$(plugindir)' --enable-gcs --enable-libcurl --enable-s3 --with-external-htscodecs configure: WARNING: unrecognized options: --disable-dependency-tracking checking for s390x-redhat-linux-gcc... gcc 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 gcc accepts -g... yes checking for gcc option to enable C23 features... none needed checking for s390x-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 gcc options to detect undeclared functions... none needed checking for gcc 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 s390x-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 gcc option to support large files... none needed checking shared library type for s390x-redhat-linux... plain .so checking whether the linker supports versioned symbols... yes checking whether the compiler accepts -fvisibility=hidden... yes checking build system type... s390x-redhat-linux-gnu checking host system type... s390x-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 for htscodecs/rANS_static4x16.h... yes checking for rans_compress_bound_4x16 in -lhtscodecs... yes checking for libdeflate.h... yes checking for libdeflate_deflate_compress in -ldeflate... yes 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... yes 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_external.mk to htscodecs.mk configure: WARNING: unrecognized options: --disable-dependency-tracking + /usr/bin/make -O -j2 V=1 VERBOSE=1 gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o kfunc.o kfunc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o kstring.o kstring.c kstring.c: In function ‘boyer_moore’: kstring.c:468:24: warning: return discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 468 | return memchr(str, pat[0], n); | ^~~~~~ gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o bcf_sr_sort.o bcf_sr_sort.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o errmod.o errmod.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o bgzf.o bgzf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o faidx.o faidx.c faidx.c: In function ‘fai_path’: faidx.c:1067:25: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 1067 | char *fai_tmp = strstr(fa, HTS_IDX_DELIM); | ^~~~~~ gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o hfile.o hfile.c echo '#define HTS_VERSION_TEXT "1.24"' > version.h printf '#define HTS_CC "%s"\n#define HTS_CPPFLAGS "%s"\n#define HTS_CFLAGS "%s"\n#define HTS_LDFLAGS "%s"\n#define HTS_LIBS "%s"\n' \ 'gcc' \ '' \ '-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden' \ '-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic' \ '-ldeflate -lhtscodecs -llzma -lbz2 -lz -lm ' > config_vars.h gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o hts_expr.o hts_expr.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o header.o header.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o hts_os.o hts_os.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o md5.o md5.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o multipart.o multipart.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o probaln.o probaln.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o realn.o realn.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o region.o region.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o regidx.o regidx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o sam_mods.o sam_mods.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o simd.o simd.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o synced_bcf_reader.o synced_bcf_reader.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o vcf_sweep.o vcf_sweep.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o tbx.o tbx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o textutils.o textutils.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o thread_pool.o thread_pool.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o sam.o sam.c sam.c: In function ‘sam_open_mode_opts’: sam.c:5222:15: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 5222 | if ((opts = strchr(format, ','))) { | ^ gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o vcfutils.o vcfutils.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/cram_codecs.o cram/cram_codecs.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o vcf.o vcf.c vcf.c: In function ‘bcf_get_version’: vcf.c:168:17: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 168 | if (!(major = strstr(version, vcf))) { //bad format | ^ gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/cram_decode.o cram/cram_decode.c cram/cram_decode.c: In function ‘cram_decode_seq’: cram/cram_decode.c:1234:35: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 1234 | char *N = memchr(refp, 'N', frag_len); | ^~~~~~ gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/cram_external.o cram/cram_external.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/cram_index.o cram/cram_index.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/cram_encode.o cram/cram_encode.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/cram_stats.o cram/cram_stats.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/mFILE.o cram/mFILE.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/open_trace_file.o cram/open_trace_file.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/string_alloc.o cram/string_alloc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -DPLUGINPATH=\"/usr/local/libexec/htslib:/usr/libexec/htslib\" -c -o plugin.o plugin.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o kfunc.pico kfunc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o kstring.pico kstring.c kstring.c: In function ‘boyer_moore’: kstring.c:468:24: warning: return discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 468 | return memchr(str, pat[0], n); | ^~~~~~ gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/cram_io.o cram/cram_io.c cram/cram_io.c: In function ‘refs_load_fai’: cram/cram_io.c:2323:22: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2323 | char *fn_delim = strstr(fn, HTS_IDX_DELIM); | ^~~~~~ cram/cram_io.c: In function ‘cram_dopen’: cram/cram_io.c:5070:29: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 5070 | fd->prefix = strdup((cp = strrchr(filename, '/')) ? cp+1 : filename); | ^ gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o bcf_sr_sort.pico bcf_sr_sort.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o errmod.pico errmod.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o bgzf.pico bgzf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o faidx.pico faidx.c faidx.c: In function ‘fai_path’: faidx.c:1067:25: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 1067 | char *fai_tmp = strstr(fa, HTS_IDX_DELIM); | ^~~~~~ gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o hfile.pico hfile.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o header.pico header.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o hts_expr.pico hts_expr.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o hts_os.pico hts_os.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o md5.pico md5.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o multipart.pico multipart.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o probaln.pico probaln.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o realn.pico realn.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o regidx.pico regidx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o region.pico region.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o hts.pico hts.c hts.c: In function ‘hts_open_format’: hts.c:942:33: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 942 | char *rmme = NULL, *fnidx = strstr(fn, HTS_IDX_DELIM); | ^~~~~~ hts.c: In function ‘hts_hopen’: hts.c:1478:13: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 1478 | if ((cp = strchr(mode, ','))) { | ^ hts.c: In function ‘idx_find_and_load’: hts.c:4929:19: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 4929 | char *fnidx = strstr(fn, HTS_IDX_DELIM); | ^~~~~~ gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o sam_mods.pico sam_mods.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o simd.pico simd.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o synced_bcf_reader.pico synced_bcf_reader.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o vcf_sweep.pico vcf_sweep.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o tbx.pico tbx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o textutils.pico textutils.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o thread_pool.pico thread_pool.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o sam.pico sam.c sam.c: In function ‘sam_open_mode_opts’: sam.c:5222:15: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 5222 | if ((opts = strchr(format, ','))) { | ^ gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o vcfutils.pico vcfutils.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o cram/cram_codecs.pico cram/cram_codecs.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o vcf.pico vcf.c vcf.c: In function ‘bcf_get_version’: vcf.c:168:17: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 168 | if (!(major = strstr(version, vcf))) { //bad format | ^ gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o cram/cram_decode.pico cram/cram_decode.c cram/cram_decode.c: In function ‘cram_decode_seq’: cram/cram_decode.c:1234:35: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 1234 | char *N = memchr(refp, 'N', frag_len); | ^~~~~~ gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o cram/cram_external.pico cram/cram_external.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o cram/cram_index.pico cram/cram_index.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o cram/cram_encode.pico cram/cram_encode.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o cram/cram_stats.pico cram/cram_stats.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o cram/mFILE.pico cram/mFILE.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o cram/open_trace_file.pico cram/open_trace_file.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o cram/pooled_alloc.pico cram/pooled_alloc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o cram/string_alloc.pico cram/string_alloc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -DPLUGINPATH=\"/usr/local/libexec/htslib:/usr/libexec/htslib\" -fpic -c -o plugin.pico plugin.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o cram/cram_io.pico cram/cram_io.c cram/cram_io.c: In function ‘refs_load_fai’: cram/cram_io.c:2323:22: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2323 | char *fn_delim = strstr(fn, HTS_IDX_DELIM); | ^~~~~~ cram/cram_io.c: In function ‘cram_dopen’: cram/cram_io.c:5070:29: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 5070 | fd->prefix = strdup((cp = strrchr(filename, '/')) ? cp+1 : filename); | ^ gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o annot-tsv.o annot-tsv.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o htsfile.o htsfile.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o bgzip.o bgzip.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o tabix.o tabix.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o hfile_gcs.pico hfile_gcs.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o hfile_libcurl.pico hfile_libcurl.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/hts_endian.o test/hts_endian.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/fieldarith.o test/fieldarith.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/hfile.o test/hfile.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/pileup.o test/pileup.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o hfile_s3.pico hfile_s3.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/plugins-dlhts.o test/plugins-dlhts.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/pileup_mod.o test/pileup_mod.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_alloc.o test/test_alloc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_bgzf.o test/test_bgzf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_expr.o test/test_expr.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/sam.o test/sam.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_kfunc.o test/test_kfunc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_faidx.o test/test_faidx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_khash.o test/test_khash.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_mod.o test/test_mod.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_nibbles.o test/test_nibbles.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_realn.o test/test_realn.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -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: In function ‘boyer_moore’: test/../kstring.c:468:24: warning: return discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 468 | return memchr(str, pat[0], n); | ^~~~~~ gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test-regidx.o test/test-regidx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_str2int.o test/test_str2int.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_time_funcs.o test/test_time_funcs.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_index.o test/test_index.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_view.o test/test_view.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test-bcf-sr.o test/test-bcf-sr.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/fuzz/hts_open_fuzzer.o test/fuzz/hts_open_fuzzer.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test-bcf-translate.o test/test-bcf-translate.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test-vcf-api.o test/test-vcf-api.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_introspection.o test/test_introspection.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test-parse-reg.o test/test-parse-reg.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_hfile_libcurl.o test/test_hfile_libcurl.c sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' htslib.pc.tmp > htslib_static.mk sed -e "s#@-includedir@#`pwd`#g;s#@-libdir@#`pwd`#g" htslib.pc.tmp > htslib-uninstalled.pc gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -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 gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -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 gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fno-delete-null-pointer-checks -I. -c -o ref_cache/listener.o ref_cache/listener.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -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 gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fno-delete-null-pointer-checks -I. -c -o ref_cache/main.o ref_cache/main.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fno-delete-null-pointer-checks -I. -c -o ref_cache/misc.o ref_cache/misc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fno-delete-null-pointer-checks -I. -c -o ref_cache/ping.o ref_cache/ping.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -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 gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -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 gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -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 gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -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 gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -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 gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fno-delete-null-pointer-checks -I. -c -o ref_cache/server.o ref_cache/server.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fno-delete-null-pointer-checks -I. -c -o ref_cache/transaction.o ref_cache/transaction.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fno-delete-null-pointer-checks -I. -c -o ref_cache/upstream.o ref_cache/upstream.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o hts.o hts.c hts.c: In function ‘hts_open_format’: hts.c:942:33: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 942 | char *rmme = NULL, *fnidx = strstr(fn, HTS_IDX_DELIM); | ^~~~~~ hts.c: In function ‘hts_hopen’: hts.c:1478:13: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 1478 | if ((cp = strchr(mode, ','))) { | ^ hts.c: In function ‘idx_find_and_load’: hts.c:4929:19: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 4929 | char *fnidx = strstr(fn, HTS_IDX_DELIM); | ^~~~~~ gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -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: In function ‘bcf_get_version’: test/../vcf.c:168:17: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 168 | if (!(major = strstr(version, vcf))) { //bad format | ^ gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/hts_endian test/hts_endian.o -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/plugins-dlhts test/plugins-dlhts.o -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test_alloc test/test_alloc.o gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test_kstring test/test_kstring.o -lm gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test_time_funcs test/test_time_funcs.o gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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 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 plugin.o ranlib libhts.a gcc -shared -Wl,-soname,libhts.so.3 -Wl,-version-script,htslib.map -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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 plugin.pico -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread ln -sf libhts.so libhts.so.3 gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/fieldarith test/fieldarith.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/hfile test/hfile.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/pileup test/pileup.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/pileup_mod test/pileup_mod.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/sam test/sam.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test_bgzf test/test_bgzf.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test_expr test/test_expr.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test_kfunc test/test_kfunc.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test_khash test/test_khash.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test_faidx test/test_faidx.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test_mod test/test_mod.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test_nibbles test/test_nibbles.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test_realn test/test_realn.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test_str2int test/test_str2int.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test-regidx test/test-regidx.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test_index test/test_index.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test_view test/test_view.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test-vcf-api test/test-vcf-api.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test_introspection test/test_introspection.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test-parse-reg test/test-parse-reg.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test_hfile_libcurl test/test_hfile_libcurl.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o annot-tsv annot-tsv.o libhts.so -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o bgzip bgzip.o libhts.so -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o htsfile htsfile.o libhts.so -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o tabix tabix.o libhts.so -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -shared -Wl,-E -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o hfile_libcurl.so hfile_libcurl.pico libhts.so -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lcurl -lpthread gcc -shared -Wl,-E -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o hfile_gcs.so hfile_gcs.pico libhts.so -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -shared -Wl,-E -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o hfile_s3.so hfile_s3.pico libhts.so -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lcrypto -lcurl -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test-bcf_set_variant_type test/test-bcf_set_variant_type.o libhts.a -ldeflate -lhtscodecs -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.wiIHiZ + 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=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -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 -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd 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 + chmod 755 /builddir/build/BUILD/htslib-1.24-build/BUILDROOT//usr/lib64/libhts.so.1.24 + rm -f /builddir/build/BUILD/htslib-1.24-build/BUILDROOT//usr/lib64/libhts.a + /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 1.24-2.fc46 --unique-debug-suffix -1.24-2.fc46.s390x --unique-debug-src-base htslib-1.24-2.fc46.s390x --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 sepdebugcrcfix: Updated 9 CRC32s, 0 CRC32s did match. Creating .debug symlinks for symlinks to ELF files Copying sources found by 'debugedit -l' to /usr/src/debug/htslib-1.24-2.fc46.s390x 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 -j2 + /usr/lib/rpm/redhat/brp-python-hardlink + /usr/bin/add-det --brp -j2 /builddir/build/BUILD/htslib-1.24-build/BUILDROOT Scanned 28 directories and 180 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 27 directories and 180 files, considered 178 files, read 46 files, linked 23 files, 0 errors sum of sizes of linked files: 448100 bytes Reading /builddir/build/BUILD/htslib-1.24-build/SPECPARTS/rpm-debuginfo.specpart Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.NytXYm + umask 022 + cd /builddir/build/BUILD/htslib-1.24-build + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z15 -mtune=z17 -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 -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd htslib-1.24 + export LD_LIBRARY_PATH=/builddir/build/BUILD/htslib-1.24-build/htslib-1.24 + LD_LIBRARY_PATH=/builddir/build/BUILD/htslib-1.24-build/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 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/WU_PP7LPlZ/index.bam.csi /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.sam > /tmp/WU_PP7LPlZ/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -c /tmp/WU_PP7LPlZ/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/WU_PP7LPlZ/index.bam.bai /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.sam > /tmp/WU_PP7LPlZ/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -b /tmp/WU_PP7LPlZ/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/WU_PP7LPlZ/index.sam.gz.csi /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.sam > /tmp/WU_PP7LPlZ/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -c /tmp/WU_PP7LPlZ/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/WU_PP7LPlZ/index.sam.gz.bai /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.sam > /tmp/WU_PP7LPlZ/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -b /tmp/WU_PP7LPlZ/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/WU_PP7LPlZ/index.sam.gz.csi /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index_dos.sam > /tmp/WU_PP7LPlZ/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -c /tmp/WU_PP7LPlZ/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/WU_PP7LPlZ/index.sam.gz.bai /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index_dos.sam > /tmp/WU_PP7LPlZ/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -b /tmp/WU_PP7LPlZ/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view -l 0 -C -x /tmp/WU_PP7LPlZ/index.cram.crai /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.sam > /tmp/WU_PP7LPlZ/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index /tmp/WU_PP7LPlZ/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view -p /tmp/WU_PP7LPlZ/index3_rgn.sam /tmp/WU_PP7LPlZ/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/WU_PP7LPlZ/index3_rgnm.sam /tmp/WU_PP7LPlZ/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/WU_PP7LPlZ/index.bcf.csi /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.vcf > /tmp/WU_PP7LPlZ/index.bcf .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -c /tmp/WU_PP7LPlZ/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/WU_PP7LPlZ/index.vcf.gz.csi /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.vcf > /tmp/WU_PP7LPlZ/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -c /tmp/WU_PP7LPlZ/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/WU_PP7LPlZ/index.vcf.gz.tbi /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.vcf > /tmp/WU_PP7LPlZ/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -t /tmp/WU_PP7LPlZ/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/tabix /tmp/WU_PP7LPlZ/index.vcf.gz##idx##/tmp/WU_PP7LPlZ/index.vcf.gz.tbi 1:10000060-10000060 .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view /tmp/WU_PP7LPlZ/index2.bam 1:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view /tmp/WU_PP7LPlZ/index2.bam 1:2000000-2000000 .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view /tmp/WU_PP7LPlZ/index2.bam 2:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view /tmp/WU_PP7LPlZ/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/WU_PP7LPlZ/index.bam.csi /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.sam > /tmp/WU_PP7LPlZ/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -c /tmp/WU_PP7LPlZ/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/WU_PP7LPlZ/index.bam.bai /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.sam > /tmp/WU_PP7LPlZ/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -b /tmp/WU_PP7LPlZ/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/WU_PP7LPlZ/index.sam.gz.csi /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.sam > /tmp/WU_PP7LPlZ/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -c /tmp/WU_PP7LPlZ/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/WU_PP7LPlZ/index.sam.gz.bai /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.sam > /tmp/WU_PP7LPlZ/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -b /tmp/WU_PP7LPlZ/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/WU_PP7LPlZ/index.sam.gz.csi /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index_dos.sam > /tmp/WU_PP7LPlZ/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -c /tmp/WU_PP7LPlZ/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/WU_PP7LPlZ/index.sam.gz.bai /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index_dos.sam > /tmp/WU_PP7LPlZ/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -b /tmp/WU_PP7LPlZ/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/WU_PP7LPlZ/index.cram.crai /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.sam > /tmp/WU_PP7LPlZ/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index /tmp/WU_PP7LPlZ/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view -@4 -p /tmp/WU_PP7LPlZ/index3_rgn.sam /tmp/WU_PP7LPlZ/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/WU_PP7LPlZ/index3_rgnm.sam /tmp/WU_PP7LPlZ/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/WU_PP7LPlZ/index.bcf.csi /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.vcf > /tmp/WU_PP7LPlZ/index.bcf .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -c /tmp/WU_PP7LPlZ/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/WU_PP7LPlZ/index.vcf.gz.csi /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.vcf > /tmp/WU_PP7LPlZ/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -c /tmp/WU_PP7LPlZ/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/WU_PP7LPlZ/index.vcf.gz.tbi /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/index.vcf > /tmp/WU_PP7LPlZ/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_index -t /tmp/WU_PP7LPlZ/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/tabix /tmp/WU_PP7LPlZ/index.vcf.gz##idx##/tmp/WU_PP7LPlZ/index.vcf.gz.tbi 1:10000060-10000060 .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view /tmp/WU_PP7LPlZ/index2.bam 1:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view /tmp/WU_PP7LPlZ/index2.bam 1:2000000-2000000 .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view /tmp/WU_PP7LPlZ/index2.bam 2:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test_view /tmp/WU_PP7LPlZ/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/WU_PP7LPlZ/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/WU_PP7LPlZ/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/WU_PP7LPlZ -s 74452500 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr.pl -t /tmp/WU_PP7LPlZ -s 34270147 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr.pl -t /tmp/WU_PP7LPlZ -s 11108528 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr.pl -t /tmp/WU_PP7LPlZ -s 42233895 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr.pl -t /tmp/WU_PP7LPlZ -s 8111117 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr.pl -t /tmp/WU_PP7LPlZ -s 85644070 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr.pl -t /tmp/WU_PP7LPlZ -s 49879942 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr.pl -t /tmp/WU_PP7LPlZ -s 47881429 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr.pl -t /tmp/WU_PP7LPlZ -s 69081244 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.24-build/htslib-1.24/test/test-bcf-sr.pl -t /tmp/WU_PP7LPlZ -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/WU_PP7LPlZ/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/WU_PP7LPlZ/no_index_2.out 2> /tmp/WU_PP7LPlZ/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/WU_PP7LPlZ/no_index_3.out 2> /tmp/WU_PP7LPlZ/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/WU_PP7LPlZ/no_index_4.out 2> /tmp/WU_PP7LPlZ/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/WU_PP7LPlZ/weird-chr-names.vcf.bcf -x /tmp/WU_PP7LPlZ/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/WU_PP7LPlZ/range_test_1.out.vcf -r '1' --args /tmp/WU_PP7LPlZ/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/WU_PP7LPlZ/range_test_2.out.vcf -r '1:1-2' --args /tmp/WU_PP7LPlZ/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/WU_PP7LPlZ/range_test_3.out.vcf -r '1:1,1:2' --args /tmp/WU_PP7LPlZ/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/WU_PP7LPlZ/range_test_4.out.vcf -r '1:1-1' --args /tmp/WU_PP7LPlZ/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/WU_PP7LPlZ/range_test_5.out.vcf -r '{1:1}' --args /tmp/WU_PP7LPlZ/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/WU_PP7LPlZ/range_test_6.out.vcf -r '{1:1}:1-2' --args /tmp/WU_PP7LPlZ/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/WU_PP7LPlZ/range_test_7.out.vcf -r '{1:1}:1,{1:1}:2' --args /tmp/WU_PP7LPlZ/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/WU_PP7LPlZ/range_test_8.out.vcf -r '{1:1}:1-1' --args /tmp/WU_PP7LPlZ/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/WU_PP7LPlZ/range_test_9.out.vcf -r '{1:1-1}' --args /tmp/WU_PP7LPlZ/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/WU_PP7LPlZ/range_test_10.out.vcf -r '{1:1-1}:1-2' --args /tmp/WU_PP7LPlZ/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/WU_PP7LPlZ/range_test_11.out.vcf -r '{1:1-1}:1,{1:1-1}:2' --args /tmp/WU_PP7LPlZ/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/WU_PP7LPlZ/range_test_12.out.vcf -r '{1:1-1}:1-1' --args /tmp/WU_PP7LPlZ/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/WU_PP7LPlZ/range_test_13.out.vcf -r '{1:1-1}-2' --args /tmp/WU_PP7LPlZ/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/WU_PP7LPlZ/range_test_14.out.vcf -t '1' --args /tmp/WU_PP7LPlZ/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/WU_PP7LPlZ/range_test_15.out.vcf -t '1:1-2' --args /tmp/WU_PP7LPlZ/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/WU_PP7LPlZ/range_test_16.out.vcf -t '1:1,1:2' --args /tmp/WU_PP7LPlZ/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/WU_PP7LPlZ/range_test_17.out.vcf -t '1:1-1' --args /tmp/WU_PP7LPlZ/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/WU_PP7LPlZ/range_test_18.out.vcf -t '{1:1}' --args /tmp/WU_PP7LPlZ/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/WU_PP7LPlZ/range_test_19.out.vcf -t '{1:1}:1-2' --args /tmp/WU_PP7LPlZ/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/WU_PP7LPlZ/range_test_20.out.vcf -t '{1:1}:1,{1:1}:2' --args /tmp/WU_PP7LPlZ/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/WU_PP7LPlZ/range_test_21.out.vcf -t '{1:1}:1-1' --args /tmp/WU_PP7LPlZ/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/WU_PP7LPlZ/range_test_22.out.vcf -t '{1:1-1}' --args /tmp/WU_PP7LPlZ/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/WU_PP7LPlZ/range_test_23.out.vcf -t '{1:1-1}:1-2' --args /tmp/WU_PP7LPlZ/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/WU_PP7LPlZ/range_test_24.out.vcf -t '{1:1-1}:1,{1:1-1}:2' --args /tmp/WU_PP7LPlZ/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/WU_PP7LPlZ/range_test_25.out.vcf -t '{1:1-1}:1-1' --args /tmp/WU_PP7LPlZ/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/WU_PP7LPlZ/range_test_26.out.vcf -t '{1:1-1}-2' --args /tmp/WU_PP7LPlZ/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/WU_PP7LPlZ/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/WU_PP7LPlZ/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/WU_PP7LPlZ/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 python3 not found, skipping libcurl retry tests + RPM_EC=0 ++ jobs -p + exit 0 Processing files: htslib-1.24-2.fc46.s390x Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.MJIMcM + 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.7dLcX1 + 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 = 1.24-2.fc46 htslib(s390-64) = 1.24-2.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_2.2)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.2)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.38)(64bit) libc.so.6(GLIBC_2.4)(64bit) libcrypto.so.4()(64bit) libcrypto.so.4(OPENSSL_4.0.0)(64bit) libcurl.so.4()(64bit) libdeflate.so.0()(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) libhtscodecs.so.2()(64bit) liblzma.so.5()(64bit) liblzma.so.5(XZ_5.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2)(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-1.24-2.fc46.s390x Provides: htslib-devel = 1.24-2.fc46 htslib-devel(s390-64) = 1.24-2.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-1.24-2.fc46.s390x Provides: htslib-tools = 1.24-2.fc46 htslib-tools(s390-64) = 1.24-2.fc46 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: libc.so.6()(64bit) libc.so.6(GLIBC_2.2)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.2)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.38)(64bit) libc.so.6(GLIBC_2.4)(64bit) libcurl.so.4()(64bit) libhts.so.3()(64bit) libhts.so.3(HTSLIB_1.0)(64bit) libhts.so.3(HTSLIB_1.10)(64bit) libhts.so.3(HTSLIB_1.15)(64bit) libhts.so.3(HTSLIB_1.2.1)(64bit) libhts.so.3(HTSLIB_1.20)(64bit) libhts.so.3(HTSLIB_1.24)(64bit) libhts.so.3(HTSLIB_1.4)(64bit) libhts.so.3(HTSLIB_1.5)(64bit) libhts.so.3(HTSLIB_1.7)(64bit) rtld(GNU_HASH) Processing files: htslib-debugsource-1.24-2.fc46.s390x Provides: htslib-debugsource = 1.24-2.fc46 htslib-debugsource(s390-64) = 1.24-2.fc46 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: htslib-debuginfo-1.24-2.fc46.s390x Provides: debuginfo(build-id) = 44c97dd83de9b929e8c6e6e0a35387951606ca46 debuginfo(build-id) = 58d158e2dda548b71452952bed5733244c4f1def debuginfo(build-id) = a0dda1e95a1f13896e499e8d8df626dda69a1b7a debuginfo(build-id) = d56774da31236f6c44622bc00e81124e78d3431f htslib-debuginfo = 1.24-2.fc46 htslib-debuginfo(s390-64) = 1.24-2.fc46 libhts.so.1.24-1.24-2.fc46.s390x.debug()(64bit) Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: htslib-debugsource(s390-64) = 1.24-2.fc46 Processing files: htslib-tools-debuginfo-1.24-2.fc46.s390x Provides: debuginfo(build-id) = 33b9ec0cb89d232ab0a90a5c53564546441d3075 debuginfo(build-id) = 41b6add2b469a6ed882907857b42510e3421067d debuginfo(build-id) = 8dcd4682c01bff97815e4a7ac206e4992c798830 debuginfo(build-id) = 996579912b54f0b673fdf168cbbce2319c4bb659 debuginfo(build-id) = 9f43adf70a8ed1ee28d7bd8a2ace88168ad11fa1 htslib-tools-debuginfo = 1.24-2.fc46 htslib-tools-debuginfo(s390-64) = 1.24-2.fc46 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: htslib-debugsource(s390-64) = 1.24-2.fc46 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILD/htslib-1.24-build/BUILDROOT Wrote: /builddir/build/RPMS/htslib-debuginfo-1.24-2.fc46.s390x.rpm Wrote: /builddir/build/RPMS/htslib-debugsource-1.24-2.fc46.s390x.rpm Wrote: /builddir/build/RPMS/htslib-1.24-2.fc46.s390x.rpm Wrote: /builddir/build/RPMS/htslib-tools-debuginfo-1.24-2.fc46.s390x.rpm Wrote: /builddir/build/RPMS/htslib-tools-1.24-2.fc46.s390x.rpm Wrote: /builddir/build/RPMS/htslib-devel-1.24-2.fc46.s390x.rpm Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.KDm9Yj + 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-1.24-2.fc46.src.rpm Finish: build phase for htslib-1.24-2.fc46.src.rpm INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-s390x-1790798737.214009/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-1.24-2.fc46.src.rpm) Config(child) 6 minutes 19 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot Finish: run Running RPMResults tool Package info: { "packages": [ { "name": "htslib-tools", "epoch": null, "version": "1.24", "release": "2.fc46", "arch": "s390x" }, { "name": "htslib-debugsource", "epoch": null, "version": "1.24", "release": "2.fc46", "arch": "s390x" }, { "name": "htslib-debuginfo", "epoch": null, "version": "1.24", "release": "2.fc46", "arch": "s390x" }, { "name": "htslib", "epoch": null, "version": "1.24", "release": "2.fc46", "arch": "s390x" }, { "name": "htslib-tools-debuginfo", "epoch": null, "version": "1.24", "release": "2.fc46", "arch": "s390x" }, { "name": "htslib", "epoch": null, "version": "1.24", "release": "2.fc46", "arch": "src" }, { "name": "htslib-devel", "epoch": null, "version": "1.24", "release": "2.fc46", "arch": "s390x" } ] } RPMResults finished