Warning: Permanently added '2620:52:3:1:dead:beef:cafe:c153' (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/6868870-amazonlinux-2023-x86_64 --chroot amazonlinux-2023-x86_64 Version: 0.70 PID: 84747 Logging PID: 84748 Task: {'appstream': False, 'background': False, 'build_id': 6868870, 'buildroot_pkgs': [], 'chroot': 'amazonlinux-2023-x86_64', 'enable_net': False, 'fedora_review': False, 'git_hash': '2d28de63a19d1aff56222c30e0f57c3bc94da81a', 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/trawets/random-al2023-pkg-builds/htslib', 'isolation': 'default', 'memory_reqs': 2048, 'package_name': 'htslib', 'package_version': '1.15.1-3', 'project_dirname': 'random-al2023-pkg-builds', 'project_name': 'random-al2023-pkg-builds', 'project_owner': 'trawets', 'repo_priority': None, 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/trawets/random-al2023-pkg-builds/amazonlinux-2023-x86_64/', 'id': 'copr_base', 'name': 'Copr repository', 'priority': None}], 'sandbox': 'trawets/random-al2023-pkg-builds--trawets', 'source_json': {}, 'source_type': None, 'submitter': 'trawets', 'tags': [], 'task_id': '6868870-amazonlinux-2023-x86_64', 'timeout': 18000, 'uses_devel_repo': False, 'with_opts': [], 'without_opts': []} Running: git clone https://copr-dist-git.fedorainfracloud.org/git/trawets/random-al2023-pkg-builds/htslib /var/lib/copr-rpmbuild/workspace/workdir-mccg0cke/htslib --depth 500 --no-single-branch --recursive cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/trawets/random-al2023-pkg-builds/htslib', '/var/lib/copr-rpmbuild/workspace/workdir-mccg0cke/htslib', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-mccg0cke/htslib'... Running: git checkout 2d28de63a19d1aff56222c30e0f57c3bc94da81a -- cmd: ['git', 'checkout', '2d28de63a19d1aff56222c30e0f57c3bc94da81a', '--'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-mccg0cke/htslib rc: 0 stdout: stderr: Note: switching to '2d28de63a19d1aff56222c30e0f57c3bc94da81a'. 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 2d28de6 automatic import of htslib Running: copr-distgit-client sources cmd: ['copr-distgit-client', 'sources'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-mccg0cke/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-1.15.1.tar.bz2 INFO: Reading stdout from command: curl --help all INFO: Calling: curl -H Pragma: -o htslib-1.15.1.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/trawets/random-al2023-pkg-builds/htslib/htslib-1.15.1.tar.bz2/md5/9ea5cff8edcebb01f31dd02bd4d2a082/htslib-1.15.1.tar.bz2 % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 4044k 100 4044k 0 0 12.7M 0 --:--:-- --:--:-- --:--:-- 12.8M INFO: Reading stdout from command: md5sum htslib-1.15.1.tar.bz2 /usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-mccg0cke/htslib/htslib.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-mccg0cke/htslib --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1704591055.887282 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 5.4 starting (python version = 3.11.3, NVR = mock-5.4-1.fc38), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-mccg0cke/htslib/htslib.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-mccg0cke/htslib --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1704591055.887282 -r /var/lib/copr-rpmbuild/results/configs/child.cfg Start(bootstrap): init plugins INFO: tmpfs initialized INFO: selinux enabled INFO: chroot_scan: initialized INFO: compress_logs: initialized Finish(bootstrap): init plugins Start: init plugins INFO: tmpfs initialized INFO: selinux enabled INFO: chroot_scan: initialized INFO: compress_logs: initialized Finish: init plugins INFO: Signal handler active Start: run INFO: Start(/var/lib/copr-rpmbuild/workspace/workdir-mccg0cke/htslib/htslib.spec) Config(amazonlinux-2023-x86_64) Start: clean chroot Finish: clean chroot Mock Version: 5.4 INFO: Mock Version: 5.4 Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/amazonlinux-2023-x86_64-bootstrap-1704591055.887282/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata INFO: Guessed host environment type: unknown INFO: Using bootstrap image: public.ecr.aws/amazonlinux/amazonlinux:2023 INFO: Pulling image: public.ecr.aws/amazonlinux/amazonlinux:2023 INFO: Copy content of container public.ecr.aws/amazonlinux/amazonlinux:2023 to /var/lib/mock/amazonlinux-2023-x86_64-bootstrap-1704591055.887282/root INFO: Checking that public.ecr.aws/amazonlinux/amazonlinux:2023 image matches host's architecture INFO: mounting public.ecr.aws/amazonlinux/amazonlinux:2023 with podman image mount INFO: image public.ecr.aws/amazonlinux/amazonlinux:2023 as /var/lib/containers/storage/overlay/feb47202015b991620a1d091d4c0e3cf93925009c823acb869c0ac54078b50fd/merged INFO: umounting image public.ecr.aws/amazonlinux/amazonlinux:2023 (/var/lib/containers/storage/overlay/feb47202015b991620a1d091d4c0e3cf93925009c823acb869c0ac54078b50fd/merged) with podman image umount INFO: Package manager dnf detected and used (fallback) INFO: Bootstrap image not marked ready Start(bootstrap): installing dnf tooling No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 228 kB/s | 151 kB 00:00 Amazon Linux 2023 repository - x86_64 14 MB/s | 22 MB 00:01 Package python3-dnf-4.12.0-2.amzn2023.0.4.noarch is already installed. Dependencies resolved. ================================================================================ Package Arch Version Repository Size ================================================================================ Installing: python3-dnf-plugins-core noarch 4.1.0-1.amzn2023.0.3 amazonlinux 219 k Installing dependencies: dbus-libs x86_64 1:1.12.28-1.amzn2023.0.1 amazonlinux 153 k python3-dateutil noarch 1:2.8.1-3.amzn2023.0.2 amazonlinux 289 k python3-dbus x86_64 1.2.18-1.amzn2023.0.2 amazonlinux 134 k python3-distro noarch 1.5.0-5.amzn2023.0.2 amazonlinux 36 k python3-setuptools noarch 59.6.0-2.amzn2023.0.4 amazonlinux 940 k python3-six noarch 1.15.0-5.amzn2023.0.2 amazonlinux 36 k systemd-libs x86_64 252.16-1.amzn2023.0.1 amazonlinux 627 k Transaction Summary ================================================================================ Install 8 Packages Total download size: 2.4 M Installed size: 11 M Downloading Packages: (1/8): dbus-libs-1.12.28-1.amzn2023.0.1.x86_64. 2.3 MB/s | 153 kB 00:00 (2/8): python3-dbus-1.2.18-1.amzn2023.0.2.x86_6 1.8 MB/s | 134 kB 00:00 (3/8): python3-six-1.15.0-5.amzn2023.0.2.noarch 2.8 MB/s | 36 kB 00:00 (4/8): systemd-libs-252.16-1.amzn2023.0.1.x86_6 6.4 MB/s | 627 kB 00:00 (5/8): python3-dateutil-2.8.1-3.amzn2023.0.2.no 12 MB/s | 289 kB 00:00 (6/8): python3-setuptools-59.6.0-2.amzn2023.0.4 22 MB/s | 940 kB 00:00 (7/8): python3-distro-1.5.0-5.amzn2023.0.2.noar 1.5 MB/s | 36 kB 00:00 (8/8): python3-dnf-plugins-core-4.1.0-1.amzn202 9.1 MB/s | 219 kB 00:00 -------------------------------------------------------------------------------- Total 5.4 MB/s | 2.4 MB 00:00 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Installing : python3-setuptools-59.6.0-2.amzn2023.0.4.noarch 1/8 Installing : python3-distro-1.5.0-5.amzn2023.0.2.noarch 2/8 Installing : python3-six-1.15.0-5.amzn2023.0.2.noarch 3/8 Installing : python3-dateutil-1:2.8.1-3.amzn2023.0.2.noarch 4/8 Installing : systemd-libs-252.16-1.amzn2023.0.1.x86_64 5/8 Installing : dbus-libs-1:1.12.28-1.amzn2023.0.1.x86_64 6/8 Installing : python3-dbus-1.2.18-1.amzn2023.0.2.x86_64 7/8 Installing : python3-dnf-plugins-core-4.1.0-1.amzn2023.0.3.noarch 8/8 Running scriptlet: python3-dnf-plugins-core-4.1.0-1.amzn2023.0.3.noarch 8/8 Verifying : python3-dbus-1.2.18-1.amzn2023.0.2.x86_64 1/8 Verifying : dbus-libs-1:1.12.28-1.amzn2023.0.1.x86_64 2/8 Verifying : systemd-libs-252.16-1.amzn2023.0.1.x86_64 3/8 Verifying : python3-six-1.15.0-5.amzn2023.0.2.noarch 4/8 Verifying : python3-dateutil-1:2.8.1-3.amzn2023.0.2.noarch 5/8 Verifying : python3-setuptools-59.6.0-2.amzn2023.0.4.noarch 6/8 Verifying : python3-distro-1.5.0-5.amzn2023.0.2.noarch 7/8 Verifying : python3-dnf-plugins-core-4.1.0-1.amzn2023.0.3.noarch 8/8 Installed: dbus-libs-1:1.12.28-1.amzn2023.0.1.x86_64 python3-dateutil-1:2.8.1-3.amzn2023.0.2.noarch python3-dbus-1.2.18-1.amzn2023.0.2.x86_64 python3-distro-1.5.0-5.amzn2023.0.2.noarch python3-dnf-plugins-core-4.1.0-1.amzn2023.0.3.noarch python3-setuptools-59.6.0-2.amzn2023.0.4.noarch python3-six-1.15.0-5.amzn2023.0.2.noarch systemd-libs-252.16-1.amzn2023.0.1.x86_64 Complete! Finish(bootstrap): installing dnf tooling Start(bootstrap): creating root cache Finish(bootstrap): creating root cache Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/amazonlinux-2023-x86_64-1704591055.887282/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 (direct choice) INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-4.16.1.3-12.amzn2023.0.6.x86_64 python3-dnf-4.12.0-2.amzn2023.0.4.noarch python3-dnf-plugins-core-4.1.0-1.amzn2023.0.3.noarch yum-4.12.0-2.amzn2023.0.4.noarch Start: installing minimal buildroot with dnf No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 23 kB/s | 1.5 kB 00:00 Copr repository 1.1 MB/s | 151 kB 00:00 Amazon Linux 2023 repository - x86_64 9.7 kB/s | 3.6 kB 00:00 Dependencies resolved. ============================================================================================ Package Arch Version Repository Size ============================================================================================ Installing: amazon-rpm-config noarch 228-3.amzn2023.0.2 amazonlinux 74 k bash x86_64 5.2.15-1.amzn2023.0.2 amazonlinux 1.8 M bzip2 x86_64 1.0.8-6.amzn2023.0.2 amazonlinux 53 k coreutils x86_64 8.32-30.amzn2023.0.3 amazonlinux 1.1 M cpio x86_64 2.13-13.amzn2023.0.2 amazonlinux 272 k diffutils x86_64 3.8-1.amzn2023.0.2 amazonlinux 370 k findutils x86_64 1:4.8.0-2.amzn2023.0.2 amazonlinux 539 k gawk x86_64 5.1.0-3.amzn2023.0.3 amazonlinux 1.0 M glibc-minimal-langpack x86_64 2.34-52.amzn2023.0.7 amazonlinux 33 k grep x86_64 3.8-1.amzn2023.0.4 amazonlinux 283 k gzip x86_64 1.12-1.amzn2023.0.1 amazonlinux 160 k info x86_64 6.7-10.amzn2023.0.2 amazonlinux 227 k patch x86_64 2.7.6-14.amzn2023.0.2 amazonlinux 129 k rpm-build x86_64 4.16.1.3-12.amzn2023.0.6 amazonlinux 92 k sed x86_64 4.8-7.amzn2023.0.2 amazonlinux 297 k system-release noarch 2023.3.20231218-0.amzn2023 amazonlinux 27 k tar x86_64 2:1.34-1.amzn2023.0.3 amazonlinux 879 k unzip x86_64 6.0-57.amzn2023.0.2 amazonlinux 182 k util-linux x86_64 2.37.4-1.amzn2023.0.3 amazonlinux 2.2 M which x86_64 2.21-26.amzn2023.0.2 amazonlinux 42 k xz x86_64 5.2.5-9.amzn2023.0.2 amazonlinux 215 k Installing dependencies: alternatives x86_64 1.15-2.amzn2023.0.2 amazonlinux 36 k amazon-linux-repo-cdn noarch 2023.3.20231218-0.amzn2023 amazonlinux 16 k audit-libs x86_64 3.0.6-1.amzn2023.0.2 amazonlinux 116 k basesystem noarch 11-11.amzn2023.0.2 amazonlinux 7.8 k binutils x86_64 2.39-6.amzn2023.0.10 amazonlinux 4.4 M bzip2-libs x86_64 1.0.8-6.amzn2023.0.2 amazonlinux 43 k ca-certificates noarch 2023.2.62-1.0.amzn2023.0.1 amazonlinux 739 k coreutils-common x86_64 8.32-30.amzn2023.0.3 amazonlinux 2.0 M cracklib x86_64 2.9.6-27.amzn2023.0.2 amazonlinux 82 k crypto-policies noarch 20220428-1.gitdfb10ea.amzn2023.0.2 amazonlinux 60 k curl x86_64 8.3.0-1.amzn2023.0.2 amazonlinux 355 k cyrus-sasl-lib x86_64 2.1.27-18.amzn2023.0.3 amazonlinux 786 k dwz x86_64 0.14-6.amzn2023.0.2 amazonlinux 129 k ed x86_64 1.14.2-10.amzn2023.0.2 amazonlinux 75 k efi-srpm-macros noarch 5-4.amzn2023.0.5 amazonlinux 23 k elfutils x86_64 0.188-3.amzn2023.0.2 amazonlinux 525 k elfutils-debuginfod-client x86_64 0.188-3.amzn2023.0.2 amazonlinux 41 k elfutils-default-yama-scope noarch 0.188-3.amzn2023.0.2 amazonlinux 17 k elfutils-libelf x86_64 0.188-3.amzn2023.0.2 amazonlinux 199 k elfutils-libs x86_64 0.188-3.amzn2023.0.2 amazonlinux 258 k file x86_64 5.39-7.amzn2023.0.4 amazonlinux 49 k file-libs x86_64 5.39-7.amzn2023.0.4 amazonlinux 588 k filesystem x86_64 3.14-5.amzn2023.0.3 amazonlinux 22 k fonts-srpm-macros noarch 1:2.0.5-12.amzn2023.0.2 amazonlinux 27 k gdb-minimal x86_64 12.1-5.amzn2023.0.3 amazonlinux 4.0 M gdbm-libs x86_64 1:1.19-2.amzn2023.0.2 amazonlinux 53 k ghc-srpm-macros noarch 1.5.0-4.amzn2023.0.2 amazonlinux 8.5 k glibc x86_64 2.34-52.amzn2023.0.7 amazonlinux 1.9 M glibc-common x86_64 2.34-52.amzn2023.0.7 amazonlinux 304 k glibc-gconv-extra x86_64 2.34-52.amzn2023.0.7 amazonlinux 1.5 M gmp x86_64 1:6.2.1-2.amzn2023.0.2 amazonlinux 324 k go-srpm-macros noarch 3.3.1-1.amzn2023 copr_base 28 k jansson x86_64 2.14-0.amzn2023 amazonlinux 46 k kernel-srpm-macros noarch 1.0-14.amzn2023.0.2 amazonlinux 10 k keyutils-libs x86_64 1.6.3-1.amzn2023 amazonlinux 33 k krb5-libs x86_64 1.21-3.amzn2023.0.3 amazonlinux 760 k libacl x86_64 2.3.1-2.amzn2023.0.2 amazonlinux 24 k libarchive x86_64 3.5.3-2.amzn2023.0.3 amazonlinux 398 k libattr x86_64 2.5.1-3.amzn2023.0.2 amazonlinux 19 k libblkid x86_64 2.37.4-1.amzn2023.0.3 amazonlinux 107 k libbrotli x86_64 1.0.9-4.amzn2023.0.2 amazonlinux 315 k libcap x86_64 2.48-2.amzn2023.0.3 amazonlinux 67 k libcap-ng x86_64 0.8.2-4.amzn2023.0.2 amazonlinux 33 k libcom_err x86_64 1.46.5-2.amzn2023.0.2 amazonlinux 27 k libcurl x86_64 8.3.0-1.amzn2023.0.2 amazonlinux 344 k libdb x86_64 5.3.28-49.amzn2023.0.2 amazonlinux 756 k libeconf x86_64 0.4.0-1.amzn2023.0.3 amazonlinux 28 k libfdisk x86_64 2.37.4-1.amzn2023.0.3 amazonlinux 154 k libffi x86_64 3.4.4-1.amzn2023.0.1 amazonlinux 39 k libgcc x86_64 11.4.1-2.amzn2023.0.2 amazonlinux 93 k libgomp x86_64 11.4.1-2.amzn2023.0.2 amazonlinux 268 k libidn2 x86_64 2.3.2-1.amzn2023.0.5 amazonlinux 104 k libmount x86_64 2.37.4-1.amzn2023.0.3 amazonlinux 133 k libnghttp2 x86_64 1.57.0-1.amzn2023.0.1 amazonlinux 78 k libpkgconf x86_64 1.8.0-4.amzn2023.0.2 amazonlinux 37 k libpsl x86_64 0.21.1-3.amzn2023.0.2 amazonlinux 61 k libpwquality x86_64 1.4.4-6.amzn2023.0.2 amazonlinux 106 k libselinux x86_64 3.4-5.amzn2023.0.2 amazonlinux 87 k libsemanage x86_64 3.4-5.amzn2023.0.2 amazonlinux 121 k libsepol x86_64 3.4-3.amzn2023.0.3 amazonlinux 320 k libsigsegv x86_64 2.13-2.amzn2023.0.2 amazonlinux 27 k libsmartcols x86_64 2.37.4-1.amzn2023.0.3 amazonlinux 63 k libssh x86_64 0.10.5-1.amzn2023.0.2 amazonlinux 215 k libssh-config noarch 0.10.5-1.amzn2023.0.2 amazonlinux 11 k libstdc++ x86_64 11.4.1-2.amzn2023.0.2 amazonlinux 731 k libtasn1 x86_64 4.19.0-1.amzn2023.0.4 amazonlinux 75 k libunistring x86_64 0.9.10-10.amzn2023.0.2 amazonlinux 499 k libutempter x86_64 1.2.1-4.amzn2023.0.2 amazonlinux 26 k libuuid x86_64 2.37.4-1.amzn2023.0.3 amazonlinux 27 k libverto x86_64 0.3.2-1.amzn2023.0.2 amazonlinux 22 k libxcrypt x86_64 4.4.33-7.amzn2023 amazonlinux 121 k libxml2 x86_64 2.10.4-1.amzn2023.0.6 amazonlinux 706 k libzstd x86_64 1.5.5-1.amzn2023.0.1 amazonlinux 309 k lua-libs x86_64 5.4.4-3.amzn2023.0.2 amazonlinux 217 k lua-srpm-macros noarch 1-4.amzn2023.0.2 amazonlinux 9.2 k lz4-libs x86_64 1.9.4-1.amzn2023.0.2 amazonlinux 81 k mpfr x86_64 4.1.0-7.amzn2023.0.2 amazonlinux 330 k ncurses-base noarch 6.2-4.20200222.amzn2023.0.4 amazonlinux 60 k ncurses-libs x86_64 6.2-4.20200222.amzn2023.0.4 amazonlinux 328 k ocaml-srpm-macros noarch 6-6.amzn2023.0.2 amazonlinux 8.8 k openblas-srpm-macros noarch 2-9.amzn2023.0.2 amazonlinux 8.2 k openldap x86_64 2.4.57-6.amzn2023.0.6 amazonlinux 257 k openssl-libs x86_64 1:3.0.8-1.amzn2023.0.10 amazonlinux 2.2 M p11-kit x86_64 0.24.1-2.amzn2023.0.3 amazonlinux 357 k p11-kit-trust x86_64 0.24.1-2.amzn2023.0.3 amazonlinux 138 k package-notes-srpm-macros noarch 0.4-18.amzn2023.0.5 amazonlinux 13 k pam x86_64 1.5.1-8.amzn2023.0.3 amazonlinux 543 k pcre2 x86_64 10.40-1.amzn2023.0.3 amazonlinux 236 k pcre2-syntax noarch 10.40-1.amzn2023.0.3 amazonlinux 142 k perl-srpm-macros noarch 1-39.amzn2023.0.2 amazonlinux 8.7 k pkgconf x86_64 1.8.0-4.amzn2023.0.2 amazonlinux 43 k pkgconf-m4 noarch 1.8.0-4.amzn2023.0.2 amazonlinux 15 k pkgconf-pkg-config x86_64 1.8.0-4.amzn2023.0.2 amazonlinux 11 k popt x86_64 1.18-6.amzn2023.0.2 amazonlinux 60 k publicsuffix-list-dafsa noarch 20221208-60.amzn2023 amazonlinux 61 k python-srpm-macros noarch 3.9-41.amzn2023.0.5 amazonlinux 22 k readline x86_64 8.1-2.amzn2023.0.2 amazonlinux 212 k rpm x86_64 4.16.1.3-12.amzn2023.0.6 amazonlinux 486 k rpm-build-libs x86_64 4.16.1.3-12.amzn2023.0.6 amazonlinux 90 k rpm-libs x86_64 4.16.1.3-12.amzn2023.0.6 amazonlinux 309 k rust-srpm-macros noarch 21-42.amzn2023.0.2 amazonlinux 10 k setup noarch 2.13.7-3.amzn2023.0.2 amazonlinux 141 k shadow-utils x86_64 2:4.9-12.amzn2023.0.4 amazonlinux 1.1 M sqlite-libs x86_64 3.40.0-1.amzn2023.0.3 amazonlinux 663 k systemd-libs x86_64 252.16-1.amzn2023.0.1 amazonlinux 627 k util-linux-core x86_64 2.37.4-1.amzn2023.0.3 amazonlinux 433 k xxhash-libs x86_64 0.8.0-3.amzn2023.0.2 amazonlinux 40 k xz-libs x86_64 5.2.5-9.amzn2023.0.2 amazonlinux 93 k zip x86_64 3.0-28.amzn2023.0.2 amazonlinux 257 k zlib x86_64 1.2.11-33.amzn2023.0.5 amazonlinux 93 k zstd x86_64 1.5.5-1.amzn2023.0.1 amazonlinux 478 k Transaction Summary ============================================================================================ Install 132 Packages Total size: 46 M Total download size: 28 k Installed size: 165 M Downloading Packages: [SKIPPED] bash-5.2.15-1.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] pam-1.5.1-8.amzn2023.0.3.x86_64.rpm: Already downloaded [SKIPPED] libselinux-3.4-5.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] diffutils-3.8-1.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] libcurl-8.3.0-1.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] libgomp-11.4.1-2.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] bzip2-1.0.8-6.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] elfutils-0.188-3.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] libcap-2.48-2.amzn2023.0.3.x86_64.rpm: Already downloaded [SKIPPED] libtasn1-4.19.0-1.amzn2023.0.4.x86_64.rpm: Already downloaded [SKIPPED] sed-4.8-7.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] binutils-2.39-6.amzn2023.0.10.x86_64.rpm: Already downloaded [SKIPPED] p11-kit-0.24.1-2.amzn2023.0.3.x86_64.rpm: Already downloaded [SKIPPED] findutils-4.8.0-2.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] pkgconf-pkg-config-1.8.0-4.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] mpfr-4.1.0-7.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] lz4-libs-1.9.4-1.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] dwz-0.14-6.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] zlib-1.2.11-33.amzn2023.0.5.x86_64.rpm: Already downloaded [SKIPPED] jansson-2.14-0.amzn2023.x86_64.rpm: Already downloaded [SKIPPED] patch-2.7.6-14.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] xz-libs-5.2.5-9.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] xz-5.2.5-9.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] libxml2-2.10.4-1.amzn2023.0.6.x86_64.rpm: Already downloaded [SKIPPED] glibc-minimal-langpack-2.34-52.amzn2023.0.7.x86_64.rpm: Already downloaded [SKIPPED] util-linux-2.37.4-1.amzn2023.0.3.x86_64.rpm: Already downloaded [SKIPPED] curl-8.3.0-1.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] libdb-5.3.28-49.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] lua-libs-5.4.4-3.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] gdbm-libs-1.19-2.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] libstdc++-11.4.1-2.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] libxcrypt-4.4.33-7.amzn2023.x86_64.rpm: Already downloaded [SKIPPED] libacl-2.3.1-2.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] glibc-common-2.34-52.amzn2023.0.7.x86_64.rpm: Already downloaded [SKIPPED] keyutils-libs-1.6.3-1.amzn2023.x86_64.rpm: Already downloaded [SKIPPED] libmount-2.37.4-1.amzn2023.0.3.x86_64.rpm: Already downloaded [SKIPPED] audit-libs-3.0.6-1.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] rpm-build-libs-4.16.1.3-12.amzn2023.0.6.x86_64.rpm: Already downloaded [SKIPPED] zstd-1.5.5-1.amzn2023.0.1.x86_64.rpm: Already downloaded [SKIPPED] alternatives-1.15-2.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] sqlite-libs-3.40.0-1.amzn2023.0.3.x86_64.rpm: Already downloaded [SKIPPED] bzip2-libs-1.0.8-6.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] rpm-build-4.16.1.3-12.amzn2023.0.6.x86_64.rpm: Already downloaded [SKIPPED] libffi-3.4.4-1.amzn2023.0.1.x86_64.rpm: Already downloaded [SKIPPED] krb5-libs-1.21-3.amzn2023.0.3.x86_64.rpm: Already downloaded [SKIPPED] libsepol-3.4-3.amzn2023.0.3.x86_64.rpm: Already downloaded [SKIPPED] glibc-2.34-52.amzn2023.0.7.x86_64.rpm: Already downloaded [SKIPPED] libidn2-2.3.2-1.amzn2023.0.5.x86_64.rpm: Already downloaded [SKIPPED] elfutils-libelf-0.188-3.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] libcom_err-1.46.5-2.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] cyrus-sasl-lib-2.1.27-18.amzn2023.0.3.x86_64.rpm: Already downloaded [SKIPPED] openssl-libs-3.0.8-1.amzn2023.0.10.x86_64.rpm: Already downloaded [SKIPPED] rpm-libs-4.16.1.3-12.amzn2023.0.6.x86_64.rpm: Already downloaded [SKIPPED] libattr-2.5.1-3.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] shadow-utils-4.9-12.amzn2023.0.4.x86_64.rpm: Already downloaded [SKIPPED] grep-3.8-1.amzn2023.0.4.x86_64.rpm: Already downloaded [SKIPPED] libfdisk-2.37.4-1.amzn2023.0.3.x86_64.rpm: Already downloaded [SKIPPED] rpm-4.16.1.3-12.amzn2023.0.6.x86_64.rpm: Already downloaded [SKIPPED] filesystem-3.14-5.amzn2023.0.3.x86_64.rpm: Already downloaded [SKIPPED] libpwquality-1.4.4-6.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] libuuid-2.37.4-1.amzn2023.0.3.x86_64.rpm: Already downloaded [SKIPPED] libpkgconf-1.8.0-4.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] ed-1.14.2-10.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] libgcc-11.4.1-2.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] info-6.7-10.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] libsemanage-3.4-5.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] libblkid-2.37.4-1.amzn2023.0.3.x86_64.rpm: Already downloaded [SKIPPED] xxhash-libs-0.8.0-3.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] gawk-5.1.0-3.amzn2023.0.3.x86_64.rpm: Already downloaded [SKIPPED] coreutils-8.32-30.amzn2023.0.3.x86_64.rpm: Already downloaded [SKIPPED] coreutils-common-8.32-30.amzn2023.0.3.x86_64.rpm: Already downloaded [SKIPPED] gzip-1.12-1.amzn2023.0.1.x86_64.rpm: Already downloaded [SKIPPED] libcap-ng-0.8.2-4.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] libunistring-0.9.10-10.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] tar-1.34-1.amzn2023.0.3.x86_64.rpm: Already downloaded [SKIPPED] gdb-minimal-12.1-5.amzn2023.0.3.x86_64.rpm: Already downloaded [SKIPPED] unzip-6.0-57.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] libsigsegv-2.13-2.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] libarchive-3.5.3-2.amzn2023.0.3.x86_64.rpm: Already downloaded [SKIPPED] which-2.21-26.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] elfutils-debuginfod-client-0.188-3.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] cpio-2.13-13.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] ncurses-libs-6.2-4.20200222.amzn2023.0.4.x86_64.rpm: Already downloaded [SKIPPED] glibc-gconv-extra-2.34-52.amzn2023.0.7.x86_64.rpm: Already downloaded [SKIPPED] libssh-0.10.5-1.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] elfutils-libs-0.188-3.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] readline-8.1-2.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] libutempter-1.2.1-4.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] util-linux-core-2.37.4-1.amzn2023.0.3.x86_64.rpm: Already downloaded [SKIPPED] cracklib-2.9.6-27.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] libzstd-1.5.5-1.amzn2023.0.1.x86_64.rpm: Already downloaded [SKIPPED] zip-3.0-28.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] p11-kit-trust-0.24.1-2.amzn2023.0.3.x86_64.rpm: Already downloaded [SKIPPED] libnghttp2-1.57.0-1.amzn2023.0.1.x86_64.rpm: Already downloaded [SKIPPED] libsmartcols-2.37.4-1.amzn2023.0.3.x86_64.rpm: Already downloaded [SKIPPED] gmp-6.2.1-2.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] file-libs-5.39-7.amzn2023.0.4.x86_64.rpm: Already downloaded [SKIPPED] popt-1.18-6.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] pcre2-10.40-1.amzn2023.0.3.x86_64.rpm: Already downloaded [SKIPPED] openldap-2.4.57-6.amzn2023.0.6.x86_64.rpm: Already downloaded [SKIPPED] file-5.39-7.amzn2023.0.4.x86_64.rpm: Already downloaded [SKIPPED] systemd-libs-252.16-1.amzn2023.0.1.x86_64.rpm: Already downloaded [SKIPPED] libpsl-0.21.1-3.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] pkgconf-1.8.0-4.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] libverto-0.3.2-1.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] libeconf-0.4.0-1.amzn2023.0.3.x86_64.rpm: Already downloaded [SKIPPED] libbrotli-1.0.9-4.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] efi-srpm-macros-5-4.amzn2023.0.5.noarch.rpm: Already downloaded [SKIPPED] ghc-srpm-macros-1.5.0-4.amzn2023.0.2.noarch.rpm: Already downloaded [SKIPPED] elfutils-default-yama-scope-0.188-3.amzn2023.0.2.noarch.rpm: Already downloaded [SKIPPED] ncurses-base-6.2-4.20200222.amzn2023.0.4.noarch.rpm: Already downloaded [SKIPPED] openblas-srpm-macros-2-9.amzn2023.0.2.noarch.rpm: Already downloaded [SKIPPED] publicsuffix-list-dafsa-20221208-60.amzn2023.noarch.rpm: Already downloaded [SKIPPED] kernel-srpm-macros-1.0-14.amzn2023.0.2.noarch.rpm: Already downloaded [SKIPPED] pcre2-syntax-10.40-1.amzn2023.0.3.noarch.rpm: Already downloaded [SKIPPED] ocaml-srpm-macros-6-6.amzn2023.0.2.noarch.rpm: Already downloaded [SKIPPED] basesystem-11-11.amzn2023.0.2.noarch.rpm: Already downloaded [SKIPPED] setup-2.13.7-3.amzn2023.0.2.noarch.rpm: Already downloaded [SKIPPED] libssh-config-0.10.5-1.amzn2023.0.2.noarch.rpm: Already downloaded [SKIPPED] amazon-rpm-config-228-3.amzn2023.0.2.noarch.rpm: Already downloaded [SKIPPED] ca-certificates-2023.2.62-1.0.amzn2023.0.1.noarch.rpm: Already downloaded [SKIPPED] python-srpm-macros-3.9-41.amzn2023.0.5.noarch.rpm: Already downloaded [SKIPPED] crypto-policies-20220428-1.gitdfb10ea.amzn2023.0.2.noarch.rpm: Already downloaded [SKIPPED] fonts-srpm-macros-2.0.5-12.amzn2023.0.2.noarch.rpm: Already downloaded [SKIPPED] package-notes-srpm-macros-0.4-18.amzn2023.0.5.noarch.rpm: Already downloaded [SKIPPED] perl-srpm-macros-1-39.amzn2023.0.2.noarch.rpm: Already downloaded [SKIPPED] lua-srpm-macros-1-4.amzn2023.0.2.noarch.rpm: Already downloaded [SKIPPED] system-release-2023.3.20231218-0.amzn2023.noarch.rpm: Already downloaded [SKIPPED] amazon-linux-repo-cdn-2023.3.20231218-0.amzn2023.noarch.rpm: Already downloaded [SKIPPED] rust-srpm-macros-21-42.amzn2023.0.2.noarch.rpm: Already downloaded [SKIPPED] pkgconf-m4-1.8.0-4.amzn2023.0.2.noarch.rpm: Already downloaded (132/132): go-srpm-macros-3.3.1-1.amzn2023.noar 613 kB/s | 28 kB 00:00 -------------------------------------------------------------------------------- Total 277 kB/s | 28 kB 00:00 Amazon Linux 2023 repository - x86_64 1.7 MB/s | 1.8 kB 00:00 Importing GPG key 0xD832C631: Userid : "Amazon Linux " Fingerprint: B21C 50FA 44A9 9720 EAA7 2F7F E951 904A D832 C631 From : /usr/share/distribution-gpg-keys/amazon-linux/RPM-GPG-KEY-amazon-linux-2023 Key imported successfully Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Running scriptlet: filesystem-3.14-5.amzn2023.0.3.x86_64 1/1 Preparing : 1/1 Installing : libgcc-11.4.1-2.amzn2023.0.2.x86_64 1/132 Running scriptlet: libgcc-11.4.1-2.amzn2023.0.2.x86_64 1/132 Installing : crypto-policies-20220428-1.gitdfb10ea.amzn2023.0 2/132 Running scriptlet: crypto-policies-20220428-1.gitdfb10ea.amzn2023.0 2/132 Installing : pkgconf-m4-1.8.0-4.amzn2023.0.2.noarch 3/132 Installing : rust-srpm-macros-21-42.amzn2023.0.2.noarch 4/132 Installing : perl-srpm-macros-1-39.amzn2023.0.2.noarch 5/132 Installing : libssh-config-0.10.5-1.amzn2023.0.2.noarch 6/132 Installing : ocaml-srpm-macros-6-6.amzn2023.0.2.noarch 7/132 Installing : pcre2-syntax-10.40-1.amzn2023.0.3.noarch 8/132 Installing : kernel-srpm-macros-1.0-14.amzn2023.0.2.noarch 9/132 Installing : publicsuffix-list-dafsa-20221208-60.amzn2023.noa 10/132 Installing : openblas-srpm-macros-2-9.amzn2023.0.2.noarch 11/132 Installing : ncurses-base-6.2-4.20200222.amzn2023.0.4.noarch 12/132 Installing : ncurses-libs-6.2-4.20200222.amzn2023.0.4.x86_64 13/132 Installing : amazon-linux-repo-cdn-2023.3.20231218-0.amzn2023 14/132 Installing : system-release-2023.3.20231218-0.amzn2023.noarch 15/132 Installing : setup-2.13.7-3.amzn2023.0.2.noarch 16/132 warning: /etc/hosts created as /etc/hosts.rpmnew Running scriptlet: setup-2.13.7-3.amzn2023.0.2.noarch 16/132 Installing : filesystem-3.14-5.amzn2023.0.3.x86_64 17/132 Installing : basesystem-11-11.amzn2023.0.2.noarch 18/132 Installing : bash-5.2.15-1.amzn2023.0.2.x86_64 19/132 Running scriptlet: bash-5.2.15-1.amzn2023.0.2.x86_64 19/132 Installing : glibc-minimal-langpack-2.34-52.amzn2023.0.7.x86_ 20/132 Installing : glibc-common-2.34-52.amzn2023.0.7.x86_64 21/132 Installing : glibc-gconv-extra-2.34-52.amzn2023.0.7.x86_64 22/132 Running scriptlet: glibc-gconv-extra-2.34-52.amzn2023.0.7.x86_64 22/132 Running scriptlet: glibc-2.34-52.amzn2023.0.7.x86_64 23/132 Installing : glibc-2.34-52.amzn2023.0.7.x86_64 23/132 Running scriptlet: glibc-2.34-52.amzn2023.0.7.x86_64 23/132 Installing : zlib-1.2.11-33.amzn2023.0.5.x86_64 24/132 Installing : xz-libs-5.2.5-9.amzn2023.0.2.x86_64 25/132 Installing : bzip2-libs-1.0.8-6.amzn2023.0.2.x86_64 26/132 Installing : elfutils-libelf-0.188-3.amzn2023.0.2.x86_64 27/132 Installing : libuuid-2.37.4-1.amzn2023.0.3.x86_64 28/132 Installing : libcap-2.48-2.amzn2023.0.3.x86_64 29/132 Installing : libxcrypt-4.4.33-7.amzn2023.x86_64 30/132 Installing : libattr-2.5.1-3.amzn2023.0.2.x86_64 31/132 Installing : libacl-2.3.1-2.amzn2023.0.2.x86_64 32/132 Installing : libzstd-1.5.5-1.amzn2023.0.1.x86_64 33/132 Installing : gmp-1:6.2.1-2.amzn2023.0.2.x86_64 34/132 Installing : popt-1.18-6.amzn2023.0.2.x86_64 35/132 Installing : libstdc++-11.4.1-2.amzn2023.0.2.x86_64 36/132 Installing : readline-8.1-2.amzn2023.0.2.x86_64 37/132 Installing : mpfr-4.1.0-7.amzn2023.0.2.x86_64 38/132 Installing : systemd-libs-252.16-1.amzn2023.0.1.x86_64 39/132 Installing : unzip-6.0-57.amzn2023.0.2.x86_64 40/132 Installing : sqlite-libs-3.40.0-1.amzn2023.0.3.x86_64 41/132 Installing : file-libs-5.39-7.amzn2023.0.4.x86_64 42/132 Installing : file-5.39-7.amzn2023.0.4.x86_64 43/132 Installing : lz4-libs-1.9.4-1.amzn2023.0.2.x86_64 44/132 Installing : lua-libs-5.4.4-3.amzn2023.0.2.x86_64 45/132 Installing : alternatives-1.15-2.amzn2023.0.2.x86_64 46/132 Installing : libsepol-3.4-3.amzn2023.0.3.x86_64 47/132 Installing : libcom_err-1.46.5-2.amzn2023.0.2.x86_64 48/132 Installing : libcap-ng-0.8.2-4.amzn2023.0.2.x86_64 49/132 Installing : audit-libs-3.0.6-1.amzn2023.0.2.x86_64 50/132 Installing : libunistring-0.9.10-10.amzn2023.0.2.x86_64 51/132 Installing : libidn2-2.3.2-1.amzn2023.0.5.x86_64 52/132 Installing : libsmartcols-2.37.4-1.amzn2023.0.3.x86_64 53/132 Installing : pcre2-10.40-1.amzn2023.0.3.x86_64 54/132 Installing : libselinux-3.4-5.amzn2023.0.2.x86_64 55/132 Installing : sed-4.8-7.amzn2023.0.2.x86_64 56/132 Installing : grep-3.8-1.amzn2023.0.4.x86_64 57/132 Installing : findutils-1:4.8.0-2.amzn2023.0.2.x86_64 58/132 Installing : xz-5.2.5-9.amzn2023.0.2.x86_64 59/132 Installing : libsemanage-3.4-5.amzn2023.0.2.x86_64 60/132 Installing : shadow-utils-2:4.9-12.amzn2023.0.4.x86_64 61/132 Running scriptlet: libutempter-1.2.1-4.amzn2023.0.2.x86_64 62/132 Installing : libutempter-1.2.1-4.amzn2023.0.2.x86_64 62/132 Installing : tar-2:1.34-1.amzn2023.0.3.x86_64 63/132 Installing : libpsl-0.21.1-3.amzn2023.0.2.x86_64 64/132 Installing : zstd-1.5.5-1.amzn2023.0.1.x86_64 65/132 Installing : zip-3.0-28.amzn2023.0.2.x86_64 66/132 Installing : dwz-0.14-6.amzn2023.0.2.x86_64 67/132 Installing : bzip2-1.0.8-6.amzn2023.0.2.x86_64 68/132 Installing : libxml2-2.10.4-1.amzn2023.0.6.x86_64 69/132 Installing : info-6.7-10.amzn2023.0.2.x86_64 70/132 Installing : ed-1.14.2-10.amzn2023.0.2.x86_64 71/132 Installing : patch-2.7.6-14.amzn2023.0.2.x86_64 72/132 Installing : diffutils-3.8-1.amzn2023.0.2.x86_64 73/132 Installing : libgomp-11.4.1-2.amzn2023.0.2.x86_64 74/132 Installing : libtasn1-4.19.0-1.amzn2023.0.4.x86_64 75/132 Installing : jansson-2.14-0.amzn2023.x86_64 76/132 Installing : libdb-5.3.28-49.amzn2023.0.2.x86_64 77/132 Installing : gdbm-libs-1:1.19-2.amzn2023.0.2.x86_64 78/132 Installing : keyutils-libs-1.6.3-1.amzn2023.x86_64 79/132 Installing : libffi-3.4.4-1.amzn2023.0.1.x86_64 80/132 Installing : p11-kit-0.24.1-2.amzn2023.0.3.x86_64 81/132 Installing : p11-kit-trust-0.24.1-2.amzn2023.0.3.x86_64 82/132 Running scriptlet: p11-kit-trust-0.24.1-2.amzn2023.0.3.x86_64 82/132 Installing : libpkgconf-1.8.0-4.amzn2023.0.2.x86_64 83/132 Installing : xxhash-libs-0.8.0-3.amzn2023.0.2.x86_64 84/132 Installing : libsigsegv-2.13-2.amzn2023.0.2.x86_64 85/132 Installing : gawk-5.1.0-3.amzn2023.0.3.x86_64 86/132 Installing : cpio-2.13-13.amzn2023.0.2.x86_64 87/132 Installing : libnghttp2-1.57.0-1.amzn2023.0.1.x86_64 88/132 Installing : libverto-0.3.2-1.amzn2023.0.2.x86_64 89/132 Installing : libeconf-0.4.0-1.amzn2023.0.3.x86_64 90/132 Installing : libbrotli-1.0.9-4.amzn2023.0.2.x86_64 91/132 Installing : elfutils-default-yama-scope-0.188-3.amzn2023.0.2 92/132 Running scriptlet: elfutils-default-yama-scope-0.188-3.amzn2023.0.2 92/132 Installing : package-notes-srpm-macros-0.4-18.amzn2023.0.5.no 93/132 Installing : ghc-srpm-macros-1.5.0-4.amzn2023.0.2.noarch 94/132 Installing : coreutils-common-8.32-30.amzn2023.0.3.x86_64 95/132 Installing : openssl-libs-1:3.0.8-1.amzn2023.0.10.x86_64 96/132 Installing : coreutils-8.32-30.amzn2023.0.3.x86_64 97/132 Running scriptlet: ca-certificates-2023.2.62-1.0.amzn2023.0.1.noarc 98/132 Installing : ca-certificates-2023.2.62-1.0.amzn2023.0.1.noarc 98/132 Running scriptlet: ca-certificates-2023.2.62-1.0.amzn2023.0.1.noarc 98/132 Installing : libblkid-2.37.4-1.amzn2023.0.3.x86_64 99/132 Running scriptlet: libblkid-2.37.4-1.amzn2023.0.3.x86_64 99/132 Installing : krb5-libs-1.21-3.amzn2023.0.3.x86_64 100/132 Installing : libmount-2.37.4-1.amzn2023.0.3.x86_64 101/132 Installing : gzip-1.12-1.amzn2023.0.1.x86_64 102/132 Installing : cracklib-2.9.6-27.amzn2023.0.2.x86_64 103/132 Installing : libpwquality-1.4.4-6.amzn2023.0.2.x86_64 104/132 Installing : pam-1.5.1-8.amzn2023.0.3.x86_64 105/132 Installing : util-linux-core-2.37.4-1.amzn2023.0.3.x86_64 106/132 Running scriptlet: util-linux-core-2.37.4-1.amzn2023.0.3.x86_64 106/132 Installing : cyrus-sasl-lib-2.1.27-18.amzn2023.0.3.x86_64 107/132 Installing : openldap-2.4.57-6.amzn2023.0.6.x86_64 108/132 Installing : libssh-0.10.5-1.amzn2023.0.2.x86_64 109/132 Installing : libcurl-8.3.0-1.amzn2023.0.2.x86_64 110/132 Installing : elfutils-libs-0.188-3.amzn2023.0.2.x86_64 111/132 Installing : elfutils-debuginfod-client-0.188-3.amzn2023.0.2. 112/132 Installing : elfutils-0.188-3.amzn2023.0.2.x86_64 113/132 Installing : binutils-2.39-6.amzn2023.0.10.x86_64 114/132 Running scriptlet: binutils-2.39-6.amzn2023.0.10.x86_64 114/132 Installing : gdb-minimal-12.1-5.amzn2023.0.3.x86_64 115/132 Installing : curl-8.3.0-1.amzn2023.0.2.x86_64 116/132 Installing : libfdisk-2.37.4-1.amzn2023.0.3.x86_64 117/132 Installing : libarchive-3.5.3-2.amzn2023.0.3.x86_64 118/132 Installing : rpm-libs-4.16.1.3-12.amzn2023.0.6.x86_64 119/132 Installing : rpm-4.16.1.3-12.amzn2023.0.6.x86_64 120/132 Installing : efi-srpm-macros-5-4.amzn2023.0.5.noarch 121/132 Installing : lua-srpm-macros-1-4.amzn2023.0.2.noarch 122/132 Installing : python-srpm-macros-3.9-41.amzn2023.0.5.noarch 123/132 Installing : fonts-srpm-macros-1:2.0.5-12.amzn2023.0.2.noarch 124/132 Installing : amazon-rpm-config-228-3.amzn2023.0.2.noarch 125/132 Running scriptlet: amazon-rpm-config-228-3.amzn2023.0.2.noarch 125/132 Installing : go-srpm-macros-3.3.1-1.amzn2023.noarch 126/132 Installing : pkgconf-1.8.0-4.amzn2023.0.2.x86_64 127/132 Installing : pkgconf-pkg-config-1.8.0-4.amzn2023.0.2.x86_64 128/132 Installing : rpm-build-libs-4.16.1.3-12.amzn2023.0.6.x86_64 129/132 Installing : rpm-build-4.16.1.3-12.amzn2023.0.6.x86_64 130/132 Installing : util-linux-2.37.4-1.amzn2023.0.3.x86_64 131/132 Running scriptlet: util-linux-2.37.4-1.amzn2023.0.3.x86_64 131/132 Installing : which-2.21-26.amzn2023.0.2.x86_64 132/132 Running scriptlet: filesystem-3.14-5.amzn2023.0.3.x86_64 132/132 Running scriptlet: ca-certificates-2023.2.62-1.0.amzn2023.0.1.noarc 132/132 Running scriptlet: pam-1.5.1-8.amzn2023.0.3.x86_64 132/132 Running scriptlet: rpm-4.16.1.3-12.amzn2023.0.6.x86_64 132/132 Running scriptlet: which-2.21-26.amzn2023.0.2.x86_64 132/132 Verifying : go-srpm-macros-3.3.1-1.amzn2023.noarch 1/132 Verifying : bash-5.2.15-1.amzn2023.0.2.x86_64 2/132 Verifying : pam-1.5.1-8.amzn2023.0.3.x86_64 3/132 Verifying : libselinux-3.4-5.amzn2023.0.2.x86_64 4/132 Verifying : diffutils-3.8-1.amzn2023.0.2.x86_64 5/132 Verifying : libcurl-8.3.0-1.amzn2023.0.2.x86_64 6/132 Verifying : libgomp-11.4.1-2.amzn2023.0.2.x86_64 7/132 Verifying : bzip2-1.0.8-6.amzn2023.0.2.x86_64 8/132 Verifying : elfutils-0.188-3.amzn2023.0.2.x86_64 9/132 Verifying : libcap-2.48-2.amzn2023.0.3.x86_64 10/132 Verifying : libtasn1-4.19.0-1.amzn2023.0.4.x86_64 11/132 Verifying : sed-4.8-7.amzn2023.0.2.x86_64 12/132 Verifying : binutils-2.39-6.amzn2023.0.10.x86_64 13/132 Verifying : p11-kit-0.24.1-2.amzn2023.0.3.x86_64 14/132 Verifying : findutils-1:4.8.0-2.amzn2023.0.2.x86_64 15/132 Verifying : pkgconf-pkg-config-1.8.0-4.amzn2023.0.2.x86_64 16/132 Verifying : mpfr-4.1.0-7.amzn2023.0.2.x86_64 17/132 Verifying : lz4-libs-1.9.4-1.amzn2023.0.2.x86_64 18/132 Verifying : dwz-0.14-6.amzn2023.0.2.x86_64 19/132 Verifying : zlib-1.2.11-33.amzn2023.0.5.x86_64 20/132 Verifying : jansson-2.14-0.amzn2023.x86_64 21/132 Verifying : patch-2.7.6-14.amzn2023.0.2.x86_64 22/132 Verifying : xz-libs-5.2.5-9.amzn2023.0.2.x86_64 23/132 Verifying : xz-5.2.5-9.amzn2023.0.2.x86_64 24/132 Verifying : libxml2-2.10.4-1.amzn2023.0.6.x86_64 25/132 Verifying : glibc-minimal-langpack-2.34-52.amzn2023.0.7.x86_ 26/132 Verifying : util-linux-2.37.4-1.amzn2023.0.3.x86_64 27/132 Verifying : curl-8.3.0-1.amzn2023.0.2.x86_64 28/132 Verifying : libdb-5.3.28-49.amzn2023.0.2.x86_64 29/132 Verifying : lua-libs-5.4.4-3.amzn2023.0.2.x86_64 30/132 Verifying : gdbm-libs-1:1.19-2.amzn2023.0.2.x86_64 31/132 Verifying : libstdc++-11.4.1-2.amzn2023.0.2.x86_64 32/132 Verifying : libxcrypt-4.4.33-7.amzn2023.x86_64 33/132 Verifying : libacl-2.3.1-2.amzn2023.0.2.x86_64 34/132 Verifying : glibc-common-2.34-52.amzn2023.0.7.x86_64 35/132 Verifying : keyutils-libs-1.6.3-1.amzn2023.x86_64 36/132 Verifying : libmount-2.37.4-1.amzn2023.0.3.x86_64 37/132 Verifying : audit-libs-3.0.6-1.amzn2023.0.2.x86_64 38/132 Verifying : rpm-build-libs-4.16.1.3-12.amzn2023.0.6.x86_64 39/132 Verifying : zstd-1.5.5-1.amzn2023.0.1.x86_64 40/132 Verifying : alternatives-1.15-2.amzn2023.0.2.x86_64 41/132 Verifying : sqlite-libs-3.40.0-1.amzn2023.0.3.x86_64 42/132 Verifying : bzip2-libs-1.0.8-6.amzn2023.0.2.x86_64 43/132 Verifying : rpm-build-4.16.1.3-12.amzn2023.0.6.x86_64 44/132 Verifying : libffi-3.4.4-1.amzn2023.0.1.x86_64 45/132 Verifying : krb5-libs-1.21-3.amzn2023.0.3.x86_64 46/132 Verifying : libsepol-3.4-3.amzn2023.0.3.x86_64 47/132 Verifying : glibc-2.34-52.amzn2023.0.7.x86_64 48/132 Verifying : libidn2-2.3.2-1.amzn2023.0.5.x86_64 49/132 Verifying : elfutils-libelf-0.188-3.amzn2023.0.2.x86_64 50/132 Verifying : libcom_err-1.46.5-2.amzn2023.0.2.x86_64 51/132 Verifying : cyrus-sasl-lib-2.1.27-18.amzn2023.0.3.x86_64 52/132 Verifying : openssl-libs-1:3.0.8-1.amzn2023.0.10.x86_64 53/132 Verifying : rpm-libs-4.16.1.3-12.amzn2023.0.6.x86_64 54/132 Verifying : libattr-2.5.1-3.amzn2023.0.2.x86_64 55/132 Verifying : shadow-utils-2:4.9-12.amzn2023.0.4.x86_64 56/132 Verifying : grep-3.8-1.amzn2023.0.4.x86_64 57/132 Verifying : libfdisk-2.37.4-1.amzn2023.0.3.x86_64 58/132 Verifying : rpm-4.16.1.3-12.amzn2023.0.6.x86_64 59/132 Verifying : filesystem-3.14-5.amzn2023.0.3.x86_64 60/132 Verifying : libpwquality-1.4.4-6.amzn2023.0.2.x86_64 61/132 Verifying : libuuid-2.37.4-1.amzn2023.0.3.x86_64 62/132 Verifying : libpkgconf-1.8.0-4.amzn2023.0.2.x86_64 63/132 Verifying : ed-1.14.2-10.amzn2023.0.2.x86_64 64/132 Verifying : libgcc-11.4.1-2.amzn2023.0.2.x86_64 65/132 Verifying : info-6.7-10.amzn2023.0.2.x86_64 66/132 Verifying : libsemanage-3.4-5.amzn2023.0.2.x86_64 67/132 Verifying : libblkid-2.37.4-1.amzn2023.0.3.x86_64 68/132 Verifying : xxhash-libs-0.8.0-3.amzn2023.0.2.x86_64 69/132 Verifying : gawk-5.1.0-3.amzn2023.0.3.x86_64 70/132 Verifying : coreutils-8.32-30.amzn2023.0.3.x86_64 71/132 Verifying : coreutils-common-8.32-30.amzn2023.0.3.x86_64 72/132 Verifying : gzip-1.12-1.amzn2023.0.1.x86_64 73/132 Verifying : libcap-ng-0.8.2-4.amzn2023.0.2.x86_64 74/132 Verifying : libunistring-0.9.10-10.amzn2023.0.2.x86_64 75/132 Verifying : tar-2:1.34-1.amzn2023.0.3.x86_64 76/132 Verifying : gdb-minimal-12.1-5.amzn2023.0.3.x86_64 77/132 Verifying : unzip-6.0-57.amzn2023.0.2.x86_64 78/132 Verifying : libsigsegv-2.13-2.amzn2023.0.2.x86_64 79/132 Verifying : libarchive-3.5.3-2.amzn2023.0.3.x86_64 80/132 Verifying : which-2.21-26.amzn2023.0.2.x86_64 81/132 Verifying : elfutils-debuginfod-client-0.188-3.amzn2023.0.2. 82/132 Verifying : cpio-2.13-13.amzn2023.0.2.x86_64 83/132 Verifying : ncurses-libs-6.2-4.20200222.amzn2023.0.4.x86_64 84/132 Verifying : glibc-gconv-extra-2.34-52.amzn2023.0.7.x86_64 85/132 Verifying : libssh-0.10.5-1.amzn2023.0.2.x86_64 86/132 Verifying : elfutils-libs-0.188-3.amzn2023.0.2.x86_64 87/132 Verifying : readline-8.1-2.amzn2023.0.2.x86_64 88/132 Verifying : libutempter-1.2.1-4.amzn2023.0.2.x86_64 89/132 Verifying : util-linux-core-2.37.4-1.amzn2023.0.3.x86_64 90/132 Verifying : cracklib-2.9.6-27.amzn2023.0.2.x86_64 91/132 Verifying : libzstd-1.5.5-1.amzn2023.0.1.x86_64 92/132 Verifying : zip-3.0-28.amzn2023.0.2.x86_64 93/132 Verifying : p11-kit-trust-0.24.1-2.amzn2023.0.3.x86_64 94/132 Verifying : libnghttp2-1.57.0-1.amzn2023.0.1.x86_64 95/132 Verifying : libsmartcols-2.37.4-1.amzn2023.0.3.x86_64 96/132 Verifying : gmp-1:6.2.1-2.amzn2023.0.2.x86_64 97/132 Verifying : file-libs-5.39-7.amzn2023.0.4.x86_64 98/132 Verifying : popt-1.18-6.amzn2023.0.2.x86_64 99/132 Verifying : pcre2-10.40-1.amzn2023.0.3.x86_64 100/132 Verifying : openldap-2.4.57-6.amzn2023.0.6.x86_64 101/132 Verifying : file-5.39-7.amzn2023.0.4.x86_64 102/132 Verifying : systemd-libs-252.16-1.amzn2023.0.1.x86_64 103/132 Verifying : libpsl-0.21.1-3.amzn2023.0.2.x86_64 104/132 Verifying : pkgconf-1.8.0-4.amzn2023.0.2.x86_64 105/132 Verifying : libverto-0.3.2-1.amzn2023.0.2.x86_64 106/132 Verifying : libeconf-0.4.0-1.amzn2023.0.3.x86_64 107/132 Verifying : libbrotli-1.0.9-4.amzn2023.0.2.x86_64 108/132 Verifying : efi-srpm-macros-5-4.amzn2023.0.5.noarch 109/132 Verifying : ghc-srpm-macros-1.5.0-4.amzn2023.0.2.noarch 110/132 Verifying : elfutils-default-yama-scope-0.188-3.amzn2023.0.2 111/132 Verifying : ncurses-base-6.2-4.20200222.amzn2023.0.4.noarch 112/132 Verifying : openblas-srpm-macros-2-9.amzn2023.0.2.noarch 113/132 Verifying : publicsuffix-list-dafsa-20221208-60.amzn2023.noa 114/132 Verifying : kernel-srpm-macros-1.0-14.amzn2023.0.2.noarch 115/132 Verifying : pcre2-syntax-10.40-1.amzn2023.0.3.noarch 116/132 Verifying : ocaml-srpm-macros-6-6.amzn2023.0.2.noarch 117/132 Verifying : basesystem-11-11.amzn2023.0.2.noarch 118/132 Verifying : setup-2.13.7-3.amzn2023.0.2.noarch 119/132 Verifying : libssh-config-0.10.5-1.amzn2023.0.2.noarch 120/132 Verifying : amazon-rpm-config-228-3.amzn2023.0.2.noarch 121/132 Verifying : ca-certificates-2023.2.62-1.0.amzn2023.0.1.noarc 122/132 Verifying : python-srpm-macros-3.9-41.amzn2023.0.5.noarch 123/132 Verifying : crypto-policies-20220428-1.gitdfb10ea.amzn2023.0 124/132 Verifying : fonts-srpm-macros-1:2.0.5-12.amzn2023.0.2.noarch 125/132 Verifying : package-notes-srpm-macros-0.4-18.amzn2023.0.5.no 126/132 Verifying : perl-srpm-macros-1-39.amzn2023.0.2.noarch 127/132 Verifying : lua-srpm-macros-1-4.amzn2023.0.2.noarch 128/132 Verifying : system-release-2023.3.20231218-0.amzn2023.noarch 129/132 Verifying : amazon-linux-repo-cdn-2023.3.20231218-0.amzn2023 130/132 Verifying : rust-srpm-macros-21-42.amzn2023.0.2.noarch 131/132 Verifying : pkgconf-m4-1.8.0-4.amzn2023.0.2.noarch 132/132 Installed: alternatives-1.15-2.amzn2023.0.2.x86_64 amazon-linux-repo-cdn-2023.3.20231218-0.amzn2023.noarch amazon-rpm-config-228-3.amzn2023.0.2.noarch audit-libs-3.0.6-1.amzn2023.0.2.x86_64 basesystem-11-11.amzn2023.0.2.noarch bash-5.2.15-1.amzn2023.0.2.x86_64 binutils-2.39-6.amzn2023.0.10.x86_64 bzip2-1.0.8-6.amzn2023.0.2.x86_64 bzip2-libs-1.0.8-6.amzn2023.0.2.x86_64 ca-certificates-2023.2.62-1.0.amzn2023.0.1.noarch coreutils-8.32-30.amzn2023.0.3.x86_64 coreutils-common-8.32-30.amzn2023.0.3.x86_64 cpio-2.13-13.amzn2023.0.2.x86_64 cracklib-2.9.6-27.amzn2023.0.2.x86_64 crypto-policies-20220428-1.gitdfb10ea.amzn2023.0.2.noarch curl-8.3.0-1.amzn2023.0.2.x86_64 cyrus-sasl-lib-2.1.27-18.amzn2023.0.3.x86_64 diffutils-3.8-1.amzn2023.0.2.x86_64 dwz-0.14-6.amzn2023.0.2.x86_64 ed-1.14.2-10.amzn2023.0.2.x86_64 efi-srpm-macros-5-4.amzn2023.0.5.noarch elfutils-0.188-3.amzn2023.0.2.x86_64 elfutils-debuginfod-client-0.188-3.amzn2023.0.2.x86_64 elfutils-default-yama-scope-0.188-3.amzn2023.0.2.noarch elfutils-libelf-0.188-3.amzn2023.0.2.x86_64 elfutils-libs-0.188-3.amzn2023.0.2.x86_64 file-5.39-7.amzn2023.0.4.x86_64 file-libs-5.39-7.amzn2023.0.4.x86_64 filesystem-3.14-5.amzn2023.0.3.x86_64 findutils-1:4.8.0-2.amzn2023.0.2.x86_64 fonts-srpm-macros-1:2.0.5-12.amzn2023.0.2.noarch gawk-5.1.0-3.amzn2023.0.3.x86_64 gdb-minimal-12.1-5.amzn2023.0.3.x86_64 gdbm-libs-1:1.19-2.amzn2023.0.2.x86_64 ghc-srpm-macros-1.5.0-4.amzn2023.0.2.noarch glibc-2.34-52.amzn2023.0.7.x86_64 glibc-common-2.34-52.amzn2023.0.7.x86_64 glibc-gconv-extra-2.34-52.amzn2023.0.7.x86_64 glibc-minimal-langpack-2.34-52.amzn2023.0.7.x86_64 gmp-1:6.2.1-2.amzn2023.0.2.x86_64 go-srpm-macros-3.3.1-1.amzn2023.noarch grep-3.8-1.amzn2023.0.4.x86_64 gzip-1.12-1.amzn2023.0.1.x86_64 info-6.7-10.amzn2023.0.2.x86_64 jansson-2.14-0.amzn2023.x86_64 kernel-srpm-macros-1.0-14.amzn2023.0.2.noarch keyutils-libs-1.6.3-1.amzn2023.x86_64 krb5-libs-1.21-3.amzn2023.0.3.x86_64 libacl-2.3.1-2.amzn2023.0.2.x86_64 libarchive-3.5.3-2.amzn2023.0.3.x86_64 libattr-2.5.1-3.amzn2023.0.2.x86_64 libblkid-2.37.4-1.amzn2023.0.3.x86_64 libbrotli-1.0.9-4.amzn2023.0.2.x86_64 libcap-2.48-2.amzn2023.0.3.x86_64 libcap-ng-0.8.2-4.amzn2023.0.2.x86_64 libcom_err-1.46.5-2.amzn2023.0.2.x86_64 libcurl-8.3.0-1.amzn2023.0.2.x86_64 libdb-5.3.28-49.amzn2023.0.2.x86_64 libeconf-0.4.0-1.amzn2023.0.3.x86_64 libfdisk-2.37.4-1.amzn2023.0.3.x86_64 libffi-3.4.4-1.amzn2023.0.1.x86_64 libgcc-11.4.1-2.amzn2023.0.2.x86_64 libgomp-11.4.1-2.amzn2023.0.2.x86_64 libidn2-2.3.2-1.amzn2023.0.5.x86_64 libmount-2.37.4-1.amzn2023.0.3.x86_64 libnghttp2-1.57.0-1.amzn2023.0.1.x86_64 libpkgconf-1.8.0-4.amzn2023.0.2.x86_64 libpsl-0.21.1-3.amzn2023.0.2.x86_64 libpwquality-1.4.4-6.amzn2023.0.2.x86_64 libselinux-3.4-5.amzn2023.0.2.x86_64 libsemanage-3.4-5.amzn2023.0.2.x86_64 libsepol-3.4-3.amzn2023.0.3.x86_64 libsigsegv-2.13-2.amzn2023.0.2.x86_64 libsmartcols-2.37.4-1.amzn2023.0.3.x86_64 libssh-0.10.5-1.amzn2023.0.2.x86_64 libssh-config-0.10.5-1.amzn2023.0.2.noarch libstdc++-11.4.1-2.amzn2023.0.2.x86_64 libtasn1-4.19.0-1.amzn2023.0.4.x86_64 libunistring-0.9.10-10.amzn2023.0.2.x86_64 libutempter-1.2.1-4.amzn2023.0.2.x86_64 libuuid-2.37.4-1.amzn2023.0.3.x86_64 libverto-0.3.2-1.amzn2023.0.2.x86_64 libxcrypt-4.4.33-7.amzn2023.x86_64 libxml2-2.10.4-1.amzn2023.0.6.x86_64 libzstd-1.5.5-1.amzn2023.0.1.x86_64 lua-libs-5.4.4-3.amzn2023.0.2.x86_64 lua-srpm-macros-1-4.amzn2023.0.2.noarch lz4-libs-1.9.4-1.amzn2023.0.2.x86_64 mpfr-4.1.0-7.amzn2023.0.2.x86_64 ncurses-base-6.2-4.20200222.amzn2023.0.4.noarch ncurses-libs-6.2-4.20200222.amzn2023.0.4.x86_64 ocaml-srpm-macros-6-6.amzn2023.0.2.noarch openblas-srpm-macros-2-9.amzn2023.0.2.noarch openldap-2.4.57-6.amzn2023.0.6.x86_64 openssl-libs-1:3.0.8-1.amzn2023.0.10.x86_64 p11-kit-0.24.1-2.amzn2023.0.3.x86_64 p11-kit-trust-0.24.1-2.amzn2023.0.3.x86_64 package-notes-srpm-macros-0.4-18.amzn2023.0.5.noarch pam-1.5.1-8.amzn2023.0.3.x86_64 patch-2.7.6-14.amzn2023.0.2.x86_64 pcre2-10.40-1.amzn2023.0.3.x86_64 pcre2-syntax-10.40-1.amzn2023.0.3.noarch perl-srpm-macros-1-39.amzn2023.0.2.noarch pkgconf-1.8.0-4.amzn2023.0.2.x86_64 pkgconf-m4-1.8.0-4.amzn2023.0.2.noarch pkgconf-pkg-config-1.8.0-4.amzn2023.0.2.x86_64 popt-1.18-6.amzn2023.0.2.x86_64 publicsuffix-list-dafsa-20221208-60.amzn2023.noarch python-srpm-macros-3.9-41.amzn2023.0.5.noarch readline-8.1-2.amzn2023.0.2.x86_64 rpm-4.16.1.3-12.amzn2023.0.6.x86_64 rpm-build-4.16.1.3-12.amzn2023.0.6.x86_64 rpm-build-libs-4.16.1.3-12.amzn2023.0.6.x86_64 rpm-libs-4.16.1.3-12.amzn2023.0.6.x86_64 rust-srpm-macros-21-42.amzn2023.0.2.noarch sed-4.8-7.amzn2023.0.2.x86_64 setup-2.13.7-3.amzn2023.0.2.noarch shadow-utils-2:4.9-12.amzn2023.0.4.x86_64 sqlite-libs-3.40.0-1.amzn2023.0.3.x86_64 system-release-2023.3.20231218-0.amzn2023.noarch systemd-libs-252.16-1.amzn2023.0.1.x86_64 tar-2:1.34-1.amzn2023.0.3.x86_64 unzip-6.0-57.amzn2023.0.2.x86_64 util-linux-2.37.4-1.amzn2023.0.3.x86_64 util-linux-core-2.37.4-1.amzn2023.0.3.x86_64 which-2.21-26.amzn2023.0.2.x86_64 xxhash-libs-0.8.0-3.amzn2023.0.2.x86_64 xz-5.2.5-9.amzn2023.0.2.x86_64 xz-libs-5.2.5-9.amzn2023.0.2.x86_64 zip-3.0-28.amzn2023.0.2.x86_64 zlib-1.2.11-33.amzn2023.0.5.x86_64 zstd-1.5.5-1.amzn2023.0.1.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-1.15-2.amzn2023.0.2.x86_64 amazon-linux-repo-cdn-2023.3.20231218-0.amzn2023.noarch amazon-rpm-config-228-3.amzn2023.0.2.noarch audit-libs-3.0.6-1.amzn2023.0.2.x86_64 basesystem-11-11.amzn2023.0.2.noarch bash-5.2.15-1.amzn2023.0.2.x86_64 binutils-2.39-6.amzn2023.0.10.x86_64 bzip2-1.0.8-6.amzn2023.0.2.x86_64 bzip2-libs-1.0.8-6.amzn2023.0.2.x86_64 ca-certificates-2023.2.62-1.0.amzn2023.0.1.noarch coreutils-8.32-30.amzn2023.0.3.x86_64 coreutils-common-8.32-30.amzn2023.0.3.x86_64 cpio-2.13-13.amzn2023.0.2.x86_64 cracklib-2.9.6-27.amzn2023.0.2.x86_64 crypto-policies-20220428-1.gitdfb10ea.amzn2023.0.2.noarch curl-8.3.0-1.amzn2023.0.2.x86_64 cyrus-sasl-lib-2.1.27-18.amzn2023.0.3.x86_64 diffutils-3.8-1.amzn2023.0.2.x86_64 dwz-0.14-6.amzn2023.0.2.x86_64 ed-1.14.2-10.amzn2023.0.2.x86_64 efi-srpm-macros-5-4.amzn2023.0.5.noarch elfutils-0.188-3.amzn2023.0.2.x86_64 elfutils-debuginfod-client-0.188-3.amzn2023.0.2.x86_64 elfutils-default-yama-scope-0.188-3.amzn2023.0.2.noarch elfutils-libelf-0.188-3.amzn2023.0.2.x86_64 elfutils-libs-0.188-3.amzn2023.0.2.x86_64 file-5.39-7.amzn2023.0.4.x86_64 file-libs-5.39-7.amzn2023.0.4.x86_64 filesystem-3.14-5.amzn2023.0.3.x86_64 findutils-4.8.0-2.amzn2023.0.2.x86_64 fonts-srpm-macros-2.0.5-12.amzn2023.0.2.noarch gawk-5.1.0-3.amzn2023.0.3.x86_64 gdb-minimal-12.1-5.amzn2023.0.3.x86_64 gdbm-libs-1.19-2.amzn2023.0.2.x86_64 ghc-srpm-macros-1.5.0-4.amzn2023.0.2.noarch glibc-2.34-52.amzn2023.0.7.x86_64 glibc-common-2.34-52.amzn2023.0.7.x86_64 glibc-gconv-extra-2.34-52.amzn2023.0.7.x86_64 glibc-minimal-langpack-2.34-52.amzn2023.0.7.x86_64 gmp-6.2.1-2.amzn2023.0.2.x86_64 go-srpm-macros-3.3.1-1.amzn2023.noarch gpg-pubkey-d832c631-6515c85e grep-3.8-1.amzn2023.0.4.x86_64 gzip-1.12-1.amzn2023.0.1.x86_64 info-6.7-10.amzn2023.0.2.x86_64 jansson-2.14-0.amzn2023.x86_64 kernel-srpm-macros-1.0-14.amzn2023.0.2.noarch keyutils-libs-1.6.3-1.amzn2023.x86_64 krb5-libs-1.21-3.amzn2023.0.3.x86_64 libacl-2.3.1-2.amzn2023.0.2.x86_64 libarchive-3.5.3-2.amzn2023.0.3.x86_64 libattr-2.5.1-3.amzn2023.0.2.x86_64 libblkid-2.37.4-1.amzn2023.0.3.x86_64 libbrotli-1.0.9-4.amzn2023.0.2.x86_64 libcap-2.48-2.amzn2023.0.3.x86_64 libcap-ng-0.8.2-4.amzn2023.0.2.x86_64 libcom_err-1.46.5-2.amzn2023.0.2.x86_64 libcurl-8.3.0-1.amzn2023.0.2.x86_64 libdb-5.3.28-49.amzn2023.0.2.x86_64 libeconf-0.4.0-1.amzn2023.0.3.x86_64 libfdisk-2.37.4-1.amzn2023.0.3.x86_64 libffi-3.4.4-1.amzn2023.0.1.x86_64 libgcc-11.4.1-2.amzn2023.0.2.x86_64 libgomp-11.4.1-2.amzn2023.0.2.x86_64 libidn2-2.3.2-1.amzn2023.0.5.x86_64 libmount-2.37.4-1.amzn2023.0.3.x86_64 libnghttp2-1.57.0-1.amzn2023.0.1.x86_64 libpkgconf-1.8.0-4.amzn2023.0.2.x86_64 libpsl-0.21.1-3.amzn2023.0.2.x86_64 libpwquality-1.4.4-6.amzn2023.0.2.x86_64 libselinux-3.4-5.amzn2023.0.2.x86_64 libsemanage-3.4-5.amzn2023.0.2.x86_64 libsepol-3.4-3.amzn2023.0.3.x86_64 libsigsegv-2.13-2.amzn2023.0.2.x86_64 libsmartcols-2.37.4-1.amzn2023.0.3.x86_64 libssh-0.10.5-1.amzn2023.0.2.x86_64 libssh-config-0.10.5-1.amzn2023.0.2.noarch libstdc++-11.4.1-2.amzn2023.0.2.x86_64 libtasn1-4.19.0-1.amzn2023.0.4.x86_64 libunistring-0.9.10-10.amzn2023.0.2.x86_64 libutempter-1.2.1-4.amzn2023.0.2.x86_64 libuuid-2.37.4-1.amzn2023.0.3.x86_64 libverto-0.3.2-1.amzn2023.0.2.x86_64 libxcrypt-4.4.33-7.amzn2023.x86_64 libxml2-2.10.4-1.amzn2023.0.6.x86_64 libzstd-1.5.5-1.amzn2023.0.1.x86_64 lua-libs-5.4.4-3.amzn2023.0.2.x86_64 lua-srpm-macros-1-4.amzn2023.0.2.noarch lz4-libs-1.9.4-1.amzn2023.0.2.x86_64 mpfr-4.1.0-7.amzn2023.0.2.x86_64 ncurses-base-6.2-4.20200222.amzn2023.0.4.noarch ncurses-libs-6.2-4.20200222.amzn2023.0.4.x86_64 ocaml-srpm-macros-6-6.amzn2023.0.2.noarch openblas-srpm-macros-2-9.amzn2023.0.2.noarch openldap-2.4.57-6.amzn2023.0.6.x86_64 openssl-libs-3.0.8-1.amzn2023.0.10.x86_64 p11-kit-0.24.1-2.amzn2023.0.3.x86_64 p11-kit-trust-0.24.1-2.amzn2023.0.3.x86_64 package-notes-srpm-macros-0.4-18.amzn2023.0.5.noarch pam-1.5.1-8.amzn2023.0.3.x86_64 patch-2.7.6-14.amzn2023.0.2.x86_64 pcre2-10.40-1.amzn2023.0.3.x86_64 pcre2-syntax-10.40-1.amzn2023.0.3.noarch perl-srpm-macros-1-39.amzn2023.0.2.noarch pkgconf-1.8.0-4.amzn2023.0.2.x86_64 pkgconf-m4-1.8.0-4.amzn2023.0.2.noarch pkgconf-pkg-config-1.8.0-4.amzn2023.0.2.x86_64 popt-1.18-6.amzn2023.0.2.x86_64 publicsuffix-list-dafsa-20221208-60.amzn2023.noarch python-srpm-macros-3.9-41.amzn2023.0.5.noarch readline-8.1-2.amzn2023.0.2.x86_64 rpm-4.16.1.3-12.amzn2023.0.6.x86_64 rpm-build-4.16.1.3-12.amzn2023.0.6.x86_64 rpm-build-libs-4.16.1.3-12.amzn2023.0.6.x86_64 rpm-libs-4.16.1.3-12.amzn2023.0.6.x86_64 rust-srpm-macros-21-42.amzn2023.0.2.noarch sed-4.8-7.amzn2023.0.2.x86_64 setup-2.13.7-3.amzn2023.0.2.noarch shadow-utils-4.9-12.amzn2023.0.4.x86_64 sqlite-libs-3.40.0-1.amzn2023.0.3.x86_64 system-release-2023.3.20231218-0.amzn2023.noarch systemd-libs-252.16-1.amzn2023.0.1.x86_64 tar-1.34-1.amzn2023.0.3.x86_64 unzip-6.0-57.amzn2023.0.2.x86_64 util-linux-2.37.4-1.amzn2023.0.3.x86_64 util-linux-core-2.37.4-1.amzn2023.0.3.x86_64 which-2.21-26.amzn2023.0.2.x86_64 xxhash-libs-0.8.0-3.amzn2023.0.2.x86_64 xz-5.2.5-9.amzn2023.0.2.x86_64 xz-libs-5.2.5-9.amzn2023.0.2.x86_64 zip-3.0-28.amzn2023.0.2.x86_64 zlib-1.2.11-33.amzn2023.0.5.x86_64 zstd-1.5.5-1.amzn2023.0.1.x86_64 Start: buildsrpm Start: rpmbuild -bs Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1689811200 Wrote: /builddir/build/SRPMS/htslib-1.15.1-3.amzn2023.src.rpm Finish: rpmbuild -bs INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/amazonlinux-2023-x86_64-1704591055.887282/root/var/log/dnf.rpm.log /var/lib/mock/amazonlinux-2023-x86_64-1704591055.887282/root/var/log/dnf.librepo.log /var/lib/mock/amazonlinux-2023-x86_64-1704591055.887282/root/var/log/dnf.log Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-mccg0cke/htslib/htslib.spec) Config(child) 0 minutes 24 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-1.15.1-3.amzn2023.src.rpm) Config(amazonlinux-2023-x86_64) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/amazonlinux-2023-x86_64-bootstrap-1704591055.887282/root. INFO: reusing tmpfs at /var/lib/mock/amazonlinux-2023-x86_64-bootstrap-1704591055.887282/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/amazonlinux-2023-x86_64-1704591055.887282/root. INFO: calling preinit hooks INFO: enabled root cache Start: unpacking root cache Finish: unpacking root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-4.16.1.3-12.amzn2023.0.6.x86_64 python3-dnf-4.12.0-2.amzn2023.0.4.noarch python3-dnf-plugins-core-4.1.0-1.amzn2023.0.3.noarch yum-4.12.0-2.amzn2023.0.4.noarch Finish: chroot init Start: build phase for htslib-1.15.1-3.amzn2023.src.rpm Start: build setup for htslib-1.15.1-3.amzn2023.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1689811200 Wrote: /builddir/build/SRPMS/htslib-1.15.1-3.amzn2023.src.rpm No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 33 kB/s | 1.5 kB 00:00 Amazon Linux 2023 repository - x86_64 9.3 kB/s | 3.6 kB 00:00 Dependencies resolved. ================================================================================ Package Arch Version Repository Size ================================================================================ Installing: bzip2-devel x86_64 1.0.8-6.amzn2023.0.2 amazonlinux 214 k gcc x86_64 11.4.1-2.amzn2023.0.2 amazonlinux 32 M libcurl-devel x86_64 8.3.0-1.amzn2023.0.2 amazonlinux 903 k make x86_64 1:4.3-5.amzn2023.0.2 amazonlinux 534 k openssl-devel x86_64 1:3.0.8-1.amzn2023.0.10 amazonlinux 3.0 M perl-Data-Dumper x86_64 2.174-460.amzn2023.0.2 amazonlinux 55 k perl-FindBin noarch 1.51-477.amzn2023.0.6 amazonlinux 14 k perl-Getopt-Long noarch 1:2.52-2.amzn2023.0.2 amazonlinux 60 k perl-interpreter x86_64 4:5.32.1-477.amzn2023.0.6 amazonlinux 71 k perl-lib x86_64 0.65-477.amzn2023.0.6 amazonlinux 15 k xz-devel x86_64 5.2.5-9.amzn2023.0.2 amazonlinux 53 k zlib-devel x86_64 1.2.11-33.amzn2023.0.5 amazonlinux 45 k Installing dependencies: annobin-docs noarch 10.93-1.amzn2023.0.1 amazonlinux 92 k annobin-plugin-gcc x86_64 10.93-1.amzn2023.0.1 amazonlinux 887 k cpp x86_64 11.4.1-2.amzn2023.0.2 amazonlinux 10 M gc x86_64 8.0.4-5.amzn2023.0.2 amazonlinux 105 k glibc-devel x86_64 2.34-52.amzn2023.0.7 amazonlinux 45 k glibc-headers-x86 noarch 2.34-52.amzn2023.0.7 amazonlinux 446 k groff-base x86_64 1.22.4-7.amzn2023.0.2 amazonlinux 1.0 M guile22 x86_64 2.2.7-2.amzn2023.0.3 amazonlinux 6.4 M kernel-headers x86_64 6.1.66-91.160.amzn2023 amazonlinux 1.4 M libmpc x86_64 1.2.1-2.amzn2023.0.2 amazonlinux 62 k libtool-ltdl x86_64 2.4.7-1.amzn2023.0.3 amazonlinux 38 k libxcrypt-devel x86_64 4.4.33-7.amzn2023 amazonlinux 32 k ncurses x86_64 6.2-4.20200222.amzn2023.0.4 amazonlinux 394 k perl-B x86_64 1.80-477.amzn2023.0.6 amazonlinux 179 k perl-Carp noarch 1.50-458.amzn2023.0.2 amazonlinux 29 k perl-Class-Struct noarch 0.66-477.amzn2023.0.6 amazonlinux 22 k perl-DynaLoader x86_64 1.47-477.amzn2023.0.6 amazonlinux 26 k perl-Encode x86_64 4:3.15-462.amzn2023.0.2 amazonlinux 1.7 M perl-Errno x86_64 1.30-477.amzn2023.0.6 amazonlinux 15 k perl-Exporter noarch 5.74-459.amzn2023.0.2 amazonlinux 31 k perl-Fcntl x86_64 1.13-477.amzn2023.0.6 amazonlinux 21 k perl-File-Basename noarch 2.85-477.amzn2023.0.6 amazonlinux 18 k perl-File-Path noarch 2.18-2.amzn2023.0.2 amazonlinux 36 k perl-File-Temp noarch 1:0.231.100-2.amzn2023.0.2 amazonlinux 60 k perl-File-stat noarch 1.09-477.amzn2023.0.6 amazonlinux 17 k perl-Getopt-Std noarch 1.12-477.amzn2023.0.6 amazonlinux 16 k perl-HTTP-Tiny noarch 0.078-1.amzn2023.0.3 amazonlinux 56 k perl-IO x86_64 1.43-477.amzn2023.0.6 amazonlinux 87 k perl-IPC-Open3 noarch 1.21-477.amzn2023.0.6 amazonlinux 23 k perl-MIME-Base64 x86_64 3.16-2.amzn2023.0.2 amazonlinux 31 k perl-POSIX x86_64 1.94-477.amzn2023.0.6 amazonlinux 97 k perl-PathTools x86_64 3.78-459.amzn2023.0.2 amazonlinux 85 k perl-Pod-Escapes noarch 1:1.07-458.amzn2023.0.2 amazonlinux 20 k perl-Pod-Perldoc noarch 3.28.01-459.amzn2023.0.3 amazonlinux 84 k perl-Pod-Simple noarch 1:3.42-2.amzn2023.0.2 amazonlinux 215 k perl-Pod-Usage noarch 4:2.01-2.amzn2023.0.2 amazonlinux 41 k perl-Scalar-List-Utils x86_64 4:1.56-459.amzn2023.0.2 amazonlinux 71 k perl-SelectSaver noarch 1.02-477.amzn2023.0.6 amazonlinux 12 k perl-Socket x86_64 4:2.032-1.amzn2023.0.2 amazonlinux 55 k perl-Storable x86_64 1:3.21-458.amzn2023.0.2 amazonlinux 96 k perl-Symbol noarch 1.08-477.amzn2023.0.6 amazonlinux 15 k perl-Term-ANSIColor noarch 5.01-459.amzn2023.0.2 amazonlinux 48 k perl-Term-Cap noarch 1.17-458.amzn2023.0.2 amazonlinux 22 k perl-Text-ParseWords noarch 3.30-458.amzn2023.0.2 amazonlinux 17 k perl-Text-Tabs+Wrap noarch 2021.0726-1.amzn2023.0.1 amazonlinux 22 k perl-Time-Local noarch 2:1.300-5.amzn2023.0.2 amazonlinux 34 k perl-constant noarch 1.33-459.amzn2023.0.2 amazonlinux 23 k perl-if noarch 0.60.800-477.amzn2023.0.6 amazonlinux 14 k perl-libs x86_64 4:5.32.1-477.amzn2023.0.6 amazonlinux 2.0 M perl-mro x86_64 1.23-477.amzn2023.0.6 amazonlinux 29 k perl-overload noarch 1.31-477.amzn2023.0.6 amazonlinux 46 k perl-overloading noarch 0.02-477.amzn2023.0.6 amazonlinux 13 k perl-parent noarch 1:0.238-458.amzn2023.0.2 amazonlinux 14 k perl-podlators noarch 1:4.14-458.amzn2023.0.2 amazonlinux 112 k perl-subs noarch 1.03-477.amzn2023.0.6 amazonlinux 12 k perl-vars noarch 1.05-477.amzn2023.0.6 amazonlinux 13 k Transaction Summary ================================================================================ Install 68 Packages Total size: 64 M Total download size: 4.3 M Installed size: 201 M Downloading Packages: [SKIPPED] perl-MIME-Base64-3.16-2.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] cpp-11.4.1-2.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] xz-devel-5.2.5-9.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] annobin-plugin-gcc-10.93-1.amzn2023.0.1.x86_64.rpm: Already downloaded [SKIPPED] perl-Encode-3.15-462.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] perl-IO-1.43-477.amzn2023.0.6.x86_64.rpm: Already downloaded [SKIPPED] gcc-11.4.1-2.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] perl-Errno-1.30-477.amzn2023.0.6.x86_64.rpm: Already downloaded [SKIPPED] libmpc-1.2.1-2.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] glibc-devel-2.34-52.amzn2023.0.7.x86_64.rpm: Already downloaded [SKIPPED] perl-PathTools-3.78-459.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] groff-base-1.22.4-7.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] perl-POSIX-1.94-477.amzn2023.0.6.x86_64.rpm: Already downloaded [SKIPPED] perl-Scalar-List-Utils-1.56-459.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] libxcrypt-devel-4.4.33-7.amzn2023.x86_64.rpm: Already downloaded [SKIPPED] gc-8.0.4-5.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] perl-libs-5.32.1-477.amzn2023.0.6.x86_64.rpm: Already downloaded [SKIPPED] perl-Storable-3.21-458.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] zlib-devel-1.2.11-33.amzn2023.0.5.x86_64.rpm: Already downloaded [SKIPPED] guile22-2.2.7-2.amzn2023.0.3.x86_64.rpm: Already downloaded [SKIPPED] libtool-ltdl-2.4.7-1.amzn2023.0.3.x86_64.rpm: Already downloaded [SKIPPED] kernel-headers-6.1.66-91.160.amzn2023.x86_64.rpm: Already downloaded [SKIPPED] perl-interpreter-5.32.1-477.amzn2023.0.6.x86_64.rpm: Already downloaded [SKIPPED] ncurses-6.2-4.20200222.amzn2023.0.4.x86_64.rpm: Already downloaded [SKIPPED] perl-mro-1.23-477.amzn2023.0.6.x86_64.rpm: Already downloaded [SKIPPED] perl-Socket-2.032-1.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] perl-DynaLoader-1.47-477.amzn2023.0.6.x86_64.rpm: Already downloaded [SKIPPED] make-4.3-5.amzn2023.0.2.x86_64.rpm: Already downloaded [SKIPPED] perl-Fcntl-1.13-477.amzn2023.0.6.x86_64.rpm: Already downloaded [SKIPPED] perl-podlators-4.14-458.amzn2023.0.2.noarch.rpm: Already downloaded [SKIPPED] perl-Carp-1.50-458.amzn2023.0.2.noarch.rpm: Already downloaded [SKIPPED] perl-parent-0.238-458.amzn2023.0.2.noarch.rpm: Already downloaded [SKIPPED] perl-Time-Local-1.300-5.amzn2023.0.2.noarch.rpm: Already downloaded [SKIPPED] perl-constant-1.33-459.amzn2023.0.2.noarch.rpm: Already downloaded [SKIPPED] perl-Text-ParseWords-3.30-458.amzn2023.0.2.noarch.rpm: Already downloaded [SKIPPED] perl-File-Temp-0.231.100-2.amzn2023.0.2.noarch.rpm: Already downloaded [SKIPPED] perl-Term-ANSIColor-5.01-459.amzn2023.0.2.noarch.rpm: Already downloaded [SKIPPED] perl-if-0.60.800-477.amzn2023.0.6.noarch.rpm: Already downloaded [SKIPPED] perl-Term-Cap-1.17-458.amzn2023.0.2.noarch.rpm: Already downloaded [SKIPPED] perl-Text-Tabs+Wrap-2021.0726-1.amzn2023.0.1.noarch.rpm: Already downloaded [SKIPPED] perl-overloading-0.02-477.amzn2023.0.6.noarch.rpm: Already downloaded [SKIPPED] perl-Exporter-5.74-459.amzn2023.0.2.noarch.rpm: Already downloaded [SKIPPED] perl-File-Basename-2.85-477.amzn2023.0.6.noarch.rpm: Already downloaded [SKIPPED] perl-subs-1.03-477.amzn2023.0.6.noarch.rpm: Already downloaded [SKIPPED] perl-File-stat-1.09-477.amzn2023.0.6.noarch.rpm: Already downloaded [SKIPPED] perl-Pod-Simple-3.42-2.amzn2023.0.2.noarch.rpm: Already downloaded [SKIPPED] perl-Getopt-Long-2.52-2.amzn2023.0.2.noarch.rpm: Already downloaded [SKIPPED] perl-overload-1.31-477.amzn2023.0.6.noarch.rpm: Already downloaded [SKIPPED] perl-Getopt-Std-1.12-477.amzn2023.0.6.noarch.rpm: Already downloaded [SKIPPED] glibc-headers-x86-2.34-52.amzn2023.0.7.noarch.rpm: Already downloaded [SKIPPED] perl-IPC-Open3-1.21-477.amzn2023.0.6.noarch.rpm: Already downloaded [SKIPPED] perl-HTTP-Tiny-0.078-1.amzn2023.0.3.noarch.rpm: Already downloaded [SKIPPED] perl-Pod-Perldoc-3.28.01-459.amzn2023.0.3.noarch.rpm: Already downloaded [SKIPPED] perl-Pod-Usage-2.01-2.amzn2023.0.2.noarch.rpm: Already downloaded [SKIPPED] perl-Symbol-1.08-477.amzn2023.0.6.noarch.rpm: Already downloaded [SKIPPED] perl-SelectSaver-1.02-477.amzn2023.0.6.noarch.rpm: Already downloaded [SKIPPED] perl-vars-1.05-477.amzn2023.0.6.noarch.rpm: Already downloaded [SKIPPED] annobin-docs-10.93-1.amzn2023.0.1.noarch.rpm: Already downloaded [SKIPPED] perl-Pod-Escapes-1.07-458.amzn2023.0.2.noarch.rpm: Already downloaded [SKIPPED] perl-File-Path-2.18-2.amzn2023.0.2.noarch.rpm: Already downloaded [SKIPPED] perl-Class-Struct-0.66-477.amzn2023.0.6.noarch.rpm: Already downloaded (62/68): perl-B-1.80-477.amzn2023.0.6.x86_64.rp 2.3 MB/s | 179 kB 00:00 (63/68): libcurl-devel-8.3.0-1.amzn2023.0.2.x86 7.8 MB/s | 903 kB 00:00 (64/68): perl-Data-Dumper-2.174-460.amzn2023.0. 1.2 MB/s | 55 kB 00:00 (65/68): openssl-devel-3.0.8-1.amzn2023.0.10.x8 23 MB/s | 3.0 MB 00:00 (66/68): perl-lib-0.65-477.amzn2023.0.6.x86_64. 917 kB/s | 15 kB 00:00 (67/68): bzip2-devel-1.0.8-6.amzn2023.0.2.x86_6 12 MB/s | 214 kB 00:00 (68/68): perl-FindBin-1.51-477.amzn2023.0.6.noa 1.2 MB/s | 14 kB 00:00 -------------------------------------------------------------------------------- Total 8.4 MB/s | 4.3 MB 00:00 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Installing : libmpc-1.2.1-2.amzn2023.0.2.x86_64 1/68 Installing : cpp-11.4.1-2.amzn2023.0.2.x86_64 2/68 Installing : annobin-docs-10.93-1.amzn2023.0.1.noarch 3/68 Installing : glibc-headers-x86-2.34-52.amzn2023.0.7.noarch 4/68 Installing : ncurses-6.2-4.20200222.amzn2023.0.4.x86_64 5/68 Installing : kernel-headers-6.1.66-91.160.amzn2023.x86_64 6/68 Installing : libxcrypt-devel-4.4.33-7.amzn2023.x86_64 7/68 Installing : glibc-devel-2.34-52.amzn2023.0.7.x86_64 8/68 Installing : libtool-ltdl-2.4.7-1.amzn2023.0.3.x86_64 9/68 Installing : gc-8.0.4-5.amzn2023.0.2.x86_64 10/68 Installing : guile22-2.2.7-2.amzn2023.0.3.x86_64 11/68 Installing : make-1:4.3-5.amzn2023.0.2.x86_64 12/68 Installing : gcc-11.4.1-2.amzn2023.0.2.x86_64 13/68 Running scriptlet: gcc-11.4.1-2.amzn2023.0.2.x86_64 13/68 Running scriptlet: groff-base-1.22.4-7.amzn2023.0.2.x86_64 14/68 Installing : groff-base-1.22.4-7.amzn2023.0.2.x86_64 14/68 Running scriptlet: groff-base-1.22.4-7.amzn2023.0.2.x86_64 14/68 Installing : perl-if-0.60.800-477.amzn2023.0.6.noarch 15/68 Installing : perl-Text-Tabs+Wrap-2021.0726-1.amzn2023.0.1.noarc 16/68 Installing : perl-Time-Local-2:1.300-5.amzn2023.0.2.noarch 17/68 Installing : perl-Pod-Escapes-1:1.07-458.amzn2023.0.2.noarch 18/68 Installing : perl-File-Path-2.18-2.amzn2023.0.2.noarch 19/68 Installing : perl-POSIX-1.94-477.amzn2023.0.6.x86_64 20/68 Installing : perl-Term-ANSIColor-5.01-459.amzn2023.0.2.noarch 21/68 Installing : perl-subs-1.03-477.amzn2023.0.6.noarch 22/68 Installing : perl-Term-Cap-1.17-458.amzn2023.0.2.noarch 23/68 Installing : perl-File-Temp-1:0.231.100-2.amzn2023.0.2.noarch 24/68 Installing : perl-IPC-Open3-1.21-477.amzn2023.0.6.noarch 25/68 Installing : perl-Class-Struct-0.66-477.amzn2023.0.6.noarch 26/68 Installing : perl-Pod-Simple-1:3.42-2.amzn2023.0.2.noarch 27/68 Installing : perl-HTTP-Tiny-0.078-1.amzn2023.0.3.noarch 28/68 Installing : perl-Socket-4:2.032-1.amzn2023.0.2.x86_64 29/68 Installing : perl-Symbol-1.08-477.amzn2023.0.6.noarch 30/68 Installing : perl-SelectSaver-1.02-477.amzn2023.0.6.noarch 31/68 Installing : perl-File-stat-1.09-477.amzn2023.0.6.noarch 32/68 Installing : perl-podlators-1:4.14-458.amzn2023.0.2.noarch 33/68 Installing : perl-Pod-Perldoc-3.28.01-459.amzn2023.0.3.noarch 34/68 Installing : perl-mro-1.23-477.amzn2023.0.6.x86_64 35/68 Installing : perl-Fcntl-1.13-477.amzn2023.0.6.x86_64 36/68 Installing : perl-overloading-0.02-477.amzn2023.0.6.noarch 37/68 Installing : perl-Text-ParseWords-3.30-458.amzn2023.0.2.noarch 38/68 Installing : perl-IO-1.43-477.amzn2023.0.6.x86_64 39/68 Installing : perl-Pod-Usage-4:2.01-2.amzn2023.0.2.noarch 40/68 Installing : perl-parent-1:0.238-458.amzn2023.0.2.noarch 41/68 Installing : perl-Errno-1.30-477.amzn2023.0.6.x86_64 42/68 Installing : perl-Scalar-List-Utils-4:1.56-459.amzn2023.0.2.x86 43/68 Installing : perl-constant-1.33-459.amzn2023.0.2.noarch 44/68 Installing : perl-File-Basename-2.85-477.amzn2023.0.6.noarch 45/68 Installing : perl-overload-1.31-477.amzn2023.0.6.noarch 46/68 Installing : perl-Getopt-Std-1.12-477.amzn2023.0.6.noarch 47/68 Installing : perl-vars-1.05-477.amzn2023.0.6.noarch 48/68 Installing : perl-Storable-1:3.21-458.amzn2023.0.2.x86_64 49/68 Installing : perl-Getopt-Long-1:2.52-2.amzn2023.0.2.noarch 50/68 Installing : perl-MIME-Base64-3.16-2.amzn2023.0.2.x86_64 51/68 Installing : perl-DynaLoader-1.47-477.amzn2023.0.6.x86_64 52/68 Installing : perl-PathTools-3.78-459.amzn2023.0.2.x86_64 53/68 Installing : perl-Carp-1.50-458.amzn2023.0.2.noarch 54/68 Installing : perl-Exporter-5.74-459.amzn2023.0.2.noarch 55/68 Installing : perl-Encode-4:3.15-462.amzn2023.0.2.x86_64 56/68 Installing : perl-libs-4:5.32.1-477.amzn2023.0.6.x86_64 57/68 Installing : perl-interpreter-4:5.32.1-477.amzn2023.0.6.x86_64 58/68 Installing : perl-Data-Dumper-2.174-460.amzn2023.0.2.x86_64 59/68 Installing : perl-B-1.80-477.amzn2023.0.6.x86_64 60/68 Installing : perl-lib-0.65-477.amzn2023.0.6.x86_64 61/68 Installing : perl-FindBin-1.51-477.amzn2023.0.6.noarch 62/68 Installing : annobin-plugin-gcc-10.93-1.amzn2023.0.1.x86_64 63/68 Running scriptlet: annobin-plugin-gcc-10.93-1.amzn2023.0.1.x86_64 63/68 Installing : bzip2-devel-1.0.8-6.amzn2023.0.2.x86_64 64/68 Installing : zlib-devel-1.2.11-33.amzn2023.0.5.x86_64 65/68 Installing : openssl-devel-1:3.0.8-1.amzn2023.0.10.x86_64 66/68 Installing : libcurl-devel-8.3.0-1.amzn2023.0.2.x86_64 67/68 Installing : xz-devel-5.2.5-9.amzn2023.0.2.x86_64 68/68 Running scriptlet: xz-devel-5.2.5-9.amzn2023.0.2.x86_64 68/68 Verifying : perl-MIME-Base64-3.16-2.amzn2023.0.2.x86_64 1/68 Verifying : cpp-11.4.1-2.amzn2023.0.2.x86_64 2/68 Verifying : xz-devel-5.2.5-9.amzn2023.0.2.x86_64 3/68 Verifying : annobin-plugin-gcc-10.93-1.amzn2023.0.1.x86_64 4/68 Verifying : perl-Encode-4:3.15-462.amzn2023.0.2.x86_64 5/68 Verifying : libcurl-devel-8.3.0-1.amzn2023.0.2.x86_64 6/68 Verifying : perl-IO-1.43-477.amzn2023.0.6.x86_64 7/68 Verifying : gcc-11.4.1-2.amzn2023.0.2.x86_64 8/68 Verifying : openssl-devel-1:3.0.8-1.amzn2023.0.10.x86_64 9/68 Verifying : perl-Errno-1.30-477.amzn2023.0.6.x86_64 10/68 Verifying : perl-B-1.80-477.amzn2023.0.6.x86_64 11/68 Verifying : perl-Data-Dumper-2.174-460.amzn2023.0.2.x86_64 12/68 Verifying : libmpc-1.2.1-2.amzn2023.0.2.x86_64 13/68 Verifying : glibc-devel-2.34-52.amzn2023.0.7.x86_64 14/68 Verifying : perl-PathTools-3.78-459.amzn2023.0.2.x86_64 15/68 Verifying : groff-base-1.22.4-7.amzn2023.0.2.x86_64 16/68 Verifying : perl-POSIX-1.94-477.amzn2023.0.6.x86_64 17/68 Verifying : perl-Scalar-List-Utils-4:1.56-459.amzn2023.0.2.x86 18/68 Verifying : libxcrypt-devel-4.4.33-7.amzn2023.x86_64 19/68 Verifying : gc-8.0.4-5.amzn2023.0.2.x86_64 20/68 Verifying : perl-libs-4:5.32.1-477.amzn2023.0.6.x86_64 21/68 Verifying : perl-Storable-1:3.21-458.amzn2023.0.2.x86_64 22/68 Verifying : zlib-devel-1.2.11-33.amzn2023.0.5.x86_64 23/68 Verifying : guile22-2.2.7-2.amzn2023.0.3.x86_64 24/68 Verifying : libtool-ltdl-2.4.7-1.amzn2023.0.3.x86_64 25/68 Verifying : perl-lib-0.65-477.amzn2023.0.6.x86_64 26/68 Verifying : kernel-headers-6.1.66-91.160.amzn2023.x86_64 27/68 Verifying : perl-interpreter-4:5.32.1-477.amzn2023.0.6.x86_64 28/68 Verifying : ncurses-6.2-4.20200222.amzn2023.0.4.x86_64 29/68 Verifying : perl-mro-1.23-477.amzn2023.0.6.x86_64 30/68 Verifying : bzip2-devel-1.0.8-6.amzn2023.0.2.x86_64 31/68 Verifying : perl-Socket-4:2.032-1.amzn2023.0.2.x86_64 32/68 Verifying : perl-DynaLoader-1.47-477.amzn2023.0.6.x86_64 33/68 Verifying : make-1:4.3-5.amzn2023.0.2.x86_64 34/68 Verifying : perl-Fcntl-1.13-477.amzn2023.0.6.x86_64 35/68 Verifying : perl-podlators-1:4.14-458.amzn2023.0.2.noarch 36/68 Verifying : perl-Carp-1.50-458.amzn2023.0.2.noarch 37/68 Verifying : perl-parent-1:0.238-458.amzn2023.0.2.noarch 38/68 Verifying : perl-Time-Local-2:1.300-5.amzn2023.0.2.noarch 39/68 Verifying : perl-constant-1.33-459.amzn2023.0.2.noarch 40/68 Verifying : perl-Text-ParseWords-3.30-458.amzn2023.0.2.noarch 41/68 Verifying : perl-FindBin-1.51-477.amzn2023.0.6.noarch 42/68 Verifying : perl-File-Temp-1:0.231.100-2.amzn2023.0.2.noarch 43/68 Verifying : perl-Term-ANSIColor-5.01-459.amzn2023.0.2.noarch 44/68 Verifying : perl-if-0.60.800-477.amzn2023.0.6.noarch 45/68 Verifying : perl-Term-Cap-1.17-458.amzn2023.0.2.noarch 46/68 Verifying : perl-Text-Tabs+Wrap-2021.0726-1.amzn2023.0.1.noarc 47/68 Verifying : perl-overloading-0.02-477.amzn2023.0.6.noarch 48/68 Verifying : perl-Exporter-5.74-459.amzn2023.0.2.noarch 49/68 Verifying : perl-File-Basename-2.85-477.amzn2023.0.6.noarch 50/68 Verifying : perl-subs-1.03-477.amzn2023.0.6.noarch 51/68 Verifying : perl-File-stat-1.09-477.amzn2023.0.6.noarch 52/68 Verifying : perl-Pod-Simple-1:3.42-2.amzn2023.0.2.noarch 53/68 Verifying : perl-Getopt-Long-1:2.52-2.amzn2023.0.2.noarch 54/68 Verifying : perl-overload-1.31-477.amzn2023.0.6.noarch 55/68 Verifying : perl-Getopt-Std-1.12-477.amzn2023.0.6.noarch 56/68 Verifying : glibc-headers-x86-2.34-52.amzn2023.0.7.noarch 57/68 Verifying : perl-IPC-Open3-1.21-477.amzn2023.0.6.noarch 58/68 Verifying : perl-HTTP-Tiny-0.078-1.amzn2023.0.3.noarch 59/68 Verifying : perl-Pod-Perldoc-3.28.01-459.amzn2023.0.3.noarch 60/68 Verifying : perl-Pod-Usage-4:2.01-2.amzn2023.0.2.noarch 61/68 Verifying : perl-Symbol-1.08-477.amzn2023.0.6.noarch 62/68 Verifying : perl-SelectSaver-1.02-477.amzn2023.0.6.noarch 63/68 Verifying : perl-vars-1.05-477.amzn2023.0.6.noarch 64/68 Verifying : annobin-docs-10.93-1.amzn2023.0.1.noarch 65/68 Verifying : perl-Pod-Escapes-1:1.07-458.amzn2023.0.2.noarch 66/68 Verifying : perl-File-Path-2.18-2.amzn2023.0.2.noarch 67/68 Verifying : perl-Class-Struct-0.66-477.amzn2023.0.6.noarch 68/68 Installed: annobin-docs-10.93-1.amzn2023.0.1.noarch annobin-plugin-gcc-10.93-1.amzn2023.0.1.x86_64 bzip2-devel-1.0.8-6.amzn2023.0.2.x86_64 cpp-11.4.1-2.amzn2023.0.2.x86_64 gc-8.0.4-5.amzn2023.0.2.x86_64 gcc-11.4.1-2.amzn2023.0.2.x86_64 glibc-devel-2.34-52.amzn2023.0.7.x86_64 glibc-headers-x86-2.34-52.amzn2023.0.7.noarch groff-base-1.22.4-7.amzn2023.0.2.x86_64 guile22-2.2.7-2.amzn2023.0.3.x86_64 kernel-headers-6.1.66-91.160.amzn2023.x86_64 libcurl-devel-8.3.0-1.amzn2023.0.2.x86_64 libmpc-1.2.1-2.amzn2023.0.2.x86_64 libtool-ltdl-2.4.7-1.amzn2023.0.3.x86_64 libxcrypt-devel-4.4.33-7.amzn2023.x86_64 make-1:4.3-5.amzn2023.0.2.x86_64 ncurses-6.2-4.20200222.amzn2023.0.4.x86_64 openssl-devel-1:3.0.8-1.amzn2023.0.10.x86_64 perl-B-1.80-477.amzn2023.0.6.x86_64 perl-Carp-1.50-458.amzn2023.0.2.noarch perl-Class-Struct-0.66-477.amzn2023.0.6.noarch perl-Data-Dumper-2.174-460.amzn2023.0.2.x86_64 perl-DynaLoader-1.47-477.amzn2023.0.6.x86_64 perl-Encode-4:3.15-462.amzn2023.0.2.x86_64 perl-Errno-1.30-477.amzn2023.0.6.x86_64 perl-Exporter-5.74-459.amzn2023.0.2.noarch perl-Fcntl-1.13-477.amzn2023.0.6.x86_64 perl-File-Basename-2.85-477.amzn2023.0.6.noarch perl-File-Path-2.18-2.amzn2023.0.2.noarch perl-File-Temp-1:0.231.100-2.amzn2023.0.2.noarch perl-File-stat-1.09-477.amzn2023.0.6.noarch perl-FindBin-1.51-477.amzn2023.0.6.noarch perl-Getopt-Long-1:2.52-2.amzn2023.0.2.noarch perl-Getopt-Std-1.12-477.amzn2023.0.6.noarch perl-HTTP-Tiny-0.078-1.amzn2023.0.3.noarch perl-IO-1.43-477.amzn2023.0.6.x86_64 perl-IPC-Open3-1.21-477.amzn2023.0.6.noarch perl-MIME-Base64-3.16-2.amzn2023.0.2.x86_64 perl-POSIX-1.94-477.amzn2023.0.6.x86_64 perl-PathTools-3.78-459.amzn2023.0.2.x86_64 perl-Pod-Escapes-1:1.07-458.amzn2023.0.2.noarch perl-Pod-Perldoc-3.28.01-459.amzn2023.0.3.noarch perl-Pod-Simple-1:3.42-2.amzn2023.0.2.noarch perl-Pod-Usage-4:2.01-2.amzn2023.0.2.noarch perl-Scalar-List-Utils-4:1.56-459.amzn2023.0.2.x86_64 perl-SelectSaver-1.02-477.amzn2023.0.6.noarch perl-Socket-4:2.032-1.amzn2023.0.2.x86_64 perl-Storable-1:3.21-458.amzn2023.0.2.x86_64 perl-Symbol-1.08-477.amzn2023.0.6.noarch perl-Term-ANSIColor-5.01-459.amzn2023.0.2.noarch perl-Term-Cap-1.17-458.amzn2023.0.2.noarch perl-Text-ParseWords-3.30-458.amzn2023.0.2.noarch perl-Text-Tabs+Wrap-2021.0726-1.amzn2023.0.1.noarch perl-Time-Local-2:1.300-5.amzn2023.0.2.noarch perl-constant-1.33-459.amzn2023.0.2.noarch perl-if-0.60.800-477.amzn2023.0.6.noarch perl-interpreter-4:5.32.1-477.amzn2023.0.6.x86_64 perl-lib-0.65-477.amzn2023.0.6.x86_64 perl-libs-4:5.32.1-477.amzn2023.0.6.x86_64 perl-mro-1.23-477.amzn2023.0.6.x86_64 perl-overload-1.31-477.amzn2023.0.6.noarch perl-overloading-0.02-477.amzn2023.0.6.noarch perl-parent-1:0.238-458.amzn2023.0.2.noarch perl-podlators-1:4.14-458.amzn2023.0.2.noarch perl-subs-1.03-477.amzn2023.0.6.noarch perl-vars-1.05-477.amzn2023.0.6.noarch xz-devel-5.2.5-9.amzn2023.0.2.x86_64 zlib-devel-1.2.11-33.amzn2023.0.5.x86_64 Complete! Finish: build setup for htslib-1.15.1-3.amzn2023.src.rpm Start: rpmbuild htslib-1.15.1-3.amzn2023.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1689811200 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.qufgio + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf htslib-1.15.1 + /usr/bin/bzip2 -dc /builddir/build/SOURCES/htslib-1.15.1.tar.bz2 + /usr/bin/tar -xof - + STATUS=0 + '[' 0 -ne 0 ']' + cd htslib-1.15.1 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . Patch #0 (htslib-1.15.1-gcc12.patch): + echo 'Patch #0 (htslib-1.15.1-gcc12.patch):' + /usr/bin/patch --no-backup-if-mismatch -p1 --fuzz=0 patching file htscodecs/htscodecs/rANS_word.h + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.X8Lhfp + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-3.amzn2023.x86_64.ld' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + '[' -f /usr/lib/rpm/generate-rpm-note.sh ']' + /usr/lib/rpm/generate-rpm-note.sh htslib 1.15.1-3.amzn2023 x86_64 + cd htslib-1.15.1 + CFLAGS='-O2 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-3.amzn2023.x86_64.ld' + 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 --- ./configure.backup 2022-04-07 15:42:52.000000000 +0000 +++ ./configure 2024-01-07 01:31:29.919304201 +0000 @@ -1697,7 +1697,7 @@ #ifdef __cplusplus extern "C" #endif -char $2 (); +__attribute__ ((used)) char $2 (); /* The GNU C library defines this for functions which it implements to always fail with ENOSYS. Some functions are actually named something starting with __ and the normal name is an alias. */ + /usr/bin/sed --in-place=.backup '1{$!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* .* \\(.*\\)$/extern char \\1;/p'\''"#' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + '[' 1 = 1 ']' +++ dirname ./configure ++ find . -name config.guess -o -name config.sub + '[' 1 = 1 ']' + '[' x '!=' 'x-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' ']' ++ find . -name ltmain.sh + ./configure --build=x86_64-amazon-linux-gnu --host=x86_64-amazon-linux-gnu --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/libexec --localstatedir=/var --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info 'CFLAGS=-O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' 'LDFLAGS=-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-3.amzn2023.x86_64.ld' --prefix=/usr --libdir=/usr/lib64 --enable-plugins '--with-plugin-path=/usr/local/libexec/htslib:$(plugindir)' --enable-gcs --enable-libcurl --enable-s3 configure: WARNING: unrecognized options: --disable-dependency-tracking checking for x86_64-amazon-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 we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for x86_64-amazon-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 x86_64-amazon-linux-gnu-pkg-config... /usr/bin/x86_64-amazon-linux-gnu-pkg-config checking pkg-config is at least version 0.9.0... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking shared library type for x86_64-amazon-linux-gnu... plain .so checking whether the compiler accepts -fvisibility=hidden... yes checking how to run the C preprocessor... gcc -E checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... yes 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 checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes 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 -j2 V=1 VERBOSE=1 gcc -O2 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 gcc -O2 -ftree-vectorize -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 echo '#define HTS_VERSION_TEXT "1.15.1"' > version.h echo '#define HTS_CC "gcc"' > config_vars.h echo '#define HTS_CPPFLAGS ""' >> config_vars.h echo '#define HTS_CFLAGS "-O2 -ftree-vectorize -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"' >> config_vars.h echo '#define HTS_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 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-3.amzn2023.x86_64.ld -fvisibility=hidden -rdynamic"' >> config_vars.h echo '#define HTS_LIBS "-llzma -lbz2 -lz -lm "' >> config_vars.h gcc -O2 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 gcc -O2 -ftree-vectorize -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 -ftree-vectorize -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 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 -ftree-vectorize -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 -ftree-vectorize -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 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 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-3.amzn2023.x86_64.ld -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 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-3.amzn2023.x86_64.ld -fvisibility=hidden -rdynamic -o test/plugins-dlhts test/plugins-dlhts.o -llzma -lbz2 -lz -lm 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 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_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o plugin.o ranlib libhts.a 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 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-3.amzn2023.x86_64.ld -fvisibility=hidden -rdynamic -o bgzip bgzip.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 12 LTRANS jobs gcc -shared -Wl,-soname,libhts.so.3 -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 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-3.amzn2023.x86_64.ld -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 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_static.pico htscodecs/htscodecs/rle.pico htscodecs/htscodecs/tokenise_name3.pico plugin.pico -llzma -lbz2 -lz -lm -lpthread ln -sf libhts.so libhts.so.3 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 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-3.amzn2023.x86_64.ld -fvisibility=hidden -rdynamic -o htsfile htsfile.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 15 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 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-3.amzn2023.x86_64.ld -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 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-3.amzn2023.x86_64.ld -fvisibility=hidden -rdynamic -o hfile_gcs.so hfile_gcs.pico libhts.so -llzma -lbz2 -lz -lm -lpthread gcc -shared -Wl,-E -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-3.amzn2023.x86_64.ld -fvisibility=hidden -rdynamic -o hfile_s3.so hfile_s3.pico libhts.so -llzma -lbz2 -lz -lm -lcrypto -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 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-3.amzn2023.x86_64.ld -fvisibility=hidden -rdynamic -o hfile_s3_write.so hfile_s3_write.pico libhts.so -llzma -lbz2 -lz -lm -lcrypto -lcurl -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-3.amzn2023.x86_64.ld -fvisibility=hidden -rdynamic -o tabix tabix.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 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-3.amzn2023.x86_64.ld -fvisibility=hidden -rdynamic -o test/fieldarith test/fieldarith.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 12 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 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-3.amzn2023.x86_64.ld -fvisibility=hidden -rdynamic -o test/hfile test/hfile.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 12 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 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-3.amzn2023.x86_64.ld -fvisibility=hidden -rdynamic -o test/pileup test/pileup.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 12 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 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-3.amzn2023.x86_64.ld -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 12 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 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-3.amzn2023.x86_64.ld -fvisibility=hidden -rdynamic -o test/sam test/sam.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 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-3.amzn2023.x86_64.ld -fvisibility=hidden -rdynamic -o test/test_expr test/test_expr.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 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-3.amzn2023.x86_64.ld -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 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-3.amzn2023.x86_64.ld -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 12 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 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-3.amzn2023.x86_64.ld -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 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-3.amzn2023.x86_64.ld -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 12 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 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-3.amzn2023.x86_64.ld -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 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 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-3.amzn2023.x86_64.ld -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 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 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-3.amzn2023.x86_64.ld -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 12 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 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-3.amzn2023.x86_64.ld -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 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 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-3.amzn2023.x86_64.ld -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 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 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-3.amzn2023.x86_64.ld -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 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 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-3.amzn2023.x86_64.ld -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 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 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-3.amzn2023.x86_64.ld -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 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 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-3.amzn2023.x86_64.ld -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 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 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-3.amzn2023.x86_64.ld -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 12 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 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-3.amzn2023.x86_64.ld -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 12 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.EOVPq5 + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.x86_64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.x86_64 ++ dirname /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.x86_64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.x86_64 + CFLAGS='-O2 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-3.amzn2023.x86_64.ld' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd htslib-1.15.1 + /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.x86_64 'INSTALL=/usr/bin/install -p' mkdir -p -m 755 /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.x86_64/usr/bin /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.x86_64/usr/include /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.x86_64/usr/include/htslib /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.x86_64/usr/lib64 /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.x86_64/usr/share/man/man1 /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.x86_64/usr/share/man/man5 /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.x86_64/usr/share/man/man7 /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.x86_64/usr/lib64/pkgconfig if test -n "/usr/libexec/htslib"; then mkdir -p -m 755 /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.x86_64/usr/libexec/htslib; fi /usr/bin/install -p -m 644 libhts.so /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.x86_64/usr/lib64/libhts.so.1.15.1 ln -sf libhts.so.1.15.1 /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.x86_64/usr/lib64/libhts.so ln -sf libhts.so.1.15.1 /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.x86_64/usr/lib64/libhts.so.3 sed -e 's#@-includedir@#/usr/include#g;s#@-libdir@#/usr/lib64#g;s#@-PACKAGE_VERSION@#1.15.1#g' htslib.pc.tmp > /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.x86_64/usr/lib64/pkgconfig/htslib.pc chmod 644 /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.x86_64/usr/lib64/pkgconfig/htslib.pc /usr/bin/install -p bgzip htsfile tabix /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.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-1.15.1-3.amzn2023.x86_64/usr/libexec/htslib; fi /usr/bin/install -p -m 644 htslib/*.h /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.x86_64/usr/include/htslib /usr/bin/install -p -m 644 libhts.a /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.x86_64/usr/lib64/libhts.a /usr/bin/install -p -m 644 bgzip.1 htsfile.1 tabix.1 /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.x86_64/usr/share/man/man1 /usr/bin/install -p -m 644 faidx.5 sam.5 vcf.5 /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.x86_64/usr/share/man/man5 /usr/bin/install -p -m 644 htslib-s3-plugin.7 /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.x86_64/usr/share/man/man7 + pushd /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.x86_64//usr/lib64 ~/build/BUILDROOT/htslib-1.15.1-3.amzn2023.x86_64/usr/lib64 ~/build/BUILD/htslib-1.15.1 + chmod 755 libhts.so.1.15.1 + popd ~/build/BUILD/htslib-1.15.1 + find /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.x86_64 -name '*.la' -delete + rm -f /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.x86_64//usr/lib64/libhts.a + /usr/lib/rpm/find-debuginfo.sh -j2 --strict-build-id -m -i --build-id-seed 1.15.1-3.amzn2023 --unique-debug-suffix -1.15.1-3.amzn2023.x86_64 --unique-debug-src-base htslib-1.15.1-3.amzn2023.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/htslib-1.15.1 explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.x86_64/usr/bin/htsfile explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.x86_64/usr/bin/bgzip extracting debug info from /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.x86_64/usr/bin/htsfile extracting debug info from /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.x86_64/usr/bin/bgzip explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.x86_64/usr/bin/tabix extracting debug info from /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.x86_64/usr/bin/tabix explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.x86_64/usr/lib64/libhts.so.1.15.1 extracting debug info from /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.x86_64/usr/lib64/libhts.so.1.15.1 explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.x86_64/usr/libexec/htslib/hfile_gcs.so extracting debug info from /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.x86_64/usr/libexec/htslib/hfile_gcs.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.x86_64/usr/libexec/htslib/hfile_libcurl.so extracting debug info from /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.x86_64/usr/libexec/htslib/hfile_libcurl.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.x86_64/usr/libexec/htslib/hfile_s3.so extracting debug info from /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.x86_64/usr/libexec/htslib/hfile_s3.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.x86_64/usr/libexec/htslib/hfile_s3_write.so extracting debug info from /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.x86_64/usr/libexec/htslib/hfile_s3_write.so original debug info size: 12312kB, size after compression: 11596kB /usr/lib/rpm/sepdebugcrcfix: Updated 8 CRC32s, 0 CRC32s did match. 5259 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/check-rpaths + /usr/lib/rpm/redhat/brp-mangle-shebangs + /usr/lib/rpm/brp-python-bytecompile '' 0 1 Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.IzMmsg + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -ftree-vectorize -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 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-3.amzn2023.x86_64.ld' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + '[' -f /usr/lib/rpm/generate-rpm-note.sh ']' + /usr/lib/rpm/generate-rpm-note.sh htslib 1.15.1-3.amzn2023 x86_64 + cd htslib-1.15.1 + make test gcc -O2 -ftree-vectorize -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 -D_POSIX_C_SOURCE=200112L -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 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-3.amzn2023.x86_64.ld -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_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.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 -ftree-vectorize -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 -D_POSIX_C_SOURCE=200112L -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 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-3.amzn2023.x86_64.ld -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_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o -llzma -lbz2 -lz -lm -lm -lpthread cd htscodecs/tests && srcdir=. && export srcdir && ./rans4x16.test Testing rans4x16 -r -o0 on ./dat/q4 11660 Testing rans4x16 -r -o1 on ./dat/q4 10848 Testing rans4x16 -r -o64 on ./dat/q4 12878 Testing rans4x16 -r -o65 on ./dat/q4 10672 Testing rans4x16 -r -o128 on ./dat/q4 10902 Testing rans4x16 -r -o129 on ./dat/q4 10890 Testing rans4x16 -r -o192 on ./dat/q4 11225 Testing rans4x16 -r -o193 on ./dat/q4 10825 Testing rans4x16 -r -o8 on ./dat/q4 11731 Testing rans4x16 -r -o9 on ./dat/q4 11111 Testing rans4x16 -r -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 -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 -o0 on ./dat/qvar 32987 Testing rans4x16 -r -o1 on ./dat/qvar 32261 gcc -O2 -ftree-vectorize -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 -D_POSIX_C_SOURCE=200112L -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 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-3.amzn2023.x86_64.ld -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_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.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 gcc -O2 -ftree-vectorize -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 -D_POSIX_C_SOURCE=200112L -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 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-3.amzn2023.x86_64.ld -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_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o -llzma -lbz2 -lz -lm -lm -lpthread cd htscodecs/tests && srcdir=. && export srcdir && ./tok3.test Testing tokenise_name3 -r -1 on ./names/01.names 3392 Testing tokenise_name3 -r -3 on ./names/01.names 2471 Testing tokenise_name3 -r -5 on ./names/01.names 2283 Testing tokenise_name3 -r -7 on ./names/01.names 2234 Testing tokenise_name3 -r -9 on ./names/01.names 2234 Testing tokenise_name3 -r -11 on ./names/01.names 3151 Testing tokenise_name3 -r -13 on ./names/01.names 2424 Testing tokenise_name3 -r -15 on ./names/01.names 2061 Testing tokenise_name3 -r -17 on ./names/01.names 2051 Testing tokenise_name3 -r -19 on ./names/01.names 2049 Testing tokenise_name3 -r -1 on ./names/02.names 6633 Testing tokenise_name3 -r -3 on ./names/02.names 4983 Testing tokenise_name3 -r -5 on ./names/02.names 4942 Testing tokenise_name3 -r -7 on ./names/02.names 4922 Testing tokenise_name3 -r -9 on ./names/02.names 4918 Testing tokenise_name3 -r -11 on ./names/02.names 6087 Testing tokenise_name3 -r -13 on ./names/02.names 4797 Testing tokenise_name3 -r -15 on ./names/02.names 4714 Testing tokenise_name3 -r -17 on ./names/02.names 4695 Testing tokenise_name3 -r -19 on ./names/02.names 4695 Testing tokenise_name3 -r -1 on ./names/03.names 10557 Testing tokenise_name3 -r -3 on ./names/03.names 7822 Testing tokenise_name3 -r -5 on ./names/03.names 7557 Testing tokenise_name3 -r -7 on ./names/03.names 7521 Testing tokenise_name3 -r -9 on ./names/03.names 7521 Testing tokenise_name3 -r -11 on ./names/03.names 9294 Testing tokenise_name3 -r -13 on ./names/03.names 7291 Testing tokenise_name3 -r -15 on ./names/03.names 7125 Testing tokenise_name3 -r -17 on ./names/03.names 7069 Testing tokenise_name3 -r -19 on ./names/03.names 7068 Testing tokenise_name3 -r -1 on ./names/05.names 5098 Testing tokenise_name3 -r -3 on ./names/05.names 3600 Testing tokenise_name3 -r -5 on ./names/05.names 3551 Testing tokenise_name3 -r -7 on ./names/05.names 3534 Testing tokenise_name3 -r -9 on ./names/05.names 3534 Testing tokenise_name3 -r -11 on ./names/05.names 4648 Testing tokenise_name3 -r -13 on ./names/05.names 3405 Testing tokenise_name3 -r -15 on ./names/05.names 3381 Testing tokenise_name3 -r -17 on ./names/05.names 3377 Testing tokenise_name3 -r -19 on ./names/05.names 3377 Testing tokenise_name3 -r -1 on ./names/08.names 6841 Testing tokenise_name3 -r -3 on ./names/08.names 5291 Testing tokenise_name3 -r -5 on ./names/08.names 5206 Testing tokenise_name3 -r -7 on ./names/08.names 5160 Testing tokenise_name3 -r -9 on ./names/08.names 5160 Testing tokenise_name3 -r -11 on ./names/08.names 6374 Testing tokenise_name3 -r -13 on ./names/08.names 4895 Testing tokenise_name3 -r -15 on ./names/08.names 4851 Testing tokenise_name3 -r -17 on ./names/08.names 4805 Testing tokenise_name3 -r -19 on ./names/08.names 4805 Testing tokenise_name3 -r -1 on ./names/09.names 5339 Testing tokenise_name3 -r -3 on ./names/09.names 3598 Testing tokenise_name3 -r -5 on ./names/09.names 3527 Testing tokenise_name3 -r -7 on ./names/09.names 3493 Testing tokenise_name3 -r -9 on ./names/09.names 3493 Testing tokenise_name3 -r -11 on ./names/09.names 4861 Testing tokenise_name3 -r -13 on ./names/09.names 3427 Testing tokenise_name3 -r -15 on ./names/09.names 3391 Testing tokenise_name3 -r -17 on ./names/09.names 3366 Testing tokenise_name3 -r -19 on ./names/09.names 3366 Testing tokenise_name3 -r -1 on ./names/10.names 6458 Testing tokenise_name3 -r -3 on ./names/10.names 4843 Testing tokenise_name3 -r -5 on ./names/10.names 4799 Testing tokenise_name3 -r -7 on ./names/10.names 4746 Testing tokenise_name3 -r -9 on ./names/10.names 4744 Testing tokenise_name3 -r -11 on ./names/10.names 5785 Testing tokenise_name3 -r -13 on ./names/10.names 4567 Testing tokenise_name3 -r -15 on ./names/10.names 4492 Testing tokenise_name3 -r -17 on ./names/10.names 4472 Testing tokenise_name3 -r -19 on ./names/10.names 4472 Testing tokenise_name3 -r -1 on ./names/20.names 2511 Testing tokenise_name3 -r -3 on ./names/20.names 1701 Testing tokenise_name3 -r -5 on ./names/20.names 1659 Testing tokenise_name3 -r -7 on ./names/20.names 1632 Testing tokenise_name3 -r -9 on ./names/20.names 1632 Testing tokenise_name3 -r -11 on ./names/20.names 2319 Testing tokenise_name3 -r -13 on ./names/20.names 1629 Testing tokenise_name3 -r -15 on ./names/20.names 1605 Testing tokenise_name3 -r -17 on ./names/20.names 1600 Testing tokenise_name3 -r -19 on ./names/20.names 1600 Testing tokenise_name3 -r -1 on ./names/nv.names 6816 Testing tokenise_name3 -r -3 on ./names/nv.names 4989 Testing tokenise_name3 -r -5 on ./names/nv.names 4972 Testing tokenise_name3 -r -7 on ./names/nv.names 4937 Testing tokenise_name3 -r -9 on ./names/nv.names 4937 Testing tokenise_name3 -r -11 on ./names/nv.names 6084 Testing tokenise_name3 -r -13 on ./names/nv.names 4825 Testing tokenise_name3 -r -15 on ./names/nv.names 4771 Testing tokenise_name3 -r -17 on ./names/nv.names 4767 Testing tokenise_name3 -r -19 on ./names/nv.names 4767 Testing tokenise_name3 -r -1 on ./names/nv2.names 1181 Testing tokenise_name3 -r -3 on ./names/nv2.names 903 Testing tokenise_name3 -r -5 on ./names/nv2.names 879 Testing tokenise_name3 -r -7 on ./names/nv2.names 846 Testing tokenise_name3 -r -9 on ./names/nv2.names 846 Testing tokenise_name3 -r -11 on ./names/nv2.names 891 Testing tokenise_name3 -r -13 on ./names/nv2.names 836 Testing tokenise_name3 -r -15 on ./names/nv2.names 764 Testing tokenise_name3 -r -17 on ./names/nv2.names 747 Testing tokenise_name3 -r -19 on ./names/nv2.names 747 Testing tokenise_name3 -r -1 on ./names/rr.names 8788 Testing tokenise_name3 -r -3 on ./names/rr.names 6290 Testing tokenise_name3 -r -5 on ./names/rr.names 6252 Testing tokenise_name3 -r -7 on ./names/rr.names 6230 Testing tokenise_name3 -r -9 on ./names/rr.names 6230 Testing tokenise_name3 -r -11 on ./names/rr.names 8319 Testing tokenise_name3 -r -13 on ./names/rr.names 6066 Testing tokenise_name3 -r -15 on ./names/rr.names 5972 Testing tokenise_name3 -r -17 on ./names/rr.names 5963 Testing tokenise_name3 -r -19 on ./names/rr.names 5963 gcc -O2 -ftree-vectorize -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 -D_POSIX_C_SOURCE=200112L -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 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-3.amzn2023.x86_64.ld -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_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.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 -ftree-vectorize -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 -D_POSIX_C_SOURCE=200112L -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 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-3.amzn2023.x86_64.ld -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_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.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/fieldarith test/fieldarith.sam test/hfile HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -g ./libhts.so HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -l ./libhts.so 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/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 |egrep -cv '^@' PASS : $tv -i 'filter=qlen/(flag*mapq+pos)>5' ../ce#1000.sam |egrep -cv '^@' PASS : $tv -i 'filter=[NM]>=10 || [MD]=~"A.*A.*A"' -t4 ../ce#1000.sam |egrep -cv '^@' PASS : $tv -i 'filter=length(seq) != qlen' ../ce#5b.sam | egrep -cv '^@' PASS : $tv -i 'filter=min(qual) >= 20' ../ce#1000.sam | egrep -cv '^@' PASS : $tv -i 'filter=max(qual) <= 20' ../ce#1000.sam | egrep -cv '^@' PASS : $tv -i 'filter=avg(qual) >= 20 && avg(qual) <= 30' ../ce#1000.sam | egrep -cv '^@' Expected passes: 14 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 Expected passes: 14 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 Expected passes: 21 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 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: 40 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 : $pileup_mod < MM-pileup.sam PASS : $pileup_mod < MM-pileup2.sam Expected passes: 5 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 REF_PATH=: test/sam test/ce.fa test/faidx.fa test/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:-} "my" variable @p masks earlier declaration in same scope at ./test.pl line 617. bgzip round-trip no threads: .. ok bgzip -b no threads: .. ok bgzip -b -I no threads: .. ok bgzip round-trip 4 threads: .. ok bgzip -b 4 threads: .. ok bgzip -b -I 4 threads: .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -b -m 14 -x /tmp/Yw0asGoY47/index.bam.csi /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/Yw0asGoY47/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/Yw0asGoY47/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -b -m 0 -x /tmp/Yw0asGoY47/index.bam.bai /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/Yw0asGoY47/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -b /tmp/Yw0asGoY47/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -z -m 14 -x /tmp/Yw0asGoY47/index.sam.gz.csi /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/Yw0asGoY47/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/Yw0asGoY47/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -z -m 0 -x /tmp/Yw0asGoY47/index.sam.gz.bai /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/Yw0asGoY47/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -b /tmp/Yw0asGoY47/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -z -m 14 -x /tmp/Yw0asGoY47/index.sam.gz.csi /builddir/build/BUILD/htslib-1.15.1/test/index_dos.sam > /tmp/Yw0asGoY47/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/Yw0asGoY47/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -z -m 0 -x /tmp/Yw0asGoY47/index.sam.gz.bai /builddir/build/BUILD/htslib-1.15.1/test/index_dos.sam > /tmp/Yw0asGoY47/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -b /tmp/Yw0asGoY47/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -C -x /tmp/Yw0asGoY47/index.cram.crai /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/Yw0asGoY47/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index /tmp/Yw0asGoY47/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -b -m 14 -x /tmp/Yw0asGoY47/index.bcf.csi /builddir/build/BUILD/htslib-1.15.1/test/index.vcf > /tmp/Yw0asGoY47/index.bcf .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/Yw0asGoY47/index.bcf .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -z -m 14 -x /tmp/Yw0asGoY47/index.vcf.gz.csi /builddir/build/BUILD/htslib-1.15.1/test/index.vcf > /tmp/Yw0asGoY47/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/Yw0asGoY47/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -z -m 0 -x /tmp/Yw0asGoY47/index.vcf.gz.tbi /builddir/build/BUILD/htslib-1.15.1/test/index.vcf > /tmp/Yw0asGoY47/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -t /tmp/Yw0asGoY47/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/tabix /tmp/Yw0asGoY47/index.vcf.gz##idx##/tmp/Yw0asGoY47/index.vcf.gz.tbi 1:10000060-10000060 .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view /tmp/Yw0asGoY47/index2.bam 1:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view /tmp/Yw0asGoY47/index2.bam 1:2000000-2000000 .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view /tmp/Yw0asGoY47/index2.bam 2:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view /tmp/Yw0asGoY47/index2.bam 2:2000000-2000000 .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -b -m 14 -x /tmp/Yw0asGoY47/index.bam.csi /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/Yw0asGoY47/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/Yw0asGoY47/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -b -m 0 -x /tmp/Yw0asGoY47/index.bam.bai /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/Yw0asGoY47/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -b /tmp/Yw0asGoY47/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -z -m 14 -x /tmp/Yw0asGoY47/index.sam.gz.csi /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/Yw0asGoY47/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/Yw0asGoY47/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -z -m 0 -x /tmp/Yw0asGoY47/index.sam.gz.bai /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/Yw0asGoY47/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -b /tmp/Yw0asGoY47/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -z -m 14 -x /tmp/Yw0asGoY47/index.sam.gz.csi /builddir/build/BUILD/htslib-1.15.1/test/index_dos.sam > /tmp/Yw0asGoY47/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/Yw0asGoY47/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -z -m 0 -x /tmp/Yw0asGoY47/index.sam.gz.bai /builddir/build/BUILD/htslib-1.15.1/test/index_dos.sam > /tmp/Yw0asGoY47/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -b /tmp/Yw0asGoY47/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -C -x /tmp/Yw0asGoY47/index.cram.crai /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/Yw0asGoY47/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index /tmp/Yw0asGoY47/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -b -m 14 -x /tmp/Yw0asGoY47/index.bcf.csi /builddir/build/BUILD/htslib-1.15.1/test/index.vcf > /tmp/Yw0asGoY47/index.bcf .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/Yw0asGoY47/index.bcf .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -z -m 14 -x /tmp/Yw0asGoY47/index.vcf.gz.csi /builddir/build/BUILD/htslib-1.15.1/test/index.vcf > /tmp/Yw0asGoY47/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/Yw0asGoY47/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -z -m 0 -x /tmp/Yw0asGoY47/index.vcf.gz.tbi /builddir/build/BUILD/htslib-1.15.1/test/index.vcf > /tmp/Yw0asGoY47/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -t /tmp/Yw0asGoY47/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/tabix /tmp/Yw0asGoY47/index.vcf.gz##idx##/tmp/Yw0asGoY47/index.vcf.gz.tbi 1:10000060-10000060 .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view /tmp/Yw0asGoY47/index2.bam 1:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view /tmp/Yw0asGoY47/index2.bam 1:2000000-2000000 .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view /tmp/Yw0asGoY47/index2.bam 2:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view /tmp/Yw0asGoY47/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 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-1.15.1/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 [W::cram_set_voption] CRAM version 3.1 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 -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 [W::cram_set_voption] CRAM version 3.1 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_ ./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 [W::cram_set_voption] CRAM version 3.1 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_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o normal ce#1000.sam > ce#1000.tmp.cram [W::cram_set_voption] CRAM version 3.1 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_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o small ce#1000.sam > ce#1000.tmp.cram [W::cram_set_voption] CRAM version 3.1 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_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#1000.sam > ce#1000.tmp.cram [W::cram_set_voption] CRAM version 3.1 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_ ./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#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 [W::cram_set_voption] CRAM version 3.1 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_ ./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 [W::cram_set_voption] CRAM version 3.1 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 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 [W::cram_set_voption] CRAM version 3.1 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_ ./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 [W::cram_set_voption] CRAM version 3.1 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_ ./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 [W::cram_set_voption] CRAM version 3.1 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 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 [W::cram_set_voption] CRAM version 3.1 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_ ./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 [W::cram_set_voption] CRAM version 3.1 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_ ./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 [W::cram_set_voption] CRAM version 3.1 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_ ./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 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-1.15.1/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-1.15.1/test/test-vcf-api /tmp/Yw0asGoY47/test-vcf-api.bcf [W::bcf_record_check] Bad BCF record at 1:1: No REF allele [E::bcf_index_build3] TBI indices for BCF files are not supported [E::idx_find_and_load] Could not retrieve index file for '/tmp/Yw0asGoY47/test-vcf-api.bcf' .. ok test_bcf2vcf: /builddir/build/BUILD/htslib-1.15.1/test/test_view /builddir/build/BUILD/htslib-1.15.1/test/tabix/vcf_file.bcf .. ok test_vcf_sweep: /builddir/build/BUILD/htslib-1.15.1/test/test-vcf-sweep /tmp/Yw0asGoY47/test-vcf-api.bcf .. ok test_vcf_various: /builddir/build/BUILD/htslib-1.15.1/htsfile -ch /builddir/build/BUILD/htslib-1.15.1/test/test-vcf-hdr-in.vcf .. ok test_vcf_various: /builddir/build/BUILD/htslib-1.15.1/htsfile -c /builddir/build/BUILD/htslib-1.15.1/test/formatcols.vcf .. ok test_vcf_various: /builddir/build/BUILD/htslib-1.15.1/htsfile -c /builddir/build/BUILD/htslib-1.15.1/test/noroundtrip.vcf .. ok test_vcf_various: /builddir/build/BUILD/htslib-1.15.1/htsfile -c /builddir/build/BUILD/htslib-1.15.1/test/formatmissing.vcf .. ok test_vcf_various: /builddir/build/BUILD/htslib-1.15.1/htsfile -c /builddir/build/BUILD/htslib-1.15.1/test/vcf_meta_meta.vcf .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/Yw0asGoY47 -s 786898085 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/Yw0asGoY47 -s 1148402887 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/Yw0asGoY47 -s 165793916 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/Yw0asGoY47 -s 61981647 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/Yw0asGoY47 -s 291670700 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/Yw0asGoY47 -s 1435451401 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/Yw0asGoY47 -s 1311135147 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/Yw0asGoY47 -s 1277066036 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/Yw0asGoY47 -s 1378638156 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/Yw0asGoY47 -s 102814046 .. ok test_command: /builddir/build/BUILD/htslib-1.15.1/test/test-bcf-translate - .. ok test_convert_padded_header: /builddir/build/BUILD/htslib-1.15.1/test/test_view -t ce.fa -C /tmp/Yw0asGoY47/headernul0.bam .. ok test_convert_padded_header: /builddir/build/BUILD/htslib-1.15.1/test/test_view -t ce.fa -C /tmp/Yw0asGoY47/headernul1.bam .. ok test_convert_padded_header: /builddir/build/BUILD/htslib-1.15.1/test/test_view -t ce.fa -C /tmp/Yw0asGoY47/headernul678.bam .. ok test_rebgzip: /builddir/build/BUILD/htslib-1.15.1/bgzip -I /builddir/build/BUILD/htslib-1.15.1/test/bgziptest.txt.gz.gzi -c -g /builddir/build/BUILD/htslib-1.15.1/test/bgziptest.txt .. ok test-logging: /builddir/build/BUILD/htslib-1.15.1/test/test-logging.pl .. ok test_plugin_loading: HTS_PATH=/builddir/build/BUILD/htslib-1.15.1 /builddir/build/BUILD/htslib-1.15.1/test/with-shlib.sh /builddir/build/BUILD/htslib-1.15.1/htsfile https://localhost:99999/invalid_port .. ok test_realn: /builddir/build/BUILD/htslib-1.15.1/test/test_realn -f /builddir/build/BUILD/htslib-1.15.1/test/realn01.fa -i /builddir/build/BUILD/htslib-1.15.1/test/realn01.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.15.1/test/test_realn -f /builddir/build/BUILD/htslib-1.15.1/test/realn02.fa -i /builddir/build/BUILD/htslib-1.15.1/test/realn02.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.15.1/test/test_realn -a -f /builddir/build/BUILD/htslib-1.15.1/test/realn01.fa -i /builddir/build/BUILD/htslib-1.15.1/test/realn01.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.15.1/test/test_realn -a -f /builddir/build/BUILD/htslib-1.15.1/test/realn02.fa -i /builddir/build/BUILD/htslib-1.15.1/test/realn02.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.15.1/test/test_realn -e -f /builddir/build/BUILD/htslib-1.15.1/test/realn01.fa -i /builddir/build/BUILD/htslib-1.15.1/test/realn01.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.15.1/test/test_realn -e -f /builddir/build/BUILD/htslib-1.15.1/test/realn02.fa -i /builddir/build/BUILD/htslib-1.15.1/test/realn02.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.15.1/test/test_realn -r -f /builddir/build/BUILD/htslib-1.15.1/test/realn02.fa -i /builddir/build/BUILD/htslib-1.15.1/test/realn02-r.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.15.1/test/test_realn -a -f /builddir/build/BUILD/htslib-1.15.1/test/realn02.fa -i /builddir/build/BUILD/htslib-1.15.1/test/realn02_exp.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.15.1/test/test_realn -f /builddir/build/BUILD/htslib-1.15.1/test/realn02.fa -i /builddir/build/BUILD/htslib-1.15.1/test/realn02_exp-a.sam -o - .. ok Number of tests: total .. 172 passed .. 172 failed .. 0 + RPM_EC=0 ++ jobs -p + exit 0 Processing files: htslib-1.15.1-3.amzn2023.x86_64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.mycpPj + umask 022 + cd /builddir/build/BUILD + cd htslib-1.15.1 + DOCDIR=/builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.x86_64/usr/share/doc/htslib + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.x86_64/usr/share/doc/htslib + cp -pr NEWS /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.x86_64/usr/share/doc/htslib + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.eGy41U + umask 022 + cd /builddir/build/BUILD + cd htslib-1.15.1 + LICENSEDIR=/builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.x86_64/usr/share/licenses/htslib + export LC_ALL=C + LC_ALL=C + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.x86_64/usr/share/licenses/htslib + cp -pr LICENSE /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.x86_64/usr/share/licenses/htslib + RPM_EC=0 ++ jobs -p + exit 0 Provides: htslib = 1.15.1-3.amzn2023 htslib(x86-64) = 1.15.1-3.amzn2023 libhts.so.3()(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) 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-1.15.1-3.amzn2023.x86_64 Provides: htslib-devel = 1.15.1-3.amzn2023 htslib-devel(x86-64) = 1.15.1-3.amzn2023 pkgconfig(htslib) = 1.15.1 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-1.15.1-3.amzn2023.x86_64 Provides: htslib-tools = 1.15.1-3.amzn2023 htslib-tools(x86-64) = 1.15.1-3.amzn2023 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_2.29)(64bit) libz.so.1()(64bit) rtld(GNU_HASH) Processing files: htslib-debugsource-1.15.1-3.amzn2023.x86_64 Provides: htslib-debugsource = 1.15.1-3.amzn2023 htslib-debugsource(x86-64) = 1.15.1-3.amzn2023 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: htslib-debuginfo-1.15.1-3.amzn2023.x86_64 Provides: debuginfo(build-id) = 64118733d1ce7f0026402d0421388ff866f0161c debuginfo(build-id) = 7cebac2cba5ab5631ae7bd78e5d205343413b038 debuginfo(build-id) = e104672aa9e64b02b197b5defbd477cc5d05d0c1 debuginfo(build-id) = e9d8a31be2b3b8d490fd6007566f9c7dd1151bee debuginfo(build-id) = f31981b5e0e2f9c2a0e0719f9db1afb081d8c461 htslib-debuginfo = 1.15.1-3.amzn2023 htslib-debuginfo(x86-64) = 1.15.1-3.amzn2023 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: htslib-debugsource(x86-64) = 1.15.1-3.amzn2023 Processing files: htslib-tools-debuginfo-1.15.1-3.amzn2023.x86_64 Provides: debuginfo(build-id) = 0ac088a9f57081ef95320915cd85b8456135ca3e debuginfo(build-id) = 373f624f4cd29245b2db8b84e76b28360c49c5c7 debuginfo(build-id) = 52062d67d562d087bf886fc2e06629dee2c1e316 htslib-tools-debuginfo = 1.15.1-3.amzn2023 htslib-tools-debuginfo(x86-64) = 1.15.1-3.amzn2023 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: htslib-debugsource(x86-64) = 1.15.1-3.amzn2023 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.x86_64 Wrote: /builddir/build/RPMS/htslib-debuginfo-1.15.1-3.amzn2023.x86_64.rpm Wrote: /builddir/build/RPMS/htslib-debugsource-1.15.1-3.amzn2023.x86_64.rpm Wrote: /builddir/build/RPMS/htslib-tools-debuginfo-1.15.1-3.amzn2023.x86_64.rpm Wrote: /builddir/build/RPMS/htslib-1.15.1-3.amzn2023.x86_64.rpm Wrote: /builddir/build/RPMS/htslib-tools-1.15.1-3.amzn2023.x86_64.rpm Wrote: /builddir/build/RPMS/htslib-devel-1.15.1-3.amzn2023.x86_64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.jxZlwM + umask 022 + cd /builddir/build/BUILD + cd htslib-1.15.1 + /usr/bin/rm -rf /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.x86_64 + RPM_EC=0 ++ jobs -p + exit 0 Finish: rpmbuild htslib-1.15.1-3.amzn2023.src.rpm Finish: build phase for htslib-1.15.1-3.amzn2023.src.rpm INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/amazonlinux-2023-x86_64-1704591055.887282/root/var/log/dnf.rpm.log /var/lib/mock/amazonlinux-2023-x86_64-1704591055.887282/root/var/log/dnf.librepo.log /var/lib/mock/amazonlinux-2023-x86_64-1704591055.887282/root/var/log/dnf.log INFO: Done(/var/lib/copr-rpmbuild/results/htslib-1.15.1-3.amzn2023.src.rpm) Config(child) 4 minutes 33 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-debuginfo", "epoch": null, "version": "1.15.1", "release": "3.amzn2023", "arch": "x86_64" }, { "name": "htslib-tools-debuginfo", "epoch": null, "version": "1.15.1", "release": "3.amzn2023", "arch": "x86_64" }, { "name": "htslib-devel", "epoch": null, "version": "1.15.1", "release": "3.amzn2023", "arch": "x86_64" }, { "name": "htslib-debugsource", "epoch": null, "version": "1.15.1", "release": "3.amzn2023", "arch": "x86_64" }, { "name": "htslib", "epoch": null, "version": "1.15.1", "release": "3.amzn2023", "arch": "x86_64" }, { "name": "htslib", "epoch": null, "version": "1.15.1", "release": "3.amzn2023", "arch": "src" }, { "name": "htslib-tools", "epoch": null, "version": "1.15.1", "release": "3.amzn2023", "arch": "x86_64" } ] } RPMResults finished