Warning: Permanently added '54.234.248.155' (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/10066099-epel-10-aarch64 --chroot epel-10-aarch64 Version: 1.6 PID: 9551 Logging PID: 9553 Task: {'allow_user_ssh': False, 'appstream': False, 'background': False, 'build_id': 10066099, 'buildroot_pkgs': [], 'chroot': 'epel-10-aarch64', 'enable_net': False, 'fedora_review': False, 'git_hash': '7f908d99caaa698e4edc070e538303e597a5ee85', 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/ron/bioinformatics/htslib', 'isolation': 'default', 'memory_reqs': 2048, 'package_name': 'htslib', 'package_version': '1.23-1', 'project_dirname': 'bioinformatics', 'project_name': 'bioinformatics', 'project_owner': 'ron', 'repo_priority': None, 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/ron/bioinformatics/epel-10-aarch64/', 'id': 'copr_base', 'name': 'Copr repository', 'priority': None}], 'sandbox': 'ron/bioinformatics--ron', 'source_json': {}, 'source_type': None, 'ssh_public_keys': None, 'storage': 0, 'submitter': 'ron', 'tags': [], 'task_id': '10066099-epel-10-aarch64', 'timeout': 18000, 'uses_devel_repo': False, 'with_opts': [], 'without_opts': []} Running: git clone https://copr-dist-git.fedorainfracloud.org/git/ron/bioinformatics/htslib /var/lib/copr-rpmbuild/workspace/workdir-hu4s1yu1/htslib --depth 500 --no-single-branch --recursive cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/ron/bioinformatics/htslib', '/var/lib/copr-rpmbuild/workspace/workdir-hu4s1yu1/htslib', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-hu4s1yu1/htslib'... Running: git checkout 7f908d99caaa698e4edc070e538303e597a5ee85 -- cmd: ['git', 'checkout', '7f908d99caaa698e4edc070e538303e597a5ee85', '--'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-hu4s1yu1/htslib rc: 0 stdout: stderr: Note: switching to '7f908d99caaa698e4edc070e538303e597a5ee85'. 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 7f908d9 automatic import of htslib Running: dist-git-client sources cmd: ['dist-git-client', 'sources'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-hu4s1yu1/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-1.23.tar.bz2 INFO: Reading stdout from command: curl --help all INFO: Calling: curl -H Pragma: -o htslib-1.23.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/ron/bioinformatics/htslib/htslib-1.23.tar.bz2/md5/686ccffe2ba88ec57d85cca0e3eb2f3a/htslib-1.23.tar.bz2 % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 4786k 100 4786k 0 0 143M 0 --:--:-- --:--:-- --:--:-- 146M INFO: Reading stdout from command: md5sum htslib-1.23.tar.bz2 tail: /var/lib/copr-rpmbuild/main.log: file truncated Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-hu4s1yu1/htslib/htslib.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-hu4s1yu1/htslib --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1769500621.779357 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 6.6 starting (python version = 3.14.2, NVR = mock-6.6-1.fc43), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-hu4s1yu1/htslib/htslib.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-hu4s1yu1/htslib --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1769500621.779357 -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-hu4s1yu1/htslib/htslib.spec) Config(centos-stream+epel-10-aarch64) Start: clean chroot Finish: clean chroot Mock Version: 6.6 INFO: Mock Version: 6.6 Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/centos-stream+epel-10-aarch64-bootstrap-1769500621.779357/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: quay.io/centos/centos:stream10 INFO: Pulling image: quay.io/centos/centos:stream10 INFO: Tagging container image as mock-bootstrap-53164ed9-a090-40e0-980a-c0836e9da128 INFO: Checking that c785a964505697d8f598018f70abee48cc50e8faf9290eec7850d3d9d4cce980 image matches host's architecture INFO: Copy content of container c785a964505697d8f598018f70abee48cc50e8faf9290eec7850d3d9d4cce980 to /var/lib/mock/centos-stream+epel-10-aarch64-bootstrap-1769500621.779357/root INFO: mounting c785a964505697d8f598018f70abee48cc50e8faf9290eec7850d3d9d4cce980 with podman image mount INFO: image c785a964505697d8f598018f70abee48cc50e8faf9290eec7850d3d9d4cce980 as /var/lib/containers/storage/overlay/1dc01b598e3ff5390652e58589fa7a58a2d5659c6ca2b463aceb2ed08c570660/merged INFO: umounting image c785a964505697d8f598018f70abee48cc50e8faf9290eec7850d3d9d4cce980 (/var/lib/containers/storage/overlay/1dc01b598e3ff5390652e58589fa7a58a2d5659c6ca2b463aceb2ed08c570660/merged) with podman image umount INFO: Removing image mock-bootstrap-53164ed9-a090-40e0-980a-c0836e9da128 INFO: Package manager dnf4 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/centos-stream+epel-10-aarch64-1769500621.779357/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 dnf4 detected and used (direct choice) INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-4.19.1.1-21.el10.aarch64 rpm-sequoia-1.9.0.3-1.el10.aarch64 python3-dnf-4.20.0-19.el10.noarch python3-dnf-plugins-core-4.7.0-10.el10.noarch yum-4.20.0-19.el10.noarch Start: installing minimal buildroot with dnf No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 1.5 kB/s | 133 B 00:00 CentOS Stream 10 - BaseOS 18 MB/s | 9.3 MB 00:00 CentOS Stream 10 - AppStream 5.5 MB/s | 3.5 MB 00:00 CentOS Stream 10 - CRB 1.5 MB/s | 778 kB 00:00 CentOS Stream 10 - Extras packages 29 kB/s | 8.3 kB 00:00 Extra Packages for Enterprise Linux 10 - aarch6 46 MB/s | 6.1 MB 00:00 Dependencies resolved. ================================================================================ Package Arch Version Repo Size ================================================================================ Installing: bash aarch64 5.2.26-6.el10 baseos 1.8 M bzip2 aarch64 1.0.8-25.el10 baseos 54 k centos-stream-release noarch 10.0-19.el10 baseos 30 k coreutils aarch64 9.5-6.el10 baseos 1.1 M cpio aarch64 2.15-3.el10 baseos 290 k diffutils aarch64 3.10-8.el10 baseos 405 k epel-rpm-macros noarch 10-6.el10_2 epel 8.2 k findutils aarch64 1:4.10.0-5.el10 baseos 555 k gawk aarch64 5.3.0-6.el10 baseos 1.1 M glibc-minimal-langpack aarch64 2.39-99.el10 baseos 39 k grep aarch64 3.11-10.el10 baseos 298 k gzip aarch64 1.13-3.el10 baseos 168 k info aarch64 7.1-6.el10 baseos 182 k patch aarch64 2.7.6-26.el10 appstream 130 k redhat-rpm-config noarch 295-1.el10 appstream 74 k rpm-build aarch64 4.19.1.1-21.el10 appstream 76 k sed aarch64 4.9-3.el10 baseos 316 k shadow-utils aarch64 2:4.15.0-9.el10 baseos 1.3 M tar aarch64 2:1.35-10.el10 baseos 857 k unzip aarch64 6.0-69.el10 baseos 186 k util-linux aarch64 2.40.2-13.el10 baseos 1.2 M which aarch64 2.21-44.el10 baseos 42 k xz aarch64 1:5.6.2-4.el10 baseos 481 k Installing dependencies: alternatives aarch64 1.30-2.el10 baseos 41 k ansible-srpm-macros noarch 1-16.1.el10_0 epel 20 k audit-libs aarch64 4.0.3-5.el10 baseos 129 k authselect aarch64 1.5.0-8.el10 baseos 144 k authselect-libs aarch64 1.5.0-8.el10 baseos 221 k basesystem noarch 11-22.el10 baseos 4.3 k binutils aarch64 2.41-60.el10 baseos 6.7 M binutils-gold aarch64 2.41-60.el10 baseos 938 k bzip2-libs aarch64 1.0.8-25.el10 baseos 42 k ca-certificates noarch 2025.2.80_v9.0.305-102.el10 baseos 1.1 M centos-gpg-keys noarch 10.0-19.el10 baseos 26 k centos-stream-repos noarch 10.0-19.el10 baseos 12 k coreutils-common aarch64 9.5-6.el10 baseos 2.1 M cracklib aarch64 2.9.11-8.el10 baseos 96 k cracklib-dicts aarch64 2.9.11-8.el10 baseos 3.6 M crypto-policies noarch 20251127-1.git27c2902.el10 baseos 98 k curl aarch64 8.12.1-4.el10 baseos 214 k cyrus-sasl-lib aarch64 2.1.28-27.el10 baseos 107 k debugedit aarch64 5.1-8.el10 appstream 80 k dwz aarch64 0.16-1.el10 appstream 137 k ed aarch64 1.20-5.el10 baseos 82 k efi-srpm-macros noarch 6-6.el10 appstream 24 k elfutils aarch64 0.194-1.el10 baseos 539 k elfutils-debuginfod-client aarch64 0.194-1.el10 baseos 42 k elfutils-default-yama-scope noarch 0.194-1.el10 baseos 8.3 k elfutils-libelf aarch64 0.194-1.el10 baseos 199 k elfutils-libs aarch64 0.194-1.el10 baseos 263 k file aarch64 5.45-8.el10 baseos 49 k file-libs aarch64 5.45-8.el10 baseos 762 k filesystem aarch64 3.18-17.el10 baseos 4.8 M fonts-srpm-macros noarch 1:2.0.5-18.el10 appstream 27 k forge-srpm-macros noarch 0.4.0-6.el10 appstream 21 k fpc-srpm-macros noarch 1.3-7.el10_1 epel 7.8 k gdb-minimal aarch64 16.3-2.el10 appstream 4.1 M gdbm aarch64 1:1.23-14.el10 baseos 150 k gdbm-libs aarch64 1:1.23-14.el10 baseos 56 k ghc-srpm-macros noarch 1.9.2-1.el10_0 epel 9.1 k glibc aarch64 2.39-99.el10 baseos 1.7 M glibc-common aarch64 2.39-99.el10 baseos 321 k glibc-gconv-extra aarch64 2.39-99.el10 baseos 1.8 M gmp aarch64 1:6.2.1-12.el10 baseos 268 k go-srpm-macros noarch 3.8.0-1.el10 appstream 27 k jansson aarch64 2.14-3.el10 baseos 47 k json-c aarch64 0.18-3.el10 baseos 46 k kernel-srpm-macros noarch 1.0-27.el10 appstream 8.7 k keyutils-libs aarch64 1.6.3-5.el10 baseos 33 k krb5-libs aarch64 1.21.3-8.el10 baseos 769 k libacl aarch64 2.3.2-4.el10 baseos 26 k libarchive aarch64 3.7.7-4.el10 baseos 406 k libattr aarch64 2.5.2-5.el10 baseos 19 k libblkid aarch64 2.40.2-13.el10 baseos 123 k libbrotli aarch64 1.1.0-7.el10 baseos 344 k libcap aarch64 2.69-7.el10 baseos 91 k libcap-ng aarch64 0.8.4-6.el10 baseos 33 k libcom_err aarch64 1.47.1-5.el10 baseos 26 k libcurl aarch64 8.12.1-4.el10 baseos 361 k libeconf aarch64 0.6.2-4.el10 baseos 33 k libevent aarch64 2.1.12-16.el10 baseos 256 k libfdisk aarch64 2.40.2-13.el10 baseos 154 k libffi aarch64 3.4.4-10.el10 baseos 38 k libgcc aarch64 14.3.1-4.2.el10 baseos 130 k libgomp aarch64 14.3.1-4.2.el10 baseos 361 k libidn2 aarch64 2.3.7-3.el10 baseos 119 k libmount aarch64 2.40.2-13.el10 baseos 153 k libnghttp2 aarch64 1.64.0-2.el10 baseos 77 k libpkgconf aarch64 2.1.0-3.el10 baseos 39 k libpsl aarch64 0.21.5-6.el10 baseos 65 k libpwquality aarch64 1.4.5-12.el10 baseos 123 k libselinux aarch64 3.9-3.el10 baseos 96 k libsemanage aarch64 3.9-2.el10 baseos 118 k libsepol aarch64 3.9-1.el10 baseos 331 k libsmartcols aarch64 2.40.2-13.el10 baseos 82 k libssh aarch64 0.11.1-3.el10 baseos 231 k libssh-config noarch 0.11.1-3.el10 baseos 8.4 k libstdc++ aarch64 14.3.1-4.2.el10 baseos 871 k libtasn1 aarch64 4.20.0-1.el10 baseos 74 k libunistring aarch64 1.1-10.el10 baseos 540 k libutempter aarch64 1.2.1-15.el10 baseos 28 k libuuid aarch64 2.40.2-13.el10 baseos 28 k libverto aarch64 0.3.2-10.el10 baseos 22 k libxcrypt aarch64 4.4.36-10.el10 baseos 124 k libxml2 aarch64 2.12.5-9.el10 baseos 673 k libzstd aarch64 1.5.5-9.el10 baseos 285 k lua-libs aarch64 5.4.6-7.el10 baseos 130 k lua-srpm-macros noarch 1-15.el10 appstream 9.8 k lz4-libs aarch64 1.9.4-8.el10 baseos 68 k mpfr aarch64 4.2.1-6.el10 baseos 324 k ncurses-base noarch 6.4-14.20240127.el10 baseos 100 k ncurses-libs aarch64 6.4-14.20240127.el10 baseos 330 k ocaml-srpm-macros noarch 10-4.el10 appstream 10 k openblas-srpm-macros noarch 2-19.el10 appstream 8.7 k openldap aarch64 2.6.10-1.el10 baseos 235 k openssl-fips-provider aarch64 1:3.5.1-6.el10 baseos 716 k openssl-libs aarch64 1:3.5.1-6.el10 baseos 2.1 M p11-kit aarch64 0.26.1-1.el10 baseos 535 k p11-kit-trust aarch64 0.26.1-1.el10 baseos 141 k package-notes-srpm-macros noarch 0.5-13.el10 appstream 10 k pam aarch64 1.6.1-9.el10 baseos 589 k pam-libs aarch64 1.6.1-9.el10 baseos 56 k pcre2 aarch64 10.44-1.el10.3 baseos 227 k pcre2-syntax noarch 10.44-1.el10.3 baseos 151 k perl-srpm-macros noarch 1-57.el10 appstream 9.5 k pkgconf aarch64 2.1.0-3.el10 baseos 44 k pkgconf-m4 noarch 2.1.0-3.el10 baseos 15 k pkgconf-pkg-config aarch64 2.1.0-3.el10 baseos 11 k popt aarch64 1.19-8.el10 baseos 65 k publicsuffix-list-dafsa noarch 20240107-5.el10 baseos 59 k pyproject-srpm-macros noarch 1.18.5-1.el10 appstream 13 k python-srpm-macros noarch 3.12-11.el10 appstream 22 k qt6-srpm-macros noarch 6.10.1-1.el10 appstream 9.1 k readline aarch64 8.2-11.el10 baseos 212 k rpm aarch64 4.19.1.1-21.el10 baseos 562 k rpm-build-libs aarch64 4.19.1.1-21.el10 baseos 88 k rpm-libs aarch64 4.19.1.1-21.el10 baseos 298 k rpm-sequoia aarch64 1.9.0.3-1.el10 baseos 902 k rust-toolset-srpm-macros noarch 1.92.0-1.el10 appstream 11 k setup noarch 2.14.5-7.el10 baseos 153 k sqlite-libs aarch64 3.46.1-5.el10 baseos 730 k systemd-libs aarch64 257-21.el10 baseos 788 k util-linux-core aarch64 2.40.2-13.el10 baseos 543 k xz-libs aarch64 1:5.6.2-4.el10 baseos 110 k zip aarch64 3.0-45.el10 baseos 264 k zlib-ng-compat aarch64 2.2.3-3.el10 baseos 63 k zstd aarch64 1.5.5-9.el10 baseos 455 k Transaction Summary ================================================================================ Install 147 Packages Total download size: 60 M Installed size: 215 M Downloading Packages: (1/147): alternatives-1.30-2.el10.aarch64.rpm 3.1 MB/s | 41 kB 00:00 (2/147): authselect-1.5.0-8.el10.aarch64.rpm 8.6 MB/s | 144 kB 00:00 (3/147): audit-libs-4.0.3-5.el10.aarch64.rpm 7.3 MB/s | 129 kB 00:00 (4/147): authselect-libs-1.5.0-8.el10.aarch64.r 37 MB/s | 221 kB 00:00 (5/147): basesystem-11-22.el10.noarch.rpm 1.9 MB/s | 4.3 kB 00:00 (6/147): bash-5.2.26-6.el10.aarch64.rpm 170 MB/s | 1.8 MB 00:00 (7/147): binutils-gold-2.41-60.el10.aarch64.rpm 62 MB/s | 938 kB 00:00 (8/147): bzip2-1.0.8-25.el10.aarch64.rpm 3.8 MB/s | 54 kB 00:00 (9/147): binutils-2.41-60.el10.aarch64.rpm 188 MB/s | 6.7 MB 00:00 (10/147): bzip2-libs-1.0.8-25.el10.aarch64.rpm 2.0 MB/s | 42 kB 00:00 (11/147): centos-gpg-keys-10.0-19.el10.noarch.r 8.6 MB/s | 26 kB 00:00 (12/147): centos-stream-release-10.0-19.el10.no 9.6 MB/s | 30 kB 00:00 (13/147): ca-certificates-2025.2.80_v9.0.305-10 60 MB/s | 1.1 MB 00:00 (14/147): centos-stream-repos-10.0-19.el10.noar 3.8 MB/s | 12 kB 00:00 (15/147): coreutils-9.5-6.el10.aarch64.rpm 148 MB/s | 1.1 MB 00:00 (16/147): cpio-2.15-3.el10.aarch64.rpm 42 MB/s | 290 kB 00:00 (17/147): coreutils-common-9.5-6.el10.aarch64.r 154 MB/s | 2.1 MB 00:00 (18/147): cracklib-2.9.11-8.el10.aarch64.rpm 9.9 MB/s | 96 kB 00:00 (19/147): crypto-policies-20251127-1.git27c2902 17 MB/s | 98 kB 00:00 (20/147): curl-8.12.1-4.el10.aarch64.rpm 35 MB/s | 214 kB 00:00 (21/147): cracklib-dicts-2.9.11-8.el10.aarch64. 160 MB/s | 3.6 MB 00:00 (22/147): cyrus-sasl-lib-2.1.28-27.el10.aarch64 9.9 MB/s | 107 kB 00:00 (23/147): diffutils-3.10-8.el10.aarch64.rpm 35 MB/s | 405 kB 00:00 (24/147): ed-1.20-5.el10.aarch64.rpm 23 MB/s | 82 kB 00:00 (25/147): elfutils-0.194-1.el10.aarch64.rpm 101 MB/s | 539 kB 00:00 (26/147): elfutils-debuginfod-client-0.194-1.el 10 MB/s | 42 kB 00:00 (27/147): elfutils-default-yama-scope-0.194-1.e 2.9 MB/s | 8.3 kB 00:00 (28/147): elfutils-libelf-0.194-1.el10.aarch64. 59 MB/s | 199 kB 00:00 (29/147): file-5.45-8.el10.aarch64.rpm 17 MB/s | 49 kB 00:00 (30/147): elfutils-libs-0.194-1.el10.aarch64.rp 61 MB/s | 263 kB 00:00 (31/147): file-libs-5.45-8.el10.aarch64.rpm 119 MB/s | 762 kB 00:00 (32/147): findutils-4.10.0-5.el10.aarch64.rpm 68 MB/s | 555 kB 00:00 (33/147): filesystem-3.18-17.el10.aarch64.rpm 200 MB/s | 4.8 MB 00:00 (34/147): gawk-5.3.0-6.el10.aarch64.rpm 50 MB/s | 1.1 MB 00:00 (35/147): gdbm-1.23-14.el10.aarch64.rpm 7.6 MB/s | 150 kB 00:00 (36/147): gdbm-libs-1.23-14.el10.aarch64.rpm 8.0 MB/s | 56 kB 00:00 (37/147): glibc-common-2.39-99.el10.aarch64.rpm 60 MB/s | 321 kB 00:00 (38/147): glibc-2.39-99.el10.aarch64.rpm 137 MB/s | 1.7 MB 00:00 (39/147): glibc-minimal-langpack-2.39-99.el10.a 5.1 MB/s | 39 kB 00:00 (40/147): glibc-gconv-extra-2.39-99.el10.aarch6 116 MB/s | 1.8 MB 00:00 (41/147): gmp-6.2.1-12.el10.aarch64.rpm 37 MB/s | 268 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(144/147): epel-rpm-macros-10-6.el10_2.noarch.r 891 kB/s | 8.2 kB 00:00 (145/147): ansible-srpm-macros-1-16.1.el10_0.no 1.9 MB/s | 20 kB 00:00 (146/147): fpc-srpm-macros-1.3-7.el10_1.noarch. 787 kB/s | 7.8 kB 00:00 (147/147): ghc-srpm-macros-1.9.2-1.el10_0.noarc 2.8 MB/s | 9.1 kB 00:00 -------------------------------------------------------------------------------- Total 84 MB/s | 60 MB 00:00 CentOS Stream 10 - BaseOS 1.6 MB/s | 1.6 kB 00:00 Importing GPG key 0x8483C65D: Userid : "CentOS (CentOS Official Signing Key) " Fingerprint: 99DB 70FA E1D7 CE22 7FB6 4882 05B5 55B3 8483 C65D From : /usr/share/distribution-gpg-keys/centos/RPM-GPG-KEY-CentOS-Official-SHA256 Key imported successfully Extra Packages for Enterprise Linux 10 - aarch6 1.6 MB/s | 1.6 kB 00:00 Importing GPG key 0xE37ED158: Userid : "Fedora (epel10) " Fingerprint: 7D8D 15CB FC4E 6268 8591 FB26 33D9 8517 E37E D158 From : /usr/share/distribution-gpg-keys/epel/RPM-GPG-KEY-EPEL-10 Key imported successfully Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Running scriptlet: filesystem-3.18-17.el10.aarch64 1/1 Preparing : 1/1 Installing : libgcc-14.3.1-4.2.el10.aarch64 1/147 Running scriptlet: libgcc-14.3.1-4.2.el10.aarch64 1/147 Installing : ghc-srpm-macros-1.9.2-1.el10_0.noarch 2/147 Installing : fpc-srpm-macros-1.3-7.el10_1.noarch 3/147 Installing : ansible-srpm-macros-1-16.1.el10_0.noarch 4/147 Installing : rust-toolset-srpm-macros-1.92.0-1.el10.noarch 5/147 Installing : qt6-srpm-macros-6.10.1-1.el10.noarch 6/147 Installing : perl-srpm-macros-1-57.el10.noarch 7/147 Installing : package-notes-srpm-macros-0.5-13.el10.noarch 8/147 Installing : openblas-srpm-macros-2-19.el10.noarch 9/147 Installing : ocaml-srpm-macros-10-4.el10.noarch 10/147 Installing : kernel-srpm-macros-1.0-27.el10.noarch 11/147 Installing : publicsuffix-list-dafsa-20240107-5.el10.noarch 12/147 Installing : pkgconf-m4-2.1.0-3.el10.noarch 13/147 Installing : pcre2-syntax-10.44-1.el10.3.noarch 14/147 Installing : 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81/147 Installing : p11-kit-0.26.1-1.el10.aarch64 82/147 Installing : p11-kit-trust-0.26.1-1.el10.aarch64 83/147 Running scriptlet: p11-kit-trust-0.26.1-1.el10.aarch64 83/147 Installing : openssl-fips-provider-1:3.5.1-6.el10.aarch64 84/147 Installing : openssl-libs-1:3.5.1-6.el10.aarch64 85/147 Installing : coreutils-9.5-6.el10.aarch64 86/147 Running scriptlet: ca-certificates-2025.2.80_v9.0.305-102.el10.noar 87/147 Installing : ca-certificates-2025.2.80_v9.0.305-102.el10.noar 87/147 Running scriptlet: ca-certificates-2025.2.80_v9.0.305-102.el10.noar 87/147 Installing : authselect-libs-1.5.0-8.el10.aarch64 88/147 Installing : gzip-1.13-3.el10.aarch64 89/147 Installing : cracklib-2.9.11-8.el10.aarch64 90/147 Installing : cracklib-dicts-2.9.11-8.el10.aarch64 91/147 Installing : libpwquality-1.4.5-12.el10.aarch64 92/147 Installing : libevent-2.1.12-16.el10.aarch64 93/147 Installing : rpm-sequoia-1.9.0.3-1.el10.aarch64 94/147 Installing : zip-3.0-45.el10.aarch64 95/147 Installing : cyrus-sasl-lib-2.1.28-27.el10.aarch64 96/147 Installing : openldap-2.6.10-1.el10.aarch64 97/147 Installing : gdbm-1:1.23-14.el10.aarch64 98/147 Installing : pam-1.6.1-9.el10.aarch64 99/147 Installing : libfdisk-2.40.2-13.el10.aarch64 100/147 Installing : libxml2-2.12.5-9.el10.aarch64 101/147 Installing : libarchive-3.7.7-4.el10.aarch64 102/147 Installing : bzip2-1.0.8-25.el10.aarch64 103/147 Installing : sqlite-libs-3.46.1-5.el10.aarch64 104/147 Installing : rpm-libs-4.19.1.1-21.el10.aarch64 105/147 Installing : ed-1.20-5.el10.aarch64 106/147 Installing : patch-2.7.6-26.el10.aarch64 107/147 Installing : elfutils-default-yama-scope-0.194-1.el10.noarch 108/147 Running scriptlet: elfutils-default-yama-scope-0.194-1.el10.noarch 108/147 Installing : cpio-2.15-3.el10.aarch64 109/147 Installing : diffutils-3.10-8.el10.aarch64 110/147 Installing : json-c-0.18-3.el10.aarch64 111/147 Installing : keyutils-libs-1.6.3-5.el10.aarch64 112/147 Installing : libbrotli-1.1.0-7.el10.aarch64 113/147 Installing : libcom_err-1.47.1-5.el10.aarch64 114/147 Installing : libgomp-14.3.1-4.2.el10.aarch64 115/147 Installing : libnghttp2-1.64.0-2.el10.aarch64 116/147 Installing : libpkgconf-2.1.0-3.el10.aarch64 117/147 Installing : pkgconf-2.1.0-3.el10.aarch64 118/147 Installing : pkgconf-pkg-config-2.1.0-3.el10.aarch64 119/147 Installing : libverto-0.3.2-10.el10.aarch64 120/147 Installing : krb5-libs-1.21.3-8.el10.aarch64 121/147 Installing : libssh-0.11.1-3.el10.aarch64 122/147 Installing : libcurl-8.12.1-4.el10.aarch64 123/147 Installing : elfutils-libs-0.194-1.el10.aarch64 124/147 Installing : elfutils-debuginfod-client-0.194-1.el10.aarch64 125/147 Installing : binutils-gold-2.41-60.el10.aarch64 126/147 Running scriptlet: binutils-gold-2.41-60.el10.aarch64 126/147 Installing : binutils-2.41-60.el10.aarch64 127/147 Running scriptlet: binutils-2.41-60.el10.aarch64 127/147 Installing : elfutils-0.194-1.el10.aarch64 128/147 Installing : gdb-minimal-16.3-2.el10.aarch64 129/147 Installing : debugedit-5.1-8.el10.aarch64 130/147 Installing : rpm-build-libs-4.19.1.1-21.el10.aarch64 131/147 Installing : curl-8.12.1-4.el10.aarch64 132/147 Running scriptlet: rpm-4.19.1.1-21.el10.aarch64 133/147 Installing : rpm-4.19.1.1-21.el10.aarch64 133/147 Installing : efi-srpm-macros-6-6.el10.noarch 134/147 Installing : lua-srpm-macros-1-15.el10.noarch 135/147 Installing : fonts-srpm-macros-1:2.0.5-18.el10.noarch 136/147 Installing : forge-srpm-macros-0.4.0-6.el10.noarch 137/147 Installing : go-srpm-macros-3.8.0-1.el10.noarch 138/147 Installing : python-srpm-macros-3.12-11.el10.noarch 139/147 Installing : redhat-rpm-config-295-1.el10.noarch 140/147 Installing : rpm-build-4.19.1.1-21.el10.aarch64 141/147 Installing : pyproject-srpm-macros-1.18.5-1.el10.noarch 142/147 Installing : util-linux-2.40.2-13.el10.aarch64 143/147 Running scriptlet: util-linux-2.40.2-13.el10.aarch64 143/147 Installing : authselect-1.5.0-8.el10.aarch64 144/147 Installing : which-2.21-44.el10.aarch64 145/147 Installing : info-7.1-6.el10.aarch64 146/147 Installing : epel-rpm-macros-10-6.el10_2.noarch 147/147 Running scriptlet: filesystem-3.18-17.el10.aarch64 147/147 Running scriptlet: ca-certificates-2025.2.80_v9.0.305-102.el10.noar 147/147 Running scriptlet: authselect-libs-1.5.0-8.el10.aarch64 147/147 Running scriptlet: rpm-4.19.1.1-21.el10.aarch64 147/147 Running scriptlet: epel-rpm-macros-10-6.el10_2.noarch 147/147 Installed: alternatives-1.30-2.el10.aarch64 ansible-srpm-macros-1-16.1.el10_0.noarch audit-libs-4.0.3-5.el10.aarch64 authselect-1.5.0-8.el10.aarch64 authselect-libs-1.5.0-8.el10.aarch64 basesystem-11-22.el10.noarch bash-5.2.26-6.el10.aarch64 binutils-2.41-60.el10.aarch64 binutils-gold-2.41-60.el10.aarch64 bzip2-1.0.8-25.el10.aarch64 bzip2-libs-1.0.8-25.el10.aarch64 ca-certificates-2025.2.80_v9.0.305-102.el10.noarch centos-gpg-keys-10.0-19.el10.noarch centos-stream-release-10.0-19.el10.noarch centos-stream-repos-10.0-19.el10.noarch coreutils-9.5-6.el10.aarch64 coreutils-common-9.5-6.el10.aarch64 cpio-2.15-3.el10.aarch64 cracklib-2.9.11-8.el10.aarch64 cracklib-dicts-2.9.11-8.el10.aarch64 crypto-policies-20251127-1.git27c2902.el10.noarch curl-8.12.1-4.el10.aarch64 cyrus-sasl-lib-2.1.28-27.el10.aarch64 debugedit-5.1-8.el10.aarch64 diffutils-3.10-8.el10.aarch64 dwz-0.16-1.el10.aarch64 ed-1.20-5.el10.aarch64 efi-srpm-macros-6-6.el10.noarch elfutils-0.194-1.el10.aarch64 elfutils-debuginfod-client-0.194-1.el10.aarch64 elfutils-default-yama-scope-0.194-1.el10.noarch elfutils-libelf-0.194-1.el10.aarch64 elfutils-libs-0.194-1.el10.aarch64 epel-rpm-macros-10-6.el10_2.noarch file-5.45-8.el10.aarch64 file-libs-5.45-8.el10.aarch64 filesystem-3.18-17.el10.aarch64 findutils-1:4.10.0-5.el10.aarch64 fonts-srpm-macros-1:2.0.5-18.el10.noarch forge-srpm-macros-0.4.0-6.el10.noarch fpc-srpm-macros-1.3-7.el10_1.noarch gawk-5.3.0-6.el10.aarch64 gdb-minimal-16.3-2.el10.aarch64 gdbm-1:1.23-14.el10.aarch64 gdbm-libs-1:1.23-14.el10.aarch64 ghc-srpm-macros-1.9.2-1.el10_0.noarch glibc-2.39-99.el10.aarch64 glibc-common-2.39-99.el10.aarch64 glibc-gconv-extra-2.39-99.el10.aarch64 glibc-minimal-langpack-2.39-99.el10.aarch64 gmp-1:6.2.1-12.el10.aarch64 go-srpm-macros-3.8.0-1.el10.noarch grep-3.11-10.el10.aarch64 gzip-1.13-3.el10.aarch64 info-7.1-6.el10.aarch64 jansson-2.14-3.el10.aarch64 json-c-0.18-3.el10.aarch64 kernel-srpm-macros-1.0-27.el10.noarch keyutils-libs-1.6.3-5.el10.aarch64 krb5-libs-1.21.3-8.el10.aarch64 libacl-2.3.2-4.el10.aarch64 libarchive-3.7.7-4.el10.aarch64 libattr-2.5.2-5.el10.aarch64 libblkid-2.40.2-13.el10.aarch64 libbrotli-1.1.0-7.el10.aarch64 libcap-2.69-7.el10.aarch64 libcap-ng-0.8.4-6.el10.aarch64 libcom_err-1.47.1-5.el10.aarch64 libcurl-8.12.1-4.el10.aarch64 libeconf-0.6.2-4.el10.aarch64 libevent-2.1.12-16.el10.aarch64 libfdisk-2.40.2-13.el10.aarch64 libffi-3.4.4-10.el10.aarch64 libgcc-14.3.1-4.2.el10.aarch64 libgomp-14.3.1-4.2.el10.aarch64 libidn2-2.3.7-3.el10.aarch64 libmount-2.40.2-13.el10.aarch64 libnghttp2-1.64.0-2.el10.aarch64 libpkgconf-2.1.0-3.el10.aarch64 libpsl-0.21.5-6.el10.aarch64 libpwquality-1.4.5-12.el10.aarch64 libselinux-3.9-3.el10.aarch64 libsemanage-3.9-2.el10.aarch64 libsepol-3.9-1.el10.aarch64 libsmartcols-2.40.2-13.el10.aarch64 libssh-0.11.1-3.el10.aarch64 libssh-config-0.11.1-3.el10.noarch libstdc++-14.3.1-4.2.el10.aarch64 libtasn1-4.20.0-1.el10.aarch64 libunistring-1.1-10.el10.aarch64 libutempter-1.2.1-15.el10.aarch64 libuuid-2.40.2-13.el10.aarch64 libverto-0.3.2-10.el10.aarch64 libxcrypt-4.4.36-10.el10.aarch64 libxml2-2.12.5-9.el10.aarch64 libzstd-1.5.5-9.el10.aarch64 lua-libs-5.4.6-7.el10.aarch64 lua-srpm-macros-1-15.el10.noarch lz4-libs-1.9.4-8.el10.aarch64 mpfr-4.2.1-6.el10.aarch64 ncurses-base-6.4-14.20240127.el10.noarch ncurses-libs-6.4-14.20240127.el10.aarch64 ocaml-srpm-macros-10-4.el10.noarch openblas-srpm-macros-2-19.el10.noarch openldap-2.6.10-1.el10.aarch64 openssl-fips-provider-1:3.5.1-6.el10.aarch64 openssl-libs-1:3.5.1-6.el10.aarch64 p11-kit-0.26.1-1.el10.aarch64 p11-kit-trust-0.26.1-1.el10.aarch64 package-notes-srpm-macros-0.5-13.el10.noarch pam-1.6.1-9.el10.aarch64 pam-libs-1.6.1-9.el10.aarch64 patch-2.7.6-26.el10.aarch64 pcre2-10.44-1.el10.3.aarch64 pcre2-syntax-10.44-1.el10.3.noarch perl-srpm-macros-1-57.el10.noarch pkgconf-2.1.0-3.el10.aarch64 pkgconf-m4-2.1.0-3.el10.noarch pkgconf-pkg-config-2.1.0-3.el10.aarch64 popt-1.19-8.el10.aarch64 publicsuffix-list-dafsa-20240107-5.el10.noarch pyproject-srpm-macros-1.18.5-1.el10.noarch python-srpm-macros-3.12-11.el10.noarch qt6-srpm-macros-6.10.1-1.el10.noarch readline-8.2-11.el10.aarch64 redhat-rpm-config-295-1.el10.noarch rpm-4.19.1.1-21.el10.aarch64 rpm-build-4.19.1.1-21.el10.aarch64 rpm-build-libs-4.19.1.1-21.el10.aarch64 rpm-libs-4.19.1.1-21.el10.aarch64 rpm-sequoia-1.9.0.3-1.el10.aarch64 rust-toolset-srpm-macros-1.92.0-1.el10.noarch sed-4.9-3.el10.aarch64 setup-2.14.5-7.el10.noarch shadow-utils-2:4.15.0-9.el10.aarch64 sqlite-libs-3.46.1-5.el10.aarch64 systemd-libs-257-21.el10.aarch64 tar-2:1.35-10.el10.aarch64 unzip-6.0-69.el10.aarch64 util-linux-2.40.2-13.el10.aarch64 util-linux-core-2.40.2-13.el10.aarch64 which-2.21-44.el10.aarch64 xz-1:5.6.2-4.el10.aarch64 xz-libs-1:5.6.2-4.el10.aarch64 zip-3.0-45.el10.aarch64 zlib-ng-compat-2.2.3-3.el10.aarch64 zstd-1.5.5-9.el10.aarch64 Complete! Finish: installing minimal buildroot with dnf Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: alternatives-1.30-2.el10.aarch64 ansible-srpm-macros-1-16.1.el10_0.noarch audit-libs-4.0.3-5.el10.aarch64 authselect-1.5.0-8.el10.aarch64 authselect-libs-1.5.0-8.el10.aarch64 basesystem-11-22.el10.noarch bash-5.2.26-6.el10.aarch64 binutils-2.41-60.el10.aarch64 binutils-gold-2.41-60.el10.aarch64 bzip2-1.0.8-25.el10.aarch64 bzip2-libs-1.0.8-25.el10.aarch64 ca-certificates-2025.2.80_v9.0.305-102.el10.noarch centos-gpg-keys-10.0-19.el10.noarch centos-stream-release-10.0-19.el10.noarch centos-stream-repos-10.0-19.el10.noarch coreutils-9.5-6.el10.aarch64 coreutils-common-9.5-6.el10.aarch64 cpio-2.15-3.el10.aarch64 cracklib-2.9.11-8.el10.aarch64 cracklib-dicts-2.9.11-8.el10.aarch64 crypto-policies-20251127-1.git27c2902.el10.noarch curl-8.12.1-4.el10.aarch64 cyrus-sasl-lib-2.1.28-27.el10.aarch64 debugedit-5.1-8.el10.aarch64 diffutils-3.10-8.el10.aarch64 dwz-0.16-1.el10.aarch64 ed-1.20-5.el10.aarch64 efi-srpm-macros-6-6.el10.noarch elfutils-0.194-1.el10.aarch64 elfutils-debuginfod-client-0.194-1.el10.aarch64 elfutils-default-yama-scope-0.194-1.el10.noarch elfutils-libelf-0.194-1.el10.aarch64 elfutils-libs-0.194-1.el10.aarch64 epel-rpm-macros-10-6.el10_2.noarch file-5.45-8.el10.aarch64 file-libs-5.45-8.el10.aarch64 filesystem-3.18-17.el10.aarch64 findutils-4.10.0-5.el10.aarch64 fonts-srpm-macros-2.0.5-18.el10.noarch forge-srpm-macros-0.4.0-6.el10.noarch fpc-srpm-macros-1.3-7.el10_1.noarch gawk-5.3.0-6.el10.aarch64 gdb-minimal-16.3-2.el10.aarch64 gdbm-1.23-14.el10.aarch64 gdbm-libs-1.23-14.el10.aarch64 ghc-srpm-macros-1.9.2-1.el10_0.noarch glibc-2.39-99.el10.aarch64 glibc-common-2.39-99.el10.aarch64 glibc-gconv-extra-2.39-99.el10.aarch64 glibc-minimal-langpack-2.39-99.el10.aarch64 gmp-6.2.1-12.el10.aarch64 go-srpm-macros-3.8.0-1.el10.noarch gpg-pubkey-8483c65d-5ccc5b19 gpg-pubkey-e37ed158-65785fa9 grep-3.11-10.el10.aarch64 gzip-1.13-3.el10.aarch64 info-7.1-6.el10.aarch64 jansson-2.14-3.el10.aarch64 json-c-0.18-3.el10.aarch64 kernel-srpm-macros-1.0-27.el10.noarch keyutils-libs-1.6.3-5.el10.aarch64 krb5-libs-1.21.3-8.el10.aarch64 libacl-2.3.2-4.el10.aarch64 libarchive-3.7.7-4.el10.aarch64 libattr-2.5.2-5.el10.aarch64 libblkid-2.40.2-13.el10.aarch64 libbrotli-1.1.0-7.el10.aarch64 libcap-2.69-7.el10.aarch64 libcap-ng-0.8.4-6.el10.aarch64 libcom_err-1.47.1-5.el10.aarch64 libcurl-8.12.1-4.el10.aarch64 libeconf-0.6.2-4.el10.aarch64 libevent-2.1.12-16.el10.aarch64 libfdisk-2.40.2-13.el10.aarch64 libffi-3.4.4-10.el10.aarch64 libgcc-14.3.1-4.2.el10.aarch64 libgomp-14.3.1-4.2.el10.aarch64 libidn2-2.3.7-3.el10.aarch64 libmount-2.40.2-13.el10.aarch64 libnghttp2-1.64.0-2.el10.aarch64 libpkgconf-2.1.0-3.el10.aarch64 libpsl-0.21.5-6.el10.aarch64 libpwquality-1.4.5-12.el10.aarch64 libselinux-3.9-3.el10.aarch64 libsemanage-3.9-2.el10.aarch64 libsepol-3.9-1.el10.aarch64 libsmartcols-2.40.2-13.el10.aarch64 libssh-0.11.1-3.el10.aarch64 libssh-config-0.11.1-3.el10.noarch libstdc++-14.3.1-4.2.el10.aarch64 libtasn1-4.20.0-1.el10.aarch64 libunistring-1.1-10.el10.aarch64 libutempter-1.2.1-15.el10.aarch64 libuuid-2.40.2-13.el10.aarch64 libverto-0.3.2-10.el10.aarch64 libxcrypt-4.4.36-10.el10.aarch64 libxml2-2.12.5-9.el10.aarch64 libzstd-1.5.5-9.el10.aarch64 lua-libs-5.4.6-7.el10.aarch64 lua-srpm-macros-1-15.el10.noarch lz4-libs-1.9.4-8.el10.aarch64 mpfr-4.2.1-6.el10.aarch64 ncurses-base-6.4-14.20240127.el10.noarch ncurses-libs-6.4-14.20240127.el10.aarch64 ocaml-srpm-macros-10-4.el10.noarch openblas-srpm-macros-2-19.el10.noarch openldap-2.6.10-1.el10.aarch64 openssl-fips-provider-3.5.1-6.el10.aarch64 openssl-libs-3.5.1-6.el10.aarch64 p11-kit-0.26.1-1.el10.aarch64 p11-kit-trust-0.26.1-1.el10.aarch64 package-notes-srpm-macros-0.5-13.el10.noarch pam-1.6.1-9.el10.aarch64 pam-libs-1.6.1-9.el10.aarch64 patch-2.7.6-26.el10.aarch64 pcre2-10.44-1.el10.3.aarch64 pcre2-syntax-10.44-1.el10.3.noarch perl-srpm-macros-1-57.el10.noarch pkgconf-2.1.0-3.el10.aarch64 pkgconf-m4-2.1.0-3.el10.noarch pkgconf-pkg-config-2.1.0-3.el10.aarch64 popt-1.19-8.el10.aarch64 publicsuffix-list-dafsa-20240107-5.el10.noarch pyproject-srpm-macros-1.18.5-1.el10.noarch python-srpm-macros-3.12-11.el10.noarch qt6-srpm-macros-6.10.1-1.el10.noarch readline-8.2-11.el10.aarch64 redhat-rpm-config-295-1.el10.noarch rpm-4.19.1.1-21.el10.aarch64 rpm-build-4.19.1.1-21.el10.aarch64 rpm-build-libs-4.19.1.1-21.el10.aarch64 rpm-libs-4.19.1.1-21.el10.aarch64 rpm-sequoia-1.9.0.3-1.el10.aarch64 rust-toolset-srpm-macros-1.92.0-1.el10.noarch sed-4.9-3.el10.aarch64 setup-2.14.5-7.el10.noarch shadow-utils-4.15.0-9.el10.aarch64 sqlite-libs-3.46.1-5.el10.aarch64 systemd-libs-257-21.el10.aarch64 tar-1.35-10.el10.aarch64 unzip-6.0-69.el10.aarch64 util-linux-2.40.2-13.el10.aarch64 util-linux-core-2.40.2-13.el10.aarch64 which-2.21-44.el10.aarch64 xz-5.6.2-4.el10.aarch64 xz-libs-5.6.2-4.el10.aarch64 zip-3.0-45.el10.aarch64 zlib-ng-compat-2.2.3-3.el10.aarch64 zstd-1.5.5-9.el10.aarch64 Start: buildsrpm Start: rpmbuild -bs Building target platforms: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1769040000 Wrote: /builddir/build/SRPMS/htslib-1.23-1.el10.src.rpm Finish: rpmbuild -bs INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/centos-stream+epel-10-aarch64-1769500621.779357/root/var/log/dnf.rpm.log /var/lib/mock/centos-stream+epel-10-aarch64-1769500621.779357/root/var/log/dnf.librepo.log /var/lib/mock/centos-stream+epel-10-aarch64-1769500621.779357/root/var/log/dnf.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-hu4s1yu1/htslib/htslib.spec) Config(child) 0 minutes 31 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-1.23-1.el10.src.rpm) Config(centos-stream+epel-10-aarch64) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/centos-stream+epel-10-aarch64-bootstrap-1769500621.779357/root. INFO: reusing tmpfs at /var/lib/mock/centos-stream+epel-10-aarch64-bootstrap-1769500621.779357/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/centos-stream+epel-10-aarch64-1769500621.779357/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-4.19.1.1-21.el10.aarch64 rpm-sequoia-1.9.0.3-1.el10.aarch64 python3-dnf-4.20.0-19.el10.noarch python3-dnf-plugins-core-4.7.0-10.el10.noarch yum-4.20.0-19.el10.noarch Finish: chroot init Start: build phase for htslib-1.23-1.el10.src.rpm Start: build setup for htslib-1.23-1.el10.src.rpm Building target platforms: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1769040000 Wrote: /builddir/build/SRPMS/htslib-1.23-1.el10.src.rpm No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 26 kB/s | 1.5 kB 00:00 CentOS Stream 10 - BaseOS 64 kB/s | 5.5 kB 00:00 CentOS Stream 10 - AppStream 110 kB/s | 5.5 kB 00:00 CentOS Stream 10 - CRB 92 kB/s | 4.4 kB 00:00 CentOS Stream 10 - Extras packages 153 kB/s | 7.4 kB 00:00 Extra Packages for Enterprise Linux 10 - aarch6 279 kB/s | 22 kB 00:00 Dependencies resolved. ================================================================================ Package Arch Version Repository Size ================================================================================ Installing: bzip2-devel aarch64 1.0.8-25.el10 appstream 215 k gcc aarch64 14.3.1-4.2.el10 appstream 35 M libcurl-devel aarch64 8.12.1-4.el10 appstream 946 k make aarch64 1:4.4.1-9.el10 baseos 585 k openssl-devel aarch64 1:3.5.1-6.el10 appstream 4.2 M perl-Data-Dumper aarch64 2.189-512.el10 baseos 56 k perl-FindBin noarch 1.54-514.el10 appstream 15 k perl-Getopt-Long noarch 1:2.58-3.el10 baseos 65 k perl-interpreter aarch64 4:5.40.2-514.el10 appstream 73 k perl-lib aarch64 0.65-514.el10 appstream 16 k xz-devel aarch64 1:5.6.2-4.el10 appstream 64 k zlib-ng-compat-devel aarch64 2.2.3-3.el10 appstream 36 k Installing dependencies: annobin-docs noarch 13.02-2.el10 appstream 87 k annobin-plugin-gcc aarch64 13.02-2.el10 appstream 997 k brotli aarch64 1.1.0-7.el10 appstream 19 k brotli-devel aarch64 1.1.0-7.el10 appstream 33 k cmake-filesystem aarch64 3.31.8-1.el10 appstream 21 k cpp aarch64 14.3.1-4.2.el10 appstream 11 M gcc-plugin-annobin aarch64 14.3.1-4.2.el10 appstream 69 k glibc-devel aarch64 2.39-99.el10 appstream 589 k groff-base aarch64 1.23.0-10.el10 baseos 1.1 M kernel-headers aarch64 6.12.0-191.el10 appstream 3.1 M keyutils-libs-devel aarch64 1.6.3-5.el10 appstream 61 k krb5-devel aarch64 1.21.3-8.el10 appstream 145 k libasan aarch64 14.3.1-4.2.el10 appstream 532 k libatomic aarch64 14.3.1-4.2.el10 baseos 58 k libcom_err-devel aarch64 1.47.1-5.el10 appstream 16 k libidn2-devel aarch64 2.3.7-3.el10 appstream 71 k libkadm5 aarch64 1.21.3-8.el10 baseos 78 k libmpc aarch64 1.3.1-7.el10 appstream 73 k libnghttp2-devel aarch64 1.64.0-2.el10 appstream 57 k libpsl-devel aarch64 0.21.5-6.el10 appstream 35 k libselinux-devel aarch64 3.9-3.el10 appstream 161 k libsepol-devel aarch64 3.9-1.el10 appstream 48 k libssh-devel aarch64 0.11.1-3.el10 appstream 41 k libubsan aarch64 14.3.1-4.2.el10 appstream 238 k libverto-devel aarch64 0.3.2-10.el10 appstream 15 k libxcrypt-devel aarch64 4.4.36-10.el10 appstream 30 k ncurses aarch64 6.4-14.20240127.el10 baseos 421 k pcre2-devel aarch64 10.44-1.el10.3 appstream 532 k pcre2-utf16 aarch64 10.44-1.el10.3 appstream 208 k pcre2-utf32 aarch64 10.44-1.el10.3 appstream 196 k perl-AutoLoader noarch 5.74-514.el10 appstream 22 k perl-B aarch64 1.89-514.el10 appstream 179 k perl-Carp noarch 1.54-511.el10 baseos 30 k perl-Class-Struct noarch 0.68-514.el10 appstream 23 k perl-Digest noarch 1.20-511.el10 baseos 26 k perl-Digest-MD5 aarch64 2.59-6.el10 baseos 37 k perl-DynaLoader aarch64 1.56-514.el10 appstream 27 k perl-Encode aarch64 4:3.21-511.el10 baseos 1.1 M perl-Errno aarch64 1.38-514.el10 appstream 16 k perl-Exporter noarch 5.78-511.el10 baseos 32 k perl-Fcntl aarch64 1.18-514.el10 appstream 30 k perl-File-Basename noarch 2.86-514.el10 appstream 18 k perl-File-Path noarch 2.18-512.el10 appstream 35 k perl-File-Temp noarch 1:0.231.100-512.el10 baseos 60 k perl-File-stat noarch 1.14-514.el10 appstream 18 k perl-FileHandle noarch 2.05-514.el10 appstream 16 k perl-Getopt-Std noarch 1.14-514.el10 appstream 16 k perl-HTTP-Tiny noarch 0.088-512.el10 baseos 57 k perl-IO aarch64 1.55-514.el10 appstream 81 k perl-IO-Socket-IP noarch 0.42-512.el10 baseos 43 k perl-IO-Socket-SSL noarch 2.085-3.el10 baseos 227 k perl-IPC-Open3 noarch 1.22-514.el10 appstream 23 k perl-MIME-Base64 aarch64 3.16-511.el10 baseos 31 k perl-Mozilla-CA noarch 20231213-5.el10 baseos 15 k perl-Net-SSLeay aarch64 1.94-8.el10 appstream 381 k perl-POSIX aarch64 2.20-514.el10 appstream 98 k perl-PathTools aarch64 3.91-512.el10 baseos 85 k perl-Pod-Escapes noarch 1:1.07-511.el10 baseos 21 k perl-Pod-Perldoc noarch 3.28.01-512.el10 baseos 84 k perl-Pod-Simple noarch 1:3.45-511.el10 baseos 218 k perl-Pod-Usage noarch 4:2.03-511.el10 baseos 41 k perl-Scalar-List-Utils aarch64 5:1.63-511.el10 baseos 73 k perl-SelectSaver noarch 1.02-514.el10 appstream 12 k perl-Socket aarch64 4:2.038-511.el10 baseos 56 k perl-Storable aarch64 1:3.32-511.el10 baseos 98 k perl-Symbol noarch 1.09-514.el10 appstream 15 k perl-Term-ANSIColor noarch 5.01-512.el10 baseos 49 k perl-Term-Cap noarch 1.18-511.el10 baseos 23 k perl-Text-ParseWords noarch 3.31-511.el10 baseos 17 k perl-Text-Tabs+Wrap noarch 2024.001-511.el10 baseos 23 k perl-Time-Local noarch 2:1.350-511.el10 baseos 35 k perl-URI noarch 5.27-3.el10 baseos 134 k perl-base noarch 2.27-514.el10 appstream 17 k perl-constant noarch 1.33-512.el10 baseos 24 k perl-if noarch 0.61.000-514.el10 appstream 15 k perl-libnet noarch 3.15-512.el10 baseos 127 k perl-libs aarch64 4:5.40.2-514.el10 appstream 2.3 M perl-locale noarch 1.12-514.el10 appstream 14 k perl-mro aarch64 1.29-514.el10 appstream 30 k perl-overload noarch 1.37-514.el10 appstream 46 k perl-overloading noarch 0.02-514.el10 appstream 14 k perl-parent noarch 1:0.241-512.el10 baseos 16 k perl-podlators noarch 1:5.01-511.el10 baseos 124 k perl-vars noarch 1.05-514.el10 appstream 14 k publicsuffix-list noarch 20240107-5.el10 appstream 88 k Transaction Summary ================================================================================ Install 97 Packages Total download size: 67 M Installed size: 189 M Downloading Packages: (1/97): libatomic-14.3.1-4.2.el10.aarch64.rpm 4.2 MB/s | 58 kB 00:00 (2/97): libkadm5-1.21.3-8.el10.aarch64.rpm 5.0 MB/s | 78 kB 00:00 (3/97): groff-base-1.23.0-10.el10.aarch64.rpm 49 MB/s | 1.1 MB 00:00 (4/97): make-4.4.1-9.el10.aarch64.rpm 54 MB/s | 585 kB 00:00 (5/97): ncurses-6.4-14.20240127.el10.aarch64.rp 40 MB/s | 421 kB 00:00 (6/97): perl-Carp-1.54-511.el10.noarch.rpm 7.4 MB/s | 30 kB 00:00 (7/97): perl-Data-Dumper-2.189-512.el10.aarch64 23 MB/s | 56 kB 00:00 (8/97): perl-Digest-1.20-511.el10.noarch.rpm 12 MB/s | 26 kB 00:00 (9/97): perl-Digest-MD5-2.59-6.el10.aarch64.rpm 13 MB/s | 37 kB 00:00 (10/97): perl-Exporter-5.78-511.el10.noarch.rpm 8.2 MB/s | 32 kB 00:00 (11/97): perl-Encode-3.21-511.el10.aarch64.rpm 137 MB/s | 1.1 MB 00:00 (12/97): perl-File-Temp-0.231.100-512.el10.noar 10 MB/s | 60 kB 00:00 (13/97): perl-Getopt-Long-2.58-3.el10.noarch.rp 17 MB/s | 65 kB 00:00 (14/97): perl-HTTP-Tiny-0.088-512.el10.noarch.r 20 MB/s | 57 kB 00:00 (15/97): perl-IO-Socket-IP-0.42-512.el10.noarch 15 MB/s | 43 kB 00:00 (16/97): perl-IO-Socket-SSL-2.085-3.el10.noarch 60 MB/s | 227 kB 00:00 (17/97): perl-MIME-Base64-3.16-511.el10.aarch64 10 MB/s | 31 kB 00:00 (18/97): perl-Mozilla-CA-20231213-5.el10.noarch 5.2 MB/s | 15 kB 00:00 (19/97): perl-Pod-Escapes-1.07-511.el10.noarch. 8.5 MB/s | 21 kB 00:00 (20/97): perl-PathTools-3.91-512.el10.aarch64.r 23 MB/s | 85 kB 00:00 (21/97): perl-Pod-Perldoc-3.28.01-512.el10.noar 23 MB/s | 84 kB 00:00 (22/97): perl-Pod-Usage-2.03-511.el10.noarch.rp 19 MB/s | 41 kB 00:00 (23/97): perl-Pod-Simple-3.45-511.el10.noarch.r 52 MB/s | 218 kB 00:00 (24/97): perl-Scalar-List-Utils-1.63-511.el10.a 19 MB/s | 73 kB 00:00 (25/97): perl-Socket-2.038-511.el10.aarch64.rpm 24 MB/s | 56 kB 00:00 (26/97): perl-Storable-3.32-511.el10.aarch64.rp 28 MB/s | 98 kB 00:00 (27/97): perl-Term-ANSIColor-5.01-512.el10.noar 19 MB/s | 49 kB 00:00 (28/97): perl-Term-Cap-1.18-511.el10.noarch.rpm 4.5 MB/s | 23 kB 00:00 (29/97): perl-Text-ParseWords-3.31-511.el10.noa 6.5 MB/s | 17 kB 00:00 (30/97): perl-Text-Tabs+Wrap-2024.001-511.el10. 7.4 MB/s | 23 kB 00:00 (31/97): perl-Time-Local-1.350-511.el10.noarch. 15 MB/s | 35 kB 00:00 (32/97): perl-constant-1.33-512.el10.noarch.rpm 9.8 MB/s | 24 kB 00:00 (33/97): perl-URI-5.27-3.el10.noarch.rpm 32 MB/s | 134 kB 00:00 (34/97): perl-parent-0.241-512.el10.noarch.rpm 8.4 MB/s | 16 kB 00:00 (35/97): perl-libnet-3.15-512.el10.noarch.rpm 36 MB/s | 127 kB 00:00 (36/97): perl-podlators-5.01-511.el10.noarch.rp 33 MB/s | 124 kB 00:00 (37/97): annobin-docs-13.02-2.el10.noarch.rpm 24 MB/s | 87 kB 00:00 (38/97): brotli-1.1.0-7.el10.aarch64.rpm 5.7 MB/s | 19 kB 00:00 (39/97): annobin-plugin-gcc-13.02-2.el10.aarch6 136 MB/s | 997 kB 00:00 (40/97): brotli-devel-1.1.0-7.el10.aarch64.rpm 7.3 MB/s | 33 kB 00:00 (41/97): cmake-filesystem-3.31.8-1.el10.aarch64 8.6 MB/s | 21 kB 00:00 (42/97): bzip2-devel-1.0.8-25.el10.aarch64.rpm 43 MB/s | 215 kB 00:00 (43/97): gcc-plugin-annobin-14.3.1-4.2.el10.aar 15 MB/s | 69 kB 00:00 (44/97): glibc-devel-2.39-99.el10.aarch64.rpm 43 MB/s | 589 kB 00:00 (45/97): kernel-headers-6.12.0-191.el10.aarch64 92 MB/s | 3.1 MB 00:00 (46/97): keyutils-libs-devel-1.6.3-5.el10.aarch 3.0 MB/s | 61 kB 00:00 (47/97): krb5-devel-1.21.3-8.el10.aarch64.rpm 3.9 MB/s | 145 kB 00:00 (48/97): gcc-14.3.1-4.2.el10.aarch64.rpm 233 MB/s | 35 MB 00:00 (49/97): cpp-14.3.1-4.2.el10.aarch64.rpm 67 MB/s | 11 MB 00:00 (50/97): libcom_err-devel-1.47.1-5.el10.aarch64 851 kB/s | 16 kB 00:00 (51/97): libasan-14.3.1-4.2.el10.aarch64.rpm 8.9 MB/s | 532 kB 00:00 (52/97): libidn2-devel-2.3.7-3.el10.aarch64.rpm 14 MB/s | 71 kB 00:00 (53/97): libcurl-devel-8.12.1-4.el10.aarch64.rp 122 MB/s | 946 kB 00:00 (54/97): libmpc-1.3.1-7.el10.aarch64.rpm 12 MB/s | 73 kB 00:00 (55/97): libnghttp2-devel-1.64.0-2.el10.aarch64 17 MB/s | 57 kB 00:00 (56/97): libsepol-devel-3.9-1.el10.aarch64.rpm 21 MB/s | 48 kB 00:00 (57/97): libpsl-devel-0.21.5-6.el10.aarch64.rpm 9.4 MB/s | 35 kB 00:00 (58/97): libselinux-devel-3.9-3.el10.aarch64.rp 41 MB/s | 161 kB 00:00 (59/97): libssh-devel-0.11.1-3.el10.aarch64.rpm 18 MB/s | 41 kB 00:00 (60/97): libverto-devel-0.3.2-10.el10.aarch64.r 7.1 MB/s | 15 kB 00:00 (61/97): libubsan-14.3.1-4.2.el10.aarch64.rpm 61 MB/s | 238 kB 00:00 (62/97): libxcrypt-devel-4.4.36-10.el10.aarch64 11 MB/s | 30 kB 00:00 (63/97): pcre2-devel-10.44-1.el10.3.aarch64.rpm 80 MB/s | 532 kB 00:00 (64/97): pcre2-utf16-10.44-1.el10.3.aarch64.rpm 18 MB/s | 208 kB 00:00 (65/97): openssl-devel-3.5.1-6.el10.aarch64.rpm 205 MB/s | 4.2 MB 00:00 (66/97): perl-AutoLoader-5.74-514.el10.noarch.r 2.8 MB/s | 22 kB 00:00 (67/97): pcre2-utf32-10.44-1.el10.3.aarch64.rpm 14 MB/s | 196 kB 00:00 (68/97): perl-Class-Struct-0.68-514.el10.noarch 11 MB/s | 23 kB 00:00 (69/97): perl-B-1.89-514.el10.aarch64.rpm 45 MB/s | 179 kB 00:00 (70/97): perl-DynaLoader-1.56-514.el10.aarch64. 9.6 MB/s | 27 kB 00:00 (71/97): perl-Errno-1.38-514.el10.aarch64.rpm 7.8 MB/s | 16 kB 00:00 (72/97): perl-Fcntl-1.18-514.el10.aarch64.rpm 14 MB/s | 30 kB 00:00 (73/97): perl-File-Basename-2.86-514.el10.noarc 6.8 MB/s | 18 kB 00:00 (74/97): perl-File-Path-2.18-512.el10.noarch.rp 14 MB/s | 35 kB 00:00 (75/97): perl-File-stat-1.14-514.el10.noarch.rp 7.7 MB/s | 18 kB 00:00 (76/97): perl-FileHandle-2.05-514.el10.noarch.r 4.3 MB/s | 16 kB 00:00 (77/97): perl-Getopt-Std-1.14-514.el10.noarch.r 7.5 MB/s | 16 kB 00:00 (78/97): perl-IPC-Open3-1.22-514.el10.noarch.rp 11 MB/s | 23 kB 00:00 (79/97): perl-IO-1.55-514.el10.aarch64.rpm 26 MB/s | 81 kB 00:00 (80/97): perl-Net-SSLeay-1.94-8.el10.aarch64.rp 82 MB/s | 381 kB 00:00 (81/97): perl-POSIX-2.20-514.el10.aarch64.rpm 22 MB/s | 98 kB 00:00 (82/97): perl-SelectSaver-1.02-514.el10.noarch. 5.4 MB/s | 12 kB 00:00 (83/97): perl-Symbol-1.09-514.el10.noarch.rpm 6.6 MB/s | 15 kB 00:00 (84/97): perl-base-2.27-514.el10.noarch.rpm 7.9 MB/s | 17 kB 00:00 (85/97): perl-if-0.61.000-514.el10.noarch.rpm 6.6 MB/s | 15 kB 00:00 (86/97): perl-lib-0.65-514.el10.aarch64.rpm 7.0 MB/s | 16 kB 00:00 (87/97): perl-interpreter-5.40.2-514.el10.aarch 22 MB/s | 73 kB 00:00 (88/97): perl-locale-1.12-514.el10.noarch.rpm 6.6 MB/s | 14 kB 00:00 (89/97): perl-mro-1.29-514.el10.aarch64.rpm 6.1 MB/s | 30 kB 00:00 (90/97): perl-libs-5.40.2-514.el10.aarch64.rpm 208 MB/s | 2.3 MB 00:00 (91/97): perl-overload-1.37-514.el10.noarch.rpm 12 MB/s | 46 kB 00:00 (92/97): perl-overloading-0.02-514.el10.noarch. 5.9 MB/s | 14 kB 00:00 (93/97): perl-vars-1.05-514.el10.noarch.rpm 5.9 MB/s | 14 kB 00:00 (94/97): xz-devel-5.6.2-4.el10.aarch64.rpm 28 MB/s | 64 kB 00:00 (95/97): publicsuffix-list-20240107-5.el10.noar 25 MB/s | 88 kB 00:00 (96/97): zlib-ng-compat-devel-2.2.3-3.el10.aarc 18 MB/s | 36 kB 00:00 (97/97): perl-FindBin-1.54-514.el10.noarch.rpm 67 kB/s | 15 kB 00:00 -------------------------------------------------------------------------------- Total 104 MB/s | 67 MB 00:00 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Installing : libmpc-1.3.1-7.el10.aarch64 1/97 Installing : cmake-filesystem-3.31.8-1.el10.aarch64 2/97 Installing : libssh-devel-0.11.1-3.el10.aarch64 3/97 Installing : zlib-ng-compat-devel-2.2.3-3.el10.aarch64 4/97 Installing : cpp-14.3.1-4.2.el10.aarch64 5/97 Installing : publicsuffix-list-20240107-5.el10.noarch 6/97 Installing : libpsl-devel-0.21.5-6.el10.aarch64 7/97 Installing : pcre2-utf32-10.44-1.el10.3.aarch64 8/97 Installing : pcre2-utf16-10.44-1.el10.3.aarch64 9/97 Installing : pcre2-devel-10.44-1.el10.3.aarch64 10/97 Installing : openssl-devel-1:3.5.1-6.el10.aarch64 11/97 Installing : libverto-devel-0.3.2-10.el10.aarch64 12/97 Installing : libubsan-14.3.1-4.2.el10.aarch64 13/97 Installing : libsepol-devel-3.9-1.el10.aarch64 14/97 Installing : libselinux-devel-3.9-3.el10.aarch64 15/97 Installing : libnghttp2-devel-1.64.0-2.el10.aarch64 16/97 Installing : libidn2-devel-2.3.7-3.el10.aarch64 17/97 Installing : libcom_err-devel-1.47.1-5.el10.aarch64 18/97 Installing : libasan-14.3.1-4.2.el10.aarch64 19/97 Installing : keyutils-libs-devel-1.6.3-5.el10.aarch64 20/97 Installing : kernel-headers-6.12.0-191.el10.aarch64 21/97 Installing : libxcrypt-devel-4.4.36-10.el10.aarch64 22/97 Installing : glibc-devel-2.39-99.el10.aarch64 23/97 Installing : brotli-1.1.0-7.el10.aarch64 24/97 Installing : brotli-devel-1.1.0-7.el10.aarch64 25/97 Installing : annobin-docs-13.02-2.el10.noarch 26/97 Installing : ncurses-6.4-14.20240127.el10.aarch64 27/97 Installing : make-1:4.4.1-9.el10.aarch64 28/97 Installing : libkadm5-1.21.3-8.el10.aarch64 29/97 Installing : krb5-devel-1.21.3-8.el10.aarch64 30/97 Installing : libatomic-14.3.1-4.2.el10.aarch64 31/97 Installing : gcc-14.3.1-4.2.el10.aarch64 32/97 Running scriptlet: gcc-14.3.1-4.2.el10.aarch64 32/97 Running scriptlet: groff-base-1.23.0-10.el10.aarch64 33/97 Installing : groff-base-1.23.0-10.el10.aarch64 33/97 Running scriptlet: groff-base-1.23.0-10.el10.aarch64 33/97 Installing : perl-Digest-1.20-511.el10.noarch 34/97 Installing : perl-Digest-MD5-2.59-6.el10.aarch64 35/97 Installing : perl-B-1.89-514.el10.aarch64 36/97 Installing : perl-FileHandle-2.05-514.el10.noarch 37/97 Installing : perl-Data-Dumper-2.189-512.el10.aarch64 38/97 Installing : perl-libnet-3.15-512.el10.noarch 39/97 Installing : perl-AutoLoader-5.74-514.el10.noarch 40/97 Installing : perl-URI-5.27-3.el10.noarch 41/97 Installing : perl-Text-Tabs+Wrap-2024.001-511.el10.noarch 42/97 Installing : perl-Time-Local-2:1.350-511.el10.noarch 43/97 Installing : perl-Mozilla-CA-20231213-5.el10.noarch 44/97 Installing : perl-if-0.61.000-514.el10.noarch 45/97 Installing : perl-locale-1.12-514.el10.noarch 46/97 Installing : perl-IO-Socket-IP-0.42-512.el10.noarch 47/97 Installing : perl-Pod-Escapes-1:1.07-511.el10.noarch 48/97 Installing : perl-File-Path-2.18-512.el10.noarch 49/97 Installing : perl-IO-Socket-SSL-2.085-3.el10.noarch 50/97 Installing : perl-Net-SSLeay-1.94-8.el10.aarch64 51/97 Installing : perl-Term-ANSIColor-5.01-512.el10.noarch 52/97 Installing : perl-Class-Struct-0.68-514.el10.noarch 53/97 Installing : perl-POSIX-2.20-514.el10.aarch64 54/97 Installing : perl-IPC-Open3-1.22-514.el10.noarch 55/97 Installing : perl-Term-Cap-1.18-511.el10.noarch 56/97 Installing : perl-File-Temp-1:0.231.100-512.el10.noarch 57/97 Installing : perl-HTTP-Tiny-0.088-512.el10.noarch 58/97 Installing : perl-Pod-Simple-1:3.45-511.el10.noarch 59/97 Installing : perl-Socket-4:2.038-511.el10.aarch64 60/97 Installing : perl-SelectSaver-1.02-514.el10.noarch 61/97 Installing : perl-Symbol-1.09-514.el10.noarch 62/97 Installing : perl-File-stat-1.14-514.el10.noarch 63/97 Installing : perl-podlators-1:5.01-511.el10.noarch 64/97 Installing : perl-Pod-Perldoc-3.28.01-512.el10.noarch 65/97 Installing : perl-Text-ParseWords-3.31-511.el10.noarch 66/97 Installing : perl-Fcntl-1.18-514.el10.aarch64 67/97 Installing : perl-base-2.27-514.el10.noarch 68/97 Installing : perl-mro-1.29-514.el10.aarch64 69/97 Installing : perl-IO-1.55-514.el10.aarch64 70/97 Installing : perl-overloading-0.02-514.el10.noarch 71/97 Installing : perl-Pod-Usage-4:2.03-511.el10.noarch 72/97 Installing : perl-MIME-Base64-3.16-511.el10.aarch64 73/97 Installing : perl-Scalar-List-Utils-5:1.63-511.el10.aarch64 74/97 Installing : perl-constant-1.33-512.el10.noarch 75/97 Installing : perl-parent-1:0.241-512.el10.noarch 76/97 Installing : perl-Errno-1.38-514.el10.aarch64 77/97 Installing : perl-File-Basename-2.86-514.el10.noarch 78/97 Installing : perl-Getopt-Std-1.14-514.el10.noarch 79/97 Installing : perl-Storable-1:3.32-511.el10.aarch64 80/97 Installing : perl-overload-1.37-514.el10.noarch 81/97 Installing : perl-vars-1.05-514.el10.noarch 82/97 Installing : perl-Getopt-Long-1:2.58-3.el10.noarch 83/97 Installing : perl-Carp-1.54-511.el10.noarch 84/97 Installing : perl-Exporter-5.78-511.el10.noarch 85/97 Installing : perl-PathTools-3.91-512.el10.aarch64 86/97 Installing : perl-DynaLoader-1.56-514.el10.aarch64 87/97 Installing : perl-Encode-4:3.21-511.el10.aarch64 88/97 Installing : perl-libs-4:5.40.2-514.el10.aarch64 89/97 Installing : perl-interpreter-4:5.40.2-514.el10.aarch64 90/97 Installing : perl-FindBin-1.54-514.el10.noarch 91/97 Installing : perl-lib-0.65-514.el10.aarch64 92/97 Installing : annobin-plugin-gcc-13.02-2.el10.aarch64 93/97 Running scriptlet: annobin-plugin-gcc-13.02-2.el10.aarch64 93/97 Installing : gcc-plugin-annobin-14.3.1-4.2.el10.aarch64 94/97 Running scriptlet: gcc-plugin-annobin-14.3.1-4.2.el10.aarch64 94/97 Installing : libcurl-devel-8.12.1-4.el10.aarch64 95/97 Installing : xz-devel-1:5.6.2-4.el10.aarch64 96/97 Installing : bzip2-devel-1.0.8-25.el10.aarch64 97/97 Running scriptlet: bzip2-devel-1.0.8-25.el10.aarch64 97/97 Installed: annobin-docs-13.02-2.el10.noarch annobin-plugin-gcc-13.02-2.el10.aarch64 brotli-1.1.0-7.el10.aarch64 brotli-devel-1.1.0-7.el10.aarch64 bzip2-devel-1.0.8-25.el10.aarch64 cmake-filesystem-3.31.8-1.el10.aarch64 cpp-14.3.1-4.2.el10.aarch64 gcc-14.3.1-4.2.el10.aarch64 gcc-plugin-annobin-14.3.1-4.2.el10.aarch64 glibc-devel-2.39-99.el10.aarch64 groff-base-1.23.0-10.el10.aarch64 kernel-headers-6.12.0-191.el10.aarch64 keyutils-libs-devel-1.6.3-5.el10.aarch64 krb5-devel-1.21.3-8.el10.aarch64 libasan-14.3.1-4.2.el10.aarch64 libatomic-14.3.1-4.2.el10.aarch64 libcom_err-devel-1.47.1-5.el10.aarch64 libcurl-devel-8.12.1-4.el10.aarch64 libidn2-devel-2.3.7-3.el10.aarch64 libkadm5-1.21.3-8.el10.aarch64 libmpc-1.3.1-7.el10.aarch64 libnghttp2-devel-1.64.0-2.el10.aarch64 libpsl-devel-0.21.5-6.el10.aarch64 libselinux-devel-3.9-3.el10.aarch64 libsepol-devel-3.9-1.el10.aarch64 libssh-devel-0.11.1-3.el10.aarch64 libubsan-14.3.1-4.2.el10.aarch64 libverto-devel-0.3.2-10.el10.aarch64 libxcrypt-devel-4.4.36-10.el10.aarch64 make-1:4.4.1-9.el10.aarch64 ncurses-6.4-14.20240127.el10.aarch64 openssl-devel-1:3.5.1-6.el10.aarch64 pcre2-devel-10.44-1.el10.3.aarch64 pcre2-utf16-10.44-1.el10.3.aarch64 pcre2-utf32-10.44-1.el10.3.aarch64 perl-AutoLoader-5.74-514.el10.noarch perl-B-1.89-514.el10.aarch64 perl-Carp-1.54-511.el10.noarch perl-Class-Struct-0.68-514.el10.noarch perl-Data-Dumper-2.189-512.el10.aarch64 perl-Digest-1.20-511.el10.noarch perl-Digest-MD5-2.59-6.el10.aarch64 perl-DynaLoader-1.56-514.el10.aarch64 perl-Encode-4:3.21-511.el10.aarch64 perl-Errno-1.38-514.el10.aarch64 perl-Exporter-5.78-511.el10.noarch perl-Fcntl-1.18-514.el10.aarch64 perl-File-Basename-2.86-514.el10.noarch perl-File-Path-2.18-512.el10.noarch perl-File-Temp-1:0.231.100-512.el10.noarch perl-File-stat-1.14-514.el10.noarch perl-FileHandle-2.05-514.el10.noarch perl-FindBin-1.54-514.el10.noarch perl-Getopt-Long-1:2.58-3.el10.noarch perl-Getopt-Std-1.14-514.el10.noarch perl-HTTP-Tiny-0.088-512.el10.noarch perl-IO-1.55-514.el10.aarch64 perl-IO-Socket-IP-0.42-512.el10.noarch perl-IO-Socket-SSL-2.085-3.el10.noarch perl-IPC-Open3-1.22-514.el10.noarch perl-MIME-Base64-3.16-511.el10.aarch64 perl-Mozilla-CA-20231213-5.el10.noarch perl-Net-SSLeay-1.94-8.el10.aarch64 perl-POSIX-2.20-514.el10.aarch64 perl-PathTools-3.91-512.el10.aarch64 perl-Pod-Escapes-1:1.07-511.el10.noarch perl-Pod-Perldoc-3.28.01-512.el10.noarch perl-Pod-Simple-1:3.45-511.el10.noarch perl-Pod-Usage-4:2.03-511.el10.noarch perl-Scalar-List-Utils-5:1.63-511.el10.aarch64 perl-SelectSaver-1.02-514.el10.noarch perl-Socket-4:2.038-511.el10.aarch64 perl-Storable-1:3.32-511.el10.aarch64 perl-Symbol-1.09-514.el10.noarch perl-Term-ANSIColor-5.01-512.el10.noarch perl-Term-Cap-1.18-511.el10.noarch perl-Text-ParseWords-3.31-511.el10.noarch perl-Text-Tabs+Wrap-2024.001-511.el10.noarch perl-Time-Local-2:1.350-511.el10.noarch perl-URI-5.27-3.el10.noarch perl-base-2.27-514.el10.noarch perl-constant-1.33-512.el10.noarch perl-if-0.61.000-514.el10.noarch perl-interpreter-4:5.40.2-514.el10.aarch64 perl-lib-0.65-514.el10.aarch64 perl-libnet-3.15-512.el10.noarch perl-libs-4:5.40.2-514.el10.aarch64 perl-locale-1.12-514.el10.noarch perl-mro-1.29-514.el10.aarch64 perl-overload-1.37-514.el10.noarch perl-overloading-0.02-514.el10.noarch perl-parent-1:0.241-512.el10.noarch perl-podlators-1:5.01-511.el10.noarch perl-vars-1.05-514.el10.noarch publicsuffix-list-20240107-5.el10.noarch xz-devel-1:5.6.2-4.el10.aarch64 zlib-ng-compat-devel-2.2.3-3.el10.aarch64 Complete! Building target platforms: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1769040000 Wrote: /builddir/build/SRPMS/htslib-1.23-1.el10.src.rpm No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 3.3 kB/s | 1.5 kB 00:00 CentOS Stream 10 - BaseOS 92 kB/s | 5.5 kB 00:00 CentOS Stream 10 - AppStream 91 kB/s | 5.5 kB 00:00 CentOS Stream 10 - CRB 22 kB/s | 4.4 kB 00:00 CentOS Stream 10 - Extras packages 162 kB/s | 7.4 kB 00:00 Extra Packages for Enterprise Linux 10 - aarch6 279 kB/s | 22 kB 00:00 Package bzip2-devel-1.0.8-25.el10.aarch64 is already installed. Package gcc-14.3.1-4.2.el10.aarch64 is already installed. Package libcurl-devel-8.12.1-4.el10.aarch64 is already installed. Package make-1:4.4.1-9.el10.aarch64 is already installed. Package openssl-devel-1:3.5.1-6.el10.aarch64 is already installed. Package perl-Data-Dumper-2.189-512.el10.aarch64 is already installed. Package perl-FindBin-1.54-514.el10.noarch is already installed. Package perl-Getopt-Long-1:2.58-3.el10.noarch is already installed. Package perl-lib-0.65-514.el10.aarch64 is already installed. Package perl-interpreter-4:5.40.2-514.el10.aarch64 is already installed. Package xz-devel-1:5.6.2-4.el10.aarch64 is already installed. Package zlib-ng-compat-devel-2.2.3-3.el10.aarch64 is already installed. Dependencies resolved. Nothing to do. Complete! Finish: build setup for htslib-1.23-1.el10.src.rpm Start: rpmbuild htslib-1.23-1.el10.src.rpm Building target platforms: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1769040000 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.fYUkCv + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf htslib-1.23 + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/htslib-1.23.tar.bz2 + STATUS=0 + '[' 0 -ne 0 ']' + cd htslib-1.23 + rm -rf /builddir/build/BUILD/htslib-1.23-SPECPARTS + /usr/bin/mkdir -p /builddir/build/BUILD/htslib-1.23-SPECPARTS + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.mAYCSr + umask 022 + cd /builddir/build/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd htslib-1.23 + 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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + '[' '-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};$!N;s/int x = 1;\nint y = 0;\nint z;\nint nan;/volatile int x = 1; volatile int y = 0; volatile int z, nan;/;P;D' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed --in-place=.backup 's#^lt_cv_sys_global_symbol_to_cdecl=.*#lt_cv_sys_global_symbol_to_cdecl="sed -n -e '\''s/^T .* \\(.*\\)$/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 $(dirname ./configure) -name config.guess -o -name config.sub) ++ basename ./config.sub + '[' -f /usr/lib/rpm/redhat/config.sub ']' + /usr/bin/rm -f ./config.sub ++ basename ./config.sub + /usr/bin/cp -fv /usr/lib/rpm/redhat/config.sub ./config.sub '/usr/lib/rpm/redhat/config.sub' -> './config.sub' + '[' 1 = 1 ']' + '[' x '!=' 'x-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors' ']' ++ find . -name ltmain.sh ++ grep -q runstatedir=DIR ./configure ++ echo --runstatedir=/run + ./configure --build=aarch64-redhat-linux --host=aarch64-redhat-linux --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/libexec --localstatedir=/var --runstatedir=/run --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info 'CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection ' 'LDFLAGS=-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' --prefix=/usr --libdir=/usr/lib64 --enable-plugins '--with-plugin-path=/usr/local/libexec/htslib:$(plugindir)' --enable-gcs --enable-libcurl --enable-s3 configure: WARNING: unrecognized options: --disable-dependency-tracking checking for aarch64-redhat-linux-gcc... 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 C11 features... none needed checking for aarch64-redhat-linux-ranlib... no checking for ranlib... ranlib checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for gcc options needed to detect all undeclared functions... none needed checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for sys/param.h... yes checking whether _XOPEN_SOURCE is declared... no checking whether __get_cpuid_max is declared... no checking whether __cpuid_count is declared... no checking for x86intrin.h... no checking for aarch64-redhat-linux-pkg-config... no checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for gcc option to enable large file support... none needed checking shared library type for aarch64-redhat-linux... plain .so checking whether the linker supports versioned symbols... yes checking whether the compiler accepts -fvisibility=hidden... yes checking build system type... aarch64-redhat-linux-gnu checking host system type... aarch64-redhat-linux-gnu checking for getpagesize... yes checking for working mmap... yes checking for gmtime_r... yes checking for fsync... yes checking for drand48... yes checking for srand48_deterministic... no checking for getauxval... yes checking for elf_aux_info... no checking for posix_memalign... yes checking whether fdatasync is declared... yes checking for fdatasync... yes checking for __attribute__((constructor))... yes checking for clock_gettime with CLOCK_PROCESS_CPUTIME_ID... yes checking for library containing dlsym... none required checking whether the compiler accepts -rdynamic... yes checking for library containing log... -lm checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing recv... none required checking for bzlib.h... yes checking for BZ2_bzBuffToBuffCompress in -lbz2... yes checking for lzma.h... yes checking for lzma_easy_buffer_encode in -llzma... yes checking whether htscodecs files are present... yes checking for libdeflate.h... no checking for libdeflate_deflate_compress in -ldeflate... no checking for curl/curl.h... yes checking for curl_easy_pause in -lcurl... yes checking for CCHmac... no checking for library containing HMAC... -lcrypto checking for fstatat... yes checking for CMSG_LEN... yes checking for epoll... yes (edge triggered) checking for sendfile... yes, Linux-style checking whether EHOSTDOWN is declared... yes checking whether ENONET is declared... yes checking whether AI_V4MAPPED is declared... yes checking whether AI_ADDRCONFIG is declared... yes checking whether the compiler accepts -Wextra... yes checking whether the compiler accepts -Wformat... yes checking whether the compiler accepts -Wformat=2... yes checking whether the compiler accepts -Wconversion... yes checking whether the compiler accepts -Wtrampolines... 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... yes checking whether the compiler accepts -fno-delete-null-pointer-checks... yes checking whether the compiler accepts -Wl,-z,noexecstack... yes checking whether the compiler accepts -Wl,-z,relro... yes checking whether the compiler accepts -Wl,-z,now... yes checking whether the compiler accepts -Wl,--as-needed... yes checking whether the compiler accepts -Wl,--no-copy-dt-needed-entries... yes checking whether the compiler accepts -Wl,-z,nodlopen... yes checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating htslib.pc.tmp config.status: creating config.h config.status: linking htscodecs_bundled.mk to htscodecs.mk configure: WARNING: unrecognized options: --disable-dependency-tracking + /usr/bin/make -O -j4 V=1 VERBOSE=1 gcc -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o kstring.o kstring.c gcc -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o faidx.o faidx.c echo '#define HTS_VERSION_TEXT "1.23"' > 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 -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden' \ '-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic' \ '-llzma -lbz2 -lz -lm ' > config_vars.h gcc -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o hfile.o hfile.c gcc -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o sam.o sam.c gcc -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/cram_decode.o cram/cram_decode.c gcc -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o vcf.o vcf.c gcc -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c gcc -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c gcc -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c gcc -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx2.c gcc -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_avx512.c gcc -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c gcc -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_sse4.c gcc -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/cram_io.o cram/cram_io.c gcc -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c gcc -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static32x16pr.c gcc -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c gcc -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/utils.o htscodecs/htscodecs/utils.c gcc -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr_neon.c gcc -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c gcc -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o kstring.pico kstring.c gcc -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c gcc -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o faidx.pico faidx.c gcc -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o hts.pico hts.c gcc -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o sam.pico sam.c gcc -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o cram/cram_decode.pico cram/cram_decode.c gcc -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o vcf.pico vcf.c gcc -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/htscodecs.pico htscodecs/htscodecs/htscodecs.c gcc -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/pack.pico htscodecs/htscodecs/pack.c gcc -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o cram/cram_io.pico cram/cram_io.c gcc -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.pico htscodecs/htscodecs/rANS_static32x16pr_avx2.c gcc -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.pico htscodecs/htscodecs/rANS_static32x16pr_avx512.c gcc -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.pico htscodecs/htscodecs/rANS_static32x16pr_sse4.c gcc -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/fqzcomp_qual.pico htscodecs/htscodecs/fqzcomp_qual.c gcc -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/arith_dynamic.pico htscodecs/htscodecs/arith_dynamic.c gcc -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rANS_static.pico htscodecs/htscodecs/rANS_static.c gcc -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rle.pico htscodecs/htscodecs/rle.c gcc -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr.pico htscodecs/htscodecs/rANS_static32x16pr.c gcc -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/utils.pico htscodecs/htscodecs/utils.c gcc -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rANS_static4x16pr.pico htscodecs/htscodecs/rANS_static4x16pr.c gcc -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr_neon.pico htscodecs/htscodecs/rANS_static32x16pr_neon.c gcc -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/tokenise_name3.pico htscodecs/htscodecs/tokenise_name3.c gcc -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_kstring.o test/test_kstring.c gcc -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test-parse-reg.o test/test-parse-reg.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 -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -mbranch-protection=standard -fno-delete-null-pointer-checks -I. -c -o ref_cache/cmsg_wrap.o ref_cache/cmsg_wrap.c gcc -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -mbranch-protection=standard -fno-delete-null-pointer-checks -I. -c -o ref_cache/listener.o ref_cache/listener.c gcc -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 -mbranch-protection=standard -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 -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -mbranch-protection=standard -fno-delete-null-pointer-checks -I. -c -o ref_cache/http_parser.o ref_cache/http_parser.c gcc -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -mbranch-protection=standard -fno-delete-null-pointer-checks -I. -c -o ref_cache/log_files.o ref_cache/log_files.c gcc -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -mbranch-protection=standard -fno-delete-null-pointer-checks -I. -c -o ref_cache/misc.o ref_cache/misc.c gcc -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -mbranch-protection=standard -fno-delete-null-pointer-checks -I. -c -o ref_cache/poll_wrap_epoll.o ref_cache/poll_wrap_epoll.c gcc -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -mbranch-protection=standard -fno-delete-null-pointer-checks -I. -c -o ref_cache/ping.o ref_cache/ping.c gcc -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -mbranch-protection=standard -fno-delete-null-pointer-checks -I. -c -o ref_cache/poll_wrap_poll.o ref_cache/poll_wrap_poll.c gcc -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -mbranch-protection=standard -fno-delete-null-pointer-checks -I. -c -o ref_cache/ref_files.o ref_cache/ref_files.c gcc -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -mbranch-protection=standard -fno-delete-null-pointer-checks -I. -c -o ref_cache/request_handler.o ref_cache/request_handler.c gcc -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -mbranch-protection=standard -fno-delete-null-pointer-checks -I. -c -o ref_cache/sendfile_wrap.o ref_cache/sendfile_wrap.c gcc -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -mbranch-protection=standard -fno-delete-null-pointer-checks -I. -c -o ref_cache/main.o ref_cache/main.c gcc -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -mbranch-protection=standard -fno-delete-null-pointer-checks -I. -c -o ref_cache/transaction.o ref_cache/transaction.c gcc -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -mbranch-protection=standard -fno-delete-null-pointer-checks -I. -c -o ref_cache/server.o ref_cache/server.c gcc -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -mbranch-protection=standard -fno-delete-null-pointer-checks -I. -c -o ref_cache/upstream.o ref_cache/upstream.c gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/hts_endian test/hts_endian.o -llzma -lbz2 -lz -lm gcc -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o hts.o hts.c gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/plugins-dlhts test/plugins-dlhts.o -llzma -lbz2 -lz -lm gcc -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 -mbranch-protection=standard -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 gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test_time_funcs test/test_time_funcs.o ar -rc libhts.a kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o sam_mods.o simd.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o plugin.o ranlib libhts.a gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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 gcc -shared -Wl,-soname,libhts.so.3 -Wl,-version-script,htslib.map -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -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 htscodecs/htscodecs/arith_dynamic.pico htscodecs/htscodecs/fqzcomp_qual.pico htscodecs/htscodecs/htscodecs.pico htscodecs/htscodecs/pack.pico htscodecs/htscodecs/rANS_static4x16pr.pico htscodecs/htscodecs/rANS_static32x16pr_avx2.pico htscodecs/htscodecs/rANS_static32x16pr_avx512.pico htscodecs/htscodecs/rANS_static32x16pr_sse4.pico htscodecs/htscodecs/rANS_static32x16pr_neon.pico htscodecs/htscodecs/rANS_static32x16pr.pico htscodecs/htscodecs/rANS_static.pico htscodecs/htscodecs/rle.pico htscodecs/htscodecs/tokenise_name3.pico htscodecs/htscodecs/utils.pico plugin.pico -llzma -lbz2 -lz -lm -lpthread ln -sf libhts.so libhts.so.3 gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o annot-tsv annot-tsv.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o bgzip bgzip.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -shared -Wl,-E -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o hfile_libcurl.so hfile_libcurl.pico libhts.so -llzma -lbz2 -lz -lm -lcurl -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o htsfile htsfile.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -shared -Wl,-E -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o hfile_gcs.so hfile_gcs.pico libhts.so -llzma -lbz2 -lz -lm -lpthread gcc -shared -Wl,-E -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o hfile_s3.so hfile_s3.pico libhts.so -llzma -lbz2 -lz -lm -lcrypto -lcurl -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o tabix tabix.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/fieldarith test/fieldarith.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/hfile test/hfile.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/pileup test/pileup.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/pileup_mod test/pileup_mod.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/sam test/sam.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test_bgzf test/test_bgzf.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test_kfunc test/test_kfunc.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test_expr test/test_expr.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test_khash test/test_khash.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test_kstring test/test_kstring.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test_faidx test/test_faidx.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test_mod test/test_mod.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test_nibbles test/test_nibbles.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test_realn test/test_realn.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test-regidx test/test-regidx.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test_str2int test/test_str2int.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test_view test/test_view.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test_index test/test_index.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test-vcf-api test/test-vcf-api.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test-parse-reg test/test-parse-reg.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test_introspection test/test_introspection.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test-bcf_set_variant_type test/test-bcf_set_variant_type.o libhts.a -llzma -lbz2 -lz -lm -lpthread + sed -i -E '/^(Libs|Requires)\.private:/d' htslib.pc.tmp + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.ZxD8mn + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/htslib-1.23-1.el10.aarch64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/htslib-1.23-1.el10.aarch64 ++ dirname /builddir/build/BUILDROOT/htslib-1.23-1.el10.aarch64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/htslib-1.23-1.el10.aarch64 + 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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd htslib-1.23 + /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/htslib-1.23-1.el10.aarch64 'INSTALL=/usr/bin/install -p' mkdir -p -m 755 /builddir/build/BUILDROOT/htslib-1.23-1.el10.aarch64/usr/bin /builddir/build/BUILDROOT/htslib-1.23-1.el10.aarch64/usr/include /builddir/build/BUILDROOT/htslib-1.23-1.el10.aarch64/usr/include/htslib /builddir/build/BUILDROOT/htslib-1.23-1.el10.aarch64/usr/lib64 /builddir/build/BUILDROOT/htslib-1.23-1.el10.aarch64/usr/share/man/man1 /builddir/build/BUILDROOT/htslib-1.23-1.el10.aarch64/usr/share/man/man5 /builddir/build/BUILDROOT/htslib-1.23-1.el10.aarch64/usr/share/man/man7 /builddir/build/BUILDROOT/htslib-1.23-1.el10.aarch64/usr/lib64/pkgconfig if test -n "/usr/libexec/htslib"; then mkdir -p -m 755 /builddir/build/BUILDROOT/htslib-1.23-1.el10.aarch64/usr/libexec/htslib; fi /usr/bin/install -p -m 644 libhts.so /builddir/build/BUILDROOT/htslib-1.23-1.el10.aarch64/usr/lib64/libhts.so.1.23 ln -sf libhts.so.1.23 /builddir/build/BUILDROOT/htslib-1.23-1.el10.aarch64/usr/lib64/libhts.so ln -sf libhts.so.1.23 /builddir/build/BUILDROOT/htslib-1.23-1.el10.aarch64/usr/lib64/libhts.so.3 sed -e 's#@-includedir@#/usr/include#g;s#@-libdir@#/usr/lib64#g;s#@-PACKAGE_VERSION@#1.23#g' htslib.pc.tmp > /builddir/build/BUILDROOT/htslib-1.23-1.el10.aarch64/usr/lib64/pkgconfig/htslib.pc chmod 644 /builddir/build/BUILDROOT/htslib-1.23-1.el10.aarch64/usr/lib64/pkgconfig/htslib.pc /usr/bin/install -p annot-tsv bgzip htsfile tabix ref_cache/ref-cache /builddir/build/BUILDROOT/htslib-1.23-1.el10.aarch64/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/BUILDROOT/htslib-1.23-1.el10.aarch64/usr/libexec/htslib; fi /usr/bin/install -p -m 644 htslib/*.h /builddir/build/BUILDROOT/htslib-1.23-1.el10.aarch64/usr/include/htslib /usr/bin/install -p -m 644 libhts.a /builddir/build/BUILDROOT/htslib-1.23-1.el10.aarch64/usr/lib64/libhts.a /usr/bin/install -p -m 644 annot-tsv.1 bgzip.1 htsfile.1 tabix.1 /builddir/build/BUILDROOT/htslib-1.23-1.el10.aarch64/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/BUILDROOT/htslib-1.23-1.el10.aarch64/usr/share/man/man1 ; \ fi /usr/bin/install -p -m 644 faidx.5 sam.5 vcf.5 /builddir/build/BUILDROOT/htslib-1.23-1.el10.aarch64/usr/share/man/man5 /usr/bin/install -p -m 644 htslib-s3-plugin.7 /builddir/build/BUILDROOT/htslib-1.23-1.el10.aarch64/usr/share/man/man7 + pushd /builddir/build/BUILDROOT/htslib-1.23-1.el10.aarch64//usr/lib64 ~/build/BUILDROOT/htslib-1.23-1.el10.aarch64/usr/lib64 ~/build/BUILD/htslib-1.23 + chmod 755 libhts.so.1.23 + popd ~/build/BUILD/htslib-1.23 + find /builddir/build/BUILDROOT/htslib-1.23-1.el10.aarch64 -name '*.la' -delete + rm -f /builddir/build/BUILDROOT/htslib-1.23-1.el10.aarch64//usr/lib64/libhts.a + /usr/bin/find-debuginfo -j4 --strict-build-id -m -i --build-id-seed 1.23-1.el10 --unique-debug-suffix -1.23-1.el10.aarch64 --unique-debug-src-base htslib-1.23-1.el10.aarch64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/htslib-1.23 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-1.23-1.el10.aarch64 find-debuginfo: done + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + /usr/lib/rpm/brp-compress + /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/check-rpaths + /usr/lib/rpm/redhat/brp-mangle-shebangs + /usr/lib/rpm/brp-remove-la-files + /usr/lib/rpm/redhat/brp-python-rpm-in-distinfo + env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j4 + /usr/lib/rpm/redhat/brp-python-hardlink Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.91erL9 + umask 022 + cd /builddir/build/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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd htslib-1.23 + 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 gcc -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -Ihtscodecs -c -o htscodecs/tests/rANS_static_test.o htscodecs/tests/rANS_static_test.c gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o htscodecs/tests/rans4x8 htscodecs/tests/rANS_static_test.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o -llzma -lbz2 -lz -lm -lm -lpthread cd htscodecs/tests && srcdir=. && export srcdir && ./rans4x8.test Testing rans4x8 -r -o0 on ./dat/q4 11674 Testing rans4x8 -r -o1 on ./dat/q4 10870 Testing rans4x8 -r -o0 on ./dat/q40+dir 50258 Testing rans4x8 -r -o1 on ./dat/q40+dir 50537 Testing rans4x8 -r -o0 on ./dat/q8 33099 Testing rans4x8 -r -o1 on ./dat/q8 31428 Testing rans4x8 -r -o0 on ./dat/qvar 32997 Testing rans4x8 -r -o1 on ./dat/qvar 32832 gcc -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -Ihtscodecs -c -o htscodecs/tests/rANS_static4x16pr_test.o htscodecs/tests/rANS_static4x16pr_test.c gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o htscodecs/tests/rans4x16pr htscodecs/tests/rANS_static4x16pr_test.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o -llzma -lbz2 -lz -lm -lm -lpthread cd htscodecs/tests && srcdir=. && export srcdir && ./rans4x16.test Testing rans4x16 -r -o0 on ./dat/q4 11660 Testing rans4x16 -r -o1 on ./dat/q4 10848 Testing rans4x16 -r -o64 on ./dat/q4 12878 Testing rans4x16 -r -o65 on ./dat/q4 10672 Testing rans4x16 -r -o128 on ./dat/q4 10902 Testing rans4x16 -r -o129 on ./dat/q4 10890 Testing rans4x16 -r -o192 on ./dat/q4 11225 Testing rans4x16 -r -o193 on ./dat/q4 10825 Testing rans4x16 -r -o8 on ./dat/q4 11731 Testing rans4x16 -r -o9 on ./dat/q4 11111 Testing rans4x16 -r -o4 on ./dat/q4 11746 11746 11746 11746 Testing rans4x16 -r -o5 on ./dat/q4 10932 10932 10932 10932 Testing rans4x16 -r -o0 on ./dat/q40+dir 50247 Testing rans4x16 -r -o1 on ./dat/q40+dir 49449 Testing rans4x16 -r -o8 on ./dat/q40+dir 50072 Testing rans4x16 -r -o9 on ./dat/q40+dir 50072 Testing rans4x16 -r -o4 on ./dat/q40+dir 50331 50331 50331 50331 Testing rans4x16 -r -o5 on ./dat/q40+dir 49537 49537 49537 49537 Testing rans4x16 -r -o0 on ./dat/q8 33088 Testing rans4x16 -r -o1 on ./dat/q8 31372 Testing rans4x16 -r -o64 on ./dat/q8 33458 Testing rans4x16 -r -o65 on ./dat/q8 31025 Testing rans4x16 -r -o128 on ./dat/q8 32237 Testing rans4x16 -r -o129 on ./dat/q8 31258 Testing rans4x16 -r -o192 on ./dat/q8 32024 Testing rans4x16 -r -o193 on ./dat/q8 31146 Testing rans4x16 -r -o4 on ./dat/q8 33176 33176 33176 33176 Testing rans4x16 -r -o5 on ./dat/q8 31458 31458 31458 31458 Testing rans4x16 -r -o69 on ./dat/qsimd 35 Testing rans4x16 -r -o4 on ./dat/qsimd 219 219 219 219 Testing rans4x16 -r -o5 on ./dat/qsimd 151 151 151 151 Testing rans4x16 -r -o0 on ./dat/qvar 32987 Testing rans4x16 -r -o1 on ./dat/qvar 32261 Testing rans4x16 -r -o4 on ./dat/qvar 33073 33073 33073 33073 Testing rans4x16 -r -o5 on ./dat/qvar 32353 32353 32353 32353 gcc -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -Ihtscodecs -c -o htscodecs/tests/arith_dynamic_test.o htscodecs/tests/arith_dynamic_test.c gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o htscodecs/tests/arith_dynamic htscodecs/tests/arith_dynamic_test.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o -llzma -lbz2 -lz -lm -lm -lpthread cd htscodecs/tests && srcdir=. && export srcdir && ./arith.test Testing arith_dynamic -r -o0 on ./dat/q4 11615 Testing arith_dynamic -r -o1 on ./dat/q4 10831 Testing arith_dynamic -r -o64 on ./dat/q4 13360 Testing arith_dynamic -r -o65 on ./dat/q4 10484 Testing arith_dynamic -r -o128 on ./dat/q4 10774 Testing arith_dynamic -r -o129 on ./dat/q4 10329 Testing arith_dynamic -r -o192 on ./dat/q4 11095 Testing arith_dynamic -r -o193 on ./dat/q4 10283 Testing arith_dynamic -r -o8 on ./dat/q4 11448 Testing arith_dynamic -r -o9 on ./dat/q4 11083 Testing arith_dynamic -r -o0 on ./dat/q40+dir 49949 Testing arith_dynamic -r -o1 on ./dat/q40+dir 49034 Testing arith_dynamic -r -o64 on ./dat/q40+dir 51242 Testing arith_dynamic -r -o65 on ./dat/q40+dir 49061 Testing arith_dynamic -r -o8 on ./dat/q40+dir 49820 Testing arith_dynamic -r -o9 on ./dat/q40+dir 49448 Testing arith_dynamic -r -o0 on ./dat/q8 32752 Testing arith_dynamic -r -o1 on ./dat/q8 31331 Testing arith_dynamic -r -o64 on ./dat/q8 35211 Testing arith_dynamic -r -o65 on ./dat/q8 30907 Testing arith_dynamic -r -o128 on ./dat/q8 32063 Testing arith_dynamic -r -o129 on ./dat/q8 31084 Testing arith_dynamic -r -o192 on ./dat/q8 32267 Testing arith_dynamic -r -o193 on ./dat/q8 30931 Testing arith_dynamic -r -o0 on ./dat/qvar 32597 Testing arith_dynamic -r -o1 on ./dat/qvar 31982 Testing arith_dynamic -r -o64 on ./dat/qvar 33237 Testing arith_dynamic -r -o65 on ./dat/qvar 31993 Testing arith_dynamic -r -o1 on ./dat/u32 27005 Testing arith_dynamic -r -o65 on ./dat/u32 23864 Testing arith_dynamic -r -o9 on ./dat/u32 24811 Testing arith_dynamic -r -o4 on ./dat/u32 20849 gcc -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -Ihtscodecs -c -o htscodecs/tests/tokenise_name3_test.o htscodecs/tests/tokenise_name3_test.c gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o htscodecs/tests/tokenise_name3 htscodecs/tests/tokenise_name3_test.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o -llzma -lbz2 -lz -lm -lm -lpthread cd htscodecs/tests && srcdir=. && export srcdir && ./tok3.test Testing tokenise_name3 -r -1 on ./names/01.names 2708 Testing tokenise_name3 -r -3 on ./names/01.names 2429 Testing tokenise_name3 -r -5 on ./names/01.names 2264 Testing tokenise_name3 -r -7 on ./names/01.names 2264 Testing tokenise_name3 -r -9 on ./names/01.names 2234 Testing tokenise_name3 -r -11 on ./names/01.names 2449 Testing tokenise_name3 -r -13 on ./names/01.names 2085 Testing tokenise_name3 -r -15 on ./names/01.names 2071 Testing tokenise_name3 -r -17 on ./names/01.names 2070 Testing tokenise_name3 -r -19 on ./names/01.names 2051 Testing tokenise_name3 -r -1 on ./names/02.names 5390 Testing tokenise_name3 -r -3 on ./names/02.names 4955 Testing tokenise_name3 -r -5 on ./names/02.names 4923 Testing tokenise_name3 -r -7 on ./names/02.names 4923 Testing tokenise_name3 -r -9 on ./names/02.names 4918 Testing tokenise_name3 -r -11 on ./names/02.names 4838 Testing tokenise_name3 -r -13 on ./names/02.names 4757 Testing tokenise_name3 -r -15 on ./names/02.names 4743 Testing tokenise_name3 -r -17 on ./names/02.names 4716 Testing tokenise_name3 -r -19 on ./names/02.names 4700 Testing tokenise_name3 -r -1 on ./names/03.names 8854 Testing tokenise_name3 -r -3 on ./names/03.names 7782 Testing tokenise_name3 -r -5 on ./names/03.names 7771 Testing tokenise_name3 -r -7 on ./names/03.names 7771 Testing tokenise_name3 -r -9 on ./names/03.names 7521 Testing tokenise_name3 -r -11 on ./names/03.names 7395 Testing tokenise_name3 -r -13 on ./names/03.names 7252 Testing tokenise_name3 -r -15 on ./names/03.names 7252 Testing tokenise_name3 -r -17 on ./names/03.names 7225 Testing tokenise_name3 -r -19 on ./names/03.names 7075 Testing tokenise_name3 -r -1 on ./names/05.names 3787 Testing tokenise_name3 -r -3 on ./names/05.names 3564 Testing tokenise_name3 -r -5 on ./names/05.names 3536 Testing tokenise_name3 -r -7 on ./names/05.names 3536 Testing tokenise_name3 -r -9 on ./names/05.names 3534 Testing tokenise_name3 -r -11 on ./names/05.names 3411 Testing tokenise_name3 -r -13 on ./names/05.names 3397 Testing tokenise_name3 -r -15 on ./names/05.names 3383 Testing tokenise_name3 -r -17 on ./names/05.names 3383 Testing tokenise_name3 -r -19 on ./names/05.names 3377 Testing tokenise_name3 -r -1 on ./names/08.names 5579 Testing tokenise_name3 -r -3 on ./names/08.names 5274 Testing tokenise_name3 -r -5 on ./names/08.names 5246 Testing tokenise_name3 -r -7 on ./names/08.names 5213 Testing tokenise_name3 -r -9 on ./names/08.names 5160 Testing tokenise_name3 -r -11 on ./names/08.names 4915 Testing tokenise_name3 -r -13 on ./names/08.names 4901 Testing tokenise_name3 -r -15 on ./names/08.names 4887 Testing tokenise_name3 -r -17 on ./names/08.names 4844 Testing tokenise_name3 -r -19 on ./names/08.names 4805 Testing tokenise_name3 -r -1 on ./names/09.names 3740 Testing tokenise_name3 -r -3 on ./names/09.names 3539 Testing tokenise_name3 -r -5 on ./names/09.names 3539 Testing tokenise_name3 -r -7 on ./names/09.names 3528 Testing tokenise_name3 -r -9 on ./names/09.names 3493 Testing tokenise_name3 -r -11 on ./names/09.names 3431 Testing tokenise_name3 -r -13 on ./names/09.names 3394 Testing tokenise_name3 -r -15 on ./names/09.names 3394 Testing tokenise_name3 -r -17 on ./names/09.names 3386 Testing tokenise_name3 -r -19 on ./names/09.names 3366 Testing tokenise_name3 -r -1 on ./names/10.names 5210 Testing tokenise_name3 -r -3 on ./names/10.names 4782 Testing tokenise_name3 -r -5 on ./names/10.names 4752 Testing tokenise_name3 -r -7 on ./names/10.names 4752 Testing tokenise_name3 -r -9 on ./names/10.names 4744 Testing tokenise_name3 -r -11 on ./names/10.names 4566 Testing tokenise_name3 -r -13 on ./names/10.names 4520 Testing tokenise_name3 -r -15 on ./names/10.names 4506 Testing tokenise_name3 -r -17 on ./names/10.names 4494 Testing tokenise_name3 -r -19 on ./names/10.names 4476 Testing tokenise_name3 -r -1 on ./names/20.names 1783 Testing tokenise_name3 -r -3 on ./names/20.names 1668 Testing tokenise_name3 -r -5 on ./names/20.names 1640 Testing tokenise_name3 -r -7 on ./names/20.names 1640 Testing tokenise_name3 -r -9 on ./names/20.names 1632 Testing tokenise_name3 -r -11 on ./names/20.names 1645 Testing tokenise_name3 -r -13 on ./names/20.names 1625 Testing tokenise_name3 -r -15 on ./names/20.names 1611 Testing tokenise_name3 -r -17 on ./names/20.names 1609 Testing tokenise_name3 -r -19 on ./names/20.names 1600 Testing tokenise_name3 -r -1 on ./names/nv.names 5273 Testing tokenise_name3 -r -3 on ./names/nv.names 4968 Testing tokenise_name3 -r -5 on ./names/nv.names 4941 Testing tokenise_name3 -r -7 on ./names/nv.names 4941 Testing tokenise_name3 -r -9 on ./names/nv.names 4937 Testing tokenise_name3 -r -11 on ./names/nv.names 4864 Testing tokenise_name3 -r -13 on ./names/nv.names 4785 Testing tokenise_name3 -r -15 on ./names/nv.names 4772 Testing tokenise_name3 -r -17 on ./names/nv.names 4772 Testing tokenise_name3 -r -19 on ./names/nv.names 4767 Testing tokenise_name3 -r -1 on ./names/nv2.names 1060 Testing tokenise_name3 -r -3 on ./names/nv2.names 891 Testing tokenise_name3 -r -5 on ./names/nv2.names 863 Testing tokenise_name3 -r -7 on ./names/nv2.names 863 Testing tokenise_name3 -r -9 on ./names/nv2.names 855 Testing tokenise_name3 -r -11 on ./names/nv2.names 836 Testing tokenise_name3 -r -13 on ./names/nv2.names 799 Testing tokenise_name3 -r -15 on ./names/nv2.names 785 Testing tokenise_name3 -r -17 on ./names/nv2.names 779 Testing tokenise_name3 -r -19 on ./names/nv2.names 767 Testing tokenise_name3 -r -1 on ./names/rr.names 6605 Testing tokenise_name3 -r -3 on ./names/rr.names 6237 Testing tokenise_name3 -r -5 on ./names/rr.names 6237 Testing tokenise_name3 -r -7 on ./names/rr.names 6237 Testing tokenise_name3 -r -9 on ./names/rr.names 6230 Testing tokenise_name3 -r -11 on ./names/rr.names 6151 Testing tokenise_name3 -r -13 on ./names/rr.names 6025 Testing tokenise_name3 -r -15 on ./names/rr.names 6025 Testing tokenise_name3 -r -17 on ./names/rr.names 6023 Testing tokenise_name3 -r -19 on ./names/rr.names 5973 gcc -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -Ihtscodecs -c -o htscodecs/tests/fqzcomp_qual_test.o htscodecs/tests/fqzcomp_qual_test.c gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o htscodecs/tests/fqzcomp_qual htscodecs/tests/fqzcomp_qual_test.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o -llzma -lbz2 -lz -lm -lm -lpthread cd htscodecs/tests && srcdir=. && export srcdir && ./fqzcomp.test gcc -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -Ihtscodecs -c -o htscodecs/tests/varint_test.o htscodecs/tests/varint_test.c gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o htscodecs/tests/varint htscodecs/tests/varint_test.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o -llzma -lbz2 -lz -lm -lm -lpthread cd htscodecs/tests && ./varint test/hts_endian test/test_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 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 vcf_file.csi.tmp.vcf.gz 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 -f -p bed bed_file.tbi.tmp.bed.gz PASS : $tabix bed_file.tbi.tmp.bed.gz Y:100200-100200 PASS : $tabix -f -p gff gff_file.tbi.tmp.gff.gz PASS : $tabix gff_file.tbi.tmp.gff.gz X:2934832-2935190 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 Expected passes: 16 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-1.23/test/test_view -l 0 -b -m 14 -x /tmp/f5YcqjFauI/index.bam.csi /builddir/build/BUILD/htslib-1.23/test/index.sam > /tmp/f5YcqjFauI/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_index -c /tmp/f5YcqjFauI/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view -l 0 -b -m 0 -x /tmp/f5YcqjFauI/index.bam.bai /builddir/build/BUILD/htslib-1.23/test/index.sam > /tmp/f5YcqjFauI/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_index -b /tmp/f5YcqjFauI/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view -l 0 -z -m 14 -x /tmp/f5YcqjFauI/index.sam.gz.csi /builddir/build/BUILD/htslib-1.23/test/index.sam > /tmp/f5YcqjFauI/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_index -c /tmp/f5YcqjFauI/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view -l 0 -z -m 0 -x /tmp/f5YcqjFauI/index.sam.gz.bai /builddir/build/BUILD/htslib-1.23/test/index.sam > /tmp/f5YcqjFauI/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_index -b /tmp/f5YcqjFauI/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view -l 0 -z -m 14 -x /tmp/f5YcqjFauI/index.sam.gz.csi /builddir/build/BUILD/htslib-1.23/test/index_dos.sam > /tmp/f5YcqjFauI/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_index -c /tmp/f5YcqjFauI/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view -l 0 -z -m 0 -x /tmp/f5YcqjFauI/index.sam.gz.bai /builddir/build/BUILD/htslib-1.23/test/index_dos.sam > /tmp/f5YcqjFauI/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_index -b /tmp/f5YcqjFauI/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view -l 0 -C -x /tmp/f5YcqjFauI/index.cram.crai /builddir/build/BUILD/htslib-1.23/test/index.sam > /tmp/f5YcqjFauI/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_index /tmp/f5YcqjFauI/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view -p /tmp/f5YcqjFauI/index3_rgn.sam /tmp/f5YcqjFauI/index3.cram CHROMOSOME_I:5000-5100 .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view -M -p /tmp/f5YcqjFauI/index3_rgnm.sam /tmp/f5YcqjFauI/index3.cram CHROMOSOME_I:5000-5100 .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view -l 0 -b -m 14 -x /tmp/f5YcqjFauI/index.bcf.csi /builddir/build/BUILD/htslib-1.23/test/index.vcf > /tmp/f5YcqjFauI/index.bcf .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_index -c /tmp/f5YcqjFauI/index.bcf .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view -l 0 -z -m 14 -x /tmp/f5YcqjFauI/index.vcf.gz.csi /builddir/build/BUILD/htslib-1.23/test/index.vcf > /tmp/f5YcqjFauI/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_index -c /tmp/f5YcqjFauI/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view -l 0 -z -m 0 -x /tmp/f5YcqjFauI/index.vcf.gz.tbi /builddir/build/BUILD/htslib-1.23/test/index.vcf > /tmp/f5YcqjFauI/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_index -t /tmp/f5YcqjFauI/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23/tabix /tmp/f5YcqjFauI/index.vcf.gz##idx##/tmp/f5YcqjFauI/index.vcf.gz.tbi 1:10000060-10000060 .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view /tmp/f5YcqjFauI/index2.bam 1:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view /tmp/f5YcqjFauI/index2.bam 1:2000000-2000000 .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view /tmp/f5YcqjFauI/index2.bam 2:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view /tmp/f5YcqjFauI/index2.bam 2:2000000-2000000 .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view -@4 -l 0 -b -m 14 -x /tmp/f5YcqjFauI/index.bam.csi /builddir/build/BUILD/htslib-1.23/test/index.sam > /tmp/f5YcqjFauI/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_index -c /tmp/f5YcqjFauI/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view -@4 -l 0 -b -m 0 -x /tmp/f5YcqjFauI/index.bam.bai /builddir/build/BUILD/htslib-1.23/test/index.sam > /tmp/f5YcqjFauI/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_index -b /tmp/f5YcqjFauI/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view -@4 -l 0 -z -m 14 -x /tmp/f5YcqjFauI/index.sam.gz.csi /builddir/build/BUILD/htslib-1.23/test/index.sam > /tmp/f5YcqjFauI/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_index -c /tmp/f5YcqjFauI/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view -@4 -l 0 -z -m 0 -x /tmp/f5YcqjFauI/index.sam.gz.bai /builddir/build/BUILD/htslib-1.23/test/index.sam > /tmp/f5YcqjFauI/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_index -b /tmp/f5YcqjFauI/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view -@4 -l 0 -z -m 14 -x /tmp/f5YcqjFauI/index.sam.gz.csi /builddir/build/BUILD/htslib-1.23/test/index_dos.sam > /tmp/f5YcqjFauI/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_index -c /tmp/f5YcqjFauI/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view -@4 -l 0 -z -m 0 -x /tmp/f5YcqjFauI/index.sam.gz.bai /builddir/build/BUILD/htslib-1.23/test/index_dos.sam > /tmp/f5YcqjFauI/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_index -b /tmp/f5YcqjFauI/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view -@4 -l 0 -C -x /tmp/f5YcqjFauI/index.cram.crai /builddir/build/BUILD/htslib-1.23/test/index.sam > /tmp/f5YcqjFauI/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_index /tmp/f5YcqjFauI/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view -@4 -p /tmp/f5YcqjFauI/index3_rgn.sam /tmp/f5YcqjFauI/index3.cram CHROMOSOME_I:5000-5100 .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view -@4 -M -p /tmp/f5YcqjFauI/index3_rgnm.sam /tmp/f5YcqjFauI/index3.cram CHROMOSOME_I:5000-5100 .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view -@4 -l 0 -b -m 14 -x /tmp/f5YcqjFauI/index.bcf.csi /builddir/build/BUILD/htslib-1.23/test/index.vcf > /tmp/f5YcqjFauI/index.bcf .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_index -c /tmp/f5YcqjFauI/index.bcf .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view -@4 -l 0 -z -m 14 -x /tmp/f5YcqjFauI/index.vcf.gz.csi /builddir/build/BUILD/htslib-1.23/test/index.vcf > /tmp/f5YcqjFauI/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_index -c /tmp/f5YcqjFauI/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view -@4 -l 0 -z -m 0 -x /tmp/f5YcqjFauI/index.vcf.gz.tbi /builddir/build/BUILD/htslib-1.23/test/index.vcf > /tmp/f5YcqjFauI/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_index -t /tmp/f5YcqjFauI/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23/tabix /tmp/f5YcqjFauI/index.vcf.gz##idx##/tmp/f5YcqjFauI/index.vcf.gz.tbi 1:10000060-10000060 .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view /tmp/f5YcqjFauI/index2.bam 1:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view /tmp/f5YcqjFauI/index2.bam 1:2000000-2000000 .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view /tmp/f5YcqjFauI/index2.bam 2:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.23/test/test_view /tmp/f5YcqjFauI/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 .. 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-1.23/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 -t auxf.fa -S -l7 -C -o VERSION=4.0 -o archive auxf#values.sam > auxf#values.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./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_ ./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=4.0 -o archive c1#pad3.sam > c1#pad3.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./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_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#1000.sam > ce#1000.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./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_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#5.sam > ce#5.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./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_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o fast ce#large_seq.sam > ce#large_seq.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./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 -S -l7 -C -o VERSION=4.0 -o normal ce#large_seq.sam > ce#large_seq.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./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 -S -l7 -C -o VERSION=4.0 -o small ce#large_seq.sam > ce#large_seq.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./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 -S -l7 -C -o VERSION=4.0 -o archive ce#large_seq.sam > ce#large_seq.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./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_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#supp.sam > ce#supp.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./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_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#blank.sam > xx#blank.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./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 -t xx.fa -S -l7 -C -o VERSION=4.0 -o fast xx#large_aux.sam > xx#large_aux.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./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 -S -l7 -C -o VERSION=4.0 -o normal xx#large_aux.sam > xx#large_aux.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./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 -S -l7 -C -o VERSION=4.0 -o small xx#large_aux.sam > xx#large_aux.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./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 -S -l7 -C -o VERSION=4.0 -o archive xx#large_aux.sam > xx#large_aux.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./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_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#MD.sam > xx#MD.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./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_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#pair.sam > xx#pair.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./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_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#tlen.sam > xx#tlen.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./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 .. 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-1.23/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-1.23/test/test-vcf-api /tmp/f5YcqjFauI/test-vcf-api.bcf .. ok test_bcf2vcf: /builddir/build/BUILD/htslib-1.23/test/test_view /builddir/build/BUILD/htslib-1.23/test/tabix/vcf_file.bcf .. ok test_vcf_sweep: /builddir/build/BUILD/htslib-1.23/test/test-vcf-sweep /tmp/f5YcqjFauI/test-vcf-api.bcf .. ok test_vcf_various: /builddir/build/BUILD/htslib-1.23/htsfile -ch /builddir/build/BUILD/htslib-1.23/test/test-vcf-hdr-in.vcf .. ok test_vcf_various: /builddir/build/BUILD/htslib-1.23/htsfile -c /builddir/build/BUILD/htslib-1.23/test/formatcols.vcf .. ok test_vcf_various: /builddir/build/BUILD/htslib-1.23/htsfile -c /builddir/build/BUILD/htslib-1.23/test/noroundtrip.vcf .. ok test_vcf_various: /builddir/build/BUILD/htslib-1.23/htsfile -c /builddir/build/BUILD/htslib-1.23/test/formatmissing.vcf .. ok test_vcf_various: /builddir/build/BUILD/htslib-1.23/htsfile -c /builddir/build/BUILD/htslib-1.23/test/vcf_meta_meta.vcf .. ok test_vcf_various: /builddir/build/BUILD/htslib-1.23/test/test_view /builddir/build/BUILD/htslib-1.23/test/modhdr.vcf.gz chr22:1-2 .. ok test_vcf_44: /builddir/build/BUILD/htslib-1.23/htsfile -c /builddir/build/BUILD/htslib-1.23/test/vcf44_1.vcf .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr.pl -t /tmp/f5YcqjFauI -s 74452500 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr.pl -t /tmp/f5YcqjFauI -s 34270147 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr.pl -t /tmp/f5YcqjFauI -s 11108528 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr.pl -t /tmp/f5YcqjFauI -s 42233895 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr.pl -t /tmp/f5YcqjFauI -s 8111117 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr.pl -t /tmp/f5YcqjFauI -s 85644070 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr.pl -t /tmp/f5YcqjFauI -s 49879942 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr.pl -t /tmp/f5YcqjFauI -s 47881429 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr.pl -t /tmp/f5YcqjFauI -s 69081244 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr.pl -t /tmp/f5YcqjFauI -s 83459376 .. ok test_bcf_sr_no_index: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr --no-index -p all --args /builddir/build/BUILD/htslib-1.23/test/bcf-sr/merge.noidx.a.vcf /builddir/build/BUILD/htslib-1.23/test/bcf-sr/merge.noidx.b.vcf /builddir/build/BUILD/htslib-1.23/test/bcf-sr/merge.noidx.c.vcf 2> /tmp/f5YcqjFauI/no_index_1.err .. ok test_bcf_sr_no_index: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr --no-index -p all --args /builddir/build/BUILD/htslib-1.23/test/bcf-sr/merge.noidx.a.vcf /builddir/build/BUILD/htslib-1.23/test/bcf-sr/merge.noidx.hdr_order.vcf > /tmp/f5YcqjFauI/no_index_2.out 2> /tmp/f5YcqjFauI/no_index_2.err (expected fail) .. ok test_bcf_sr_no_index: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr --no-index -p all --args /builddir/build/BUILD/htslib-1.23/test/bcf-sr/merge.noidx.a.vcf /builddir/build/BUILD/htslib-1.23/test/bcf-sr/merge.noidx.rec_order.vcf > /tmp/f5YcqjFauI/no_index_3.out 2> /tmp/f5YcqjFauI/no_index_3.err (expected fail) .. ok test_bcf_sr_no_index: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr --no-index -p all --args /builddir/build/BUILD/htslib-1.23/test/bcf-sr/merge.noidx.rec_order.vcf /builddir/build/BUILD/htslib-1.23/test/bcf-sr/merge.noidx.a.vcf > /tmp/f5YcqjFauI/no_index_4.out 2> /tmp/f5YcqjFauI/no_index_4.err (expected fail) .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23/test/test_view -b -p /tmp/f5YcqjFauI/weird-chr-names.vcf.bcf -x /tmp/f5YcqjFauI/weird-chr-names.vcf.bcf.csi /builddir/build/BUILD/htslib-1.23/test/bcf-sr/weird-chr-names.vcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/f5YcqjFauI/range_test_1.out.vcf -r '1' --args /tmp/f5YcqjFauI/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/f5YcqjFauI/range_test_2.out.vcf -r '1:1-2' --args /tmp/f5YcqjFauI/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/f5YcqjFauI/range_test_3.out.vcf -r '1:1,1:2' --args /tmp/f5YcqjFauI/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/f5YcqjFauI/range_test_4.out.vcf -r '1:1-1' --args /tmp/f5YcqjFauI/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/f5YcqjFauI/range_test_5.out.vcf -r '{1:1}' --args /tmp/f5YcqjFauI/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/f5YcqjFauI/range_test_6.out.vcf -r '{1:1}:1-2' --args /tmp/f5YcqjFauI/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/f5YcqjFauI/range_test_7.out.vcf -r '{1:1}:1,{1:1}:2' --args /tmp/f5YcqjFauI/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/f5YcqjFauI/range_test_8.out.vcf -r '{1:1}:1-1' --args /tmp/f5YcqjFauI/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/f5YcqjFauI/range_test_9.out.vcf -r '{1:1-1}' --args /tmp/f5YcqjFauI/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/f5YcqjFauI/range_test_10.out.vcf -r '{1:1-1}:1-2' --args /tmp/f5YcqjFauI/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/f5YcqjFauI/range_test_11.out.vcf -r '{1:1-1}:1,{1:1-1}:2' --args /tmp/f5YcqjFauI/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/f5YcqjFauI/range_test_12.out.vcf -r '{1:1-1}:1-1' --args /tmp/f5YcqjFauI/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/f5YcqjFauI/range_test_13.out.vcf -r '{1:1-1}-2' --args /tmp/f5YcqjFauI/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-1.23/test/test-bcf-sr -O vcf -o /tmp/f5YcqjFauI/range_test_14.out.vcf -t '1' --args /tmp/f5YcqjFauI/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/f5YcqjFauI/range_test_15.out.vcf -t '1:1-2' --args /tmp/f5YcqjFauI/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/f5YcqjFauI/range_test_16.out.vcf -t '1:1,1:2' --args /tmp/f5YcqjFauI/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/f5YcqjFauI/range_test_17.out.vcf -t '1:1-1' --args /tmp/f5YcqjFauI/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/f5YcqjFauI/range_test_18.out.vcf -t '{1:1}' --args /tmp/f5YcqjFauI/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/f5YcqjFauI/range_test_19.out.vcf -t '{1:1}:1-2' --args /tmp/f5YcqjFauI/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/f5YcqjFauI/range_test_20.out.vcf -t '{1:1}:1,{1:1}:2' --args /tmp/f5YcqjFauI/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/f5YcqjFauI/range_test_21.out.vcf -t '{1:1}:1-1' --args /tmp/f5YcqjFauI/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/f5YcqjFauI/range_test_22.out.vcf -t '{1:1-1}' --args /tmp/f5YcqjFauI/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/f5YcqjFauI/range_test_23.out.vcf -t '{1:1-1}:1-2' --args /tmp/f5YcqjFauI/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/f5YcqjFauI/range_test_24.out.vcf -t '{1:1-1}:1,{1:1-1}:2' --args /tmp/f5YcqjFauI/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/f5YcqjFauI/range_test_25.out.vcf -t '{1:1-1}:1-1' --args /tmp/f5YcqjFauI/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/f5YcqjFauI/range_test_26.out.vcf -t '{1:1-1}-2' --args /tmp/f5YcqjFauI/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-1.23/test/test-bcf-translate - .. ok test_convert_padded_header: /builddir/build/BUILD/htslib-1.23/test/test_view -t ce.fa -C /tmp/f5YcqjFauI/headernul0.bam .. ok test_convert_padded_header: /builddir/build/BUILD/htslib-1.23/test/test_view -t ce.fa -C /tmp/f5YcqjFauI/headernul1.bam .. ok test_convert_padded_header: /builddir/build/BUILD/htslib-1.23/test/test_view -t ce.fa -C /tmp/f5YcqjFauI/headernul678.bam .. ok test_rebgzip: Alternate zlib/deflate library detected test_rebgzip: /builddir/build/BUILD/htslib-1.23/bgzip -I /builddir/build/BUILD/htslib-1.23/test/bgziptest.txt.tmp.gz.gzi -c -g /builddir/build/BUILD/htslib-1.23/test/bgziptest.txt .. ok test-logging: /builddir/build/BUILD/htslib-1.23/test/test-logging.pl .. ok test_plugin_loading: HTS_PATH=/builddir/build/BUILD/htslib-1.23 /builddir/build/BUILD/htslib-1.23/test/with-shlib.sh /builddir/build/BUILD/htslib-1.23/htsfile https://localhost:99999/invalid_port .. ok test_realn: /builddir/build/BUILD/htslib-1.23/test/test_realn -f /builddir/build/BUILD/htslib-1.23/test/realn01.fa -i /builddir/build/BUILD/htslib-1.23/test/realn01.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.23/test/test_realn -f /builddir/build/BUILD/htslib-1.23/test/realn02.fa -i /builddir/build/BUILD/htslib-1.23/test/realn02.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.23/test/test_realn -a -f /builddir/build/BUILD/htslib-1.23/test/realn01.fa -i /builddir/build/BUILD/htslib-1.23/test/realn01.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.23/test/test_realn -a -f /builddir/build/BUILD/htslib-1.23/test/realn02.fa -i /builddir/build/BUILD/htslib-1.23/test/realn02.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.23/test/test_realn -e -f /builddir/build/BUILD/htslib-1.23/test/realn01.fa -i /builddir/build/BUILD/htslib-1.23/test/realn01.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.23/test/test_realn -e -f /builddir/build/BUILD/htslib-1.23/test/realn02.fa -i /builddir/build/BUILD/htslib-1.23/test/realn02.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.23/test/test_realn -r -f /builddir/build/BUILD/htslib-1.23/test/realn02.fa -i /builddir/build/BUILD/htslib-1.23/test/realn02-r.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.23/test/test_realn -a -f /builddir/build/BUILD/htslib-1.23/test/realn02.fa -i /builddir/build/BUILD/htslib-1.23/test/realn02_exp.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.23/test/test_realn -f /builddir/build/BUILD/htslib-1.23/test/realn02.fa -i /builddir/build/BUILD/htslib-1.23/test/realn02_exp-a.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.23/test/test_realn -f /builddir/build/BUILD/htslib-1.23/test/realn03.fa -e -i /builddir/build/BUILD/htslib-1.23/test/realn03.sam -o - .. ok test-bcf_set_variant_type: /builddir/build/BUILD/htslib-1.23/test/test-bcf_set_variant_type .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -f smpl:overlap --allow-dups -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.1.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.1.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -f smpl:overlap --allow-dups -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.1.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -f smpl:overlap --allow-dups -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -f smpl:overlap -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.1.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.1.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -f smpl:overlap -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.1.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -f smpl:overlap -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -f smpl:overlap -c chr,beg,end -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.1.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.1.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -f smpl:overlap -c chr,beg,end -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.1.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -f smpl:overlap -c chr,beg,end -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -f smpl,value:overlap,value -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.1.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.1.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -f smpl,value:overlap,value -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.1.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -f smpl,value:overlap,value -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -f smpl:overlap -O 0.5 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.1.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.1.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -f smpl:overlap -O 0.5 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.1.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -f smpl:overlap -O 0.5 -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -f smpl:overlap -rO 0.5 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.1.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.1.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -f smpl:overlap -rO 0.5 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.1.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -f smpl:overlap -rO 0.5 -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -f smpl:overlap --allow-dups --max-annots 2 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.1.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.1.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -f smpl:overlap --allow-dups --max-annots 2 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.1.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -f smpl:overlap --allow-dups --max-annots 2 -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.2.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.2.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.2.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.2.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.2.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.2.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4,value:5,value -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.2.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.2.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4,value:5,value -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.2.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4,value:5,value -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.2.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.2.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.2.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -a nbp,frac -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.2.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.2.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -a nbp,frac -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.2.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -a nbp,frac -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups --max-annots 2 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.2.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.2.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups --max-annots 2 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.2.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups --max-annots 2 -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -f smpl:overlap -a nbp,frac -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.3.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.3.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.3.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -f smpl:overlap -a nbp,frac -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.3.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.3.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -f smpl:overlap -a nbp,frac -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.3.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -c 2,3,4:2,3,4 -m 1:1 -f 1:1 -a nbp,frac -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.4.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.4.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.4.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 2,3,4:2,3,4 -m 1:1 -f 1:1 -a nbp,frac -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.4.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.4.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 2,3,4:2,3,4 -m 1:1 -f 1:1 -a nbp,frac -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.4.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -c 2,3,4:2,3,4 -a nbp,frac -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.5.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.5.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.5.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 2,3,4:2,3,4 -a nbp,frac -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.5.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.5.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 2,3,4:2,3,4 -a nbp,frac -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.5.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,2:1,2,2 -a nbp -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.6.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.6.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.6.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,2:1,2,2 -a nbp -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.6.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.6.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,2:1,2,2 -a nbp -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.6.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,2:1,2,2 -f overlap -H -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.7.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.7.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.7.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,2:1,2,2 -f overlap -H -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.7.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.7.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,2:1,2,2 -f overlap -H -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.7.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -c chr,beg,end:chr,start,end -m sample -f is_tp -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.8.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.8.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.8.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c chr,beg,end:chr,start,end -m sample -f is_tp -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.8.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.8.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c chr,beg,end:chr,start,end -m sample -f is_tp -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.8.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:chr,beg,end -a nbp,frac,cnt -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.9.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.9.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.9.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:chr,beg,end -a nbp,frac,cnt -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.9.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.9.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:chr,beg,end -a nbp,frac,cnt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.9.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -f smpl -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.10.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.10.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -f smpl -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.10.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -f smpl -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.10.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.10.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.10.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -x -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.10.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.10.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -x -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.10.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -x -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -m smpl -f smpl -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.10.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.10.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -m smpl -f smpl -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.10.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -m smpl -f smpl -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -m smpl -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.10.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.10.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -m smpl -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.10.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -m smpl -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -m smpl -x -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.10.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.10.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -m smpl -x -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.10.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -m smpl -x -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.11.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.11.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.11.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -II -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.11.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.11.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -II -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.11.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -II -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:-1 -II -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.11.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.11.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:-1 -II -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.11.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:-1 -II -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.11.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.11.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.11.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.11.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.11.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.11.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -I -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.11.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.11.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -I -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.11.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -I -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -I -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.11.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.11.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -I -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.11.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -I -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d , -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.12.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.12.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.12.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d , -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.12.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.12.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d , -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.12.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d $',:\t' -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.12.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.11.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d $',:\t' -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.12.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.12.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d $',:\t' -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -r -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -r -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -r -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 0.5,0.5 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 0.5,0.5 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 0.5,0.5 -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 0,1 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 0,1 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 0,1 -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 1,0 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 1,0 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 1,0 -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.13.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3 -C 11:11 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.14.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.14.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.14.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3 -C 11:11 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.14.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.14.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3 -C 11:11 -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.14.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3 -C 01:01 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.14.txt -t /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.14.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/dst.14.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3 -C 01:01 -s /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.14.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23/test/annot-tsv/src.14.txt | /builddir/build/BUILD/htslib-1.23/annot-tsv -c 1,2,3 -C 01:01 -t /builddir/build/BUILD/htslib-1.23/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 + RPM_EC=0 ++ jobs -p + exit 0 Processing files: htslib-1.23-1.el10.aarch64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.hy6rGl + umask 022 + cd /builddir/build/BUILD + cd htslib-1.23 + DOCDIR=/builddir/build/BUILDROOT/htslib-1.23-1.el10.aarch64/usr/share/doc/htslib + export LC_ALL= + LC_ALL= + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/htslib-1.23-1.el10.aarch64/usr/share/doc/htslib + cp -pr /builddir/build/BUILD/htslib-1.23/NEWS /builddir/build/BUILDROOT/htslib-1.23-1.el10.aarch64/usr/share/doc/htslib + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.phAVcA + umask 022 + cd /builddir/build/BUILD + cd htslib-1.23 + LICENSEDIR=/builddir/build/BUILDROOT/htslib-1.23-1.el10.aarch64/usr/share/licenses/htslib + export LC_ALL= + LC_ALL= + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/htslib-1.23-1.el10.aarch64/usr/share/licenses/htslib + cp -pr /builddir/build/BUILD/htslib-1.23/LICENSE /builddir/build/BUILDROOT/htslib-1.23-1.el10.aarch64/usr/share/licenses/htslib + RPM_EC=0 ++ jobs -p + exit 0 Provides: htslib = 1.23-1.el10 htslib(aarch-64) = 1.23-1.el10 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_1.3)(64bit) libhts.so.3(HTSLIB_1.4)(64bit) libhts.so.3(HTSLIB_1.5)(64bit) libhts.so.3(HTSLIB_1.6)(64bit) libhts.so.3(HTSLIB_1.7)(64bit) libhts.so.3(HTSLIB_1.9)(64bit) Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: ld-linux-aarch64.so.1()(64bit) ld-linux-aarch64.so.1(GLIBC_2.17)(64bit) libbz2.so.1()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.17)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_ABI_DT_RELR)(64bit) libcrypto.so.3()(64bit) libcrypto.so.3(OPENSSL_3.0.0)(64bit) libcurl.so.4()(64bit) libhts.so.3()(64bit) libhts.so.3(HTSLIB_1.0)(64bit) libhts.so.3(HTSLIB_1.3)(64bit) libhts.so.3(HTSLIB_1.4)(64bit) libhts.so.3(HTSLIB_1.5)(64bit) libhts.so.3(HTSLIB_1.7)(64bit) liblzma.so.5()(64bit) liblzma.so.5(XZ_5.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.17)(64bit) libm.so.6(GLIBC_2.23)(64bit) libm.so.6(GLIBC_2.29)(64bit) libz.so.1()(64bit) rtld(GNU_HASH) Processing files: htslib-devel-1.23-1.el10.aarch64 Provides: htslib-devel = 1.23-1.el10 htslib-devel(aarch-64) = 1.23-1.el10 pkgconfig(htslib) = 1.23 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-1.23-1.el10.aarch64 Provides: htslib-tools = 1.23-1.el10 htslib-tools(aarch-64) = 1.23-1.el10 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: ld-linux-aarch64.so.1()(64bit) ld-linux-aarch64.so.1(GLIBC_2.17)(64bit) libbz2.so.1()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.17)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_ABI_DT_RELR)(64bit) libcurl.so.4()(64bit) liblzma.so.5()(64bit) liblzma.so.5(XZ_5.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.17)(64bit) libm.so.6(GLIBC_2.29)(64bit) libz.so.1()(64bit) rtld(GNU_HASH) Processing files: htslib-debugsource-1.23-1.el10.aarch64 Provides: htslib-debugsource = 1.23-1.el10 htslib-debugsource(aarch-64) = 1.23-1.el10 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: htslib-debuginfo-1.23-1.el10.aarch64 Provides: debuginfo(build-id) = 5858fd579ccbbe67aafdaf4c76e9cfe8951d40d4 debuginfo(build-id) = 9c810b25a791eb79fe7e810a237aa59bacbd2e28 debuginfo(build-id) = e36dc3d242090ae121ebfdf3a659da727da0f720 debuginfo(build-id) = e372dcd3342d62efeaeadfd0bfc847c2f207ff60 htslib-debuginfo = 1.23-1.el10 htslib-debuginfo(aarch-64) = 1.23-1.el10 libhts.so.1.23-1.23-1.el10.aarch64.debug()(64bit) Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: htslib-debugsource(aarch-64) = 1.23-1.el10 Processing files: htslib-tools-debuginfo-1.23-1.el10.aarch64 Provides: debuginfo(build-id) = 3a0ff6810b3eda3bca59cb89fea3f5053a4de906 debuginfo(build-id) = 4cad327479e78da7295f7ffaf537326814abb4c2 debuginfo(build-id) = 9d298062a253373a3c5c8b77bbf7999ad9035407 debuginfo(build-id) = e380f1aa5680510114a9710daec8de11ab092893 debuginfo(build-id) = eec39de0b956b75438c0cb3d33a0b9f241aed21f htslib-tools-debuginfo = 1.23-1.el10 htslib-tools-debuginfo(aarch-64) = 1.23-1.el10 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: htslib-debugsource(aarch-64) = 1.23-1.el10 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/htslib-1.23-1.el10.aarch64 Wrote: /builddir/build/RPMS/htslib-debuginfo-1.23-1.el10.aarch64.rpm Wrote: /builddir/build/RPMS/htslib-tools-1.23-1.el10.aarch64.rpm Wrote: /builddir/build/RPMS/htslib-debugsource-1.23-1.el10.aarch64.rpm Wrote: /builddir/build/RPMS/htslib-devel-1.23-1.el10.aarch64.rpm Wrote: /builddir/build/RPMS/htslib-1.23-1.el10.aarch64.rpm Wrote: /builddir/build/RPMS/htslib-tools-debuginfo-1.23-1.el10.aarch64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.DUHtLg + umask 022 + cd /builddir/build/BUILD + cd htslib-1.23 + /usr/bin/rm -rf /builddir/build/BUILDROOT/htslib-1.23-1.el10.aarch64 + RPM_EC=0 ++ jobs -p + exit 0 Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.DWhEKr + umask 022 + cd /builddir/build/BUILD + rm -rf /builddir/build/BUILD/htslib-1.23-SPECPARTS + rm -rf htslib-1.23 htslib-1.23.gemspec + RPM_EC=0 ++ jobs -p + exit 0 Finish: rpmbuild htslib-1.23-1.el10.src.rpm Finish: build phase for htslib-1.23-1.el10.src.rpm INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/centos-stream+epel-10-aarch64-1769500621.779357/root/var/log/dnf.rpm.log /var/lib/mock/centos-stream+epel-10-aarch64-1769500621.779357/root/var/log/dnf.librepo.log /var/lib/mock/centos-stream+epel-10-aarch64-1769500621.779357/root/var/log/dnf.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-1.23-1.el10.src.rpm) Config(child) 4 minutes 47 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-devel", "epoch": null, "version": "1.23", "release": "1.el10", "arch": "aarch64" }, { "name": "htslib", "epoch": null, "version": "1.23", "release": "1.el10", "arch": "aarch64" }, { "name": "htslib", "epoch": null, "version": "1.23", "release": "1.el10", "arch": "src" }, { "name": "htslib-debugsource", "epoch": null, "version": "1.23", "release": "1.el10", "arch": "aarch64" }, { "name": "htslib-tools", "epoch": null, "version": "1.23", "release": "1.el10", "arch": "aarch64" }, { "name": "htslib-tools-debuginfo", "epoch": null, "version": "1.23", "release": "1.el10", "arch": "aarch64" }, { "name": "htslib-debuginfo", "epoch": null, "version": "1.23", "release": "1.el10", "arch": "aarch64" } ] } RPMResults finished