Warning: Permanently added '3.93.242.113' (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/7524263-epel-9-x86_64 --chroot epel-9-x86_64 Version: 0.73 PID: 6603 Logging PID: 6604 Task: {'allow_user_ssh': False, 'appstream': False, 'background': False, 'bootstrap': 'off', 'build_id': 7524263, 'buildroot_pkgs': [], 'chroot': 'epel-9-x86_64', 'enable_net': False, 'fedora_review': False, 'git_hash': 'c599a627a8d7f25c2fc367c91f40be3c44190c7f', 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/yamaura/genomics/htslib', 'isolation': 'default', 'memory_reqs': 2048, 'package_name': 'htslib', 'package_version': '1.20-1', 'project_dirname': 'genomics', 'project_name': 'genomics', 'project_owner': 'yamaura', 'repo_priority': None, 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/yamaura/genomics/epel-9-x86_64/', 'id': 'copr_base', 'name': 'Copr repository', 'priority': None}], 'sandbox': 'yamaura/genomics--yamaura', 'source_json': {}, 'source_type': None, 'ssh_public_keys': None, 'submitter': 'yamaura', 'tags': [], 'task_id': '7524263-epel-9-x86_64', 'timeout': 18000, 'uses_devel_repo': False, 'with_opts': [], 'without_opts': []} Running: git clone https://copr-dist-git.fedorainfracloud.org/git/yamaura/genomics/htslib /var/lib/copr-rpmbuild/workspace/workdir-4jea4873/htslib --depth 500 --no-single-branch --recursive cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/yamaura/genomics/htslib', '/var/lib/copr-rpmbuild/workspace/workdir-4jea4873/htslib', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-4jea4873/htslib'... Running: git checkout c599a627a8d7f25c2fc367c91f40be3c44190c7f -- cmd: ['git', 'checkout', 'c599a627a8d7f25c2fc367c91f40be3c44190c7f', '--'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-4jea4873/htslib rc: 0 stdout: stderr: Note: switching to 'c599a627a8d7f25c2fc367c91f40be3c44190c7f'. 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 c599a62 automatic import of htslib Running: copr-distgit-client sources cmd: ['copr-distgit-client', 'sources'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-4jea4873/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-1.20.tar.bz2 INFO: Reading stdout from command: curl --help all INFO: Calling: curl -H Pragma: -o htslib-1.20.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/yamaura/genomics/htslib/htslib-1.20.tar.bz2/md5/127cbea4e9a8c084fb09c3fd24bd825d/htslib-1.20.tar.bz2 /usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 4667k 100 4667k 0 0 154M 0 --:--:-- --:--:-- --:--:-- 157M INFO: Reading stdout from command: md5sum htslib-1.20.tar.bz2 Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-4jea4873/htslib/htslib.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-4jea4873/htslib --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1717413251.506071 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 5.6 starting (python version = 3.12.1, NVR = mock-5.6-1.fc39), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-4jea4873/htslib/htslib.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-4jea4873/htslib --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1717413251.506071 -r /var/lib/copr-rpmbuild/results/configs/child.cfg 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-4jea4873/htslib/htslib.spec) Config(rhel+epel-9-x86_64) Start: clean chroot Finish: clean chroot Mock Version: 5.6 INFO: Mock Version: 5.6 Start: chroot init INFO: mounting tmpfs at /var/lib/mock/rhel+epel-9-x86_64-1717413251.506071/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 dnf detected and used (fallback) INFO: Buildroot is handled by package management from host and used with --installroot: rpm-4.19.1.1-1.fc39.x86_64 rpm-sequoia-1.6.0-1.fc39.x86_64 python3-dnf-4.19.2-1.fc39.noarch python3-dnf-plugins-core-4.6.0-1.fc39.noarch yum-4.19.2-1.fc39.noarch dnf5-5.1.17-1.fc39.x86_64 dnf5-plugins-5.1.17-1.fc39.x86_64 Start: installing minimal buildroot with dnf No matches found for the following disable plugin patterns: local, spacewalk, versionlock Updating Subscription Management repositories. Unable to read consumer identity This system is not registered with an entitlement server. You can use subscription-manager to register. Copr repository 268 kB/s | 14 kB 00:00 Red Hat Enterprise Linux - BaseOS 91 MB/s | 22 MB 00:00 Red Hat Enterprise Linux - AppStream 149 MB/s | 35 MB 00:00 Red Hat Enterprise Linux - CodeReady Linux Buil 28 MB/s | 7.8 MB 00:00 Extra Packages for Enterprise Linux 9 - x86_64 134 MB/s | 21 MB 00:00 Dependencies resolved. ================================================================================ Package Arch Version Repo Size ================================================================================ Installing: bash x86_64 5.1.8-9.el9 baseos 1.7 M bzip2 x86_64 1.0.8-8.el9 baseos 60 k coreutils x86_64 8.32-35.el9 baseos 1.2 M cpio x86_64 2.13-16.el9 baseos 279 k diffutils x86_64 3.7-12.el9 baseos 402 k epel-rpm-macros noarch 9-14.el9 epel 15 k findutils x86_64 1:4.8.0-6.el9 baseos 550 k gawk x86_64 5.1.0-6.el9 baseos 1.0 M glibc-minimal-langpack x86_64 2.34-100.el9_4.2 baseos 28 k grep x86_64 3.6-5.el9 baseos 273 k gzip x86_64 1.12-1.el9 baseos 167 k info x86_64 6.7-15.el9 baseos 228 k patch x86_64 2.7.6-16.el9 appstream 130 k redhat-release x86_64 9.4-0.4.el9 baseos 46 k redhat-rpm-config noarch 207-1.el9 appstream 76 k rpm-build x86_64 4.16.1.3-29.el9 appstream 72 k sed x86_64 4.8-9.el9 baseos 309 k tar x86_64 2:1.34-6.el9_1 baseos 889 k unzip x86_64 6.0-56.el9 baseos 186 k util-linux x86_64 2.37.4-18.el9 baseos 2.3 M which x86_64 2.21-29.el9 baseos 45 k xz x86_64 5.2.5-8.el9_0 baseos 230 k Installing dependencies: alternatives x86_64 1.24-1.el9 baseos 42 k ansible-srpm-macros noarch 1-12.el9 epel 21 k audit-libs x86_64 3.1.2-2.el9 baseos 121 k basesystem noarch 11-13.el9 baseos 8.0 k binutils x86_64 2.35.2-43.el9 baseos 4.6 M binutils-gold x86_64 2.35.2-43.el9 baseos 736 k bzip2-libs x86_64 1.0.8-8.el9 baseos 42 k ca-certificates noarch 2023.2.60_v7.0.306-90.1.el9_2 baseos 846 k coreutils-common x86_64 8.32-35.el9 baseos 2.0 M cracklib x86_64 2.9.6-27.el9 baseos 99 k cracklib-dicts x86_64 2.9.6-27.el9 baseos 3.6 M crypto-policies noarch 20240202-1.git283706d.el9 baseos 88 k curl x86_64 7.76.1-29.el9_4 baseos 298 k cyrus-sasl-lib x86_64 2.1.27-21.el9 baseos 774 k debugedit x86_64 5.0-5.el9 appstream 81 k dwz x86_64 0.14-3.el9 appstream 130 k ed x86_64 1.14.2-12.el9 baseos 78 k efi-srpm-macros noarch 6-2.el9_0 appstream 24 k elfutils x86_64 0.190-2.el9 baseos 559 k elfutils-debuginfod-client x86_64 0.190-2.el9 baseos 39 k elfutils-default-yama-scope noarch 0.190-2.el9 baseos 12 k elfutils-libelf x86_64 0.190-2.el9 baseos 196 k elfutils-libs x86_64 0.190-2.el9 baseos 258 k file x86_64 5.39-16.el9 baseos 52 k file-libs x86_64 5.39-16.el9 baseos 593 k filesystem x86_64 3.16-2.el9 baseos 4.7 M fonts-srpm-macros noarch 1:2.0.5-7.el9.1 appstream 29 k forge-srpm-macros noarch 0.3.1-1.el9 epel 19 k fpc-srpm-macros noarch 1.3-7.el9 epel 7.5 k gdb-minimal x86_64 10.2-13.el9 appstream 3.5 M gdbm-libs x86_64 1:1.19-4.el9 baseos 56 k ghc-srpm-macros noarch 1.5.0-6.el9 appstream 9.0 k glibc x86_64 2.34-100.el9_4.2 baseos 2.0 M glibc-common x86_64 2.34-100.el9_4.2 baseos 313 k glibc-gconv-extra x86_64 2.34-100.el9_4.2 baseos 1.7 M gmp x86_64 1:6.2.0-13.el9 baseos 319 k go-srpm-macros noarch 3.2.0-3.el9 appstream 28 k go-srpm-macros-epel noarch 3.3.0.5-1.el9 epel 27 k groff-base x86_64 1.22.4-10.el9 baseos 1.1 M kernel-srpm-macros noarch 1.0-13.el9 appstream 17 k keyutils-libs x86_64 1.6.3-1.el9 baseos 34 k krb5-libs x86_64 1.21.1-1.el9 baseos 770 k libacl x86_64 2.3.1-4.el9 baseos 24 k libarchive x86_64 3.5.3-4.el9 baseos 392 k libattr x86_64 2.5.1-3.el9 baseos 20 k libblkid x86_64 2.37.4-18.el9 baseos 110 k libbrotli x86_64 1.0.9-6.el9 baseos 317 k libcap x86_64 2.48-9.el9_2 baseos 74 k libcap-ng x86_64 0.8.2-7.el9 baseos 36 k libcom_err x86_64 1.46.5-5.el9 baseos 28 k libcurl x86_64 7.76.1-29.el9_4 baseos 286 k libdb x86_64 5.3.28-53.el9 baseos 740 k libeconf x86_64 0.4.1-3.el9_2 baseos 30 k libevent x86_64 2.1.12-6.el9 baseos 268 k libfdisk x86_64 2.37.4-18.el9 baseos 157 k libffi x86_64 3.4.2-8.el9 baseos 40 k libgcc x86_64 11.4.1-3.el9 baseos 95 k libgcrypt x86_64 1.10.0-10.el9_2 baseos 508 k libgomp x86_64 11.4.1-3.el9 baseos 270 k libgpg-error x86_64 1.42-5.el9 baseos 220 k libidn2 x86_64 2.3.0-7.el9 baseos 105 k libmount x86_64 2.37.4-18.el9 baseos 138 k libnghttp2 x86_64 1.43.0-5.el9_4.3 baseos 75 k libpkgconf x86_64 1.7.3-10.el9 baseos 37 k libpsl x86_64 0.21.1-5.el9 baseos 66 k libpwquality x86_64 1.4.4-8.el9 baseos 123 k libselinux x86_64 3.6-1.el9 baseos 88 k libsemanage x86_64 3.6-1.el9 baseos 121 k libsepol x86_64 3.6-1.el9 baseos 331 k libsigsegv x86_64 2.13-4.el9 baseos 30 k libsmartcols x86_64 2.37.4-18.el9 baseos 66 k libssh x86_64 0.10.4-13.el9 baseos 220 k libssh-config noarch 0.10.4-13.el9 baseos 11 k libstdc++ x86_64 11.4.1-3.el9 baseos 747 k libtasn1 x86_64 4.16.0-8.el9_1 baseos 77 k libunistring x86_64 0.9.10-15.el9 baseos 499 k libutempter x86_64 1.2.1-6.el9 baseos 30 k libuuid x86_64 2.37.4-18.el9 baseos 30 k libverto x86_64 0.3.2-3.el9 baseos 24 k libxcrypt x86_64 4.4.18-3.el9 baseos 120 k libxml2 x86_64 2.9.13-6.el9_4 baseos 752 k libzstd x86_64 1.5.1-2.el9 baseos 332 k lua-libs x86_64 5.4.4-4.el9 baseos 132 k lua-srpm-macros noarch 1-6.el9 appstream 10 k lz4-libs x86_64 1.9.3-5.el9 baseos 69 k mpfr x86_64 4.1.0-7.el9 baseos 329 k ncurses x86_64 6.2-10.20210508.el9 baseos 410 k ncurses-base noarch 6.2-10.20210508.el9 baseos 99 k ncurses-libs x86_64 6.2-10.20210508.el9 baseos 332 k ocaml-srpm-macros noarch 6-6.el9 appstream 9.1 k openblas-srpm-macros noarch 2-11.el9 appstream 8.6 k openldap x86_64 2.6.6-3.el9 baseos 286 k openssl x86_64 1:3.0.7-27.el9 baseos 1.2 M openssl-fips-provider x86_64 3.0.7-2.el9 baseos 576 k openssl-libs x86_64 1:3.0.7-27.el9 baseos 1.9 M p11-kit x86_64 0.25.3-2.el9 baseos 537 k p11-kit-trust x86_64 0.25.3-2.el9 baseos 145 k pam x86_64 1.5.1-19.el9 baseos 631 k pcre x86_64 8.44-3.el9.3 baseos 202 k pcre2 x86_64 10.40-5.el9 baseos 236 k pcre2-syntax noarch 10.40-5.el9 baseos 145 k perl-AutoLoader noarch 5.74-481.el9 appstream 21 k perl-B x86_64 1.80-481.el9 appstream 184 k perl-Carp noarch 1.50-460.el9 appstream 31 k perl-Class-Struct noarch 0.66-481.el9 appstream 22 k perl-Data-Dumper x86_64 2.174-462.el9 appstream 59 k perl-Digest noarch 1.19-4.el9 appstream 29 k perl-Digest-MD5 x86_64 2.58-4.el9 appstream 39 k perl-Encode x86_64 4:3.08-462.el9 appstream 1.7 M perl-Errno x86_64 1.30-481.el9 appstream 15 k perl-Exporter noarch 5.74-461.el9 appstream 34 k perl-Fcntl x86_64 1.13-481.el9 appstream 22 k perl-File-Basename noarch 2.85-481.el9 appstream 17 k perl-File-Path noarch 2.18-4.el9 appstream 38 k perl-File-Temp noarch 1:0.231.100-4.el9 appstream 63 k perl-File-stat noarch 1.09-481.el9 appstream 17 k perl-FileHandle noarch 2.03-481.el9 appstream 16 k perl-Getopt-Long noarch 1:2.52-4.el9 appstream 64 k perl-Getopt-Std noarch 1.12-481.el9 appstream 16 k perl-HTTP-Tiny noarch 0.076-462.el9 appstream 57 k perl-IO x86_64 1.43-481.el9 appstream 92 k perl-IO-Socket-IP noarch 0.41-5.el9 appstream 45 k perl-IO-Socket-SSL noarch 2.073-1.el9 appstream 223 k perl-IPC-Open3 noarch 1.21-481.el9 appstream 24 k perl-MIME-Base64 x86_64 3.16-4.el9 appstream 34 k perl-Mozilla-CA noarch 20200520-6.el9 appstream 14 k perl-Net-SSLeay x86_64 1.92-2.el9 appstream 392 k perl-POSIX x86_64 1.94-481.el9 appstream 98 k perl-PathTools x86_64 3.78-461.el9 appstream 92 k perl-Pod-Escapes noarch 1:1.07-460.el9 appstream 22 k perl-Pod-Perldoc noarch 3.28.01-461.el9 appstream 92 k perl-Pod-Simple noarch 1:3.42-4.el9 appstream 229 k perl-Pod-Usage noarch 4:2.01-4.el9 appstream 43 k perl-Scalar-List-Utils x86_64 4:1.56-461.el9 appstream 77 k perl-SelectSaver noarch 1.02-481.el9 appstream 12 k perl-Socket x86_64 4:2.031-4.el9 appstream 58 k perl-Storable x86_64 1:3.21-460.el9 appstream 98 k perl-Symbol noarch 1.08-481.el9 appstream 14 k perl-Term-ANSIColor noarch 5.01-461.el9 appstream 51 k perl-Term-Cap noarch 1.17-460.el9 appstream 24 k perl-Text-ParseWords noarch 3.30-460.el9 appstream 18 k perl-Text-Tabs+Wrap noarch 2013.0523-460.el9 appstream 25 k perl-Time-Local noarch 2:1.300-7.el9 appstream 37 k perl-URI noarch 5.09-3.el9 appstream 125 k perl-base noarch 2.27-481.el9 appstream 16 k perl-constant noarch 1.33-461.el9 appstream 25 k perl-if noarch 0.60.800-481.el9 appstream 14 k perl-interpreter x86_64 4:5.32.1-481.el9 appstream 73 k perl-libnet noarch 3.13-4.el9 appstream 134 k perl-libs x86_64 4:5.32.1-481.el9 appstream 2.2 M perl-mro x86_64 1.23-481.el9 appstream 29 k perl-overload noarch 1.31-481.el9 appstream 46 k perl-overloading noarch 0.02-481.el9 appstream 13 k perl-parent noarch 1:0.238-460.el9 appstream 16 k perl-podlators noarch 1:4.14-460.el9 appstream 118 k perl-srpm-macros noarch 1-41.el9 appstream 9.4 k perl-subs noarch 1.03-481.el9 appstream 12 k perl-vars noarch 1.05-481.el9 appstream 13 k pkgconf x86_64 1.7.3-10.el9 baseos 45 k pkgconf-m4 noarch 1.7.3-10.el9 baseos 16 k pkgconf-pkg-config x86_64 1.7.3-10.el9 baseos 12 k popt x86_64 1.18-8.el9 baseos 69 k publicsuffix-list-dafsa noarch 20210518-3.el9 baseos 59 k pyproject-srpm-macros noarch 1.12.0-1.el9 appstream 14 k python-srpm-macros noarch 3.9-53.el9 appstream 19 k qt5-srpm-macros noarch 5.15.9-1.el9 appstream 9.1 k qt6-srpm-macros noarch 6.6.2-1.el9 epel 8.7 k readline x86_64 8.1-4.el9 baseos 215 k rpm x86_64 4.16.1.3-29.el9 baseos 541 k rpm-build-libs x86_64 4.16.1.3-29.el9 baseos 90 k rpm-libs x86_64 4.16.1.3-29.el9 baseos 310 k rpmautospec-rpm-macros noarch 0.6.3-1.el9 epel 9.9 k rust-srpm-macros noarch 17-4.el9 appstream 11 k rust-srpm-macros-epel noarch 26.3-1.el9 epel 10 k setup noarch 2.13.7-10.el9 baseos 150 k shadow-utils x86_64 2:4.9-8.el9 baseos 1.2 M sqlite-libs x86_64 3.34.1-7.el9_3 baseos 622 k systemd-libs x86_64 252-32.el9_4 baseos 679 k tzdata noarch 2024a-1.el9 baseos 842 k util-linux-core x86_64 2.37.4-18.el9 baseos 469 k xz-libs x86_64 5.2.5-8.el9_0 baseos 94 k zip x86_64 3.0-35.el9 baseos 270 k zlib x86_64 1.2.11-40.el9 baseos 93 k zstd x86_64 1.5.1-2.el9 baseos 552 k Transaction Summary ================================================================================ Install 206 Packages Total download size: 68 M Installed size: 215 M Downloading Packages: (1/206): bzip2-libs-1.0.8-8.el9.x86_64.rpm 652 kB/s | 42 kB 00:00 (2/206): bzip2-1.0.8-8.el9.x86_64.rpm 918 kB/s | 60 kB 00:00 (3/206): basesystem-11-13.el9.noarch.rpm 70 kB/s | 8.0 kB 00:00 (4/206): cpio-2.13-16.el9.x86_64.rpm 3.9 MB/s | 279 kB 00:00 (5/206): cracklib-2.9.6-27.el9.x86_64.rpm 1.3 MB/s | 99 kB 00:00 (6/206): ed-1.14.2-12.el9.x86_64.rpm 1.2 MB/s | 78 kB 00:00 (7/206): filesystem-3.16-2.el9.x86_64.rpm 86 MB/s | 4.7 MB 00:00 (8/206): grep-3.6-5.el9.x86_64.rpm 5.4 MB/s | 273 kB 00:00 (9/206): libattr-2.5.1-3.el9.x86_64.rpm 438 kB/s | 20 kB 00:00 (10/206): groff-base-1.22.4-10.el9.x86_64.rpm 18 MB/s | 1.1 MB 00:00 (11/206): info-6.7-15.el9.x86_64.rpm 3.4 MB/s | 228 kB 00:00 (12/206): libcap-ng-0.8.2-7.el9.x86_64.rpm 869 kB/s | 36 kB 00:00 (13/206): libbrotli-1.0.9-6.el9.x86_64.rpm 6.8 MB/s | 317 kB 00:00 (14/206): libevent-2.1.12-6.el9.x86_64.rpm 5.9 MB/s | 268 kB 00:00 (15/206): libdb-5.3.28-53.el9.x86_64.rpm 9.9 MB/s | 740 kB 00:00 (16/206): libgpg-error-1.42-5.el9.x86_64.rpm 4.5 MB/s | 220 kB 00:00 (17/206): libidn2-2.3.0-7.el9.x86_64.rpm 2.3 MB/s | 105 kB 00:00 (18/206): libpwquality-1.4.4-8.el9.x86_64.rpm 2.9 MB/s | 123 kB 00:00 (19/206): libpsl-0.21.1-5.el9.x86_64.rpm 1.2 MB/s | 66 kB 00:00 (20/206): libsigsegv-2.13-4.el9.x86_64.rpm 661 kB/s | 30 kB 00:00 (21/206): libunistring-0.9.10-15.el9.x86_64.rpm 6.4 MB/s | 499 kB 00:00 (22/206): libverto-0.3.2-3.el9.x86_64.rpm 524 kB/s | 24 kB 00:00 (23/206): libutempter-1.2.1-6.el9.x86_64.rpm 354 kB/s | 30 kB 00:00 (24/206): libxcrypt-4.4.18-3.el9.x86_64.rpm 2.6 MB/s | 120 kB 00:00 (25/206): libzstd-1.5.1-2.el9.x86_64.rpm 7.3 MB/s | 332 kB 00:00 (26/206): mpfr-4.1.0-7.el9.x86_64.rpm 7.4 MB/s | 329 kB 00:00 (27/206): pcre-8.44-3.el9.3.x86_64.rpm 4.4 MB/s | 202 kB 00:00 (28/206): lz4-libs-1.9.3-5.el9.x86_64.rpm 700 kB/s | 69 kB 00:00 (29/206): popt-1.18-8.el9.x86_64.rpm 1.5 MB/s | 69 kB 00:00 (30/206): publicsuffix-list-dafsa-20210518-3.el 1.4 MB/s | 59 kB 00:00 (31/206): readline-8.1-4.el9.x86_64.rpm 4.1 MB/s | 215 kB 00:00 (32/206): sed-4.8-9.el9.x86_64.rpm 6.4 MB/s | 309 kB 00:00 (33/206): unzip-6.0-56.el9.x86_64.rpm 3.3 MB/s | 186 kB 00:00 (34/206): diffutils-3.7-12.el9.x86_64.rpm 8.5 MB/s | 402 kB 00:00 (35/206): gawk-5.1.0-6.el9.x86_64.rpm 20 MB/s | 1.0 MB 00:00 (36/206): cracklib-dicts-2.9.6-27.el9.x86_64.rp 35 MB/s | 3.6 MB 00:00 (37/206): gdbm-libs-1.19-4.el9.x86_64.rpm 1.1 MB/s | 56 kB 00:00 (38/206): xz-5.2.5-8.el9_0.x86_64.rpm 4.9 MB/s | 230 kB 00:00 (39/206): xz-libs-5.2.5-8.el9_0.x86_64.rpm 2.1 MB/s | 94 kB 00:00 (40/206): zstd-1.5.1-2.el9.x86_64.rpm 13 MB/s | 552 kB 00:00 (41/206): cyrus-sasl-lib-2.1.27-21.el9.x86_64.r 15 MB/s | 774 kB 00:00 (42/206): libtasn1-4.16.0-8.el9_1.x86_64.rpm 1.8 MB/s | 77 kB 00:00 (43/206): tar-1.34-6.el9_1.x86_64.rpm 18 MB/s | 889 kB 00:00 (44/206): gzip-1.12-1.el9.x86_64.rpm 1.8 MB/s | 167 kB 00:00 (45/206): ca-certificates-2023.2.60_v7.0.306-90 18 MB/s | 846 kB 00:00 (46/206): keyutils-libs-1.6.3-1.el9.x86_64.rpm 792 kB/s | 34 kB 00:00 (47/206): libcap-2.48-9.el9_2.x86_64.rpm 1.8 MB/s | 74 kB 00:00 (48/206): libeconf-0.4.1-3.el9_2.x86_64.rpm 707 kB/s | 30 kB 00:00 (49/206): libgcrypt-1.10.0-10.el9_2.x86_64.rpm 11 MB/s | 508 kB 00:00 (50/206): libarchive-3.5.3-4.el9.x86_64.rpm 4.1 MB/s | 392 kB 00:00 (51/206): libpkgconf-1.7.3-10.el9.x86_64.rpm 824 kB/s | 37 kB 00:00 (52/206): pkgconf-1.7.3-10.el9.x86_64.rpm 942 kB/s | 45 kB 00:00 (53/206): pkgconf-pkg-config-1.7.3-10.el9.x86_6 293 kB/s | 12 kB 00:00 (54/206): pkgconf-m4-1.7.3-10.el9.noarch.rpm 245 kB/s | 16 kB 00:00 (55/206): zip-3.0-35.el9.x86_64.rpm 5.8 MB/s | 270 kB 00:00 (56/206): alternatives-1.24-1.el9.x86_64.rpm 1.0 MB/s | 42 kB 00:00 (57/206): findutils-4.8.0-6.el9.x86_64.rpm 11 MB/s | 550 kB 00:00 (58/206): gmp-6.2.0-13.el9.x86_64.rpm 6.5 MB/s | 319 kB 00:00 (59/206): krb5-libs-1.21.1-1.el9.x86_64.rpm 17 MB/s | 770 kB 00:00 (60/206): libffi-3.4.2-8.el9.x86_64.rpm 609 kB/s | 40 kB 00:00 (61/206): lua-libs-5.4.4-4.el9.x86_64.rpm 2.6 MB/s | 132 kB 00:00 (62/206): ncurses-6.2-10.20210508.el9.x86_64.rp 7.5 MB/s | 410 kB 00:00 (63/206): ncurses-base-6.2-10.20210508.el9.noar 1.8 MB/s | 99 kB 00:00 (64/206): ncurses-libs-6.2-10.20210508.el9.x86_ 5.6 MB/s | 332 kB 00:00 (65/206): shadow-utils-4.9-8.el9.x86_64.rpm 26 MB/s | 1.2 MB 00:00 (66/206): which-2.21-29.el9.x86_64.rpm 872 kB/s | 45 kB 00:00 (67/206): zlib-1.2.11-40.el9.x86_64.rpm 2.1 MB/s | 93 kB 00:00 (68/206): audit-libs-3.1.2-2.el9.x86_64.rpm 2.5 MB/s | 121 kB 00:00 (69/206): binutils-gold-2.35.2-43.el9.x86_64.rp 15 MB/s | 736 kB 00:00 (70/206): bash-5.1.8-9.el9.x86_64.rpm 26 MB/s | 1.7 MB 00:00 (71/206): binutils-2.35.2-43.el9.x86_64.rpm 54 MB/s | 4.6 MB 00:00 (72/206): coreutils-8.32-35.el9.x86_64.rpm 27 MB/s | 1.2 MB 00:00 (73/206): coreutils-common-8.32-35.el9.x86_64.r 29 MB/s | 2.0 MB 00:00 (74/206): curl-7.76.1-29.el9_4.x86_64.rpm 6.3 MB/s | 298 kB 00:00 (75/206): elfutils-0.190-2.el9.x86_64.rpm 12 MB/s | 559 kB 00:00 (76/206): elfutils-default-yama-scope-0.190-2.e 294 kB/s | 12 kB 00:00 (77/206): elfutils-libs-0.190-2.el9.x86_64.rpm 4.8 MB/s | 258 kB 00:00 (78/206): file-5.39-16.el9.x86_64.rpm 1.1 MB/s | 52 kB 00:00 (79/206): libacl-2.3.1-4.el9.x86_64.rpm 584 kB/s | 24 kB 00:00 (80/206): file-libs-5.39-16.el9.x86_64.rpm 11 MB/s | 593 kB 00:00 (81/206): libblkid-2.37.4-18.el9.x86_64.rpm 1.6 MB/s | 110 kB 00:00 (82/206): libfdisk-2.37.4-18.el9.x86_64.rpm 3.5 MB/s | 157 kB 00:00 (83/206): libgcc-11.4.1-3.el9.x86_64.rpm 1.4 MB/s | 95 kB 00:00 (84/206): libgomp-11.4.1-3.el9.x86_64.rpm 5.7 MB/s | 270 kB 00:00 (85/206): libmount-2.37.4-18.el9.x86_64.rpm 3.2 MB/s | 138 kB 00:00 (86/206): libsemanage-3.6-1.el9.x86_64.rpm 2.8 MB/s | 121 kB 00:00 (87/206): libsepol-3.6-1.el9.x86_64.rpm 7.7 MB/s | 331 kB 00:00 (88/206): libselinux-3.6-1.el9.x86_64.rpm 1.3 MB/s | 88 kB 00:00 (89/206): libsmartcols-2.37.4-18.el9.x86_64.rpm 1.5 MB/s | 66 kB 00:00 (90/206): libstdc++-11.4.1-3.el9.x86_64.rpm 16 MB/s | 747 kB 00:00 (91/206): libuuid-2.37.4-18.el9.x86_64.rpm 617 kB/s | 30 kB 00:00 (92/206): openldap-2.6.6-3.el9.x86_64.rpm 6.2 MB/s | 286 kB 00:00 (93/206): openssl-3.0.7-27.el9.x86_64.rpm 26 MB/s | 1.2 MB 00:00 (94/206): openssl-libs-3.0.7-27.el9.x86_64.rpm 38 MB/s | 1.9 MB 00:00 (95/206): openssl-fips-provider-3.0.7-2.el9.x86 7.1 MB/s | 576 kB 00:00 (96/206): p11-kit-0.25.3-2.el9.x86_64.rpm 9.9 MB/s | 537 kB 00:00 (97/206): pam-1.5.1-19.el9.x86_64.rpm 14 MB/s | 631 kB 00:00 (98/206): p11-kit-trust-0.25.3-2.el9.x86_64.rpm 2.6 MB/s | 145 kB 00:00 (99/206): pcre2-10.40-5.el9.x86_64.rpm 4.2 MB/s | 236 kB 00:00 (100/206): rpm-4.16.1.3-29.el9.x86_64.rpm 12 MB/s | 541 kB 00:00 (101/206): rpm-build-libs-4.16.1.3-29.el9.x86_6 2.0 MB/s | 90 kB 00:00 (102/206): rpm-libs-4.16.1.3-29.el9.x86_64.rpm 6.9 MB/s | 310 kB 00:00 (103/206): setup-2.13.7-10.el9.noarch.rpm 3.2 MB/s | 150 kB 00:00 (104/206): systemd-libs-252-32.el9_4.x86_64.rpm 12 MB/s | 679 kB 00:00 (105/206): tzdata-2024a-1.el9.noarch.rpm 17 MB/s | 842 kB 00:00 (106/206): sqlite-libs-3.34.1-7.el9_3.x86_64.rp 6.7 MB/s | 622 kB 00:00 (107/206): util-linux-2.37.4-18.el9.x86_64.rpm 42 MB/s | 2.3 MB 00:00 (108/206): util-linux-core-2.37.4-18.el9.x86_64 10 MB/s | 469 kB 00:00 (109/206): crypto-policies-20240202-1.git283706 1.5 MB/s | 88 kB 00:00 (110/206): elfutils-debuginfod-client-0.190-2.e 878 kB/s | 39 kB 00:00 (111/206): elfutils-libelf-0.190-2.el9.x86_64.r 4.4 MB/s | 196 kB 00:00 (112/206): libcom_err-1.46.5-5.el9.x86_64.rpm 611 kB/s | 28 kB 00:00 (113/206): libcurl-7.76.1-29.el9_4.x86_64.rpm 6.4 MB/s | 286 kB 00:00 (114/206): libssh-0.10.4-13.el9.x86_64.rpm 5.0 MB/s | 220 kB 00:00 (115/206): libssh-config-0.10.4-13.el9.noarch.r 207 kB/s | 11 kB 00:00 (116/206): pcre2-syntax-10.40-5.el9.noarch.rpm 3.1 MB/s | 145 kB 00:00 (117/206): redhat-release-9.4-0.4.el9.x86_64.rp 1.0 MB/s | 46 kB 00:00 (118/206): libxml2-2.9.13-6.el9_4.x86_64.rpm 16 MB/s | 752 kB 00:00 (119/206): glibc-2.34-100.el9_4.2.x86_64.rpm 43 MB/s | 2.0 MB 00:00 (120/206): glibc-common-2.34-100.el9_4.2.x86_64 6.6 MB/s | 313 kB 00:00 (121/206): glibc-minimal-langpack-2.34-100.el9_ 666 kB/s | 28 kB 00:00 (122/206): glibc-gconv-extra-2.34-100.el9_4.2.x 25 MB/s | 1.7 MB 00:00 (123/206): libnghttp2-1.43.0-5.el9_4.3.x86_64.r 1.4 MB/s | 75 kB 00:00 (124/206): ghc-srpm-macros-1.5.0-6.el9.noarch.r 200 kB/s | 9.0 kB 00:00 (125/206): perl-Data-Dumper-2.174-462.el9.x86_6 1.4 MB/s | 59 kB 00:00 (126/206): lua-srpm-macros-1-6.el9.noarch.rpm 174 kB/s | 10 kB 00:00 (127/206): perl-Digest-MD5-2.58-4.el9.x86_64.rp 959 kB/s | 39 kB 00:00 (128/206): perl-Encode-3.08-462.el9.x86_64.rpm 31 MB/s | 1.7 MB 00:00 (129/206): perl-IO-Socket-SSL-2.073-1.el9.noarc 4.8 MB/s | 223 kB 00:00 (130/206): perl-Mozilla-CA-20200520-6.el9.noarc 345 kB/s | 14 kB 00:00 (131/206): perl-Pod-Simple-3.42-4.el9.noarch.rp 4.8 MB/s | 229 kB 00:00 (132/206): perl-Term-Cap-1.17-460.el9.noarch.rp 417 kB/s | 24 kB 00:00 (133/206): rust-srpm-macros-17-4.el9.noarch.rpm 257 kB/s | 11 kB 00:00 (134/206): perl-Time-Local-1.300-7.el9.noarch.r 434 kB/s | 37 kB 00:00 (135/206): perl-Pod-Escapes-1.07-460.el9.noarch 467 kB/s | 22 kB 00:00 (136/206): perl-Storable-3.21-460.el9.x86_64.rp 2.3 MB/s | 98 kB 00:00 (137/206): dwz-0.14-3.el9.x86_64.rpm 2.7 MB/s | 130 kB 00:00 (138/206): perl-Exporter-5.74-461.el9.noarch.rp 774 kB/s | 34 kB 00:00 (139/206): perl-File-Temp-0.231.100-4.el9.noarc 1.4 MB/s | 63 kB 00:00 (140/206): perl-Getopt-Long-2.52-4.el9.noarch.r 1.5 MB/s | 64 kB 00:00 (141/206): perl-MIME-Base64-3.16-4.el9.x86_64.r 667 kB/s | 34 kB 00:00 (142/206): perl-Text-Tabs+Wrap-2013.0523-460.el 604 kB/s | 25 kB 00:00 (143/206): perl-podlators-4.14-460.el9.noarch.r 694 kB/s | 118 kB 00:00 (144/206): perl-parent-0.238-460.el9.noarch.rpm 352 kB/s | 16 kB 00:00 (145/206): perl-srpm-macros-1-41.el9.noarch.rpm 219 kB/s | 9.4 kB 00:00 (146/206): efi-srpm-macros-6-2.el9_0.noarch.rpm 427 kB/s | 24 kB 00:00 (147/206): perl-Digest-1.19-4.el9.noarch.rpm 663 kB/s | 29 kB 00:00 (148/206): openblas-srpm-macros-2-11.el9.noarch 175 kB/s | 8.6 kB 00:00 (149/206): perl-File-Path-2.18-4.el9.noarch.rpm 926 kB/s | 38 kB 00:00 (150/206): perl-IO-Socket-IP-0.41-5.el9.noarch. 1.1 MB/s | 45 kB 00:00 (151/206): perl-Pod-Usage-2.01-4.el9.noarch.rpm 1.0 MB/s | 43 kB 00:00 (152/206): perl-Socket-2.031-4.el9.x86_64.rpm 1.4 MB/s | 58 kB 00:00 (153/206): perl-Term-ANSIColor-5.01-461.el9.noa 1.2 MB/s | 51 kB 00:00 (154/206): perl-Scalar-List-Utils-1.56-461.el9. 722 kB/s | 77 kB 00:00 (155/206): perl-Text-ParseWords-3.30-460.el9.no 410 kB/s | 18 kB 00:00 (156/206): perl-URI-5.09-3.el9.noarch.rpm 2.8 MB/s | 125 kB 00:00 (157/206): fonts-srpm-macros-2.0.5-7.el9.1.noar 703 kB/s | 29 kB 00:00 (158/206): ocaml-srpm-macros-6-6.el9.noarch.rpm 216 kB/s | 9.1 kB 00:00 (159/206): perl-Pod-Perldoc-3.28.01-461.el9.noa 2.0 MB/s | 92 kB 00:00 (160/206): perl-constant-1.33-461.el9.noarch.rp 275 kB/s | 25 kB 00:00 (161/206): patch-2.7.6-16.el9.x86_64.rpm 2.5 MB/s | 130 kB 00:00 (162/206): perl-Carp-1.50-460.el9.noarch.rpm 774 kB/s | 31 kB 00:00 (163/206): perl-libnet-3.13-4.el9.noarch.rpm 3.0 MB/s | 134 kB 00:00 (164/206): perl-PathTools-3.78-461.el9.x86_64.r 2.0 MB/s | 92 kB 00:00 (165/206): kernel-srpm-macros-1.0-13.el9.noarch 411 kB/s | 17 kB 00:00 (166/206): perl-Net-SSLeay-1.92-2.el9.x86_64.rp 6.5 MB/s | 392 kB 00:00 (167/206): qt5-srpm-macros-5.15.9-1.el9.noarch. 121 kB/s | 9.1 kB 00:00 (168/206): perl-AutoLoader-5.74-481.el9.noarch. 499 kB/s | 21 kB 00:00 (169/206): perl-SelectSaver-1.02-481.el9.noarch 206 kB/s | 12 kB 00:00 (170/206): perl-if-0.60.800-481.el9.noarch.rpm 314 kB/s | 14 kB 00:00 (171/206): perl-overloading-0.02-481.el9.noarch 313 kB/s | 13 kB 00:00 (172/206): python-srpm-macros-3.9-53.el9.noarch 386 kB/s | 19 kB 00:00 (173/206): redhat-rpm-config-207-1.el9.noarch.r 1.5 MB/s | 76 kB 00:00 (174/206): gdb-minimal-10.2-13.el9.x86_64.rpm 66 MB/s | 3.5 MB 00:00 (175/206): go-srpm-macros-3.2.0-3.el9.noarch.rp 701 kB/s | 28 kB 00:00 (176/206): perl-Class-Struct-0.66-481.el9.noarc 515 kB/s | 22 kB 00:00 (177/206): perl-B-1.80-481.el9.x86_64.rpm 3.2 MB/s | 184 kB 00:00 (178/206): perl-File-Basename-2.85-481.el9.noar 402 kB/s | 17 kB 00:00 (179/206): perl-File-stat-1.09-481.el9.noarch.r 252 kB/s | 17 kB 00:00 (180/206): perl-FileHandle-2.03-481.el9.noarch. 275 kB/s | 16 kB 00:00 (181/206): perl-Errno-1.30-481.el9.x86_64.rpm 121 kB/s | 15 kB 00:00 (182/206): perl-Getopt-Std-1.12-481.el9.noarch. 359 kB/s | 16 kB 00:00 (183/206): perl-HTTP-Tiny-0.076-462.el9.noarch. 1.3 MB/s | 57 kB 00:00 (184/206): perl-POSIX-1.94-481.el9.x86_64.rpm 2.2 MB/s | 98 kB 00:00 (185/206): perl-IPC-Open3-1.21-481.el9.noarch.r 283 kB/s | 24 kB 00:00 (186/206): perl-IO-1.43-481.el9.x86_64.rpm 881 kB/s | 92 kB 00:00 (187/206): perl-Symbol-1.08-481.el9.noarch.rpm 233 kB/s | 14 kB 00:00 (188/206): perl-interpreter-5.32.1-481.el9.x86_ 1.6 MB/s | 73 kB 00:00 (189/206): perl-base-2.27-481.el9.noarch.rpm 268 kB/s | 16 kB 00:00 (190/206): perl-mro-1.23-481.el9.x86_64.rpm 715 kB/s | 29 kB 00:00 (191/206): perl-libs-5.32.1-481.el9.x86_64.rpm 43 MB/s | 2.2 MB 00:00 (192/206): perl-overload-1.31-481.el9.noarch.rp 861 kB/s | 46 kB 00:00 (193/206): perl-vars-1.05-481.el9.noarch.rpm 308 kB/s | 13 kB 00:00 (194/206): pyproject-srpm-macros-1.12.0-1.el9.n 324 kB/s | 14 kB 00:00 (195/206): debugedit-5.0-5.el9.x86_64.rpm 1.2 MB/s | 81 kB 00:00 (196/206): perl-subs-1.03-481.el9.noarch.rpm 264 kB/s | 12 kB 00:00 (197/206): perl-Fcntl-1.13-481.el9.x86_64.rpm 351 kB/s | 22 kB 00:00 (198/206): ansible-srpm-macros-1-12.el9.noarch. 1.9 MB/s | 21 kB 00:00 (199/206): epel-rpm-macros-9-14.el9.noarch.rpm 5.0 MB/s | 15 kB 00:00 (200/206): forge-srpm-macros-0.3.1-1.el9.noarch 10 MB/s | 19 kB 00:00 (201/206): fpc-srpm-macros-1.3-7.el9.noarch.rpm 3.0 MB/s | 7.5 kB 00:00 (202/206): go-srpm-macros-epel-3.3.0.5-1.el9.no 11 MB/s | 27 kB 00:00 (203/206): qt6-srpm-macros-6.6.2-1.el9.noarch.r 5.7 MB/s | 8.7 kB 00:00 (204/206): rpmautospec-rpm-macros-0.6.3-1.el9.n 6.2 MB/s | 9.9 kB 00:00 (205/206): rust-srpm-macros-epel-26.3-1.el9.noa 10 MB/s | 10 kB 00:00 (206/206): rpm-build-4.16.1.3-29.el9.x86_64.rpm 1.1 MB/s | 72 kB 00:00 -------------------------------------------------------------------------------- Total 18 MB/s | 68 MB 00:03 Red Hat Enterprise Linux - BaseOS 3.5 MB/s | 3.6 kB 00:00 Importing GPG key 0x5A6340B3: Userid : "Red Hat, Inc. (auxiliary key 3) " Fingerprint: 7E46 2425 8C40 6535 D56D 6F13 5054 E4A4 5A63 40B3 From : /usr/share/distribution-gpg-keys/redhat/RPM-GPG-KEY-redhat9-release Key imported successfully Importing GPG key 0xFD431D51: Userid : "Red Hat, Inc. (release key 2) " Fingerprint: 567E 347A D004 4ADE 55BA 8A5F 199E 2F91 FD43 1D51 From : /usr/share/distribution-gpg-keys/redhat/RPM-GPG-KEY-redhat9-release Key imported successfully Extra Packages for Enterprise Linux 9 - x86_64 1.6 MB/s | 1.6 kB 00:00 Importing GPG key 0x3228467C: Userid : "Fedora (epel9) " Fingerprint: FF8A D134 4597 106E CE81 3B91 8A38 72BF 3228 467C From : /usr/share/distribution-gpg-keys/epel/RPM-GPG-KEY-EPEL-9 Key imported successfully Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Running scriptlet: filesystem-3.16-2.el9.x86_64 1/1 Preparing : 1/1 Installing : libgcc-11.4.1-3.el9.x86_64 1/206 Running scriptlet: libgcc-11.4.1-3.el9.x86_64 1/206 Installing : crypto-policies-20240202-1.git283706d.el9.noarch 2/206 Running scriptlet: crypto-policies-20240202-1.git283706d.el9.noarch 2/206 Installing : rust-srpm-macros-17-4.el9.noarch 3/206 Installing : redhat-release-9.4-0.4.el9.x86_64 4/206 Installing : setup-2.13.7-10.el9.noarch 5/206 warning: /etc/hosts created as /etc/hosts.rpmnew Running scriptlet: setup-2.13.7-10.el9.noarch 5/206 Installing : filesystem-3.16-2.el9.x86_64 6/206 Installing : basesystem-11-13.el9.noarch 7/206 Installing : rust-srpm-macros-epel-26.3-1.el9.noarch 8/206 Installing : qt6-srpm-macros-6.6.2-1.el9.noarch 9/206 Installing : fpc-srpm-macros-1.3-7.el9.noarch 10/206 Installing : ansible-srpm-macros-1-12.el9.noarch 11/206 Installing : qt5-srpm-macros-5.15.9-1.el9.noarch 12/206 Installing : ocaml-srpm-macros-6-6.el9.noarch 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Installing : perl-Getopt-Std-1.12-481.el9.noarch 152/206 Installing : perl-Storable-1:3.21-460.el9.x86_64 153/206 Installing : perl-overload-1.31-481.el9.noarch 154/206 Installing : perl-vars-1.05-481.el9.noarch 155/206 Installing : perl-Getopt-Long-1:2.52-4.el9.noarch 156/206 Installing : perl-Exporter-5.74-461.el9.noarch 157/206 Installing : perl-Carp-1.50-460.el9.noarch 158/206 Installing : perl-PathTools-3.78-461.el9.x86_64 159/206 Installing : perl-Encode-4:3.08-462.el9.x86_64 160/206 Installing : perl-libs-4:5.32.1-481.el9.x86_64 161/206 Installing : perl-interpreter-4:5.32.1-481.el9.x86_64 162/206 Installing : kernel-srpm-macros-1.0-13.el9.noarch 163/206 Installing : openssl-1:3.0.7-27.el9.x86_64 164/206 Installing : libpwquality-1.4.4-8.el9.x86_64 165/206 Installing : pam-1.5.1-19.el9.x86_64 166/206 Installing : libevent-2.1.12-6.el9.x86_64 167/206 Installing : libarchive-3.5.3-4.el9.x86_64 168/206 Installing : tar-2:1.34-6.el9_1.x86_64 169/206 Installing : 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: go-srpm-macros-epel-3.3.0.5-1.el9.noarch 203/206 Installing : epel-rpm-macros-9-14.el9.noarch 204/206 Installing : util-linux-2.37.4-18.el9.x86_64 205/206 Installing : which-2.21-29.el9.x86_64 206/206 Running scriptlet: filesystem-3.16-2.el9.x86_64 206/206 Running scriptlet: ca-certificates-2023.2.60_v7.0.306-90.1.el9_2.no 206/206 Running scriptlet: rpm-4.16.1.3-29.el9.x86_64 206/206 Running scriptlet: which-2.21-29.el9.x86_64 206/206 Verifying : basesystem-11-13.el9.noarch 1/206 Verifying : bzip2-1.0.8-8.el9.x86_64 2/206 Verifying : bzip2-libs-1.0.8-8.el9.x86_64 3/206 Verifying : cpio-2.13-16.el9.x86_64 4/206 Verifying : cracklib-2.9.6-27.el9.x86_64 5/206 Verifying : ed-1.14.2-12.el9.x86_64 6/206 Verifying : filesystem-3.16-2.el9.x86_64 7/206 Verifying : grep-3.6-5.el9.x86_64 8/206 Verifying : groff-base-1.22.4-10.el9.x86_64 9/206 Verifying : info-6.7-15.el9.x86_64 10/206 Verifying : libattr-2.5.1-3.el9.x86_64 11/206 Verifying : libbrotli-1.0.9-6.el9.x86_64 12/206 Verifying : libcap-ng-0.8.2-7.el9.x86_64 13/206 Verifying : libdb-5.3.28-53.el9.x86_64 14/206 Verifying : libevent-2.1.12-6.el9.x86_64 15/206 Verifying : libgpg-error-1.42-5.el9.x86_64 16/206 Verifying : libidn2-2.3.0-7.el9.x86_64 17/206 Verifying : libpsl-0.21.1-5.el9.x86_64 18/206 Verifying : libpwquality-1.4.4-8.el9.x86_64 19/206 Verifying : libsigsegv-2.13-4.el9.x86_64 20/206 Verifying : libunistring-0.9.10-15.el9.x86_64 21/206 Verifying : libutempter-1.2.1-6.el9.x86_64 22/206 Verifying : libverto-0.3.2-3.el9.x86_64 23/206 Verifying : libxcrypt-4.4.18-3.el9.x86_64 24/206 Verifying : libzstd-1.5.1-2.el9.x86_64 25/206 Verifying : lz4-libs-1.9.3-5.el9.x86_64 26/206 Verifying : mpfr-4.1.0-7.el9.x86_64 27/206 Verifying : pcre-8.44-3.el9.3.x86_64 28/206 Verifying : popt-1.18-8.el9.x86_64 29/206 Verifying : publicsuffix-list-dafsa-20210518-3.el9.noarch 30/206 Verifying : readline-8.1-4.el9.x86_64 31/206 Verifying : sed-4.8-9.el9.x86_64 32/206 Verifying : unzip-6.0-56.el9.x86_64 33/206 Verifying : cracklib-dicts-2.9.6-27.el9.x86_64 34/206 Verifying : diffutils-3.7-12.el9.x86_64 35/206 Verifying : gawk-5.1.0-6.el9.x86_64 36/206 Verifying : gdbm-libs-1:1.19-4.el9.x86_64 37/206 Verifying : xz-5.2.5-8.el9_0.x86_64 38/206 Verifying : xz-libs-5.2.5-8.el9_0.x86_64 39/206 Verifying : zstd-1.5.1-2.el9.x86_64 40/206 Verifying : cyrus-sasl-lib-2.1.27-21.el9.x86_64 41/206 Verifying : gzip-1.12-1.el9.x86_64 42/206 Verifying : libtasn1-4.16.0-8.el9_1.x86_64 43/206 Verifying : tar-2:1.34-6.el9_1.x86_64 44/206 Verifying : ca-certificates-2023.2.60_v7.0.306-90.1.el9_2.no 45/206 Verifying : keyutils-libs-1.6.3-1.el9.x86_64 46/206 Verifying : libarchive-3.5.3-4.el9.x86_64 47/206 Verifying : libcap-2.48-9.el9_2.x86_64 48/206 Verifying : libeconf-0.4.1-3.el9_2.x86_64 49/206 Verifying : libgcrypt-1.10.0-10.el9_2.x86_64 50/206 Verifying : libpkgconf-1.7.3-10.el9.x86_64 51/206 Verifying : pkgconf-1.7.3-10.el9.x86_64 52/206 Verifying : pkgconf-m4-1.7.3-10.el9.noarch 53/206 Verifying : pkgconf-pkg-config-1.7.3-10.el9.x86_64 54/206 Verifying : zip-3.0-35.el9.x86_64 55/206 Verifying : alternatives-1.24-1.el9.x86_64 56/206 Verifying : findutils-1:4.8.0-6.el9.x86_64 57/206 Verifying : gmp-1:6.2.0-13.el9.x86_64 58/206 Verifying : krb5-libs-1.21.1-1.el9.x86_64 59/206 Verifying : libffi-3.4.2-8.el9.x86_64 60/206 Verifying : lua-libs-5.4.4-4.el9.x86_64 61/206 Verifying : ncurses-6.2-10.20210508.el9.x86_64 62/206 Verifying : ncurses-base-6.2-10.20210508.el9.noarch 63/206 Verifying : ncurses-libs-6.2-10.20210508.el9.x86_64 64/206 Verifying : shadow-utils-2:4.9-8.el9.x86_64 65/206 Verifying : which-2.21-29.el9.x86_64 66/206 Verifying : zlib-1.2.11-40.el9.x86_64 67/206 Verifying : audit-libs-3.1.2-2.el9.x86_64 68/206 Verifying : bash-5.1.8-9.el9.x86_64 69/206 Verifying : binutils-2.35.2-43.el9.x86_64 70/206 Verifying : binutils-gold-2.35.2-43.el9.x86_64 71/206 Verifying : coreutils-8.32-35.el9.x86_64 72/206 Verifying : coreutils-common-8.32-35.el9.x86_64 73/206 Verifying : curl-7.76.1-29.el9_4.x86_64 74/206 Verifying : elfutils-0.190-2.el9.x86_64 75/206 Verifying : elfutils-default-yama-scope-0.190-2.el9.noarch 76/206 Verifying : elfutils-libs-0.190-2.el9.x86_64 77/206 Verifying : file-5.39-16.el9.x86_64 78/206 Verifying : file-libs-5.39-16.el9.x86_64 79/206 Verifying : libacl-2.3.1-4.el9.x86_64 80/206 Verifying : libblkid-2.37.4-18.el9.x86_64 81/206 Verifying : libfdisk-2.37.4-18.el9.x86_64 82/206 Verifying : libgcc-11.4.1-3.el9.x86_64 83/206 Verifying : libgomp-11.4.1-3.el9.x86_64 84/206 Verifying : libmount-2.37.4-18.el9.x86_64 85/206 Verifying : libselinux-3.6-1.el9.x86_64 86/206 Verifying : libsemanage-3.6-1.el9.x86_64 87/206 Verifying : libsepol-3.6-1.el9.x86_64 88/206 Verifying : libsmartcols-2.37.4-18.el9.x86_64 89/206 Verifying : libstdc++-11.4.1-3.el9.x86_64 90/206 Verifying : libuuid-2.37.4-18.el9.x86_64 91/206 Verifying : openldap-2.6.6-3.el9.x86_64 92/206 Verifying : openssl-1:3.0.7-27.el9.x86_64 93/206 Verifying : openssl-fips-provider-3.0.7-2.el9.x86_64 94/206 Verifying : openssl-libs-1:3.0.7-27.el9.x86_64 95/206 Verifying : p11-kit-0.25.3-2.el9.x86_64 96/206 Verifying : p11-kit-trust-0.25.3-2.el9.x86_64 97/206 Verifying : pam-1.5.1-19.el9.x86_64 98/206 Verifying : pcre2-10.40-5.el9.x86_64 99/206 Verifying : rpm-4.16.1.3-29.el9.x86_64 100/206 Verifying : rpm-build-libs-4.16.1.3-29.el9.x86_64 101/206 Verifying : rpm-libs-4.16.1.3-29.el9.x86_64 102/206 Verifying : setup-2.13.7-10.el9.noarch 103/206 Verifying : sqlite-libs-3.34.1-7.el9_3.x86_64 104/206 Verifying : systemd-libs-252-32.el9_4.x86_64 105/206 Verifying : tzdata-2024a-1.el9.noarch 106/206 Verifying : util-linux-2.37.4-18.el9.x86_64 107/206 Verifying : util-linux-core-2.37.4-18.el9.x86_64 108/206 Verifying : crypto-policies-20240202-1.git283706d.el9.noarch 109/206 Verifying : elfutils-debuginfod-client-0.190-2.el9.x86_64 110/206 Verifying : elfutils-libelf-0.190-2.el9.x86_64 111/206 Verifying : libcom_err-1.46.5-5.el9.x86_64 112/206 Verifying : libcurl-7.76.1-29.el9_4.x86_64 113/206 Verifying : libssh-0.10.4-13.el9.x86_64 114/206 Verifying : libssh-config-0.10.4-13.el9.noarch 115/206 Verifying : pcre2-syntax-10.40-5.el9.noarch 116/206 Verifying : redhat-release-9.4-0.4.el9.x86_64 117/206 Verifying : libxml2-2.9.13-6.el9_4.x86_64 118/206 Verifying : glibc-2.34-100.el9_4.2.x86_64 119/206 Verifying : glibc-common-2.34-100.el9_4.2.x86_64 120/206 Verifying : glibc-gconv-extra-2.34-100.el9_4.2.x86_64 121/206 Verifying : glibc-minimal-langpack-2.34-100.el9_4.2.x86_64 122/206 Verifying : libnghttp2-1.43.0-5.el9_4.3.x86_64 123/206 Verifying : ghc-srpm-macros-1.5.0-6.el9.noarch 124/206 Verifying : lua-srpm-macros-1-6.el9.noarch 125/206 Verifying : perl-Data-Dumper-2.174-462.el9.x86_64 126/206 Verifying : perl-Digest-MD5-2.58-4.el9.x86_64 127/206 Verifying : perl-Encode-4:3.08-462.el9.x86_64 128/206 Verifying : perl-IO-Socket-SSL-2.073-1.el9.noarch 129/206 Verifying : perl-Mozilla-CA-20200520-6.el9.noarch 130/206 Verifying : perl-Pod-Simple-1:3.42-4.el9.noarch 131/206 Verifying : perl-Term-Cap-1.17-460.el9.noarch 132/206 Verifying : perl-Time-Local-2:1.300-7.el9.noarch 133/206 Verifying : rust-srpm-macros-17-4.el9.noarch 134/206 Verifying : perl-Pod-Escapes-1:1.07-460.el9.noarch 135/206 Verifying : perl-Storable-1:3.21-460.el9.x86_64 136/206 Verifying : perl-podlators-1:4.14-460.el9.noarch 137/206 Verifying : dwz-0.14-3.el9.x86_64 138/206 Verifying : perl-Exporter-5.74-461.el9.noarch 139/206 Verifying : perl-File-Temp-1:0.231.100-4.el9.noarch 140/206 Verifying : perl-Getopt-Long-1:2.52-4.el9.noarch 141/206 Verifying : perl-MIME-Base64-3.16-4.el9.x86_64 142/206 Verifying : perl-Text-Tabs+Wrap-2013.0523-460.el9.noarch 143/206 Verifying : perl-parent-1:0.238-460.el9.noarch 144/206 Verifying : perl-srpm-macros-1-41.el9.noarch 145/206 Verifying : efi-srpm-macros-6-2.el9_0.noarch 146/206 Verifying : openblas-srpm-macros-2-11.el9.noarch 147/206 Verifying : perl-Digest-1.19-4.el9.noarch 148/206 Verifying : perl-File-Path-2.18-4.el9.noarch 149/206 Verifying : perl-IO-Socket-IP-0.41-5.el9.noarch 150/206 Verifying : perl-Pod-Usage-4:2.01-4.el9.noarch 151/206 Verifying : perl-Scalar-List-Utils-4:1.56-461.el9.x86_64 152/206 Verifying : perl-Socket-4:2.031-4.el9.x86_64 153/206 Verifying : perl-Term-ANSIColor-5.01-461.el9.noarch 154/206 Verifying : perl-Text-ParseWords-3.30-460.el9.noarch 155/206 Verifying : perl-URI-5.09-3.el9.noarch 156/206 Verifying : perl-constant-1.33-461.el9.noarch 157/206 Verifying : fonts-srpm-macros-1:2.0.5-7.el9.1.noarch 158/206 Verifying : ocaml-srpm-macros-6-6.el9.noarch 159/206 Verifying : patch-2.7.6-16.el9.x86_64 160/206 Verifying : perl-Pod-Perldoc-3.28.01-461.el9.noarch 161/206 Verifying : perl-libnet-3.13-4.el9.noarch 162/206 Verifying : perl-Carp-1.50-460.el9.noarch 163/206 Verifying : perl-PathTools-3.78-461.el9.x86_64 164/206 Verifying : perl-Net-SSLeay-1.92-2.el9.x86_64 165/206 Verifying : kernel-srpm-macros-1.0-13.el9.noarch 166/206 Verifying : qt5-srpm-macros-5.15.9-1.el9.noarch 167/206 Verifying : perl-AutoLoader-5.74-481.el9.noarch 168/206 Verifying : perl-SelectSaver-1.02-481.el9.noarch 169/206 Verifying : perl-if-0.60.800-481.el9.noarch 170/206 Verifying : perl-overloading-0.02-481.el9.noarch 171/206 Verifying : python-srpm-macros-3.9-53.el9.noarch 172/206 Verifying : redhat-rpm-config-207-1.el9.noarch 173/206 Verifying : gdb-minimal-10.2-13.el9.x86_64 174/206 Verifying : go-srpm-macros-3.2.0-3.el9.noarch 175/206 Verifying : perl-B-1.80-481.el9.x86_64 176/206 Verifying : perl-Class-Struct-0.66-481.el9.noarch 177/206 Verifying : perl-Errno-1.30-481.el9.x86_64 178/206 Verifying : perl-File-Basename-2.85-481.el9.noarch 179/206 Verifying : perl-File-stat-1.09-481.el9.noarch 180/206 Verifying : perl-FileHandle-2.03-481.el9.noarch 181/206 Verifying : perl-Getopt-Std-1.12-481.el9.noarch 182/206 Verifying : perl-HTTP-Tiny-0.076-462.el9.noarch 183/206 Verifying : perl-IO-1.43-481.el9.x86_64 184/206 Verifying : perl-IPC-Open3-1.21-481.el9.noarch 185/206 Verifying : perl-POSIX-1.94-481.el9.x86_64 186/206 Verifying : perl-Symbol-1.08-481.el9.noarch 187/206 Verifying : perl-base-2.27-481.el9.noarch 188/206 Verifying : perl-interpreter-4:5.32.1-481.el9.x86_64 189/206 Verifying : perl-libs-4:5.32.1-481.el9.x86_64 190/206 Verifying : perl-mro-1.23-481.el9.x86_64 191/206 Verifying : perl-overload-1.31-481.el9.noarch 192/206 Verifying : perl-vars-1.05-481.el9.noarch 193/206 Verifying : pyproject-srpm-macros-1.12.0-1.el9.noarch 194/206 Verifying : debugedit-5.0-5.el9.x86_64 195/206 Verifying : perl-Fcntl-1.13-481.el9.x86_64 196/206 Verifying : perl-subs-1.03-481.el9.noarch 197/206 Verifying : rpm-build-4.16.1.3-29.el9.x86_64 198/206 Verifying : ansible-srpm-macros-1-12.el9.noarch 199/206 Verifying : epel-rpm-macros-9-14.el9.noarch 200/206 Verifying : forge-srpm-macros-0.3.1-1.el9.noarch 201/206 Verifying : fpc-srpm-macros-1.3-7.el9.noarch 202/206 Verifying : go-srpm-macros-epel-3.3.0.5-1.el9.noarch 203/206 Verifying : qt6-srpm-macros-6.6.2-1.el9.noarch 204/206 Verifying : rpmautospec-rpm-macros-0.6.3-1.el9.noarch 205/206 Verifying : rust-srpm-macros-epel-26.3-1.el9.noarch 206/206 Installed products updated. Installed: alternatives-1.24-1.el9.x86_64 ansible-srpm-macros-1-12.el9.noarch audit-libs-3.1.2-2.el9.x86_64 basesystem-11-13.el9.noarch bash-5.1.8-9.el9.x86_64 binutils-2.35.2-43.el9.x86_64 binutils-gold-2.35.2-43.el9.x86_64 bzip2-1.0.8-8.el9.x86_64 bzip2-libs-1.0.8-8.el9.x86_64 ca-certificates-2023.2.60_v7.0.306-90.1.el9_2.noarch coreutils-8.32-35.el9.x86_64 coreutils-common-8.32-35.el9.x86_64 cpio-2.13-16.el9.x86_64 cracklib-2.9.6-27.el9.x86_64 cracklib-dicts-2.9.6-27.el9.x86_64 crypto-policies-20240202-1.git283706d.el9.noarch curl-7.76.1-29.el9_4.x86_64 cyrus-sasl-lib-2.1.27-21.el9.x86_64 debugedit-5.0-5.el9.x86_64 diffutils-3.7-12.el9.x86_64 dwz-0.14-3.el9.x86_64 ed-1.14.2-12.el9.x86_64 efi-srpm-macros-6-2.el9_0.noarch elfutils-0.190-2.el9.x86_64 elfutils-debuginfod-client-0.190-2.el9.x86_64 elfutils-default-yama-scope-0.190-2.el9.noarch elfutils-libelf-0.190-2.el9.x86_64 elfutils-libs-0.190-2.el9.x86_64 epel-rpm-macros-9-14.el9.noarch file-5.39-16.el9.x86_64 file-libs-5.39-16.el9.x86_64 filesystem-3.16-2.el9.x86_64 findutils-1:4.8.0-6.el9.x86_64 fonts-srpm-macros-1:2.0.5-7.el9.1.noarch forge-srpm-macros-0.3.1-1.el9.noarch fpc-srpm-macros-1.3-7.el9.noarch gawk-5.1.0-6.el9.x86_64 gdb-minimal-10.2-13.el9.x86_64 gdbm-libs-1:1.19-4.el9.x86_64 ghc-srpm-macros-1.5.0-6.el9.noarch glibc-2.34-100.el9_4.2.x86_64 glibc-common-2.34-100.el9_4.2.x86_64 glibc-gconv-extra-2.34-100.el9_4.2.x86_64 glibc-minimal-langpack-2.34-100.el9_4.2.x86_64 gmp-1:6.2.0-13.el9.x86_64 go-srpm-macros-3.2.0-3.el9.noarch go-srpm-macros-epel-3.3.0.5-1.el9.noarch grep-3.6-5.el9.x86_64 groff-base-1.22.4-10.el9.x86_64 gzip-1.12-1.el9.x86_64 info-6.7-15.el9.x86_64 kernel-srpm-macros-1.0-13.el9.noarch keyutils-libs-1.6.3-1.el9.x86_64 krb5-libs-1.21.1-1.el9.x86_64 libacl-2.3.1-4.el9.x86_64 libarchive-3.5.3-4.el9.x86_64 libattr-2.5.1-3.el9.x86_64 libblkid-2.37.4-18.el9.x86_64 libbrotli-1.0.9-6.el9.x86_64 libcap-2.48-9.el9_2.x86_64 libcap-ng-0.8.2-7.el9.x86_64 libcom_err-1.46.5-5.el9.x86_64 libcurl-7.76.1-29.el9_4.x86_64 libdb-5.3.28-53.el9.x86_64 libeconf-0.4.1-3.el9_2.x86_64 libevent-2.1.12-6.el9.x86_64 libfdisk-2.37.4-18.el9.x86_64 libffi-3.4.2-8.el9.x86_64 libgcc-11.4.1-3.el9.x86_64 libgcrypt-1.10.0-10.el9_2.x86_64 libgomp-11.4.1-3.el9.x86_64 libgpg-error-1.42-5.el9.x86_64 libidn2-2.3.0-7.el9.x86_64 libmount-2.37.4-18.el9.x86_64 libnghttp2-1.43.0-5.el9_4.3.x86_64 libpkgconf-1.7.3-10.el9.x86_64 libpsl-0.21.1-5.el9.x86_64 libpwquality-1.4.4-8.el9.x86_64 libselinux-3.6-1.el9.x86_64 libsemanage-3.6-1.el9.x86_64 libsepol-3.6-1.el9.x86_64 libsigsegv-2.13-4.el9.x86_64 libsmartcols-2.37.4-18.el9.x86_64 libssh-0.10.4-13.el9.x86_64 libssh-config-0.10.4-13.el9.noarch libstdc++-11.4.1-3.el9.x86_64 libtasn1-4.16.0-8.el9_1.x86_64 libunistring-0.9.10-15.el9.x86_64 libutempter-1.2.1-6.el9.x86_64 libuuid-2.37.4-18.el9.x86_64 libverto-0.3.2-3.el9.x86_64 libxcrypt-4.4.18-3.el9.x86_64 libxml2-2.9.13-6.el9_4.x86_64 libzstd-1.5.1-2.el9.x86_64 lua-libs-5.4.4-4.el9.x86_64 lua-srpm-macros-1-6.el9.noarch lz4-libs-1.9.3-5.el9.x86_64 mpfr-4.1.0-7.el9.x86_64 ncurses-6.2-10.20210508.el9.x86_64 ncurses-base-6.2-10.20210508.el9.noarch ncurses-libs-6.2-10.20210508.el9.x86_64 ocaml-srpm-macros-6-6.el9.noarch openblas-srpm-macros-2-11.el9.noarch openldap-2.6.6-3.el9.x86_64 openssl-1:3.0.7-27.el9.x86_64 openssl-fips-provider-3.0.7-2.el9.x86_64 openssl-libs-1:3.0.7-27.el9.x86_64 p11-kit-0.25.3-2.el9.x86_64 p11-kit-trust-0.25.3-2.el9.x86_64 pam-1.5.1-19.el9.x86_64 patch-2.7.6-16.el9.x86_64 pcre-8.44-3.el9.3.x86_64 pcre2-10.40-5.el9.x86_64 pcre2-syntax-10.40-5.el9.noarch perl-AutoLoader-5.74-481.el9.noarch perl-B-1.80-481.el9.x86_64 perl-Carp-1.50-460.el9.noarch perl-Class-Struct-0.66-481.el9.noarch perl-Data-Dumper-2.174-462.el9.x86_64 perl-Digest-1.19-4.el9.noarch perl-Digest-MD5-2.58-4.el9.x86_64 perl-Encode-4:3.08-462.el9.x86_64 perl-Errno-1.30-481.el9.x86_64 perl-Exporter-5.74-461.el9.noarch perl-Fcntl-1.13-481.el9.x86_64 perl-File-Basename-2.85-481.el9.noarch perl-File-Path-2.18-4.el9.noarch perl-File-Temp-1:0.231.100-4.el9.noarch perl-File-stat-1.09-481.el9.noarch perl-FileHandle-2.03-481.el9.noarch perl-Getopt-Long-1:2.52-4.el9.noarch perl-Getopt-Std-1.12-481.el9.noarch perl-HTTP-Tiny-0.076-462.el9.noarch perl-IO-1.43-481.el9.x86_64 perl-IO-Socket-IP-0.41-5.el9.noarch perl-IO-Socket-SSL-2.073-1.el9.noarch perl-IPC-Open3-1.21-481.el9.noarch perl-MIME-Base64-3.16-4.el9.x86_64 perl-Mozilla-CA-20200520-6.el9.noarch perl-Net-SSLeay-1.92-2.el9.x86_64 perl-POSIX-1.94-481.el9.x86_64 perl-PathTools-3.78-461.el9.x86_64 perl-Pod-Escapes-1:1.07-460.el9.noarch perl-Pod-Perldoc-3.28.01-461.el9.noarch perl-Pod-Simple-1:3.42-4.el9.noarch perl-Pod-Usage-4:2.01-4.el9.noarch perl-Scalar-List-Utils-4:1.56-461.el9.x86_64 perl-SelectSaver-1.02-481.el9.noarch perl-Socket-4:2.031-4.el9.x86_64 perl-Storable-1:3.21-460.el9.x86_64 perl-Symbol-1.08-481.el9.noarch perl-Term-ANSIColor-5.01-461.el9.noarch perl-Term-Cap-1.17-460.el9.noarch perl-Text-ParseWords-3.30-460.el9.noarch perl-Text-Tabs+Wrap-2013.0523-460.el9.noarch perl-Time-Local-2:1.300-7.el9.noarch perl-URI-5.09-3.el9.noarch perl-base-2.27-481.el9.noarch perl-constant-1.33-461.el9.noarch perl-if-0.60.800-481.el9.noarch perl-interpreter-4:5.32.1-481.el9.x86_64 perl-libnet-3.13-4.el9.noarch perl-libs-4:5.32.1-481.el9.x86_64 perl-mro-1.23-481.el9.x86_64 perl-overload-1.31-481.el9.noarch perl-overloading-0.02-481.el9.noarch perl-parent-1:0.238-460.el9.noarch perl-podlators-1:4.14-460.el9.noarch perl-srpm-macros-1-41.el9.noarch perl-subs-1.03-481.el9.noarch perl-vars-1.05-481.el9.noarch pkgconf-1.7.3-10.el9.x86_64 pkgconf-m4-1.7.3-10.el9.noarch pkgconf-pkg-config-1.7.3-10.el9.x86_64 popt-1.18-8.el9.x86_64 publicsuffix-list-dafsa-20210518-3.el9.noarch pyproject-srpm-macros-1.12.0-1.el9.noarch python-srpm-macros-3.9-53.el9.noarch qt5-srpm-macros-5.15.9-1.el9.noarch qt6-srpm-macros-6.6.2-1.el9.noarch readline-8.1-4.el9.x86_64 redhat-release-9.4-0.4.el9.x86_64 redhat-rpm-config-207-1.el9.noarch rpm-4.16.1.3-29.el9.x86_64 rpm-build-4.16.1.3-29.el9.x86_64 rpm-build-libs-4.16.1.3-29.el9.x86_64 rpm-libs-4.16.1.3-29.el9.x86_64 rpmautospec-rpm-macros-0.6.3-1.el9.noarch rust-srpm-macros-17-4.el9.noarch rust-srpm-macros-epel-26.3-1.el9.noarch sed-4.8-9.el9.x86_64 setup-2.13.7-10.el9.noarch shadow-utils-2:4.9-8.el9.x86_64 sqlite-libs-3.34.1-7.el9_3.x86_64 systemd-libs-252-32.el9_4.x86_64 tar-2:1.34-6.el9_1.x86_64 tzdata-2024a-1.el9.noarch unzip-6.0-56.el9.x86_64 util-linux-2.37.4-18.el9.x86_64 util-linux-core-2.37.4-18.el9.x86_64 which-2.21-29.el9.x86_64 xz-5.2.5-8.el9_0.x86_64 xz-libs-5.2.5-8.el9_0.x86_64 zip-3.0-35.el9.x86_64 zlib-1.2.11-40.el9.x86_64 zstd-1.5.1-2.el9.x86_64 Complete! Finish: installing minimal buildroot with dnf Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: alternatives-1.24-1.el9.x86_64 ansible-srpm-macros-1-12.el9.noarch audit-libs-3.1.2-2.el9.x86_64 basesystem-11-13.el9.noarch bash-5.1.8-9.el9.x86_64 binutils-2.35.2-43.el9.x86_64 binutils-gold-2.35.2-43.el9.x86_64 bzip2-1.0.8-8.el9.x86_64 bzip2-libs-1.0.8-8.el9.x86_64 ca-certificates-2023.2.60_v7.0.306-90.1.el9_2.noarch coreutils-8.32-35.el9.x86_64 coreutils-common-8.32-35.el9.x86_64 cpio-2.13-16.el9.x86_64 cracklib-2.9.6-27.el9.x86_64 cracklib-dicts-2.9.6-27.el9.x86_64 crypto-policies-20240202-1.git283706d.el9.noarch curl-7.76.1-29.el9_4.x86_64 cyrus-sasl-lib-2.1.27-21.el9.x86_64 debugedit-5.0-5.el9.x86_64 diffutils-3.7-12.el9.x86_64 dwz-0.14-3.el9.x86_64 ed-1.14.2-12.el9.x86_64 efi-srpm-macros-6-2.el9_0.noarch elfutils-0.190-2.el9.x86_64 elfutils-debuginfod-client-0.190-2.el9.x86_64 elfutils-default-yama-scope-0.190-2.el9.noarch elfutils-libelf-0.190-2.el9.x86_64 elfutils-libs-0.190-2.el9.x86_64 epel-rpm-macros-9-14.el9.noarch file-5.39-16.el9.x86_64 file-libs-5.39-16.el9.x86_64 filesystem-3.16-2.el9.x86_64 findutils-4.8.0-6.el9.x86_64 fonts-srpm-macros-2.0.5-7.el9.1.noarch forge-srpm-macros-0.3.1-1.el9.noarch fpc-srpm-macros-1.3-7.el9.noarch gawk-5.1.0-6.el9.x86_64 gdb-minimal-10.2-13.el9.x86_64 gdbm-libs-1.19-4.el9.x86_64 ghc-srpm-macros-1.5.0-6.el9.noarch glibc-2.34-100.el9_4.2.x86_64 glibc-common-2.34-100.el9_4.2.x86_64 glibc-gconv-extra-2.34-100.el9_4.2.x86_64 glibc-minimal-langpack-2.34-100.el9_4.2.x86_64 gmp-6.2.0-13.el9.x86_64 go-srpm-macros-3.2.0-3.el9.noarch go-srpm-macros-epel-3.3.0.5-1.el9.noarch gpg-pubkey-3228467c-613798eb gpg-pubkey-5a6340b3-6229229e gpg-pubkey-fd431d51-4ae0493b grep-3.6-5.el9.x86_64 groff-base-1.22.4-10.el9.x86_64 gzip-1.12-1.el9.x86_64 info-6.7-15.el9.x86_64 kernel-srpm-macros-1.0-13.el9.noarch keyutils-libs-1.6.3-1.el9.x86_64 krb5-libs-1.21.1-1.el9.x86_64 libacl-2.3.1-4.el9.x86_64 libarchive-3.5.3-4.el9.x86_64 libattr-2.5.1-3.el9.x86_64 libblkid-2.37.4-18.el9.x86_64 libbrotli-1.0.9-6.el9.x86_64 libcap-2.48-9.el9_2.x86_64 libcap-ng-0.8.2-7.el9.x86_64 libcom_err-1.46.5-5.el9.x86_64 libcurl-7.76.1-29.el9_4.x86_64 libdb-5.3.28-53.el9.x86_64 libeconf-0.4.1-3.el9_2.x86_64 libevent-2.1.12-6.el9.x86_64 libfdisk-2.37.4-18.el9.x86_64 libffi-3.4.2-8.el9.x86_64 libgcc-11.4.1-3.el9.x86_64 libgcrypt-1.10.0-10.el9_2.x86_64 libgomp-11.4.1-3.el9.x86_64 libgpg-error-1.42-5.el9.x86_64 libidn2-2.3.0-7.el9.x86_64 libmount-2.37.4-18.el9.x86_64 libnghttp2-1.43.0-5.el9_4.3.x86_64 libpkgconf-1.7.3-10.el9.x86_64 libpsl-0.21.1-5.el9.x86_64 libpwquality-1.4.4-8.el9.x86_64 libselinux-3.6-1.el9.x86_64 libsemanage-3.6-1.el9.x86_64 libsepol-3.6-1.el9.x86_64 libsigsegv-2.13-4.el9.x86_64 libsmartcols-2.37.4-18.el9.x86_64 libssh-0.10.4-13.el9.x86_64 libssh-config-0.10.4-13.el9.noarch libstdc++-11.4.1-3.el9.x86_64 libtasn1-4.16.0-8.el9_1.x86_64 libunistring-0.9.10-15.el9.x86_64 libutempter-1.2.1-6.el9.x86_64 libuuid-2.37.4-18.el9.x86_64 libverto-0.3.2-3.el9.x86_64 libxcrypt-4.4.18-3.el9.x86_64 libxml2-2.9.13-6.el9_4.x86_64 libzstd-1.5.1-2.el9.x86_64 lua-libs-5.4.4-4.el9.x86_64 lua-srpm-macros-1-6.el9.noarch lz4-libs-1.9.3-5.el9.x86_64 mpfr-4.1.0-7.el9.x86_64 ncurses-6.2-10.20210508.el9.x86_64 ncurses-base-6.2-10.20210508.el9.noarch ncurses-libs-6.2-10.20210508.el9.x86_64 ocaml-srpm-macros-6-6.el9.noarch openblas-srpm-macros-2-11.el9.noarch openldap-2.6.6-3.el9.x86_64 openssl-3.0.7-27.el9.x86_64 openssl-fips-provider-3.0.7-2.el9.x86_64 openssl-libs-3.0.7-27.el9.x86_64 p11-kit-0.25.3-2.el9.x86_64 p11-kit-trust-0.25.3-2.el9.x86_64 pam-1.5.1-19.el9.x86_64 patch-2.7.6-16.el9.x86_64 pcre-8.44-3.el9.3.x86_64 pcre2-10.40-5.el9.x86_64 pcre2-syntax-10.40-5.el9.noarch perl-AutoLoader-5.74-481.el9.noarch perl-B-1.80-481.el9.x86_64 perl-Carp-1.50-460.el9.noarch perl-Class-Struct-0.66-481.el9.noarch perl-Data-Dumper-2.174-462.el9.x86_64 perl-Digest-1.19-4.el9.noarch perl-Digest-MD5-2.58-4.el9.x86_64 perl-Encode-3.08-462.el9.x86_64 perl-Errno-1.30-481.el9.x86_64 perl-Exporter-5.74-461.el9.noarch perl-Fcntl-1.13-481.el9.x86_64 perl-File-Basename-2.85-481.el9.noarch perl-File-Path-2.18-4.el9.noarch perl-File-Temp-0.231.100-4.el9.noarch perl-File-stat-1.09-481.el9.noarch perl-FileHandle-2.03-481.el9.noarch perl-Getopt-Long-2.52-4.el9.noarch perl-Getopt-Std-1.12-481.el9.noarch perl-HTTP-Tiny-0.076-462.el9.noarch perl-IO-1.43-481.el9.x86_64 perl-IO-Socket-IP-0.41-5.el9.noarch perl-IO-Socket-SSL-2.073-1.el9.noarch perl-IPC-Open3-1.21-481.el9.noarch perl-MIME-Base64-3.16-4.el9.x86_64 perl-Mozilla-CA-20200520-6.el9.noarch perl-Net-SSLeay-1.92-2.el9.x86_64 perl-POSIX-1.94-481.el9.x86_64 perl-PathTools-3.78-461.el9.x86_64 perl-Pod-Escapes-1.07-460.el9.noarch perl-Pod-Perldoc-3.28.01-461.el9.noarch perl-Pod-Simple-3.42-4.el9.noarch perl-Pod-Usage-2.01-4.el9.noarch perl-Scalar-List-Utils-1.56-461.el9.x86_64 perl-SelectSaver-1.02-481.el9.noarch perl-Socket-2.031-4.el9.x86_64 perl-Storable-3.21-460.el9.x86_64 perl-Symbol-1.08-481.el9.noarch perl-Term-ANSIColor-5.01-461.el9.noarch perl-Term-Cap-1.17-460.el9.noarch perl-Text-ParseWords-3.30-460.el9.noarch perl-Text-Tabs+Wrap-2013.0523-460.el9.noarch perl-Time-Local-1.300-7.el9.noarch perl-URI-5.09-3.el9.noarch perl-base-2.27-481.el9.noarch perl-constant-1.33-461.el9.noarch perl-if-0.60.800-481.el9.noarch perl-interpreter-5.32.1-481.el9.x86_64 perl-libnet-3.13-4.el9.noarch perl-libs-5.32.1-481.el9.x86_64 perl-mro-1.23-481.el9.x86_64 perl-overload-1.31-481.el9.noarch perl-overloading-0.02-481.el9.noarch perl-parent-0.238-460.el9.noarch perl-podlators-4.14-460.el9.noarch perl-srpm-macros-1-41.el9.noarch perl-subs-1.03-481.el9.noarch perl-vars-1.05-481.el9.noarch pkgconf-1.7.3-10.el9.x86_64 pkgconf-m4-1.7.3-10.el9.noarch pkgconf-pkg-config-1.7.3-10.el9.x86_64 popt-1.18-8.el9.x86_64 publicsuffix-list-dafsa-20210518-3.el9.noarch pyproject-srpm-macros-1.12.0-1.el9.noarch python-srpm-macros-3.9-53.el9.noarch qt5-srpm-macros-5.15.9-1.el9.noarch qt6-srpm-macros-6.6.2-1.el9.noarch readline-8.1-4.el9.x86_64 redhat-release-9.4-0.4.el9.x86_64 redhat-rpm-config-207-1.el9.noarch rpm-4.16.1.3-29.el9.x86_64 rpm-build-4.16.1.3-29.el9.x86_64 rpm-build-libs-4.16.1.3-29.el9.x86_64 rpm-libs-4.16.1.3-29.el9.x86_64 rpmautospec-rpm-macros-0.6.3-1.el9.noarch rust-srpm-macros-17-4.el9.noarch rust-srpm-macros-epel-26.3-1.el9.noarch sed-4.8-9.el9.x86_64 setup-2.13.7-10.el9.noarch shadow-utils-4.9-8.el9.x86_64 sqlite-libs-3.34.1-7.el9_3.x86_64 systemd-libs-252-32.el9_4.x86_64 tar-1.34-6.el9_1.x86_64 tzdata-2024a-1.el9.noarch unzip-6.0-56.el9.x86_64 util-linux-2.37.4-18.el9.x86_64 util-linux-core-2.37.4-18.el9.x86_64 which-2.21-29.el9.x86_64 xz-5.2.5-8.el9_0.x86_64 xz-libs-5.2.5-8.el9_0.x86_64 zip-3.0-35.el9.x86_64 zlib-1.2.11-40.el9.x86_64 zstd-1.5.1-2.el9.x86_64 Start: buildsrpm Start: rpmbuild -bs Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1717372800 Wrote: /builddir/build/SRPMS/htslib-1.20-1.el9.src.rpm Finish: rpmbuild -bs cp: preserving permissions for ‘/var/lib/copr-rpmbuild/results/chroot_scan/var/lib/mock/rhel+epel-9-x86_64-1717413251.506071/root/var/log’: No such file or directory INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/rhel+epel-9-x86_64-1717413251.506071/root/var/log/dnf.rpm.log /var/lib/mock/rhel+epel-9-x86_64-1717413251.506071/root/var/log/dnf.librepo.log /var/lib/mock/rhel+epel-9-x86_64-1717413251.506071/root/var/log/dnf.log Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-4jea4873/htslib/htslib.spec) Config(child) 0 minutes 27 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-1.20-1.el9.src.rpm) Config(rhel+epel-9-x86_64) Start: chroot init INFO: mounting tmpfs at /var/lib/mock/rhel+epel-9-x86_64-1717413251.506071/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 from host and used with --installroot: rpm-4.19.1.1-1.fc39.x86_64 rpm-sequoia-1.6.0-1.fc39.x86_64 python3-dnf-4.19.2-1.fc39.noarch python3-dnf-plugins-core-4.6.0-1.fc39.noarch yum-4.19.2-1.fc39.noarch dnf5-5.1.17-1.fc39.x86_64 dnf5-plugins-5.1.17-1.fc39.x86_64 Finish: chroot init Start: build phase for htslib-1.20-1.el9.src.rpm Start: build setup for htslib-1.20-1.el9.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1717372800 Wrote: /builddir/build/SRPMS/htslib-1.20-1.el9.src.rpm No matches found for the following disable plugin patterns: local, spacewalk, versionlock Updating Subscription Management repositories. Unable to read consumer identity This system is not registered with an entitlement server. You can use subscription-manager to register. Copr repository 41 kB/s | 1.8 kB 00:00 Red Hat Enterprise Linux - BaseOS 52 kB/s | 4.1 kB 00:00 Red Hat Enterprise Linux - AppStream 45 kB/s | 4.5 kB 00:00 Red Hat Enterprise Linux - CodeReady Linux Buil 62 kB/s | 4.5 kB 00:00 Extra Packages for Enterprise Linux 9 - x86_64 43 kB/s | 12 kB 00:00 Package perl-Data-Dumper-2.174-462.el9.x86_64 is already installed. Package perl-Getopt-Long-1:2.52-4.el9.noarch is already installed. Package perl-interpreter-4:5.32.1-481.el9.x86_64 is already installed. Dependencies resolved. ================================================================================ Package Arch Version Repository Size ================================================================================ Installing: bzip2-devel x86_64 1.0.8-8.el9 appstream 216 k gcc x86_64 11.4.1-3.el9 appstream 32 M libcurl-devel x86_64 7.76.1-29.el9_4 appstream 980 k make x86_64 1:4.3-8.el9 baseos 541 k openssl-devel x86_64 1:3.0.7-27.el9 appstream 4.1 M perl-FindBin noarch 1.51-481.el9 appstream 14 k perl-lib x86_64 0.65-481.el9 appstream 15 k xz-devel x86_64 5.2.5-8.el9_0 appstream 59 k zlib-devel x86_64 1.2.11-40.el9 appstream 47 k Installing dependencies: annobin x86_64 12.31-2.el9 appstream 1.0 M cpp x86_64 11.4.1-3.el9 appstream 11 M gcc-plugin-annobin x86_64 11.4.1-3.el9 appstream 49 k glibc-devel x86_64 2.34-100.el9_4.2 appstream 42 k glibc-headers x86_64 2.34-100.el9_4.2 appstream 548 k kernel-headers x86_64 5.14.0-427.18.1.el9_4 appstream 7.4 M libedit x86_64 3.1-38.20210216cvs.el9 baseos 107 k libmpc x86_64 1.2.1-4.el9 appstream 65 k libxcrypt-devel x86_64 4.4.18-3.el9 appstream 32 k llvm-libs x86_64 17.0.6-5.el9 appstream 25 M Transaction Summary ================================================================================ Install 19 Packages Total download size: 83 M Installed size: 234 M Downloading Packages: (1/19): libedit-3.1-38.20210216cvs.el9.x86_64.r 973 kB/s | 107 kB 00:00 (2/19): make-4.3-8.el9.x86_64.rpm 4.4 MB/s | 541 kB 00:00 (3/19): libmpc-1.2.1-4.el9.x86_64.rpm 1.2 MB/s | 65 kB 00:00 (4/19): bzip2-devel-1.0.8-8.el9.x86_64.rpm 1.3 MB/s | 216 kB 00:00 (5/19): libxcrypt-devel-4.4.18-3.el9.x86_64.rpm 346 kB/s | 32 kB 00:00 (6/19): zlib-devel-1.2.11-40.el9.x86_64.rpm 933 kB/s | 47 kB 00:00 (7/19): gcc-plugin-annobin-11.4.1-3.el9.x86_64. 1.1 MB/s | 49 kB 00:00 (8/19): xz-devel-5.2.5-8.el9_0.x86_64.rpm 591 kB/s | 59 kB 00:00 (9/19): perl-FindBin-1.51-481.el9.noarch.rpm 216 kB/s | 14 kB 00:00 (10/19): annobin-12.31-2.el9.x86_64.rpm 18 MB/s | 1.0 MB 00:00 (11/19): libcurl-devel-7.76.1-29.el9_4.x86_64.r 14 MB/s | 980 kB 00:00 (12/19): cpp-11.4.1-3.el9.x86_64.rpm 83 MB/s | 11 MB 00:00 (13/19): llvm-libs-17.0.6-5.el9.x86_64.rpm 172 MB/s | 25 MB 00:00 (14/19): openssl-devel-3.0.7-27.el9.x86_64.rpm 24 MB/s | 4.1 MB 00:00 (15/19): perl-lib-0.65-481.el9.x86_64.rpm 105 kB/s | 15 kB 00:00 (16/19): kernel-headers-5.14.0-427.18.1.el9_4.x 113 MB/s | 7.4 MB 00:00 (17/19): gcc-11.4.1-3.el9.x86_64.rpm 185 MB/s | 32 MB 00:00 (18/19): glibc-devel-2.34-100.el9_4.2.x86_64.rp 431 kB/s | 42 kB 00:00 (19/19): glibc-headers-2.34-100.el9_4.2.x86_64. 6.3 MB/s | 548 kB 00:00 -------------------------------------------------------------------------------- Total 121 MB/s | 83 MB 00:00 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Installing : libmpc-1.2.1-4.el9.x86_64 1/19 Installing : cpp-11.4.1-3.el9.x86_64 2/19 Installing : glibc-headers-2.34-100.el9_4.2.x86_64 3/19 Installing : kernel-headers-5.14.0-427.18.1.el9_4.x86_64 4/19 Installing : glibc-devel-2.34-100.el9_4.2.x86_64 5/19 Installing : libxcrypt-devel-4.4.18-3.el9.x86_64 6/19 Installing : make-1:4.3-8.el9.x86_64 7/19 Installing : gcc-11.4.1-3.el9.x86_64 8/19 Running scriptlet: gcc-11.4.1-3.el9.x86_64 8/19 Installing : libedit-3.1-38.20210216cvs.el9.x86_64 9/19 Installing : llvm-libs-17.0.6-5.el9.x86_64 10/19 Installing : annobin-12.31-2.el9.x86_64 11/19 Running scriptlet: annobin-12.31-2.el9.x86_64 11/19 Installing : gcc-plugin-annobin-11.4.1-3.el9.x86_64 12/19 Running scriptlet: gcc-plugin-annobin-11.4.1-3.el9.x86_64 12/19 Installing : perl-lib-0.65-481.el9.x86_64 13/19 Installing : openssl-devel-1:3.0.7-27.el9.x86_64 14/19 Installing : libcurl-devel-7.76.1-29.el9_4.x86_64 15/19 Installing : perl-FindBin-1.51-481.el9.noarch 16/19 Installing : zlib-devel-1.2.11-40.el9.x86_64 17/19 Installing : xz-devel-5.2.5-8.el9_0.x86_64 18/19 Installing : bzip2-devel-1.0.8-8.el9.x86_64 19/19 Running scriptlet: bzip2-devel-1.0.8-8.el9.x86_64 19/19 Verifying : libedit-3.1-38.20210216cvs.el9.x86_64 1/19 Verifying : make-1:4.3-8.el9.x86_64 2/19 Verifying : bzip2-devel-1.0.8-8.el9.x86_64 3/19 Verifying : libmpc-1.2.1-4.el9.x86_64 4/19 Verifying : libxcrypt-devel-4.4.18-3.el9.x86_64 5/19 Verifying : xz-devel-5.2.5-8.el9_0.x86_64 6/19 Verifying : zlib-devel-1.2.11-40.el9.x86_64 7/19 Verifying : gcc-plugin-annobin-11.4.1-3.el9.x86_64 8/19 Verifying : perl-FindBin-1.51-481.el9.noarch 9/19 Verifying : annobin-12.31-2.el9.x86_64 10/19 Verifying : cpp-11.4.1-3.el9.x86_64 11/19 Verifying : libcurl-devel-7.76.1-29.el9_4.x86_64 12/19 Verifying : llvm-libs-17.0.6-5.el9.x86_64 13/19 Verifying : openssl-devel-1:3.0.7-27.el9.x86_64 14/19 Verifying : perl-lib-0.65-481.el9.x86_64 15/19 Verifying : gcc-11.4.1-3.el9.x86_64 16/19 Verifying : kernel-headers-5.14.0-427.18.1.el9_4.x86_64 17/19 Verifying : glibc-devel-2.34-100.el9_4.2.x86_64 18/19 Verifying : glibc-headers-2.34-100.el9_4.2.x86_64 19/19 Installed products updated. Installed: annobin-12.31-2.el9.x86_64 bzip2-devel-1.0.8-8.el9.x86_64 cpp-11.4.1-3.el9.x86_64 gcc-11.4.1-3.el9.x86_64 gcc-plugin-annobin-11.4.1-3.el9.x86_64 glibc-devel-2.34-100.el9_4.2.x86_64 glibc-headers-2.34-100.el9_4.2.x86_64 kernel-headers-5.14.0-427.18.1.el9_4.x86_64 libcurl-devel-7.76.1-29.el9_4.x86_64 libedit-3.1-38.20210216cvs.el9.x86_64 libmpc-1.2.1-4.el9.x86_64 libxcrypt-devel-4.4.18-3.el9.x86_64 llvm-libs-17.0.6-5.el9.x86_64 make-1:4.3-8.el9.x86_64 openssl-devel-1:3.0.7-27.el9.x86_64 perl-FindBin-1.51-481.el9.noarch perl-lib-0.65-481.el9.x86_64 xz-devel-5.2.5-8.el9_0.x86_64 zlib-devel-1.2.11-40.el9.x86_64 Complete! Finish: build setup for htslib-1.20-1.el9.src.rpm Start: rpmbuild htslib-1.20-1.el9.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1717372800 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.gwvY47 + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf htslib-1.20 + /usr/bin/bzip2 -dc /builddir/build/SOURCES/htslib-1.20.tar.bz2 + /usr/bin/tar -xof - + STATUS=0 + '[' 0 -ne 0 ']' + cd htslib-1.20 + /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.SSpEAz + umask 022 + cd /builddir/build/BUILD + cd htslib-1.20 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FCFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 ' + 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 $(dirname ./configure) -name config.guess -o -name config.sub) ++ basename ./config.sub + '[' -f /usr/lib/rpm/redhat/config.sub ']' + /usr/bin/rm -f ./config.sub ++ basename ./config.sub + /usr/bin/cp -fv /usr/lib/rpm/redhat/config.sub ./config.sub '/usr/lib/rpm/redhat/config.sub' -> './config.sub' + '[' 1 = 1 ']' + '[' x '!=' 'x-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' ']' ++ find . -name ltmain.sh + ./configure --build=x86_64-redhat-linux-gnu --host=x86_64-redhat-linux-gnu --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/libexec --localstatedir=/var --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info 'CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' 'LDFLAGS=-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 ' --prefix=/usr --libdir=/usr/lib64 --enable-plugins '--with-plugin-path=/usr/local/libexec/htslib:$(plugindir)' --enable-gcs --enable-libcurl --enable-s3 configure: WARNING: unrecognized options: --disable-dependency-tracking checking for x86_64-redhat-linux-gnu-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 x86_64-redhat-linux-gnu-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 C compiler flags needed for sse4.1... none checking C compiler flags needed for avx2... -mavx2 -mpopcnt checking C compiler flags needed for avx512f... -mavx512f -mpopcnt checking for x86_64-redhat-linux-gnu-pkg-config... /usr/bin/x86_64-redhat-linux-gnu-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 x86_64-redhat-linux-gnu... plain .so checking whether the linker supports versioned symbols... yes checking whether the compiler accepts -fvisibility=hidden... yes checking build system type... x86_64-redhat-linux-gnu checking host system type... x86_64-redhat-linux-gnu checking for getpagesize... yes checking for working mmap... yes checking for gmtime_r... yes checking for fsync... yes checking for drand48... yes checking for srand48_deterministic... no checking whether fdatasync is declared... yes checking for fdatasync... 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 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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o kfunc.o kfunc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o kstring.o kstring.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o errmod.o errmod.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o bcf_sr_sort.o bcf_sr_sort.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o faidx.o faidx.c echo '#define HTS_VERSION_TEXT "1.20"' > version.h printf '#define HTS_CC "%s"\n#define HTS_CPPFLAGS "%s"\n#define HTS_CFLAGS "%s"\n#define HTS_LDFLAGS "%s"\n#define HTS_LIBS "%s"\n' \ 'gcc' \ '' \ '-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden' \ '-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fvisibility=hidden -rdynamic' \ '-llzma -lbz2 -lz -lm ' > config_vars.h gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o bgzf.o bgzf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o hts_os.o hts_os.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o md5.o md5.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o hfile.o hfile.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o multipart.o multipart.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o hts_expr.o hts_expr.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o probaln.o probaln.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o realn.o realn.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o region.o region.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o header.o header.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o regidx.o regidx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o sam_mods.o sam_mods.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o vcf_sweep.o vcf_sweep.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o tbx.o tbx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o textutils.o textutils.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o thread_pool.o thread_pool.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o synced_bcf_reader.o synced_bcf_reader.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o vcfutils.o vcfutils.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o cram/cram_codecs.o cram/cram_codecs.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o cram/cram_external.o cram/cram_external.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o sam.o sam.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o cram/cram_index.o cram/cram_index.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o cram/cram_stats.o cram/cram_stats.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o cram/mFILE.o cram/mFILE.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o cram/open_trace_file.o cram/open_trace_file.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o cram/string_alloc.o cram/string_alloc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o cram/cram_encode.o cram/cram_encode.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o vcf.o vcf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -mavx512f -mpopcnt -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -mavx2 -mpopcnt -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -DPLUGINPATH=\"/usr/local/libexec/htslib:/usr/libexec/htslib\" -c -o plugin.o plugin.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o kfunc.pico kfunc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o errmod.pico errmod.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o bcf_sr_sort.pico bcf_sr_sort.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o bgzf.pico bgzf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o hfile.pico hfile.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o hts_os.pico hts_os.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o md5.pico md5.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o multipart.pico multipart.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o hts_expr.pico hts_expr.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o probaln.pico probaln.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o header.pico header.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o realn.pico realn.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o region.pico region.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o regidx.pico regidx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o sam_mods.pico sam_mods.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o vcf_sweep.pico vcf_sweep.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o tbx.pico tbx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o textutils.pico textutils.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o synced_bcf_reader.pico synced_bcf_reader.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o thread_pool.pico thread_pool.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o vcfutils.pico vcfutils.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o cram/cram_codecs.pico cram/cram_codecs.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o cram/cram_external.pico cram/cram_external.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o cram/cram_index.pico cram/cram_index.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o cram/cram_stats.pico cram/cram_stats.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o cram/mFILE.pico cram/mFILE.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o cram/open_trace_file.pico cram/open_trace_file.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o cram/pooled_alloc.pico cram/pooled_alloc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o cram/string_alloc.pico cram/string_alloc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o cram/cram_encode.pico cram/cram_encode.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -mavx2 -mpopcnt -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -mavx512f -mpopcnt -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -DPLUGINPATH=\"/usr/local/libexec/htslib:/usr/libexec/htslib\" -fpic -c -o plugin.pico plugin.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o bgzip.o bgzip.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o htsfile.o htsfile.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o annot-tsv.o annot-tsv.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o hfile_gcs.pico hfile_gcs.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o tabix.o tabix.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o hfile_s3_write.pico hfile_s3_write.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o test/fieldarith.o test/fieldarith.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o test/hts_endian.o test/hts_endian.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o hfile_libcurl.pico hfile_libcurl.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o test/pileup.o test/pileup.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o test/plugins-dlhts.o test/plugins-dlhts.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o test/pileup_mod.o test/pileup_mod.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o test/hfile.o test/hfile.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o hfile_s3.pico hfile_s3.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o test/test_expr.o test/test_expr.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o test/test_kfunc.o test/test_kfunc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o test/test_faidx.o test/test_faidx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o test/test_mod.o test/test_mod.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o test/test_bgzf.o test/test_bgzf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o test/test_realn.o test/test_realn.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o test/test_time_funcs.o test/test_time_funcs.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o test/test_str2int.o test/test_str2int.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o test/test-regidx.o test/test-regidx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o test/test_index.o test/test_index.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o test/test_view.o test/test_view.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o test/sam.o test/sam.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o test/test-bcf-sr.o test/test-bcf-sr.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o test/test-vcf-api.o test/test-vcf-api.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o test/test-bcf-translate.o test/test-bcf-translate.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o test/fuzz/hts_open_fuzzer.o test/fuzz/hts_open_fuzzer.c sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' htslib.pc.tmp > htslib_static.mk sed -e 's#@-includedir@#'`pwd`'#g;s#@-libdir@#'`pwd`'#g' htslib.pc.tmp > htslib-uninstalled.pc gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o test/test_introspection.o test/test_introspection.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o test/test-parse-reg.o test/test-parse-reg.c gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fvisibility=hidden -rdynamic -o test/hts_endian test/hts_endian.o -llzma -lbz2 -lz -lm gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fvisibility=hidden -rdynamic -o test/plugins-dlhts test/plugins-dlhts.o -llzma -lbz2 -lz -lm gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fvisibility=hidden -rdynamic -o test/test_time_funcs test/test_time_funcs.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o hts.o hts.c 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 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 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fvisibility=hidden -rdynamic -o bgzip bgzip.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 14 LTRANS jobs gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fvisibility=hidden -rdynamic -o annot-tsv annot-tsv.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 14 LTRANS jobs gcc -shared -Wl,-soname,libhts.so.3 -Wl,-version-script,htslib.map -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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 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 lto-wrapper: warning: using serial compilation of 18 LTRANS jobs gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fvisibility=hidden -rdynamic -o htsfile htsfile.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 17 LTRANS jobs gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fvisibility=hidden -rdynamic -o test/fieldarith test/fieldarith.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 14 LTRANS jobs gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fvisibility=hidden -rdynamic -o test/hfile test/hfile.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 14 LTRANS jobs gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fvisibility=hidden -rdynamic -o tabix tabix.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 18 LTRANS jobs gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fvisibility=hidden -rdynamic -o test/pileup test/pileup.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 14 LTRANS jobs gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fvisibility=hidden -rdynamic -o test/pileup_mod test/pileup_mod.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 13 LTRANS jobs gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fvisibility=hidden -rdynamic -o test/sam test/sam.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 15 LTRANS jobs gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fvisibility=hidden -rdynamic -o test/test_kfunc test/test_kfunc.o libhts.a -lz -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fvisibility=hidden -rdynamic -o test/test_kstring test/test_kstring.o libhts.a -lz -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fvisibility=hidden -rdynamic -o test/test_bgzf test/test_bgzf.o libhts.a -lz -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 14 LTRANS jobs gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fvisibility=hidden -rdynamic -o test/test_expr test/test_expr.o libhts.a -lz -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 14 LTRANS jobs gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fvisibility=hidden -rdynamic -o test/test_faidx test/test_faidx.o libhts.a -lz -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 14 LTRANS jobs gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fvisibility=hidden -rdynamic -o test/test_mod test/test_mod.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 14 LTRANS jobs gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fvisibility=hidden -rdynamic -o test/test_realn test/test_realn.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 14 LTRANS jobs gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fvisibility=hidden -rdynamic -o test/test-regidx test/test-regidx.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 14 LTRANS jobs gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fvisibility=hidden -rdynamic -o test/test_str2int test/test_str2int.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 14 LTRANS jobs gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fvisibility=hidden -rdynamic -o test/test_view test/test_view.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 18 LTRANS jobs gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fvisibility=hidden -rdynamic -o test/test_index test/test_index.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 18 LTRANS jobs gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fvisibility=hidden -rdynamic -o test/test-vcf-api test/test-vcf-api.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 18 LTRANS jobs gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fvisibility=hidden -rdynamic -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 17 LTRANS jobs gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fvisibility=hidden -rdynamic -o test/test-parse-reg test/test-parse-reg.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 14 LTRANS jobs gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fvisibility=hidden -rdynamic -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -lz -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 18 LTRANS jobs gcc -shared -Wl,-E -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fvisibility=hidden -rdynamic -o hfile_libcurl.so hfile_libcurl.pico libhts.so -llzma -lbz2 -lz -lm -lcurl -lpthread gcc -shared -Wl,-E -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fvisibility=hidden -rdynamic -o hfile_gcs.so hfile_gcs.pico libhts.so -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fvisibility=hidden -rdynamic -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 18 LTRANS jobs gcc -shared -Wl,-E -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fvisibility=hidden -rdynamic -o hfile_s3_write.so hfile_s3_write.pico libhts.so -llzma -lbz2 -lz -lm -lcrypto -lcurl -lpthread gcc -shared -Wl,-E -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fvisibility=hidden -rdynamic -o hfile_s3.so hfile_s3.pico libhts.so -llzma -lbz2 -lz -lm -lcrypto -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fvisibility=hidden -rdynamic -o test/test_introspection test/test_introspection.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 14 LTRANS jobs gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fvisibility=hidden -rdynamic -o test/test-bcf_set_variant_type test/test-bcf_set_variant_type.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 17 LTRANS jobs + 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.4u4bcl + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/htslib-1.20-1.el9.x86_64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/htslib-1.20-1.el9.x86_64 ++ dirname /builddir/build/BUILDROOT/htslib-1.20-1.el9.x86_64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/htslib-1.20-1.el9.x86_64 + cd htslib-1.20 + /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/htslib-1.20-1.el9.x86_64 'INSTALL=/usr/bin/install -p' mkdir -p -m 755 /builddir/build/BUILDROOT/htslib-1.20-1.el9.x86_64/usr/bin /builddir/build/BUILDROOT/htslib-1.20-1.el9.x86_64/usr/include /builddir/build/BUILDROOT/htslib-1.20-1.el9.x86_64/usr/include/htslib /builddir/build/BUILDROOT/htslib-1.20-1.el9.x86_64/usr/lib64 /builddir/build/BUILDROOT/htslib-1.20-1.el9.x86_64/usr/share/man/man1 /builddir/build/BUILDROOT/htslib-1.20-1.el9.x86_64/usr/share/man/man5 /builddir/build/BUILDROOT/htslib-1.20-1.el9.x86_64/usr/share/man/man7 /builddir/build/BUILDROOT/htslib-1.20-1.el9.x86_64/usr/lib64/pkgconfig if test -n "/usr/libexec/htslib"; then mkdir -p -m 755 /builddir/build/BUILDROOT/htslib-1.20-1.el9.x86_64/usr/libexec/htslib; fi /usr/bin/install -p -m 644 libhts.so /builddir/build/BUILDROOT/htslib-1.20-1.el9.x86_64/usr/lib64/libhts.so.1.20 ln -sf libhts.so.1.20 /builddir/build/BUILDROOT/htslib-1.20-1.el9.x86_64/usr/lib64/libhts.so ln -sf libhts.so.1.20 /builddir/build/BUILDROOT/htslib-1.20-1.el9.x86_64/usr/lib64/libhts.so.3 sed -e 's#@-includedir@#/usr/include#g;s#@-libdir@#/usr/lib64#g;s#@-PACKAGE_VERSION@#1.20#g' htslib.pc.tmp > /builddir/build/BUILDROOT/htslib-1.20-1.el9.x86_64/usr/lib64/pkgconfig/htslib.pc chmod 644 /builddir/build/BUILDROOT/htslib-1.20-1.el9.x86_64/usr/lib64/pkgconfig/htslib.pc /usr/bin/install -p annot-tsv bgzip htsfile tabix /builddir/build/BUILDROOT/htslib-1.20-1.el9.x86_64/usr/bin if test -n "hfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so"; then /usr/bin/install -p hfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so /builddir/build/BUILDROOT/htslib-1.20-1.el9.x86_64/usr/libexec/htslib; fi /usr/bin/install -p -m 644 htslib/*.h /builddir/build/BUILDROOT/htslib-1.20-1.el9.x86_64/usr/include/htslib /usr/bin/install -p -m 644 libhts.a /builddir/build/BUILDROOT/htslib-1.20-1.el9.x86_64/usr/lib64/libhts.a /usr/bin/install -p -m 644 annot-tsv.1 bgzip.1 htsfile.1 tabix.1 /builddir/build/BUILDROOT/htslib-1.20-1.el9.x86_64/usr/share/man/man1 /usr/bin/install -p -m 644 faidx.5 sam.5 vcf.5 /builddir/build/BUILDROOT/htslib-1.20-1.el9.x86_64/usr/share/man/man5 /usr/bin/install -p -m 644 htslib-s3-plugin.7 /builddir/build/BUILDROOT/htslib-1.20-1.el9.x86_64/usr/share/man/man7 + pushd /builddir/build/BUILDROOT/htslib-1.20-1.el9.x86_64//usr/lib64 ~/build/BUILDROOT/htslib-1.20-1.el9.x86_64/usr/lib64 ~/build/BUILD/htslib-1.20 + chmod 755 libhts.so.1.20 ~/build/BUILD/htslib-1.20 + popd + find /builddir/build/BUILDROOT/htslib-1.20-1.el9.x86_64 -name '*.la' -delete + rm -f /builddir/build/BUILDROOT/htslib-1.20-1.el9.x86_64//usr/lib64/libhts.a + /usr/bin/find-debuginfo -j4 --strict-build-id -m -i --build-id-seed 1.20-1.el9 --unique-debug-suffix -1.20-1.el9.x86_64 --unique-debug-src-base htslib-1.20-1.el9.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 --remove-section .gnu.build.attributes -S debugsourcefiles.list /builddir/build/BUILD/htslib-1.20 extracting debug info from /builddir/build/BUILDROOT/htslib-1.20-1.el9.x86_64/usr/bin/annot-tsv extracting debug info from /builddir/build/BUILDROOT/htslib-1.20-1.el9.x86_64/usr/bin/tabix extracting debug info from /builddir/build/BUILDROOT/htslib-1.20-1.el9.x86_64/usr/bin/htsfile extracting debug info from /builddir/build/BUILDROOT/htslib-1.20-1.el9.x86_64/usr/bin/bgzip extracting debug info from /builddir/build/BUILDROOT/htslib-1.20-1.el9.x86_64/usr/lib64/libhts.so.1.20 extracting debug info from /builddir/build/BUILDROOT/htslib-1.20-1.el9.x86_64/usr/libexec/htslib/hfile_gcs.so extracting debug info from /builddir/build/BUILDROOT/htslib-1.20-1.el9.x86_64/usr/libexec/htslib/hfile_libcurl.so extracting debug info from /builddir/build/BUILDROOT/htslib-1.20-1.el9.x86_64/usr/libexec/htslib/hfile_s3.so extracting debug info from /builddir/build/BUILDROOT/htslib-1.20-1.el9.x86_64/usr/libexec/htslib/hfile_s3_write.so original debug info size: 17500kB, size after compression: 16388kB /usr/bin/sepdebugcrcfix: Updated 9 CRC32s, 0 CRC32s did match. 6439 blocks + /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/redhat/brp-python-bytecompile '' 1 0 + /usr/lib/rpm/brp-python-hardlink + /usr/lib/rpm/redhat/brp-mangle-shebangs Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.19Omcy + umask 022 + cd /builddir/build/BUILD + cd htslib-1.20 + 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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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 lto-wrapper: warning: using serial compilation of 3 LTRANS jobs 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 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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 lto-wrapper: warning: using serial compilation of 3 LTRANS jobs 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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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 Testing fqzcomp_qual -r -s 0 on ./dat/q4 9307 Testing fqzcomp_qual -r -s 1 on ./dat/q4 9618 Testing fqzcomp_qual -r -s 2 on ./dat/q4 9453 Testing fqzcomp_qual -r -s 3 on ./dat/q4 10481 Testing fqzcomp_qual -r -s 0 on ./dat/q40+dir 47674 Testing fqzcomp_qual -r -s 1 on ./dat/q40+dir 45016 Testing fqzcomp_qual -r -s 2 on ./dat/q40+dir 47760 Testing fqzcomp_qual -r -s 3 on ./dat/q40+dir 48583 Testing fqzcomp_qual -r -s 0 on ./dat/q8 30012 Testing fqzcomp_qual -r -s 1 on ./dat/q8 33742 Testing fqzcomp_qual -r -s 2 on ./dat/q8 30982 Testing fqzcomp_qual -r -s 3 on ./dat/q8 31709 Testing fqzcomp_qual -r -s 0 on ./dat/qvar 32868 Testing fqzcomp_qual -r -s 1 on ./dat/qvar 35007 Testing fqzcomp_qual -r -s 2 on ./dat/qvar 32400 Testing fqzcomp_qual -r -s 3 on ./dat/qvar 32073 gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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_kstring 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 hfile_s3_write.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 hfile_s3_write.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 -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 Expected passes: 41 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) Expected passes: 16 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 && REF_PATH=: ./test.pl ${TEST_OPTS:-} 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-1.20/test/test_view -l 0 -b -m 14 -x /tmp/smFSq11Epi/index.bam.csi /builddir/build/BUILD/htslib-1.20/test/index.sam > /tmp/smFSq11Epi/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.20/test/test_index -c /tmp/smFSq11Epi/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.20/test/test_view -l 0 -b -m 0 -x /tmp/smFSq11Epi/index.bam.bai /builddir/build/BUILD/htslib-1.20/test/index.sam > /tmp/smFSq11Epi/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.20/test/test_index -b /tmp/smFSq11Epi/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.20/test/test_view -l 0 -z -m 14 -x /tmp/smFSq11Epi/index.sam.gz.csi /builddir/build/BUILD/htslib-1.20/test/index.sam > /tmp/smFSq11Epi/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.20/test/test_index -c /tmp/smFSq11Epi/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.20/test/test_view -l 0 -z -m 0 -x /tmp/smFSq11Epi/index.sam.gz.bai /builddir/build/BUILD/htslib-1.20/test/index.sam > /tmp/smFSq11Epi/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.20/test/test_index -b /tmp/smFSq11Epi/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.20/test/test_view -l 0 -z -m 14 -x /tmp/smFSq11Epi/index.sam.gz.csi /builddir/build/BUILD/htslib-1.20/test/index_dos.sam > /tmp/smFSq11Epi/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.20/test/test_index -c /tmp/smFSq11Epi/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.20/test/test_view -l 0 -z -m 0 -x /tmp/smFSq11Epi/index.sam.gz.bai /builddir/build/BUILD/htslib-1.20/test/index_dos.sam > /tmp/smFSq11Epi/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.20/test/test_index -b /tmp/smFSq11Epi/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.20/test/test_view -l 0 -C -x /tmp/smFSq11Epi/index.cram.crai /builddir/build/BUILD/htslib-1.20/test/index.sam > /tmp/smFSq11Epi/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.20/test/test_index /tmp/smFSq11Epi/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.20/test/test_view -l 0 -b -m 14 -x /tmp/smFSq11Epi/index.bcf.csi /builddir/build/BUILD/htslib-1.20/test/index.vcf > /tmp/smFSq11Epi/index.bcf .. ok test_index: /builddir/build/BUILD/htslib-1.20/test/test_index -c /tmp/smFSq11Epi/index.bcf .. ok test_index: /builddir/build/BUILD/htslib-1.20/test/test_view -l 0 -z -m 14 -x /tmp/smFSq11Epi/index.vcf.gz.csi /builddir/build/BUILD/htslib-1.20/test/index.vcf > /tmp/smFSq11Epi/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.20/test/test_index -c /tmp/smFSq11Epi/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.20/test/test_view -l 0 -z -m 0 -x /tmp/smFSq11Epi/index.vcf.gz.tbi /builddir/build/BUILD/htslib-1.20/test/index.vcf > /tmp/smFSq11Epi/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.20/test/test_index -t /tmp/smFSq11Epi/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.20/tabix /tmp/smFSq11Epi/index.vcf.gz##idx##/tmp/smFSq11Epi/index.vcf.gz.tbi 1:10000060-10000060 .. ok test_index: /builddir/build/BUILD/htslib-1.20/test/test_view /tmp/smFSq11Epi/index2.bam 1:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.20/test/test_view /tmp/smFSq11Epi/index2.bam 1:2000000-2000000 .. ok test_index: /builddir/build/BUILD/htslib-1.20/test/test_view /tmp/smFSq11Epi/index2.bam 2:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.20/test/test_view /tmp/smFSq11Epi/index2.bam 2:2000000-2000000 .. ok test_index: /builddir/build/BUILD/htslib-1.20/test/test_view -@4 -l 0 -b -m 14 -x /tmp/smFSq11Epi/index.bam.csi /builddir/build/BUILD/htslib-1.20/test/index.sam > /tmp/smFSq11Epi/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.20/test/test_index -c /tmp/smFSq11Epi/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.20/test/test_view -@4 -l 0 -b -m 0 -x /tmp/smFSq11Epi/index.bam.bai /builddir/build/BUILD/htslib-1.20/test/index.sam > /tmp/smFSq11Epi/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.20/test/test_index -b /tmp/smFSq11Epi/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.20/test/test_view -@4 -l 0 -z -m 14 -x /tmp/smFSq11Epi/index.sam.gz.csi /builddir/build/BUILD/htslib-1.20/test/index.sam > /tmp/smFSq11Epi/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.20/test/test_index -c /tmp/smFSq11Epi/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.20/test/test_view -@4 -l 0 -z -m 0 -x /tmp/smFSq11Epi/index.sam.gz.bai /builddir/build/BUILD/htslib-1.20/test/index.sam > /tmp/smFSq11Epi/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.20/test/test_index -b /tmp/smFSq11Epi/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.20/test/test_view -@4 -l 0 -z -m 14 -x /tmp/smFSq11Epi/index.sam.gz.csi /builddir/build/BUILD/htslib-1.20/test/index_dos.sam > /tmp/smFSq11Epi/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.20/test/test_index -c /tmp/smFSq11Epi/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.20/test/test_view -@4 -l 0 -z -m 0 -x /tmp/smFSq11Epi/index.sam.gz.bai /builddir/build/BUILD/htslib-1.20/test/index_dos.sam > /tmp/smFSq11Epi/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.20/test/test_index -b /tmp/smFSq11Epi/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.20/test/test_view -@4 -l 0 -C -x /tmp/smFSq11Epi/index.cram.crai /builddir/build/BUILD/htslib-1.20/test/index.sam > /tmp/smFSq11Epi/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.20/test/test_index /tmp/smFSq11Epi/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.20/test/test_view -@4 -l 0 -b -m 14 -x /tmp/smFSq11Epi/index.bcf.csi /builddir/build/BUILD/htslib-1.20/test/index.vcf > /tmp/smFSq11Epi/index.bcf .. ok test_index: /builddir/build/BUILD/htslib-1.20/test/test_index -c /tmp/smFSq11Epi/index.bcf .. ok test_index: /builddir/build/BUILD/htslib-1.20/test/test_view -@4 -l 0 -z -m 14 -x /tmp/smFSq11Epi/index.vcf.gz.csi /builddir/build/BUILD/htslib-1.20/test/index.vcf > /tmp/smFSq11Epi/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.20/test/test_index -c /tmp/smFSq11Epi/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.20/test/test_view -@4 -l 0 -z -m 0 -x /tmp/smFSq11Epi/index.vcf.gz.tbi /builddir/build/BUILD/htslib-1.20/test/index.vcf > /tmp/smFSq11Epi/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.20/test/test_index -t /tmp/smFSq11Epi/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.20/tabix /tmp/smFSq11Epi/index.vcf.gz##idx##/tmp/smFSq11Epi/index.vcf.gz.tbi 1:10000060-10000060 .. ok test_index: /builddir/build/BUILD/htslib-1.20/test/test_view /tmp/smFSq11Epi/index2.bam 1:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.20/test/test_view /tmp/smFSq11Epi/index2.bam 1:2000000-2000000 .. ok test_index: /builddir/build/BUILD/htslib-1.20/test/test_view /tmp/smFSq11Epi/index2.bam 2:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.20/test/test_view /tmp/smFSq11Epi/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#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#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 embed_ref=2: ./test_view -C -p ce#1000_er.tmp.cram ce#1000.sam [W::cram_get_ref] Failed to populate reference for id 0 [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 .. 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 .. 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-1.20/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#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#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#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 embed_ref=2: ./test_view -@4 -C -p ce#1000_er.tmp.cram ce#1000.sam [W::cram_get_ref] Failed to populate reference for id 0 [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 .. 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 .. 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-1.20/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-1.20/test/test-vcf-api /tmp/smFSq11Epi/test-vcf-api.bcf .. ok test_bcf2vcf: /builddir/build/BUILD/htslib-1.20/test/test_view /builddir/build/BUILD/htslib-1.20/test/tabix/vcf_file.bcf .. ok test_vcf_sweep: /builddir/build/BUILD/htslib-1.20/test/test-vcf-sweep /tmp/smFSq11Epi/test-vcf-api.bcf .. ok test_vcf_various: /builddir/build/BUILD/htslib-1.20/htsfile -ch /builddir/build/BUILD/htslib-1.20/test/test-vcf-hdr-in.vcf .. ok test_vcf_various: /builddir/build/BUILD/htslib-1.20/htsfile -c /builddir/build/BUILD/htslib-1.20/test/formatcols.vcf .. ok test_vcf_various: /builddir/build/BUILD/htslib-1.20/htsfile -c /builddir/build/BUILD/htslib-1.20/test/noroundtrip.vcf .. ok test_vcf_various: /builddir/build/BUILD/htslib-1.20/htsfile -c /builddir/build/BUILD/htslib-1.20/test/formatmissing.vcf .. ok test_vcf_various: /builddir/build/BUILD/htslib-1.20/htsfile -c /builddir/build/BUILD/htslib-1.20/test/vcf_meta_meta.vcf .. ok test_vcf_various: /builddir/build/BUILD/htslib-1.20/test/test_view /builddir/build/BUILD/htslib-1.20/test/modhdr.vcf.gz chr22:1-2 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.20/test/test-bcf-sr.pl -t /tmp/smFSq11Epi -s 74452500 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.20/test/test-bcf-sr.pl -t /tmp/smFSq11Epi -s 34270147 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.20/test/test-bcf-sr.pl -t /tmp/smFSq11Epi -s 11108528 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.20/test/test-bcf-sr.pl -t /tmp/smFSq11Epi -s 42233895 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.20/test/test-bcf-sr.pl -t /tmp/smFSq11Epi -s 8111117 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.20/test/test-bcf-sr.pl -t /tmp/smFSq11Epi -s 85644070 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.20/test/test-bcf-sr.pl -t /tmp/smFSq11Epi -s 49879942 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.20/test/test-bcf-sr.pl -t /tmp/smFSq11Epi -s 47881429 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.20/test/test-bcf-sr.pl -t /tmp/smFSq11Epi -s 69081244 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.20/test/test-bcf-sr.pl -t /tmp/smFSq11Epi -s 83459376 .. ok test_bcf_sr_no_index: /builddir/build/BUILD/htslib-1.20/test/test-bcf-sr --no-index -p all --args /builddir/build/BUILD/htslib-1.20/test/bcf-sr/merge.noidx.a.vcf /builddir/build/BUILD/htslib-1.20/test/bcf-sr/merge.noidx.b.vcf /builddir/build/BUILD/htslib-1.20/test/bcf-sr/merge.noidx.c.vcf 2> /tmp/smFSq11Epi/no_index_1.err .. ok test_bcf_sr_no_index: /builddir/build/BUILD/htslib-1.20/test/test-bcf-sr --no-index -p all --args /builddir/build/BUILD/htslib-1.20/test/bcf-sr/merge.noidx.a.vcf /builddir/build/BUILD/htslib-1.20/test/bcf-sr/merge.noidx.hdr_order.vcf > /tmp/smFSq11Epi/no_index_2.out 2> /tmp/smFSq11Epi/no_index_2.err (expected fail) .. ok test_bcf_sr_no_index: /builddir/build/BUILD/htslib-1.20/test/test-bcf-sr --no-index -p all --args /builddir/build/BUILD/htslib-1.20/test/bcf-sr/merge.noidx.a.vcf /builddir/build/BUILD/htslib-1.20/test/bcf-sr/merge.noidx.rec_order.vcf > /tmp/smFSq11Epi/no_index_3.out 2> /tmp/smFSq11Epi/no_index_3.err (expected fail) .. ok test_bcf_sr_no_index: /builddir/build/BUILD/htslib-1.20/test/test-bcf-sr --no-index -p all --args /builddir/build/BUILD/htslib-1.20/test/bcf-sr/merge.noidx.rec_order.vcf /builddir/build/BUILD/htslib-1.20/test/bcf-sr/merge.noidx.a.vcf > /tmp/smFSq11Epi/no_index_4.out 2> /tmp/smFSq11Epi/no_index_4.err (expected fail) .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.20/test/test_view -b -p /tmp/smFSq11Epi/weird-chr-names.vcf.bcf -x /tmp/smFSq11Epi/weird-chr-names.vcf.bcf.csi /builddir/build/BUILD/htslib-1.20/test/bcf-sr/weird-chr-names.vcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.20/test/test-bcf-sr -O vcf -o /tmp/smFSq11Epi/range_test_1.out.vcf -r '1' --args /tmp/smFSq11Epi/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.20/test/test-bcf-sr -O vcf -o /tmp/smFSq11Epi/range_test_2.out.vcf -r '1:1-2' --args /tmp/smFSq11Epi/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.20/test/test-bcf-sr -O vcf -o /tmp/smFSq11Epi/range_test_3.out.vcf -r '1:1,1:2' --args /tmp/smFSq11Epi/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.20/test/test-bcf-sr -O vcf -o /tmp/smFSq11Epi/range_test_4.out.vcf -r '1:1-1' --args /tmp/smFSq11Epi/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.20/test/test-bcf-sr -O vcf -o /tmp/smFSq11Epi/range_test_5.out.vcf -r '{1:1}' --args /tmp/smFSq11Epi/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.20/test/test-bcf-sr -O vcf -o /tmp/smFSq11Epi/range_test_6.out.vcf -r '{1:1}:1-2' --args /tmp/smFSq11Epi/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.20/test/test-bcf-sr -O vcf -o /tmp/smFSq11Epi/range_test_7.out.vcf -r '{1:1}:1,{1:1}:2' --args /tmp/smFSq11Epi/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.20/test/test-bcf-sr -O vcf -o /tmp/smFSq11Epi/range_test_8.out.vcf -r '{1:1}:1-1' --args /tmp/smFSq11Epi/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.20/test/test-bcf-sr -O vcf -o /tmp/smFSq11Epi/range_test_9.out.vcf -r '{1:1-1}' --args /tmp/smFSq11Epi/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.20/test/test-bcf-sr -O vcf -o /tmp/smFSq11Epi/range_test_10.out.vcf -r '{1:1-1}:1-2' --args /tmp/smFSq11Epi/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.20/test/test-bcf-sr -O vcf -o /tmp/smFSq11Epi/range_test_11.out.vcf -r '{1:1-1}:1,{1:1-1}:2' --args /tmp/smFSq11Epi/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.20/test/test-bcf-sr -O vcf -o /tmp/smFSq11Epi/range_test_12.out.vcf -r '{1:1-1}:1-1' --args /tmp/smFSq11Epi/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.20/test/test-bcf-sr -O vcf -o /tmp/smFSq11Epi/range_test_13.out.vcf -r '{1:1-1}-2' --args /tmp/smFSq11Epi/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-1.20/test/test-bcf-sr -O vcf -o /tmp/smFSq11Epi/range_test_14.out.vcf -t '1' --args /tmp/smFSq11Epi/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.20/test/test-bcf-sr -O vcf -o /tmp/smFSq11Epi/range_test_15.out.vcf -t '1:1-2' --args /tmp/smFSq11Epi/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.20/test/test-bcf-sr -O vcf -o /tmp/smFSq11Epi/range_test_16.out.vcf -t '1:1,1:2' --args /tmp/smFSq11Epi/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.20/test/test-bcf-sr -O vcf -o /tmp/smFSq11Epi/range_test_17.out.vcf -t '1:1-1' --args /tmp/smFSq11Epi/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.20/test/test-bcf-sr -O vcf -o /tmp/smFSq11Epi/range_test_18.out.vcf -t '{1:1}' --args /tmp/smFSq11Epi/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.20/test/test-bcf-sr -O vcf -o /tmp/smFSq11Epi/range_test_19.out.vcf -t '{1:1}:1-2' --args /tmp/smFSq11Epi/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.20/test/test-bcf-sr -O vcf -o /tmp/smFSq11Epi/range_test_20.out.vcf -t '{1:1}:1,{1:1}:2' --args /tmp/smFSq11Epi/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.20/test/test-bcf-sr -O vcf -o /tmp/smFSq11Epi/range_test_21.out.vcf -t '{1:1}:1-1' --args /tmp/smFSq11Epi/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.20/test/test-bcf-sr -O vcf -o /tmp/smFSq11Epi/range_test_22.out.vcf -t '{1:1-1}' --args /tmp/smFSq11Epi/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.20/test/test-bcf-sr -O vcf -o /tmp/smFSq11Epi/range_test_23.out.vcf -t '{1:1-1}:1-2' --args /tmp/smFSq11Epi/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.20/test/test-bcf-sr -O vcf -o /tmp/smFSq11Epi/range_test_24.out.vcf -t '{1:1-1}:1,{1:1-1}:2' --args /tmp/smFSq11Epi/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.20/test/test-bcf-sr -O vcf -o /tmp/smFSq11Epi/range_test_25.out.vcf -t '{1:1-1}:1-1' --args /tmp/smFSq11Epi/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.20/test/test-bcf-sr -O vcf -o /tmp/smFSq11Epi/range_test_26.out.vcf -t '{1:1-1}-2' --args /tmp/smFSq11Epi/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 test_command: /builddir/build/BUILD/htslib-1.20/test/test-bcf-translate - .. ok test_convert_padded_header: /builddir/build/BUILD/htslib-1.20/test/test_view -t ce.fa -C /tmp/smFSq11Epi/headernul0.bam .. ok test_convert_padded_header: /builddir/build/BUILD/htslib-1.20/test/test_view -t ce.fa -C /tmp/smFSq11Epi/headernul1.bam .. ok test_convert_padded_header: /builddir/build/BUILD/htslib-1.20/test/test_view -t ce.fa -C /tmp/smFSq11Epi/headernul678.bam .. ok test_rebgzip: /builddir/build/BUILD/htslib-1.20/bgzip -I /builddir/build/BUILD/htslib-1.20/test/bgziptest.txt.gz.gzi -c -g /builddir/build/BUILD/htslib-1.20/test/bgziptest.txt .. ok test-logging: /builddir/build/BUILD/htslib-1.20/test/test-logging.pl .. ok test_plugin_loading: HTS_PATH=/builddir/build/BUILD/htslib-1.20 /builddir/build/BUILD/htslib-1.20/test/with-shlib.sh /builddir/build/BUILD/htslib-1.20/htsfile https://localhost:99999/invalid_port .. ok test_realn: /builddir/build/BUILD/htslib-1.20/test/test_realn -f /builddir/build/BUILD/htslib-1.20/test/realn01.fa -i /builddir/build/BUILD/htslib-1.20/test/realn01.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.20/test/test_realn -f /builddir/build/BUILD/htslib-1.20/test/realn02.fa -i /builddir/build/BUILD/htslib-1.20/test/realn02.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.20/test/test_realn -a -f /builddir/build/BUILD/htslib-1.20/test/realn01.fa -i /builddir/build/BUILD/htslib-1.20/test/realn01.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.20/test/test_realn -a -f /builddir/build/BUILD/htslib-1.20/test/realn02.fa -i /builddir/build/BUILD/htslib-1.20/test/realn02.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.20/test/test_realn -e -f /builddir/build/BUILD/htslib-1.20/test/realn01.fa -i /builddir/build/BUILD/htslib-1.20/test/realn01.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.20/test/test_realn -e -f /builddir/build/BUILD/htslib-1.20/test/realn02.fa -i /builddir/build/BUILD/htslib-1.20/test/realn02.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.20/test/test_realn -r -f /builddir/build/BUILD/htslib-1.20/test/realn02.fa -i /builddir/build/BUILD/htslib-1.20/test/realn02-r.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.20/test/test_realn -a -f /builddir/build/BUILD/htslib-1.20/test/realn02.fa -i /builddir/build/BUILD/htslib-1.20/test/realn02_exp.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.20/test/test_realn -f /builddir/build/BUILD/htslib-1.20/test/realn02.fa -i /builddir/build/BUILD/htslib-1.20/test/realn02_exp-a.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.20/test/test_realn -f /builddir/build/BUILD/htslib-1.20/test/realn03.fa -e -i /builddir/build/BUILD/htslib-1.20/test/realn03.sam -o - .. ok test-bcf_set_variant_type: /builddir/build/BUILD/htslib-1.20/test/test-bcf_set_variant_type .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.20/annot-tsv -f smpl:overlap --allow-dups -s /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.1.txt -t /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.1.txt | /builddir/build/BUILD/htslib-1.20/annot-tsv -f smpl:overlap --allow-dups -s /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.1.txt | /builddir/build/BUILD/htslib-1.20/annot-tsv -f smpl:overlap --allow-dups -t /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.20/annot-tsv -f smpl:overlap -s /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.1.txt -t /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.1.txt | /builddir/build/BUILD/htslib-1.20/annot-tsv -f smpl:overlap -s /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.1.txt | /builddir/build/BUILD/htslib-1.20/annot-tsv -f smpl:overlap -t /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.20/annot-tsv -f smpl:overlap -c chr,beg,end -s /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.1.txt -t /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.1.txt | /builddir/build/BUILD/htslib-1.20/annot-tsv -f smpl:overlap -c chr,beg,end -s /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.1.txt | /builddir/build/BUILD/htslib-1.20/annot-tsv -f smpl:overlap -c chr,beg,end -t /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.20/annot-tsv -f smpl,value:overlap,value -s /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.1.txt -t /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.1.txt | /builddir/build/BUILD/htslib-1.20/annot-tsv -f smpl,value:overlap,value -s /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.1.txt | /builddir/build/BUILD/htslib-1.20/annot-tsv -f smpl,value:overlap,value -t /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.20/annot-tsv -f smpl:overlap -O 0.5 -s /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.1.txt -t /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.1.txt | /builddir/build/BUILD/htslib-1.20/annot-tsv -f smpl:overlap -O 0.5 -s /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.1.txt | /builddir/build/BUILD/htslib-1.20/annot-tsv -f smpl:overlap -O 0.5 -t /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.20/annot-tsv -f smpl:overlap -rO 0.5 -s /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.1.txt -t /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.1.txt | /builddir/build/BUILD/htslib-1.20/annot-tsv -f smpl:overlap -rO 0.5 -s /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.1.txt | /builddir/build/BUILD/htslib-1.20/annot-tsv -f smpl:overlap -rO 0.5 -t /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.20/annot-tsv -f smpl:overlap --allow-dups --max-annots 2 -s /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.1.txt -t /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.1.txt | /builddir/build/BUILD/htslib-1.20/annot-tsv -f smpl:overlap --allow-dups --max-annots 2 -s /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.1.txt | /builddir/build/BUILD/htslib-1.20/annot-tsv -f smpl:overlap --allow-dups --max-annots 2 -t /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.20/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups -s /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.2.txt -t /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.2.txt | /builddir/build/BUILD/htslib-1.20/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups -s /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.2.txt | /builddir/build/BUILD/htslib-1.20/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups -t /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.20/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -s /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.2.txt -t /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.2.txt | /builddir/build/BUILD/htslib-1.20/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -s /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.2.txt | /builddir/build/BUILD/htslib-1.20/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -t /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.20/annot-tsv -c 1,2,3:1,2,3 -f 4,value:5,value -s /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.2.txt -t /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.2.txt | /builddir/build/BUILD/htslib-1.20/annot-tsv -c 1,2,3:1,2,3 -f 4,value:5,value -s /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.2.txt | /builddir/build/BUILD/htslib-1.20/annot-tsv -c 1,2,3:1,2,3 -f 4,value:5,value -t /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.20/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -s /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.2.txt -t /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.2.txt | /builddir/build/BUILD/htslib-1.20/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -s /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.2.txt | /builddir/build/BUILD/htslib-1.20/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -t /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.20/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -a nbp,frac -s /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.2.txt -t /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.2.txt | /builddir/build/BUILD/htslib-1.20/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -a nbp,frac -s /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.2.txt | /builddir/build/BUILD/htslib-1.20/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -a nbp,frac -t /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.20/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups --max-annots 2 -s /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.2.txt -t /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.2.txt | /builddir/build/BUILD/htslib-1.20/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups --max-annots 2 -s /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.2.txt | /builddir/build/BUILD/htslib-1.20/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups --max-annots 2 -t /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.20/annot-tsv -f smpl:overlap -a nbp,frac -s /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.3.txt -t /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.3.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.3.txt | /builddir/build/BUILD/htslib-1.20/annot-tsv -f smpl:overlap -a nbp,frac -s /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.3.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.3.txt | /builddir/build/BUILD/htslib-1.20/annot-tsv -f smpl:overlap -a nbp,frac -t /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.3.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.20/annot-tsv -c 2,3,4:2,3,4 -m 1:1 -f 1:1 -a nbp,frac -s /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.4.txt -t /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.4.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.4.txt | /builddir/build/BUILD/htslib-1.20/annot-tsv -c 2,3,4:2,3,4 -m 1:1 -f 1:1 -a nbp,frac -s /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.4.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.4.txt | /builddir/build/BUILD/htslib-1.20/annot-tsv -c 2,3,4:2,3,4 -m 1:1 -f 1:1 -a nbp,frac -t /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.4.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.20/annot-tsv -c 2,3,4:2,3,4 -a nbp,frac -s /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.5.txt -t /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.5.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.5.txt | /builddir/build/BUILD/htslib-1.20/annot-tsv -c 2,3,4:2,3,4 -a nbp,frac -s /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.5.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.5.txt | /builddir/build/BUILD/htslib-1.20/annot-tsv -c 2,3,4:2,3,4 -a nbp,frac -t /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.5.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.20/annot-tsv -c 1,2,2:1,2,2 -a nbp -s /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.6.txt -t /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.6.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.6.txt | /builddir/build/BUILD/htslib-1.20/annot-tsv -c 1,2,2:1,2,2 -a nbp -s /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.6.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.6.txt | /builddir/build/BUILD/htslib-1.20/annot-tsv -c 1,2,2:1,2,2 -a nbp -t /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.6.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.20/annot-tsv -c 1,2,2:1,2,2 -f overlap -H -s /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.7.txt -t /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.7.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.7.txt | /builddir/build/BUILD/htslib-1.20/annot-tsv -c 1,2,2:1,2,2 -f overlap -H -s /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.7.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.7.txt | /builddir/build/BUILD/htslib-1.20/annot-tsv -c 1,2,2:1,2,2 -f overlap -H -t /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.7.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.20/annot-tsv -c chr,beg,end:chr,start,end -m sample -f is_tp -s /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.8.txt -t /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.8.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.8.txt | /builddir/build/BUILD/htslib-1.20/annot-tsv -c chr,beg,end:chr,start,end -m sample -f is_tp -s /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.8.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.8.txt | /builddir/build/BUILD/htslib-1.20/annot-tsv -c chr,beg,end:chr,start,end -m sample -f is_tp -t /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.8.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.20/annot-tsv -c 1,2,3:chr,beg,end -a nbp,frac,cnt -s /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.9.txt -t /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.9.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.9.txt | /builddir/build/BUILD/htslib-1.20/annot-tsv -c 1,2,3:chr,beg,end -a nbp,frac,cnt -s /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.9.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.9.txt | /builddir/build/BUILD/htslib-1.20/annot-tsv -c 1,2,3:chr,beg,end -a nbp,frac,cnt -t /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.9.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.20/annot-tsv -f smpl -s /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.10.txt -t /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.10.txt | /builddir/build/BUILD/htslib-1.20/annot-tsv -f smpl -s /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.10.txt | /builddir/build/BUILD/htslib-1.20/annot-tsv -f smpl -t /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.20/annot-tsv -s /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.10.txt -t /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.10.txt | /builddir/build/BUILD/htslib-1.20/annot-tsv -s /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.10.txt | /builddir/build/BUILD/htslib-1.20/annot-tsv -t /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.20/annot-tsv -x -s /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.10.txt -t /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.10.txt | /builddir/build/BUILD/htslib-1.20/annot-tsv -x -s /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.10.txt | /builddir/build/BUILD/htslib-1.20/annot-tsv -x -t /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.20/annot-tsv -m smpl -f smpl -s /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.10.txt -t /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.10.txt | /builddir/build/BUILD/htslib-1.20/annot-tsv -m smpl -f smpl -s /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.10.txt | /builddir/build/BUILD/htslib-1.20/annot-tsv -m smpl -f smpl -t /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.20/annot-tsv -m smpl -s /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.10.txt -t /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.10.txt | /builddir/build/BUILD/htslib-1.20/annot-tsv -m smpl -s /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.10.txt | /builddir/build/BUILD/htslib-1.20/annot-tsv -m smpl -t /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.20/annot-tsv -m smpl -x -s /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.10.txt -t /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.10.txt | /builddir/build/BUILD/htslib-1.20/annot-tsv -m smpl -x -s /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.20/test/annot-tsv/src.10.txt | /builddir/build/BUILD/htslib-1.20/annot-tsv -m smpl -x -t /builddir/build/BUILD/htslib-1.20/test/annot-tsv/dst.10.txt .. ok Number of tests: total .. 293 passed .. 293 failed .. 0 + RPM_EC=0 ++ jobs -p + exit 0 Processing files: htslib-1.20-1.el9.x86_64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.RPiikM + umask 022 + cd /builddir/build/BUILD + cd htslib-1.20 + DOCDIR=/builddir/build/BUILDROOT/htslib-1.20-1.el9.x86_64/usr/share/doc/htslib + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/htslib-1.20-1.el9.x86_64/usr/share/doc/htslib + cp -pr NEWS /builddir/build/BUILDROOT/htslib-1.20-1.el9.x86_64/usr/share/doc/htslib + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.XccInt + umask 022 + cd /builddir/build/BUILD + cd htslib-1.20 + LICENSEDIR=/builddir/build/BUILDROOT/htslib-1.20-1.el9.x86_64/usr/share/licenses/htslib + export LC_ALL=C + LC_ALL=C + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/htslib-1.20-1.el9.x86_64/usr/share/licenses/htslib + cp -pr LICENSE /builddir/build/BUILDROOT/htslib-1.20-1.el9.x86_64/usr/share/licenses/htslib + RPM_EC=0 ++ jobs -p + exit 0 Provides: htslib = 1.20-1.el9 htslib(x86-64) = 1.20-1.el9 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_1.3)(64bit) libhts.so.3(HTSLIB_1.4)(64bit) libhts.so.3(HTSLIB_1.5)(64bit) libhts.so.3(HTSLIB_1.6)(64bit) libhts.so.3(HTSLIB_1.7)(64bit) libhts.so.3(HTSLIB_1.9)(64bit) Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: libbz2.so.1()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.2)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.7)(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_2.2.5)(64bit) libm.so.6(GLIBC_2.23)(64bit) libm.so.6(GLIBC_2.29)(64bit) libz.so.1()(64bit) rtld(GNU_HASH) Processing files: htslib-devel-1.20-1.el9.x86_64 Provides: htslib-devel = 1.20-1.el9 htslib-devel(x86-64) = 1.20-1.el9 pkgconfig(htslib) = 1.20 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-1.20-1.el9.x86_64 Provides: htslib-tools = 1.20-1.el9 htslib-tools(x86-64) = 1.20-1.el9 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: libbz2.so.1()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.2)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.7)(64bit) liblzma.so.5()(64bit) liblzma.so.5(XZ_5.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.29)(64bit) libz.so.1()(64bit) rtld(GNU_HASH) Processing files: htslib-debugsource-1.20-1.el9.x86_64 Provides: htslib-debugsource = 1.20-1.el9 htslib-debugsource(x86-64) = 1.20-1.el9 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: htslib-debuginfo-1.20-1.el9.x86_64 Provides: debuginfo(build-id) = 1e248c0bb186d0385d087b1f7f3a0b71afaa7c64 debuginfo(build-id) = 1ef6d24887e897a90e16e8278cdb1c242d819908 debuginfo(build-id) = 94135256a665b7d8560e726fc1096d5585f5dbd0 debuginfo(build-id) = ae534ccd846fdf4ef76c110eb0f5a1106161acc2 debuginfo(build-id) = e2bd8afa119870e537081e0f36207648f6092116 htslib-debuginfo = 1.20-1.el9 htslib-debuginfo(x86-64) = 1.20-1.el9 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: htslib-debugsource(x86-64) = 1.20-1.el9 Processing files: htslib-tools-debuginfo-1.20-1.el9.x86_64 Provides: debuginfo(build-id) = 1e91200b8f558f536caca3d5bc55601c72fb34ba debuginfo(build-id) = 61dde071c57571f51c92e3ae0d316756f37704ed debuginfo(build-id) = da3bd6d2ad1a007bd95a83c4fd5f9a85ba70cdd6 debuginfo(build-id) = fd591c972364d393ba7df37f2943aa363f1163b7 htslib-tools-debuginfo = 1.20-1.el9 htslib-tools-debuginfo(x86-64) = 1.20-1.el9 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: htslib-debugsource(x86-64) = 1.20-1.el9 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/htslib-1.20-1.el9.x86_64 Wrote: /builddir/build/RPMS/htslib-debuginfo-1.20-1.el9.x86_64.rpm Wrote: /builddir/build/RPMS/htslib-debugsource-1.20-1.el9.x86_64.rpm Wrote: /builddir/build/RPMS/htslib-tools-1.20-1.el9.x86_64.rpm Wrote: /builddir/build/RPMS/htslib-devel-1.20-1.el9.x86_64.rpm Wrote: /builddir/build/RPMS/htslib-1.20-1.el9.x86_64.rpm Wrote: /builddir/build/RPMS/htslib-tools-debuginfo-1.20-1.el9.x86_64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.5zXg4M + umask 022 + cd /builddir/build/BUILD + cd htslib-1.20 + /usr/bin/rm -rf /builddir/build/BUILDROOT/htslib-1.20-1.el9.x86_64 + RPM_EC=0 ++ jobs -p + exit 0 Finish: rpmbuild htslib-1.20-1.el9.src.rpm Finish: build phase for htslib-1.20-1.el9.src.rpm INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/rhel+epel-9-x86_64-1717413251.506071/root/var/log/dnf.rpm.log /var/lib/mock/rhel+epel-9-x86_64-1717413251.506071/root/var/log/dnf.librepo.log /var/lib/mock/rhel+epel-9-x86_64-1717413251.506071/root/var/log/dnf.log INFO: Done(/var/lib/copr-rpmbuild/results/htslib-1.20-1.el9.src.rpm) Config(child) 3 minutes 41 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", "epoch": null, "version": "1.20", "release": "1.el9", "arch": "src" }, { "name": "htslib-tools", "epoch": null, "version": "1.20", "release": "1.el9", "arch": "x86_64" }, { "name": "htslib-debuginfo", "epoch": null, "version": "1.20", "release": "1.el9", "arch": "x86_64" }, { "name": "htslib-devel", "epoch": null, "version": "1.20", "release": "1.el9", "arch": "x86_64" }, { "name": "htslib-tools-debuginfo", "epoch": null, "version": "1.20", "release": "1.el9", "arch": "x86_64" }, { "name": "htslib-debugsource", "epoch": null, "version": "1.20", "release": "1.el9", "arch": "x86_64" }, { "name": "htslib", "epoch": null, "version": "1.20", "release": "1.el9", "arch": "x86_64" } ] } RPMResults finished