Warning: Permanently added '162.133.131.141' (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/6407951-fedora-rawhide-s390x --chroot fedora-rawhide-s390x Version: 0.69 PID: 13916 Logging PID: 13917 Task: {'appstream': False, 'background': True, 'build_id': 6407951, 'buildroot_pkgs': [], 'chroot': 'fedora-rawhide-s390x', 'enable_net': False, 'fedora_review': False, 'git_hash': '513b3642bc72b4ff0e5bd71bc544f558162538b4', 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/tuliom/zlib-ng-compat-mpb/htslib', 'isolation': 'default', 'memory_reqs': 2048, 'package_name': 'htslib', 'package_version': '1.15.1-3', 'project_dirname': 'zlib-ng-compat-mpb', 'project_name': 'zlib-ng-compat-mpb', 'project_owner': 'tuliom', 'repo_priority': None, 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/tuliom/zlib-ng-compat-mpb/fedora-rawhide-s390x/', 'id': 'copr_base', 'name': 'Copr repository', 'priority': None}], 'sandbox': 'tuliom/zlib-ng-compat-mpb--tuliom', 'source_json': {}, 'source_type': None, 'submitter': 'tuliom', 'tags': [], 'task_id': '6407951-fedora-rawhide-s390x', 'timeout': 115200, 'uses_devel_repo': False, 'with_opts': [], 'without_opts': []} Running: git clone https://copr-dist-git.fedorainfracloud.org/git/tuliom/zlib-ng-compat-mpb/htslib /var/lib/copr-rpmbuild/workspace/workdir-k5v2bpfm/htslib --depth 500 --no-single-branch --recursive cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/tuliom/zlib-ng-compat-mpb/htslib', '/var/lib/copr-rpmbuild/workspace/workdir-k5v2bpfm/htslib', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-k5v2bpfm/htslib'... Running: git checkout 513b3642bc72b4ff0e5bd71bc544f558162538b4 -- cmd: ['git', 'checkout', '513b3642bc72b4ff0e5bd71bc544f558162538b4', '--'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-k5v2bpfm/htslib rc: 0 stdout: stderr: Note: switching to '513b3642bc72b4ff0e5bd71bc544f558162538b4'. 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 513b364 automatic import of htslib Running: copr-distgit-client sources /usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated cmd: ['copr-distgit-client', 'sources'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-k5v2bpfm/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/tuliom/zlib-ng-compat-mpb/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 2419k 0 0:00:01 0:00:01 --:--:-- 2418k INFO: Reading stdout from command: md5sum htslib-1.15.1.tar.bz2 Running (timeout=115200): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-k5v2bpfm/htslib/htslib.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-k5v2bpfm/htslib --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1695021298.041424 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 5.1 starting (python version = 3.11.3, NVR = mock-5.1-1.fc38)... 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-k5v2bpfm/htslib/htslib.spec) Config(fedora-rawhide-s390x) Start: clean chroot Finish: clean chroot Mock Version: 5.1 INFO: Mock Version: 5.1 Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-s390x-bootstrap-1695021298.041424/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: registry.fedoraproject.org/fedora:rawhide INFO: Pulling image: registry.fedoraproject.org/fedora:rawhide INFO: Copy content of container registry.fedoraproject.org/fedora:rawhide to /var/lib/mock/fedora-rawhide-s390x-bootstrap-1695021298.041424/root INFO: Checking that registry.fedoraproject.org/fedora:rawhide image matches host's architecture INFO: mounting registry.fedoraproject.org/fedora:rawhide with podman image mount INFO: image registry.fedoraproject.org/fedora:rawhide as /var/lib/containers/storage/overlay/048a30d242435471510b8c750dbc9cf86e41860183b8bd626e06a27f1e4c6a85/merged INFO: umounting image registry.fedoraproject.org/fedora:rawhide (/var/lib/containers/storage/overlay/048a30d242435471510b8c750dbc9cf86e41860183b8bd626e06a27f1e4c6a85/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 273 kB/s | 2.9 MB 00:10 fedora 184 kB/s | 63 MB 05:52 Last metadata expiration check: 0:00:05 ago on Mon Sep 18 07:17:39 2023. Package python3-dnf-4.16.2-4.fc40.noarch is already installed. Dependencies resolved. ================================================================================ Package Arch Version Repository Size ================================================================================ Installing: python3-dnf-plugins-core noarch 4.4.2-1.fc39 fedora 293 k Installing dependencies: dbus-libs s390x 1:1.14.10-1.fc40 fedora 159 k python3-dateutil noarch 1:2.8.2-10.fc39 fedora 355 k python3-dbus s390x 1.3.2-4.fc39 fedora 157 k python3-distro noarch 1.8.0-6.fc39 fedora 49 k python3-six noarch 1.16.0-12.fc39 fedora 41 k python3-systemd s390x 235-5.fc39 fedora 106 k Transaction Summary ================================================================================ Install 7 Packages Total download size: 1.1 M Installed size: 3.5 M Downloading Packages: (1/7): python3-dbus-1.3.2-4.fc39.s390x.rpm 138 kB/s | 157 kB 00:01 (2/7): dbus-libs-1.14.10-1.fc40.s390x.rpm 32 kB/s | 159 kB 00:05 (3/7): python3-dateutil-2.8.2-10.fc39.noarch.rp 71 kB/s | 355 kB 00:05 (4/7): python3-distro-1.8.0-6.fc39.noarch.rpm 13 kB/s | 49 kB 00:03 (5/7): python3-six-1.16.0-12.fc39.noarch.rpm 248 kB/s | 41 kB 00:00 (6/7): python3-systemd-235-5.fc39.s390x.rpm 463 kB/s | 106 kB 00:00 (7/7): python3-dnf-plugins-core-4.4.2-1.fc39.no 749 kB/s | 293 kB 00:00 -------------------------------------------------------------------------------- Total 171 kB/s | 1.1 MB 00:06 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Installing : python3-systemd-235-5.fc39.s390x 1/7 Installing : python3-six-1.16.0-12.fc39.noarch 2/7 Installing : python3-dateutil-1:2.8.2-10.fc39.noarch 3/7 Installing : python3-distro-1.8.0-6.fc39.noarch 4/7 Installing : dbus-libs-1:1.14.10-1.fc40.s390x 5/7 Installing : python3-dbus-1.3.2-4.fc39.s390x 6/7 Installing : python3-dnf-plugins-core-4.4.2-1.fc39.noarch 7/7 Running scriptlet: python3-dnf-plugins-core-4.4.2-1.fc39.noarch 7/7 Verifying : dbus-libs-1:1.14.10-1.fc40.s390x 1/7 Verifying : python3-dateutil-1:2.8.2-10.fc39.noarch 2/7 Verifying : python3-dbus-1.3.2-4.fc39.s390x 3/7 Verifying : python3-distro-1.8.0-6.fc39.noarch 4/7 Verifying : python3-dnf-plugins-core-4.4.2-1.fc39.noarch 5/7 Verifying : python3-six-1.16.0-12.fc39.noarch 6/7 Verifying : python3-systemd-235-5.fc39.s390x 7/7 Installed: dbus-libs-1:1.14.10-1.fc40.s390x python3-dateutil-1:2.8.2-10.fc39.noarch python3-dbus-1.3.2-4.fc39.s390x python3-distro-1.8.0-6.fc39.noarch python3-dnf-plugins-core-4.4.2-1.fc39.noarch python3-six-1.16.0-12.fc39.noarch python3-systemd-235-5.fc39.s390x 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/fedora-rawhide-s390x-1695021298.041424/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) Start: installing minimal buildroot with dnf No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 940 B/s | 1.5 kB 00:01 Copr repository 475 kB/s | 2.9 MB 00:06 fedora 8.0 kB/s | 5.5 kB 00:00 Dependencies resolved. ================================================================================ Package Arch Version Repo Size ================================================================================ Installing group/module packages: bash s390x 5.2.15-5.fc39 fedora 1.8 M bzip2 s390x 1.0.8-16.fc39 fedora 53 k coreutils s390x 9.4-1.fc40 fedora 1.2 M cpio s390x 2.14-4.fc39 fedora 283 k diffutils s390x 3.10-3.fc39 fedora 407 k fedora-release-common noarch 40-0.7 fedora 18 k findutils s390x 1:4.9.0-6.fc40 fedora 497 k gawk s390x 5.2.2-2.fc39 fedora 1.1 M glibc-minimal-langpack s390x 2.38.9000-8.fc40 copr_base 73 k grep s390x 3.11-5.fc40 fedora 305 k gzip s390x 1.12-6.fc39 fedora 173 k info s390x 7.0.3-3.fc39 fedora 192 k patch s390x 2.7.6-22.fc39 fedora 134 k redhat-rpm-config noarch 270-1.fc40 copr_base 74 k rpm-build s390x 4.18.99-1.fc40 fedora 78 k sed s390x 4.8-14.fc39 fedora 309 k shadow-utils s390x 2:4.14.0-1.fc40 fedora 1.3 M tar s390x 2:1.35-2.fc40 fedora 874 k unzip s390x 6.0-62.fc39 fedora 194 k util-linux s390x 2.39.2-1.fc40 copr_base 1.1 M which s390x 2.21-40.fc39 fedora 43 k xz s390x 5.4.4-1.fc39 fedora 557 k Installing dependencies: alternatives s390x 1.25-1.fc39 fedora 39 k ansible-srpm-macros noarch 1-11.fc39 fedora 21 k audit-libs s390x 3.1.2-4.fc40 fedora 121 k authselect s390x 1.4.2-3.fc39 fedora 144 k authselect-libs s390x 1.4.2-3.fc39 fedora 247 k basesystem noarch 11-18.fc39 fedora 7.2 k binutils s390x 2.41-5.fc40 fedora 5.9 M binutils-gold s390x 2.41-5.fc40 fedora 993 k bzip2-libs s390x 1.0.8-16.fc39 fedora 46 k ca-certificates noarch 2023.2.60_v7.0.306-3.fc40 fedora 837 k coreutils-common s390x 9.4-1.fc40 fedora 2.1 M cracklib s390x 2.9.11-2.fc40 copr_base 84 k crypto-policies noarch 20230731-1.git5ed06e0.fc39 fedora 99 k curl s390x 8.3.0-1.fc40 copr_base 354 k cyrus-sasl-lib s390x 2.1.28-11.fc39 fedora 819 k debugedit s390x 5.0-10.fc39 fedora 81 k dwz s390x 0.15-3.fc39 fedora 144 k ed s390x 1.19-4.fc39 fedora 80 k efi-srpm-macros noarch 5-9.fc39 fedora 22 k elfutils s390x 0.189-6.fc40 copr_base 555 k elfutils-debuginfod-client s390x 0.189-6.fc40 copr_base 39 k elfutils-default-yama-scope noarch 0.189-6.fc40 copr_base 14 k elfutils-libelf s390x 0.189-6.fc40 copr_base 201 k elfutils-libs s390x 0.189-6.fc40 copr_base 275 k fedora-gpg-keys noarch 40-0.1 fedora 130 k fedora-release noarch 40-0.7 fedora 8.0 k fedora-release-identity-basic noarch 40-0.7 fedora 8.8 k fedora-repos noarch 40-0.1 fedora 9.4 k fedora-repos-rawhide noarch 40-0.1 fedora 9.0 k file s390x 5.45-1.fc40 copr_base 50 k file-libs s390x 5.45-1.fc40 copr_base 770 k filesystem s390x 3.18-6.fc39 fedora 1.1 M fonts-srpm-macros noarch 1:2.0.5-12.fc39 fedora 26 k forge-srpm-macros noarch 0.1.0-1.fc40 fedora 18 k fpc-srpm-macros noarch 1.3-8.fc39 fedora 7.4 k gdb-minimal s390x 13.2-8.fc40 fedora 4.0 M gdbm-libs s390x 1:1.23-4.fc39 fedora 58 k ghc-srpm-macros noarch 1.6.1-2.fc39 fedora 7.8 k glibc s390x 2.38.9000-8.fc40 copr_base 1.8 M glibc-common s390x 2.38.9000-8.fc40 copr_base 368 k glibc-gconv-extra s390x 2.38.9000-8.fc40 copr_base 1.6 M gmp s390x 1:6.2.1-5.fc39 fedora 325 k gnat-srpm-macros noarch 6-3.fc39 fedora 8.8 k go-srpm-macros noarch 3.2.0-7.fc40 fedora 27 k jansson s390x 2.13.1-7.fc39 fedora 44 k kernel-srpm-macros noarch 1.0-20.fc39 fedora 10 k keyutils-libs s390x 1.6.1-7.fc39 fedora 31 k krb5-libs s390x 1.21.2-1.fc40 fedora 780 k libacl s390x 2.3.1-9.fc40 fedora 24 k libarchive s390x 3.7.2-1.fc40 fedora 440 k libattr s390x 2.5.1-9.fc40 fedora 18 k libblkid s390x 2.39.2-1.fc40 copr_base 121 k libbrotli s390x 1.1.0-1.fc40 fedora 379 k libcap s390x 2.48-7.fc39 fedora 69 k libcap-ng s390x 0.8.3-8.fc40 fedora 32 k libcom_err s390x 1.47.0-2.fc39 fedora 26 k libcurl s390x 8.3.0-1.fc40 copr_base 362 k libdb s390x 5.3.28-58.fc40 copr_base 775 k libeconf s390x 0.5.2-1.fc40 fedora 32 k libevent s390x 2.1.12-9.fc39 fedora 260 k libfdisk s390x 2.39.2-1.fc40 copr_base 166 k libffi s390x 3.4.4-4.fc39 fedora 36 k libgcc s390x 13.2.1-1.fc40 copr_base 82 k libgomp s390x 13.2.1-1.fc40 copr_base 323 k libidn2 s390x 2.3.4-3.fc39 fedora 118 k libmount s390x 2.39.2-1.fc40 copr_base 159 k libnghttp2 s390x 1.56.0-1.fc40 fedora 78 k libnsl2 s390x 2.0.0-6.fc39 fedora 30 k libpkgconf s390x 1.9.5-2.fc39 fedora 38 k libpsl s390x 0.21.2-4.fc39 fedora 63 k libpwquality s390x 1.4.5-6.fc39 fedora 121 k libselinux s390x 3.5-5.fc39 fedora 91 k libsemanage s390x 3.5-4.fc39 fedora 122 k libsepol s390x 3.5-2.fc39 fedora 330 k libsigsegv s390x 2.14-5.fc39 fedora 27 k libsmartcols s390x 2.39.2-1.fc40 copr_base 70 k libssh s390x 0.10.5-2.fc39 fedora 209 k libssh-config noarch 0.10.5-2.fc39 fedora 9.2 k libstdc++ s390x 13.2.1-1.fc40 copr_base 949 k libtasn1 s390x 4.19.0-3.fc39 fedora 77 k libtirpc s390x 1.3.3-1.rc2.fc39 fedora 95 k libunistring s390x 1.1-5.fc40 fedora 556 k libutempter s390x 1.2.1-10.fc39 fedora 26 k libuuid s390x 2.39.2-1.fc40 copr_base 29 k libverto s390x 0.3.2-6.fc39 fedora 21 k libxcrypt s390x 4.4.36-2.fc39 fedora 124 k libxml2 s390x 2.11.5-1.fc40 copr_base 711 k libzstd s390x 1.5.5-4.fc40 copr_base 343 k lua-libs s390x 5.4.6-3.fc39 fedora 142 k lua-srpm-macros noarch 1-9.fc39 fedora 8.6 k lz4-libs s390x 1.9.4-4.fc39 fedora 81 k mpfr s390x 4.2.0-3.fc39 fedora 298 k ncurses-base noarch 6.4-7.20230520.fc40 fedora 88 k ncurses-libs s390x 6.4-7.20230520.fc40 fedora 361 k ocaml-srpm-macros noarch 8-2.fc39 fedora 14 k openblas-srpm-macros noarch 2-14.fc39 fedora 7.5 k openldap s390x 2.6.6-1.fc39 fedora 262 k openssl-libs s390x 1:3.1.1-4.fc40 copr_base 1.9 M p11-kit s390x 0.25.0-2.fc39 fedora 507 k p11-kit-trust s390x 0.25.0-2.fc39 fedora 141 k package-notes-srpm-macros noarch 0.5-9.fc39 fedora 11 k pam s390x 1.5.3-2.fc39 fedora 558 k pam-libs s390x 1.5.3-2.fc39 fedora 59 k pcre2 s390x 10.42-1.fc39.2 fedora 250 k pcre2-syntax noarch 10.42-1.fc39.2 fedora 143 k perl-srpm-macros noarch 1-51.fc39 fedora 8.0 k pkgconf s390x 1.9.5-2.fc39 fedora 43 k pkgconf-m4 noarch 1.9.5-2.fc39 fedora 14 k pkgconf-pkg-config s390x 1.9.5-2.fc39 fedora 9.6 k popt s390x 1.19-3.fc39 fedora 69 k publicsuffix-list-dafsa noarch 20230812-1.fc40 fedora 57 k pyproject-srpm-macros noarch 1.9.0-2.fc39 fedora 14 k python-srpm-macros noarch 3.12-4.fc40 fedora 25 k qt5-srpm-macros noarch 5.15.10-2.fc39 fedora 8.3 k qt6-srpm-macros noarch 6.5.2-2.fc39 fedora 9.2 k readline s390x 8.2-4.fc39 fedora 229 k rpm s390x 4.18.99-1.fc40 fedora 538 k rpm-build-libs s390x 4.18.99-1.fc40 fedora 97 k rpm-libs s390x 4.18.99-1.fc40 fedora 323 k rpm-sequoia s390x 1.5.0-1.fc40 fedora 1.0 M rust-srpm-macros noarch 24-5.fc40 fedora 12 k setup noarch 2.14.4-1.fc39 fedora 154 k sqlite-libs s390x 3.43.1-1.fc40 fedora 737 k systemd-libs s390x 254.1-2.fc40 fedora 696 k tzdata noarch 2023c-3.fc40 fedora 718 k util-linux-core s390x 2.39.2-1.fc40 copr_base 483 k xxhash-libs s390x 0.8.2-1.fc39 fedora 37 k xz-libs s390x 5.4.4-1.fc39 fedora 114 k zip s390x 3.0-38.fc39 fedora 283 k zlib-ng-compat s390x 2.1.3-3.fc40 copr_base 71 k zstd s390x 1.5.5-4.fc40 copr_base 506 k Installing Groups: Buildsystem building group Transaction Summary ================================================================================ Install 153 Packages Total size: 53 M Installed size: 181 M Downloading Packages: [SKIPPED] cracklib-2.9.11-2.fc40.s390x.rpm: Already downloaded [SKIPPED] curl-8.3.0-1.fc40.s390x.rpm: Already downloaded [SKIPPED] elfutils-0.189-6.fc40.s390x.rpm: Already downloaded [SKIPPED] elfutils-debuginfod-client-0.189-6.fc40.s390x.rpm: Already downloaded [SKIPPED] elfutils-default-yama-scope-0.189-6.fc40.noarch.rpm: Already downloaded [SKIPPED] elfutils-libelf-0.189-6.fc40.s390x.rpm: Already downloaded [SKIPPED] elfutils-libs-0.189-6.fc40.s390x.rpm: Already downloaded [SKIPPED] file-5.45-1.fc40.s390x.rpm: Already downloaded [SKIPPED] file-libs-5.45-1.fc40.s390x.rpm: Already downloaded [SKIPPED] glibc-2.38.9000-8.fc40.s390x.rpm: Already downloaded [SKIPPED] glibc-common-2.38.9000-8.fc40.s390x.rpm: Already downloaded [SKIPPED] glibc-gconv-extra-2.38.9000-8.fc40.s390x.rpm: Already downloaded [SKIPPED] glibc-minimal-langpack-2.38.9000-8.fc40.s390x.rpm: Already downloaded [SKIPPED] libblkid-2.39.2-1.fc40.s390x.rpm: Already downloaded [SKIPPED] libcurl-8.3.0-1.fc40.s390x.rpm: Already downloaded [SKIPPED] libdb-5.3.28-58.fc40.s390x.rpm: Already downloaded [SKIPPED] libfdisk-2.39.2-1.fc40.s390x.rpm: Already downloaded [SKIPPED] libgcc-13.2.1-1.fc40.s390x.rpm: Already downloaded [SKIPPED] libgomp-13.2.1-1.fc40.s390x.rpm: Already downloaded [SKIPPED] libmount-2.39.2-1.fc40.s390x.rpm: Already downloaded [SKIPPED] libsmartcols-2.39.2-1.fc40.s390x.rpm: Already downloaded [SKIPPED] libstdc++-13.2.1-1.fc40.s390x.rpm: Already downloaded [SKIPPED] libuuid-2.39.2-1.fc40.s390x.rpm: Already downloaded [SKIPPED] libxml2-2.11.5-1.fc40.s390x.rpm: Already downloaded [SKIPPED] libzstd-1.5.5-4.fc40.s390x.rpm: Already downloaded [SKIPPED] openssl-libs-3.1.1-4.fc40.s390x.rpm: Already downloaded [SKIPPED] redhat-rpm-config-270-1.fc40.noarch.rpm: Already downloaded [SKIPPED] util-linux-2.39.2-1.fc40.s390x.rpm: Already downloaded [SKIPPED] util-linux-core-2.39.2-1.fc40.s390x.rpm: Already downloaded [SKIPPED] zlib-ng-compat-2.1.3-3.fc40.s390x.rpm: Already downloaded [SKIPPED] zstd-1.5.5-4.fc40.s390x.rpm: Already downloaded [SKIPPED] alternatives-1.25-1.fc39.s390x.rpm: Already downloaded [SKIPPED] ansible-srpm-macros-1-11.fc39.noarch.rpm: Already downloaded [SKIPPED] audit-libs-3.1.2-4.fc40.s390x.rpm: Already downloaded [SKIPPED] authselect-1.4.2-3.fc39.s390x.rpm: Already downloaded [SKIPPED] authselect-libs-1.4.2-3.fc39.s390x.rpm: Already downloaded [SKIPPED] basesystem-11-18.fc39.noarch.rpm: Already downloaded [SKIPPED] bash-5.2.15-5.fc39.s390x.rpm: Already downloaded [SKIPPED] binutils-2.41-5.fc40.s390x.rpm: Already downloaded [SKIPPED] binutils-gold-2.41-5.fc40.s390x.rpm: Already downloaded [SKIPPED] bzip2-1.0.8-16.fc39.s390x.rpm: Already downloaded [SKIPPED] bzip2-libs-1.0.8-16.fc39.s390x.rpm: Already downloaded [SKIPPED] ca-certificates-2023.2.60_v7.0.306-3.fc40.noarch.rpm: Already downloaded [SKIPPED] coreutils-9.4-1.fc40.s390x.rpm: Already downloaded [SKIPPED] coreutils-common-9.4-1.fc40.s390x.rpm: Already downloaded [SKIPPED] cpio-2.14-4.fc39.s390x.rpm: Already downloaded [SKIPPED] crypto-policies-20230731-1.git5ed06e0.fc39.noarch.rpm: Already downloaded [SKIPPED] cyrus-sasl-lib-2.1.28-11.fc39.s390x.rpm: Already downloaded [SKIPPED] 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/usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-40-primary Key imported successfully fedora 1.6 MB/s | 1.6 kB 00:00 GPG key at file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-40-primary (0xA15B79CC) is already installed fedora 1.6 MB/s | 1.6 kB 00:00 Importing GPG key 0x18B8E74C: Userid : "Fedora (39) " Fingerprint: E8F2 3996 F232 1864 0CB4 4CBE 75CF 5AC4 18B8 E74C From : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-39-primary Key imported successfully Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. 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p11-kit-trust-0.25.0-2.fc39.s390x 104/153 Installing : libverto-0.3.2-6.fc39.s390x 105/153 Installing : xxhash-libs-0.8.2-1.fc39.s390x 106/153 Installing : libssh-config-0.10.5-2.fc39.noarch 107/153 Installing : kernel-srpm-macros-1.0-20.fc39.noarch 108/153 Installing : gnat-srpm-macros-6-3.fc39.noarch 109/153 Installing : ghc-srpm-macros-1.6.1-2.fc39.noarch 110/153 Installing : fpc-srpm-macros-1.3-8.fc39.noarch 111/153 Installing : coreutils-common-9.4-1.fc40.s390x 112/153 Installing : openssl-libs-1:3.1.1-4.fc40.s390x 113/153 Installing : coreutils-9.4-1.fc40.s390x 114/153 Running scriptlet: ca-certificates-2023.2.60_v7.0.306-3.fc40.noarch 115/153 Installing : ca-certificates-2023.2.60_v7.0.306-3.fc40.noarch 115/153 Running scriptlet: ca-certificates-2023.2.60_v7.0.306-3.fc40.noarch 115/153 Installing : krb5-libs-1.21.2-1.fc40.s390x 116/153 Installing : libtirpc-1.3.3-1.rc2.fc39.s390x 117/153 Running scriptlet: authselect-libs-1.4.2-3.fc39.s390x 118/153 Installing : authselect-libs-1.4.2-3.fc39.s390x 118/153 Installing : gzip-1.12-6.fc39.s390x 119/153 Installing : cracklib-2.9.11-2.fc40.s390x 120/153 Installing : libpwquality-1.4.5-6.fc39.s390x 121/153 Installing : authselect-1.4.2-3.fc39.s390x 122/153 Installing : libnsl2-2.0.0-6.fc39.s390x 123/153 Installing : pam-1.5.3-2.fc39.s390x 124/153 Installing : libssh-0.10.5-2.fc39.s390x 125/153 Installing : libarchive-3.7.2-1.fc40.s390x 126/153 Installing : libevent-2.1.12-9.fc39.s390x 127/153 Installing : openldap-2.6.6-1.fc39.s390x 128/153 Installing : libcurl-8.3.0-1.fc40.s390x 129/153 Installing : elfutils-libs-0.189-6.fc40.s390x 130/153 Installing : elfutils-debuginfod-client-0.189-6.fc40.s390x 131/153 Installing : binutils-gold-2.41-5.fc40.s390x 132/153 Running scriptlet: binutils-gold-2.41-5.fc40.s390x 132/153 Installing : binutils-2.41-5.fc40.s390x 133/153 Running scriptlet: binutils-2.41-5.fc40.s390x 133/153 Installing : elfutils-0.189-6.fc40.s390x 134/153 Installing : gdb-minimal-13.2-8.fc40.s390x 135/153 Installing : debugedit-5.0-10.fc39.s390x 136/153 Installing : curl-8.3.0-1.fc40.s390x 137/153 Installing : rpm-sequoia-1.5.0-1.fc40.s390x 138/153 Installing : rpm-libs-4.18.99-1.fc40.s390x 139/153 Running scriptlet: rpm-4.18.99-1.fc40.s390x 140/153 Installing : rpm-4.18.99-1.fc40.s390x 140/153 Installing : efi-srpm-macros-5-9.fc39.noarch 141/153 Installing : lua-srpm-macros-1-9.fc39.noarch 142/153 Installing : rpm-build-libs-4.18.99-1.fc40.s390x 143/153 Installing : ansible-srpm-macros-1-11.fc39.noarch 144/153 Installing : fonts-srpm-macros-1:2.0.5-12.fc39.noarch 145/153 Installing : forge-srpm-macros-0.1.0-1.fc40.noarch 146/153 Installing : go-srpm-macros-3.2.0-7.fc40.noarch 147/153 Installing : python-srpm-macros-3.12-4.fc40.noarch 148/153 Installing : redhat-rpm-config-270-1.fc40.noarch 149/153 Installing : rpm-build-4.18.99-1.fc40.s390x 150/153 Installing : util-linux-2.39.2-1.fc40.s390x 151/153 Installing : which-2.21-40.fc39.s390x 152/153 Installing : info-7.0.3-3.fc39.s390x 153/153 Running scriptlet: filesystem-3.18-6.fc39.s390x 153/153 Running scriptlet: ca-certificates-2023.2.60_v7.0.306-3.fc40.noarch 153/153 Running scriptlet: authselect-libs-1.4.2-3.fc39.s390x 153/153 Running scriptlet: rpm-4.18.99-1.fc40.s390x 153/153 Running scriptlet: info-7.0.3-3.fc39.s390x 153/153 Verifying : cracklib-2.9.11-2.fc40.s390x 1/153 Verifying : curl-8.3.0-1.fc40.s390x 2/153 Verifying : elfutils-0.189-6.fc40.s390x 3/153 Verifying : elfutils-debuginfod-client-0.189-6.fc40.s390x 4/153 Verifying : elfutils-default-yama-scope-0.189-6.fc40.noarch 5/153 Verifying : elfutils-libelf-0.189-6.fc40.s390x 6/153 Verifying : elfutils-libs-0.189-6.fc40.s390x 7/153 Verifying : file-5.45-1.fc40.s390x 8/153 Verifying : file-libs-5.45-1.fc40.s390x 9/153 Verifying : glibc-2.38.9000-8.fc40.s390x 10/153 Verifying : glibc-common-2.38.9000-8.fc40.s390x 11/153 Verifying : glibc-gconv-extra-2.38.9000-8.fc40.s390x 12/153 Verifying : glibc-minimal-langpack-2.38.9000-8.fc40.s390x 13/153 Verifying : libblkid-2.39.2-1.fc40.s390x 14/153 Verifying : libcurl-8.3.0-1.fc40.s390x 15/153 Verifying : libdb-5.3.28-58.fc40.s390x 16/153 Verifying : libfdisk-2.39.2-1.fc40.s390x 17/153 Verifying : libgcc-13.2.1-1.fc40.s390x 18/153 Verifying : libgomp-13.2.1-1.fc40.s390x 19/153 Verifying : libmount-2.39.2-1.fc40.s390x 20/153 Verifying : libsmartcols-2.39.2-1.fc40.s390x 21/153 Verifying : libstdc++-13.2.1-1.fc40.s390x 22/153 Verifying : libuuid-2.39.2-1.fc40.s390x 23/153 Verifying : libxml2-2.11.5-1.fc40.s390x 24/153 Verifying : libzstd-1.5.5-4.fc40.s390x 25/153 Verifying : openssl-libs-1:3.1.1-4.fc40.s390x 26/153 Verifying : redhat-rpm-config-270-1.fc40.noarch 27/153 Verifying : util-linux-2.39.2-1.fc40.s390x 28/153 Verifying : util-linux-core-2.39.2-1.fc40.s390x 29/153 Verifying : zlib-ng-compat-2.1.3-3.fc40.s390x 30/153 Verifying : zstd-1.5.5-4.fc40.s390x 31/153 Verifying : alternatives-1.25-1.fc39.s390x 32/153 Verifying : ansible-srpm-macros-1-11.fc39.noarch 33/153 Verifying : audit-libs-3.1.2-4.fc40.s390x 34/153 Verifying : authselect-1.4.2-3.fc39.s390x 35/153 Verifying : authselect-libs-1.4.2-3.fc39.s390x 36/153 Verifying : basesystem-11-18.fc39.noarch 37/153 Verifying : bash-5.2.15-5.fc39.s390x 38/153 Verifying : binutils-2.41-5.fc40.s390x 39/153 Verifying : binutils-gold-2.41-5.fc40.s390x 40/153 Verifying : bzip2-1.0.8-16.fc39.s390x 41/153 Verifying : bzip2-libs-1.0.8-16.fc39.s390x 42/153 Verifying : ca-certificates-2023.2.60_v7.0.306-3.fc40.noarch 43/153 Verifying : coreutils-9.4-1.fc40.s390x 44/153 Verifying : coreutils-common-9.4-1.fc40.s390x 45/153 Verifying : cpio-2.14-4.fc39.s390x 46/153 Verifying : crypto-policies-20230731-1.git5ed06e0.fc39.noarc 47/153 Verifying : cyrus-sasl-lib-2.1.28-11.fc39.s390x 48/153 Verifying : debugedit-5.0-10.fc39.s390x 49/153 Verifying : diffutils-3.10-3.fc39.s390x 50/153 Verifying : dwz-0.15-3.fc39.s390x 51/153 Verifying : ed-1.19-4.fc39.s390x 52/153 Verifying : efi-srpm-macros-5-9.fc39.noarch 53/153 Verifying : fedora-gpg-keys-40-0.1.noarch 54/153 Verifying : fedora-release-40-0.7.noarch 55/153 Verifying : fedora-release-common-40-0.7.noarch 56/153 Verifying : fedora-release-identity-basic-40-0.7.noarch 57/153 Verifying : fedora-repos-40-0.1.noarch 58/153 Verifying : fedora-repos-rawhide-40-0.1.noarch 59/153 Verifying : filesystem-3.18-6.fc39.s390x 60/153 Verifying : findutils-1:4.9.0-6.fc40.s390x 61/153 Verifying : fonts-srpm-macros-1:2.0.5-12.fc39.noarch 62/153 Verifying : forge-srpm-macros-0.1.0-1.fc40.noarch 63/153 Verifying : fpc-srpm-macros-1.3-8.fc39.noarch 64/153 Verifying : gawk-5.2.2-2.fc39.s390x 65/153 Verifying : gdb-minimal-13.2-8.fc40.s390x 66/153 Verifying : gdbm-libs-1:1.23-4.fc39.s390x 67/153 Verifying : ghc-srpm-macros-1.6.1-2.fc39.noarch 68/153 Verifying : gmp-1:6.2.1-5.fc39.s390x 69/153 Verifying : gnat-srpm-macros-6-3.fc39.noarch 70/153 Verifying : go-srpm-macros-3.2.0-7.fc40.noarch 71/153 Verifying : grep-3.11-5.fc40.s390x 72/153 Verifying : gzip-1.12-6.fc39.s390x 73/153 Verifying : info-7.0.3-3.fc39.s390x 74/153 Verifying : jansson-2.13.1-7.fc39.s390x 75/153 Verifying : kernel-srpm-macros-1.0-20.fc39.noarch 76/153 Verifying : keyutils-libs-1.6.1-7.fc39.s390x 77/153 Verifying : krb5-libs-1.21.2-1.fc40.s390x 78/153 Verifying : libacl-2.3.1-9.fc40.s390x 79/153 Verifying : libarchive-3.7.2-1.fc40.s390x 80/153 Verifying : libattr-2.5.1-9.fc40.s390x 81/153 Verifying : libbrotli-1.1.0-1.fc40.s390x 82/153 Verifying : libcap-2.48-7.fc39.s390x 83/153 Verifying : libcap-ng-0.8.3-8.fc40.s390x 84/153 Verifying : libcom_err-1.47.0-2.fc39.s390x 85/153 Verifying : libeconf-0.5.2-1.fc40.s390x 86/153 Verifying : libevent-2.1.12-9.fc39.s390x 87/153 Verifying : libffi-3.4.4-4.fc39.s390x 88/153 Verifying : libidn2-2.3.4-3.fc39.s390x 89/153 Verifying : libnghttp2-1.56.0-1.fc40.s390x 90/153 Verifying : libnsl2-2.0.0-6.fc39.s390x 91/153 Verifying : libpkgconf-1.9.5-2.fc39.s390x 92/153 Verifying : libpsl-0.21.2-4.fc39.s390x 93/153 Verifying : libpwquality-1.4.5-6.fc39.s390x 94/153 Verifying : libselinux-3.5-5.fc39.s390x 95/153 Verifying : libsemanage-3.5-4.fc39.s390x 96/153 Verifying : libsepol-3.5-2.fc39.s390x 97/153 Verifying : libsigsegv-2.14-5.fc39.s390x 98/153 Verifying : libssh-0.10.5-2.fc39.s390x 99/153 Verifying : libssh-config-0.10.5-2.fc39.noarch 100/153 Verifying : libtasn1-4.19.0-3.fc39.s390x 101/153 Verifying : libtirpc-1.3.3-1.rc2.fc39.s390x 102/153 Verifying : libunistring-1.1-5.fc40.s390x 103/153 Verifying : libutempter-1.2.1-10.fc39.s390x 104/153 Verifying : libverto-0.3.2-6.fc39.s390x 105/153 Verifying : libxcrypt-4.4.36-2.fc39.s390x 106/153 Verifying : lua-libs-5.4.6-3.fc39.s390x 107/153 Verifying : lua-srpm-macros-1-9.fc39.noarch 108/153 Verifying : lz4-libs-1.9.4-4.fc39.s390x 109/153 Verifying : mpfr-4.2.0-3.fc39.s390x 110/153 Verifying : ncurses-base-6.4-7.20230520.fc40.noarch 111/153 Verifying : ncurses-libs-6.4-7.20230520.fc40.s390x 112/153 Verifying : ocaml-srpm-macros-8-2.fc39.noarch 113/153 Verifying : openblas-srpm-macros-2-14.fc39.noarch 114/153 Verifying : openldap-2.6.6-1.fc39.s390x 115/153 Verifying : p11-kit-0.25.0-2.fc39.s390x 116/153 Verifying : p11-kit-trust-0.25.0-2.fc39.s390x 117/153 Verifying : package-notes-srpm-macros-0.5-9.fc39.noarch 118/153 Verifying : pam-1.5.3-2.fc39.s390x 119/153 Verifying : pam-libs-1.5.3-2.fc39.s390x 120/153 Verifying : patch-2.7.6-22.fc39.s390x 121/153 Verifying : pcre2-10.42-1.fc39.2.s390x 122/153 Verifying : pcre2-syntax-10.42-1.fc39.2.noarch 123/153 Verifying : perl-srpm-macros-1-51.fc39.noarch 124/153 Verifying : pkgconf-1.9.5-2.fc39.s390x 125/153 Verifying : pkgconf-m4-1.9.5-2.fc39.noarch 126/153 Verifying : pkgconf-pkg-config-1.9.5-2.fc39.s390x 127/153 Verifying : popt-1.19-3.fc39.s390x 128/153 Verifying : publicsuffix-list-dafsa-20230812-1.fc40.noarch 129/153 Verifying : pyproject-srpm-macros-1.9.0-2.fc39.noarch 130/153 Verifying : python-srpm-macros-3.12-4.fc40.noarch 131/153 Verifying : qt5-srpm-macros-5.15.10-2.fc39.noarch 132/153 Verifying : qt6-srpm-macros-6.5.2-2.fc39.noarch 133/153 Verifying : readline-8.2-4.fc39.s390x 134/153 Verifying : rpm-4.18.99-1.fc40.s390x 135/153 Verifying : rpm-build-4.18.99-1.fc40.s390x 136/153 Verifying : rpm-build-libs-4.18.99-1.fc40.s390x 137/153 Verifying : rpm-libs-4.18.99-1.fc40.s390x 138/153 Verifying : rpm-sequoia-1.5.0-1.fc40.s390x 139/153 Verifying : rust-srpm-macros-24-5.fc40.noarch 140/153 Verifying : sed-4.8-14.fc39.s390x 141/153 Verifying : setup-2.14.4-1.fc39.noarch 142/153 Verifying : shadow-utils-2:4.14.0-1.fc40.s390x 143/153 Verifying : sqlite-libs-3.43.1-1.fc40.s390x 144/153 Verifying : systemd-libs-254.1-2.fc40.s390x 145/153 Verifying : tar-2:1.35-2.fc40.s390x 146/153 Verifying : tzdata-2023c-3.fc40.noarch 147/153 Verifying : unzip-6.0-62.fc39.s390x 148/153 Verifying : which-2.21-40.fc39.s390x 149/153 Verifying : xxhash-libs-0.8.2-1.fc39.s390x 150/153 Verifying : xz-5.4.4-1.fc39.s390x 151/153 Verifying : xz-libs-5.4.4-1.fc39.s390x 152/153 Verifying : zip-3.0-38.fc39.s390x 153/153 Installed: alternatives-1.25-1.fc39.s390x ansible-srpm-macros-1-11.fc39.noarch audit-libs-3.1.2-4.fc40.s390x authselect-1.4.2-3.fc39.s390x authselect-libs-1.4.2-3.fc39.s390x basesystem-11-18.fc39.noarch bash-5.2.15-5.fc39.s390x binutils-2.41-5.fc40.s390x binutils-gold-2.41-5.fc40.s390x bzip2-1.0.8-16.fc39.s390x bzip2-libs-1.0.8-16.fc39.s390x ca-certificates-2023.2.60_v7.0.306-3.fc40.noarch coreutils-9.4-1.fc40.s390x coreutils-common-9.4-1.fc40.s390x cpio-2.14-4.fc39.s390x cracklib-2.9.11-2.fc40.s390x crypto-policies-20230731-1.git5ed06e0.fc39.noarch curl-8.3.0-1.fc40.s390x cyrus-sasl-lib-2.1.28-11.fc39.s390x debugedit-5.0-10.fc39.s390x diffutils-3.10-3.fc39.s390x dwz-0.15-3.fc39.s390x ed-1.19-4.fc39.s390x efi-srpm-macros-5-9.fc39.noarch elfutils-0.189-6.fc40.s390x elfutils-debuginfod-client-0.189-6.fc40.s390x elfutils-default-yama-scope-0.189-6.fc40.noarch elfutils-libelf-0.189-6.fc40.s390x elfutils-libs-0.189-6.fc40.s390x fedora-gpg-keys-40-0.1.noarch fedora-release-40-0.7.noarch fedora-release-common-40-0.7.noarch fedora-release-identity-basic-40-0.7.noarch fedora-repos-40-0.1.noarch fedora-repos-rawhide-40-0.1.noarch file-5.45-1.fc40.s390x file-libs-5.45-1.fc40.s390x filesystem-3.18-6.fc39.s390x findutils-1:4.9.0-6.fc40.s390x fonts-srpm-macros-1:2.0.5-12.fc39.noarch forge-srpm-macros-0.1.0-1.fc40.noarch fpc-srpm-macros-1.3-8.fc39.noarch gawk-5.2.2-2.fc39.s390x gdb-minimal-13.2-8.fc40.s390x gdbm-libs-1:1.23-4.fc39.s390x ghc-srpm-macros-1.6.1-2.fc39.noarch glibc-2.38.9000-8.fc40.s390x glibc-common-2.38.9000-8.fc40.s390x glibc-gconv-extra-2.38.9000-8.fc40.s390x glibc-minimal-langpack-2.38.9000-8.fc40.s390x gmp-1:6.2.1-5.fc39.s390x gnat-srpm-macros-6-3.fc39.noarch go-srpm-macros-3.2.0-7.fc40.noarch grep-3.11-5.fc40.s390x gzip-1.12-6.fc39.s390x info-7.0.3-3.fc39.s390x jansson-2.13.1-7.fc39.s390x kernel-srpm-macros-1.0-20.fc39.noarch keyutils-libs-1.6.1-7.fc39.s390x krb5-libs-1.21.2-1.fc40.s390x libacl-2.3.1-9.fc40.s390x libarchive-3.7.2-1.fc40.s390x libattr-2.5.1-9.fc40.s390x libblkid-2.39.2-1.fc40.s390x libbrotli-1.1.0-1.fc40.s390x libcap-2.48-7.fc39.s390x libcap-ng-0.8.3-8.fc40.s390x libcom_err-1.47.0-2.fc39.s390x libcurl-8.3.0-1.fc40.s390x libdb-5.3.28-58.fc40.s390x libeconf-0.5.2-1.fc40.s390x libevent-2.1.12-9.fc39.s390x libfdisk-2.39.2-1.fc40.s390x libffi-3.4.4-4.fc39.s390x libgcc-13.2.1-1.fc40.s390x libgomp-13.2.1-1.fc40.s390x libidn2-2.3.4-3.fc39.s390x libmount-2.39.2-1.fc40.s390x libnghttp2-1.56.0-1.fc40.s390x libnsl2-2.0.0-6.fc39.s390x libpkgconf-1.9.5-2.fc39.s390x libpsl-0.21.2-4.fc39.s390x libpwquality-1.4.5-6.fc39.s390x libselinux-3.5-5.fc39.s390x libsemanage-3.5-4.fc39.s390x libsepol-3.5-2.fc39.s390x libsigsegv-2.14-5.fc39.s390x libsmartcols-2.39.2-1.fc40.s390x libssh-0.10.5-2.fc39.s390x libssh-config-0.10.5-2.fc39.noarch libstdc++-13.2.1-1.fc40.s390x libtasn1-4.19.0-3.fc39.s390x libtirpc-1.3.3-1.rc2.fc39.s390x libunistring-1.1-5.fc40.s390x libutempter-1.2.1-10.fc39.s390x libuuid-2.39.2-1.fc40.s390x libverto-0.3.2-6.fc39.s390x libxcrypt-4.4.36-2.fc39.s390x libxml2-2.11.5-1.fc40.s390x libzstd-1.5.5-4.fc40.s390x lua-libs-5.4.6-3.fc39.s390x lua-srpm-macros-1-9.fc39.noarch lz4-libs-1.9.4-4.fc39.s390x mpfr-4.2.0-3.fc39.s390x ncurses-base-6.4-7.20230520.fc40.noarch ncurses-libs-6.4-7.20230520.fc40.s390x ocaml-srpm-macros-8-2.fc39.noarch openblas-srpm-macros-2-14.fc39.noarch openldap-2.6.6-1.fc39.s390x openssl-libs-1:3.1.1-4.fc40.s390x p11-kit-0.25.0-2.fc39.s390x p11-kit-trust-0.25.0-2.fc39.s390x package-notes-srpm-macros-0.5-9.fc39.noarch pam-1.5.3-2.fc39.s390x pam-libs-1.5.3-2.fc39.s390x patch-2.7.6-22.fc39.s390x pcre2-10.42-1.fc39.2.s390x pcre2-syntax-10.42-1.fc39.2.noarch perl-srpm-macros-1-51.fc39.noarch pkgconf-1.9.5-2.fc39.s390x pkgconf-m4-1.9.5-2.fc39.noarch pkgconf-pkg-config-1.9.5-2.fc39.s390x popt-1.19-3.fc39.s390x publicsuffix-list-dafsa-20230812-1.fc40.noarch pyproject-srpm-macros-1.9.0-2.fc39.noarch python-srpm-macros-3.12-4.fc40.noarch qt5-srpm-macros-5.15.10-2.fc39.noarch qt6-srpm-macros-6.5.2-2.fc39.noarch readline-8.2-4.fc39.s390x redhat-rpm-config-270-1.fc40.noarch rpm-4.18.99-1.fc40.s390x rpm-build-4.18.99-1.fc40.s390x rpm-build-libs-4.18.99-1.fc40.s390x rpm-libs-4.18.99-1.fc40.s390x rpm-sequoia-1.5.0-1.fc40.s390x rust-srpm-macros-24-5.fc40.noarch sed-4.8-14.fc39.s390x setup-2.14.4-1.fc39.noarch shadow-utils-2:4.14.0-1.fc40.s390x sqlite-libs-3.43.1-1.fc40.s390x systemd-libs-254.1-2.fc40.s390x tar-2:1.35-2.fc40.s390x tzdata-2023c-3.fc40.noarch unzip-6.0-62.fc39.s390x util-linux-2.39.2-1.fc40.s390x util-linux-core-2.39.2-1.fc40.s390x which-2.21-40.fc39.s390x xxhash-libs-0.8.2-1.fc39.s390x xz-5.4.4-1.fc39.s390x xz-libs-5.4.4-1.fc39.s390x zip-3.0-38.fc39.s390x zlib-ng-compat-2.1.3-3.fc40.s390x zstd-1.5.5-4.fc40.s390x Complete! Finish: installing minimal buildroot with dnf Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: alternatives-1.25-1.fc39.s390x ansible-srpm-macros-1-11.fc39.noarch audit-libs-3.1.2-4.fc40.s390x authselect-1.4.2-3.fc39.s390x authselect-libs-1.4.2-3.fc39.s390x basesystem-11-18.fc39.noarch bash-5.2.15-5.fc39.s390x binutils-2.41-5.fc40.s390x binutils-gold-2.41-5.fc40.s390x bzip2-1.0.8-16.fc39.s390x bzip2-libs-1.0.8-16.fc39.s390x ca-certificates-2023.2.60_v7.0.306-3.fc40.noarch coreutils-9.4-1.fc40.s390x coreutils-common-9.4-1.fc40.s390x cpio-2.14-4.fc39.s390x cracklib-2.9.11-2.fc40.s390x crypto-policies-20230731-1.git5ed06e0.fc39.noarch curl-8.3.0-1.fc40.s390x cyrus-sasl-lib-2.1.28-11.fc39.s390x debugedit-5.0-10.fc39.s390x diffutils-3.10-3.fc39.s390x dwz-0.15-3.fc39.s390x ed-1.19-4.fc39.s390x efi-srpm-macros-5-9.fc39.noarch elfutils-0.189-6.fc40.s390x elfutils-debuginfod-client-0.189-6.fc40.s390x elfutils-default-yama-scope-0.189-6.fc40.noarch elfutils-libelf-0.189-6.fc40.s390x elfutils-libs-0.189-6.fc40.s390x fedora-gpg-keys-40-0.1.noarch fedora-release-40-0.7.noarch fedora-release-common-40-0.7.noarch fedora-release-identity-basic-40-0.7.noarch fedora-repos-40-0.1.noarch fedora-repos-rawhide-40-0.1.noarch file-5.45-1.fc40.s390x file-libs-5.45-1.fc40.s390x filesystem-3.18-6.fc39.s390x findutils-4.9.0-6.fc40.s390x fonts-srpm-macros-2.0.5-12.fc39.noarch forge-srpm-macros-0.1.0-1.fc40.noarch fpc-srpm-macros-1.3-8.fc39.noarch gawk-5.2.2-2.fc39.s390x gdb-minimal-13.2-8.fc40.s390x gdbm-libs-1.23-4.fc39.s390x ghc-srpm-macros-1.6.1-2.fc39.noarch glibc-2.38.9000-8.fc40.s390x glibc-common-2.38.9000-8.fc40.s390x glibc-gconv-extra-2.38.9000-8.fc40.s390x glibc-minimal-langpack-2.38.9000-8.fc40.s390x gmp-6.2.1-5.fc39.s390x gnat-srpm-macros-6-3.fc39.noarch go-srpm-macros-3.2.0-7.fc40.noarch gpg-pubkey-18b8e74c-62f2920f gpg-pubkey-a15b79cc-63d04c2c grep-3.11-5.fc40.s390x gzip-1.12-6.fc39.s390x info-7.0.3-3.fc39.s390x jansson-2.13.1-7.fc39.s390x kernel-srpm-macros-1.0-20.fc39.noarch keyutils-libs-1.6.1-7.fc39.s390x krb5-libs-1.21.2-1.fc40.s390x libacl-2.3.1-9.fc40.s390x libarchive-3.7.2-1.fc40.s390x libattr-2.5.1-9.fc40.s390x libblkid-2.39.2-1.fc40.s390x libbrotli-1.1.0-1.fc40.s390x libcap-2.48-7.fc39.s390x libcap-ng-0.8.3-8.fc40.s390x libcom_err-1.47.0-2.fc39.s390x libcurl-8.3.0-1.fc40.s390x libdb-5.3.28-58.fc40.s390x libeconf-0.5.2-1.fc40.s390x libevent-2.1.12-9.fc39.s390x libfdisk-2.39.2-1.fc40.s390x libffi-3.4.4-4.fc39.s390x libgcc-13.2.1-1.fc40.s390x libgomp-13.2.1-1.fc40.s390x libidn2-2.3.4-3.fc39.s390x libmount-2.39.2-1.fc40.s390x libnghttp2-1.56.0-1.fc40.s390x libnsl2-2.0.0-6.fc39.s390x libpkgconf-1.9.5-2.fc39.s390x libpsl-0.21.2-4.fc39.s390x libpwquality-1.4.5-6.fc39.s390x libselinux-3.5-5.fc39.s390x libsemanage-3.5-4.fc39.s390x libsepol-3.5-2.fc39.s390x libsigsegv-2.14-5.fc39.s390x libsmartcols-2.39.2-1.fc40.s390x libssh-0.10.5-2.fc39.s390x libssh-config-0.10.5-2.fc39.noarch libstdc++-13.2.1-1.fc40.s390x libtasn1-4.19.0-3.fc39.s390x libtirpc-1.3.3-1.rc2.fc39.s390x libunistring-1.1-5.fc40.s390x libutempter-1.2.1-10.fc39.s390x libuuid-2.39.2-1.fc40.s390x libverto-0.3.2-6.fc39.s390x libxcrypt-4.4.36-2.fc39.s390x libxml2-2.11.5-1.fc40.s390x libzstd-1.5.5-4.fc40.s390x lua-libs-5.4.6-3.fc39.s390x lua-srpm-macros-1-9.fc39.noarch lz4-libs-1.9.4-4.fc39.s390x mpfr-4.2.0-3.fc39.s390x ncurses-base-6.4-7.20230520.fc40.noarch ncurses-libs-6.4-7.20230520.fc40.s390x ocaml-srpm-macros-8-2.fc39.noarch openblas-srpm-macros-2-14.fc39.noarch openldap-2.6.6-1.fc39.s390x openssl-libs-3.1.1-4.fc40.s390x p11-kit-0.25.0-2.fc39.s390x p11-kit-trust-0.25.0-2.fc39.s390x package-notes-srpm-macros-0.5-9.fc39.noarch pam-1.5.3-2.fc39.s390x pam-libs-1.5.3-2.fc39.s390x patch-2.7.6-22.fc39.s390x pcre2-10.42-1.fc39.2.s390x pcre2-syntax-10.42-1.fc39.2.noarch perl-srpm-macros-1-51.fc39.noarch pkgconf-1.9.5-2.fc39.s390x pkgconf-m4-1.9.5-2.fc39.noarch pkgconf-pkg-config-1.9.5-2.fc39.s390x popt-1.19-3.fc39.s390x publicsuffix-list-dafsa-20230812-1.fc40.noarch pyproject-srpm-macros-1.9.0-2.fc39.noarch python-srpm-macros-3.12-4.fc40.noarch qt5-srpm-macros-5.15.10-2.fc39.noarch qt6-srpm-macros-6.5.2-2.fc39.noarch readline-8.2-4.fc39.s390x redhat-rpm-config-270-1.fc40.noarch rpm-4.18.99-1.fc40.s390x rpm-build-4.18.99-1.fc40.s390x rpm-build-libs-4.18.99-1.fc40.s390x rpm-libs-4.18.99-1.fc40.s390x rpm-sequoia-1.5.0-1.fc40.s390x rust-srpm-macros-24-5.fc40.noarch sed-4.8-14.fc39.s390x setup-2.14.4-1.fc39.noarch shadow-utils-4.14.0-1.fc40.s390x sqlite-libs-3.43.1-1.fc40.s390x systemd-libs-254.1-2.fc40.s390x tar-1.35-2.fc40.s390x tzdata-2023c-3.fc40.noarch unzip-6.0-62.fc39.s390x util-linux-2.39.2-1.fc40.s390x util-linux-core-2.39.2-1.fc40.s390x which-2.21-40.fc39.s390x xxhash-libs-0.8.2-1.fc39.s390x xz-5.4.4-1.fc39.s390x xz-libs-5.4.4-1.fc39.s390x zip-3.0-38.fc39.s390x zlib-ng-compat-2.1.3-3.fc40.s390x zstd-1.5.5-4.fc40.s390x Start: buildsrpm Start: rpmbuild -bs warning: %patchN is deprecated (1 usages found), use %patch N (or %patch -P N) Building target platforms: s390x Building for target s390x setting SOURCE_DATE_EPOCH=1689811200 Wrote: /builddir/build/SRPMS/htslib-1.15.1-3.fc40.src.rpm RPM build warnings: %patchN is deprecated (1 usages found), use %patch N (or %patch -P N) Finish: rpmbuild -bs INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-s390x-1695021298.041424/root/var/log/dnf.rpm.log /var/lib/mock/fedora-rawhide-s390x-1695021298.041424/root/var/log/dnf.librepo.log /var/lib/mock/fedora-rawhide-s390x-1695021298.041424/root/var/log/dnf.log Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-k5v2bpfm/htslib/htslib.spec) Config(child) 7 minutes 9 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.fc40.src.rpm) Config(fedora-rawhide-s390x) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-s390x-bootstrap-1695021298.041424/root. INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-s390x-bootstrap-1695021298.041424/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-s390x-1695021298.041424/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 Finish: chroot init INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-4.18.99-1.fc40.s390x rpm-sequoia-1.5.0-1.fc40.s390x python3-dnf-4.16.2-4.fc40.noarch python3-dnf-plugins-core-4.4.2-1.fc39.noarch yum-4.16.2-4.fc40.noarch Start: build phase for htslib-1.15.1-3.fc40.src.rpm Start: build setup for htslib-1.15.1-3.fc40.src.rpm warning: %patchN is deprecated (1 usages found), use %patch N (or %patch -P N) Building target platforms: s390x Building for target s390x setting SOURCE_DATE_EPOCH=1689811200 Wrote: /builddir/build/SRPMS/htslib-1.15.1-3.fc40.src.rpm RPM build warnings: %patchN is deprecated (1 usages found), use %patch N (or %patch -P N) No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 2.9 kB/s | 1.5 kB 00:00 Copr repository 1.2 MB/s | 3.0 MB 00:02 fedora 16 kB/s | 5.5 kB 00:00 Last metadata expiration check: 0:00:01 ago on Mon Sep 18 07:22:15 2023. Dependencies resolved. ================================================================================ Package Arch Version Repository Size ================================================================================ Installing: bzip2-devel s390x 1.0.8-16.fc39 fedora 214 k gcc s390x 13.2.1-1.fc40 copr_base 28 M libcurl-devel s390x 8.3.0-1.fc40 copr_base 901 k make s390x 1:4.4.1-2.fc39 fedora 605 k openssl-devel s390x 1:3.1.1-4.fc40 copr_base 2.5 M perl-Data-Dumper s390x 2.188-501.fc39 fedora 57 k perl-FindBin noarch 1.53-500.fc39 fedora 14 k perl-Getopt-Long noarch 1:2.54-500.fc39 fedora 60 k perl-interpreter s390x 4:5.38.0-500.fc39 fedora 72 k perl-lib s390x 0.65-500.fc39 fedora 15 k xz-devel s390x 5.4.4-1.fc39 fedora 66 k zlib-ng-compat-devel s390x 2.1.3-3.fc40 copr_base 34 k Installing dependencies: annobin-docs noarch 12.26-1.fc40 fedora 94 k annobin-plugin-gcc s390x 12.26-1.fc40 fedora 958 k cpp s390x 13.2.1-1.fc40 copr_base 8.8 M gc s390x 8.2.2-4.fc39 fedora 114 k gcc-plugin-annobin s390x 13.2.1-1.fc40 copr_base 46 k glibc-devel s390x 2.38.9000-8.fc40 copr_base 96 k glibc-headers-s390 noarch 2.38.9000-8.fc40 copr_base 489 k groff-base s390x 1.23.0-2.fc39 fedora 1.2 M guile22 s390x 2.2.7-9.fc39 fedora 6.5 M kernel-headers s390x 6.6.0-0.rc1.git0.1.fc40 fedora 1.5 M libasan s390x 13.2.1-1.fc40 copr_base 507 k libatomic s390x 13.2.1-1.fc40 copr_base 34 k libmpc s390x 1.3.1-3.fc39 fedora 73 k libtool-ltdl s390x 2.4.7-8.fc40 fedora 37 k libubsan s390x 13.2.1-1.fc40 copr_base 219 k libxcrypt-devel s390x 4.4.36-2.fc39 fedora 30 k ncurses s390x 6.4-7.20230520.fc40 fedora 424 k perl-AutoLoader noarch 5.74-500.fc39 fedora 21 k perl-B s390x 1.88-500.fc39 fedora 178 k perl-Carp noarch 1.54-500.fc39 fedora 29 k perl-Class-Struct noarch 0.68-500.fc39 fedora 22 k perl-Digest noarch 1.20-500.fc39 fedora 25 k perl-Digest-MD5 s390x 2.58-500.fc39 fedora 35 k perl-DynaLoader s390x 1.54-500.fc39 fedora 26 k perl-Encode s390x 4:3.19-500.fc39 fedora 1.7 M perl-Errno s390x 1.37-500.fc39 fedora 15 k perl-Exporter noarch 5.77-500.fc39 fedora 31 k perl-Fcntl s390x 1.15-500.fc39 fedora 21 k perl-File-Basename noarch 2.86-500.fc39 fedora 17 k perl-File-Path noarch 2.18-500.fc39 fedora 35 k perl-File-Temp noarch 1:0.231.100-500.fc39 fedora 58 k perl-File-stat noarch 1.13-500.fc39 fedora 17 k perl-FileHandle noarch 2.05-500.fc39 fedora 16 k perl-Getopt-Std noarch 1.13-500.fc39 fedora 16 k perl-HTTP-Tiny noarch 0.088-3.fc39 fedora 56 k perl-IO s390x 1.52-500.fc39 fedora 82 k perl-IO-Socket-IP noarch 0.42-1.fc39 fedora 42 k perl-IO-Socket-SSL noarch 2.083-3.fc39 fedora 225 k perl-IPC-Open3 noarch 1.22-500.fc39 fedora 22 k perl-MIME-Base64 s390x 3.16-500.fc39 fedora 30 k perl-Mozilla-CA noarch 20230821-1.fc40 fedora 13 k perl-Net-SSLeay s390x 1.92-10.fc39 fedora 363 k perl-POSIX s390x 2.13-500.fc39 fedora 98 k perl-PathTools s390x 3.89-500.fc39 fedora 87 k perl-Pod-Escapes noarch 1:1.07-501.fc40 fedora 19 k perl-Pod-Perldoc noarch 3.28.01-501.fc39 fedora 86 k perl-Pod-Simple noarch 1:3.45-4.fc39 fedora 218 k perl-Pod-Usage noarch 4:2.03-500.fc39 fedora 39 k perl-Scalar-List-Utils s390x 5:1.63-500.fc39 fedora 74 k perl-SelectSaver noarch 1.02-500.fc39 fedora 12 k perl-Socket s390x 4:2.037-3.fc39 fedora 55 k perl-Storable s390x 1:3.32-500.fc39 fedora 100 k perl-Symbol noarch 1.09-500.fc39 fedora 14 k perl-Term-ANSIColor noarch 5.01-501.fc39 fedora 47 k perl-Term-Cap noarch 1.18-500.fc39 fedora 22 k perl-Text-ParseWords noarch 3.31-500.fc39 fedora 16 k perl-Text-Tabs+Wrap noarch 2023.0511-3.fc39 fedora 22 k perl-Time-Local noarch 2:1.350-3.fc39 fedora 34 k perl-URI noarch 5.21-1.fc40 fedora 125 k perl-base noarch 2.27-500.fc39 fedora 16 k perl-constant noarch 1.33-501.fc39 fedora 22 k perl-if noarch 0.61.000-500.fc39 fedora 14 k perl-libnet noarch 3.15-501.fc39 fedora 129 k perl-libs s390x 4:5.38.0-500.fc39 fedora 2.5 M perl-locale noarch 1.10-500.fc39 fedora 14 k perl-mro s390x 1.28-500.fc39 fedora 29 k perl-overload noarch 1.37-500.fc39 fedora 46 k perl-overloading noarch 0.02-500.fc39 fedora 13 k perl-parent noarch 1:0.241-500.fc39 fedora 14 k perl-podlators noarch 1:5.01-500.fc39 fedora 125 k perl-vars noarch 1.05-500.fc39 fedora 13 k Transaction Summary ================================================================================ Install 83 Packages Total size: 61 M Total download size: 12 M Installed size: 189 M Downloading Packages: [SKIPPED] cpp-13.2.1-1.fc40.s390x.rpm: Already downloaded [SKIPPED] gcc-13.2.1-1.fc40.s390x.rpm: Already downloaded [SKIPPED] gcc-plugin-annobin-13.2.1-1.fc40.s390x.rpm: Already downloaded [SKIPPED] glibc-devel-2.38.9000-8.fc40.s390x.rpm: Already downloaded [SKIPPED] glibc-headers-s390-2.38.9000-8.fc40.noarch.rpm: Already downloaded [SKIPPED] libasan-13.2.1-1.fc40.s390x.rpm: Already downloaded [SKIPPED] libatomic-13.2.1-1.fc40.s390x.rpm: Already downloaded [SKIPPED] libubsan-13.2.1-1.fc40.s390x.rpm: Already downloaded [SKIPPED] zlib-ng-compat-devel-2.1.3-3.fc40.s390x.rpm: Already downloaded [SKIPPED] annobin-docs-12.26-1.fc40.noarch.rpm: Already downloaded [SKIPPED] annobin-plugin-gcc-12.26-1.fc40.s390x.rpm: Already downloaded [SKIPPED] bzip2-devel-1.0.8-16.fc39.s390x.rpm: Already downloaded [SKIPPED] gc-8.2.2-4.fc39.s390x.rpm: Already downloaded [SKIPPED] guile22-2.2.7-9.fc39.s390x.rpm: Already downloaded [SKIPPED] kernel-headers-6.6.0-0.rc1.git0.1.fc40.s390x.rpm: Already downloaded [SKIPPED] libmpc-1.3.1-3.fc39.s390x.rpm: Already downloaded [SKIPPED] libtool-ltdl-2.4.7-8.fc40.s390x.rpm: Already downloaded [SKIPPED] libxcrypt-devel-4.4.36-2.fc39.s390x.rpm: Already downloaded [SKIPPED] make-4.4.1-2.fc39.s390x.rpm: Already downloaded [SKIPPED] xz-devel-5.4.4-1.fc39.s390x.rpm: Already downloaded (21/83): libcurl-devel-8.3.0-1.fc40.s390x.rpm 23 MB/s | 901 kB 00:00 (22/83): openssl-devel-3.1.1-4.fc40.s390x.rpm 32 MB/s | 2.5 MB 00:00 (23/83): perl-AutoLoader-5.74-500.fc39.noarch.r 45 kB/s | 21 kB 00:00 (24/83): perl-B-1.88-500.fc39.s390x.rpm 306 kB/s | 178 kB 00:00 (25/83): ncurses-6.4-7.20230520.fc40.s390x.rpm 384 kB/s | 424 kB 00:01 (26/83): perl-Carp-1.54-500.fc39.noarch.rpm 173 kB/s | 29 kB 00:00 (27/83): perl-Class-Struct-0.68-500.fc39.noarch 142 kB/s | 22 kB 00:00 (28/83): groff-base-1.23.0-2.fc39.s390x.rpm 888 kB/s | 1.2 MB 00:01 (29/83): perl-Digest-1.20-500.fc39.noarch.rpm 158 kB/s | 25 kB 00:00 (30/83): perl-Data-Dumper-2.188-501.fc39.s390x. 314 kB/s | 57 kB 00:00 (31/83): perl-Digest-MD5-2.58-500.fc39.s390x.rp 230 kB/s | 35 kB 00:00 (32/83): perl-DynaLoader-1.54-500.fc39.s390x.rp 165 kB/s | 26 kB 00:00 (33/83): perl-Errno-1.37-500.fc39.s390x.rpm 98 kB/s | 15 kB 00:00 (34/83): perl-Exporter-5.77-500.fc39.noarch.rpm 194 kB/s | 31 kB 00:00 (35/83): perl-Fcntl-1.15-500.fc39.s390x.rpm 135 kB/s | 21 kB 00:00 (36/83): perl-File-Basename-2.86-500.fc39.noarc 111 kB/s | 17 kB 00:00 (37/83): perl-File-Path-2.18-500.fc39.noarch.rp 228 kB/s | 35 kB 00:00 (38/83): perl-File-Temp-0.231.100-500.fc39.noar 354 kB/s | 58 kB 00:00 (39/83): perl-File-stat-1.13-500.fc39.noarch.rp 113 kB/s | 17 kB 00:00 (40/83): perl-Encode-3.19-500.fc39.s390x.rpm 2.5 MB/s | 1.7 MB 00:00 (41/83): perl-FileHandle-2.05-500.fc39.noarch.r 101 kB/s | 16 kB 00:00 (42/83): perl-FindBin-1.53-500.fc39.noarch.rpm 86 kB/s | 14 kB 00:00 (43/83): perl-Getopt-Long-2.54-500.fc39.noarch. 390 kB/s | 60 kB 00:00 (44/83): perl-Getopt-Std-1.13-500.fc39.noarch.r 102 kB/s | 16 kB 00:00 (45/83): perl-HTTP-Tiny-0.088-3.fc39.noarch.rpm 358 kB/s | 56 kB 00:00 (46/83): perl-IO-1.52-500.fc39.s390x.rpm 528 kB/s | 82 kB 00:00 (47/83): perl-IO-Socket-IP-0.42-1.fc39.noarch.r 259 kB/s | 42 kB 00:00 (48/83): perl-IO-Socket-SSL-2.083-3.fc39.noarch 1.3 MB/s | 225 kB 00:00 (49/83): perl-IPC-Open3-1.22-500.fc39.noarch.rp 144 kB/s | 22 kB 00:00 (50/83): perl-MIME-Base64-3.16-500.fc39.s390x.r 189 kB/s | 30 kB 00:00 (51/83): perl-Mozilla-CA-20230821-1.fc40.noarch 89 kB/s | 13 kB 00:00 (52/83): perl-Net-SSLeay-1.92-10.fc39.s390x.rpm 2.1 MB/s | 363 kB 00:00 (53/83): perl-POSIX-2.13-500.fc39.s390x.rpm 559 kB/s | 98 kB 00:00 (54/83): perl-PathTools-3.89-500.fc39.s390x.rpm 551 kB/s | 87 kB 00:00 (55/83): perl-Pod-Escapes-1.07-501.fc40.noarch. 128 kB/s | 19 kB 00:00 (56/83): perl-Pod-Simple-3.45-4.fc39.noarch.rpm 1.3 MB/s | 218 kB 00:00 (57/83): perl-Pod-Perldoc-3.28.01-501.fc39.noar 498 kB/s | 86 kB 00:00 (58/83): perl-Pod-Usage-2.03-500.fc39.noarch.rp 257 kB/s | 39 kB 00:00 (59/83): perl-SelectSaver-1.02-500.fc39.noarch. 77 kB/s | 12 kB 00:00 (60/83): perl-Scalar-List-Utils-1.63-500.fc39.s 471 kB/s | 74 kB 00:00 (61/83): perl-Socket-2.037-3.fc39.s390x.rpm 358 kB/s | 55 kB 00:00 (62/83): perl-Symbol-1.09-500.fc39.noarch.rpm 94 kB/s | 14 kB 00:00 (63/83): perl-Term-ANSIColor-5.01-501.fc39.noar 306 kB/s | 47 kB 00:00 (64/83): perl-Storable-3.32-500.fc39.s390x.rpm 567 kB/s | 100 kB 00:00 (65/83): perl-Term-Cap-1.18-500.fc39.noarch.rpm 143 kB/s | 22 kB 00:00 (66/83): perl-Text-ParseWords-3.31-500.fc39.noa 105 kB/s | 16 kB 00:00 (67/83): perl-Text-Tabs+Wrap-2023.0511-3.fc39.n 144 kB/s | 22 kB 00:00 (68/83): perl-Time-Local-1.350-3.fc39.noarch.rp 224 kB/s | 34 kB 00:00 (69/83): perl-URI-5.21-1.fc40.noarch.rpm 790 kB/s | 125 kB 00:00 (70/83): perl-base-2.27-500.fc39.noarch.rpm 105 kB/s | 16 kB 00:00 (71/83): perl-constant-1.33-501.fc39.noarch.rpm 147 kB/s | 22 kB 00:00 (72/83): perl-if-0.61.000-500.fc39.noarch.rpm 93 kB/s | 14 kB 00:00 (73/83): perl-interpreter-5.38.0-500.fc39.s390x 424 kB/s | 72 kB 00:00 (74/83): perl-lib-0.65-500.fc39.s390x.rpm 88 kB/s | 15 kB 00:00 (75/83): perl-libnet-3.15-501.fc39.noarch.rpm 810 kB/s | 129 kB 00:00 (76/83): perl-locale-1.10-500.fc39.noarch.rpm 90 kB/s | 14 kB 00:00 (77/83): perl-mro-1.28-500.fc39.s390x.rpm 190 kB/s | 29 kB 00:00 (78/83): perl-overload-1.37-500.fc39.noarch.rpm 295 kB/s | 46 kB 00:00 (79/83): perl-overloading-0.02-500.fc39.noarch. 85 kB/s | 13 kB 00:00 (80/83): perl-libs-5.38.0-500.fc39.s390x.rpm 4.2 MB/s | 2.5 MB 00:00 (81/83): perl-parent-0.241-500.fc39.noarch.rpm 94 kB/s | 14 kB 00:00 (82/83): perl-podlators-5.01-500.fc39.noarch.rp 789 kB/s | 125 kB 00:00 (83/83): perl-vars-1.05-500.fc39.noarch.rpm 86 kB/s | 13 kB 00:00 -------------------------------------------------------------------------------- Total 2.3 MB/s | 12 MB 00:05 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Installing : libmpc-1.3.1-3.fc39.s390x 1/83 Installing : cpp-13.2.1-1.fc40.s390x 2/83 Installing : ncurses-6.4-7.20230520.fc40.s390x 3/83 Installing : libtool-ltdl-2.4.7-8.fc40.s390x 4/83 Installing : kernel-headers-6.6.0-0.rc1.git0.1.fc40.s390x 5/83 Running scriptlet: groff-base-1.23.0-2.fc39.s390x 6/83 Installing : groff-base-1.23.0-2.fc39.s390x 6/83 Running scriptlet: groff-base-1.23.0-2.fc39.s390x 6/83 Installing : perl-Digest-1.20-500.fc39.noarch 7/83 Installing : perl-Digest-MD5-2.58-500.fc39.s390x 8/83 Installing : perl-B-1.88-500.fc39.s390x 9/83 Installing : perl-FileHandle-2.05-500.fc39.noarch 10/83 Installing : perl-Data-Dumper-2.188-501.fc39.s390x 11/83 Installing : perl-libnet-3.15-501.fc39.noarch 12/83 Installing : perl-AutoLoader-5.74-500.fc39.noarch 13/83 Installing : perl-base-2.27-500.fc39.noarch 14/83 Installing : perl-URI-5.21-1.fc40.noarch 15/83 Installing : perl-Text-Tabs+Wrap-2023.0511-3.fc39.noarch 16/83 Installing : perl-Mozilla-CA-20230821-1.fc40.noarch 17/83 Installing : perl-if-0.61.000-500.fc39.noarch 18/83 Installing : perl-locale-1.10-500.fc39.noarch 19/83 Installing : perl-IO-Socket-IP-0.42-1.fc39.noarch 20/83 Installing : perl-Time-Local-2:1.350-3.fc39.noarch 21/83 Installing : perl-File-Path-2.18-500.fc39.noarch 22/83 Installing : perl-IO-Socket-SSL-2.083-3.fc39.noarch 23/83 Installing : perl-Net-SSLeay-1.92-10.fc39.s390x 24/83 Installing : perl-Pod-Escapes-1:1.07-501.fc40.noarch 25/83 Installing : perl-Class-Struct-0.68-500.fc39.noarch 26/83 Installing : perl-Term-ANSIColor-5.01-501.fc39.noarch 27/83 Installing : perl-POSIX-2.13-500.fc39.s390x 28/83 Installing : perl-IPC-Open3-1.22-500.fc39.noarch 29/83 Installing : perl-File-Temp-1:0.231.100-500.fc39.noarch 30/83 Installing : perl-HTTP-Tiny-0.088-3.fc39.noarch 31/83 Installing : perl-Term-Cap-1.18-500.fc39.noarch 32/83 Installing : perl-Pod-Simple-1:3.45-4.fc39.noarch 33/83 Installing : perl-Socket-4:2.037-3.fc39.s390x 34/83 Installing : perl-SelectSaver-1.02-500.fc39.noarch 35/83 Installing : perl-Symbol-1.09-500.fc39.noarch 36/83 Installing : perl-File-stat-1.13-500.fc39.noarch 37/83 Installing : perl-podlators-1:5.01-500.fc39.noarch 38/83 Installing : perl-Pod-Perldoc-3.28.01-501.fc39.noarch 39/83 Installing : perl-Fcntl-1.15-500.fc39.s390x 40/83 Installing : perl-Text-ParseWords-3.31-500.fc39.noarch 41/83 Installing : perl-mro-1.28-500.fc39.s390x 42/83 Installing : perl-IO-1.52-500.fc39.s390x 43/83 Installing : perl-overloading-0.02-500.fc39.noarch 44/83 Installing : perl-Pod-Usage-4:2.03-500.fc39.noarch 45/83 Installing : perl-Errno-1.37-500.fc39.s390x 46/83 Installing : perl-File-Basename-2.86-500.fc39.noarch 47/83 Installing : perl-Getopt-Std-1.13-500.fc39.noarch 48/83 Installing : perl-MIME-Base64-3.16-500.fc39.s390x 49/83 Installing : perl-Scalar-List-Utils-5:1.63-500.fc39.s390x 50/83 Installing : perl-constant-1.33-501.fc39.noarch 51/83 Installing : perl-Storable-1:3.32-500.fc39.s390x 52/83 Installing : perl-overload-1.37-500.fc39.noarch 53/83 Installing : perl-parent-1:0.241-500.fc39.noarch 54/83 Installing : perl-vars-1.05-500.fc39.noarch 55/83 Installing : perl-Getopt-Long-1:2.54-500.fc39.noarch 56/83 Installing : perl-Carp-1.54-500.fc39.noarch 57/83 Installing : perl-Exporter-5.77-500.fc39.noarch 58/83 Installing : perl-PathTools-3.89-500.fc39.s390x 59/83 Installing : perl-DynaLoader-1.54-500.fc39.s390x 60/83 Installing : perl-Encode-4:3.19-500.fc39.s390x 61/83 Installing : perl-libs-4:5.38.0-500.fc39.s390x 62/83 Installing : perl-interpreter-4:5.38.0-500.fc39.s390x 63/83 Installing : gc-8.2.2-4.fc39.s390x 64/83 Installing : guile22-2.2.7-9.fc39.s390x 65/83 Installing : make-1:4.4.1-2.fc39.s390x 66/83 Installing : annobin-docs-12.26-1.fc40.noarch 67/83 Installing : libubsan-13.2.1-1.fc40.s390x 68/83 Installing : libatomic-13.2.1-1.fc40.s390x 69/83 Installing : libasan-13.2.1-1.fc40.s390x 70/83 Installing : glibc-headers-s390-2.38.9000-8.fc40.noarch 71/83 Installing : libxcrypt-devel-4.4.36-2.fc39.s390x 72/83 Installing : glibc-devel-2.38.9000-8.fc40.s390x 73/83 Installing : gcc-13.2.1-1.fc40.s390x 74/83 Running scriptlet: gcc-13.2.1-1.fc40.s390x 74/83 Installing : gcc-plugin-annobin-13.2.1-1.fc40.s390x 75/83 Running scriptlet: gcc-plugin-annobin-13.2.1-1.fc40.s390x 75/83 Installing : annobin-plugin-gcc-12.26-1.fc40.s390x 76/83 Running scriptlet: annobin-plugin-gcc-12.26-1.fc40.s390x 76/83 Installing : perl-FindBin-1.53-500.fc39.noarch 77/83 Installing : perl-lib-0.65-500.fc39.s390x 78/83 Installing : xz-devel-5.4.4-1.fc39.s390x 79/83 Installing : bzip2-devel-1.0.8-16.fc39.s390x 80/83 Installing : zlib-ng-compat-devel-2.1.3-3.fc40.s390x 81/83 Installing : openssl-devel-1:3.1.1-4.fc40.s390x 82/83 Installing : libcurl-devel-8.3.0-1.fc40.s390x 83/83 Running scriptlet: libcurl-devel-8.3.0-1.fc40.s390x 83/83 Verifying : cpp-13.2.1-1.fc40.s390x 1/83 Verifying : gcc-13.2.1-1.fc40.s390x 2/83 Verifying : gcc-plugin-annobin-13.2.1-1.fc40.s390x 3/83 Verifying : glibc-devel-2.38.9000-8.fc40.s390x 4/83 Verifying : glibc-headers-s390-2.38.9000-8.fc40.noarch 5/83 Verifying : libasan-13.2.1-1.fc40.s390x 6/83 Verifying : libatomic-13.2.1-1.fc40.s390x 7/83 Verifying : libcurl-devel-8.3.0-1.fc40.s390x 8/83 Verifying : libubsan-13.2.1-1.fc40.s390x 9/83 Verifying : openssl-devel-1:3.1.1-4.fc40.s390x 10/83 Verifying : zlib-ng-compat-devel-2.1.3-3.fc40.s390x 11/83 Verifying : annobin-docs-12.26-1.fc40.noarch 12/83 Verifying : annobin-plugin-gcc-12.26-1.fc40.s390x 13/83 Verifying : bzip2-devel-1.0.8-16.fc39.s390x 14/83 Verifying : gc-8.2.2-4.fc39.s390x 15/83 Verifying : groff-base-1.23.0-2.fc39.s390x 16/83 Verifying : guile22-2.2.7-9.fc39.s390x 17/83 Verifying : kernel-headers-6.6.0-0.rc1.git0.1.fc40.s390x 18/83 Verifying : libmpc-1.3.1-3.fc39.s390x 19/83 Verifying : libtool-ltdl-2.4.7-8.fc40.s390x 20/83 Verifying : libxcrypt-devel-4.4.36-2.fc39.s390x 21/83 Verifying : make-1:4.4.1-2.fc39.s390x 22/83 Verifying : ncurses-6.4-7.20230520.fc40.s390x 23/83 Verifying : perl-AutoLoader-5.74-500.fc39.noarch 24/83 Verifying : perl-B-1.88-500.fc39.s390x 25/83 Verifying : perl-Carp-1.54-500.fc39.noarch 26/83 Verifying : perl-Class-Struct-0.68-500.fc39.noarch 27/83 Verifying : perl-Data-Dumper-2.188-501.fc39.s390x 28/83 Verifying : perl-Digest-1.20-500.fc39.noarch 29/83 Verifying : perl-Digest-MD5-2.58-500.fc39.s390x 30/83 Verifying : perl-DynaLoader-1.54-500.fc39.s390x 31/83 Verifying : perl-Encode-4:3.19-500.fc39.s390x 32/83 Verifying : perl-Errno-1.37-500.fc39.s390x 33/83 Verifying : perl-Exporter-5.77-500.fc39.noarch 34/83 Verifying : perl-Fcntl-1.15-500.fc39.s390x 35/83 Verifying : perl-File-Basename-2.86-500.fc39.noarch 36/83 Verifying : perl-File-Path-2.18-500.fc39.noarch 37/83 Verifying : perl-File-Temp-1:0.231.100-500.fc39.noarch 38/83 Verifying : perl-File-stat-1.13-500.fc39.noarch 39/83 Verifying : perl-FileHandle-2.05-500.fc39.noarch 40/83 Verifying : perl-FindBin-1.53-500.fc39.noarch 41/83 Verifying : perl-Getopt-Long-1:2.54-500.fc39.noarch 42/83 Verifying : perl-Getopt-Std-1.13-500.fc39.noarch 43/83 Verifying : perl-HTTP-Tiny-0.088-3.fc39.noarch 44/83 Verifying : perl-IO-1.52-500.fc39.s390x 45/83 Verifying : perl-IO-Socket-IP-0.42-1.fc39.noarch 46/83 Verifying : perl-IO-Socket-SSL-2.083-3.fc39.noarch 47/83 Verifying : perl-IPC-Open3-1.22-500.fc39.noarch 48/83 Verifying : perl-MIME-Base64-3.16-500.fc39.s390x 49/83 Verifying : perl-Mozilla-CA-20230821-1.fc40.noarch 50/83 Verifying : perl-Net-SSLeay-1.92-10.fc39.s390x 51/83 Verifying : perl-POSIX-2.13-500.fc39.s390x 52/83 Verifying : perl-PathTools-3.89-500.fc39.s390x 53/83 Verifying : perl-Pod-Escapes-1:1.07-501.fc40.noarch 54/83 Verifying : perl-Pod-Perldoc-3.28.01-501.fc39.noarch 55/83 Verifying : perl-Pod-Simple-1:3.45-4.fc39.noarch 56/83 Verifying : perl-Pod-Usage-4:2.03-500.fc39.noarch 57/83 Verifying : perl-Scalar-List-Utils-5:1.63-500.fc39.s390x 58/83 Verifying : perl-SelectSaver-1.02-500.fc39.noarch 59/83 Verifying : perl-Socket-4:2.037-3.fc39.s390x 60/83 Verifying : perl-Storable-1:3.32-500.fc39.s390x 61/83 Verifying : perl-Symbol-1.09-500.fc39.noarch 62/83 Verifying : perl-Term-ANSIColor-5.01-501.fc39.noarch 63/83 Verifying : perl-Term-Cap-1.18-500.fc39.noarch 64/83 Verifying : perl-Text-ParseWords-3.31-500.fc39.noarch 65/83 Verifying : perl-Text-Tabs+Wrap-2023.0511-3.fc39.noarch 66/83 Verifying : perl-Time-Local-2:1.350-3.fc39.noarch 67/83 Verifying : perl-URI-5.21-1.fc40.noarch 68/83 Verifying : perl-base-2.27-500.fc39.noarch 69/83 Verifying : perl-constant-1.33-501.fc39.noarch 70/83 Verifying : perl-if-0.61.000-500.fc39.noarch 71/83 Verifying : perl-interpreter-4:5.38.0-500.fc39.s390x 72/83 Verifying : perl-lib-0.65-500.fc39.s390x 73/83 Verifying : perl-libnet-3.15-501.fc39.noarch 74/83 Verifying : perl-libs-4:5.38.0-500.fc39.s390x 75/83 Verifying : perl-locale-1.10-500.fc39.noarch 76/83 Verifying : perl-mro-1.28-500.fc39.s390x 77/83 Verifying : perl-overload-1.37-500.fc39.noarch 78/83 Verifying : perl-overloading-0.02-500.fc39.noarch 79/83 Verifying : perl-parent-1:0.241-500.fc39.noarch 80/83 Verifying : perl-podlators-1:5.01-500.fc39.noarch 81/83 Verifying : perl-vars-1.05-500.fc39.noarch 82/83 Verifying : xz-devel-5.4.4-1.fc39.s390x 83/83 Installed: annobin-docs-12.26-1.fc40.noarch annobin-plugin-gcc-12.26-1.fc40.s390x bzip2-devel-1.0.8-16.fc39.s390x cpp-13.2.1-1.fc40.s390x gc-8.2.2-4.fc39.s390x gcc-13.2.1-1.fc40.s390x gcc-plugin-annobin-13.2.1-1.fc40.s390x glibc-devel-2.38.9000-8.fc40.s390x glibc-headers-s390-2.38.9000-8.fc40.noarch groff-base-1.23.0-2.fc39.s390x guile22-2.2.7-9.fc39.s390x kernel-headers-6.6.0-0.rc1.git0.1.fc40.s390x libasan-13.2.1-1.fc40.s390x libatomic-13.2.1-1.fc40.s390x libcurl-devel-8.3.0-1.fc40.s390x libmpc-1.3.1-3.fc39.s390x libtool-ltdl-2.4.7-8.fc40.s390x libubsan-13.2.1-1.fc40.s390x libxcrypt-devel-4.4.36-2.fc39.s390x make-1:4.4.1-2.fc39.s390x ncurses-6.4-7.20230520.fc40.s390x openssl-devel-1:3.1.1-4.fc40.s390x perl-AutoLoader-5.74-500.fc39.noarch perl-B-1.88-500.fc39.s390x perl-Carp-1.54-500.fc39.noarch perl-Class-Struct-0.68-500.fc39.noarch perl-Data-Dumper-2.188-501.fc39.s390x perl-Digest-1.20-500.fc39.noarch perl-Digest-MD5-2.58-500.fc39.s390x perl-DynaLoader-1.54-500.fc39.s390x perl-Encode-4:3.19-500.fc39.s390x perl-Errno-1.37-500.fc39.s390x perl-Exporter-5.77-500.fc39.noarch perl-Fcntl-1.15-500.fc39.s390x perl-File-Basename-2.86-500.fc39.noarch perl-File-Path-2.18-500.fc39.noarch perl-File-Temp-1:0.231.100-500.fc39.noarch perl-File-stat-1.13-500.fc39.noarch perl-FileHandle-2.05-500.fc39.noarch perl-FindBin-1.53-500.fc39.noarch perl-Getopt-Long-1:2.54-500.fc39.noarch perl-Getopt-Std-1.13-500.fc39.noarch perl-HTTP-Tiny-0.088-3.fc39.noarch perl-IO-1.52-500.fc39.s390x perl-IO-Socket-IP-0.42-1.fc39.noarch perl-IO-Socket-SSL-2.083-3.fc39.noarch perl-IPC-Open3-1.22-500.fc39.noarch perl-MIME-Base64-3.16-500.fc39.s390x perl-Mozilla-CA-20230821-1.fc40.noarch perl-Net-SSLeay-1.92-10.fc39.s390x perl-POSIX-2.13-500.fc39.s390x perl-PathTools-3.89-500.fc39.s390x perl-Pod-Escapes-1:1.07-501.fc40.noarch perl-Pod-Perldoc-3.28.01-501.fc39.noarch perl-Pod-Simple-1:3.45-4.fc39.noarch perl-Pod-Usage-4:2.03-500.fc39.noarch perl-Scalar-List-Utils-5:1.63-500.fc39.s390x perl-SelectSaver-1.02-500.fc39.noarch perl-Socket-4:2.037-3.fc39.s390x perl-Storable-1:3.32-500.fc39.s390x perl-Symbol-1.09-500.fc39.noarch perl-Term-ANSIColor-5.01-501.fc39.noarch perl-Term-Cap-1.18-500.fc39.noarch perl-Text-ParseWords-3.31-500.fc39.noarch perl-Text-Tabs+Wrap-2023.0511-3.fc39.noarch perl-Time-Local-2:1.350-3.fc39.noarch perl-URI-5.21-1.fc40.noarch perl-base-2.27-500.fc39.noarch perl-constant-1.33-501.fc39.noarch perl-if-0.61.000-500.fc39.noarch perl-interpreter-4:5.38.0-500.fc39.s390x perl-lib-0.65-500.fc39.s390x perl-libnet-3.15-501.fc39.noarch perl-libs-4:5.38.0-500.fc39.s390x perl-locale-1.10-500.fc39.noarch perl-mro-1.28-500.fc39.s390x perl-overload-1.37-500.fc39.noarch perl-overloading-0.02-500.fc39.noarch perl-parent-1:0.241-500.fc39.noarch perl-podlators-1:5.01-500.fc39.noarch perl-vars-1.05-500.fc39.noarch xz-devel-5.4.4-1.fc39.s390x zlib-ng-compat-devel-2.1.3-3.fc40.s390x Complete! Finish: build setup for htslib-1.15.1-3.fc40.src.rpm Start: rpmbuild htslib-1.15.1-3.fc40.src.rpm warning: %patchN is deprecated (1 usages found), use %patch N (or %patch -P N) Building target platforms: s390x Building for target s390x setting SOURCE_DATE_EPOCH=1689811200 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.9a25FM + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf htslib-1.15.1 + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/htslib-1.15.1.tar.bz2 + STATUS=0 + '[' 0 -ne 0 ']' + cd htslib-1.15.1 + rm -rf /builddir/build/BUILD/htslib-1.15.1-SPECPARTS + /usr/bin/mkdir -p /builddir/build/BUILD/htslib-1.15.1-SPECPARTS + /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 -f -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.5OKRll + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd htslib-1.15.1 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + '[' '-flto=auto -ffat-lto-objectsx' '!=' x ']' ++ find . -type f -name configure -print + for file in $(find . -type f -name configure -print) + /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\) = /__attribute__ ((used)) char (*f) () = /g' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\);/__attribute__ ((used)) char (*f) ();/g' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed -r --in-place=.backup 's/^char \$2 \(\);/__attribute__ ((used)) char \$2 ();/g' ./configure + diff -u ./configure.backup ./configure --- ./configure.backup 2022-04-07 15:42:52.000000000 +0000 +++ ./configure 2023-09-18 07:22:26.992349675 +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* .* \\(.*\\)$/extern char \\1;/p'\''"#' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + '[' 1 = 1 ']' +++ dirname ./configure ++ find . -name config.guess -o -name config.sub + '[' 1 = 1 ']' + '[' x '!=' 'x-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' ']' ++ find . -name ltmain.sh ++ grep -q runstatedir=DIR ./configure ++ echo --runstatedir=/run + ./configure --build=s390x-redhat-linux --host=s390x-redhat-linux --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/libexec --localstatedir=/var --runstatedir=/run --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info 'CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection' 'LDFLAGS=-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' --prefix=/usr --libdir=/usr/lib64 --enable-plugins '--with-plugin-path=/usr/local/libexec/htslib:$(plugindir)' --enable-gcs --enable-libcurl --enable-s3 configure: WARNING: unrecognized options: --disable-dependency-tracking checking for s390x-redhat-linux-gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether 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 s390x-redhat-linux-ranlib... no checking for ranlib... ranlib checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for s390x-redhat-linux-pkg-config... no checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for 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 s390x-redhat-linux... 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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o kfunc.o kfunc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o kstring.o kstring.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o bcf_sr_sort.o bcf_sr_sort.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o errmod.o errmod.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o bgzf.o bgzf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o faidx.o faidx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-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 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic"' >> config_vars.h echo '#define HTS_LIBS "-llzma -lbz2 -lz -lm "' >> config_vars.h gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o hts_expr.o hts_expr.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o hts_os.o hts_os.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o header.o header.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o md5.o md5.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o multipart.o multipart.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o probaln.o probaln.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o realn.o realn.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o region.o region.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o regidx.o regidx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o synced_bcf_reader.o synced_bcf_reader.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o vcf_sweep.o vcf_sweep.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o tbx.o tbx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o textutils.o textutils.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o thread_pool.o thread_pool.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o sam.o sam.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o vcfutils.o vcfutils.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o vcf.o vcf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/cram_codecs.o cram/cram_codecs.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/cram_decode.o cram/cram_decode.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/cram_external.o cram/cram_external.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/cram_index.o cram/cram_index.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/cram_encode.o cram/cram_encode.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/cram_stats.o cram/cram_stats.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/mFILE.o cram/mFILE.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/open_trace_file.o cram/open_trace_file.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/string_alloc.o cram/string_alloc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/cram_io.o cram/cram_io.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -DPLUGINPATH=\"/usr/local/libexec/htslib:/usr/libexec/htslib\" -c -o plugin.o plugin.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o kfunc.pico kfunc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o kstring.pico kstring.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o bcf_sr_sort.pico bcf_sr_sort.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o errmod.pico errmod.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o bgzf.pico bgzf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o faidx.pico faidx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o hfile.pico hfile.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o header.pico header.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o hts_expr.pico hts_expr.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o hts_os.pico hts_os.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o md5.pico md5.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o multipart.pico multipart.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o probaln.pico probaln.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o realn.pico realn.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o regidx.pico regidx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o region.pico region.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o hts.pico hts.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o synced_bcf_reader.pico synced_bcf_reader.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o vcf_sweep.pico vcf_sweep.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o tbx.pico tbx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o textutils.pico textutils.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o thread_pool.pico thread_pool.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o sam.pico sam.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o vcfutils.pico vcfutils.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o vcf.pico vcf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o cram/cram_codecs.pico cram/cram_codecs.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o cram/cram_decode.pico cram/cram_decode.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o cram/cram_external.pico cram/cram_external.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o cram/cram_index.pico cram/cram_index.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o cram/cram_encode.pico cram/cram_encode.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o cram/cram_stats.pico cram/cram_stats.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o cram/mFILE.pico cram/mFILE.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o cram/open_trace_file.pico cram/open_trace_file.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o cram/pooled_alloc.pico cram/pooled_alloc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o cram/string_alloc.pico cram/string_alloc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/arith_dynamic.pico htscodecs/htscodecs/arith_dynamic.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o cram/cram_io.pico cram/cram_io.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/htscodecs.pico htscodecs/htscodecs/htscodecs.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/pack.pico htscodecs/htscodecs/pack.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/fqzcomp_qual.pico htscodecs/htscodecs/fqzcomp_qual.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rANS_static4x16pr.pico htscodecs/htscodecs/rANS_static4x16pr.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rANS_static.pico htscodecs/htscodecs/rANS_static.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rle.pico htscodecs/htscodecs/rle.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -DPLUGINPATH=\"/usr/local/libexec/htslib:/usr/libexec/htslib\" -fpic -c -o plugin.pico plugin.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o bgzip.o bgzip.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o htsfile.o htsfile.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/tokenise_name3.pico htscodecs/htscodecs/tokenise_name3.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o tabix.o tabix.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o hfile_gcs.pico hfile_gcs.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o hfile_libcurl.pico hfile_libcurl.c hfile_libcurl.c: In function ‘libcurl_open’: hfile_libcurl.c:1335:9: warning: ‘CURLINFO_CONTENT_LENGTH_DOWNLOAD’ is deprecated: since 7.55.0. Use CURLINFO_CONTENT_LENGTH_DOWNLOAD_T [-Wdeprecated-declarations] 1335 | if (curl_easy_getinfo(fp->easy, CURLINFO_CONTENT_LENGTH_DOWNLOAD, | ^~ In file included from hfile_libcurl.c:47: /usr/include/curl/curl.h:2883:3: note: declared here 2883 | CURLINFO_CONTENT_LENGTH_DOWNLOAD | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o hfile_s3.pico hfile_s3.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o hfile_s3_write.pico hfile_s3_write.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/fieldarith.o test/fieldarith.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/hfile.o test/hfile.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/hts_endian.o test/hts_endian.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/pileup.o test/pileup.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/pileup_mod.o test/pileup_mod.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/plugins-dlhts.o test/plugins-dlhts.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_bgzf.o test/test_bgzf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_expr.o test/test_expr.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_kfunc.o test/test_kfunc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_kstring.o test/test_kstring.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_mod.o test/test_mod.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/sam.o test/sam.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_realn.o test/test_realn.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test-regidx.o test/test-regidx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_str2int.o test/test_str2int.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_index.o test/test_index.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_view.o test/test_view.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test-vcf-api.o test/test-vcf-api.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test-bcf-sr.o test/test-bcf-sr.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/fuzz/hts_open_fuzzer.o test/fuzz/hts_open_fuzzer.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test-bcf-translate.o test/test-bcf-translate.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_introspection.o test/test_introspection.c sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' htslib.pc.tmp > htslib_static.mk sed -e 's#@-includedir@#'`pwd`'#g;s#@-libdir@#'`pwd`'#g' htslib.pc.tmp > htslib-uninstalled.pc gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test-parse-reg.o test/test-parse-reg.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-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 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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 -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 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o libhts.so kfunc.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico header.pico hfile.pico hts.pico hts_expr.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico region.pico sam.pico 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 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 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o bgzip bgzip.o libhts.a -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 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o htsfile htsfile.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -shared -Wl,-E -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o hfile_libcurl.so hfile_libcurl.pico libhts.so -llzma -lbz2 -lz -lm -lcurl -lpthread gcc -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 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o hfile_gcs.so hfile_gcs.pico libhts.so -llzma -lbz2 -lz -lm -lpthread gcc -shared -Wl,-E -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o hfile_s3.so hfile_s3.pico libhts.so -llzma -lbz2 -lz -lm -lcrypto -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 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o tabix tabix.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/fieldarith test/fieldarith.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/hfile test/hfile.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/pileup test/pileup.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/pileup_mod test/pileup_mod.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/sam test/sam.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test_expr test/test_expr.o libhts.a -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 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test_bgzf test/test_bgzf.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 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test_mod test/test_mod.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test-regidx test/test-regidx.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test_realn test/test_realn.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test_str2int test/test_str2int.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test_view test/test_view.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test_index test/test_index.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test-vcf-api test/test-vcf-api.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -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 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test-bcf-sr test/test-bcf-sr.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 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test-parse-reg test/test-parse-reg.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test_introspection test/test_introspection.o libhts.a -llzma -lbz2 -lz -lm -lpthread + 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.aXevSy + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/htslib-1.15.1-3.fc40.s390x '!=' / ']' + rm -rf /builddir/build/BUILDROOT/htslib-1.15.1-3.fc40.s390x ++ dirname /builddir/build/BUILDROOT/htslib-1.15.1-3.fc40.s390x + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/htslib-1.15.1-3.fc40.s390x + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd htslib-1.15.1 + /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/htslib-1.15.1-3.fc40.s390x 'INSTALL=/usr/bin/install -p' mkdir -p -m 755 /builddir/build/BUILDROOT/htslib-1.15.1-3.fc40.s390x/usr/bin /builddir/build/BUILDROOT/htslib-1.15.1-3.fc40.s390x/usr/include /builddir/build/BUILDROOT/htslib-1.15.1-3.fc40.s390x/usr/include/htslib /builddir/build/BUILDROOT/htslib-1.15.1-3.fc40.s390x/usr/lib64 /builddir/build/BUILDROOT/htslib-1.15.1-3.fc40.s390x/usr/share/man/man1 /builddir/build/BUILDROOT/htslib-1.15.1-3.fc40.s390x/usr/share/man/man5 /builddir/build/BUILDROOT/htslib-1.15.1-3.fc40.s390x/usr/share/man/man7 /builddir/build/BUILDROOT/htslib-1.15.1-3.fc40.s390x/usr/lib64/pkgconfig if test -n "/usr/libexec/htslib"; then mkdir -p -m 755 /builddir/build/BUILDROOT/htslib-1.15.1-3.fc40.s390x/usr/libexec/htslib; fi /usr/bin/install -p -m 644 libhts.so /builddir/build/BUILDROOT/htslib-1.15.1-3.fc40.s390x/usr/lib64/libhts.so.1.15.1 ln -sf libhts.so.1.15.1 /builddir/build/BUILDROOT/htslib-1.15.1-3.fc40.s390x/usr/lib64/libhts.so ln -sf libhts.so.1.15.1 /builddir/build/BUILDROOT/htslib-1.15.1-3.fc40.s390x/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.fc40.s390x/usr/lib64/pkgconfig/htslib.pc chmod 644 /builddir/build/BUILDROOT/htslib-1.15.1-3.fc40.s390x/usr/lib64/pkgconfig/htslib.pc /usr/bin/install -p bgzip htsfile tabix /builddir/build/BUILDROOT/htslib-1.15.1-3.fc40.s390x/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.fc40.s390x/usr/libexec/htslib; fi /usr/bin/install -p -m 644 htslib/*.h /builddir/build/BUILDROOT/htslib-1.15.1-3.fc40.s390x/usr/include/htslib /usr/bin/install -p -m 644 libhts.a /builddir/build/BUILDROOT/htslib-1.15.1-3.fc40.s390x/usr/lib64/libhts.a /usr/bin/install -p -m 644 bgzip.1 htsfile.1 tabix.1 /builddir/build/BUILDROOT/htslib-1.15.1-3.fc40.s390x/usr/share/man/man1 /usr/bin/install -p -m 644 faidx.5 sam.5 vcf.5 /builddir/build/BUILDROOT/htslib-1.15.1-3.fc40.s390x/usr/share/man/man5 /usr/bin/install -p -m 644 htslib-s3-plugin.7 /builddir/build/BUILDROOT/htslib-1.15.1-3.fc40.s390x/usr/share/man/man7 + pushd /builddir/build/BUILDROOT/htslib-1.15.1-3.fc40.s390x//usr/lib64 ~/build/BUILDROOT/htslib-1.15.1-3.fc40.s390x/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.fc40.s390x -name '*.la' -delete + rm -f /builddir/build/BUILDROOT/htslib-1.15.1-3.fc40.s390x//usr/lib64/libhts.a + /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 1.15.1-3.fc40 --unique-debug-suffix -1.15.1-3.fc40.s390x --unique-debug-src-base htslib-1.15.1-3.fc40.s390x --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/htslib-1.15.1 find-debuginfo: starting Extracting debug info from 8 files DWARF-compressing 8 files sepdebugcrcfix: Updated 8 CRC32s, 0 CRC32s did match. Creating .debug symlinks for symlinks to ELF files Copying sources found by 'debugedit -l' to /usr/src/debug/htslib-1.15.1-3.fc40.s390x 5259 blocks find-debuginfo: done + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + /usr/lib/rpm/brp-compress + /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/check-rpaths + /usr/lib/rpm/redhat/brp-mangle-shebangs + /usr/lib/rpm/brp-remove-la-files + env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j2 + /usr/lib/rpm/redhat/brp-python-hardlink Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.ZfRDyk + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd htslib-1.15.1 + make test gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-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 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o htscodecs/tests/rans4x8 htscodecs/tests/rANS_static_test.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-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 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o htscodecs/tests/rans4x16pr htscodecs/tests/rANS_static4x16pr_test.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-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 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o htscodecs/tests/arith_dynamic htscodecs/tests/arith_dynamic_test.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-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 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o htscodecs/tests/tokenise_name3 htscodecs/tests/tokenise_name3_test.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-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 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o htscodecs/tests/fqzcomp_qual htscodecs/tests/fqzcomp_qual_test.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-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 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o htscodecs/tests/varint htscodecs/tests/varint_test.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_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/VBpL0vdXLF/index.bam.csi /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/VBpL0vdXLF/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/VBpL0vdXLF/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -b -m 0 -x /tmp/VBpL0vdXLF/index.bam.bai /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/VBpL0vdXLF/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -b /tmp/VBpL0vdXLF/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -z -m 14 -x /tmp/VBpL0vdXLF/index.sam.gz.csi /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/VBpL0vdXLF/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/VBpL0vdXLF/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -z -m 0 -x /tmp/VBpL0vdXLF/index.sam.gz.bai /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/VBpL0vdXLF/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -b /tmp/VBpL0vdXLF/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -z -m 14 -x /tmp/VBpL0vdXLF/index.sam.gz.csi /builddir/build/BUILD/htslib-1.15.1/test/index_dos.sam > /tmp/VBpL0vdXLF/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/VBpL0vdXLF/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -z -m 0 -x /tmp/VBpL0vdXLF/index.sam.gz.bai /builddir/build/BUILD/htslib-1.15.1/test/index_dos.sam > /tmp/VBpL0vdXLF/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -b /tmp/VBpL0vdXLF/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -C -x /tmp/VBpL0vdXLF/index.cram.crai /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/VBpL0vdXLF/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index /tmp/VBpL0vdXLF/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -b -m 14 -x /tmp/VBpL0vdXLF/index.bcf.csi /builddir/build/BUILD/htslib-1.15.1/test/index.vcf > /tmp/VBpL0vdXLF/index.bcf .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/VBpL0vdXLF/index.bcf .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -z -m 14 -x /tmp/VBpL0vdXLF/index.vcf.gz.csi /builddir/build/BUILD/htslib-1.15.1/test/index.vcf > /tmp/VBpL0vdXLF/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/VBpL0vdXLF/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -z -m 0 -x /tmp/VBpL0vdXLF/index.vcf.gz.tbi /builddir/build/BUILD/htslib-1.15.1/test/index.vcf > /tmp/VBpL0vdXLF/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -t /tmp/VBpL0vdXLF/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/tabix /tmp/VBpL0vdXLF/index.vcf.gz##idx##/tmp/VBpL0vdXLF/index.vcf.gz.tbi 1:10000060-10000060 .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view /tmp/VBpL0vdXLF/index2.bam 1:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view /tmp/VBpL0vdXLF/index2.bam 1:2000000-2000000 .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view /tmp/VBpL0vdXLF/index2.bam 2:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view /tmp/VBpL0vdXLF/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/VBpL0vdXLF/index.bam.csi /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/VBpL0vdXLF/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/VBpL0vdXLF/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -b -m 0 -x /tmp/VBpL0vdXLF/index.bam.bai /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/VBpL0vdXLF/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -b /tmp/VBpL0vdXLF/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -z -m 14 -x /tmp/VBpL0vdXLF/index.sam.gz.csi /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/VBpL0vdXLF/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/VBpL0vdXLF/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -z -m 0 -x /tmp/VBpL0vdXLF/index.sam.gz.bai /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/VBpL0vdXLF/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -b /tmp/VBpL0vdXLF/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -z -m 14 -x /tmp/VBpL0vdXLF/index.sam.gz.csi /builddir/build/BUILD/htslib-1.15.1/test/index_dos.sam > /tmp/VBpL0vdXLF/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/VBpL0vdXLF/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -z -m 0 -x /tmp/VBpL0vdXLF/index.sam.gz.bai /builddir/build/BUILD/htslib-1.15.1/test/index_dos.sam > /tmp/VBpL0vdXLF/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -b /tmp/VBpL0vdXLF/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -C -x /tmp/VBpL0vdXLF/index.cram.crai /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/VBpL0vdXLF/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index /tmp/VBpL0vdXLF/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -b -m 14 -x /tmp/VBpL0vdXLF/index.bcf.csi /builddir/build/BUILD/htslib-1.15.1/test/index.vcf > /tmp/VBpL0vdXLF/index.bcf .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/VBpL0vdXLF/index.bcf .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -z -m 14 -x /tmp/VBpL0vdXLF/index.vcf.gz.csi /builddir/build/BUILD/htslib-1.15.1/test/index.vcf > /tmp/VBpL0vdXLF/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/VBpL0vdXLF/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -z -m 0 -x /tmp/VBpL0vdXLF/index.vcf.gz.tbi /builddir/build/BUILD/htslib-1.15.1/test/index.vcf > /tmp/VBpL0vdXLF/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -t /tmp/VBpL0vdXLF/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/tabix /tmp/VBpL0vdXLF/index.vcf.gz##idx##/tmp/VBpL0vdXLF/index.vcf.gz.tbi 1:10000060-10000060 .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view /tmp/VBpL0vdXLF/index2.bam 1:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view /tmp/VBpL0vdXLF/index2.bam 1:2000000-2000000 .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view /tmp/VBpL0vdXLF/index2.bam 2:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view /tmp/VBpL0vdXLF/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/VBpL0vdXLF/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/VBpL0vdXLF/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/VBpL0vdXLF/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/VBpL0vdXLF -s 327302407 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/VBpL0vdXLF -s 480588831 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/VBpL0vdXLF -s 261685168 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/VBpL0vdXLF -s 841904611 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/VBpL0vdXLF -s 592018304 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/VBpL0vdXLF -s 1511636193 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/VBpL0vdXLF -s 906119943 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/VBpL0vdXLF -s 1012786201 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/VBpL0vdXLF -s 1043743286 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/VBpL0vdXLF -s 1271299577 .. 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/VBpL0vdXLF/headernul0.bam .. ok test_convert_padded_header: /builddir/build/BUILD/htslib-1.15.1/test/test_view -t ce.fa -C /tmp/VBpL0vdXLF/headernul1.bam .. ok test_convert_padded_header: /builddir/build/BUILD/htslib-1.15.1/test/test_view -t ce.fa -C /tmp/VBpL0vdXLF/headernul678.bam .. ok test_rebgzip: Alternate zlib/deflate library detected test_rebgzip: /builddir/build/BUILD/htslib-1.15.1/bgzip -I /builddir/build/BUILD/htslib-1.15.1/test/bgziptest.txt.tmp.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.fc40.s390x Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.ZA93Jr + umask 022 + cd /builddir/build/BUILD + cd htslib-1.15.1 + DOCDIR=/builddir/build/BUILDROOT/htslib-1.15.1-3.fc40.s390x/usr/share/doc/htslib + export LC_ALL= + LC_ALL= + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/htslib-1.15.1-3.fc40.s390x/usr/share/doc/htslib + cp -pr /builddir/build/BUILD/htslib-1.15.1/NEWS /builddir/build/BUILDROOT/htslib-1.15.1-3.fc40.s390x/usr/share/doc/htslib + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.Vdzm5H + umask 022 + cd /builddir/build/BUILD + cd htslib-1.15.1 + LICENSEDIR=/builddir/build/BUILDROOT/htslib-1.15.1-3.fc40.s390x/usr/share/licenses/htslib + export LC_ALL= + LC_ALL= + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/htslib-1.15.1-3.fc40.s390x/usr/share/licenses/htslib + cp -pr /builddir/build/BUILD/htslib-1.15.1/LICENSE /builddir/build/BUILDROOT/htslib-1.15.1-3.fc40.s390x/usr/share/licenses/htslib + RPM_EC=0 ++ jobs -p + exit 0 Provides: htslib = 1.15.1-3.fc40 htslib(s390-64) = 1.15.1-3.fc40 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_2.2)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.2)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.4)(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)(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.fc40.s390x Provides: htslib-devel = 1.15.1-3.fc40 htslib-devel(s390-64) = 1.15.1-3.fc40 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.fc40.s390x Provides: htslib-tools = 1.15.1-3.fc40 htslib-tools(s390-64) = 1.15.1-3.fc40 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: libbz2.so.1()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.2)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.2)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.4)(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.fc40.s390x Provides: htslib-debugsource = 1.15.1-3.fc40 htslib-debugsource(s390-64) = 1.15.1-3.fc40 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.fc40.s390x Provides: debuginfo(build-id) = 12efca1b4150794407f72afe4efcc9b846bcb0ff debuginfo(build-id) = 2af1dfdbaf0337846b31968d393c7d8cc0ee0a5d debuginfo(build-id) = 4b3924834e14107df96ce9b7987c97b4300dbf25 debuginfo(build-id) = 7880137872aaf9e72838766b326a9f1a302160e9 debuginfo(build-id) = a863a02ad57126deefcb12fc146c5e9f6599c103 htslib-debuginfo = 1.15.1-3.fc40 htslib-debuginfo(s390-64) = 1.15.1-3.fc40 libhts.so.1.15.1-1.15.1-3.fc40.s390x.debug()(64bit) Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: htslib-debugsource(s390-64) = 1.15.1-3.fc40 Processing files: htslib-tools-debuginfo-1.15.1-3.fc40.s390x Provides: debuginfo(build-id) = 8eb51a7f64e3e464df464b5c7b66a1b4076779f1 debuginfo(build-id) = eb1a75f844b4374b6f7da1802fb98a82661bfff0 debuginfo(build-id) = ecd813097eabeec66a29f86dbbbf51793b6fa92d htslib-tools-debuginfo = 1.15.1-3.fc40 htslib-tools-debuginfo(s390-64) = 1.15.1-3.fc40 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: htslib-debugsource(s390-64) = 1.15.1-3.fc40 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/htslib-1.15.1-3.fc40.s390x Wrote: /builddir/build/RPMS/htslib-debuginfo-1.15.1-3.fc40.s390x.rpm Wrote: /builddir/build/RPMS/htslib-tools-1.15.1-3.fc40.s390x.rpm Wrote: /builddir/build/RPMS/htslib-tools-debuginfo-1.15.1-3.fc40.s390x.rpm Wrote: /builddir/build/RPMS/htslib-1.15.1-3.fc40.s390x.rpm Wrote: /builddir/build/RPMS/htslib-devel-1.15.1-3.fc40.s390x.rpm Wrote: /builddir/build/RPMS/htslib-debugsource-1.15.1-3.fc40.s390x.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.TlxSEV + umask 022 + cd /builddir/build/BUILD + cd htslib-1.15.1 + /usr/bin/rm -rf /builddir/build/BUILDROOT/htslib-1.15.1-3.fc40.s390x + RPM_EC=0 ++ jobs -p + exit 0 Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.gkeYB2 + umask 022 + cd /builddir/build/BUILD + rm -rf /builddir/build/BUILD/htslib-1.15.1-SPECPARTS + rm -rf htslib-1.15.1 htslib-1.15.1.gemspec + RPM_EC=0 ++ jobs -p + exit 0 RPM build warnings: %patchN is deprecated (1 usages found), use %patch N (or %patch -P N) Finish: rpmbuild htslib-1.15.1-3.fc40.src.rpm Finish: build phase for htslib-1.15.1-3.fc40.src.rpm INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-s390x-1695021298.041424/root/var/log/dnf.rpm.log /var/lib/mock/fedora-rawhide-s390x-1695021298.041424/root/var/log/dnf.librepo.log /var/lib/mock/fedora-rawhide-s390x-1695021298.041424/root/var/log/dnf.log INFO: Done(/var/lib/copr-rpmbuild/results/htslib-1.15.1-3.fc40.src.rpm) Config(child) 6 minutes 25 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.fc40", "arch": "s390x" }, { "name": "htslib-tools-debuginfo", "epoch": null, "version": "1.15.1", "release": "3.fc40", "arch": "s390x" }, { "name": "htslib-tools", "epoch": null, "version": "1.15.1", "release": "3.fc40", "arch": "s390x" }, { "name": "htslib", "epoch": null, "version": "1.15.1", "release": "3.fc40", "arch": "src" }, { "name": "htslib", "epoch": null, "version": "1.15.1", "release": "3.fc40", "arch": "s390x" }, { "name": "htslib-debugsource", "epoch": null, "version": "1.15.1", "release": "3.fc40", "arch": "s390x" }, { "name": "htslib-devel", "epoch": null, "version": "1.15.1", "release": "3.fc40", "arch": "s390x" } ] } RPMResults finished