Warning: Permanently added '162.133.138.184' (ED25519) to the list of known hosts. Running: /usr/bin/copr-rpmbuild --verbose --drop-resultdir --build-id 5171082 --chroot fedora-rawhide-s390x --detached Version: 0.62 PID: 19839 Logging PID: 19840 Task: {'appstream': False, 'background': True, 'build_id': 5171082, 'buildroot_pkgs': [], 'chroot': 'fedora-rawhide-s390x', 'enable_net': False, 'fedora_review': False, 'git_hash': '2e8067a3d2106d0f694fdea14d7f475152026227', 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/jakub/gcc-13-test/htslib', 'isolation': 'default', 'memory_reqs': 2048, 'package_name': 'htslib', 'package_version': '1.15.1-1', 'project_dirname': 'gcc-13-test', 'project_name': 'gcc-13-test', 'project_owner': 'jakub', 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/jakub/gcc-13-test/fedora-rawhide-s390x/', 'id': 'copr_base', 'name': 'Copr repository'}, {'baseurl': 'https://jakub.fedorapeople.org/fedora-gcc13-$arch/', 'id': 'https_jakub_fedorapeople_org_fedora_gcc13_arch', 'name': 'Additional repo https_jakub_fedorapeople_org_fedora_gcc13_arch'}], 'sandbox': 'jakub/gcc-13-test--jakub', 'source_json': {}, 'source_type': None, 'submitter': 'jakub', 'tags': [], 'task_id': '5171082-fedora-rawhide-s390x', 'timeout': 115200, 'uses_devel_repo': False, 'with_opts': [], 'without_opts': []} Running: git clone https://copr-dist-git.fedorainfracloud.org/git/jakub/gcc-13-test/htslib /var/lib/copr-rpmbuild/workspace/workdir-xbkpkar1/htslib --depth 500 --no-single-branch --recursive cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/jakub/gcc-13-test/htslib', '/var/lib/copr-rpmbuild/workspace/workdir-xbkpkar1/htslib', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-xbkpkar1/htslib'... Running: git checkout 2e8067a3d2106d0f694fdea14d7f475152026227 cmd: ['git', 'checkout', '2e8067a3d2106d0f694fdea14d7f475152026227'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-xbkpkar1/htslib rc: 0 stdout: stderr: Note: switching to '2e8067a3d2106d0f694fdea14d7f475152026227'. 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 2e8067a automatic import of htslib Running: copr-distgit-client sources cmd: ['copr-distgit-client', 'sources'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-xbkpkar1/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: Calling: curl -H Pragma: -o htslib-1.15.1.tar.bz2 --location --remote-time --show-error --fail https://copr-dist-git.fedorainfracloud.org/repo/pkgs/jakub/gcc-13-test/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 2417k 0 0:00:01 0:00:01 --:--:-- 2418k INFO: Reading stdout from command: md5sum htslib-1.15.1.tar.bz2 /usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated Running (timeout=115200): unbuffer mock --buildsrpm --spec /var/lib/copr-rpmbuild/workspace/workdir-xbkpkar1/htslib/htslib.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-xbkpkar1/htslib --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1671942858.428762 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 3.5 starting (python version = 3.11.0, NVR = mock-3.5-1.fc37)... 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-xbkpkar1/htslib/htslib.spec) Config(fedora-rawhide-s390x) Start: clean chroot Finish: clean chroot Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-s390x-bootstrap-1671942858.428762/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: enabled HW Info plugin Mock Version: 3.5 INFO: Mock Version: 3.5 Start(bootstrap): dnf install No matches found for the following disable plugin patterns: local, spacewalk, versionlock Updating Subscription Management repositories. Unable to read consumer identity This system is not registered with an entitlement server. You can use subscription-manager to register. Copr repository 1.9 MB/s | 16 MB 00:08 Additional repo https_jakub_fedorapeople_org_fe 52 kB/s | 86 kB 00:01 fedora 5.5 MB/s | 59 MB 00:10 Dependencies resolved. ========================================================================================================================= Package Arch Version Repository Size ========================================================================================================================= Installing: dnf noarch 4.14.0-1.fc38 fedora 480 k dnf-plugins-core noarch 4.3.1-1.fc38 fedora 34 k Installing dependencies: alternatives s390x 1.21-1.fc38 copr_base 39 k audit-libs s390x 3.0.9-2.fc38 fedora 114 k basesystem noarch 11-14.fc37 fedora 7.0 k bash s390x 5.2.9-3.fc38 copr_base 1.8 M bzip2-libs s390x 1.0.8-12.fc38 copr_base 47 k ca-certificates noarch 2022.2.54-5.fc37 fedora 829 k coreutils s390x 9.1-8.fc38 copr_base 1.1 M coreutils-common s390x 9.1-8.fc38 copr_base 2.0 M crypto-policies noarch 20221215-1.gita4c31a3.fc38 fedora 90 k curl s390x 7.87.0-1.fc38 copr_base 345 k cyrus-sasl-lib s390x 2.1.28-8.fc38 copr_base 773 k dbus-libs s390x 1:1.14.4-1.fc38 copr_base 159 k dnf-data noarch 4.14.0-1.fc38 fedora 43 k elfutils-default-yama-scope noarch 0.188-3.fc38 copr_base 16 k elfutils-libelf s390x 0.188-3.fc38 copr_base 202 k elfutils-libs s390x 0.188-3.fc38 copr_base 275 k expat s390x 2.5.0-1.fc38 copr_base 114 k fedora-gpg-keys noarch 38-0.3 fedora 125 k fedora-release noarch 38-0.6 fedora 11 k fedora-release-common noarch 38-0.6 fedora 21 k fedora-release-identity-basic noarch 38-0.6 fedora 11 k fedora-repos noarch 38-0.3 fedora 10 k fedora-repos-rawhide noarch 38-0.3 fedora 9.7 k file-libs s390x 5.42-4.fc38 copr_base 683 k filesystem s390x 3.18-2.fc37 fedora 1.1 M findutils s390x 1:4.9.0-2.fc38 copr_base 489 k gawk s390x 5.1.1-4.fc38 copr_base 1.0 M gdbm-libs s390x 1:1.23-2.fc38 copr_base 59 k glib2 s390x 2.74.1-2.fc38 copr_base 2.7 M glibc s390x 2.36.9000-19.fc38 fedora 1.6 M glibc-common s390x 2.36.9000-19.fc38 fedora 306 k glibc-minimal-langpack s390x 2.36.9000-19.fc38 fedora 30 k gmp s390x 1:6.2.1-3.fc38 copr_base 326 k gnupg2 s390x 2.3.8-1.fc38 copr_base 2.6 M gnutls s390x 3.7.8-9.fc38 copr_base 1.0 M gpgme s390x 1.17.1-3.fc38 copr_base 219 k grep s390x 3.8-1.fc38 copr_base 290 k ima-evm-utils s390x 1.4-6.fc37 fedora 62 k json-c s390x 0.16-3.fc38 fedora 41 k keyutils-libs s390x 1.6.1-5.fc37 fedora 31 k krb5-libs s390x 1.20.1-3.fc38 fedora 706 k libacl s390x 2.3.1-4.fc38 copr_base 25 k libarchive s390x 3.6.1-3.fc38 fedora 394 k libassuan s390x 2.5.5-5.fc37 fedora 64 k libattr s390x 2.5.1-5.fc38 copr_base 19 k libb2 s390x 0.98.1-7.fc37 fedora 26 k libblkid s390x 2.38.1-3.fc38 fedora 103 k libbrotli s390x 1.0.9-9.fc38 copr_base 344 k libcap s390x 2.48-5.fc37 fedora 66 k libcap-ng s390x 0.8.3-4.fc38 fedora 32 k libcom_err s390x 1.46.5-3.fc38 copr_base 26 k libcomps s390x 0.1.18-4.fc37 fedora 74 k libcurl s390x 7.87.0-1.fc38 copr_base 320 k libdnf s390x 0.68.0-1.fc38 fedora 627 k libevent s390x 2.1.12-7.fc37 fedora 252 k libffi s390x 3.4.4-1.fc38 fedora 34 k libfsverity s390x 1.4-8.fc38 copr_base 20 k libgcc s390x 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 66 k libgcrypt s390x 1.10.1-6.fc38 fedora 457 k libgomp s390x 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 305 k libgpg-error s390x 1.46-1.fc38 fedora 226 k libidn2 s390x 2.3.4-1.fc38 fedora 161 k libksba s390x 1.6.3-1.fc38 fedora 152 k libmodulemd s390x 2.14.0-4.fc37 fedora 210 k libmount s390x 2.38.1-3.fc38 fedora 132 k libnghttp2 s390x 1.51.0-1.fc38 fedora 73 k libnsl2 s390x 2.0.0-4.fc37 fedora 30 k libpsl s390x 0.21.1-6.fc37 fedora 63 k librepo s390x 1.15.1-1.fc38 fedora 92 k libreport-filesystem noarch 2.17.6-1.fc38 fedora 14 k libselinux s390x 3.4-6.fc38 fedora 85 k libsemanage s390x 3.4-6.fc38 fedora 115 k libsepol s390x 3.4-4.fc38 fedora 302 k libsigsegv s390x 2.14-3.fc37 fedora 27 k libsmartcols s390x 2.38.1-3.fc38 fedora 63 k libsolv s390x 0.7.22-3.fc37 fedora 387 k libssh s390x 0.10.4-2.fc38 fedora 199 k libssh-config noarch 0.10.4-2.fc38 fedora 8.8 k libstdc++ s390x 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 889 k libtasn1 s390x 4.19.0-1.fc38 fedora 74 k libtirpc s390x 1.3.3-0.fc37 fedora 90 k libunistring s390x 1.0-2.fc37 fedora 547 k libuuid s390x 2.38.1-3.fc38 fedora 27 k libverto s390x 0.3.2-4.fc37 fedora 20 k libxcrypt s390x 4.4.33-5.fc38 fedora 121 k libxml2 s390x 2.10.3-2.fc38 fedora 670 k libyaml s390x 0.2.5-8.fc37 fedora 55 k libzstd s390x 1.5.2-3.fc37 fedora 274 k lua-libs s390x 5.4.4-6.fc38 fedora 129 k lz4-libs s390x 1.9.3-5.fc37 fedora 68 k mpdecimal s390x 2.5.1-4.fc37 fedora 104 k mpfr s390x 4.1.1-2.fc38 fedora 522 k ncurses-base noarch 6.3-5.20221126.fc38 fedora 86 k ncurses-libs s390x 6.3-5.20221126.fc38 fedora 324 k nettle s390x 3.8-2.fc37 fedora 430 k npth s390x 1.6-10.fc38 fedora 24 k openldap s390x 2.6.3-1.fc38 fedora 248 k openssl-libs s390x 1:3.0.5-6.fc38 fedora 1.8 M p11-kit s390x 0.24.1-5.fc38 fedora 378 k p11-kit-trust s390x 0.24.1-5.fc38 fedora 131 k pcre2 s390x 10.40-1.fc37.1 fedora 219 k pcre2-syntax noarch 10.40-1.fc37.1 fedora 142 k popt s390x 1.19-1.fc38 fedora 67 k publicsuffix-list-dafsa noarch 20221208-1.fc38 fedora 59 k python-pip-wheel noarch 22.3.1-1.fc38 fedora 1.4 M python-setuptools-wheel noarch 65.5.1-1.fc38 fedora 715 k python3 s390x 3.11.1-1.fc38 fedora 27 k python3-dateutil noarch 1:2.8.2-4.fc37 fedora 361 k python3-dbus s390x 1.3.2-1.fc38 copr_base 147 k python3-distro noarch 1.8.0-1.fc38 fedora 49 k python3-dnf noarch 4.14.0-1.fc38 fedora 607 k python3-dnf-plugins-core noarch 4.3.1-1.fc38 fedora 277 k python3-gpg s390x 1.17.1-3.fc38 copr_base 281 k python3-hawkey s390x 0.68.0-1.fc38 fedora 99 k python3-libcomps s390x 0.1.18-4.fc37 fedora 47 k python3-libdnf s390x 0.68.0-1.fc38 fedora 738 k python3-libs s390x 3.11.1-1.fc38 fedora 9.5 M python3-rpm s390x 4.18.0-8.fc38 fedora 95 k python3-six noarch 1.16.0-8.fc37 fedora 42 k readline s390x 8.2-2.fc38 fedora 213 k rpm s390x 4.18.0-8.fc38 fedora 569 k rpm-build-libs s390x 4.18.0-8.fc38 fedora 92 k rpm-libs s390x 4.18.0-8.fc38 fedora 307 k rpm-sequoia s390x 1.2.0-1.fc38 fedora 960 k rpm-sign-libs s390x 4.18.0-8.fc38 fedora 26 k sed s390x 4.8-11.fc37 fedora 304 k setup noarch 2.14.3-1.fc38 fedora 152 k shadow-utils s390x 2:4.13-3.fc38 fedora 1.2 M sqlite-libs s390x 3.40.0-1.fc38 fedora 651 k systemd-libs s390x 252.4-598.fc38 fedora 591 k tpm2-tss s390x 4.0.0-0.1.rc2.fc38 fedora 630 k tzdata noarch 2022g-1.fc38 fedora 716 k xz-libs s390x 5.2.9-1.fc38 fedora 93 k zchunk-libs s390x 1.2.3-1.fc38 fedora 49 k zlib s390x 1.2.13-1.fc38 fedora 96 k Transaction Summary ========================================================================================================================= Install 137 Packages Total download size: 56 M Installed size: 200 M Downloading Packages: (1/137): bzip2-libs-1.0.8-12.fc38.s390x.rpm 517 kB/s | 47 kB 00:00 (2/137): alternatives-1.21-1.fc38.s390x.rpm 416 kB/s | 39 kB 00:00 (3/137): bash-5.2.9-3.fc38.s390x.rpm 12 MB/s | 1.8 MB 00:00 (4/137): coreutils-9.1-8.fc38.s390x.rpm 15 MB/s | 1.1 MB 00:00 (5/137): curl-7.87.0-1.fc38.s390x.rpm 13 MB/s | 345 kB 00:00 (6/137): cyrus-sasl-lib-2.1.28-8.fc38.s390x.rpm 35 MB/s | 773 kB 00:00 (7/137): dbus-libs-1.14.4-1.fc38.s390x.rpm 15 MB/s | 159 kB 00:00 (8/137): elfutils-default-yama-scope-0.188-3.fc 1.6 MB/s | 16 kB 00:00 (9/137): coreutils-common-9.1-8.fc38.s390x.rpm 17 MB/s | 2.0 MB 00:00 (10/137): elfutils-libelf-0.188-3.fc38.s390x.rp 8.8 MB/s | 202 kB 00:00 (11/137): expat-2.5.0-1.fc38.s390x.rpm 9.4 MB/s | 114 kB 00:00 (12/137): elfutils-libs-0.188-3.fc38.s390x.rpm 9.8 MB/s | 275 kB 00:00 (13/137): findutils-4.9.0-2.fc38.s390x.rpm 37 MB/s | 489 kB 00:00 (14/137): gdbm-libs-1.23-2.fc38.s390x.rpm 12 MB/s | 59 kB 00:00 (15/137): file-libs-5.42-4.fc38.s390x.rpm 8.9 MB/s | 683 kB 00:00 (16/137): gmp-6.2.1-3.fc38.s390x.rpm 24 MB/s | 326 kB 00:00 (17/137): gawk-5.1.1-4.fc38.s390x.rpm 10 MB/s | 1.0 MB 00:00 (18/137): gnutls-3.7.8-9.fc38.s390x.rpm 17 MB/s | 1.0 MB 00:00 (19/137): gpgme-1.17.1-3.fc38.s390x.rpm 14 MB/s | 219 kB 00:00 (20/137): glib2-2.74.1-2.fc38.s390x.rpm 16 MB/s | 2.7 MB 00:00 (21/137): libacl-2.3.1-4.fc38.s390x.rpm 1.6 MB/s | 25 kB 00:00 (22/137): grep-3.8-1.fc38.s390x.rpm 12 MB/s | 290 kB 00:00 (23/137): libattr-2.5.1-5.fc38.s390x.rpm 3.7 MB/s | 19 kB 00:00 (24/137): libcom_err-1.46.5-3.fc38.s390x.rpm 6.2 MB/s | 26 kB 00:00 (25/137): gnupg2-2.3.8-1.fc38.s390x.rpm 18 MB/s | 2.6 MB 00:00 (26/137): libbrotli-1.0.9-9.fc38.s390x.rpm 15 MB/s | 344 kB 00:00 (27/137): libcurl-7.87.0-1.fc38.s390x.rpm 19 MB/s | 320 kB 00:00 (28/137): libfsverity-1.4-8.fc38.s390x.rpm 4.3 MB/s | 20 kB 00:00 (29/137): python3-dbus-1.3.2-1.fc38.s390x.rpm 15 MB/s | 147 kB 00:00 (30/137): python3-gpg-1.17.1-3.fc38.s390x.rpm 20 MB/s | 281 kB 00:00 (31/137): libgcc-13.0.0-0.4.fc38.s390x.rpm 68 kB/s | 66 kB 00:00 (32/137): libgomp-13.0.0-0.4.fc38.s390x.rpm 236 kB/s | 305 kB 00:01 (33/137): basesystem-11-14.fc37.noarch.rpm 23 kB/s | 7.0 kB 00:00 (34/137): libstdc++-13.0.0-0.4.fc38.s390x.rpm 536 kB/s | 889 kB 00:01 (35/137): audit-libs-3.0.9-2.fc38.s390x.rpm 123 kB/s | 114 kB 00:00 (36/137): dnf-4.14.0-1.fc38.noarch.rpm 908 kB/s | 480 kB 00:00 (37/137): crypto-policies-20221215-1.gita4c31a3 117 kB/s | 90 kB 00:00 (38/137): dnf-data-4.14.0-1.fc38.noarch.rpm 266 kB/s | 43 kB 00:00 (39/137): ca-certificates-2022.2.54-5.fc37.noar 830 kB/s | 829 kB 00:00 (40/137): dnf-plugins-core-4.3.1-1.fc38.noarch. 165 kB/s | 34 kB 00:00 (41/137): fedora-release-38-0.6.noarch.rpm 70 kB/s | 11 kB 00:00 (42/137): fedora-gpg-keys-38-0.3.noarch.rpm 712 kB/s | 125 kB 00:00 (43/137): fedora-release-common-38-0.6.noarch.r 114 kB/s | 21 kB 00:00 (44/137): fedora-release-identity-basic-38-0.6. 75 kB/s | 11 kB 00:00 (45/137): fedora-repos-38-0.3.noarch.rpm 67 kB/s | 10 kB 00:00 (46/137): fedora-repos-rawhide-38-0.3.noarch.rp 58 kB/s | 9.7 kB 00:00 (47/137): filesystem-3.18-2.fc37.s390x.rpm 3.3 MB/s | 1.1 MB 00:00 (48/137): glibc-2.36.9000-19.fc38.s390x.rpm 3.6 MB/s | 1.6 MB 00:00 (49/137): glibc-minimal-langpack-2.36.9000-19.f 197 kB/s | 30 kB 00:00 (50/137): ima-evm-utils-1.4-6.fc37.s390x.rpm 402 kB/s | 62 kB 00:00 (51/137): glibc-common-2.36.9000-19.fc38.s390x. 584 kB/s | 306 kB 00:00 (52/137): json-c-0.16-3.fc38.s390x.rpm 264 kB/s | 41 kB 00:00 (53/137): keyutils-libs-1.6.1-5.fc37.s390x.rpm 202 kB/s | 31 kB 00:00 (54/137): libarchive-3.6.1-3.fc38.s390x.rpm 2.2 MB/s | 394 kB 00:00 (55/137): libassuan-2.5.5-5.fc37.s390x.rpm 415 kB/s | 64 kB 00:00 (56/137): libb2-0.98.1-7.fc37.s390x.rpm 169 kB/s | 26 kB 00:00 (57/137): krb5-libs-1.20.1-3.fc38.s390x.rpm 1.6 MB/s | 706 kB 00:00 (58/137): libblkid-2.38.1-3.fc38.s390x.rpm 658 kB/s | 103 kB 00:00 (59/137): libcap-2.48-5.fc37.s390x.rpm 427 kB/s | 66 kB 00:00 (60/137): libcap-ng-0.8.3-4.fc38.s390x.rpm 199 kB/s | 32 kB 00:00 (61/137): libcomps-0.1.18-4.fc37.s390x.rpm 478 kB/s | 74 kB 00:00 (62/137): libdnf-0.68.0-1.fc38.s390x.rpm 3.2 MB/s | 627 kB 00:00 (63/137): libffi-3.4.4-1.fc38.s390x.rpm 226 kB/s | 34 kB 00:00 (64/137): libevent-2.1.12-7.fc37.s390x.rpm 1.3 MB/s | 252 kB 00:00 (65/137): libgcrypt-1.10.1-6.fc38.s390x.rpm 2.5 MB/s | 457 kB 00:00 (66/137): libgpg-error-1.46-1.fc38.s390x.rpm 1.3 MB/s | 226 kB 00:00 (67/137): libidn2-2.3.4-1.fc38.s390x.rpm 900 kB/s | 161 kB 00:00 (68/137): libksba-1.6.3-1.fc38.s390x.rpm 950 kB/s | 152 kB 00:00 (69/137): libmodulemd-2.14.0-4.fc37.s390x.rpm 1.3 MB/s | 210 kB 00:00 (70/137): libmount-2.38.1-3.fc38.s390x.rpm 752 kB/s | 132 kB 00:00 (71/137): libnghttp2-1.51.0-1.fc38.s390x.rpm 474 kB/s | 73 kB 00:00 (72/137): libnsl2-2.0.0-4.fc37.s390x.rpm 194 kB/s | 30 kB 00:00 (73/137): libpsl-0.21.1-6.fc37.s390x.rpm 383 kB/s | 63 kB 00:00 (74/137): librepo-1.15.1-1.fc38.s390x.rpm 591 kB/s | 92 kB 00:00 (75/137): libreport-filesystem-2.17.6-1.fc38.no 91 kB/s | 14 kB 00:00 (76/137): libselinux-3.4-6.fc38.s390x.rpm 509 kB/s | 85 kB 00:00 (77/137): libsemanage-3.4-6.fc38.s390x.rpm 729 kB/s | 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zchunk-libs-1.2.3-1.fc38.s390x.rpm 318 kB/s | 49 kB 00:00 (137/137): zlib-1.2.13-1.fc38.s390x.rpm 596 kB/s | 96 kB 00:00 -------------------------------------------------------------------------------- Total 5.7 MB/s | 56 MB 00:09 fedora 1.6 MB/s | 1.6 kB 00:00 Importing GPG key 0xEB10B464: Userid : "Fedora (38) " Fingerprint: 6A51 BBAB BA3D 5467 B617 1221 809A 8D7C EB10 B464 From : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-38-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-38-primary (0xEB10B464) is already installed fedora 1.6 MB/s | 1.6 kB 00:00 Importing GPG key 0x5323552A: Userid : "Fedora (37) " Fingerprint: ACB5 EE4E 831C 74BB 7C16 8D27 F55A D3FB 5323 552A From : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-37-primary Key imported successfully Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Running scriptlet: filesystem-3.18-2.fc37.s390x 1/1 Preparing : 1/1 Installing : libgcc-13.0.0-0.4.fc38.s390x 1/137 Running scriptlet: libgcc-13.0.0-0.4.fc38.s390x 1/137 Installing : crypto-policies-20221215-1.gita4c31a3.fc38.noarc 2/137 Running scriptlet: crypto-policies-20221215-1.gita4c31a3.fc38.noarc 2/137 Installing : tzdata-2022g-1.fc38.noarch 3/137 Installing : fedora-release-identity-basic-38-0.6.noarch 4/137 Installing : python-setuptools-wheel-65.5.1-1.fc38.noarch 5/137 Installing : publicsuffix-list-dafsa-20221208-1.fc38.noarch 6/137 Installing : pcre2-syntax-10.40-1.fc37.1.noarch 7/137 Installing : ncurses-base-6.3-5.20221126.fc38.noarch 8/137 Installing : libssh-config-0.10.4-2.fc38.noarch 9/137 Installing : libreport-filesystem-2.17.6-1.fc38.noarch 10/137 Installing : dnf-data-4.14.0-1.fc38.noarch 11/137 warning: /etc/dnf/dnf.conf created as /etc/dnf/dnf.conf.rpmnew Installing : fedora-gpg-keys-38-0.3.noarch 12/137 Installing : 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gpgme-1.17.1-3.fc38.s390x 122/137 Installing : python3-gpg-1.17.1-3.fc38.s390x 123/137 Installing : librepo-1.15.1-1.fc38.s390x 124/137 Installing : libdnf-0.68.0-1.fc38.s390x 125/137 Installing : python3-libdnf-0.68.0-1.fc38.s390x 126/137 Installing : python3-hawkey-0.68.0-1.fc38.s390x 127/137 Installing : curl-7.87.0-1.fc38.s390x 128/137 Running scriptlet: tpm2-tss-4.0.0-0.1.rc2.fc38.s390x 129/137 useradd: Warning: missing or non-executable shell '/usr/sbin/nologin' Installing : tpm2-tss-4.0.0-0.1.rc2.fc38.s390x 129/137 Installing : ima-evm-utils-1.4-6.fc37.s390x 130/137 Installing : rpm-sign-libs-4.18.0-8.fc38.s390x 131/137 Installing : python3-rpm-4.18.0-8.fc38.s390x 132/137 Installing : python3-dnf-4.14.0-1.fc38.noarch 133/137 Installing : python3-dnf-plugins-core-4.3.1-1.fc38.noarch 134/137 Installing : dnf-plugins-core-4.3.1-1.fc38.noarch 135/137 Installing : dnf-4.14.0-1.fc38.noarch 136/137 Running scriptlet: dnf-4.14.0-1.fc38.noarch 136/137 Running scriptlet: rpm-4.18.0-8.fc38.s390x 137/137 Installing : rpm-4.18.0-8.fc38.s390x 137/137 Running scriptlet: filesystem-3.18-2.fc37.s390x 137/137 Running scriptlet: ca-certificates-2022.2.54-5.fc37.noarch 137/137 Running scriptlet: rpm-4.18.0-8.fc38.s390x 137/137 Verifying : alternatives-1.21-1.fc38.s390x 1/137 Verifying : bash-5.2.9-3.fc38.s390x 2/137 Verifying : bzip2-libs-1.0.8-12.fc38.s390x 3/137 Verifying : coreutils-9.1-8.fc38.s390x 4/137 Verifying : coreutils-common-9.1-8.fc38.s390x 5/137 Verifying : curl-7.87.0-1.fc38.s390x 6/137 Verifying : cyrus-sasl-lib-2.1.28-8.fc38.s390x 7/137 Verifying : dbus-libs-1:1.14.4-1.fc38.s390x 8/137 Verifying : elfutils-default-yama-scope-0.188-3.fc38.noarch 9/137 Verifying : elfutils-libelf-0.188-3.fc38.s390x 10/137 Verifying : elfutils-libs-0.188-3.fc38.s390x 11/137 Verifying : expat-2.5.0-1.fc38.s390x 12/137 Verifying : file-libs-5.42-4.fc38.s390x 13/137 Verifying : findutils-1:4.9.0-2.fc38.s390x 14/137 Verifying : gawk-5.1.1-4.fc38.s390x 15/137 Verifying : gdbm-libs-1:1.23-2.fc38.s390x 16/137 Verifying : glib2-2.74.1-2.fc38.s390x 17/137 Verifying : gmp-1:6.2.1-3.fc38.s390x 18/137 Verifying : gnupg2-2.3.8-1.fc38.s390x 19/137 Verifying : gnutls-3.7.8-9.fc38.s390x 20/137 Verifying : gpgme-1.17.1-3.fc38.s390x 21/137 Verifying : grep-3.8-1.fc38.s390x 22/137 Verifying : libacl-2.3.1-4.fc38.s390x 23/137 Verifying : libattr-2.5.1-5.fc38.s390x 24/137 Verifying : libbrotli-1.0.9-9.fc38.s390x 25/137 Verifying : libcom_err-1.46.5-3.fc38.s390x 26/137 Verifying : libcurl-7.87.0-1.fc38.s390x 27/137 Verifying : libfsverity-1.4-8.fc38.s390x 28/137 Verifying : python3-dbus-1.3.2-1.fc38.s390x 29/137 Verifying : python3-gpg-1.17.1-3.fc38.s390x 30/137 Verifying : libgcc-13.0.0-0.4.fc38.s390x 31/137 Verifying : libgomp-13.0.0-0.4.fc38.s390x 32/137 Verifying : libstdc++-13.0.0-0.4.fc38.s390x 33/137 Verifying : audit-libs-3.0.9-2.fc38.s390x 34/137 Verifying : basesystem-11-14.fc37.noarch 35/137 Verifying : ca-certificates-2022.2.54-5.fc37.noarch 36/137 Verifying : crypto-policies-20221215-1.gita4c31a3.fc38.noarc 37/137 Verifying : dnf-4.14.0-1.fc38.noarch 38/137 Verifying : dnf-data-4.14.0-1.fc38.noarch 39/137 Verifying : dnf-plugins-core-4.3.1-1.fc38.noarch 40/137 Verifying : fedora-gpg-keys-38-0.3.noarch 41/137 Verifying : fedora-release-38-0.6.noarch 42/137 Verifying : fedora-release-common-38-0.6.noarch 43/137 Verifying : fedora-release-identity-basic-38-0.6.noarch 44/137 Verifying : fedora-repos-38-0.3.noarch 45/137 Verifying : fedora-repos-rawhide-38-0.3.noarch 46/137 Verifying : filesystem-3.18-2.fc37.s390x 47/137 Verifying : glibc-2.36.9000-19.fc38.s390x 48/137 Verifying : glibc-common-2.36.9000-19.fc38.s390x 49/137 Verifying : glibc-minimal-langpack-2.36.9000-19.fc38.s390x 50/137 Verifying : ima-evm-utils-1.4-6.fc37.s390x 51/137 Verifying : json-c-0.16-3.fc38.s390x 52/137 Verifying : keyutils-libs-1.6.1-5.fc37.s390x 53/137 Verifying : krb5-libs-1.20.1-3.fc38.s390x 54/137 Verifying : libarchive-3.6.1-3.fc38.s390x 55/137 Verifying : libassuan-2.5.5-5.fc37.s390x 56/137 Verifying : libb2-0.98.1-7.fc37.s390x 57/137 Verifying : libblkid-2.38.1-3.fc38.s390x 58/137 Verifying : libcap-2.48-5.fc37.s390x 59/137 Verifying : libcap-ng-0.8.3-4.fc38.s390x 60/137 Verifying : libcomps-0.1.18-4.fc37.s390x 61/137 Verifying : libdnf-0.68.0-1.fc38.s390x 62/137 Verifying : libevent-2.1.12-7.fc37.s390x 63/137 Verifying : libffi-3.4.4-1.fc38.s390x 64/137 Verifying : libgcrypt-1.10.1-6.fc38.s390x 65/137 Verifying : libgpg-error-1.46-1.fc38.s390x 66/137 Verifying : libidn2-2.3.4-1.fc38.s390x 67/137 Verifying : libksba-1.6.3-1.fc38.s390x 68/137 Verifying : libmodulemd-2.14.0-4.fc37.s390x 69/137 Verifying : libmount-2.38.1-3.fc38.s390x 70/137 Verifying : libnghttp2-1.51.0-1.fc38.s390x 71/137 Verifying : libnsl2-2.0.0-4.fc37.s390x 72/137 Verifying : libpsl-0.21.1-6.fc37.s390x 73/137 Verifying : librepo-1.15.1-1.fc38.s390x 74/137 Verifying : libreport-filesystem-2.17.6-1.fc38.noarch 75/137 Verifying : libselinux-3.4-6.fc38.s390x 76/137 Verifying : libsemanage-3.4-6.fc38.s390x 77/137 Verifying : libsepol-3.4-4.fc38.s390x 78/137 Verifying : libsigsegv-2.14-3.fc37.s390x 79/137 Verifying : libsmartcols-2.38.1-3.fc38.s390x 80/137 Verifying : libsolv-0.7.22-3.fc37.s390x 81/137 Verifying : libssh-0.10.4-2.fc38.s390x 82/137 Verifying : libssh-config-0.10.4-2.fc38.noarch 83/137 Verifying : libtasn1-4.19.0-1.fc38.s390x 84/137 Verifying : libtirpc-1.3.3-0.fc37.s390x 85/137 Verifying : libunistring-1.0-2.fc37.s390x 86/137 Verifying : libuuid-2.38.1-3.fc38.s390x 87/137 Verifying : libverto-0.3.2-4.fc37.s390x 88/137 Verifying : libxcrypt-4.4.33-5.fc38.s390x 89/137 Verifying : libxml2-2.10.3-2.fc38.s390x 90/137 Verifying : libyaml-0.2.5-8.fc37.s390x 91/137 Verifying : libzstd-1.5.2-3.fc37.s390x 92/137 Verifying : lua-libs-5.4.4-6.fc38.s390x 93/137 Verifying : lz4-libs-1.9.3-5.fc37.s390x 94/137 Verifying : mpdecimal-2.5.1-4.fc37.s390x 95/137 Verifying : mpfr-4.1.1-2.fc38.s390x 96/137 Verifying : ncurses-base-6.3-5.20221126.fc38.noarch 97/137 Verifying : ncurses-libs-6.3-5.20221126.fc38.s390x 98/137 Verifying : nettle-3.8-2.fc37.s390x 99/137 Verifying : npth-1.6-10.fc38.s390x 100/137 Verifying : openldap-2.6.3-1.fc38.s390x 101/137 Verifying : openssl-libs-1:3.0.5-6.fc38.s390x 102/137 Verifying : p11-kit-0.24.1-5.fc38.s390x 103/137 Verifying : p11-kit-trust-0.24.1-5.fc38.s390x 104/137 Verifying : pcre2-10.40-1.fc37.1.s390x 105/137 Verifying : pcre2-syntax-10.40-1.fc37.1.noarch 106/137 Verifying : popt-1.19-1.fc38.s390x 107/137 Verifying : publicsuffix-list-dafsa-20221208-1.fc38.noarch 108/137 Verifying : python-pip-wheel-22.3.1-1.fc38.noarch 109/137 Verifying : python-setuptools-wheel-65.5.1-1.fc38.noarch 110/137 Verifying : python3-3.11.1-1.fc38.s390x 111/137 Verifying : python3-dateutil-1:2.8.2-4.fc37.noarch 112/137 Verifying : python3-distro-1.8.0-1.fc38.noarch 113/137 Verifying : python3-dnf-4.14.0-1.fc38.noarch 114/137 Verifying : python3-dnf-plugins-core-4.3.1-1.fc38.noarch 115/137 Verifying : python3-hawkey-0.68.0-1.fc38.s390x 116/137 Verifying : python3-libcomps-0.1.18-4.fc37.s390x 117/137 Verifying : python3-libdnf-0.68.0-1.fc38.s390x 118/137 Verifying : python3-libs-3.11.1-1.fc38.s390x 119/137 Verifying : python3-rpm-4.18.0-8.fc38.s390x 120/137 Verifying : python3-six-1.16.0-8.fc37.noarch 121/137 Verifying : readline-8.2-2.fc38.s390x 122/137 Verifying : rpm-4.18.0-8.fc38.s390x 123/137 Verifying : rpm-build-libs-4.18.0-8.fc38.s390x 124/137 Verifying : rpm-libs-4.18.0-8.fc38.s390x 125/137 Verifying : rpm-sequoia-1.2.0-1.fc38.s390x 126/137 Verifying : rpm-sign-libs-4.18.0-8.fc38.s390x 127/137 Verifying : sed-4.8-11.fc37.s390x 128/137 Verifying : setup-2.14.3-1.fc38.noarch 129/137 Verifying : shadow-utils-2:4.13-3.fc38.s390x 130/137 Verifying : sqlite-libs-3.40.0-1.fc38.s390x 131/137 Verifying : systemd-libs-252.4-598.fc38.s390x 132/137 Verifying : tpm2-tss-4.0.0-0.1.rc2.fc38.s390x 133/137 Verifying : tzdata-2022g-1.fc38.noarch 134/137 Verifying : xz-libs-5.2.9-1.fc38.s390x 135/137 Verifying : zchunk-libs-1.2.3-1.fc38.s390x 136/137 Verifying : zlib-1.2.13-1.fc38.s390x 137/137 Installed products updated. Installed: alternatives-1.21-1.fc38.s390x audit-libs-3.0.9-2.fc38.s390x basesystem-11-14.fc37.noarch bash-5.2.9-3.fc38.s390x bzip2-libs-1.0.8-12.fc38.s390x ca-certificates-2022.2.54-5.fc37.noarch coreutils-9.1-8.fc38.s390x coreutils-common-9.1-8.fc38.s390x crypto-policies-20221215-1.gita4c31a3.fc38.noarch curl-7.87.0-1.fc38.s390x cyrus-sasl-lib-2.1.28-8.fc38.s390x dbus-libs-1:1.14.4-1.fc38.s390x dnf-4.14.0-1.fc38.noarch dnf-data-4.14.0-1.fc38.noarch dnf-plugins-core-4.3.1-1.fc38.noarch elfutils-default-yama-scope-0.188-3.fc38.noarch elfutils-libelf-0.188-3.fc38.s390x elfutils-libs-0.188-3.fc38.s390x expat-2.5.0-1.fc38.s390x fedora-gpg-keys-38-0.3.noarch fedora-release-38-0.6.noarch fedora-release-common-38-0.6.noarch fedora-release-identity-basic-38-0.6.noarch fedora-repos-38-0.3.noarch fedora-repos-rawhide-38-0.3.noarch file-libs-5.42-4.fc38.s390x filesystem-3.18-2.fc37.s390x findutils-1:4.9.0-2.fc38.s390x gawk-5.1.1-4.fc38.s390x gdbm-libs-1:1.23-2.fc38.s390x glib2-2.74.1-2.fc38.s390x glibc-2.36.9000-19.fc38.s390x glibc-common-2.36.9000-19.fc38.s390x glibc-minimal-langpack-2.36.9000-19.fc38.s390x gmp-1:6.2.1-3.fc38.s390x gnupg2-2.3.8-1.fc38.s390x gnutls-3.7.8-9.fc38.s390x gpgme-1.17.1-3.fc38.s390x grep-3.8-1.fc38.s390x ima-evm-utils-1.4-6.fc37.s390x json-c-0.16-3.fc38.s390x keyutils-libs-1.6.1-5.fc37.s390x krb5-libs-1.20.1-3.fc38.s390x libacl-2.3.1-4.fc38.s390x libarchive-3.6.1-3.fc38.s390x libassuan-2.5.5-5.fc37.s390x libattr-2.5.1-5.fc38.s390x libb2-0.98.1-7.fc37.s390x libblkid-2.38.1-3.fc38.s390x libbrotli-1.0.9-9.fc38.s390x libcap-2.48-5.fc37.s390x libcap-ng-0.8.3-4.fc38.s390x libcom_err-1.46.5-3.fc38.s390x libcomps-0.1.18-4.fc37.s390x libcurl-7.87.0-1.fc38.s390x libdnf-0.68.0-1.fc38.s390x libevent-2.1.12-7.fc37.s390x libffi-3.4.4-1.fc38.s390x libfsverity-1.4-8.fc38.s390x libgcc-13.0.0-0.4.fc38.s390x libgcrypt-1.10.1-6.fc38.s390x libgomp-13.0.0-0.4.fc38.s390x libgpg-error-1.46-1.fc38.s390x libidn2-2.3.4-1.fc38.s390x libksba-1.6.3-1.fc38.s390x libmodulemd-2.14.0-4.fc37.s390x libmount-2.38.1-3.fc38.s390x libnghttp2-1.51.0-1.fc38.s390x libnsl2-2.0.0-4.fc37.s390x libpsl-0.21.1-6.fc37.s390x librepo-1.15.1-1.fc38.s390x libreport-filesystem-2.17.6-1.fc38.noarch libselinux-3.4-6.fc38.s390x libsemanage-3.4-6.fc38.s390x libsepol-3.4-4.fc38.s390x libsigsegv-2.14-3.fc37.s390x libsmartcols-2.38.1-3.fc38.s390x libsolv-0.7.22-3.fc37.s390x libssh-0.10.4-2.fc38.s390x libssh-config-0.10.4-2.fc38.noarch libstdc++-13.0.0-0.4.fc38.s390x libtasn1-4.19.0-1.fc38.s390x libtirpc-1.3.3-0.fc37.s390x libunistring-1.0-2.fc37.s390x libuuid-2.38.1-3.fc38.s390x libverto-0.3.2-4.fc37.s390x libxcrypt-4.4.33-5.fc38.s390x libxml2-2.10.3-2.fc38.s390x libyaml-0.2.5-8.fc37.s390x libzstd-1.5.2-3.fc37.s390x lua-libs-5.4.4-6.fc38.s390x lz4-libs-1.9.3-5.fc37.s390x mpdecimal-2.5.1-4.fc37.s390x mpfr-4.1.1-2.fc38.s390x ncurses-base-6.3-5.20221126.fc38.noarch ncurses-libs-6.3-5.20221126.fc38.s390x nettle-3.8-2.fc37.s390x npth-1.6-10.fc38.s390x openldap-2.6.3-1.fc38.s390x openssl-libs-1:3.0.5-6.fc38.s390x p11-kit-0.24.1-5.fc38.s390x p11-kit-trust-0.24.1-5.fc38.s390x pcre2-10.40-1.fc37.1.s390x pcre2-syntax-10.40-1.fc37.1.noarch popt-1.19-1.fc38.s390x publicsuffix-list-dafsa-20221208-1.fc38.noarch python-pip-wheel-22.3.1-1.fc38.noarch python-setuptools-wheel-65.5.1-1.fc38.noarch python3-3.11.1-1.fc38.s390x python3-dateutil-1:2.8.2-4.fc37.noarch python3-dbus-1.3.2-1.fc38.s390x python3-distro-1.8.0-1.fc38.noarch python3-dnf-4.14.0-1.fc38.noarch python3-dnf-plugins-core-4.3.1-1.fc38.noarch python3-gpg-1.17.1-3.fc38.s390x python3-hawkey-0.68.0-1.fc38.s390x python3-libcomps-0.1.18-4.fc37.s390x python3-libdnf-0.68.0-1.fc38.s390x python3-libs-3.11.1-1.fc38.s390x python3-rpm-4.18.0-8.fc38.s390x python3-six-1.16.0-8.fc37.noarch readline-8.2-2.fc38.s390x rpm-4.18.0-8.fc38.s390x rpm-build-libs-4.18.0-8.fc38.s390x rpm-libs-4.18.0-8.fc38.s390x rpm-sequoia-1.2.0-1.fc38.s390x rpm-sign-libs-4.18.0-8.fc38.s390x sed-4.8-11.fc37.s390x setup-2.14.3-1.fc38.noarch shadow-utils-2:4.13-3.fc38.s390x sqlite-libs-3.40.0-1.fc38.s390x systemd-libs-252.4-598.fc38.s390x tpm2-tss-4.0.0-0.1.rc2.fc38.s390x tzdata-2022g-1.fc38.noarch xz-libs-5.2.9-1.fc38.s390x zchunk-libs-1.2.3-1.fc38.s390x zlib-1.2.13-1.fc38.s390x Complete! Finish(bootstrap): dnf install 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-1671942858.428762/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 Mock Version: 3.5 INFO: Mock Version: 3.5 Start: dnf install No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 4.4 kB/s | 3.0 kB 00:00 Copr repository 3.0 MB/s | 16 MB 00:05 Additional repo https_jakub_fedorapeople_org_fe 4.2 kB/s | 3.0 kB 00:00 fedora 1.0 kB/s | 6.3 kB 00:05 Dependencies resolved. ========================================================================================================================= Package Arch Version Repository Size ========================================================================================================================= Installing group/module packages: bash s390x 5.2.9-3.fc38 copr_base 1.8 M bzip2 s390x 1.0.8-12.fc38 copr_base 54 k coreutils s390x 9.1-8.fc38 copr_base 1.1 M cpio s390x 2.13-13.fc38 copr_base 275 k diffutils s390x 3.8-3.fc38 copr_base 381 k fedora-release-common noarch 38-0.6 fedora 21 k findutils s390x 1:4.9.0-2.fc38 copr_base 489 k gawk s390x 5.1.1-4.fc38 copr_base 1.0 M glibc-minimal-langpack s390x 2.36.9000-19.fc38 fedora 30 k grep s390x 3.8-1.fc38 copr_base 290 k gzip s390x 1.12-2.fc38 copr_base 165 k info s390x 7.0.1-1.fc38 fedora 180 k patch s390x 2.7.6-17.fc37 fedora 122 k redhat-rpm-config noarch 235-1.fc38 fedora 80 k rpm-build s390x 4.18.0-8.fc38 fedora 76 k sed s390x 4.8-11.fc37 fedora 304 k shadow-utils s390x 2:4.13-3.fc38 fedora 1.2 M tar s390x 2:1.34-5.fc38 fedora 876 k unzip s390x 6.0-58.fc38 fedora 177 k util-linux s390x 2.38.1-3.fc38 fedora 2.3 M which s390x 2.21-36.fc38 fedora 42 k xz s390x 5.2.9-1.fc38 fedora 306 k Installing dependencies: alternatives s390x 1.21-1.fc38 copr_base 39 k ansible-srpm-macros noarch 1-8.1.fc38 fedora 8.6 k audit-libs s390x 3.0.9-2.fc38 fedora 114 k authselect s390x 1.4.2-1.fc38 copr_base 139 k authselect-libs s390x 1.4.2-1.fc38 copr_base 235 k basesystem noarch 11-14.fc37 fedora 7.0 k binutils s390x 2.39-6.fc38 copr_base 5.7 M binutils-gold s390x 2.39-6.fc38 copr_base 994 k bzip2-libs s390x 1.0.8-12.fc38 copr_base 47 k ca-certificates noarch 2022.2.54-5.fc37 fedora 829 k coreutils-common s390x 9.1-8.fc38 copr_base 2.0 M cracklib s390x 2.9.7-30.fc38 copr_base 82 k crypto-policies noarch 20221215-1.gita4c31a3.fc38 fedora 90 k curl s390x 7.87.0-1.fc38 copr_base 345 k cyrus-sasl-lib s390x 2.1.28-8.fc38 copr_base 773 k debugedit s390x 5.0-5.fc37 fedora 76 k dwz s390x 0.15-1.fc38 copr_base 144 k ed s390x 1.18-2.fc38 copr_base 80 k efi-srpm-macros noarch 5-6.fc37 fedora 22 k elfutils s390x 0.188-3.fc38 copr_base 547 k elfutils-debuginfod-client s390x 0.188-3.fc38 copr_base 41 k elfutils-default-yama-scope noarch 0.188-3.fc38 copr_base 16 k elfutils-libelf s390x 0.188-3.fc38 copr_base 202 k elfutils-libs s390x 0.188-3.fc38 copr_base 275 k fedora-gpg-keys noarch 38-0.3 fedora 125 k fedora-release noarch 38-0.6 fedora 11 k fedora-release-identity-basic noarch 38-0.6 fedora 11 k fedora-repos noarch 38-0.3 fedora 10 k fedora-repos-rawhide noarch 38-0.3 fedora 9.7 k file s390x 5.42-4.fc38 copr_base 49 k file-libs s390x 5.42-4.fc38 copr_base 683 k filesystem s390x 3.18-2.fc37 fedora 1.1 M fonts-srpm-macros noarch 1:2.0.5-10.fc38 fedora 26 k fpc-srpm-macros noarch 1.3-6.fc37 fedora 7.7 k gdb-minimal s390x 12.1-10.fc38 fedora 3.3 M gdbm-libs s390x 1:1.23-2.fc38 copr_base 59 k ghc-srpm-macros noarch 1.5.0-7.fc37 fedora 7.8 k glibc s390x 2.36.9000-19.fc38 fedora 1.6 M glibc-common s390x 2.36.9000-19.fc38 fedora 306 k glibc-gconv-extra s390x 2.36.9000-19.fc38 fedora 1.6 M gmp s390x 1:6.2.1-3.fc38 copr_base 326 k gnat-srpm-macros noarch 4-16.fc37 fedora 8.3 k go-srpm-macros noarch 3.2.0-1.fc38 fedora 27 k jansson s390x 2.13.1-5.fc37 fedora 42 k kernel-srpm-macros noarch 1.0-15.fc37 fedora 9.4 k keyutils-libs s390x 1.6.1-5.fc37 fedora 31 k krb5-libs s390x 1.20.1-3.fc38 fedora 706 k libacl s390x 2.3.1-4.fc38 copr_base 25 k libarchive s390x 3.6.1-3.fc38 fedora 394 k libattr s390x 2.5.1-5.fc38 copr_base 19 k libblkid s390x 2.38.1-3.fc38 fedora 103 k libbrotli s390x 1.0.9-9.fc38 copr_base 344 k libcap s390x 2.48-5.fc37 fedora 66 k libcap-ng s390x 0.8.3-4.fc38 fedora 32 k libcom_err s390x 1.46.5-3.fc38 copr_base 26 k libcurl s390x 7.87.0-1.fc38 copr_base 320 k libdb s390x 5.3.28-54.fc38 fedora 727 k libeconf s390x 0.4.0-4.fc37 fedora 26 k libevent s390x 2.1.12-7.fc37 fedora 252 k libfdisk s390x 2.38.1-3.fc38 fedora 156 k libffi s390x 3.4.4-1.fc38 fedora 34 k libgcc s390x 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 66 k libgomp s390x 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 305 k libidn2 s390x 2.3.4-1.fc38 fedora 161 k libmount s390x 2.38.1-3.fc38 fedora 132 k libnghttp2 s390x 1.51.0-1.fc38 fedora 73 k libnsl2 s390x 2.0.0-4.fc37 fedora 30 k libpkgconf s390x 1.8.0-3.fc37 fedora 34 k libpsl s390x 0.21.1-6.fc37 fedora 63 k libpwquality s390x 1.4.5-1.fc38 fedora 119 k libselinux s390x 3.4-6.fc38 fedora 85 k libsemanage s390x 3.4-6.fc38 fedora 115 k libsepol s390x 3.4-4.fc38 fedora 302 k libsigsegv s390x 2.14-3.fc37 fedora 27 k libsmartcols s390x 2.38.1-3.fc38 fedora 63 k libssh s390x 0.10.4-2.fc38 fedora 199 k libssh-config noarch 0.10.4-2.fc38 fedora 8.8 k libstdc++ s390x 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 889 k libtasn1 s390x 4.19.0-1.fc38 fedora 74 k libtirpc s390x 1.3.3-0.fc37 fedora 90 k libunistring s390x 1.0-2.fc37 fedora 547 k libutempter s390x 1.2.1-7.fc37 fedora 26 k libuuid s390x 2.38.1-3.fc38 fedora 27 k libverto s390x 0.3.2-4.fc37 fedora 20 k libxcrypt s390x 4.4.33-5.fc38 fedora 121 k libxml2 s390x 2.10.3-2.fc38 fedora 670 k libzstd s390x 1.5.2-3.fc37 fedora 274 k lua-libs s390x 5.4.4-6.fc38 fedora 129 k lua-srpm-macros noarch 1-7.fc37 fedora 8.8 k lz4-libs s390x 1.9.3-5.fc37 fedora 68 k mpfr s390x 4.1.1-2.fc38 fedora 522 k ncurses-base noarch 6.3-5.20221126.fc38 fedora 86 k ncurses-libs s390x 6.3-5.20221126.fc38 fedora 324 k nettle s390x 3.8-2.fc37 fedora 430 k nim-srpm-macros noarch 3-7.fc37 fedora 8.4 k ocaml-srpm-macros noarch 7-2.fc37 fedora 13 k openblas-srpm-macros noarch 2-12.fc37 fedora 7.5 k openldap s390x 2.6.3-1.fc38 fedora 248 k openssl-libs s390x 1:3.0.5-6.fc38 fedora 1.8 M p11-kit s390x 0.24.1-5.fc38 fedora 378 k p11-kit-trust s390x 0.24.1-5.fc38 fedora 131 k package-notes-srpm-macros noarch 0.5-6.fc38 fedora 11 k pam s390x 1.5.2-15.fc38 fedora 554 k pam-libs s390x 1.5.2-15.fc38 fedora 56 k pcre2 s390x 10.40-1.fc37.1 fedora 219 k pcre2-syntax noarch 10.40-1.fc37.1 fedora 142 k perl-srpm-macros noarch 1-47.fc38 fedora 8.2 k pkgconf s390x 1.8.0-3.fc37 fedora 41 k pkgconf-m4 noarch 1.8.0-3.fc37 fedora 14 k pkgconf-pkg-config s390x 1.8.0-3.fc37 fedora 10 k popt s390x 1.19-1.fc38 fedora 67 k publicsuffix-list-dafsa noarch 20221208-1.fc38 fedora 59 k python-srpm-macros noarch 3.11-6.fc38 fedora 25 k qt5-srpm-macros noarch 5.15.7-1.fc38 fedora 7.9 k readline s390x 8.2-2.fc38 fedora 213 k rpm s390x 4.18.0-8.fc38 fedora 569 k rpm-build-libs s390x 4.18.0-8.fc38 fedora 92 k rpm-libs s390x 4.18.0-8.fc38 fedora 307 k rpm-sequoia s390x 1.2.0-1.fc38 fedora 960 k rpmautospec-rpm-macros noarch 0.3.1-1.fc38 fedora 8.8 k rust-srpm-macros noarch 23-1.fc38 fedora 9.4 k setup noarch 2.14.3-1.fc38 fedora 152 k sqlite-libs s390x 3.40.0-1.fc38 fedora 651 k systemd-libs s390x 252.4-598.fc38 fedora 591 k tzdata noarch 2022g-1.fc38 fedora 716 k util-linux-core s390x 2.38.1-3.fc38 fedora 462 k xxhash-libs s390x 0.8.1-3.fc37 fedora 36 k xz-libs s390x 5.2.9-1.fc38 fedora 93 k zip s390x 3.0-35.fc38 fedora 261 k zlib s390x 1.2.13-1.fc38 fedora 96 k zstd s390x 1.5.2-3.fc37 fedora 410 k Installing Groups: Buildsystem building group Transaction Summary ========================================================================================================================= Install 153 Packages Total size: 52 M Installed size: 182 M Downloading Packages: [SKIPPED] alternatives-1.21-1.fc38.s390x.rpm: Already downloaded [SKIPPED] authselect-1.4.2-1.fc38.s390x.rpm: Already downloaded [SKIPPED] authselect-libs-1.4.2-1.fc38.s390x.rpm: Already downloaded [SKIPPED] bash-5.2.9-3.fc38.s390x.rpm: Already downloaded [SKIPPED] binutils-2.39-6.fc38.s390x.rpm: Already downloaded [SKIPPED] binutils-gold-2.39-6.fc38.s390x.rpm: Already downloaded [SKIPPED] bzip2-1.0.8-12.fc38.s390x.rpm: Already downloaded [SKIPPED] bzip2-libs-1.0.8-12.fc38.s390x.rpm: Already downloaded [SKIPPED] coreutils-9.1-8.fc38.s390x.rpm: Already downloaded [SKIPPED] coreutils-common-9.1-8.fc38.s390x.rpm: Already downloaded [SKIPPED] cpio-2.13-13.fc38.s390x.rpm: Already downloaded [SKIPPED] cracklib-2.9.7-30.fc38.s390x.rpm: Already downloaded [SKIPPED] curl-7.87.0-1.fc38.s390x.rpm: Already downloaded [SKIPPED] cyrus-sasl-lib-2.1.28-8.fc38.s390x.rpm: Already downloaded [SKIPPED] diffutils-3.8-3.fc38.s390x.rpm: Already downloaded [SKIPPED] dwz-0.15-1.fc38.s390x.rpm: Already downloaded [SKIPPED] ed-1.18-2.fc38.s390x.rpm: Already downloaded [SKIPPED] elfutils-0.188-3.fc38.s390x.rpm: Already downloaded [SKIPPED] elfutils-debuginfod-client-0.188-3.fc38.s390x.rpm: Already downloaded [SKIPPED] elfutils-default-yama-scope-0.188-3.fc38.noarch.rpm: Already downloaded [SKIPPED] elfutils-libelf-0.188-3.fc38.s390x.rpm: Already downloaded [SKIPPED] elfutils-libs-0.188-3.fc38.s390x.rpm: Already downloaded [SKIPPED] file-5.42-4.fc38.s390x.rpm: Already downloaded [SKIPPED] file-libs-5.42-4.fc38.s390x.rpm: Already downloaded [SKIPPED] findutils-4.9.0-2.fc38.s390x.rpm: Already downloaded [SKIPPED] gawk-5.1.1-4.fc38.s390x.rpm: Already downloaded [SKIPPED] gdbm-libs-1.23-2.fc38.s390x.rpm: Already downloaded [SKIPPED] gmp-6.2.1-3.fc38.s390x.rpm: Already downloaded [SKIPPED] grep-3.8-1.fc38.s390x.rpm: Already downloaded [SKIPPED] gzip-1.12-2.fc38.s390x.rpm: Already downloaded [SKIPPED] libacl-2.3.1-4.fc38.s390x.rpm: Already downloaded [SKIPPED] libattr-2.5.1-5.fc38.s390x.rpm: Already downloaded [SKIPPED] libbrotli-1.0.9-9.fc38.s390x.rpm: Already downloaded [SKIPPED] libcom_err-1.46.5-3.fc38.s390x.rpm: Already downloaded [SKIPPED] libcurl-7.87.0-1.fc38.s390x.rpm: Already downloaded [SKIPPED] libgcc-13.0.0-0.4.fc38.s390x.rpm: Already downloaded [SKIPPED] libgomp-13.0.0-0.4.fc38.s390x.rpm: Already downloaded [SKIPPED] libstdc++-13.0.0-0.4.fc38.s390x.rpm: Already downloaded [SKIPPED] ansible-srpm-macros-1-8.1.fc38.noarch.rpm: Already downloaded [SKIPPED] audit-libs-3.0.9-2.fc38.s390x.rpm: Already downloaded [SKIPPED] basesystem-11-14.fc37.noarch.rpm: Already downloaded [SKIPPED] ca-certificates-2022.2.54-5.fc37.noarch.rpm: Already downloaded [SKIPPED] crypto-policies-20221215-1.gita4c31a3.fc38.noarch.rpm: Already downloaded [SKIPPED] debugedit-5.0-5.fc37.s390x.rpm: Already downloaded [SKIPPED] efi-srpm-macros-5-6.fc37.noarch.rpm: Already downloaded [SKIPPED] fedora-gpg-keys-38-0.3.noarch.rpm: Already downloaded [SKIPPED] fedora-release-38-0.6.noarch.rpm: Already downloaded [SKIPPED] fedora-release-common-38-0.6.noarch.rpm: Already downloaded [SKIPPED] fedora-release-identity-basic-38-0.6.noarch.rpm: Already downloaded [SKIPPED] fedora-repos-38-0.3.noarch.rpm: Already downloaded [SKIPPED] fedora-repos-rawhide-38-0.3.noarch.rpm: Already downloaded [SKIPPED] filesystem-3.18-2.fc37.s390x.rpm: Already downloaded [SKIPPED] fonts-srpm-macros-2.0.5-10.fc38.noarch.rpm: Already downloaded [SKIPPED] fpc-srpm-macros-1.3-6.fc37.noarch.rpm: Already downloaded [SKIPPED] gdb-minimal-12.1-10.fc38.s390x.rpm: Already downloaded [SKIPPED] ghc-srpm-macros-1.5.0-7.fc37.noarch.rpm: Already downloaded [SKIPPED] glibc-2.36.9000-19.fc38.s390x.rpm: Already downloaded [SKIPPED] glibc-common-2.36.9000-19.fc38.s390x.rpm: Already downloaded [SKIPPED] glibc-gconv-extra-2.36.9000-19.fc38.s390x.rpm: Already downloaded [SKIPPED] glibc-minimal-langpack-2.36.9000-19.fc38.s390x.rpm: Already downloaded [SKIPPED] gnat-srpm-macros-4-16.fc37.noarch.rpm: Already downloaded [SKIPPED] go-srpm-macros-3.2.0-1.fc38.noarch.rpm: Already downloaded [SKIPPED] info-7.0.1-1.fc38.s390x.rpm: Already downloaded [SKIPPED] jansson-2.13.1-5.fc37.s390x.rpm: Already downloaded [SKIPPED] kernel-srpm-macros-1.0-15.fc37.noarch.rpm: Already downloaded [SKIPPED] keyutils-libs-1.6.1-5.fc37.s390x.rpm: Already downloaded [SKIPPED] krb5-libs-1.20.1-3.fc38.s390x.rpm: Already downloaded [SKIPPED] libarchive-3.6.1-3.fc38.s390x.rpm: Already downloaded [SKIPPED] libblkid-2.38.1-3.fc38.s390x.rpm: Already downloaded [SKIPPED] libcap-2.48-5.fc37.s390x.rpm: Already downloaded [SKIPPED] libcap-ng-0.8.3-4.fc38.s390x.rpm: Already downloaded [SKIPPED] libdb-5.3.28-54.fc38.s390x.rpm: Already downloaded [SKIPPED] libeconf-0.4.0-4.fc37.s390x.rpm: Already downloaded [SKIPPED] libevent-2.1.12-7.fc37.s390x.rpm: Already downloaded [SKIPPED] libfdisk-2.38.1-3.fc38.s390x.rpm: Already downloaded [SKIPPED] libffi-3.4.4-1.fc38.s390x.rpm: Already downloaded [SKIPPED] libidn2-2.3.4-1.fc38.s390x.rpm: Already downloaded [SKIPPED] libmount-2.38.1-3.fc38.s390x.rpm: Already downloaded [SKIPPED] libnghttp2-1.51.0-1.fc38.s390x.rpm: Already downloaded [SKIPPED] libnsl2-2.0.0-4.fc37.s390x.rpm: Already downloaded [SKIPPED] libpkgconf-1.8.0-3.fc37.s390x.rpm: Already downloaded [SKIPPED] libpsl-0.21.1-6.fc37.s390x.rpm: Already downloaded [SKIPPED] libpwquality-1.4.5-1.fc38.s390x.rpm: Already downloaded [SKIPPED] libselinux-3.4-6.fc38.s390x.rpm: Already downloaded [SKIPPED] libsemanage-3.4-6.fc38.s390x.rpm: Already downloaded [SKIPPED] libsepol-3.4-4.fc38.s390x.rpm: Already downloaded [SKIPPED] libsigsegv-2.14-3.fc37.s390x.rpm: Already downloaded [SKIPPED] libsmartcols-2.38.1-3.fc38.s390x.rpm: Already downloaded [SKIPPED] libssh-0.10.4-2.fc38.s390x.rpm: Already downloaded [SKIPPED] libssh-config-0.10.4-2.fc38.noarch.rpm: Already downloaded [SKIPPED] libtasn1-4.19.0-1.fc38.s390x.rpm: Already downloaded [SKIPPED] libtirpc-1.3.3-0.fc37.s390x.rpm: Already downloaded [SKIPPED] libunistring-1.0-2.fc37.s390x.rpm: Already downloaded [SKIPPED] libutempter-1.2.1-7.fc37.s390x.rpm: Already downloaded [SKIPPED] libuuid-2.38.1-3.fc38.s390x.rpm: Already downloaded [SKIPPED] libverto-0.3.2-4.fc37.s390x.rpm: Already downloaded [SKIPPED] libxcrypt-4.4.33-5.fc38.s390x.rpm: Already downloaded [SKIPPED] libxml2-2.10.3-2.fc38.s390x.rpm: Already downloaded [SKIPPED] libzstd-1.5.2-3.fc37.s390x.rpm: Already downloaded [SKIPPED] lua-libs-5.4.4-6.fc38.s390x.rpm: Already downloaded [SKIPPED] lua-srpm-macros-1-7.fc37.noarch.rpm: Already downloaded [SKIPPED] lz4-libs-1.9.3-5.fc37.s390x.rpm: Already downloaded [SKIPPED] mpfr-4.1.1-2.fc38.s390x.rpm: Already downloaded [SKIPPED] ncurses-base-6.3-5.20221126.fc38.noarch.rpm: Already downloaded [SKIPPED] ncurses-libs-6.3-5.20221126.fc38.s390x.rpm: Already downloaded [SKIPPED] nettle-3.8-2.fc37.s390x.rpm: Already downloaded [SKIPPED] nim-srpm-macros-3-7.fc37.noarch.rpm: Already downloaded [SKIPPED] ocaml-srpm-macros-7-2.fc37.noarch.rpm: Already downloaded [SKIPPED] openblas-srpm-macros-2-12.fc37.noarch.rpm: Already downloaded [SKIPPED] openldap-2.6.3-1.fc38.s390x.rpm: Already downloaded [SKIPPED] openssl-libs-3.0.5-6.fc38.s390x.rpm: Already downloaded [SKIPPED] p11-kit-0.24.1-5.fc38.s390x.rpm: Already downloaded [SKIPPED] p11-kit-trust-0.24.1-5.fc38.s390x.rpm: Already downloaded [SKIPPED] package-notes-srpm-macros-0.5-6.fc38.noarch.rpm: Already downloaded [SKIPPED] pam-1.5.2-15.fc38.s390x.rpm: Already downloaded [SKIPPED] pam-libs-1.5.2-15.fc38.s390x.rpm: Already downloaded [SKIPPED] patch-2.7.6-17.fc37.s390x.rpm: Already downloaded [SKIPPED] pcre2-10.40-1.fc37.1.s390x.rpm: Already downloaded [SKIPPED] pcre2-syntax-10.40-1.fc37.1.noarch.rpm: Already downloaded [SKIPPED] perl-srpm-macros-1-47.fc38.noarch.rpm: Already downloaded [SKIPPED] pkgconf-1.8.0-3.fc37.s390x.rpm: Already downloaded [SKIPPED] pkgconf-m4-1.8.0-3.fc37.noarch.rpm: Already downloaded [SKIPPED] pkgconf-pkg-config-1.8.0-3.fc37.s390x.rpm: Already downloaded [SKIPPED] popt-1.19-1.fc38.s390x.rpm: Already downloaded [SKIPPED] publicsuffix-list-dafsa-20221208-1.fc38.noarch.rpm: Already downloaded [SKIPPED] python-srpm-macros-3.11-6.fc38.noarch.rpm: Already downloaded [SKIPPED] qt5-srpm-macros-5.15.7-1.fc38.noarch.rpm: Already downloaded [SKIPPED] readline-8.2-2.fc38.s390x.rpm: Already downloaded [SKIPPED] redhat-rpm-config-235-1.fc38.noarch.rpm: Already downloaded [SKIPPED] rpm-4.18.0-8.fc38.s390x.rpm: Already downloaded [SKIPPED] rpm-build-4.18.0-8.fc38.s390x.rpm: Already downloaded [SKIPPED] rpm-build-libs-4.18.0-8.fc38.s390x.rpm: Already downloaded [SKIPPED] rpm-libs-4.18.0-8.fc38.s390x.rpm: Already downloaded [SKIPPED] rpm-sequoia-1.2.0-1.fc38.s390x.rpm: Already downloaded [SKIPPED] rpmautospec-rpm-macros-0.3.1-1.fc38.noarch.rpm: Already downloaded [SKIPPED] rust-srpm-macros-23-1.fc38.noarch.rpm: Already downloaded [SKIPPED] sed-4.8-11.fc37.s390x.rpm: Already downloaded [SKIPPED] setup-2.14.3-1.fc38.noarch.rpm: Already downloaded [SKIPPED] shadow-utils-4.13-3.fc38.s390x.rpm: Already downloaded [SKIPPED] sqlite-libs-3.40.0-1.fc38.s390x.rpm: Already downloaded [SKIPPED] systemd-libs-252.4-598.fc38.s390x.rpm: Already downloaded [SKIPPED] tar-1.34-5.fc38.s390x.rpm: Already downloaded [SKIPPED] tzdata-2022g-1.fc38.noarch.rpm: Already downloaded [SKIPPED] unzip-6.0-58.fc38.s390x.rpm: Already downloaded [SKIPPED] util-linux-2.38.1-3.fc38.s390x.rpm: Already downloaded [SKIPPED] util-linux-core-2.38.1-3.fc38.s390x.rpm: Already downloaded [SKIPPED] which-2.21-36.fc38.s390x.rpm: Already downloaded [SKIPPED] xxhash-libs-0.8.1-3.fc37.s390x.rpm: Already downloaded [SKIPPED] xz-5.2.9-1.fc38.s390x.rpm: Already downloaded [SKIPPED] xz-libs-5.2.9-1.fc38.s390x.rpm: Already downloaded [SKIPPED] zip-3.0-35.fc38.s390x.rpm: Already downloaded [SKIPPED] zlib-1.2.13-1.fc38.s390x.rpm: Already downloaded [SKIPPED] zstd-1.5.2-3.fc37.s390x.rpm: Already downloaded fedora 1.6 MB/s | 1.6 kB 00:00 Importing GPG key 0xEB10B464: Userid : "Fedora (38) " Fingerprint: 6A51 BBAB BA3D 5467 B617 1221 809A 8D7C EB10 B464 From : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-38-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-38-primary (0xEB10B464) is already installed fedora 1.6 MB/s | 1.6 kB 00:00 Importing GPG key 0x5323552A: Userid : "Fedora (37) " Fingerprint: ACB5 EE4E 831C 74BB 7C16 8D27 F55A D3FB 5323 552A From : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-37-primary Key imported successfully Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Running scriptlet: filesystem-3.18-2.fc37.s390x 1/1 Preparing : 1/1 Installing : libgcc-13.0.0-0.4.fc38.s390x 1/153 Running scriptlet: libgcc-13.0.0-0.4.fc38.s390x 1/153 Installing : crypto-policies-20221215-1.gita4c31a3.fc38.noarc 2/153 Running scriptlet: crypto-policies-20221215-1.gita4c31a3.fc38.noarc 2/153 Installing : fedora-release-identity-basic-38-0.6.noarch 3/153 Installing : tzdata-2022g-1.fc38.noarch 4/153 Installing : rust-srpm-macros-23-1.fc38.noarch 5/153 Installing : qt5-srpm-macros-5.15.7-1.fc38.noarch 6/153 Installing : publicsuffix-list-dafsa-20221208-1.fc38.noarch 7/153 Installing : pkgconf-m4-1.8.0-3.fc37.noarch 8/153 Installing : perl-srpm-macros-1-47.fc38.noarch 9/153 Installing : pcre2-syntax-10.40-1.fc37.1.noarch 10/153 Installing : package-notes-srpm-macros-0.5-6.fc38.noarch 11/153 Installing : openblas-srpm-macros-2-12.fc37.noarch 12/153 Installing : ocaml-srpm-macros-7-2.fc37.noarch 13/153 Installing : nim-srpm-macros-3-7.fc37.noarch 14/153 Installing : ncurses-base-6.3-5.20221126.fc38.noarch 15/153 Installing : libssh-config-0.10.4-2.fc38.noarch 16/153 Installing : kernel-srpm-macros-1.0-15.fc37.noarch 17/153 Installing : gnat-srpm-macros-4-16.fc37.noarch 18/153 Installing : ghc-srpm-macros-1.5.0-7.fc37.noarch 19/153 Installing : fpc-srpm-macros-1.3-6.fc37.noarch 20/153 Installing : fedora-gpg-keys-38-0.3.noarch 21/153 Installing : fedora-release-38-0.6.noarch 22/153 Installing : fedora-release-common-38-0.6.noarch 23/153 Installing : fedora-repos-rawhide-38-0.3.noarch 24/153 Installing : fedora-repos-38-0.3.noarch 25/153 Installing : setup-2.14.3-1.fc38.noarch 26/153 warning: /etc/hosts created as /etc/hosts.rpmnew Running scriptlet: setup-2.14.3-1.fc38.noarch 26/153 Installing : filesystem-3.18-2.fc37.s390x 27/153 Installing : basesystem-11-14.fc37.noarch 28/153 Installing : glibc-gconv-extra-2.36.9000-19.fc38.s390x 29/153 Running scriptlet: glibc-gconv-extra-2.36.9000-19.fc38.s390x 29/153 Installing : ncurses-libs-6.3-5.20221126.fc38.s390x 30/153 Running scriptlet: glibc-2.36.9000-19.fc38.s390x 31/153 Installing : glibc-2.36.9000-19.fc38.s390x 31/153 Running scriptlet: glibc-2.36.9000-19.fc38.s390x 31/153 Installing : bash-5.2.9-3.fc38.s390x 32/153 Running scriptlet: bash-5.2.9-3.fc38.s390x 32/153 Installing : glibc-common-2.36.9000-19.fc38.s390x 33/153 Installing : glibc-minimal-langpack-2.36.9000-19.fc38.s390x 34/153 Installing : zlib-1.2.13-1.fc38.s390x 35/153 Installing : xz-libs-5.2.9-1.fc38.s390x 36/153 Installing : bzip2-libs-1.0.8-12.fc38.s390x 37/153 Installing : elfutils-libelf-0.188-3.fc38.s390x 38/153 Installing : gmp-1:6.2.1-3.fc38.s390x 39/153 Installing : libstdc++-13.0.0-0.4.fc38.s390x 40/153 Installing : libuuid-2.38.1-3.fc38.s390x 41/153 Installing : libzstd-1.5.2-3.fc37.s390x 42/153 Installing : popt-1.19-1.fc38.s390x 43/153 Installing : libblkid-2.38.1-3.fc38.s390x 44/153 Installing : libattr-2.5.1-5.fc38.s390x 45/153 Installing : libacl-2.3.1-4.fc38.s390x 46/153 Installing : libcap-2.48-5.fc37.s390x 47/153 Installing : libxcrypt-4.4.33-5.fc38.s390x 48/153 Installing : readline-8.2-2.fc38.s390x 49/153 Installing : lz4-libs-1.9.3-5.fc37.s390x 50/153 Installing : systemd-libs-252.4-598.fc38.s390x 51/153 Installing : mpfr-4.1.1-2.fc38.s390x 52/153 Installing : dwz-0.15-1.fc38.s390x 53/153 Installing : unzip-6.0-58.fc38.s390x 54/153 Installing : file-libs-5.42-4.fc38.s390x 55/153 Installing : file-5.42-4.fc38.s390x 56/153 Installing : sqlite-libs-3.40.0-1.fc38.s390x 57/153 Installing : alternatives-1.21-1.fc38.s390x 58/153 Installing : libcom_err-1.46.5-3.fc38.s390x 59/153 Installing : libcap-ng-0.8.3-4.fc38.s390x 60/153 Installing : audit-libs-3.0.9-2.fc38.s390x 61/153 Installing : libeconf-0.4.0-4.fc37.s390x 62/153 Installing : pam-libs-1.5.2-15.fc38.s390x 63/153 Installing : libsepol-3.4-4.fc38.s390x 64/153 Installing : libsmartcols-2.38.1-3.fc38.s390x 65/153 Installing : libunistring-1.0-2.fc37.s390x 66/153 Installing : libidn2-2.3.4-1.fc38.s390x 67/153 Installing : lua-libs-5.4.4-6.fc38.s390x 68/153 Installing : pcre2-10.40-1.fc37.1.s390x 69/153 Installing : libselinux-3.4-6.fc38.s390x 70/153 Installing : sed-4.8-11.fc37.s390x 71/153 Installing : grep-3.8-1.fc38.s390x 72/153 Installing : findutils-1:4.9.0-2.fc38.s390x 73/153 Installing : xz-5.2.9-1.fc38.s390x 74/153 Installing : libmount-2.38.1-3.fc38.s390x 75/153 Installing : util-linux-core-2.38.1-3.fc38.s390x 76/153 Installing : libsemanage-3.4-6.fc38.s390x 77/153 Installing : shadow-utils-2:4.13-3.fc38.s390x 78/153 Running scriptlet: libutempter-1.2.1-7.fc37.s390x 79/153 Installing : libutempter-1.2.1-7.fc37.s390x 79/153 Installing : tar-2:1.34-5.fc38.s390x 80/153 Installing : libpsl-0.21.1-6.fc37.s390x 81/153 Installing : zip-3.0-35.fc38.s390x 82/153 Installing : zstd-1.5.2-3.fc37.s390x 83/153 Installing : libfdisk-2.38.1-3.fc38.s390x 84/153 Installing : nettle-3.8-2.fc37.s390x 85/153 Installing : rpm-sequoia-1.2.0-1.fc38.s390x 86/153 Installing : rpm-libs-4.18.0-8.fc38.s390x 87/153 Installing : bzip2-1.0.8-12.fc38.s390x 88/153 Installing : libxml2-2.10.3-2.fc38.s390x 89/153 Installing : ed-1.18-2.fc38.s390x 90/153 Installing : patch-2.7.6-17.fc37.s390x 91/153 Installing : elfutils-default-yama-scope-0.188-3.fc38.noarch 92/153 Running scriptlet: elfutils-default-yama-scope-0.188-3.fc38.noarch 92/153 Installing : cpio-2.13-13.fc38.s390x 93/153 Installing : diffutils-3.8-3.fc38.s390x 94/153 Installing : gdbm-libs-1:1.23-2.fc38.s390x 95/153 Installing : cyrus-sasl-lib-2.1.28-8.fc38.s390x 96/153 Installing : libbrotli-1.0.9-9.fc38.s390x 97/153 Installing : libgomp-13.0.0-0.4.fc38.s390x 98/153 Installing : jansson-2.13.1-5.fc37.s390x 99/153 Installing : keyutils-libs-1.6.1-5.fc37.s390x 100/153 Installing : libdb-5.3.28-54.fc38.s390x 101/153 Installing : libffi-3.4.4-1.fc38.s390x 102/153 Installing : p11-kit-0.24.1-5.fc38.s390x 103/153 Installing : libnghttp2-1.51.0-1.fc38.s390x 104/153 Installing : libpkgconf-1.8.0-3.fc37.s390x 105/153 Installing : pkgconf-1.8.0-3.fc37.s390x 106/153 Installing : pkgconf-pkg-config-1.8.0-3.fc37.s390x 107/153 Installing : libsigsegv-2.14-3.fc37.s390x 108/153 Installing : gawk-5.1.1-4.fc38.s390x 109/153 Installing : libtasn1-4.19.0-1.fc38.s390x 110/153 Installing : p11-kit-trust-0.24.1-5.fc38.s390x 111/153 Running scriptlet: p11-kit-trust-0.24.1-5.fc38.s390x 111/153 Installing : libverto-0.3.2-4.fc37.s390x 112/153 Installing : xxhash-libs-0.8.1-3.fc37.s390x 113/153 Installing : ansible-srpm-macros-1-8.1.fc38.noarch 114/153 Installing : coreutils-common-9.1-8.fc38.s390x 115/153 Installing : openssl-libs-1:3.0.5-6.fc38.s390x 116/153 Installing : coreutils-9.1-8.fc38.s390x 117/153 Running scriptlet: ca-certificates-2022.2.54-5.fc37.noarch 118/153 Installing : ca-certificates-2022.2.54-5.fc37.noarch 118/153 Running scriptlet: ca-certificates-2022.2.54-5.fc37.noarch 118/153 Installing : krb5-libs-1.20.1-3.fc38.s390x 119/153 Installing : libtirpc-1.3.3-0.fc37.s390x 120/153 Running scriptlet: authselect-libs-1.4.2-1.fc38.s390x 121/153 Installing : authselect-libs-1.4.2-1.fc38.s390x 121/153 Installing : gzip-1.12-2.fc38.s390x 122/153 Installing : cracklib-2.9.7-30.fc38.s390x 123/153 Installing : libpwquality-1.4.5-1.fc38.s390x 124/153 Installing : authselect-1.4.2-1.fc38.s390x 125/153 Installing : libnsl2-2.0.0-4.fc37.s390x 126/153 Installing : pam-1.5.2-15.fc38.s390x 127/153 Installing : libssh-0.10.4-2.fc38.s390x 128/153 Installing : libarchive-3.6.1-3.fc38.s390x 129/153 Installing : libevent-2.1.12-7.fc37.s390x 130/153 Installing : openldap-2.6.3-1.fc38.s390x 131/153 Installing : libcurl-7.87.0-1.fc38.s390x 132/153 Installing : elfutils-libs-0.188-3.fc38.s390x 133/153 Installing : elfutils-debuginfod-client-0.188-3.fc38.s390x 134/153 Installing : binutils-gold-2.39-6.fc38.s390x 135/153 Installing : binutils-2.39-6.fc38.s390x 136/153 Running scriptlet: binutils-2.39-6.fc38.s390x 136/153 Installing : elfutils-0.188-3.fc38.s390x 137/153 Installing : gdb-minimal-12.1-10.fc38.s390x 138/153 Installing : debugedit-5.0-5.fc37.s390x 139/153 Installing : rpm-build-libs-4.18.0-8.fc38.s390x 140/153 Installing : curl-7.87.0-1.fc38.s390x 141/153 Running scriptlet: rpm-4.18.0-8.fc38.s390x 142/153 Installing : rpm-4.18.0-8.fc38.s390x 142/153 Installing : efi-srpm-macros-5-6.fc37.noarch 143/153 Installing : lua-srpm-macros-1-7.fc37.noarch 144/153 Installing : rpmautospec-rpm-macros-0.3.1-1.fc38.noarch 145/153 Installing : fonts-srpm-macros-1:2.0.5-10.fc38.noarch 146/153 Installing : go-srpm-macros-3.2.0-1.fc38.noarch 147/153 Installing : python-srpm-macros-3.11-6.fc38.noarch 148/153 Installing : redhat-rpm-config-235-1.fc38.noarch 149/153 Installing : rpm-build-4.18.0-8.fc38.s390x 150/153 Installing : util-linux-2.38.1-3.fc38.s390x 151/153 Installing : which-2.21-36.fc38.s390x 152/153 Installing : info-7.0.1-1.fc38.s390x 153/153 Running scriptlet: filesystem-3.18-2.fc37.s390x 153/153 Running scriptlet: ca-certificates-2022.2.54-5.fc37.noarch 153/153 Running scriptlet: authselect-libs-1.4.2-1.fc38.s390x 153/153 Running scriptlet: rpm-4.18.0-8.fc38.s390x 153/153 Running scriptlet: info-7.0.1-1.fc38.s390x 153/153 Verifying : alternatives-1.21-1.fc38.s390x 1/153 Verifying : authselect-1.4.2-1.fc38.s390x 2/153 Verifying : authselect-libs-1.4.2-1.fc38.s390x 3/153 Verifying : bash-5.2.9-3.fc38.s390x 4/153 Verifying : binutils-2.39-6.fc38.s390x 5/153 Verifying : binutils-gold-2.39-6.fc38.s390x 6/153 Verifying : bzip2-1.0.8-12.fc38.s390x 7/153 Verifying : bzip2-libs-1.0.8-12.fc38.s390x 8/153 Verifying : coreutils-9.1-8.fc38.s390x 9/153 Verifying : coreutils-common-9.1-8.fc38.s390x 10/153 Verifying : cpio-2.13-13.fc38.s390x 11/153 Verifying : cracklib-2.9.7-30.fc38.s390x 12/153 Verifying : curl-7.87.0-1.fc38.s390x 13/153 Verifying : cyrus-sasl-lib-2.1.28-8.fc38.s390x 14/153 Verifying : diffutils-3.8-3.fc38.s390x 15/153 Verifying : dwz-0.15-1.fc38.s390x 16/153 Verifying : ed-1.18-2.fc38.s390x 17/153 Verifying : elfutils-0.188-3.fc38.s390x 18/153 Verifying : elfutils-debuginfod-client-0.188-3.fc38.s390x 19/153 Verifying : elfutils-default-yama-scope-0.188-3.fc38.noarch 20/153 Verifying : elfutils-libelf-0.188-3.fc38.s390x 21/153 Verifying : elfutils-libs-0.188-3.fc38.s390x 22/153 Verifying : file-5.42-4.fc38.s390x 23/153 Verifying : file-libs-5.42-4.fc38.s390x 24/153 Verifying : findutils-1:4.9.0-2.fc38.s390x 25/153 Verifying : gawk-5.1.1-4.fc38.s390x 26/153 Verifying : gdbm-libs-1:1.23-2.fc38.s390x 27/153 Verifying : gmp-1:6.2.1-3.fc38.s390x 28/153 Verifying : grep-3.8-1.fc38.s390x 29/153 Verifying : gzip-1.12-2.fc38.s390x 30/153 Verifying : libacl-2.3.1-4.fc38.s390x 31/153 Verifying : libattr-2.5.1-5.fc38.s390x 32/153 Verifying : libbrotli-1.0.9-9.fc38.s390x 33/153 Verifying : libcom_err-1.46.5-3.fc38.s390x 34/153 Verifying : libcurl-7.87.0-1.fc38.s390x 35/153 Verifying : libgcc-13.0.0-0.4.fc38.s390x 36/153 Verifying : libgomp-13.0.0-0.4.fc38.s390x 37/153 Verifying : libstdc++-13.0.0-0.4.fc38.s390x 38/153 Verifying : ansible-srpm-macros-1-8.1.fc38.noarch 39/153 Verifying : audit-libs-3.0.9-2.fc38.s390x 40/153 Verifying : basesystem-11-14.fc37.noarch 41/153 Verifying : ca-certificates-2022.2.54-5.fc37.noarch 42/153 Verifying : crypto-policies-20221215-1.gita4c31a3.fc38.noarc 43/153 Verifying : debugedit-5.0-5.fc37.s390x 44/153 Verifying : efi-srpm-macros-5-6.fc37.noarch 45/153 Verifying : fedora-gpg-keys-38-0.3.noarch 46/153 Verifying : fedora-release-38-0.6.noarch 47/153 Verifying : fedora-release-common-38-0.6.noarch 48/153 Verifying : fedora-release-identity-basic-38-0.6.noarch 49/153 Verifying : fedora-repos-38-0.3.noarch 50/153 Verifying : fedora-repos-rawhide-38-0.3.noarch 51/153 Verifying : filesystem-3.18-2.fc37.s390x 52/153 Verifying : fonts-srpm-macros-1:2.0.5-10.fc38.noarch 53/153 Verifying : fpc-srpm-macros-1.3-6.fc37.noarch 54/153 Verifying : gdb-minimal-12.1-10.fc38.s390x 55/153 Verifying : ghc-srpm-macros-1.5.0-7.fc37.noarch 56/153 Verifying : glibc-2.36.9000-19.fc38.s390x 57/153 Verifying : glibc-common-2.36.9000-19.fc38.s390x 58/153 Verifying : glibc-gconv-extra-2.36.9000-19.fc38.s390x 59/153 Verifying : glibc-minimal-langpack-2.36.9000-19.fc38.s390x 60/153 Verifying : gnat-srpm-macros-4-16.fc37.noarch 61/153 Verifying : go-srpm-macros-3.2.0-1.fc38.noarch 62/153 Verifying : info-7.0.1-1.fc38.s390x 63/153 Verifying : jansson-2.13.1-5.fc37.s390x 64/153 Verifying : kernel-srpm-macros-1.0-15.fc37.noarch 65/153 Verifying : keyutils-libs-1.6.1-5.fc37.s390x 66/153 Verifying : krb5-libs-1.20.1-3.fc38.s390x 67/153 Verifying : libarchive-3.6.1-3.fc38.s390x 68/153 Verifying : libblkid-2.38.1-3.fc38.s390x 69/153 Verifying : libcap-2.48-5.fc37.s390x 70/153 Verifying : libcap-ng-0.8.3-4.fc38.s390x 71/153 Verifying : libdb-5.3.28-54.fc38.s390x 72/153 Verifying : libeconf-0.4.0-4.fc37.s390x 73/153 Verifying : libevent-2.1.12-7.fc37.s390x 74/153 Verifying : libfdisk-2.38.1-3.fc38.s390x 75/153 Verifying : libffi-3.4.4-1.fc38.s390x 76/153 Verifying : libidn2-2.3.4-1.fc38.s390x 77/153 Verifying : libmount-2.38.1-3.fc38.s390x 78/153 Verifying : libnghttp2-1.51.0-1.fc38.s390x 79/153 Verifying : libnsl2-2.0.0-4.fc37.s390x 80/153 Verifying : libpkgconf-1.8.0-3.fc37.s390x 81/153 Verifying : libpsl-0.21.1-6.fc37.s390x 82/153 Verifying : libpwquality-1.4.5-1.fc38.s390x 83/153 Verifying : libselinux-3.4-6.fc38.s390x 84/153 Verifying : libsemanage-3.4-6.fc38.s390x 85/153 Verifying : libsepol-3.4-4.fc38.s390x 86/153 Verifying : libsigsegv-2.14-3.fc37.s390x 87/153 Verifying : libsmartcols-2.38.1-3.fc38.s390x 88/153 Verifying : libssh-0.10.4-2.fc38.s390x 89/153 Verifying : libssh-config-0.10.4-2.fc38.noarch 90/153 Verifying : libtasn1-4.19.0-1.fc38.s390x 91/153 Verifying : libtirpc-1.3.3-0.fc37.s390x 92/153 Verifying : libunistring-1.0-2.fc37.s390x 93/153 Verifying : libutempter-1.2.1-7.fc37.s390x 94/153 Verifying : libuuid-2.38.1-3.fc38.s390x 95/153 Verifying : libverto-0.3.2-4.fc37.s390x 96/153 Verifying : libxcrypt-4.4.33-5.fc38.s390x 97/153 Verifying : libxml2-2.10.3-2.fc38.s390x 98/153 Verifying : libzstd-1.5.2-3.fc37.s390x 99/153 Verifying : lua-libs-5.4.4-6.fc38.s390x 100/153 Verifying : lua-srpm-macros-1-7.fc37.noarch 101/153 Verifying : lz4-libs-1.9.3-5.fc37.s390x 102/153 Verifying : mpfr-4.1.1-2.fc38.s390x 103/153 Verifying : ncurses-base-6.3-5.20221126.fc38.noarch 104/153 Verifying : ncurses-libs-6.3-5.20221126.fc38.s390x 105/153 Verifying : nettle-3.8-2.fc37.s390x 106/153 Verifying : nim-srpm-macros-3-7.fc37.noarch 107/153 Verifying : ocaml-srpm-macros-7-2.fc37.noarch 108/153 Verifying : openblas-srpm-macros-2-12.fc37.noarch 109/153 Verifying : openldap-2.6.3-1.fc38.s390x 110/153 Verifying : openssl-libs-1:3.0.5-6.fc38.s390x 111/153 Verifying : p11-kit-0.24.1-5.fc38.s390x 112/153 Verifying : p11-kit-trust-0.24.1-5.fc38.s390x 113/153 Verifying : package-notes-srpm-macros-0.5-6.fc38.noarch 114/153 Verifying : pam-1.5.2-15.fc38.s390x 115/153 Verifying : pam-libs-1.5.2-15.fc38.s390x 116/153 Verifying : patch-2.7.6-17.fc37.s390x 117/153 Verifying : pcre2-10.40-1.fc37.1.s390x 118/153 Verifying : pcre2-syntax-10.40-1.fc37.1.noarch 119/153 Verifying : perl-srpm-macros-1-47.fc38.noarch 120/153 Verifying : pkgconf-1.8.0-3.fc37.s390x 121/153 Verifying : pkgconf-m4-1.8.0-3.fc37.noarch 122/153 Verifying : pkgconf-pkg-config-1.8.0-3.fc37.s390x 123/153 Verifying : popt-1.19-1.fc38.s390x 124/153 Verifying : publicsuffix-list-dafsa-20221208-1.fc38.noarch 125/153 Verifying : python-srpm-macros-3.11-6.fc38.noarch 126/153 Verifying : qt5-srpm-macros-5.15.7-1.fc38.noarch 127/153 Verifying : readline-8.2-2.fc38.s390x 128/153 Verifying : redhat-rpm-config-235-1.fc38.noarch 129/153 Verifying : rpm-4.18.0-8.fc38.s390x 130/153 Verifying : rpm-build-4.18.0-8.fc38.s390x 131/153 Verifying : rpm-build-libs-4.18.0-8.fc38.s390x 132/153 Verifying : rpm-libs-4.18.0-8.fc38.s390x 133/153 Verifying : rpm-sequoia-1.2.0-1.fc38.s390x 134/153 Verifying : rpmautospec-rpm-macros-0.3.1-1.fc38.noarch 135/153 Verifying : rust-srpm-macros-23-1.fc38.noarch 136/153 Verifying : sed-4.8-11.fc37.s390x 137/153 Verifying : setup-2.14.3-1.fc38.noarch 138/153 Verifying : shadow-utils-2:4.13-3.fc38.s390x 139/153 Verifying : sqlite-libs-3.40.0-1.fc38.s390x 140/153 Verifying : systemd-libs-252.4-598.fc38.s390x 141/153 Verifying : tar-2:1.34-5.fc38.s390x 142/153 Verifying : tzdata-2022g-1.fc38.noarch 143/153 Verifying : unzip-6.0-58.fc38.s390x 144/153 Verifying : util-linux-2.38.1-3.fc38.s390x 145/153 Verifying : util-linux-core-2.38.1-3.fc38.s390x 146/153 Verifying : which-2.21-36.fc38.s390x 147/153 Verifying : xxhash-libs-0.8.1-3.fc37.s390x 148/153 Verifying : xz-5.2.9-1.fc38.s390x 149/153 Verifying : xz-libs-5.2.9-1.fc38.s390x 150/153 Verifying : zip-3.0-35.fc38.s390x 151/153 Verifying : zlib-1.2.13-1.fc38.s390x 152/153 Verifying : zstd-1.5.2-3.fc37.s390x 153/153 Installed: alternatives-1.21-1.fc38.s390x ansible-srpm-macros-1-8.1.fc38.noarch audit-libs-3.0.9-2.fc38.s390x authselect-1.4.2-1.fc38.s390x authselect-libs-1.4.2-1.fc38.s390x basesystem-11-14.fc37.noarch bash-5.2.9-3.fc38.s390x binutils-2.39-6.fc38.s390x binutils-gold-2.39-6.fc38.s390x bzip2-1.0.8-12.fc38.s390x bzip2-libs-1.0.8-12.fc38.s390x ca-certificates-2022.2.54-5.fc37.noarch coreutils-9.1-8.fc38.s390x coreutils-common-9.1-8.fc38.s390x cpio-2.13-13.fc38.s390x cracklib-2.9.7-30.fc38.s390x crypto-policies-20221215-1.gita4c31a3.fc38.noarch curl-7.87.0-1.fc38.s390x cyrus-sasl-lib-2.1.28-8.fc38.s390x debugedit-5.0-5.fc37.s390x diffutils-3.8-3.fc38.s390x dwz-0.15-1.fc38.s390x ed-1.18-2.fc38.s390x efi-srpm-macros-5-6.fc37.noarch elfutils-0.188-3.fc38.s390x elfutils-debuginfod-client-0.188-3.fc38.s390x elfutils-default-yama-scope-0.188-3.fc38.noarch elfutils-libelf-0.188-3.fc38.s390x elfutils-libs-0.188-3.fc38.s390x fedora-gpg-keys-38-0.3.noarch fedora-release-38-0.6.noarch fedora-release-common-38-0.6.noarch fedora-release-identity-basic-38-0.6.noarch fedora-repos-38-0.3.noarch fedora-repos-rawhide-38-0.3.noarch file-5.42-4.fc38.s390x file-libs-5.42-4.fc38.s390x filesystem-3.18-2.fc37.s390x findutils-1:4.9.0-2.fc38.s390x fonts-srpm-macros-1:2.0.5-10.fc38.noarch fpc-srpm-macros-1.3-6.fc37.noarch gawk-5.1.1-4.fc38.s390x gdb-minimal-12.1-10.fc38.s390x gdbm-libs-1:1.23-2.fc38.s390x ghc-srpm-macros-1.5.0-7.fc37.noarch glibc-2.36.9000-19.fc38.s390x glibc-common-2.36.9000-19.fc38.s390x glibc-gconv-extra-2.36.9000-19.fc38.s390x glibc-minimal-langpack-2.36.9000-19.fc38.s390x gmp-1:6.2.1-3.fc38.s390x gnat-srpm-macros-4-16.fc37.noarch go-srpm-macros-3.2.0-1.fc38.noarch grep-3.8-1.fc38.s390x gzip-1.12-2.fc38.s390x info-7.0.1-1.fc38.s390x jansson-2.13.1-5.fc37.s390x kernel-srpm-macros-1.0-15.fc37.noarch keyutils-libs-1.6.1-5.fc37.s390x krb5-libs-1.20.1-3.fc38.s390x libacl-2.3.1-4.fc38.s390x libarchive-3.6.1-3.fc38.s390x libattr-2.5.1-5.fc38.s390x libblkid-2.38.1-3.fc38.s390x libbrotli-1.0.9-9.fc38.s390x libcap-2.48-5.fc37.s390x libcap-ng-0.8.3-4.fc38.s390x libcom_err-1.46.5-3.fc38.s390x libcurl-7.87.0-1.fc38.s390x libdb-5.3.28-54.fc38.s390x libeconf-0.4.0-4.fc37.s390x libevent-2.1.12-7.fc37.s390x libfdisk-2.38.1-3.fc38.s390x libffi-3.4.4-1.fc38.s390x libgcc-13.0.0-0.4.fc38.s390x libgomp-13.0.0-0.4.fc38.s390x libidn2-2.3.4-1.fc38.s390x libmount-2.38.1-3.fc38.s390x libnghttp2-1.51.0-1.fc38.s390x libnsl2-2.0.0-4.fc37.s390x libpkgconf-1.8.0-3.fc37.s390x libpsl-0.21.1-6.fc37.s390x libpwquality-1.4.5-1.fc38.s390x libselinux-3.4-6.fc38.s390x libsemanage-3.4-6.fc38.s390x libsepol-3.4-4.fc38.s390x libsigsegv-2.14-3.fc37.s390x libsmartcols-2.38.1-3.fc38.s390x libssh-0.10.4-2.fc38.s390x libssh-config-0.10.4-2.fc38.noarch libstdc++-13.0.0-0.4.fc38.s390x libtasn1-4.19.0-1.fc38.s390x libtirpc-1.3.3-0.fc37.s390x libunistring-1.0-2.fc37.s390x libutempter-1.2.1-7.fc37.s390x libuuid-2.38.1-3.fc38.s390x libverto-0.3.2-4.fc37.s390x libxcrypt-4.4.33-5.fc38.s390x libxml2-2.10.3-2.fc38.s390x libzstd-1.5.2-3.fc37.s390x lua-libs-5.4.4-6.fc38.s390x lua-srpm-macros-1-7.fc37.noarch lz4-libs-1.9.3-5.fc37.s390x mpfr-4.1.1-2.fc38.s390x ncurses-base-6.3-5.20221126.fc38.noarch ncurses-libs-6.3-5.20221126.fc38.s390x nettle-3.8-2.fc37.s390x nim-srpm-macros-3-7.fc37.noarch ocaml-srpm-macros-7-2.fc37.noarch openblas-srpm-macros-2-12.fc37.noarch openldap-2.6.3-1.fc38.s390x openssl-libs-1:3.0.5-6.fc38.s390x p11-kit-0.24.1-5.fc38.s390x p11-kit-trust-0.24.1-5.fc38.s390x package-notes-srpm-macros-0.5-6.fc38.noarch pam-1.5.2-15.fc38.s390x pam-libs-1.5.2-15.fc38.s390x patch-2.7.6-17.fc37.s390x pcre2-10.40-1.fc37.1.s390x pcre2-syntax-10.40-1.fc37.1.noarch perl-srpm-macros-1-47.fc38.noarch pkgconf-1.8.0-3.fc37.s390x pkgconf-m4-1.8.0-3.fc37.noarch pkgconf-pkg-config-1.8.0-3.fc37.s390x popt-1.19-1.fc38.s390x publicsuffix-list-dafsa-20221208-1.fc38.noarch python-srpm-macros-3.11-6.fc38.noarch qt5-srpm-macros-5.15.7-1.fc38.noarch readline-8.2-2.fc38.s390x redhat-rpm-config-235-1.fc38.noarch rpm-4.18.0-8.fc38.s390x rpm-build-4.18.0-8.fc38.s390x rpm-build-libs-4.18.0-8.fc38.s390x rpm-libs-4.18.0-8.fc38.s390x rpm-sequoia-1.2.0-1.fc38.s390x rpmautospec-rpm-macros-0.3.1-1.fc38.noarch rust-srpm-macros-23-1.fc38.noarch sed-4.8-11.fc37.s390x setup-2.14.3-1.fc38.noarch shadow-utils-2:4.13-3.fc38.s390x sqlite-libs-3.40.0-1.fc38.s390x systemd-libs-252.4-598.fc38.s390x tar-2:1.34-5.fc38.s390x tzdata-2022g-1.fc38.noarch unzip-6.0-58.fc38.s390x util-linux-2.38.1-3.fc38.s390x util-linux-core-2.38.1-3.fc38.s390x which-2.21-36.fc38.s390x xxhash-libs-0.8.1-3.fc37.s390x xz-5.2.9-1.fc38.s390x xz-libs-5.2.9-1.fc38.s390x zip-3.0-35.fc38.s390x zlib-1.2.13-1.fc38.s390x zstd-1.5.2-3.fc37.s390x Complete! Finish: dnf install Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: libcap-ng-0.8.3-4.fc38.s390x lua-libs-5.4.4-6.fc38.s390x coreutils-common-9.1-8.fc38.s390x libffi-3.4.4-1.fc38.s390x libbrotli-1.0.9-9.fc38.s390x rpm-libs-4.18.0-8.fc38.s390x lz4-libs-1.9.3-5.fc37.s390x cpio-2.13-13.fc38.s390x crypto-policies-20221215-1.gita4c31a3.fc38.noarch grep-3.8-1.fc38.s390x lua-srpm-macros-1-7.fc37.noarch libgomp-13.0.0-0.4.fc38.s390x openssl-libs-3.0.5-6.fc38.s390x libblkid-2.38.1-3.fc38.s390x jansson-2.13.1-5.fc37.s390x patch-2.7.6-17.fc37.s390x glibc-minimal-langpack-2.36.9000-19.fc38.s390x libpsl-0.21.1-6.fc37.s390x p11-kit-trust-0.24.1-5.fc38.s390x binutils-2.39-6.fc38.s390x libcom_err-1.46.5-3.fc38.s390x glibc-2.36.9000-19.fc38.s390x cyrus-sasl-lib-2.1.28-8.fc38.s390x libattr-2.5.1-5.fc38.s390x p11-kit-0.24.1-5.fc38.s390x rpm-sequoia-1.2.0-1.fc38.s390x ed-1.18-2.fc38.s390x elfutils-debuginfod-client-0.188-3.fc38.s390x gmp-6.2.1-3.fc38.s390x libsigsegv-2.14-3.fc37.s390x gdb-minimal-12.1-10.fc38.s390x ansible-srpm-macros-1-8.1.fc38.noarch filesystem-3.18-2.fc37.s390x util-linux-2.38.1-3.fc38.s390x rpmautospec-rpm-macros-0.3.1-1.fc38.noarch libtasn1-4.19.0-1.fc38.s390x popt-1.19-1.fc38.s390x package-notes-srpm-macros-0.5-6.fc38.noarch elfutils-libelf-0.188-3.fc38.s390x shadow-utils-4.13-3.fc38.s390x basesystem-11-14.fc37.noarch efi-srpm-macros-5-6.fc37.noarch libacl-2.3.1-4.fc38.s390x glibc-common-2.36.9000-19.fc38.s390x kernel-srpm-macros-1.0-15.fc37.noarch gpg-pubkey-5323552a-6112bcdc xxhash-libs-0.8.1-3.fc37.s390x openldap-2.6.3-1.fc38.s390x libarchive-3.6.1-3.fc38.s390x gpg-pubkey-eb10b464-6202d9c6 dwz-0.15-1.fc38.s390x pkgconf-pkg-config-1.8.0-3.fc37.s390x info-7.0.1-1.fc38.s390x pam-1.5.2-15.fc38.s390x libssh-0.10.4-2.fc38.s390x sqlite-libs-3.40.0-1.fc38.s390x pkgconf-m4-1.8.0-3.fc37.noarch libevent-2.1.12-7.fc37.s390x elfutils-libs-0.188-3.fc38.s390x libpwquality-1.4.5-1.fc38.s390x audit-libs-3.0.9-2.fc38.s390x libeconf-0.4.0-4.fc37.s390x keyutils-libs-1.6.1-5.fc37.s390x unzip-6.0-58.fc38.s390x qt5-srpm-macros-5.15.7-1.fc38.noarch libselinux-3.4-6.fc38.s390x libsmartcols-2.38.1-3.fc38.s390x authselect-libs-1.4.2-1.fc38.s390x openblas-srpm-macros-2-12.fc37.noarch elfutils-0.188-3.fc38.s390x libdb-5.3.28-54.fc38.s390x libssh-config-0.10.4-2.fc38.noarch elfutils-default-yama-scope-0.188-3.fc38.noarch systemd-libs-252.4-598.fc38.s390x fedora-repos-38-0.3.noarch authselect-1.4.2-1.fc38.s390x libcurl-7.87.0-1.fc38.s390x zstd-1.5.2-3.fc37.s390x readline-8.2-2.fc38.s390x mpfr-4.1.1-2.fc38.s390x glibc-gconv-extra-2.36.9000-19.fc38.s390x nim-srpm-macros-3-7.fc37.noarch publicsuffix-list-dafsa-20221208-1.fc38.noarch ocaml-srpm-macros-7-2.fc37.noarch rpm-build-4.18.0-8.fc38.s390x perl-srpm-macros-1-47.fc38.noarch libxml2-2.10.3-2.fc38.s390x libmount-2.38.1-3.fc38.s390x alternatives-1.21-1.fc38.s390x libutempter-1.2.1-7.fc37.s390x file-libs-5.42-4.fc38.s390x ghc-srpm-macros-1.5.0-7.fc37.noarch curl-7.87.0-1.fc38.s390x which-2.21-36.fc38.s390x setup-2.14.3-1.fc38.noarch libtirpc-1.3.3-0.fc37.s390x coreutils-9.1-8.fc38.s390x pkgconf-1.8.0-3.fc37.s390x diffutils-3.8-3.fc38.s390x tzdata-2022g-1.fc38.noarch gdbm-libs-1.23-2.fc38.s390x gnat-srpm-macros-4-16.fc37.noarch fedora-release-38-0.6.noarch pam-libs-1.5.2-15.fc38.s390x libxcrypt-4.4.33-5.fc38.s390x bzip2-1.0.8-12.fc38.s390x redhat-rpm-config-235-1.fc38.noarch fedora-release-common-38-0.6.noarch rust-srpm-macros-23-1.fc38.noarch xz-5.2.9-1.fc38.s390x nettle-3.8-2.fc37.s390x fpc-srpm-macros-1.3-6.fc37.noarch pcre2-10.40-1.fc37.1.s390x pcre2-syntax-10.40-1.fc37.1.noarch python-srpm-macros-3.11-6.fc38.noarch libunistring-1.0-2.fc37.s390x xz-libs-5.2.9-1.fc38.s390x rpm-build-libs-4.18.0-8.fc38.s390x fonts-srpm-macros-2.0.5-10.fc38.noarch tar-1.34-5.fc38.s390x util-linux-core-2.38.1-3.fc38.s390x go-srpm-macros-3.2.0-1.fc38.noarch zlib-1.2.13-1.fc38.s390x krb5-libs-1.20.1-3.fc38.s390x rpm-4.18.0-8.fc38.s390x libsemanage-3.4-6.fc38.s390x file-5.42-4.fc38.s390x ncurses-base-6.3-5.20221126.fc38.noarch fedora-release-identity-basic-38-0.6.noarch bzip2-libs-1.0.8-12.fc38.s390x libidn2-2.3.4-1.fc38.s390x gawk-5.1.1-4.fc38.s390x libpkgconf-1.8.0-3.fc37.s390x libnsl2-2.0.0-4.fc37.s390x libstdc++-13.0.0-0.4.fc38.s390x findutils-4.9.0-2.fc38.s390x cracklib-2.9.7-30.fc38.s390x fedora-repos-rawhide-38-0.3.noarch libzstd-1.5.2-3.fc37.s390x debugedit-5.0-5.fc37.s390x bash-5.2.9-3.fc38.s390x zip-3.0-35.fc38.s390x libfdisk-2.38.1-3.fc38.s390x ncurses-libs-6.3-5.20221126.fc38.s390x libsepol-3.4-4.fc38.s390x libverto-0.3.2-4.fc37.s390x binutils-gold-2.39-6.fc38.s390x libnghttp2-1.51.0-1.fc38.s390x fedora-gpg-keys-38-0.3.noarch libuuid-2.38.1-3.fc38.s390x sed-4.8-11.fc37.s390x ca-certificates-2022.2.54-5.fc37.noarch gzip-1.12-2.fc38.s390x libgcc-13.0.0-0.4.fc38.s390x libcap-2.48-5.fc37.s390x Start: buildsrpm Start: rpmbuild -bs Building target platforms: s390x Building for target s390x setting SOURCE_DATE_EPOCH=1660521600 Wrote: /builddir/build/SRPMS/htslib-1.15.1-1.fc38.src.rpm Finish: rpmbuild -bs cp: ‘var/lib/mock/fedora-rawhide-s390x-1671942858.428762/root/var/log’: No such file or directory INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-s390x-1671942858.428762/root/var/log/dnf.rpm.log /var/lib/mock/fedora-rawhide-s390x-1671942858.428762/root/var/log/dnf.librepo.log /var/lib/mock/fedora-rawhide-s390x-1671942858.428762/root/var/log/dnf.log Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-xbkpkar1/htslib/htslib.spec) Config(child) 1 minutes 42 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 (timeout=115200): unbuffer mock --rebuild /var/lib/copr-rpmbuild/results/htslib-1.15.1-1.fc38.src.rpm --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1671942858.428762 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 3.5 starting (python version = 3.11.0, NVR = mock-3.5-1.fc37)... 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/results/htslib-1.15.1-1.fc38.src.rpm) Config(fedora-rawhide-s390x) Start: clean chroot Finish: clean chroot Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-s390x-bootstrap-1671942858.428762/root. INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-s390x-bootstrap-1671942858.428762/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: enabled HW Info plugin Mock Version: 3.5 INFO: Mock Version: 3.5 Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-s390x-1671942858.428762/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 Mock Version: 3.5 INFO: Mock Version: 3.5 Start: dnf update No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 599 B/s | 3.0 kB 00:05 Copr repository 2.8 MB/s | 16 MB 00:05 Additional repo https_jakub_fedorapeople_org_fe 4.2 kB/s | 3.0 kB 00:00 fedora 8.3 kB/s | 6.3 kB 00:00 Dependencies resolved. Nothing to do. Complete! Finish: dnf update Finish: chroot init Start: build phase for htslib-1.15.1-1.fc38.src.rpm Start: build setup for htslib-1.15.1-1.fc38.src.rpm Building target platforms: s390x Building for target s390x setting SOURCE_DATE_EPOCH=1660521600 Wrote: /builddir/build/SRPMS/htslib-1.15.1-1.fc38.src.rpm No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 3.8 kB/s | 3.0 kB 00:00 Copr repository 21 MB/s | 16 MB 00:00 Additional repo https_jakub_fedorapeople_org_fe 4.2 kB/s | 3.0 kB 00:00 fedora 8.4 kB/s | 6.3 kB 00:00 Dependencies resolved. ============================================================================================================ Package Arch Version Repository Size ============================================================================================================ Installing: bzip2-devel s390x 1.0.8-12.fc38 copr_base 214 k gcc s390x 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 28 M libcurl-devel s390x 7.87.0-1.fc38 copr_base 895 k make s390x 1:4.3-11.fc37 fedora 536 k openssl-devel s390x 1:3.0.5-6.fc38 fedora 3.1 M perl-Data-Dumper s390x 2.184-490.fc37 fedora 56 k perl-FindBin noarch 1.53-492.fc38 fedora 17 k perl-Getopt-Long noarch 1:2.54-1.fc38 fedora 60 k perl-interpreter s390x 4:5.36.0-492.fc38 fedora 75 k perl-lib s390x 0.65-492.fc38 fedora 18 k xz-devel s390x 5.2.9-1.fc38 fedora 58 k zlib-devel s390x 1.2.13-1.fc38 fedora 45 k Installing dependencies: annobin-docs noarch 10.99-1.0.1.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 93 k annobin-plugin-gcc s390x 10.99-1.0.1.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 888 k cpp s390x 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 8.9 M gc s390x 8.2.2-1.fc38 copr_base 114 k gcc-plugin-annobin s390x 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 28 k glibc-devel s390x 2.36.9000-19.fc38 fedora 55 k glibc-headers-s390 noarch 2.36.9000-19.fc38 fedora 516 k groff-base s390x 1.22.4-10.fc38 copr_base 1.1 M guile22 s390x 2.2.7-6.fc38 copr_base 6.4 M kernel-headers s390x 6.1.0-1.fc38 fedora 1.5 M libasan s390x 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 492 k libatomic s390x 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 18 k libmpc s390x 1.2.1-5.fc37 fedora 61 k libtool-ltdl s390x 2.4.7-3.0.1.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 38 k libubsan s390x 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 203 k libxcrypt-devel s390x 4.4.33-5.fc38 fedora 30 k ncurses s390x 6.3-5.20221126.fc38 fedora 413 k perl-B s390x 1.83-492.fc38 fedora 184 k perl-Carp noarch 1.52-489.fc37 fedora 29 k perl-Class-Struct noarch 0.66-492.fc38 fedora 25 k perl-DynaLoader s390x 1.52-492.fc38 fedora 29 k perl-Encode s390x 4:3.19-492.fc38 fedora 1.7 M perl-Errno s390x 1.36-492.fc38 fedora 18 k perl-Exporter noarch 5.77-489.fc37 fedora 31 k perl-Fcntl s390x 1.15-492.fc38 fedora 23 k perl-File-Basename noarch 2.85-492.fc38 fedora 20 k perl-File-Path noarch 2.18-489.fc37 fedora 35 k perl-File-Temp noarch 1:0.231.100-489.fc37 fedora 59 k perl-File-stat noarch 1.12-492.fc38 fedora 20 k perl-Getopt-Std noarch 1.13-492.fc38 fedora 19 k perl-HTTP-Tiny noarch 0.082-1.fc37 fedora 55 k perl-IO s390x 1.50-492.fc38 fedora 95 k perl-IPC-Open3 noarch 1.22-492.fc38 fedora 26 k perl-MIME-Base64 s390x 3.16-489.fc37 fedora 30 k perl-POSIX s390x 2.03-492.fc38 fedora 99 k perl-PathTools s390x 3.84-489.fc37 fedora 89 k perl-Pod-Escapes noarch 1:1.07-489.fc37 fedora 20 k perl-Pod-Perldoc noarch 3.28.01-490.fc37 fedora 90 k perl-Pod-Simple noarch 1:3.43-490.fc37 fedora 225 k perl-Pod-Usage noarch 4:2.03-3.fc37 fedora 40 k perl-Scalar-List-Utils s390x 5:1.63-489.fc38 fedora 71 k perl-SelectSaver noarch 1.02-492.fc38 fedora 15 k perl-Socket s390x 4:2.036-1.fc38 fedora 55 k perl-Storable s390x 1:3.26-489.fc37 fedora 93 k perl-Symbol noarch 1.09-492.fc38 fedora 17 k perl-Term-ANSIColor noarch 5.01-490.fc37 fedora 48 k perl-Term-Cap noarch 1.17-489.fc37 fedora 22 k perl-Text-ParseWords noarch 3.31-489.fc37 fedora 16 k perl-Text-Tabs+Wrap noarch 2021.0814-489.fc37 fedora 22 k perl-Time-Local noarch 2:1.300-489.fc37 fedora 33 k perl-constant noarch 1.33-490.fc37 fedora 23 k perl-if noarch 0.61.000-492.fc38 fedora 17 k perl-libs s390x 4:5.36.0-492.fc38 fedora 2.2 M perl-mro s390x 1.26-492.fc38 fedora 31 k perl-overload noarch 1.35-492.fc38 fedora 49 k perl-overloading noarch 0.02-492.fc38 fedora 16 k perl-parent noarch 1:0.239-1.fc38 fedora 14 k perl-podlators noarch 1:5.00-1.fc38 fedora 127 k perl-vars noarch 1.05-492.fc38 fedora 16 k Transaction Summary ============================================================================================================ Install 71 Packages Total size: 60 M Total download size: 1.2 M Installed size: 183 M Downloading Packages: [SKIPPED] gc-8.2.2-1.fc38.s390x.rpm: Already downloaded [SKIPPED] groff-base-1.22.4-10.fc38.s390x.rpm: Already downloaded [SKIPPED] guile22-2.2.7-6.fc38.s390x.rpm: Already downloaded [SKIPPED] annobin-docs-10.99-1.0.1.fc38.noarch.rpm: Already downloaded [SKIPPED] annobin-plugin-gcc-10.99-1.0.1.fc38.s390x.rpm: Already downloaded [SKIPPED] cpp-13.0.0-0.4.fc38.s390x.rpm: Already downloaded [SKIPPED] gcc-13.0.0-0.4.fc38.s390x.rpm: Already downloaded [SKIPPED] gcc-plugin-annobin-13.0.0-0.4.fc38.s390x.rpm: Already downloaded [SKIPPED] libasan-13.0.0-0.4.fc38.s390x.rpm: Already downloaded [SKIPPED] libatomic-13.0.0-0.4.fc38.s390x.rpm: Already downloaded [SKIPPED] libtool-ltdl-2.4.7-3.0.1.fc38.s390x.rpm: Already downloaded [SKIPPED] libubsan-13.0.0-0.4.fc38.s390x.rpm: Already downloaded [SKIPPED] glibc-devel-2.36.9000-19.fc38.s390x.rpm: Already downloaded [SKIPPED] glibc-headers-s390-2.36.9000-19.fc38.noarch.rpm: Already downloaded [SKIPPED] kernel-headers-6.1.0-1.fc38.s390x.rpm: Already downloaded [SKIPPED] libmpc-1.2.1-5.fc37.s390x.rpm: Already downloaded [SKIPPED] libxcrypt-devel-4.4.33-5.fc38.s390x.rpm: Already downloaded [SKIPPED] make-4.3-11.fc37.s390x.rpm: Already downloaded [SKIPPED] ncurses-6.3-5.20221126.fc38.s390x.rpm: Already downloaded [SKIPPED] openssl-devel-3.0.5-6.fc38.s390x.rpm: Already downloaded [SKIPPED] perl-B-1.83-492.fc38.s390x.rpm: Already downloaded [SKIPPED] perl-Carp-1.52-489.fc37.noarch.rpm: Already downloaded [SKIPPED] perl-Class-Struct-0.66-492.fc38.noarch.rpm: Already downloaded [SKIPPED] perl-Data-Dumper-2.184-490.fc37.s390x.rpm: Already downloaded [SKIPPED] perl-DynaLoader-1.52-492.fc38.s390x.rpm: Already downloaded [SKIPPED] perl-Encode-3.19-492.fc38.s390x.rpm: Already downloaded [SKIPPED] perl-Errno-1.36-492.fc38.s390x.rpm: Already downloaded [SKIPPED] perl-Exporter-5.77-489.fc37.noarch.rpm: Already downloaded [SKIPPED] perl-Fcntl-1.15-492.fc38.s390x.rpm: Already downloaded [SKIPPED] perl-File-Basename-2.85-492.fc38.noarch.rpm: Already downloaded [SKIPPED] perl-File-Path-2.18-489.fc37.noarch.rpm: Already downloaded [SKIPPED] perl-File-Temp-0.231.100-489.fc37.noarch.rpm: Already downloaded [SKIPPED] perl-File-stat-1.12-492.fc38.noarch.rpm: Already downloaded [SKIPPED] perl-Getopt-Long-2.54-1.fc38.noarch.rpm: Already downloaded [SKIPPED] perl-Getopt-Std-1.13-492.fc38.noarch.rpm: Already downloaded [SKIPPED] perl-HTTP-Tiny-0.082-1.fc37.noarch.rpm: Already downloaded [SKIPPED] perl-IO-1.50-492.fc38.s390x.rpm: Already downloaded [SKIPPED] perl-IPC-Open3-1.22-492.fc38.noarch.rpm: Already downloaded [SKIPPED] perl-MIME-Base64-3.16-489.fc37.s390x.rpm: Already downloaded [SKIPPED] perl-POSIX-2.03-492.fc38.s390x.rpm: Already downloaded [SKIPPED] perl-PathTools-3.84-489.fc37.s390x.rpm: Already downloaded [SKIPPED] perl-Pod-Escapes-1.07-489.fc37.noarch.rpm: Already downloaded [SKIPPED] perl-Pod-Perldoc-3.28.01-490.fc37.noarch.rpm: Already downloaded [SKIPPED] perl-Pod-Simple-3.43-490.fc37.noarch.rpm: Already downloaded [SKIPPED] perl-Pod-Usage-2.03-3.fc37.noarch.rpm: Already downloaded [SKIPPED] perl-Scalar-List-Utils-1.63-489.fc38.s390x.rpm: Already downloaded [SKIPPED] perl-SelectSaver-1.02-492.fc38.noarch.rpm: Already downloaded [SKIPPED] perl-Socket-2.036-1.fc38.s390x.rpm: Already downloaded [SKIPPED] perl-Storable-3.26-489.fc37.s390x.rpm: Already downloaded [SKIPPED] perl-Symbol-1.09-492.fc38.noarch.rpm: Already downloaded [SKIPPED] perl-Term-ANSIColor-5.01-490.fc37.noarch.rpm: Already downloaded [SKIPPED] perl-Term-Cap-1.17-489.fc37.noarch.rpm: Already downloaded [SKIPPED] perl-Text-ParseWords-3.31-489.fc37.noarch.rpm: Already downloaded [SKIPPED] perl-Text-Tabs+Wrap-2021.0814-489.fc37.noarch.rpm: Already downloaded [SKIPPED] perl-Time-Local-1.300-489.fc37.noarch.rpm: Already downloaded [SKIPPED] perl-constant-1.33-490.fc37.noarch.rpm: Already downloaded [SKIPPED] perl-if-0.61.000-492.fc38.noarch.rpm: Already downloaded [SKIPPED] perl-interpreter-5.36.0-492.fc38.s390x.rpm: Already downloaded [SKIPPED] perl-libs-5.36.0-492.fc38.s390x.rpm: Already downloaded [SKIPPED] perl-mro-1.26-492.fc38.s390x.rpm: Already downloaded [SKIPPED] perl-overload-1.35-492.fc38.noarch.rpm: Already downloaded [SKIPPED] perl-overloading-0.02-492.fc38.noarch.rpm: Already downloaded [SKIPPED] perl-parent-0.239-1.fc38.noarch.rpm: Already downloaded [SKIPPED] perl-podlators-5.00-1.fc38.noarch.rpm: Already downloaded [SKIPPED] perl-vars-1.05-492.fc38.noarch.rpm: Already downloaded [SKIPPED] zlib-devel-1.2.13-1.fc38.s390x.rpm: Already downloaded (67/71): bzip2-devel-1.0.8-12.fc38.s390x.rpm 3.8 MB/s | 214 kB 00:00 (68/71): libcurl-devel-7.87.0-1.fc38.s390x.rpm 177 kB/s | 895 kB 00:05 (69/71): perl-lib-0.65-492.fc38.s390x.rpm 3.4 kB/s | 18 kB 00:05 (70/71): perl-FindBin-1.53-492.fc38.noarch.rpm 3.2 kB/s | 17 kB 00:05 (71/71): xz-devel-5.2.9-1.fc38.s390x.rpm 102 kB/s | 58 kB 00:00 -------------------------------------------------------------------------------- Total 186 kB/s | 1.2 MB 00:06 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Installing : libmpc-1.2.1-5.fc37.s390x 1/71 Installing : cpp-13.0.0-0.4.fc38.s390x 2/71 Installing : ncurses-6.3-5.20221126.fc38.s390x 3/71 Installing : kernel-headers-6.1.0-1.fc38.s390x 4/71 Installing : glibc-headers-s390-2.36.9000-19.fc38.noarch 5/71 Installing : libxcrypt-devel-4.4.33-5.fc38.s390x 6/71 Installing : glibc-devel-2.36.9000-19.fc38.s390x 7/71 Installing : libubsan-13.0.0-0.4.fc38.s390x 8/71 Installing : libtool-ltdl-2.4.7-3.0.1.fc38.s390x 9/71 Installing : libatomic-13.0.0-0.4.fc38.s390x 10/71 Installing : libasan-13.0.0-0.4.fc38.s390x 11/71 Installing : annobin-docs-10.99-1.0.1.fc38.noarch 12/71 Running scriptlet: groff-base-1.22.4-10.fc38.s390x 13/71 Installing : groff-base-1.22.4-10.fc38.s390x 13/71 Running scriptlet: groff-base-1.22.4-10.fc38.s390x 13/71 Installing : perl-Text-Tabs+Wrap-2021.0814-489.fc37.noarch 14/71 Installing : perl-if-0.61.000-492.fc38.noarch 15/71 Installing : perl-Time-Local-2:1.300-489.fc37.noarch 16/71 Installing : perl-File-Path-2.18-489.fc37.noarch 17/71 Installing : perl-Pod-Escapes-1:1.07-489.fc37.noarch 18/71 Installing : perl-Class-Struct-0.66-492.fc38.noarch 19/71 Installing : perl-POSIX-2.03-492.fc38.s390x 20/71 Installing : perl-Term-ANSIColor-5.01-490.fc37.noarch 21/71 Installing : perl-IPC-Open3-1.22-492.fc38.noarch 22/71 Installing : perl-HTTP-Tiny-0.082-1.fc37.noarch 23/71 Installing : perl-File-Temp-1:0.231.100-489.fc37.noarch 24/71 Installing : perl-Term-Cap-1.17-489.fc37.noarch 25/71 Installing : perl-Pod-Simple-1:3.43-490.fc37.noarch 26/71 Installing : perl-Socket-4:2.036-1.fc38.s390x 27/71 Installing : perl-SelectSaver-1.02-492.fc38.noarch 28/71 Installing : perl-Symbol-1.09-492.fc38.noarch 29/71 Installing : perl-File-stat-1.12-492.fc38.noarch 30/71 Installing : perl-podlators-1:5.00-1.fc38.noarch 31/71 Installing : perl-Pod-Perldoc-3.28.01-490.fc37.noarch 32/71 Installing : perl-Fcntl-1.15-492.fc38.s390x 33/71 Installing : perl-Text-ParseWords-3.31-489.fc37.noarch 34/71 Installing : perl-mro-1.26-492.fc38.s390x 35/71 Installing : perl-IO-1.50-492.fc38.s390x 36/71 Installing : perl-overloading-0.02-492.fc38.noarch 37/71 Installing : perl-Pod-Usage-4:2.03-3.fc37.noarch 38/71 Installing : perl-Errno-1.36-492.fc38.s390x 39/71 Installing : perl-File-Basename-2.85-492.fc38.noarch 40/71 Installing : perl-Getopt-Std-1.13-492.fc38.noarch 41/71 Installing : perl-MIME-Base64-3.16-489.fc37.s390x 42/71 Installing : perl-Scalar-List-Utils-5:1.63-489.fc38.s390x 43/71 Installing : perl-constant-1.33-490.fc37.noarch 44/71 Installing : perl-Storable-1:3.26-489.fc37.s390x 45/71 Installing : perl-overload-1.35-492.fc38.noarch 46/71 Installing : perl-parent-1:0.239-1.fc38.noarch 47/71 Installing : perl-vars-1.05-492.fc38.noarch 48/71 Installing : perl-Getopt-Long-1:2.54-1.fc38.noarch 49/71 Installing : perl-Carp-1.52-489.fc37.noarch 50/71 Installing : perl-Exporter-5.77-489.fc37.noarch 51/71 Installing : perl-PathTools-3.84-489.fc37.s390x 52/71 Installing : perl-DynaLoader-1.52-492.fc38.s390x 53/71 Installing : perl-Encode-4:3.19-492.fc38.s390x 54/71 Installing : perl-libs-4:5.36.0-492.fc38.s390x 55/71 Installing : perl-interpreter-4:5.36.0-492.fc38.s390x 56/71 Installing : perl-Data-Dumper-2.184-490.fc37.s390x 57/71 Installing : perl-B-1.83-492.fc38.s390x 58/71 Installing : gc-8.2.2-1.fc38.s390x 59/71 Installing : guile22-2.2.7-6.fc38.s390x 60/71 Installing : make-1:4.3-11.fc37.s390x 61/71 Installing : gcc-13.0.0-0.4.fc38.s390x 62/71 Running scriptlet: gcc-13.0.0-0.4.fc38.s390x 62/71 Installing : annobin-plugin-gcc-10.99-1.0.1.fc38.s390x 63/71 Running scriptlet: annobin-plugin-gcc-10.99-1.0.1.fc38.s390x 63/71 Installing : gcc-plugin-annobin-13.0.0-0.4.fc38.s390x 64/71 Installing : perl-FindBin-1.53-492.fc38.noarch 65/71 Installing : perl-lib-0.65-492.fc38.s390x 66/71 Installing : zlib-devel-1.2.13-1.fc38.s390x 67/71 Installing : xz-devel-5.2.9-1.fc38.s390x 68/71 Installing : openssl-devel-1:3.0.5-6.fc38.s390x 69/71 Installing : libcurl-devel-7.87.0-1.fc38.s390x 70/71 Installing : bzip2-devel-1.0.8-12.fc38.s390x 71/71 Running scriptlet: bzip2-devel-1.0.8-12.fc38.s390x 71/71 Verifying : bzip2-devel-1.0.8-12.fc38.s390x 1/71 Verifying : gc-8.2.2-1.fc38.s390x 2/71 Verifying : groff-base-1.22.4-10.fc38.s390x 3/71 Verifying : guile22-2.2.7-6.fc38.s390x 4/71 Verifying : libcurl-devel-7.87.0-1.fc38.s390x 5/71 Verifying : annobin-docs-10.99-1.0.1.fc38.noarch 6/71 Verifying : annobin-plugin-gcc-10.99-1.0.1.fc38.s390x 7/71 Verifying : cpp-13.0.0-0.4.fc38.s390x 8/71 Verifying : gcc-13.0.0-0.4.fc38.s390x 9/71 Verifying : gcc-plugin-annobin-13.0.0-0.4.fc38.s390x 10/71 Verifying : libasan-13.0.0-0.4.fc38.s390x 11/71 Verifying : libatomic-13.0.0-0.4.fc38.s390x 12/71 Verifying : libtool-ltdl-2.4.7-3.0.1.fc38.s390x 13/71 Verifying : libubsan-13.0.0-0.4.fc38.s390x 14/71 Verifying : glibc-devel-2.36.9000-19.fc38.s390x 15/71 Verifying : glibc-headers-s390-2.36.9000-19.fc38.noarch 16/71 Verifying : kernel-headers-6.1.0-1.fc38.s390x 17/71 Verifying : libmpc-1.2.1-5.fc37.s390x 18/71 Verifying : libxcrypt-devel-4.4.33-5.fc38.s390x 19/71 Verifying : make-1:4.3-11.fc37.s390x 20/71 Verifying : ncurses-6.3-5.20221126.fc38.s390x 21/71 Verifying : openssl-devel-1:3.0.5-6.fc38.s390x 22/71 Verifying : perl-B-1.83-492.fc38.s390x 23/71 Verifying : perl-Carp-1.52-489.fc37.noarch 24/71 Verifying : perl-Class-Struct-0.66-492.fc38.noarch 25/71 Verifying : perl-Data-Dumper-2.184-490.fc37.s390x 26/71 Verifying : perl-DynaLoader-1.52-492.fc38.s390x 27/71 Verifying : perl-Encode-4:3.19-492.fc38.s390x 28/71 Verifying : perl-Errno-1.36-492.fc38.s390x 29/71 Verifying : perl-Exporter-5.77-489.fc37.noarch 30/71 Verifying : perl-Fcntl-1.15-492.fc38.s390x 31/71 Verifying : perl-File-Basename-2.85-492.fc38.noarch 32/71 Verifying : perl-File-Path-2.18-489.fc37.noarch 33/71 Verifying : perl-File-Temp-1:0.231.100-489.fc37.noarch 34/71 Verifying : perl-File-stat-1.12-492.fc38.noarch 35/71 Verifying : perl-FindBin-1.53-492.fc38.noarch 36/71 Verifying : perl-Getopt-Long-1:2.54-1.fc38.noarch 37/71 Verifying : perl-Getopt-Std-1.13-492.fc38.noarch 38/71 Verifying : perl-HTTP-Tiny-0.082-1.fc37.noarch 39/71 Verifying : perl-IO-1.50-492.fc38.s390x 40/71 Verifying : perl-IPC-Open3-1.22-492.fc38.noarch 41/71 Verifying : perl-MIME-Base64-3.16-489.fc37.s390x 42/71 Verifying : perl-POSIX-2.03-492.fc38.s390x 43/71 Verifying : perl-PathTools-3.84-489.fc37.s390x 44/71 Verifying : perl-Pod-Escapes-1:1.07-489.fc37.noarch 45/71 Verifying : perl-Pod-Perldoc-3.28.01-490.fc37.noarch 46/71 Verifying : perl-Pod-Simple-1:3.43-490.fc37.noarch 47/71 Verifying : perl-Pod-Usage-4:2.03-3.fc37.noarch 48/71 Verifying : perl-Scalar-List-Utils-5:1.63-489.fc38.s390x 49/71 Verifying : perl-SelectSaver-1.02-492.fc38.noarch 50/71 Verifying : perl-Socket-4:2.036-1.fc38.s390x 51/71 Verifying : perl-Storable-1:3.26-489.fc37.s390x 52/71 Verifying : perl-Symbol-1.09-492.fc38.noarch 53/71 Verifying : perl-Term-ANSIColor-5.01-490.fc37.noarch 54/71 Verifying : perl-Term-Cap-1.17-489.fc37.noarch 55/71 Verifying : perl-Text-ParseWords-3.31-489.fc37.noarch 56/71 Verifying : perl-Text-Tabs+Wrap-2021.0814-489.fc37.noarch 57/71 Verifying : perl-Time-Local-2:1.300-489.fc37.noarch 58/71 Verifying : perl-constant-1.33-490.fc37.noarch 59/71 Verifying : perl-if-0.61.000-492.fc38.noarch 60/71 Verifying : perl-interpreter-4:5.36.0-492.fc38.s390x 61/71 Verifying : perl-lib-0.65-492.fc38.s390x 62/71 Verifying : perl-libs-4:5.36.0-492.fc38.s390x 63/71 Verifying : perl-mro-1.26-492.fc38.s390x 64/71 Verifying : perl-overload-1.35-492.fc38.noarch 65/71 Verifying : perl-overloading-0.02-492.fc38.noarch 66/71 Verifying : perl-parent-1:0.239-1.fc38.noarch 67/71 Verifying : perl-podlators-1:5.00-1.fc38.noarch 68/71 Verifying : perl-vars-1.05-492.fc38.noarch 69/71 Verifying : xz-devel-5.2.9-1.fc38.s390x 70/71 Verifying : zlib-devel-1.2.13-1.fc38.s390x 71/71 Installed: annobin-docs-10.99-1.0.1.fc38.noarch annobin-plugin-gcc-10.99-1.0.1.fc38.s390x bzip2-devel-1.0.8-12.fc38.s390x cpp-13.0.0-0.4.fc38.s390x gc-8.2.2-1.fc38.s390x gcc-13.0.0-0.4.fc38.s390x gcc-plugin-annobin-13.0.0-0.4.fc38.s390x glibc-devel-2.36.9000-19.fc38.s390x glibc-headers-s390-2.36.9000-19.fc38.noarch groff-base-1.22.4-10.fc38.s390x guile22-2.2.7-6.fc38.s390x kernel-headers-6.1.0-1.fc38.s390x libasan-13.0.0-0.4.fc38.s390x libatomic-13.0.0-0.4.fc38.s390x libcurl-devel-7.87.0-1.fc38.s390x libmpc-1.2.1-5.fc37.s390x libtool-ltdl-2.4.7-3.0.1.fc38.s390x libubsan-13.0.0-0.4.fc38.s390x libxcrypt-devel-4.4.33-5.fc38.s390x make-1:4.3-11.fc37.s390x ncurses-6.3-5.20221126.fc38.s390x openssl-devel-1:3.0.5-6.fc38.s390x perl-B-1.83-492.fc38.s390x perl-Carp-1.52-489.fc37.noarch perl-Class-Struct-0.66-492.fc38.noarch perl-Data-Dumper-2.184-490.fc37.s390x perl-DynaLoader-1.52-492.fc38.s390x perl-Encode-4:3.19-492.fc38.s390x perl-Errno-1.36-492.fc38.s390x perl-Exporter-5.77-489.fc37.noarch perl-Fcntl-1.15-492.fc38.s390x perl-File-Basename-2.85-492.fc38.noarch perl-File-Path-2.18-489.fc37.noarch perl-File-Temp-1:0.231.100-489.fc37.noarch perl-File-stat-1.12-492.fc38.noarch perl-FindBin-1.53-492.fc38.noarch perl-Getopt-Long-1:2.54-1.fc38.noarch perl-Getopt-Std-1.13-492.fc38.noarch perl-HTTP-Tiny-0.082-1.fc37.noarch perl-IO-1.50-492.fc38.s390x perl-IPC-Open3-1.22-492.fc38.noarch perl-MIME-Base64-3.16-489.fc37.s390x perl-POSIX-2.03-492.fc38.s390x perl-PathTools-3.84-489.fc37.s390x perl-Pod-Escapes-1:1.07-489.fc37.noarch perl-Pod-Perldoc-3.28.01-490.fc37.noarch perl-Pod-Simple-1:3.43-490.fc37.noarch perl-Pod-Usage-4:2.03-3.fc37.noarch perl-Scalar-List-Utils-5:1.63-489.fc38.s390x perl-SelectSaver-1.02-492.fc38.noarch perl-Socket-4:2.036-1.fc38.s390x perl-Storable-1:3.26-489.fc37.s390x perl-Symbol-1.09-492.fc38.noarch perl-Term-ANSIColor-5.01-490.fc37.noarch perl-Term-Cap-1.17-489.fc37.noarch perl-Text-ParseWords-3.31-489.fc37.noarch perl-Text-Tabs+Wrap-2021.0814-489.fc37.noarch perl-Time-Local-2:1.300-489.fc37.noarch perl-constant-1.33-490.fc37.noarch perl-if-0.61.000-492.fc38.noarch perl-interpreter-4:5.36.0-492.fc38.s390x perl-lib-0.65-492.fc38.s390x perl-libs-4:5.36.0-492.fc38.s390x perl-mro-1.26-492.fc38.s390x perl-overload-1.35-492.fc38.noarch perl-overloading-0.02-492.fc38.noarch perl-parent-1:0.239-1.fc38.noarch perl-podlators-1:5.00-1.fc38.noarch perl-vars-1.05-492.fc38.noarch xz-devel-5.2.9-1.fc38.s390x zlib-devel-1.2.13-1.fc38.s390x Complete! Finish: build setup for htslib-1.15.1-1.fc38.src.rpm Start: rpmbuild htslib-1.15.1-1.fc38.src.rpm Building target platforms: s390x Building for target s390x setting SOURCE_DATE_EPOCH=1660521600 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.3u2vl3 + 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 + /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.sLVtyf + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=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,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 + 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,-D_FORTIFY_SOURCE=2 -Wp,-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,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 + 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 2022-12-25 04:36:46.345505494 +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* .* \\(.*\\)$/extern char \\1;/p'\''"#' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + '[' 1 = 1 ']' +++ dirname ./configure ++ find . -name config.guess -o -name config.sub + '[' 1 = 1 ']' + '[' x '!=' 'x-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' ']' ++ find . -name ltmain.sh ++ grep -q runstatedir=DIR ./configure ++ echo --runstatedir=/run + ./configure --build=s390x-redhat-linux-gnu --host=s390x-redhat-linux-gnu --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/libexec --localstatedir=/var --runstatedir=/run --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info 'CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection' 'LDFLAGS=-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes' --prefix=/usr --libdir=/usr/lib64 --enable-plugins '--with-plugin-path=/usr/local/libexec/htslib:$(plugindir)' --enable-gcs --enable-libcurl --enable-s3 configure: WARNING: unrecognized options: --disable-dependency-tracking checking for s390x-redhat-linux-gnu-gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for s390x-redhat-linux-gnu-ranlib... no checking for ranlib... ranlib checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for s390x-redhat-linux-gnu-pkg-config... /usr/bin/s390x-redhat-linux-gnu-pkg-config checking pkg-config is at least version 0.9.0... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking shared library type for s390x-redhat-linux-gnu... plain .so checking whether the compiler accepts -fvisibility=hidden... yes checking how to run the C preprocessor... gcc -E checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... yes checking for getpagesize... yes checking for working mmap... yes checking for gmtime_r... yes checking for fsync... yes checking for drand48... yes checking for srand48_deterministic... no checking whether fdatasync is declared... yes checking for fdatasync... yes checking for library containing dlsym... none required checking whether the compiler accepts -rdynamic... yes checking for library containing log... -lm checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing recv... none required checking for bzlib.h... yes checking for BZ2_bzBuffToBuffCompress in -lbz2... yes checking for lzma.h... yes checking for lzma_easy_buffer_encode in -llzma... yes checking whether htscodecs files are present... yes checking for libdeflate.h... no checking for libdeflate_deflate_compress in -ldeflate... no checking for curl/curl.h... yes checking for curl_easy_pause in -lcurl... yes checking for CCHmac... no checking for library containing HMAC... -lcrypto checking for library containing regcomp... none required checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes configure: creating ./config.status config.status: creating config.mk config.status: creating htslib.pc.tmp config.status: creating config.h config.status: linking htscodecs_bundled.mk to htscodecs.mk configure: WARNING: unrecognized options: --disable-dependency-tracking + /usr/bin/make -O -j2 V=1 VERBOSE=1 gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' htslib.pc.tmp > htslib_static.mk sed -e 's#@-includedir@#'`pwd`'#g;s#@-libdir@#'`pwd`'#g' htslib.pc.tmp > htslib-uninstalled.pc gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_introspection.o test/test_introspection.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -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 -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 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 -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 -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 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_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-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_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-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-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-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.hsVnsK + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x '!=' / ']' + rm -rf /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x ++ dirname /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=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,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 + 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-1.15.1-1.fc38.s390x 'INSTALL=/usr/bin/install -p' mkdir -p -m 755 /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/bin /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/include /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/include/htslib /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/lib64 /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/share/man/man1 /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/share/man/man5 /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/share/man/man7 /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/lib64/pkgconfig if test -n "/usr/libexec/htslib"; then mkdir -p -m 755 /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/libexec/htslib; fi /usr/bin/install -p -m 644 libhts.so /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/lib64/libhts.so.1.15.1 ln -sf libhts.so.1.15.1 /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/lib64/libhts.so ln -sf libhts.so.1.15.1 /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.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-1.15.1-1.fc38.s390x/usr/lib64/pkgconfig/htslib.pc chmod 644 /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/lib64/pkgconfig/htslib.pc /usr/bin/install -p bgzip htsfile tabix /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.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-1.15.1-1.fc38.s390x/usr/libexec/htslib; fi /usr/bin/install -p -m 644 htslib/*.h /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/include/htslib /usr/bin/install -p -m 644 libhts.a /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/lib64/libhts.a /usr/bin/install -p -m 644 bgzip.1 htsfile.1 tabix.1 /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/share/man/man1 /usr/bin/install -p -m 644 faidx.5 sam.5 vcf.5 /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/share/man/man5 /usr/bin/install -p -m 644 htslib-s3-plugin.7 /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/share/man/man7 + pushd /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x//usr/lib64 ~/build/BUILDROOT/htslib-1.15.1-1.fc38.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-1.15.1-1.fc38.s390x -name '*.la' -delete + rm -f /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x//usr/lib64/libhts.a + /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 1.15.1-1.fc38 --unique-debug-suffix -1.15.1-1.fc38.s390x --unique-debug-src-base htslib-1.15.1-1.fc38.s390x --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/htslib-1.15.1 extracting debug info from /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/bin/bgzip extracting debug info from /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/bin/htsfile extracting debug info from /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/bin/tabix extracting debug info from /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/lib64/libhts.so.1.15.1 extracting debug info from /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/libexec/htslib/hfile_gcs.so extracting debug info from /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/libexec/htslib/hfile_libcurl.so extracting debug info from /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/libexec/htslib/hfile_s3.so extracting debug info from /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/libexec/htslib/hfile_s3_write.so original debug info size: 12552kB, size after compression: 10988kB /usr/bin/sepdebugcrcfix: Updated 8 CRC32s, 0 CRC32s did match. 5259 blocks + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + /usr/lib/rpm/brp-compress + /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/check-rpaths + /usr/lib/rpm/redhat/brp-mangle-shebangs + /usr/lib/rpm/brp-remove-la-files + /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 + /usr/lib/rpm/redhat/brp-python-hardlink Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.PQ43uw + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=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,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 + 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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-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/2QdanlUByc/index.bam.csi /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/2QdanlUByc/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/2QdanlUByc/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -b -m 0 -x /tmp/2QdanlUByc/index.bam.bai /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/2QdanlUByc/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -b /tmp/2QdanlUByc/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -z -m 14 -x /tmp/2QdanlUByc/index.sam.gz.csi /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/2QdanlUByc/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/2QdanlUByc/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -z -m 0 -x /tmp/2QdanlUByc/index.sam.gz.bai /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/2QdanlUByc/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -b /tmp/2QdanlUByc/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -z -m 14 -x /tmp/2QdanlUByc/index.sam.gz.csi /builddir/build/BUILD/htslib-1.15.1/test/index_dos.sam > /tmp/2QdanlUByc/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/2QdanlUByc/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -z -m 0 -x /tmp/2QdanlUByc/index.sam.gz.bai /builddir/build/BUILD/htslib-1.15.1/test/index_dos.sam > /tmp/2QdanlUByc/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -b /tmp/2QdanlUByc/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -C -x /tmp/2QdanlUByc/index.cram.crai /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/2QdanlUByc/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index /tmp/2QdanlUByc/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -b -m 14 -x /tmp/2QdanlUByc/index.bcf.csi /builddir/build/BUILD/htslib-1.15.1/test/index.vcf > /tmp/2QdanlUByc/index.bcf .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/2QdanlUByc/index.bcf .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -z -m 14 -x /tmp/2QdanlUByc/index.vcf.gz.csi /builddir/build/BUILD/htslib-1.15.1/test/index.vcf > /tmp/2QdanlUByc/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/2QdanlUByc/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -z -m 0 -x /tmp/2QdanlUByc/index.vcf.gz.tbi /builddir/build/BUILD/htslib-1.15.1/test/index.vcf > /tmp/2QdanlUByc/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -t /tmp/2QdanlUByc/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/tabix /tmp/2QdanlUByc/index.vcf.gz##idx##/tmp/2QdanlUByc/index.vcf.gz.tbi 1:10000060-10000060 .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view /tmp/2QdanlUByc/index2.bam 1:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view /tmp/2QdanlUByc/index2.bam 1:2000000-2000000 .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view /tmp/2QdanlUByc/index2.bam 2:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view /tmp/2QdanlUByc/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/2QdanlUByc/index.bam.csi /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/2QdanlUByc/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/2QdanlUByc/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -b -m 0 -x /tmp/2QdanlUByc/index.bam.bai /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/2QdanlUByc/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -b /tmp/2QdanlUByc/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -z -m 14 -x /tmp/2QdanlUByc/index.sam.gz.csi /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/2QdanlUByc/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/2QdanlUByc/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -z -m 0 -x /tmp/2QdanlUByc/index.sam.gz.bai /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/2QdanlUByc/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -b /tmp/2QdanlUByc/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -z -m 14 -x /tmp/2QdanlUByc/index.sam.gz.csi /builddir/build/BUILD/htslib-1.15.1/test/index_dos.sam > /tmp/2QdanlUByc/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/2QdanlUByc/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -z -m 0 -x /tmp/2QdanlUByc/index.sam.gz.bai /builddir/build/BUILD/htslib-1.15.1/test/index_dos.sam > /tmp/2QdanlUByc/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -b /tmp/2QdanlUByc/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -C -x /tmp/2QdanlUByc/index.cram.crai /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/2QdanlUByc/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index /tmp/2QdanlUByc/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -b -m 14 -x /tmp/2QdanlUByc/index.bcf.csi /builddir/build/BUILD/htslib-1.15.1/test/index.vcf > /tmp/2QdanlUByc/index.bcf .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/2QdanlUByc/index.bcf .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -z -m 14 -x /tmp/2QdanlUByc/index.vcf.gz.csi /builddir/build/BUILD/htslib-1.15.1/test/index.vcf > /tmp/2QdanlUByc/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/2QdanlUByc/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -z -m 0 -x /tmp/2QdanlUByc/index.vcf.gz.tbi /builddir/build/BUILD/htslib-1.15.1/test/index.vcf > /tmp/2QdanlUByc/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -t /tmp/2QdanlUByc/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/tabix /tmp/2QdanlUByc/index.vcf.gz##idx##/tmp/2QdanlUByc/index.vcf.gz.tbi 1:10000060-10000060 .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view /tmp/2QdanlUByc/index2.bam 1:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view /tmp/2QdanlUByc/index2.bam 1:2000000-2000000 .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view /tmp/2QdanlUByc/index2.bam 2:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view /tmp/2QdanlUByc/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/2QdanlUByc/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/2QdanlUByc/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/2QdanlUByc/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/2QdanlUByc -s 1420980187 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/2QdanlUByc -s 320815204 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/2QdanlUByc -s 458742908 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/2QdanlUByc -s 1626428260 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/2QdanlUByc -s 1449092975 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/2QdanlUByc -s 875773942 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/2QdanlUByc -s 730838607 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/2QdanlUByc -s 537161593 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/2QdanlUByc -s 1128300927 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/2QdanlUByc -s 973442679 .. 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/2QdanlUByc/headernul0.bam .. ok test_convert_padded_header: /builddir/build/BUILD/htslib-1.15.1/test/test_view -t ce.fa -C /tmp/2QdanlUByc/headernul1.bam .. ok test_convert_padded_header: /builddir/build/BUILD/htslib-1.15.1/test/test_view -t ce.fa -C /tmp/2QdanlUByc/headernul678.bam .. ok test_rebgzip: /builddir/build/BUILD/htslib-1.15.1/bgzip -I /builddir/build/BUILD/htslib-1.15.1/test/bgziptest.txt.gz.gzi -c -g /builddir/build/BUILD/htslib-1.15.1/test/bgziptest.txt .. ok test-logging: /builddir/build/BUILD/htslib-1.15.1/test/test-logging.pl .. ok test_plugin_loading: HTS_PATH=/builddir/build/BUILD/htslib-1.15.1 /builddir/build/BUILD/htslib-1.15.1/test/with-shlib.sh /builddir/build/BUILD/htslib-1.15.1/htsfile https://localhost:99999/invalid_port .. ok test_realn: /builddir/build/BUILD/htslib-1.15.1/test/test_realn -f /builddir/build/BUILD/htslib-1.15.1/test/realn01.fa -i /builddir/build/BUILD/htslib-1.15.1/test/realn01.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.15.1/test/test_realn -f /builddir/build/BUILD/htslib-1.15.1/test/realn02.fa -i /builddir/build/BUILD/htslib-1.15.1/test/realn02.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.15.1/test/test_realn -a -f /builddir/build/BUILD/htslib-1.15.1/test/realn01.fa -i /builddir/build/BUILD/htslib-1.15.1/test/realn01.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.15.1/test/test_realn -a -f /builddir/build/BUILD/htslib-1.15.1/test/realn02.fa -i /builddir/build/BUILD/htslib-1.15.1/test/realn02.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.15.1/test/test_realn -e -f /builddir/build/BUILD/htslib-1.15.1/test/realn01.fa -i /builddir/build/BUILD/htslib-1.15.1/test/realn01.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.15.1/test/test_realn -e -f /builddir/build/BUILD/htslib-1.15.1/test/realn02.fa -i /builddir/build/BUILD/htslib-1.15.1/test/realn02.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.15.1/test/test_realn -r -f /builddir/build/BUILD/htslib-1.15.1/test/realn02.fa -i /builddir/build/BUILD/htslib-1.15.1/test/realn02-r.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.15.1/test/test_realn -a -f /builddir/build/BUILD/htslib-1.15.1/test/realn02.fa -i /builddir/build/BUILD/htslib-1.15.1/test/realn02_exp.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.15.1/test/test_realn -f /builddir/build/BUILD/htslib-1.15.1/test/realn02.fa -i /builddir/build/BUILD/htslib-1.15.1/test/realn02_exp-a.sam -o - .. ok Number of tests: total .. 172 passed .. 172 failed .. 0 + RPM_EC=0 ++ jobs -p + exit 0 Processing files: htslib-1.15.1-1.fc38.s390x Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.rzw0LP + umask 022 + cd /builddir/build/BUILD + cd htslib-1.15.1 + DOCDIR=/builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/share/doc/htslib + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/share/doc/htslib + cp -pr NEWS /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/share/doc/htslib + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.16Mb0i + umask 022 + cd /builddir/build/BUILD + cd htslib-1.15.1 + LICENSEDIR=/builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/share/licenses/htslib + export LC_ALL=C + LC_ALL=C + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/share/licenses/htslib + cp -pr LICENSE /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/share/licenses/htslib + RPM_EC=0 ++ jobs -p + exit 0 Provides: htslib = 1.15.1-1.fc38 htslib(s390-64) = 1.15.1-1.fc38 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-1.15.1-1.fc38.s390x Provides: htslib-devel = 1.15.1-1.fc38 htslib-devel(s390-64) = 1.15.1-1.fc38 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-1.15.1-1.fc38.s390x Provides: htslib-tools = 1.15.1-1.fc38 htslib-tools(s390-64) = 1.15.1-1.fc38 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-1.15.1-1.fc38.s390x Provides: htslib-debugsource = 1.15.1-1.fc38 htslib-debugsource(s390-64) = 1.15.1-1.fc38 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: htslib-debuginfo-1.15.1-1.fc38.s390x Provides: debuginfo(build-id) = 86e1cad18638eabbaf6147f3130c4b919d8a2658 debuginfo(build-id) = 8f9e64718f387d5f290b91fa61abda861ae9741f debuginfo(build-id) = 962a4d6e90b26743c8845984b9c5f0c6371976d3 debuginfo(build-id) = c3ed2da1748f8c7532be8066306a26e5bf530df8 debuginfo(build-id) = f679b7efa696b33d6f3386e387f66b75ae3321ee htslib-debuginfo = 1.15.1-1.fc38 htslib-debuginfo(s390-64) = 1.15.1-1.fc38 libhts.so.1.15.1-1.15.1-1.fc38.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) = 1.15.1-1.fc38 Processing files: htslib-tools-debuginfo-1.15.1-1.fc38.s390x Provides: debuginfo(build-id) = b72b5dba3f9adfe70fd998bba77b9a04d1ffb99d debuginfo(build-id) = ca569f4491501f64040812f05b187d6f2d4d7486 debuginfo(build-id) = d06e7812f25ee0aabfb7003278c67f7e6c1557df htslib-tools-debuginfo = 1.15.1-1.fc38 htslib-tools-debuginfo(s390-64) = 1.15.1-1.fc38 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: htslib-debugsource(s390-64) = 1.15.1-1.fc38 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x Wrote: /builddir/build/RPMS/htslib-debuginfo-1.15.1-1.fc38.s390x.rpm Wrote: /builddir/build/RPMS/htslib-tools-1.15.1-1.fc38.s390x.rpm Wrote: /builddir/build/RPMS/htslib-tools-debuginfo-1.15.1-1.fc38.s390x.rpm Wrote: /builddir/build/RPMS/htslib-1.15.1-1.fc38.s390x.rpm Wrote: /builddir/build/RPMS/htslib-devel-1.15.1-1.fc38.s390x.rpm Wrote: /builddir/build/RPMS/htslib-debugsource-1.15.1-1.fc38.s390x.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.mbTYmE + umask 022 + cd /builddir/build/BUILD + cd htslib-1.15.1 + /usr/bin/rm -rf /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x + RPM_EC=0 ++ jobs -p + exit 0 Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.WwF8yq + umask 022 + cd /builddir/build/BUILD + rm -rf htslib-1.15.1 htslib-1.15.1.gemspec + RPM_EC=0 ++ jobs -p + exit 0 Finish: rpmbuild htslib-1.15.1-1.fc38.src.rpm Finish: build phase for htslib-1.15.1-1.fc38.src.rpm INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-s390x-1671942858.428762/root/var/log/dnf.rpm.log /var/lib/mock/fedora-rawhide-s390x-1671942858.428762/root/var/log/dnf.librepo.log /var/lib/mock/fedora-rawhide-s390x-1671942858.428762/root/var/log/dnf.log INFO: Done(/var/lib/copr-rpmbuild/results/htslib-1.15.1-1.fc38.src.rpm) Config(child) 6 minutes 39 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