Warning: Permanently added '2620:52:3:1:dead:beef:cafe:c18e' (ED25519) to the list of known hosts. Running: /usr/bin/copr-rpmbuild --verbose --drop-resultdir --build-id 5008328 --chroot fedora-rawhide-x86_64 --detached Version: 0.61 PID: 43788 Logging PID: 43789 Task: {'appstream': False, 'background': True, 'build_id': 5008328, 'buildroot_pkgs': [], 'chroot': 'fedora-rawhide-x86_64', 'enable_net': False, 'fedora_review': False, 'git_hash': 'bfef6cdc75ca2e53fba4d6007bc125e86b17866e', 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/djdelorie/make-4.4/htslib', 'isolation': 'default', 'memory_reqs': 2048, 'package_name': 'htslib', 'package_version': '1.15.1-1', 'project_dirname': 'make-4.4', 'project_name': 'make-4.4', 'project_owner': 'djdelorie', 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/djdelorie/make-4.4/fedora-rawhide-x86_64/', 'id': 'copr_base', 'name': 'Copr repository'}], 'sandbox': 'djdelorie/make-4.4--djdelorie', 'source_json': {}, 'source_type': None, 'submitter': 'djdelorie', 'tags': [], 'task_id': '5008328-fedora-rawhide-x86_64', 'timeout': 108000, 'uses_devel_repo': False, 'with_opts': [], 'without_opts': []} Running: git clone https://copr-dist-git.fedorainfracloud.org/git/djdelorie/make-4.4/htslib /var/lib/copr-rpmbuild/workspace/workdir-5i5wa9c5/htslib --depth 500 --no-single-branch --recursive cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/djdelorie/make-4.4/htslib', '/var/lib/copr-rpmbuild/workspace/workdir-5i5wa9c5/htslib', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-5i5wa9c5/htslib'... Running: git checkout bfef6cdc75ca2e53fba4d6007bc125e86b17866e cmd: ['git', 'checkout', 'bfef6cdc75ca2e53fba4d6007bc125e86b17866e'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-5i5wa9c5/htslib rc: 0 stdout: stderr: Note: switching to 'bfef6cdc75ca2e53fba4d6007bc125e86b17866e'. 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 bfef6cd automatic import of htslib Running: copr-distgit-client sources /usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated cmd: ['copr-distgit-client', 'sources'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-5i5wa9c5/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/djdelorie/make-4.4/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 16.2M 0 --:--:-- --:--:-- --:--:-- 16.2M INFO: Reading stdout from command: md5sum htslib-1.15.1.tar.bz2 Running (timeout=108000): unbuffer mock --buildsrpm --spec /var/lib/copr-rpmbuild/workspace/workdir-5i5wa9c5/htslib/htslib.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-5i5wa9c5/htslib --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1667627884.349232 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 3.3 starting (python version = 3.10.4, NVR = mock-3.3-1.fc35)... 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-5i5wa9c5/htslib/htslib.spec) Config(fedora-rawhide-x86_64) Start: clean chroot Finish: clean chroot Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1667627884.349232/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: 3.3 INFO: Mock Version: 3.3 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 33 MB/s | 8.0 MB 00:00 fedora 29 MB/s | 65 MB 00:02 Last metadata expiration check: 0:00:02 ago on Sat Nov 5 05:58:08 2022. Dependencies resolved. ================================================================================ Package Arch Version Repo 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 x86_64 1.21-1.fc38 fedora 38 k audit-libs x86_64 3.0.9-1.fc38 fedora 116 k basesystem noarch 11-14.fc37 fedora 7.0 k bash x86_64 5.2.2-2.fc38 fedora 1.8 M bzip2-libs x86_64 1.0.8-12.fc38 copr_base 42 k ca-certificates noarch 2022.2.54-5.fc37 fedora 829 k coreutils x86_64 9.1-8.fc38 copr_base 1.1 M coreutils-common x86_64 9.1-8.fc38 copr_base 2.0 M crypto-policies noarch 20221003-1.gitcb1ad32.fc38 fedora 86 k curl x86_64 7.86.0-2.fc38 fedora 334 k cyrus-sasl-lib x86_64 2.1.28-8.fc38 fedora 792 k dbus-libs x86_64 1:1.14.4-1.fc38 fedora 156 k dnf-data noarch 4.14.0-1.fc38 fedora 43 k elfutils-default-yama-scope noarch 0.188-2.fc38 fedora 15 k elfutils-libelf x86_64 0.188-2.fc38 fedora 196 k elfutils-libs x86_64 0.188-2.fc38 fedora 257 k expat x86_64 2.4.8-2.fc37 fedora 110 k fedora-gpg-keys noarch 38-0.3 fedora 125 k fedora-release noarch 38-0.4 fedora 11 k fedora-release-common noarch 38-0.4 fedora 22 k fedora-release-identity-basic noarch 38-0.4 fedora 12 k fedora-repos noarch 38-0.3 fedora 10 k fedora-repos-rawhide noarch 38-0.3 fedora 9.7 k file-libs x86_64 5.42-4.fc37 fedora 676 k filesystem x86_64 3.18-2.fc37 fedora 1.1 M findutils x86_64 1:4.9.0-2.fc37 fedora 492 k gawk x86_64 5.1.1-4.fc37 fedora 1.0 M gdbm-libs x86_64 1:1.23-2.fc37 fedora 56 k glib2 x86_64 2.74.1-2.fc38 fedora 2.7 M glibc x86_64 2.36.9000-11.fc38 fedora 2.1 M glibc-common x86_64 2.36.9000-11.fc38 fedora 301 k glibc-minimal-langpack x86_64 2.36.9000-11.fc38 fedora 22 k gmp x86_64 1:6.2.1-3.fc37 fedora 315 k gnupg2 x86_64 2.3.8-1.fc38 fedora 2.6 M gnutls x86_64 3.7.8-8.fc38 fedora 1.1 M gpgme x86_64 1.17.0-4.fc37 fedora 210 k grep x86_64 3.8-1.fc38 fedora 292 k ima-evm-utils x86_64 1.4-6.fc37 fedora 63 k json-c x86_64 0.16-3.fc38 fedora 41 k keyutils-libs x86_64 1.6.1-5.fc37 fedora 31 k krb5-libs x86_64 1.19.2-11.fc37.1 fedora 727 k libacl x86_64 2.3.1-4.fc37 fedora 23 k libarchive x86_64 3.6.1-2.fc37 fedora 397 k libassuan x86_64 2.5.5-5.fc37 fedora 67 k libattr x86_64 2.5.1-5.fc37 fedora 18 k libb2 x86_64 0.98.1-7.fc37 fedora 25 k libblkid x86_64 2.38.1-2.fc38 fedora 107 k libbrotli x86_64 1.0.9-9.fc37 fedora 315 k libcap x86_64 2.48-5.fc37 fedora 67 k libcap-ng x86_64 0.8.3-3.fc37 fedora 33 k libcom_err x86_64 1.46.5-3.fc37 fedora 25 k libcomps x86_64 0.1.18-4.fc37 fedora 76 k libcurl x86_64 7.86.0-2.fc38 fedora 305 k libdnf x86_64 0.68.0-1.fc38 fedora 673 k libevent x86_64 2.1.12-7.fc37 fedora 261 k libffi x86_64 3.4.2-9.fc37 fedora 37 k libfsverity x86_64 1.4-8.fc38 copr_base 20 k libgcc x86_64 12.2.1-2.fc38 fedora 106 k libgcrypt x86_64 1.10.1-4.fc37 fedora 512 k libgomp x86_64 12.2.1-2.fc38 fedora 293 k libgpg-error x86_64 1.46-1.fc38 fedora 227 k libidn2 x86_64 2.3.4-1.fc38 fedora 160 k libksba x86_64 1.6.2-1.fc38 fedora 158 k libmodulemd x86_64 2.14.0-4.fc37 fedora 234 k libmount x86_64 2.38.1-2.fc38 fedora 135 k libnghttp2 x86_64 1.50.0-1.fc38 copr_base 75 k libnsl2 x86_64 2.0.0-4.fc37 fedora 30 k libpsl x86_64 0.21.1-6.fc37 fedora 63 k librepo x86_64 1.14.4-1.fc38 fedora 94 k libreport-filesystem noarch 2.17.5-2.fc38 fedora 14 k libselinux x86_64 3.4-5.fc37 fedora 86 k libsemanage x86_64 3.4-5.fc37 fedora 120 k libsepol x86_64 3.4-3.fc37 fedora 322 k libsigsegv x86_64 2.14-3.fc37 fedora 27 k libsmartcols x86_64 2.38.1-2.fc38 fedora 64 k libsolv x86_64 0.7.22-3.fc37 fedora 405 k libssh x86_64 0.10.4-2.fc38 fedora 209 k libssh-config noarch 0.10.4-2.fc38 fedora 8.8 k libstdc++ x86_64 12.2.1-2.fc38 fedora 800 k libtasn1 x86_64 4.18.0-3.fc37 fedora 75 k libtirpc x86_64 1.3.3-0.fc37 fedora 93 k libunistring x86_64 1.0-2.fc37 fedora 549 k libuuid x86_64 2.38.1-2.fc38 fedora 28 k libverto x86_64 0.3.2-4.fc37 fedora 21 k libxcrypt x86_64 4.4.30-1.fc38 fedora 118 k libxml2 x86_64 2.10.3-2.fc38 fedora 705 k libyaml x86_64 0.2.5-8.fc37 fedora 60 k libzstd x86_64 1.5.2-3.fc37 fedora 294 k lua-libs x86_64 5.4.4-6.fc38 fedora 131 k lz4-libs x86_64 1.9.3-5.fc37 fedora 70 k mpdecimal x86_64 2.5.1-4.fc37 fedora 102 k mpfr x86_64 4.1.0-10.fc37 fedora 331 k ncurses-base noarch 6.3-3.20220501.fc37 fedora 86 k ncurses-libs x86_64 6.3-3.20220501.fc37 fedora 329 k nettle x86_64 3.8-2.fc37 fedora 414 k npth x86_64 1.6-10.fc38 fedora 24 k openldap x86_64 2.6.3-1.fc38 fedora 254 k openssl-libs x86_64 1:3.0.5-6.fc38 fedora 2.1 M p11-kit x86_64 0.24.1-3.fc37 fedora 376 k p11-kit-trust x86_64 0.24.1-3.fc37 fedora 138 k pcre2 x86_64 10.40-1.fc37.1 fedora 236 k pcre2-syntax noarch 10.40-1.fc37.1 fedora 142 k popt x86_64 1.19-1.fc38 fedora 66 k publicsuffix-list-dafsa noarch 20210518-5.fc37 fedora 58 k python-pip-wheel noarch 22.2.2-2.fc38 fedora 1.4 M python-setuptools-wheel noarch 65.5.0-1.fc38 fedora 715 k python3 x86_64 3.11.0-1.fc38 fedora 27 k python3-dateutil noarch 1:2.8.2-4.fc38 copr_base 350 k python3-dbus x86_64 1.3.2-1.fc38 fedora 157 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 x86_64 1.17.0-4.fc37 fedora 298 k python3-hawkey x86_64 0.68.0-1.fc38 fedora 108 k python3-libcomps x86_64 0.1.18-4.fc37 fedora 48 k python3-libdnf x86_64 0.68.0-1.fc38 fedora 818 k python3-libs x86_64 3.11.0-1.fc38 fedora 9.6 M python3-rpm x86_64 4.18.0-3.fc38 fedora 94 k python3-six noarch 1.16.0-8.fc37 fedora 42 k readline x86_64 8.2-2.fc38 fedora 211 k rpm x86_64 4.18.0-3.fc38 fedora 570 k rpm-build-libs x86_64 4.18.0-3.fc38 fedora 94 k rpm-libs x86_64 4.18.0-3.fc38 fedora 320 k rpm-sign-libs x86_64 4.18.0-3.fc38 fedora 27 k sed x86_64 4.8-11.fc37 fedora 306 k setup noarch 2.14.2-1.fc38 fedora 151 k shadow-utils x86_64 2:4.12.3-3.fc38 fedora 1.3 M sqlite-libs x86_64 3.39.4-1.fc38 fedora 658 k systemd-libs x86_64 252-587.fc38 fedora 631 k tpm2-tss x86_64 3.2.0-3.fc37 fedora 600 k tzdata noarch 2022f-1.fc38 fedora 715 k xz-libs x86_64 5.2.7-1.fc38 fedora 93 k zchunk-libs x86_64 1.2.3-1.fc38 fedora 51 k zlib x86_64 1.2.12-5.fc38 fedora 94 k Transaction Summary ================================================================================ Install 136 Packages Total download size: 56 M Installed size: 196 M Downloading Packages: (1/136): bzip2-libs-1.0.8-12.fc38.x86_64.rpm 894 kB/s | 42 kB 00:00 (2/136): coreutils-9.1-8.fc38.x86_64.rpm 9.1 MB/s | 1.1 MB 00:00 (3/136): coreutils-common-9.1-8.fc38.x86_64.rpm 15 MB/s | 2.0 MB 00:00 (4/136): libfsverity-1.4-8.fc38.x86_64.rpm 215 kB/s | 20 kB 00:00 (5/136): libnghttp2-1.50.0-1.fc38.x86_64.rpm 3.6 MB/s | 75 kB 00:00 (6/136): python3-dateutil-2.8.2-4.fc38.noarch.r 8.7 MB/s | 350 kB 00:00 (7/136): alternatives-1.21-1.fc38.x86_64.rpm 283 kB/s | 38 kB 00:00 (8/136): basesystem-11-14.fc37.noarch.rpm 69 kB/s | 7.0 kB 00:00 (9/136): audit-libs-3.0.9-1.fc38.x86_64.rpm 649 kB/s | 116 kB 00:00 (10/136): crypto-policies-20221003-1.gitcb1ad32 2.1 MB/s | 86 kB 00:00 (11/136): curl-7.86.0-2.fc38.x86_64.rpm 5.0 MB/s | 334 kB 00:00 (12/136): ca-certificates-2022.2.54-5.fc37.noar 5.0 MB/s | 829 kB 00:00 (13/136): bash-5.2.2-2.fc38.x86_64.rpm 10 MB/s | 1.8 MB 00:00 (14/136): dbus-libs-1.14.4-1.fc38.x86_64.rpm 6.3 MB/s | 156 kB 00:00 (15/136): dnf-4.14.0-1.fc38.noarch.rpm 17 MB/s | 480 kB 00:00 (16/136): cyrus-sasl-lib-2.1.28-8.fc38.x86_64.r 13 MB/s | 792 kB 00:00 (17/136): dnf-data-4.14.0-1.fc38.noarch.rpm 1.9 MB/s | 43 kB 00:00 (18/136): dnf-plugins-core-4.3.1-1.fc38.noarch. 1.5 MB/s | 34 kB 00:00 (19/136): elfutils-default-yama-scope-0.188-2.f 708 kB/s | 15 kB 00:00 (20/136): elfutils-libelf-0.188-2.fc38.x86_64.r 7.6 MB/s | 196 kB 00:00 (21/136): elfutils-libs-0.188-2.fc38.x86_64.rpm 11 MB/s | 257 kB 00:00 (22/136): expat-2.4.8-2.fc37.x86_64.rpm 4.7 MB/s | 110 kB 00:00 (23/136): fedora-gpg-keys-38-0.3.noarch.rpm 5.1 MB/s | 125 kB 00:00 (24/136): fedora-release-38-0.4.noarch.rpm 520 kB/s | 11 kB 00:00 (25/136): fedora-release-common-38-0.4.noarch.r 998 kB/s | 22 kB 00:00 (26/136): fedora-release-identity-basic-38-0.4. 550 kB/s | 12 kB 00:00 (27/136): fedora-repos-38-0.3.noarch.rpm 472 kB/s | 10 kB 00:00 (28/136): fedora-repos-rawhide-38-0.3.noarch.rp 451 kB/s | 9.7 kB 00:00 (29/136): file-libs-5.42-4.fc37.x86_64.rpm 17 MB/s | 676 kB 00:00 (30/136): filesystem-3.18-2.fc37.x86_64.rpm 29 MB/s | 1.1 MB 00:00 (31/136): findutils-4.9.0-2.fc37.x86_64.rpm 14 MB/s | 492 kB 00:00 (32/136): gdbm-libs-1.23-2.fc37.x86_64.rpm 2.4 MB/s | 56 kB 00:00 (33/136): gawk-5.1.1-4.fc37.x86_64.rpm 23 MB/s | 1.0 MB 00:00 (34/136): glibc-common-2.36.9000-11.fc38.x86_64 5.1 MB/s | 301 kB 00:00 (35/136): glib2-2.74.1-2.fc38.x86_64.rpm 28 MB/s | 2.7 MB 00:00 (36/136): glibc-2.36.9000-11.fc38.x86_64.rpm 22 MB/s | 2.1 MB 00:00 (37/136): glibc-minimal-langpack-2.36.9000-11.f 1.0 MB/s | 22 kB 00:00 (38/136): gmp-6.2.1-3.fc37.x86_64.rpm 13 MB/s | 315 kB 00:00 (39/136): gpgme-1.17.0-4.fc37.x86_64.rpm 6.6 MB/s | 210 kB 00:00 (40/136): grep-3.8-1.fc38.x86_64.rpm 12 MB/s | 292 kB 00:00 (41/136): gnupg2-2.3.8-1.fc38.x86_64.rpm 33 MB/s | 2.6 MB 00:00 (42/136): ima-evm-utils-1.4-6.fc37.x86_64.rpm 2.8 MB/s | 63 kB 00:00 (43/136): gnutls-3.7.8-8.fc38.x86_64.rpm 12 MB/s | 1.1 MB 00:00 (44/136): json-c-0.16-3.fc38.x86_64.rpm 1.8 MB/s | 41 kB 00:00 (45/136): keyutils-libs-1.6.1-5.fc37.x86_64.rpm 1.4 MB/s | 31 kB 00:00 (46/136): libacl-2.3.1-4.fc37.x86_64.rpm 1.0 MB/s | 23 kB 00:00 (47/136): krb5-libs-1.19.2-11.fc37.1.x86_64.rpm 22 MB/s | 727 kB 00:00 (48/136): libarchive-3.6.1-2.fc37.x86_64.rpm 15 MB/s | 397 kB 00:00 (49/136): libassuan-2.5.5-5.fc37.x86_64.rpm 3.0 MB/s | 67 kB 00:00 (50/136): libattr-2.5.1-5.fc37.x86_64.rpm 823 kB/s | 18 kB 00:00 (51/136): libb2-0.98.1-7.fc37.x86_64.rpm 1.1 MB/s | 25 kB 00:00 (52/136): libblkid-2.38.1-2.fc38.x86_64.rpm 4.7 MB/s | 107 kB 00:00 (53/136): libbrotli-1.0.9-9.fc37.x86_64.rpm 12 MB/s | 315 kB 00:00 (54/136): libcap-2.48-5.fc37.x86_64.rpm 2.9 MB/s | 67 kB 00:00 (55/136): libcap-ng-0.8.3-3.fc37.x86_64.rpm 1.5 MB/s | 33 kB 00:00 (56/136): libcom_err-1.46.5-3.fc37.x86_64.rpm 1.1 MB/s | 25 kB 00:00 (57/136): libcomps-0.1.18-4.fc37.x86_64.rpm 3.3 MB/s | 76 kB 00:00 (58/136): libcurl-7.86.0-2.fc38.x86_64.rpm 12 MB/s | 305 kB 00:00 (59/136): libevent-2.1.12-7.fc37.x86_64.rpm 9.6 MB/s | 261 kB 00:00 (60/136): libdnf-0.68.0-1.fc38.x86_64.rpm 19 MB/s | 673 kB 00:00 (61/136): libffi-3.4.2-9.fc37.x86_64.rpm 1.7 MB/s | 37 kB 00:00 (62/136): libgcc-12.2.1-2.fc38.x86_64.rpm 4.5 MB/s | 106 kB 00:00 (63/136): libgcrypt-1.10.1-4.fc37.x86_64.rpm 14 MB/s | 512 kB 00:00 (64/136): libgomp-12.2.1-2.fc38.x86_64.rpm 9.1 MB/s | 293 kB 00:00 (65/136): libgpg-error-1.46-1.fc38.x86_64.rpm 7.8 MB/s | 227 kB 00:00 (66/136): libidn2-2.3.4-1.fc38.x86_64.rpm 6.5 MB/s | 160 kB 00:00 (67/136): libksba-1.6.2-1.fc38.x86_64.rpm 6.6 MB/s | 158 kB 00:00 (68/136): libmodulemd-2.14.0-4.fc37.x86_64.rpm 9.6 MB/s | 234 kB 00:00 (69/136): libmount-2.38.1-2.fc38.x86_64.rpm 5.6 MB/s | 135 kB 00:00 (70/136): libnsl2-2.0.0-4.fc37.x86_64.rpm 1.4 MB/s | 30 kB 00:00 (71/136): libpsl-0.21.1-6.fc37.x86_64.rpm 2.8 MB/s | 63 kB 00:00 (72/136): librepo-1.14.4-1.fc38.x86_64.rpm 4.0 MB/s | 94 kB 00:00 (73/136): libreport-filesystem-2.17.5-2.fc38.no 638 kB/s | 14 kB 00:00 (74/136): libselinux-3.4-5.fc37.x86_64.rpm 3.7 MB/s | 86 kB 00:00 (75/136): libsemanage-3.4-5.fc37.x86_64.rpm 4.9 MB/s | 120 kB 00:00 (76/136): libsepol-3.4-3.fc37.x86_64.rpm 12 MB/s | 322 kB 00:00 (77/136): libsigsegv-2.14-3.fc37.x86_64.rpm 1.2 MB/s | 27 kB 00:00 (78/136): libsmartcols-2.38.1-2.fc38.x86_64.rpm 2.8 MB/s | 64 kB 00:00 (79/136): libsolv-0.7.22-3.fc37.x86_64.rpm 16 MB/s | 405 kB 00:00 (80/136): libssh-0.10.4-2.fc38.x86_64.rpm 8.7 MB/s | 209 kB 00:00 (81/136): libssh-config-0.10.4-2.fc38.noarch.rp 405 kB/s | 8.8 kB 00:00 (82/136): libstdc++-12.2.1-2.fc38.x86_64.rpm 27 MB/s | 800 kB 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sed-4.8-11.fc37.x86_64.rpm 12 MB/s | 306 kB 00:00 (127/136): setup-2.14.2-1.fc38.noarch.rpm 6.0 MB/s | 151 kB 00:00 (128/136): sqlite-libs-3.39.4-1.fc38.x86_64.rpm 11 MB/s | 658 kB 00:00 (129/136): systemd-libs-252-587.fc38.x86_64.rpm 22 MB/s | 631 kB 00:00 (130/136): python3-libs-3.11.0-1.fc38.x86_64.rp 36 MB/s | 9.6 MB 00:00 (131/136): tpm2-tss-3.2.0-3.fc37.x86_64.rpm 21 MB/s | 600 kB 00:00 (132/136): tzdata-2022f-1.fc38.noarch.rpm 23 MB/s | 715 kB 00:00 (133/136): xz-libs-5.2.7-1.fc38.x86_64.rpm 3.8 MB/s | 93 kB 00:00 (134/136): zchunk-libs-1.2.3-1.fc38.x86_64.rpm 2.2 MB/s | 51 kB 00:00 (135/136): zlib-1.2.12-5.fc38.x86_64.rpm 4.1 MB/s | 94 kB 00:00 (136/136): shadow-utils-4.12.3-3.fc38.x86_64.rp 5.2 MB/s | 1.3 MB 00:00 -------------------------------------------------------------------------------- Total 30 MB/s | 56 MB 00:01 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.x86_64 1/1 Preparing : 1/1 Installing : libgcc-12.2.1-2.fc38.x86_64 1/136 Running scriptlet: libgcc-12.2.1-2.fc38.x86_64 1/136 Installing : crypto-policies-20221003-1.gitcb1ad32.fc38.noarc 2/136 Running scriptlet: crypto-policies-20221003-1.gitcb1ad32.fc38.noarc 2/136 Installing : tzdata-2022f-1.fc38.noarch 3/136 Installing : fedora-release-identity-basic-38-0.4.noarch 4/136 Installing : python-setuptools-wheel-65.5.0-1.fc38.noarch 5/136 Installing : publicsuffix-list-dafsa-20210518-5.fc37.noarch 6/136 Installing : pcre2-syntax-10.40-1.fc37.1.noarch 7/136 Installing : ncurses-base-6.3-3.20220501.fc37.noarch 8/136 Installing : libssh-config-0.10.4-2.fc38.noarch 9/136 Installing : libreport-filesystem-2.17.5-2.fc38.noarch 10/136 Installing : dnf-data-4.14.0-1.fc38.noarch 11/136 warning: /etc/dnf/dnf.conf created as /etc/dnf/dnf.conf.rpmnew Installing : fedora-gpg-keys-38-0.3.noarch 12/136 Installing : 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15/136 Verifying : dnf-4.14.0-1.fc38.noarch 16/136 Verifying : dnf-data-4.14.0-1.fc38.noarch 17/136 Verifying : dnf-plugins-core-4.3.1-1.fc38.noarch 18/136 Verifying : elfutils-default-yama-scope-0.188-2.fc38.noarch 19/136 Verifying : elfutils-libelf-0.188-2.fc38.x86_64 20/136 Verifying : elfutils-libs-0.188-2.fc38.x86_64 21/136 Verifying : expat-2.4.8-2.fc37.x86_64 22/136 Verifying : fedora-gpg-keys-38-0.3.noarch 23/136 Verifying : fedora-release-38-0.4.noarch 24/136 Verifying : fedora-release-common-38-0.4.noarch 25/136 Verifying : fedora-release-identity-basic-38-0.4.noarch 26/136 Verifying : fedora-repos-38-0.3.noarch 27/136 Verifying : fedora-repos-rawhide-38-0.3.noarch 28/136 Verifying : file-libs-5.42-4.fc37.x86_64 29/136 Verifying : filesystem-3.18-2.fc37.x86_64 30/136 Verifying : findutils-1:4.9.0-2.fc37.x86_64 31/136 Verifying : gawk-5.1.1-4.fc37.x86_64 32/136 Verifying : gdbm-libs-1:1.23-2.fc37.x86_64 33/136 Verifying : glib2-2.74.1-2.fc38.x86_64 34/136 Verifying : glibc-2.36.9000-11.fc38.x86_64 35/136 Verifying : glibc-common-2.36.9000-11.fc38.x86_64 36/136 Verifying : glibc-minimal-langpack-2.36.9000-11.fc38.x86_64 37/136 Verifying : gmp-1:6.2.1-3.fc37.x86_64 38/136 Verifying : gnupg2-2.3.8-1.fc38.x86_64 39/136 Verifying : gnutls-3.7.8-8.fc38.x86_64 40/136 Verifying : gpgme-1.17.0-4.fc37.x86_64 41/136 Verifying : grep-3.8-1.fc38.x86_64 42/136 Verifying : ima-evm-utils-1.4-6.fc37.x86_64 43/136 Verifying : json-c-0.16-3.fc38.x86_64 44/136 Verifying : keyutils-libs-1.6.1-5.fc37.x86_64 45/136 Verifying : krb5-libs-1.19.2-11.fc37.1.x86_64 46/136 Verifying : libacl-2.3.1-4.fc37.x86_64 47/136 Verifying : libarchive-3.6.1-2.fc37.x86_64 48/136 Verifying : libassuan-2.5.5-5.fc37.x86_64 49/136 Verifying : libattr-2.5.1-5.fc37.x86_64 50/136 Verifying : libb2-0.98.1-7.fc37.x86_64 51/136 Verifying : libblkid-2.38.1-2.fc38.x86_64 52/136 Verifying : libbrotli-1.0.9-9.fc37.x86_64 53/136 Verifying : libcap-2.48-5.fc37.x86_64 54/136 Verifying : libcap-ng-0.8.3-3.fc37.x86_64 55/136 Verifying : libcom_err-1.46.5-3.fc37.x86_64 56/136 Verifying : libcomps-0.1.18-4.fc37.x86_64 57/136 Verifying : libcurl-7.86.0-2.fc38.x86_64 58/136 Verifying : libdnf-0.68.0-1.fc38.x86_64 59/136 Verifying : libevent-2.1.12-7.fc37.x86_64 60/136 Verifying : libffi-3.4.2-9.fc37.x86_64 61/136 Verifying : libgcc-12.2.1-2.fc38.x86_64 62/136 Verifying : libgcrypt-1.10.1-4.fc37.x86_64 63/136 Verifying : libgomp-12.2.1-2.fc38.x86_64 64/136 Verifying : libgpg-error-1.46-1.fc38.x86_64 65/136 Verifying : libidn2-2.3.4-1.fc38.x86_64 66/136 Verifying : libksba-1.6.2-1.fc38.x86_64 67/136 Verifying : libmodulemd-2.14.0-4.fc37.x86_64 68/136 Verifying : libmount-2.38.1-2.fc38.x86_64 69/136 Verifying : libnsl2-2.0.0-4.fc37.x86_64 70/136 Verifying : libpsl-0.21.1-6.fc37.x86_64 71/136 Verifying : librepo-1.14.4-1.fc38.x86_64 72/136 Verifying : libreport-filesystem-2.17.5-2.fc38.noarch 73/136 Verifying : libselinux-3.4-5.fc37.x86_64 74/136 Verifying : libsemanage-3.4-5.fc37.x86_64 75/136 Verifying : libsepol-3.4-3.fc37.x86_64 76/136 Verifying : libsigsegv-2.14-3.fc37.x86_64 77/136 Verifying : libsmartcols-2.38.1-2.fc38.x86_64 78/136 Verifying : libsolv-0.7.22-3.fc37.x86_64 79/136 Verifying : libssh-0.10.4-2.fc38.x86_64 80/136 Verifying : libssh-config-0.10.4-2.fc38.noarch 81/136 Verifying : libstdc++-12.2.1-2.fc38.x86_64 82/136 Verifying : libtasn1-4.18.0-3.fc37.x86_64 83/136 Verifying : libtirpc-1.3.3-0.fc37.x86_64 84/136 Verifying : libunistring-1.0-2.fc37.x86_64 85/136 Verifying : libuuid-2.38.1-2.fc38.x86_64 86/136 Verifying : libverto-0.3.2-4.fc37.x86_64 87/136 Verifying : libxcrypt-4.4.30-1.fc38.x86_64 88/136 Verifying : libxml2-2.10.3-2.fc38.x86_64 89/136 Verifying : libyaml-0.2.5-8.fc37.x86_64 90/136 Verifying : libzstd-1.5.2-3.fc37.x86_64 91/136 Verifying : lua-libs-5.4.4-6.fc38.x86_64 92/136 Verifying : lz4-libs-1.9.3-5.fc37.x86_64 93/136 Verifying : mpdecimal-2.5.1-4.fc37.x86_64 94/136 Verifying : mpfr-4.1.0-10.fc37.x86_64 95/136 Verifying : ncurses-base-6.3-3.20220501.fc37.noarch 96/136 Verifying : ncurses-libs-6.3-3.20220501.fc37.x86_64 97/136 Verifying : nettle-3.8-2.fc37.x86_64 98/136 Verifying : npth-1.6-10.fc38.x86_64 99/136 Verifying : openldap-2.6.3-1.fc38.x86_64 100/136 Verifying : openssl-libs-1:3.0.5-6.fc38.x86_64 101/136 Verifying : p11-kit-0.24.1-3.fc37.x86_64 102/136 Verifying : p11-kit-trust-0.24.1-3.fc37.x86_64 103/136 Verifying : pcre2-10.40-1.fc37.1.x86_64 104/136 Verifying : pcre2-syntax-10.40-1.fc37.1.noarch 105/136 Verifying : popt-1.19-1.fc38.x86_64 106/136 Verifying : publicsuffix-list-dafsa-20210518-5.fc37.noarch 107/136 Verifying : python-pip-wheel-22.2.2-2.fc38.noarch 108/136 Verifying : python-setuptools-wheel-65.5.0-1.fc38.noarch 109/136 Verifying : python3-3.11.0-1.fc38.x86_64 110/136 Verifying : python3-dbus-1.3.2-1.fc38.x86_64 111/136 Verifying : python3-distro-1.8.0-1.fc38.noarch 112/136 Verifying : python3-dnf-4.14.0-1.fc38.noarch 113/136 Verifying : python3-dnf-plugins-core-4.3.1-1.fc38.noarch 114/136 Verifying : python3-gpg-1.17.0-4.fc37.x86_64 115/136 Verifying : python3-hawkey-0.68.0-1.fc38.x86_64 116/136 Verifying : python3-libcomps-0.1.18-4.fc37.x86_64 117/136 Verifying : python3-libdnf-0.68.0-1.fc38.x86_64 118/136 Verifying : python3-libs-3.11.0-1.fc38.x86_64 119/136 Verifying : python3-rpm-4.18.0-3.fc38.x86_64 120/136 Verifying : python3-six-1.16.0-8.fc37.noarch 121/136 Verifying : readline-8.2-2.fc38.x86_64 122/136 Verifying : rpm-4.18.0-3.fc38.x86_64 123/136 Verifying : rpm-build-libs-4.18.0-3.fc38.x86_64 124/136 Verifying : rpm-libs-4.18.0-3.fc38.x86_64 125/136 Verifying : rpm-sign-libs-4.18.0-3.fc38.x86_64 126/136 Verifying : sed-4.8-11.fc37.x86_64 127/136 Verifying : setup-2.14.2-1.fc38.noarch 128/136 Verifying : shadow-utils-2:4.12.3-3.fc38.x86_64 129/136 Verifying : sqlite-libs-3.39.4-1.fc38.x86_64 130/136 Verifying : systemd-libs-252-587.fc38.x86_64 131/136 Verifying : tpm2-tss-3.2.0-3.fc37.x86_64 132/136 Verifying : tzdata-2022f-1.fc38.noarch 133/136 Verifying : xz-libs-5.2.7-1.fc38.x86_64 134/136 Verifying : zchunk-libs-1.2.3-1.fc38.x86_64 135/136 Verifying : zlib-1.2.12-5.fc38.x86_64 136/136 Installed products updated. Installed: alternatives-1.21-1.fc38.x86_64 audit-libs-3.0.9-1.fc38.x86_64 basesystem-11-14.fc37.noarch bash-5.2.2-2.fc38.x86_64 bzip2-libs-1.0.8-12.fc38.x86_64 ca-certificates-2022.2.54-5.fc37.noarch coreutils-9.1-8.fc38.x86_64 coreutils-common-9.1-8.fc38.x86_64 crypto-policies-20221003-1.gitcb1ad32.fc38.noarch curl-7.86.0-2.fc38.x86_64 cyrus-sasl-lib-2.1.28-8.fc38.x86_64 dbus-libs-1:1.14.4-1.fc38.x86_64 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-0.188-2.fc38.noarch elfutils-libelf-0.188-2.fc38.x86_64 elfutils-libs-0.188-2.fc38.x86_64 expat-2.4.8-2.fc37.x86_64 fedora-gpg-keys-38-0.3.noarch fedora-release-38-0.4.noarch fedora-release-common-38-0.4.noarch fedora-release-identity-basic-38-0.4.noarch fedora-repos-38-0.3.noarch fedora-repos-rawhide-38-0.3.noarch file-libs-5.42-4.fc37.x86_64 filesystem-3.18-2.fc37.x86_64 findutils-1:4.9.0-2.fc37.x86_64 gawk-5.1.1-4.fc37.x86_64 gdbm-libs-1:1.23-2.fc37.x86_64 glib2-2.74.1-2.fc38.x86_64 glibc-2.36.9000-11.fc38.x86_64 glibc-common-2.36.9000-11.fc38.x86_64 glibc-minimal-langpack-2.36.9000-11.fc38.x86_64 gmp-1:6.2.1-3.fc37.x86_64 gnupg2-2.3.8-1.fc38.x86_64 gnutls-3.7.8-8.fc38.x86_64 gpgme-1.17.0-4.fc37.x86_64 grep-3.8-1.fc38.x86_64 ima-evm-utils-1.4-6.fc37.x86_64 json-c-0.16-3.fc38.x86_64 keyutils-libs-1.6.1-5.fc37.x86_64 krb5-libs-1.19.2-11.fc37.1.x86_64 libacl-2.3.1-4.fc37.x86_64 libarchive-3.6.1-2.fc37.x86_64 libassuan-2.5.5-5.fc37.x86_64 libattr-2.5.1-5.fc37.x86_64 libb2-0.98.1-7.fc37.x86_64 libblkid-2.38.1-2.fc38.x86_64 libbrotli-1.0.9-9.fc37.x86_64 libcap-2.48-5.fc37.x86_64 libcap-ng-0.8.3-3.fc37.x86_64 libcom_err-1.46.5-3.fc37.x86_64 libcomps-0.1.18-4.fc37.x86_64 libcurl-7.86.0-2.fc38.x86_64 libdnf-0.68.0-1.fc38.x86_64 libevent-2.1.12-7.fc37.x86_64 libffi-3.4.2-9.fc37.x86_64 libfsverity-1.4-8.fc38.x86_64 libgcc-12.2.1-2.fc38.x86_64 libgcrypt-1.10.1-4.fc37.x86_64 libgomp-12.2.1-2.fc38.x86_64 libgpg-error-1.46-1.fc38.x86_64 libidn2-2.3.4-1.fc38.x86_64 libksba-1.6.2-1.fc38.x86_64 libmodulemd-2.14.0-4.fc37.x86_64 libmount-2.38.1-2.fc38.x86_64 libnghttp2-1.50.0-1.fc38.x86_64 libnsl2-2.0.0-4.fc37.x86_64 libpsl-0.21.1-6.fc37.x86_64 librepo-1.14.4-1.fc38.x86_64 libreport-filesystem-2.17.5-2.fc38.noarch libselinux-3.4-5.fc37.x86_64 libsemanage-3.4-5.fc37.x86_64 libsepol-3.4-3.fc37.x86_64 libsigsegv-2.14-3.fc37.x86_64 libsmartcols-2.38.1-2.fc38.x86_64 libsolv-0.7.22-3.fc37.x86_64 libssh-0.10.4-2.fc38.x86_64 libssh-config-0.10.4-2.fc38.noarch libstdc++-12.2.1-2.fc38.x86_64 libtasn1-4.18.0-3.fc37.x86_64 libtirpc-1.3.3-0.fc37.x86_64 libunistring-1.0-2.fc37.x86_64 libuuid-2.38.1-2.fc38.x86_64 libverto-0.3.2-4.fc37.x86_64 libxcrypt-4.4.30-1.fc38.x86_64 libxml2-2.10.3-2.fc38.x86_64 libyaml-0.2.5-8.fc37.x86_64 libzstd-1.5.2-3.fc37.x86_64 lua-libs-5.4.4-6.fc38.x86_64 lz4-libs-1.9.3-5.fc37.x86_64 mpdecimal-2.5.1-4.fc37.x86_64 mpfr-4.1.0-10.fc37.x86_64 ncurses-base-6.3-3.20220501.fc37.noarch ncurses-libs-6.3-3.20220501.fc37.x86_64 nettle-3.8-2.fc37.x86_64 npth-1.6-10.fc38.x86_64 openldap-2.6.3-1.fc38.x86_64 openssl-libs-1:3.0.5-6.fc38.x86_64 p11-kit-0.24.1-3.fc37.x86_64 p11-kit-trust-0.24.1-3.fc37.x86_64 pcre2-10.40-1.fc37.1.x86_64 pcre2-syntax-10.40-1.fc37.1.noarch popt-1.19-1.fc38.x86_64 publicsuffix-list-dafsa-20210518-5.fc37.noarch python-pip-wheel-22.2.2-2.fc38.noarch python-setuptools-wheel-65.5.0-1.fc38.noarch python3-3.11.0-1.fc38.x86_64 python3-dateutil-1:2.8.2-4.fc38.noarch python3-dbus-1.3.2-1.fc38.x86_64 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-1.17.0-4.fc37.x86_64 python3-hawkey-0.68.0-1.fc38.x86_64 python3-libcomps-0.1.18-4.fc37.x86_64 python3-libdnf-0.68.0-1.fc38.x86_64 python3-libs-3.11.0-1.fc38.x86_64 python3-rpm-4.18.0-3.fc38.x86_64 python3-six-1.16.0-8.fc37.noarch readline-8.2-2.fc38.x86_64 rpm-4.18.0-3.fc38.x86_64 rpm-build-libs-4.18.0-3.fc38.x86_64 rpm-libs-4.18.0-3.fc38.x86_64 rpm-sign-libs-4.18.0-3.fc38.x86_64 sed-4.8-11.fc37.x86_64 setup-2.14.2-1.fc38.noarch shadow-utils-2:4.12.3-3.fc38.x86_64 sqlite-libs-3.39.4-1.fc38.x86_64 systemd-libs-252-587.fc38.x86_64 tpm2-tss-3.2.0-3.fc37.x86_64 tzdata-2022f-1.fc38.noarch xz-libs-5.2.7-1.fc38.x86_64 zchunk-libs-1.2.3-1.fc38.x86_64 zlib-1.2.12-5.fc38.x86_64 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-x86_64-1667627884.349232/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: 3.3 INFO: Mock Version: 3.3 Start: dnf install No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 43 kB/s | 3.0 kB 00:00 Copr repository 33 MB/s | 8.0 MB 00:00 fedora 197 kB/s | 9.1 kB 00:00 Last metadata expiration check: 0:00:01 ago on Sat Nov 5 05:58:43 2022. Dependencies resolved. ================================================================================ Package Arch Version Repo Size ================================================================================ Installing group/module packages: bash x86_64 5.2.2-2.fc38 fedora 1.8 M bzip2 x86_64 1.0.8-12.fc38 copr_base 53 k coreutils x86_64 9.1-8.fc38 copr_base 1.1 M cpio x86_64 2.13-13.fc38 fedora 276 k diffutils x86_64 3.8-3.fc37 fedora 378 k fedora-release-common noarch 38-0.4 fedora 22 k findutils x86_64 1:4.9.0-2.fc37 fedora 492 k gawk x86_64 5.1.1-4.fc37 fedora 1.0 M glibc-minimal-langpack x86_64 2.36.9000-11.fc38 fedora 22 k grep x86_64 3.8-1.fc38 fedora 292 k gzip x86_64 1.12-2.fc37 fedora 166 k info x86_64 6.8-4.fc37 fedora 225 k patch x86_64 2.7.6-17.fc37 fedora 124 k redhat-rpm-config noarch 232-1.fc38 fedora 81 k rpm-build x86_64 4.18.0-3.fc38 fedora 77 k sed x86_64 4.8-11.fc37 fedora 306 k shadow-utils x86_64 2:4.12.3-3.fc38 fedora 1.3 M tar x86_64 2:1.34-5.fc38 fedora 885 k unzip x86_64 6.0-58.fc37 fedora 182 k util-linux x86_64 2.38.1-2.fc38 fedora 2.3 M which x86_64 2.21-35.fc37 fedora 41 k xz x86_64 5.2.7-1.fc38 fedora 304 k Installing dependencies: alternatives x86_64 1.21-1.fc38 fedora 38 k ansible-srpm-macros noarch 1-8.1.fc38 fedora 8.6 k audit-libs x86_64 3.0.9-1.fc38 fedora 116 k authselect x86_64 1.4.0-3.fc37 fedora 144 k authselect-libs x86_64 1.4.0-3.fc37 fedora 248 k basesystem noarch 11-14.fc37 fedora 7.0 k binutils x86_64 2.39-3.fc38 fedora 5.4 M binutils-gold x86_64 2.39-3.fc38 fedora 778 k bzip2-libs x86_64 1.0.8-12.fc38 copr_base 42 k ca-certificates noarch 2022.2.54-5.fc37 fedora 829 k coreutils-common x86_64 9.1-8.fc38 copr_base 2.0 M cracklib x86_64 2.9.7-30.fc38 fedora 92 k crypto-policies noarch 20221003-1.gitcb1ad32.fc38 fedora 86 k curl x86_64 7.86.0-2.fc38 fedora 334 k cyrus-sasl-lib x86_64 2.1.28-8.fc38 fedora 792 k debugedit x86_64 5.0-5.fc37 fedora 77 k dwz x86_64 0.15-1.fc38 fedora 136 k ed x86_64 1.18-2.fc37 fedora 78 k efi-srpm-macros noarch 5-6.fc37 fedora 22 k elfutils x86_64 0.188-2.fc38 fedora 529 k elfutils-debuginfod-client x86_64 0.188-2.fc38 fedora 39 k elfutils-default-yama-scope noarch 0.188-2.fc38 fedora 15 k elfutils-libelf x86_64 0.188-2.fc38 fedora 196 k elfutils-libs x86_64 0.188-2.fc38 fedora 257 k fedora-gpg-keys noarch 38-0.3 fedora 125 k fedora-release noarch 38-0.4 fedora 11 k fedora-release-identity-basic noarch 38-0.4 fedora 12 k fedora-repos noarch 38-0.3 fedora 10 k fedora-repos-rawhide noarch 38-0.3 fedora 9.7 k file x86_64 5.42-4.fc37 fedora 49 k file-libs x86_64 5.42-4.fc37 fedora 676 k filesystem x86_64 3.18-2.fc37 fedora 1.1 M fonts-srpm-macros noarch 1:2.0.5-9.fc38 fedora 26 k fpc-srpm-macros noarch 1.3-6.fc37 fedora 7.7 k gdb-minimal x86_64 12.1-9.fc38 fedora 3.7 M gdbm-libs x86_64 1:1.23-2.fc37 fedora 56 k ghc-srpm-macros noarch 1.5.0-7.fc37 fedora 7.8 k glibc x86_64 2.36.9000-11.fc38 fedora 2.1 M glibc-common x86_64 2.36.9000-11.fc38 fedora 301 k glibc-gconv-extra x86_64 2.36.9000-11.fc38 fedora 1.6 M gmp x86_64 1:6.2.1-3.fc37 fedora 315 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 x86_64 2.13.1-5.fc37 fedora 44 k kernel-srpm-macros noarch 1.0-15.fc37 fedora 9.4 k keyutils-libs x86_64 1.6.1-5.fc37 fedora 31 k krb5-libs x86_64 1.19.2-11.fc37.1 fedora 727 k libacl x86_64 2.3.1-4.fc37 fedora 23 k libarchive x86_64 3.6.1-2.fc37 fedora 397 k libattr x86_64 2.5.1-5.fc37 fedora 18 k libblkid x86_64 2.38.1-2.fc38 fedora 107 k libbrotli x86_64 1.0.9-9.fc37 fedora 315 k libcap x86_64 2.48-5.fc37 fedora 67 k libcap-ng x86_64 0.8.3-3.fc37 fedora 33 k libcom_err x86_64 1.46.5-3.fc37 fedora 25 k libcurl x86_64 7.86.0-2.fc38 fedora 305 k libdb x86_64 5.3.28-53.fc37 fedora 760 k libeconf x86_64 0.4.0-4.fc37 fedora 27 k libevent x86_64 2.1.12-7.fc37 fedora 261 k libfdisk x86_64 2.38.1-2.fc38 fedora 160 k libffi x86_64 3.4.2-9.fc37 fedora 37 k libgcc x86_64 12.2.1-2.fc38 fedora 106 k libgomp x86_64 12.2.1-2.fc38 fedora 293 k libidn2 x86_64 2.3.4-1.fc38 fedora 160 k libmount x86_64 2.38.1-2.fc38 fedora 135 k libnghttp2 x86_64 1.50.0-1.fc38 copr_base 75 k libnsl2 x86_64 2.0.0-4.fc37 fedora 30 k libpkgconf x86_64 1.8.0-3.fc37 fedora 36 k libpsl x86_64 0.21.1-6.fc37 fedora 63 k libpwquality x86_64 1.4.4-11.fc37 fedora 116 k libselinux x86_64 3.4-5.fc37 fedora 86 k libsemanage x86_64 3.4-5.fc37 fedora 120 k libsepol x86_64 3.4-3.fc37 fedora 322 k libsigsegv x86_64 2.14-3.fc37 fedora 27 k libsmartcols x86_64 2.38.1-2.fc38 fedora 64 k libssh x86_64 0.10.4-2.fc38 fedora 209 k libssh-config noarch 0.10.4-2.fc38 fedora 8.8 k libstdc++ x86_64 12.2.1-2.fc38 fedora 800 k libtasn1 x86_64 4.18.0-3.fc37 fedora 75 k libtirpc x86_64 1.3.3-0.fc37 fedora 93 k libunistring x86_64 1.0-2.fc37 fedora 549 k libutempter x86_64 1.2.1-7.fc37 fedora 26 k libuuid x86_64 2.38.1-2.fc38 fedora 28 k libverto x86_64 0.3.2-4.fc37 fedora 21 k libxcrypt x86_64 4.4.30-1.fc38 fedora 118 k libxml2 x86_64 2.10.3-2.fc38 fedora 705 k libzstd x86_64 1.5.2-3.fc37 fedora 294 k lua-libs x86_64 5.4.4-6.fc38 fedora 131 k lua-srpm-macros noarch 1-7.fc37 fedora 8.8 k lz4-libs x86_64 1.9.3-5.fc37 fedora 70 k mpfr x86_64 4.1.0-10.fc37 fedora 331 k ncurses-base noarch 6.3-3.20220501.fc37 fedora 86 k ncurses-libs x86_64 6.3-3.20220501.fc37 fedora 329 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 x86_64 2.6.3-1.fc38 fedora 254 k openssl-libs x86_64 1:3.0.5-6.fc38 fedora 2.1 M p11-kit x86_64 0.24.1-3.fc37 fedora 376 k p11-kit-trust x86_64 0.24.1-3.fc37 fedora 138 k package-notes-srpm-macros noarch 0.5-6.fc38 fedora 11 k pam x86_64 1.5.2-14.fc37 fedora 560 k pam-libs x86_64 1.5.2-14.fc37 fedora 58 k pcre2 x86_64 10.40-1.fc37.1 fedora 236 k pcre2-syntax noarch 10.40-1.fc37.1 fedora 142 k perl-srpm-macros noarch 1-46.fc37 fedora 8.3 k pkgconf x86_64 1.8.0-3.fc37 fedora 41 k pkgconf-m4 noarch 1.8.0-3.fc37 fedora 14 k pkgconf-pkg-config x86_64 1.8.0-3.fc37 fedora 10 k popt x86_64 1.19-1.fc38 fedora 66 k publicsuffix-list-dafsa noarch 20210518-5.fc37 fedora 58 k python-srpm-macros noarch 3.11-5.fc38 fedora 24 k qt5-srpm-macros noarch 5.15.7-1.fc38 fedora 7.9 k readline x86_64 8.2-2.fc38 fedora 211 k rpm x86_64 4.18.0-3.fc38 fedora 570 k rpm-build-libs x86_64 4.18.0-3.fc38 fedora 94 k rpm-libs x86_64 4.18.0-3.fc38 fedora 320 k rpmautospec-rpm-macros noarch 0.3.0-1.fc37 fedora 8.8 k rust-srpm-macros noarch 23-1.fc38 fedora 9.4 k setup noarch 2.14.2-1.fc38 fedora 151 k sqlite-libs x86_64 3.39.4-1.fc38 fedora 658 k systemd-libs x86_64 252-587.fc38 fedora 631 k tzdata noarch 2022f-1.fc38 fedora 715 k util-linux-core x86_64 2.38.1-2.fc38 fedora 470 k xxhash-libs x86_64 0.8.1-3.fc37 fedora 41 k xz-libs x86_64 5.2.7-1.fc38 fedora 93 k zip x86_64 3.0-33.fc37 fedora 259 k zlib x86_64 1.2.12-5.fc38 fedora 94 k zstd x86_64 1.5.2-3.fc37 fedora 447 k Installing Groups: Buildsystem building group Transaction Summary ================================================================================ Install 151 Packages Total size: 51 M Installed size: 176 M Downloading Packages: [SKIPPED] bzip2-1.0.8-12.fc38.x86_64.rpm: Already downloaded [SKIPPED] bzip2-libs-1.0.8-12.fc38.x86_64.rpm: Already downloaded [SKIPPED] coreutils-9.1-8.fc38.x86_64.rpm: Already downloaded [SKIPPED] coreutils-common-9.1-8.fc38.x86_64.rpm: Already downloaded [SKIPPED] libnghttp2-1.50.0-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] alternatives-1.21-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] ansible-srpm-macros-1-8.1.fc38.noarch.rpm: Already downloaded [SKIPPED] audit-libs-3.0.9-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] authselect-1.4.0-3.fc37.x86_64.rpm: Already downloaded [SKIPPED] authselect-libs-1.4.0-3.fc37.x86_64.rpm: Already downloaded [SKIPPED] basesystem-11-14.fc37.noarch.rpm: Already downloaded [SKIPPED] bash-5.2.2-2.fc38.x86_64.rpm: Already downloaded [SKIPPED] binutils-2.39-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] binutils-gold-2.39-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] ca-certificates-2022.2.54-5.fc37.noarch.rpm: Already downloaded [SKIPPED] cpio-2.13-13.fc38.x86_64.rpm: Already downloaded [SKIPPED] cracklib-2.9.7-30.fc38.x86_64.rpm: Already downloaded [SKIPPED] crypto-policies-20221003-1.gitcb1ad32.fc38.noarch.rpm: Already downloaded [SKIPPED] curl-7.86.0-2.fc38.x86_64.rpm: Already downloaded [SKIPPED] cyrus-sasl-lib-2.1.28-8.fc38.x86_64.rpm: Already downloaded [SKIPPED] debugedit-5.0-5.fc37.x86_64.rpm: Already downloaded [SKIPPED] diffutils-3.8-3.fc37.x86_64.rpm: Already downloaded [SKIPPED] dwz-0.15-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] ed-1.18-2.fc37.x86_64.rpm: Already downloaded [SKIPPED] efi-srpm-macros-5-6.fc37.noarch.rpm: Already downloaded [SKIPPED] elfutils-0.188-2.fc38.x86_64.rpm: Already downloaded [SKIPPED] elfutils-debuginfod-client-0.188-2.fc38.x86_64.rpm: Already downloaded [SKIPPED] elfutils-default-yama-scope-0.188-2.fc38.noarch.rpm: Already downloaded [SKIPPED] elfutils-libelf-0.188-2.fc38.x86_64.rpm: Already downloaded [SKIPPED] elfutils-libs-0.188-2.fc38.x86_64.rpm: Already downloaded [SKIPPED] fedora-gpg-keys-38-0.3.noarch.rpm: Already downloaded [SKIPPED] fedora-release-38-0.4.noarch.rpm: Already downloaded [SKIPPED] fedora-release-common-38-0.4.noarch.rpm: Already downloaded [SKIPPED] fedora-release-identity-basic-38-0.4.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] file-5.42-4.fc37.x86_64.rpm: Already downloaded [SKIPPED] file-libs-5.42-4.fc37.x86_64.rpm: Already downloaded [SKIPPED] filesystem-3.18-2.fc37.x86_64.rpm: Already downloaded [SKIPPED] findutils-4.9.0-2.fc37.x86_64.rpm: Already downloaded [SKIPPED] fonts-srpm-macros-2.0.5-9.fc38.noarch.rpm: Already downloaded [SKIPPED] fpc-srpm-macros-1.3-6.fc37.noarch.rpm: Already downloaded [SKIPPED] gawk-5.1.1-4.fc37.x86_64.rpm: Already downloaded [SKIPPED] gdb-minimal-12.1-9.fc38.x86_64.rpm: Already downloaded [SKIPPED] gdbm-libs-1.23-2.fc37.x86_64.rpm: Already downloaded [SKIPPED] ghc-srpm-macros-1.5.0-7.fc37.noarch.rpm: Already downloaded [SKIPPED] glibc-2.36.9000-11.fc38.x86_64.rpm: Already downloaded [SKIPPED] glibc-common-2.36.9000-11.fc38.x86_64.rpm: Already downloaded [SKIPPED] glibc-gconv-extra-2.36.9000-11.fc38.x86_64.rpm: Already downloaded [SKIPPED] glibc-minimal-langpack-2.36.9000-11.fc38.x86_64.rpm: Already downloaded [SKIPPED] gmp-6.2.1-3.fc37.x86_64.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] grep-3.8-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] gzip-1.12-2.fc37.x86_64.rpm: Already downloaded [SKIPPED] info-6.8-4.fc37.x86_64.rpm: Already downloaded [SKIPPED] jansson-2.13.1-5.fc37.x86_64.rpm: Already downloaded [SKIPPED] kernel-srpm-macros-1.0-15.fc37.noarch.rpm: Already downloaded [SKIPPED] keyutils-libs-1.6.1-5.fc37.x86_64.rpm: Already downloaded [SKIPPED] krb5-libs-1.19.2-11.fc37.1.x86_64.rpm: Already downloaded [SKIPPED] libacl-2.3.1-4.fc37.x86_64.rpm: Already downloaded [SKIPPED] libarchive-3.6.1-2.fc37.x86_64.rpm: Already downloaded [SKIPPED] libattr-2.5.1-5.fc37.x86_64.rpm: Already downloaded [SKIPPED] libblkid-2.38.1-2.fc38.x86_64.rpm: Already downloaded [SKIPPED] libbrotli-1.0.9-9.fc37.x86_64.rpm: Already downloaded [SKIPPED] libcap-2.48-5.fc37.x86_64.rpm: Already downloaded [SKIPPED] libcap-ng-0.8.3-3.fc37.x86_64.rpm: Already downloaded [SKIPPED] libcom_err-1.46.5-3.fc37.x86_64.rpm: Already downloaded [SKIPPED] libcurl-7.86.0-2.fc38.x86_64.rpm: Already downloaded [SKIPPED] libdb-5.3.28-53.fc37.x86_64.rpm: Already downloaded [SKIPPED] libeconf-0.4.0-4.fc37.x86_64.rpm: Already downloaded [SKIPPED] libevent-2.1.12-7.fc37.x86_64.rpm: Already downloaded [SKIPPED] libfdisk-2.38.1-2.fc38.x86_64.rpm: Already downloaded [SKIPPED] libffi-3.4.2-9.fc37.x86_64.rpm: Already downloaded [SKIPPED] libgcc-12.2.1-2.fc38.x86_64.rpm: Already downloaded [SKIPPED] libgomp-12.2.1-2.fc38.x86_64.rpm: Already downloaded [SKIPPED] libidn2-2.3.4-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] libmount-2.38.1-2.fc38.x86_64.rpm: Already downloaded [SKIPPED] libnsl2-2.0.0-4.fc37.x86_64.rpm: Already downloaded [SKIPPED] libpkgconf-1.8.0-3.fc37.x86_64.rpm: Already downloaded [SKIPPED] libpsl-0.21.1-6.fc37.x86_64.rpm: Already downloaded [SKIPPED] libpwquality-1.4.4-11.fc37.x86_64.rpm: Already downloaded [SKIPPED] libselinux-3.4-5.fc37.x86_64.rpm: Already downloaded [SKIPPED] libsemanage-3.4-5.fc37.x86_64.rpm: Already downloaded [SKIPPED] libsepol-3.4-3.fc37.x86_64.rpm: Already downloaded [SKIPPED] libsigsegv-2.14-3.fc37.x86_64.rpm: Already downloaded [SKIPPED] libsmartcols-2.38.1-2.fc38.x86_64.rpm: Already downloaded [SKIPPED] libssh-0.10.4-2.fc38.x86_64.rpm: Already downloaded [SKIPPED] libssh-config-0.10.4-2.fc38.noarch.rpm: Already downloaded [SKIPPED] libstdc++-12.2.1-2.fc38.x86_64.rpm: Already downloaded [SKIPPED] libtasn1-4.18.0-3.fc37.x86_64.rpm: Already downloaded [SKIPPED] libtirpc-1.3.3-0.fc37.x86_64.rpm: Already downloaded [SKIPPED] libunistring-1.0-2.fc37.x86_64.rpm: Already downloaded [SKIPPED] libutempter-1.2.1-7.fc37.x86_64.rpm: Already downloaded [SKIPPED] libuuid-2.38.1-2.fc38.x86_64.rpm: Already downloaded [SKIPPED] libverto-0.3.2-4.fc37.x86_64.rpm: Already downloaded [SKIPPED] libxcrypt-4.4.30-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] libxml2-2.10.3-2.fc38.x86_64.rpm: Already downloaded [SKIPPED] libzstd-1.5.2-3.fc37.x86_64.rpm: Already downloaded [SKIPPED] lua-libs-5.4.4-6.fc38.x86_64.rpm: Already downloaded [SKIPPED] lua-srpm-macros-1-7.fc37.noarch.rpm: Already downloaded [SKIPPED] lz4-libs-1.9.3-5.fc37.x86_64.rpm: Already downloaded [SKIPPED] mpfr-4.1.0-10.fc37.x86_64.rpm: Already downloaded [SKIPPED] ncurses-base-6.3-3.20220501.fc37.noarch.rpm: Already downloaded [SKIPPED] ncurses-libs-6.3-3.20220501.fc37.x86_64.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.x86_64.rpm: Already downloaded [SKIPPED] openssl-libs-3.0.5-6.fc38.x86_64.rpm: Already downloaded [SKIPPED] p11-kit-0.24.1-3.fc37.x86_64.rpm: Already downloaded [SKIPPED] p11-kit-trust-0.24.1-3.fc37.x86_64.rpm: Already downloaded [SKIPPED] package-notes-srpm-macros-0.5-6.fc38.noarch.rpm: Already downloaded [SKIPPED] pam-1.5.2-14.fc37.x86_64.rpm: Already downloaded [SKIPPED] pam-libs-1.5.2-14.fc37.x86_64.rpm: Already downloaded [SKIPPED] patch-2.7.6-17.fc37.x86_64.rpm: Already downloaded [SKIPPED] pcre2-10.40-1.fc37.1.x86_64.rpm: Already downloaded [SKIPPED] pcre2-syntax-10.40-1.fc37.1.noarch.rpm: Already downloaded [SKIPPED] perl-srpm-macros-1-46.fc37.noarch.rpm: Already downloaded [SKIPPED] pkgconf-1.8.0-3.fc37.x86_64.rpm: Already downloaded [SKIPPED] pkgconf-m4-1.8.0-3.fc37.noarch.rpm: Already downloaded [SKIPPED] pkgconf-pkg-config-1.8.0-3.fc37.x86_64.rpm: Already downloaded [SKIPPED] popt-1.19-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] publicsuffix-list-dafsa-20210518-5.fc37.noarch.rpm: Already downloaded [SKIPPED] python-srpm-macros-3.11-5.fc38.noarch.rpm: Already downloaded [SKIPPED] qt5-srpm-macros-5.15.7-1.fc38.noarch.rpm: Already downloaded [SKIPPED] readline-8.2-2.fc38.x86_64.rpm: Already downloaded [SKIPPED] redhat-rpm-config-232-1.fc38.noarch.rpm: Already downloaded [SKIPPED] rpm-4.18.0-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] rpm-build-4.18.0-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] rpm-build-libs-4.18.0-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] rpm-libs-4.18.0-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] rpmautospec-rpm-macros-0.3.0-1.fc37.noarch.rpm: Already downloaded [SKIPPED] rust-srpm-macros-23-1.fc38.noarch.rpm: Already downloaded [SKIPPED] sed-4.8-11.fc37.x86_64.rpm: Already downloaded [SKIPPED] setup-2.14.2-1.fc38.noarch.rpm: Already downloaded [SKIPPED] shadow-utils-4.12.3-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] sqlite-libs-3.39.4-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] systemd-libs-252-587.fc38.x86_64.rpm: Already downloaded [SKIPPED] tar-1.34-5.fc38.x86_64.rpm: Already downloaded [SKIPPED] tzdata-2022f-1.fc38.noarch.rpm: Already downloaded [SKIPPED] unzip-6.0-58.fc37.x86_64.rpm: Already downloaded [SKIPPED] util-linux-2.38.1-2.fc38.x86_64.rpm: Already downloaded [SKIPPED] util-linux-core-2.38.1-2.fc38.x86_64.rpm: Already downloaded [SKIPPED] which-2.21-35.fc37.x86_64.rpm: Already downloaded [SKIPPED] xxhash-libs-0.8.1-3.fc37.x86_64.rpm: Already downloaded [SKIPPED] xz-5.2.7-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] xz-libs-5.2.7-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] zip-3.0-33.fc37.x86_64.rpm: Already downloaded [SKIPPED] zlib-1.2.12-5.fc38.x86_64.rpm: Already downloaded [SKIPPED] zstd-1.5.2-3.fc37.x86_64.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.x86_64 1/1 Preparing : 1/1 Installing : libgcc-12.2.1-2.fc38.x86_64 1/151 Running scriptlet: libgcc-12.2.1-2.fc38.x86_64 1/151 Installing : crypto-policies-20221003-1.gitcb1ad32.fc38.noarc 2/151 Running scriptlet: crypto-policies-20221003-1.gitcb1ad32.fc38.noarc 2/151 Installing : fedora-release-identity-basic-38-0.4.noarch 3/151 Installing : tzdata-2022f-1.fc38.noarch 4/151 Installing : rust-srpm-macros-23-1.fc38.noarch 5/151 Installing : qt5-srpm-macros-5.15.7-1.fc38.noarch 6/151 Installing : publicsuffix-list-dafsa-20210518-5.fc37.noarch 7/151 Installing : pkgconf-m4-1.8.0-3.fc37.noarch 8/151 Installing : perl-srpm-macros-1-46.fc37.noarch 9/151 Installing : pcre2-syntax-10.40-1.fc37.1.noarch 10/151 Installing : package-notes-srpm-macros-0.5-6.fc38.noarch 11/151 Installing : openblas-srpm-macros-2-12.fc37.noarch 12/151 Installing : ocaml-srpm-macros-7-2.fc37.noarch 13/151 Installing : nim-srpm-macros-3-7.fc37.noarch 14/151 Installing : ncurses-base-6.3-3.20220501.fc37.noarch 15/151 Installing : libssh-config-0.10.4-2.fc38.noarch 16/151 Installing : kernel-srpm-macros-1.0-15.fc37.noarch 17/151 Installing : gnat-srpm-macros-4-16.fc37.noarch 18/151 Installing : ghc-srpm-macros-1.5.0-7.fc37.noarch 19/151 Installing : fpc-srpm-macros-1.3-6.fc37.noarch 20/151 Installing : fedora-gpg-keys-38-0.3.noarch 21/151 Installing : fedora-release-38-0.4.noarch 22/151 Installing : fedora-release-common-38-0.4.noarch 23/151 Installing : fedora-repos-rawhide-38-0.3.noarch 24/151 Installing : fedora-repos-38-0.3.noarch 25/151 Installing : setup-2.14.2-1.fc38.noarch 26/151 warning: /etc/hosts created as /etc/hosts.rpmnew Running scriptlet: setup-2.14.2-1.fc38.noarch 26/151 Installing : filesystem-3.18-2.fc37.x86_64 27/151 Installing : basesystem-11-14.fc37.noarch 28/151 Installing : glibc-gconv-extra-2.36.9000-11.fc38.x86_64 29/151 Running scriptlet: glibc-gconv-extra-2.36.9000-11.fc38.x86_64 29/151 Installing : glibc-minimal-langpack-2.36.9000-11.fc38.x86_64 30/151 Installing : glibc-common-2.36.9000-11.fc38.x86_64 31/151 Running scriptlet: glibc-2.36.9000-11.fc38.x86_64 32/151 Installing : glibc-2.36.9000-11.fc38.x86_64 32/151 Running scriptlet: glibc-2.36.9000-11.fc38.x86_64 32/151 Installing : ncurses-libs-6.3-3.20220501.fc37.x86_64 33/151 Installing : bash-5.2.2-2.fc38.x86_64 34/151 Running scriptlet: bash-5.2.2-2.fc38.x86_64 34/151 Installing : zlib-1.2.12-5.fc38.x86_64 35/151 Installing : xz-libs-5.2.7-1.fc38.x86_64 36/151 Installing : bzip2-libs-1.0.8-12.fc38.x86_64 37/151 Installing : elfutils-libelf-0.188-2.fc38.x86_64 38/151 Installing : libstdc++-12.2.1-2.fc38.x86_64 39/151 Installing : libuuid-2.38.1-2.fc38.x86_64 40/151 Installing : libzstd-1.5.2-3.fc37.x86_64 41/151 Installing : popt-1.19-1.fc38.x86_64 42/151 Installing : libblkid-2.38.1-2.fc38.x86_64 43/151 Installing : readline-8.2-2.fc38.x86_64 44/151 Installing : gmp-1:6.2.1-3.fc37.x86_64 45/151 Installing : libattr-2.5.1-5.fc37.x86_64 46/151 Installing : libacl-2.3.1-4.fc37.x86_64 47/151 Installing : libcap-2.48-5.fc37.x86_64 48/151 Installing : libxcrypt-4.4.30-1.fc38.x86_64 49/151 Installing : lz4-libs-1.9.3-5.fc37.x86_64 50/151 Installing : systemd-libs-252-587.fc38.x86_64 51/151 Installing : mpfr-4.1.0-10.fc37.x86_64 52/151 Installing : dwz-0.15-1.fc38.x86_64 53/151 Installing : unzip-6.0-58.fc37.x86_64 54/151 Installing : file-libs-5.42-4.fc37.x86_64 55/151 Installing : file-5.42-4.fc37.x86_64 56/151 Installing : sqlite-libs-3.39.4-1.fc38.x86_64 57/151 Installing : alternatives-1.21-1.fc38.x86_64 58/151 Installing : libcap-ng-0.8.3-3.fc37.x86_64 59/151 Installing : audit-libs-3.0.9-1.fc38.x86_64 60/151 Installing : libcom_err-1.46.5-3.fc37.x86_64 61/151 Installing : libeconf-0.4.0-4.fc37.x86_64 62/151 Installing : pam-libs-1.5.2-14.fc37.x86_64 63/151 Installing : libsepol-3.4-3.fc37.x86_64 64/151 Installing : libsmartcols-2.38.1-2.fc38.x86_64 65/151 Installing : libunistring-1.0-2.fc37.x86_64 66/151 Installing : libidn2-2.3.4-1.fc38.x86_64 67/151 Installing : lua-libs-5.4.4-6.fc38.x86_64 68/151 Installing : pcre2-10.40-1.fc37.1.x86_64 69/151 Installing : libselinux-3.4-5.fc37.x86_64 70/151 Installing : sed-4.8-11.fc37.x86_64 71/151 Installing : grep-3.8-1.fc38.x86_64 72/151 Installing : findutils-1:4.9.0-2.fc37.x86_64 73/151 Installing : xz-5.2.7-1.fc38.x86_64 74/151 Installing : libmount-2.38.1-2.fc38.x86_64 75/151 Installing : util-linux-core-2.38.1-2.fc38.x86_64 76/151 Installing : libsemanage-3.4-5.fc37.x86_64 77/151 Installing : shadow-utils-2:4.12.3-3.fc38.x86_64 78/151 Running scriptlet: libutempter-1.2.1-7.fc37.x86_64 79/151 Installing : libutempter-1.2.1-7.fc37.x86_64 79/151 Installing : tar-2:1.34-5.fc38.x86_64 80/151 Installing : libpsl-0.21.1-6.fc37.x86_64 81/151 Installing : zip-3.0-33.fc37.x86_64 82/151 Installing : zstd-1.5.2-3.fc37.x86_64 83/151 Installing : libfdisk-2.38.1-2.fc38.x86_64 84/151 Installing : bzip2-1.0.8-12.fc38.x86_64 85/151 Installing : libxml2-2.10.3-2.fc38.x86_64 86/151 Installing : ed-1.18-2.fc37.x86_64 87/151 Installing : patch-2.7.6-17.fc37.x86_64 88/151 Installing : elfutils-default-yama-scope-0.188-2.fc38.noarch 89/151 Running scriptlet: elfutils-default-yama-scope-0.188-2.fc38.noarch 89/151 Installing : libnghttp2-1.50.0-1.fc38.x86_64 90/151 Installing : cpio-2.13-13.fc38.x86_64 91/151 Installing : diffutils-3.8-3.fc37.x86_64 92/151 Installing : gdbm-libs-1:1.23-2.fc37.x86_64 93/151 Installing : cyrus-sasl-lib-2.1.28-8.fc38.x86_64 94/151 Installing : jansson-2.13.1-5.fc37.x86_64 95/151 Installing : keyutils-libs-1.6.1-5.fc37.x86_64 96/151 Installing : libbrotli-1.0.9-9.fc37.x86_64 97/151 Installing : libdb-5.3.28-53.fc37.x86_64 98/151 Installing : libffi-3.4.2-9.fc37.x86_64 99/151 Installing : p11-kit-0.24.1-3.fc37.x86_64 100/151 Installing : libgomp-12.2.1-2.fc38.x86_64 101/151 Installing : libpkgconf-1.8.0-3.fc37.x86_64 102/151 Installing : pkgconf-1.8.0-3.fc37.x86_64 103/151 Installing : pkgconf-pkg-config-1.8.0-3.fc37.x86_64 104/151 Installing : libsigsegv-2.14-3.fc37.x86_64 105/151 Installing : gawk-5.1.1-4.fc37.x86_64 106/151 Installing : libtasn1-4.18.0-3.fc37.x86_64 107/151 Installing : p11-kit-trust-0.24.1-3.fc37.x86_64 108/151 Running scriptlet: p11-kit-trust-0.24.1-3.fc37.x86_64 108/151 Installing : libverto-0.3.2-4.fc37.x86_64 109/151 Installing : xxhash-libs-0.8.1-3.fc37.x86_64 110/151 Installing : ansible-srpm-macros-1-8.1.fc38.noarch 111/151 Installing : coreutils-common-9.1-8.fc38.x86_64 112/151 Installing : openssl-libs-1:3.0.5-6.fc38.x86_64 113/151 Installing : coreutils-9.1-8.fc38.x86_64 114/151 Running scriptlet: ca-certificates-2022.2.54-5.fc37.noarch 115/151 Installing : ca-certificates-2022.2.54-5.fc37.noarch 115/151 Running scriptlet: ca-certificates-2022.2.54-5.fc37.noarch 115/151 Installing : krb5-libs-1.19.2-11.fc37.1.x86_64 116/151 Installing : rpm-libs-4.18.0-3.fc38.x86_64 117/151 Installing : libtirpc-1.3.3-0.fc37.x86_64 118/151 Running scriptlet: authselect-libs-1.4.0-3.fc37.x86_64 119/151 Installing : authselect-libs-1.4.0-3.fc37.x86_64 119/151 Installing : gzip-1.12-2.fc37.x86_64 120/151 Installing : cracklib-2.9.7-30.fc38.x86_64 121/151 Installing : libpwquality-1.4.4-11.fc37.x86_64 122/151 Installing : authselect-1.4.0-3.fc37.x86_64 123/151 Installing : libnsl2-2.0.0-4.fc37.x86_64 124/151 Installing : pam-1.5.2-14.fc37.x86_64 125/151 Installing : libssh-0.10.4-2.fc38.x86_64 126/151 Installing : libarchive-3.6.1-2.fc37.x86_64 127/151 Installing : libevent-2.1.12-7.fc37.x86_64 128/151 Installing : openldap-2.6.3-1.fc38.x86_64 129/151 Installing : libcurl-7.86.0-2.fc38.x86_64 130/151 Installing : elfutils-debuginfod-client-0.188-2.fc38.x86_64 131/151 Installing : elfutils-libs-0.188-2.fc38.x86_64 132/151 Installing : binutils-gold-2.39-3.fc38.x86_64 133/151 Installing : binutils-2.39-3.fc38.x86_64 134/151 Running scriptlet: binutils-2.39-3.fc38.x86_64 134/151 Installing : elfutils-0.188-2.fc38.x86_64 135/151 Installing : gdb-minimal-12.1-9.fc38.x86_64 136/151 Installing : debugedit-5.0-5.fc37.x86_64 137/151 Installing : rpm-build-libs-4.18.0-3.fc38.x86_64 138/151 Installing : curl-7.86.0-2.fc38.x86_64 139/151 Running scriptlet: rpm-4.18.0-3.fc38.x86_64 140/151 Installing : rpm-4.18.0-3.fc38.x86_64 140/151 Installing : efi-srpm-macros-5-6.fc37.noarch 141/151 Installing : lua-srpm-macros-1-7.fc37.noarch 142/151 Installing : rpmautospec-rpm-macros-0.3.0-1.fc37.noarch 143/151 Installing : fonts-srpm-macros-1:2.0.5-9.fc38.noarch 144/151 Installing : go-srpm-macros-3.2.0-1.fc38.noarch 145/151 Installing : python-srpm-macros-3.11-5.fc38.noarch 146/151 Installing : redhat-rpm-config-232-1.fc38.noarch 147/151 Installing : rpm-build-4.18.0-3.fc38.x86_64 148/151 Installing : util-linux-2.38.1-2.fc38.x86_64 149/151 Installing : which-2.21-35.fc37.x86_64 150/151 Installing : info-6.8-4.fc37.x86_64 151/151 Running scriptlet: filesystem-3.18-2.fc37.x86_64 151/151 Running scriptlet: ca-certificates-2022.2.54-5.fc37.noarch 151/151 Running scriptlet: authselect-libs-1.4.0-3.fc37.x86_64 151/151 Running scriptlet: rpm-4.18.0-3.fc38.x86_64 151/151 Running scriptlet: info-6.8-4.fc37.x86_64 151/151 Verifying : bzip2-1.0.8-12.fc38.x86_64 1/151 Verifying : bzip2-libs-1.0.8-12.fc38.x86_64 2/151 Verifying : coreutils-9.1-8.fc38.x86_64 3/151 Verifying : coreutils-common-9.1-8.fc38.x86_64 4/151 Verifying : libnghttp2-1.50.0-1.fc38.x86_64 5/151 Verifying : alternatives-1.21-1.fc38.x86_64 6/151 Verifying : ansible-srpm-macros-1-8.1.fc38.noarch 7/151 Verifying : audit-libs-3.0.9-1.fc38.x86_64 8/151 Verifying : authselect-1.4.0-3.fc37.x86_64 9/151 Verifying : authselect-libs-1.4.0-3.fc37.x86_64 10/151 Verifying : basesystem-11-14.fc37.noarch 11/151 Verifying : bash-5.2.2-2.fc38.x86_64 12/151 Verifying : binutils-2.39-3.fc38.x86_64 13/151 Verifying : binutils-gold-2.39-3.fc38.x86_64 14/151 Verifying : ca-certificates-2022.2.54-5.fc37.noarch 15/151 Verifying : cpio-2.13-13.fc38.x86_64 16/151 Verifying : cracklib-2.9.7-30.fc38.x86_64 17/151 Verifying : crypto-policies-20221003-1.gitcb1ad32.fc38.noarc 18/151 Verifying : curl-7.86.0-2.fc38.x86_64 19/151 Verifying : cyrus-sasl-lib-2.1.28-8.fc38.x86_64 20/151 Verifying : debugedit-5.0-5.fc37.x86_64 21/151 Verifying : diffutils-3.8-3.fc37.x86_64 22/151 Verifying : dwz-0.15-1.fc38.x86_64 23/151 Verifying : ed-1.18-2.fc37.x86_64 24/151 Verifying : efi-srpm-macros-5-6.fc37.noarch 25/151 Verifying : elfutils-0.188-2.fc38.x86_64 26/151 Verifying : elfutils-debuginfod-client-0.188-2.fc38.x86_64 27/151 Verifying : elfutils-default-yama-scope-0.188-2.fc38.noarch 28/151 Verifying : elfutils-libelf-0.188-2.fc38.x86_64 29/151 Verifying : elfutils-libs-0.188-2.fc38.x86_64 30/151 Verifying : fedora-gpg-keys-38-0.3.noarch 31/151 Verifying : fedora-release-38-0.4.noarch 32/151 Verifying : fedora-release-common-38-0.4.noarch 33/151 Verifying : fedora-release-identity-basic-38-0.4.noarch 34/151 Verifying : fedora-repos-38-0.3.noarch 35/151 Verifying : fedora-repos-rawhide-38-0.3.noarch 36/151 Verifying : file-5.42-4.fc37.x86_64 37/151 Verifying : file-libs-5.42-4.fc37.x86_64 38/151 Verifying : filesystem-3.18-2.fc37.x86_64 39/151 Verifying : findutils-1:4.9.0-2.fc37.x86_64 40/151 Verifying : fonts-srpm-macros-1:2.0.5-9.fc38.noarch 41/151 Verifying : fpc-srpm-macros-1.3-6.fc37.noarch 42/151 Verifying : gawk-5.1.1-4.fc37.x86_64 43/151 Verifying : gdb-minimal-12.1-9.fc38.x86_64 44/151 Verifying : gdbm-libs-1:1.23-2.fc37.x86_64 45/151 Verifying : ghc-srpm-macros-1.5.0-7.fc37.noarch 46/151 Verifying : glibc-2.36.9000-11.fc38.x86_64 47/151 Verifying : glibc-common-2.36.9000-11.fc38.x86_64 48/151 Verifying : glibc-gconv-extra-2.36.9000-11.fc38.x86_64 49/151 Verifying : glibc-minimal-langpack-2.36.9000-11.fc38.x86_64 50/151 Verifying : gmp-1:6.2.1-3.fc37.x86_64 51/151 Verifying : gnat-srpm-macros-4-16.fc37.noarch 52/151 Verifying : go-srpm-macros-3.2.0-1.fc38.noarch 53/151 Verifying : grep-3.8-1.fc38.x86_64 54/151 Verifying : gzip-1.12-2.fc37.x86_64 55/151 Verifying : info-6.8-4.fc37.x86_64 56/151 Verifying : jansson-2.13.1-5.fc37.x86_64 57/151 Verifying : kernel-srpm-macros-1.0-15.fc37.noarch 58/151 Verifying : keyutils-libs-1.6.1-5.fc37.x86_64 59/151 Verifying : krb5-libs-1.19.2-11.fc37.1.x86_64 60/151 Verifying : libacl-2.3.1-4.fc37.x86_64 61/151 Verifying : libarchive-3.6.1-2.fc37.x86_64 62/151 Verifying : libattr-2.5.1-5.fc37.x86_64 63/151 Verifying : libblkid-2.38.1-2.fc38.x86_64 64/151 Verifying : libbrotli-1.0.9-9.fc37.x86_64 65/151 Verifying : libcap-2.48-5.fc37.x86_64 66/151 Verifying : libcap-ng-0.8.3-3.fc37.x86_64 67/151 Verifying : libcom_err-1.46.5-3.fc37.x86_64 68/151 Verifying : libcurl-7.86.0-2.fc38.x86_64 69/151 Verifying : libdb-5.3.28-53.fc37.x86_64 70/151 Verifying : libeconf-0.4.0-4.fc37.x86_64 71/151 Verifying : libevent-2.1.12-7.fc37.x86_64 72/151 Verifying : libfdisk-2.38.1-2.fc38.x86_64 73/151 Verifying : libffi-3.4.2-9.fc37.x86_64 74/151 Verifying : libgcc-12.2.1-2.fc38.x86_64 75/151 Verifying : libgomp-12.2.1-2.fc38.x86_64 76/151 Verifying : libidn2-2.3.4-1.fc38.x86_64 77/151 Verifying : libmount-2.38.1-2.fc38.x86_64 78/151 Verifying : libnsl2-2.0.0-4.fc37.x86_64 79/151 Verifying : libpkgconf-1.8.0-3.fc37.x86_64 80/151 Verifying : libpsl-0.21.1-6.fc37.x86_64 81/151 Verifying : libpwquality-1.4.4-11.fc37.x86_64 82/151 Verifying : libselinux-3.4-5.fc37.x86_64 83/151 Verifying : libsemanage-3.4-5.fc37.x86_64 84/151 Verifying : libsepol-3.4-3.fc37.x86_64 85/151 Verifying : libsigsegv-2.14-3.fc37.x86_64 86/151 Verifying : libsmartcols-2.38.1-2.fc38.x86_64 87/151 Verifying : libssh-0.10.4-2.fc38.x86_64 88/151 Verifying : libssh-config-0.10.4-2.fc38.noarch 89/151 Verifying : libstdc++-12.2.1-2.fc38.x86_64 90/151 Verifying : libtasn1-4.18.0-3.fc37.x86_64 91/151 Verifying : libtirpc-1.3.3-0.fc37.x86_64 92/151 Verifying : libunistring-1.0-2.fc37.x86_64 93/151 Verifying : libutempter-1.2.1-7.fc37.x86_64 94/151 Verifying : libuuid-2.38.1-2.fc38.x86_64 95/151 Verifying : libverto-0.3.2-4.fc37.x86_64 96/151 Verifying : libxcrypt-4.4.30-1.fc38.x86_64 97/151 Verifying : libxml2-2.10.3-2.fc38.x86_64 98/151 Verifying : libzstd-1.5.2-3.fc37.x86_64 99/151 Verifying : lua-libs-5.4.4-6.fc38.x86_64 100/151 Verifying : lua-srpm-macros-1-7.fc37.noarch 101/151 Verifying : lz4-libs-1.9.3-5.fc37.x86_64 102/151 Verifying : mpfr-4.1.0-10.fc37.x86_64 103/151 Verifying : ncurses-base-6.3-3.20220501.fc37.noarch 104/151 Verifying : ncurses-libs-6.3-3.20220501.fc37.x86_64 105/151 Verifying : nim-srpm-macros-3-7.fc37.noarch 106/151 Verifying : ocaml-srpm-macros-7-2.fc37.noarch 107/151 Verifying : openblas-srpm-macros-2-12.fc37.noarch 108/151 Verifying : openldap-2.6.3-1.fc38.x86_64 109/151 Verifying : openssl-libs-1:3.0.5-6.fc38.x86_64 110/151 Verifying : p11-kit-0.24.1-3.fc37.x86_64 111/151 Verifying : p11-kit-trust-0.24.1-3.fc37.x86_64 112/151 Verifying : package-notes-srpm-macros-0.5-6.fc38.noarch 113/151 Verifying : pam-1.5.2-14.fc37.x86_64 114/151 Verifying : pam-libs-1.5.2-14.fc37.x86_64 115/151 Verifying : patch-2.7.6-17.fc37.x86_64 116/151 Verifying : pcre2-10.40-1.fc37.1.x86_64 117/151 Verifying : pcre2-syntax-10.40-1.fc37.1.noarch 118/151 Verifying : perl-srpm-macros-1-46.fc37.noarch 119/151 Verifying : pkgconf-1.8.0-3.fc37.x86_64 120/151 Verifying : pkgconf-m4-1.8.0-3.fc37.noarch 121/151 Verifying : pkgconf-pkg-config-1.8.0-3.fc37.x86_64 122/151 Verifying : popt-1.19-1.fc38.x86_64 123/151 Verifying : publicsuffix-list-dafsa-20210518-5.fc37.noarch 124/151 Verifying : python-srpm-macros-3.11-5.fc38.noarch 125/151 Verifying : qt5-srpm-macros-5.15.7-1.fc38.noarch 126/151 Verifying : readline-8.2-2.fc38.x86_64 127/151 Verifying : redhat-rpm-config-232-1.fc38.noarch 128/151 Verifying : rpm-4.18.0-3.fc38.x86_64 129/151 Verifying : rpm-build-4.18.0-3.fc38.x86_64 130/151 Verifying : rpm-build-libs-4.18.0-3.fc38.x86_64 131/151 Verifying : rpm-libs-4.18.0-3.fc38.x86_64 132/151 Verifying : rpmautospec-rpm-macros-0.3.0-1.fc37.noarch 133/151 Verifying : rust-srpm-macros-23-1.fc38.noarch 134/151 Verifying : sed-4.8-11.fc37.x86_64 135/151 Verifying : setup-2.14.2-1.fc38.noarch 136/151 Verifying : shadow-utils-2:4.12.3-3.fc38.x86_64 137/151 Verifying : sqlite-libs-3.39.4-1.fc38.x86_64 138/151 Verifying : systemd-libs-252-587.fc38.x86_64 139/151 Verifying : tar-2:1.34-5.fc38.x86_64 140/151 Verifying : tzdata-2022f-1.fc38.noarch 141/151 Verifying : unzip-6.0-58.fc37.x86_64 142/151 Verifying : util-linux-2.38.1-2.fc38.x86_64 143/151 Verifying : util-linux-core-2.38.1-2.fc38.x86_64 144/151 Verifying : which-2.21-35.fc37.x86_64 145/151 Verifying : xxhash-libs-0.8.1-3.fc37.x86_64 146/151 Verifying : xz-5.2.7-1.fc38.x86_64 147/151 Verifying : xz-libs-5.2.7-1.fc38.x86_64 148/151 Verifying : zip-3.0-33.fc37.x86_64 149/151 Verifying : zlib-1.2.12-5.fc38.x86_64 150/151 Verifying : zstd-1.5.2-3.fc37.x86_64 151/151 Installed: alternatives-1.21-1.fc38.x86_64 ansible-srpm-macros-1-8.1.fc38.noarch audit-libs-3.0.9-1.fc38.x86_64 authselect-1.4.0-3.fc37.x86_64 authselect-libs-1.4.0-3.fc37.x86_64 basesystem-11-14.fc37.noarch bash-5.2.2-2.fc38.x86_64 binutils-2.39-3.fc38.x86_64 binutils-gold-2.39-3.fc38.x86_64 bzip2-1.0.8-12.fc38.x86_64 bzip2-libs-1.0.8-12.fc38.x86_64 ca-certificates-2022.2.54-5.fc37.noarch coreutils-9.1-8.fc38.x86_64 coreutils-common-9.1-8.fc38.x86_64 cpio-2.13-13.fc38.x86_64 cracklib-2.9.7-30.fc38.x86_64 crypto-policies-20221003-1.gitcb1ad32.fc38.noarch curl-7.86.0-2.fc38.x86_64 cyrus-sasl-lib-2.1.28-8.fc38.x86_64 debugedit-5.0-5.fc37.x86_64 diffutils-3.8-3.fc37.x86_64 dwz-0.15-1.fc38.x86_64 ed-1.18-2.fc37.x86_64 efi-srpm-macros-5-6.fc37.noarch elfutils-0.188-2.fc38.x86_64 elfutils-debuginfod-client-0.188-2.fc38.x86_64 elfutils-default-yama-scope-0.188-2.fc38.noarch elfutils-libelf-0.188-2.fc38.x86_64 elfutils-libs-0.188-2.fc38.x86_64 fedora-gpg-keys-38-0.3.noarch fedora-release-38-0.4.noarch fedora-release-common-38-0.4.noarch fedora-release-identity-basic-38-0.4.noarch fedora-repos-38-0.3.noarch fedora-repos-rawhide-38-0.3.noarch file-5.42-4.fc37.x86_64 file-libs-5.42-4.fc37.x86_64 filesystem-3.18-2.fc37.x86_64 findutils-1:4.9.0-2.fc37.x86_64 fonts-srpm-macros-1:2.0.5-9.fc38.noarch fpc-srpm-macros-1.3-6.fc37.noarch gawk-5.1.1-4.fc37.x86_64 gdb-minimal-12.1-9.fc38.x86_64 gdbm-libs-1:1.23-2.fc37.x86_64 ghc-srpm-macros-1.5.0-7.fc37.noarch glibc-2.36.9000-11.fc38.x86_64 glibc-common-2.36.9000-11.fc38.x86_64 glibc-gconv-extra-2.36.9000-11.fc38.x86_64 glibc-minimal-langpack-2.36.9000-11.fc38.x86_64 gmp-1:6.2.1-3.fc37.x86_64 gnat-srpm-macros-4-16.fc37.noarch go-srpm-macros-3.2.0-1.fc38.noarch grep-3.8-1.fc38.x86_64 gzip-1.12-2.fc37.x86_64 info-6.8-4.fc37.x86_64 jansson-2.13.1-5.fc37.x86_64 kernel-srpm-macros-1.0-15.fc37.noarch keyutils-libs-1.6.1-5.fc37.x86_64 krb5-libs-1.19.2-11.fc37.1.x86_64 libacl-2.3.1-4.fc37.x86_64 libarchive-3.6.1-2.fc37.x86_64 libattr-2.5.1-5.fc37.x86_64 libblkid-2.38.1-2.fc38.x86_64 libbrotli-1.0.9-9.fc37.x86_64 libcap-2.48-5.fc37.x86_64 libcap-ng-0.8.3-3.fc37.x86_64 libcom_err-1.46.5-3.fc37.x86_64 libcurl-7.86.0-2.fc38.x86_64 libdb-5.3.28-53.fc37.x86_64 libeconf-0.4.0-4.fc37.x86_64 libevent-2.1.12-7.fc37.x86_64 libfdisk-2.38.1-2.fc38.x86_64 libffi-3.4.2-9.fc37.x86_64 libgcc-12.2.1-2.fc38.x86_64 libgomp-12.2.1-2.fc38.x86_64 libidn2-2.3.4-1.fc38.x86_64 libmount-2.38.1-2.fc38.x86_64 libnghttp2-1.50.0-1.fc38.x86_64 libnsl2-2.0.0-4.fc37.x86_64 libpkgconf-1.8.0-3.fc37.x86_64 libpsl-0.21.1-6.fc37.x86_64 libpwquality-1.4.4-11.fc37.x86_64 libselinux-3.4-5.fc37.x86_64 libsemanage-3.4-5.fc37.x86_64 libsepol-3.4-3.fc37.x86_64 libsigsegv-2.14-3.fc37.x86_64 libsmartcols-2.38.1-2.fc38.x86_64 libssh-0.10.4-2.fc38.x86_64 libssh-config-0.10.4-2.fc38.noarch libstdc++-12.2.1-2.fc38.x86_64 libtasn1-4.18.0-3.fc37.x86_64 libtirpc-1.3.3-0.fc37.x86_64 libunistring-1.0-2.fc37.x86_64 libutempter-1.2.1-7.fc37.x86_64 libuuid-2.38.1-2.fc38.x86_64 libverto-0.3.2-4.fc37.x86_64 libxcrypt-4.4.30-1.fc38.x86_64 libxml2-2.10.3-2.fc38.x86_64 libzstd-1.5.2-3.fc37.x86_64 lua-libs-5.4.4-6.fc38.x86_64 lua-srpm-macros-1-7.fc37.noarch lz4-libs-1.9.3-5.fc37.x86_64 mpfr-4.1.0-10.fc37.x86_64 ncurses-base-6.3-3.20220501.fc37.noarch ncurses-libs-6.3-3.20220501.fc37.x86_64 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.x86_64 openssl-libs-1:3.0.5-6.fc38.x86_64 p11-kit-0.24.1-3.fc37.x86_64 p11-kit-trust-0.24.1-3.fc37.x86_64 package-notes-srpm-macros-0.5-6.fc38.noarch pam-1.5.2-14.fc37.x86_64 pam-libs-1.5.2-14.fc37.x86_64 patch-2.7.6-17.fc37.x86_64 pcre2-10.40-1.fc37.1.x86_64 pcre2-syntax-10.40-1.fc37.1.noarch perl-srpm-macros-1-46.fc37.noarch pkgconf-1.8.0-3.fc37.x86_64 pkgconf-m4-1.8.0-3.fc37.noarch pkgconf-pkg-config-1.8.0-3.fc37.x86_64 popt-1.19-1.fc38.x86_64 publicsuffix-list-dafsa-20210518-5.fc37.noarch python-srpm-macros-3.11-5.fc38.noarch qt5-srpm-macros-5.15.7-1.fc38.noarch readline-8.2-2.fc38.x86_64 redhat-rpm-config-232-1.fc38.noarch rpm-4.18.0-3.fc38.x86_64 rpm-build-4.18.0-3.fc38.x86_64 rpm-build-libs-4.18.0-3.fc38.x86_64 rpm-libs-4.18.0-3.fc38.x86_64 rpmautospec-rpm-macros-0.3.0-1.fc37.noarch rust-srpm-macros-23-1.fc38.noarch sed-4.8-11.fc37.x86_64 setup-2.14.2-1.fc38.noarch shadow-utils-2:4.12.3-3.fc38.x86_64 sqlite-libs-3.39.4-1.fc38.x86_64 systemd-libs-252-587.fc38.x86_64 tar-2:1.34-5.fc38.x86_64 tzdata-2022f-1.fc38.noarch unzip-6.0-58.fc37.x86_64 util-linux-2.38.1-2.fc38.x86_64 util-linux-core-2.38.1-2.fc38.x86_64 which-2.21-35.fc37.x86_64 xxhash-libs-0.8.1-3.fc37.x86_64 xz-5.2.7-1.fc38.x86_64 xz-libs-5.2.7-1.fc38.x86_64 zip-3.0-33.fc37.x86_64 zlib-1.2.12-5.fc38.x86_64 zstd-1.5.2-3.fc37.x86_64 Complete! Finish: dnf install Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: libnsl2-2.0.0-4.fc37.x86_64 libtirpc-1.3.3-0.fc37.x86_64 gnat-srpm-macros-4-16.fc37.noarch libzstd-1.5.2-3.fc37.x86_64 curl-7.86.0-2.fc38.x86_64 sqlite-libs-3.39.4-1.fc38.x86_64 mpfr-4.1.0-10.fc37.x86_64 kernel-srpm-macros-1.0-15.fc37.noarch elfutils-libs-0.188-2.fc38.x86_64 efi-srpm-macros-5-6.fc37.noarch libcap-ng-0.8.3-3.fc37.x86_64 authselect-libs-1.4.0-3.fc37.x86_64 libpwquality-1.4.4-11.fc37.x86_64 openssl-libs-3.0.5-6.fc38.x86_64 glibc-gconv-extra-2.36.9000-11.fc38.x86_64 pam-1.5.2-14.fc37.x86_64 ncurses-base-6.3-3.20220501.fc37.noarch jansson-2.13.1-5.fc37.x86_64 authselect-1.4.0-3.fc37.x86_64 libssh-config-0.10.4-2.fc38.noarch openblas-srpm-macros-2-12.fc37.noarch systemd-libs-252-587.fc38.x86_64 rpm-build-libs-4.18.0-3.fc38.x86_64 ansible-srpm-macros-1-8.1.fc38.noarch info-6.8-4.fc37.x86_64 fedora-repos-rawhide-38-0.3.noarch zstd-1.5.2-3.fc37.x86_64 zip-3.0-33.fc37.x86_64 fpc-srpm-macros-1.3-6.fc37.noarch xz-5.2.7-1.fc38.x86_64 gdbm-libs-1.23-2.fc37.x86_64 coreutils-9.1-8.fc38.x86_64 zlib-1.2.12-5.fc38.x86_64 libsigsegv-2.14-3.fc37.x86_64 qt5-srpm-macros-5.15.7-1.fc38.noarch cyrus-sasl-lib-2.1.28-8.fc38.x86_64 debugedit-5.0-5.fc37.x86_64 xz-libs-5.2.7-1.fc38.x86_64 patch-2.7.6-17.fc37.x86_64 libcurl-7.86.0-2.fc38.x86_64 openldap-2.6.3-1.fc38.x86_64 gmp-6.2.1-3.fc37.x86_64 fedora-repos-38-0.3.noarch rpm-build-4.18.0-3.fc38.x86_64 gdb-minimal-12.1-9.fc38.x86_64 libunistring-1.0-2.fc37.x86_64 util-linux-2.38.1-2.fc38.x86_64 tzdata-2022f-1.fc38.noarch gzip-1.12-2.fc37.x86_64 ocaml-srpm-macros-7-2.fc37.noarch elfutils-debuginfod-client-0.188-2.fc38.x86_64 grep-3.8-1.fc38.x86_64 fonts-srpm-macros-2.0.5-9.fc38.noarch glibc-minimal-langpack-2.36.9000-11.fc38.x86_64 findutils-4.9.0-2.fc37.x86_64 libbrotli-1.0.9-9.fc37.x86_64 pcre2-10.40-1.fc37.1.x86_64 p11-kit-0.24.1-3.fc37.x86_64 popt-1.19-1.fc38.x86_64 unzip-6.0-58.fc37.x86_64 perl-srpm-macros-1-46.fc37.noarch fedora-release-common-38-0.4.noarch libselinux-3.4-5.fc37.x86_64 ncurses-libs-6.3-3.20220501.fc37.x86_64 elfutils-0.188-2.fc38.x86_64 libstdc++-12.2.1-2.fc38.x86_64 xxhash-libs-0.8.1-3.fc37.x86_64 util-linux-core-2.38.1-2.fc38.x86_64 gpg-pubkey-5323552a-6112bcdc audit-libs-3.0.9-1.fc38.x86_64 rust-srpm-macros-23-1.fc38.noarch rpmautospec-rpm-macros-0.3.0-1.fc37.noarch libcom_err-1.46.5-3.fc37.x86_64 bzip2-libs-1.0.8-12.fc38.x86_64 fedora-gpg-keys-38-0.3.noarch krb5-libs-1.19.2-11.fc37.1.x86_64 coreutils-common-9.1-8.fc38.x86_64 libuuid-2.38.1-2.fc38.x86_64 gpg-pubkey-eb10b464-6202d9c6 lua-srpm-macros-1-7.fc37.noarch lua-libs-5.4.4-6.fc38.x86_64 go-srpm-macros-3.2.0-1.fc38.noarch publicsuffix-list-dafsa-20210518-5.fc37.noarch libssh-0.10.4-2.fc38.x86_64 libffi-3.4.2-9.fc37.x86_64 libmount-2.38.1-2.fc38.x86_64 libtasn1-4.18.0-3.fc37.x86_64 elfutils-default-yama-scope-0.188-2.fc38.noarch glibc-2.36.9000-11.fc38.x86_64 libarchive-3.6.1-2.fc37.x86_64 binutils-gold-2.39-3.fc38.x86_64 ghc-srpm-macros-1.5.0-7.fc37.noarch p11-kit-trust-0.24.1-3.fc37.x86_64 crypto-policies-20221003-1.gitcb1ad32.fc38.noarch bzip2-1.0.8-12.fc38.x86_64 libsepol-3.4-3.fc37.x86_64 readline-8.2-2.fc38.x86_64 ca-certificates-2022.2.54-5.fc37.noarch libverto-0.3.2-4.fc37.x86_64 dwz-0.15-1.fc38.x86_64 libattr-2.5.1-5.fc37.x86_64 libevent-2.1.12-7.fc37.x86_64 filesystem-3.18-2.fc37.x86_64 libpsl-0.21.1-6.fc37.x86_64 pcre2-syntax-10.40-1.fc37.1.noarch file-5.42-4.fc37.x86_64 libeconf-0.4.0-4.fc37.x86_64 libxcrypt-4.4.30-1.fc38.x86_64 shadow-utils-4.12.3-3.fc38.x86_64 binutils-2.39-3.fc38.x86_64 libgcc-12.2.1-2.fc38.x86_64 diffutils-3.8-3.fc37.x86_64 python-srpm-macros-3.11-5.fc38.noarch cracklib-2.9.7-30.fc38.x86_64 bash-5.2.2-2.fc38.x86_64 which-2.21-35.fc37.x86_64 basesystem-11-14.fc37.noarch libcap-2.48-5.fc37.x86_64 redhat-rpm-config-232-1.fc38.noarch libfdisk-2.38.1-2.fc38.x86_64 rpm-4.18.0-3.fc38.x86_64 ed-1.18-2.fc37.x86_64 libutempter-1.2.1-7.fc37.x86_64 sed-4.8-11.fc37.x86_64 package-notes-srpm-macros-0.5-6.fc38.noarch pkgconf-1.8.0-3.fc37.x86_64 glibc-common-2.36.9000-11.fc38.x86_64 libgomp-12.2.1-2.fc38.x86_64 fedora-release-identity-basic-38-0.4.noarch tar-1.34-5.fc38.x86_64 libpkgconf-1.8.0-3.fc37.x86_64 fedora-release-38-0.4.noarch libxml2-2.10.3-2.fc38.x86_64 libblkid-2.38.1-2.fc38.x86_64 file-libs-5.42-4.fc37.x86_64 nim-srpm-macros-3-7.fc37.noarch pkgconf-m4-1.8.0-3.fc37.noarch lz4-libs-1.9.3-5.fc37.x86_64 pkgconf-pkg-config-1.8.0-3.fc37.x86_64 alternatives-1.21-1.fc38.x86_64 libdb-5.3.28-53.fc37.x86_64 gawk-5.1.1-4.fc37.x86_64 libsmartcols-2.38.1-2.fc38.x86_64 elfutils-libelf-0.188-2.fc38.x86_64 cpio-2.13-13.fc38.x86_64 libsemanage-3.4-5.fc37.x86_64 keyutils-libs-1.6.1-5.fc37.x86_64 rpm-libs-4.18.0-3.fc38.x86_64 libacl-2.3.1-4.fc37.x86_64 setup-2.14.2-1.fc38.noarch libnghttp2-1.50.0-1.fc38.x86_64 libidn2-2.3.4-1.fc38.x86_64 pam-libs-1.5.2-14.fc37.x86_64 Start: buildsrpm Start: rpmbuild -bs Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1660521600 Wrote: /builddir/build/SRPMS/htslib-1.15.1-1.fc38.src.rpm Finish: rpmbuild -bs INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-x86_64-1667627884.349232/root/var/log/dnf.rpm.log /var/lib/mock/fedora-rawhide-x86_64-1667627884.349232/root/var/log/dnf.librepo.log /var/lib/mock/fedora-rawhide-x86_64-1667627884.349232/root/var/log/dnf.log Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-5i5wa9c5/htslib/htslib.spec) Config(child) 0 minutes 53 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=108000): unbuffer mock --rebuild /var/lib/copr-rpmbuild/results/htslib-1.15.1-1.fc38.src.rpm --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1667627884.349232 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 3.3 starting (python version = 3.10.4, NVR = mock-3.3-1.fc35)... 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-x86_64) Start: clean chroot Finish: clean chroot Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1667627884.349232/root. INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1667627884.349232/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: 3.3 INFO: Mock Version: 3.3 Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-1667627884.349232/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: 3.3 INFO: Mock Version: 3.3 Start: dnf update No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 36 kB/s | 3.0 kB 00:00 Copr repository 33 MB/s | 8.0 MB 00:00 fedora 196 kB/s | 9.1 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: x86_64 Building for target x86_64 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 55 kB/s | 3.0 kB 00:00 Copr repository 21 MB/s | 8.0 MB 00:00 fedora 207 kB/s | 9.1 kB 00:00 Dependencies resolved. ================================================================================ Package Arch Version Repository Size ================================================================================ Installing: bzip2-devel x86_64 1.0.8-12.fc38 copr_base 214 k gcc x86_64 12.2.1-2.fc38 fedora 33 M libcurl-devel x86_64 7.86.0-2.fc38 fedora 987 k make x86_64 1:4.4-1.fc38 copr_base 571 k openssl-devel x86_64 1:3.0.5-6.fc38 fedora 3.1 M perl-Data-Dumper x86_64 2.184-490.fc37 fedora 56 k perl-FindBin noarch 1.53-492.fc38 fedora 17 k perl-Getopt-Long noarch 1:2.52-489.fc37 fedora 60 k perl-interpreter x86_64 4:5.36.0-492.fc38 fedora 75 k perl-lib x86_64 0.65-492.fc38 fedora 18 k xz-devel x86_64 5.2.7-1.fc38 fedora 57 k zlib-devel x86_64 1.2.12-5.fc38 fedora 44 k Installing dependencies: annobin-docs noarch 10.91-1.fc38 fedora 92 k annobin-plugin-gcc x86_64 10.91-1.fc38 fedora 888 k cpp x86_64 12.2.1-2.fc38 fedora 11 M gc x86_64 8.2.2-1.fc38 fedora 110 k gcc-plugin-annobin x86_64 12.2.1-2.fc38 fedora 51 k glibc-devel x86_64 2.36.9000-11.fc38 fedora 39 k glibc-headers-x86 noarch 2.36.9000-11.fc38 fedora 516 k groff-base x86_64 1.22.4-10.fc37 fedora 1.1 M guile22 x86_64 2.2.7-6.fc37 fedora 6.5 M kernel-headers x86_64 6.1.0-0.rc2.git0.1.fc38 fedora 1.5 M libmpc x86_64 1.2.1-5.fc37 fedora 61 k libtool-ltdl x86_64 2.4.7-2.fc37 fedora 37 k libxcrypt-devel x86_64 4.4.30-1.fc38 fedora 28 k ncurses x86_64 6.3-3.20220501.fc37 fedora 409 k perl-B x86_64 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 x86_64 1.52-492.fc38 fedora 29 k perl-Encode x86_64 4:3.19-492.fc38 fedora 1.7 M perl-Errno x86_64 1.36-492.fc38 fedora 18 k perl-Exporter noarch 5.77-489.fc37 fedora 31 k perl-Fcntl x86_64 1.15-492.fc38 fedora 24 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 x86_64 1.50-492.fc38 fedora 95 k perl-IPC-Open3 noarch 1.22-492.fc38 fedora 26 k perl-MIME-Base64 x86_64 3.16-489.fc37 fedora 30 k perl-POSIX x86_64 2.03-492.fc38 fedora 101 k perl-PathTools x86_64 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 x86_64 5:1.63-489.fc38 fedora 72 k perl-SelectSaver noarch 1.02-492.fc38 fedora 15 k perl-Socket x86_64 4:2.036-1.fc38 fedora 55 k perl-Storable x86_64 1:3.26-489.fc37 fedora 97 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 x86_64 4:5.36.0-492.fc38 fedora 2.2 M perl-mro x86_64 1.26-492.fc38 fedora 32 k perl-overload noarch 1.35-492.fc38 fedora 49 k perl-overloading noarch 0.02-492.fc38 fedora 16 k perl-parent noarch 1:0.238-489.fc37 fedora 14 k perl-podlators noarch 1:4.14-489.fc37 fedora 116 k perl-subs noarch 1.04-492.fc38 fedora 15 k perl-vars noarch 1.05-492.fc38 fedora 16 k Transaction Summary ================================================================================ Install 69 Packages Total size: 66 M Total download size: 1.3 M Installed size: 210 M Downloading Packages: [SKIPPED] make-4.4-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] annobin-docs-10.91-1.fc38.noarch.rpm: Already downloaded [SKIPPED] annobin-plugin-gcc-10.91-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] cpp-12.2.1-2.fc38.x86_64.rpm: Already downloaded [SKIPPED] gc-8.2.2-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] gcc-12.2.1-2.fc38.x86_64.rpm: Already downloaded [SKIPPED] gcc-plugin-annobin-12.2.1-2.fc38.x86_64.rpm: Already downloaded [SKIPPED] glibc-devel-2.36.9000-11.fc38.x86_64.rpm: Already downloaded [SKIPPED] glibc-headers-x86-2.36.9000-11.fc38.noarch.rpm: Already downloaded [SKIPPED] groff-base-1.22.4-10.fc37.x86_64.rpm: Already downloaded [SKIPPED] guile22-2.2.7-6.fc37.x86_64.rpm: Already downloaded [SKIPPED] kernel-headers-6.1.0-0.rc2.git0.1.fc38.x86_64.rpm: Already downloaded [SKIPPED] libmpc-1.2.1-5.fc37.x86_64.rpm: Already downloaded [SKIPPED] libtool-ltdl-2.4.7-2.fc37.x86_64.rpm: Already downloaded [SKIPPED] libxcrypt-devel-4.4.30-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] ncurses-6.3-3.20220501.fc37.x86_64.rpm: Already downloaded [SKIPPED] openssl-devel-3.0.5-6.fc38.x86_64.rpm: Already downloaded [SKIPPED] perl-B-1.83-492.fc38.x86_64.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.x86_64.rpm: Already downloaded [SKIPPED] perl-DynaLoader-1.52-492.fc38.x86_64.rpm: Already downloaded [SKIPPED] perl-Encode-3.19-492.fc38.x86_64.rpm: Already downloaded [SKIPPED] perl-Errno-1.36-492.fc38.x86_64.rpm: Already downloaded [SKIPPED] perl-Exporter-5.77-489.fc37.noarch.rpm: Already downloaded [SKIPPED] perl-Fcntl-1.15-492.fc38.x86_64.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-2.52-489.fc37.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.x86_64.rpm: Already downloaded [SKIPPED] perl-IPC-Open3-1.22-492.fc38.noarch.rpm: Already downloaded [SKIPPED] perl-MIME-Base64-3.16-489.fc37.x86_64.rpm: Already downloaded [SKIPPED] perl-POSIX-2.03-492.fc38.x86_64.rpm: Already downloaded [SKIPPED] perl-PathTools-3.84-489.fc37.x86_64.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.x86_64.rpm: Already downloaded [SKIPPED] perl-SelectSaver-1.02-492.fc38.noarch.rpm: Already downloaded [SKIPPED] perl-Socket-2.036-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] perl-Storable-3.26-489.fc37.x86_64.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.x86_64.rpm: Already downloaded [SKIPPED] perl-libs-5.36.0-492.fc38.x86_64.rpm: Already downloaded [SKIPPED] perl-mro-1.26-492.fc38.x86_64.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-0.238-489.fc37.noarch.rpm: Already downloaded [SKIPPED] perl-podlators-4.14-489.fc37.noarch.rpm: Already downloaded [SKIPPED] perl-subs-1.04-492.fc38.noarch.rpm: Already downloaded [SKIPPED] perl-vars-1.05-492.fc38.noarch.rpm: Already downloaded [SKIPPED] zlib-devel-1.2.12-5.fc38.x86_64.rpm: Already downloaded (65/69): bzip2-devel-1.0.8-12.fc38.x86_64.rpm 2.3 MB/s | 214 kB 00:00 (66/69): perl-FindBin-1.53-492.fc38.noarch.rpm 141 kB/s | 17 kB 00:00 (67/69): perl-lib-0.65-492.fc38.x86_64.rpm 224 kB/s | 18 kB 00:00 (68/69): xz-devel-5.2.7-1.fc38.x86_64.rpm 1.1 MB/s | 57 kB 00:00 (69/69): libcurl-devel-7.86.0-2.fc38.x86_64.rpm 4.2 MB/s | 987 kB 00:00 -------------------------------------------------------------------------------- Total 3.7 MB/s | 1.3 MB 00:00 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Installing : libmpc-1.2.1-5.fc37.x86_64 1/69 Installing : cpp-12.2.1-2.fc38.x86_64 2/69 Installing : ncurses-6.3-3.20220501.fc37.x86_64 3/69 Installing : libtool-ltdl-2.4.7-2.fc37.x86_64 4/69 Installing : kernel-headers-6.1.0-0.rc2.git0.1.fc38.x86_64 5/69 Running scriptlet: groff-base-1.22.4-10.fc37.x86_64 6/69 Installing : groff-base-1.22.4-10.fc37.x86_64 6/69 Running scriptlet: groff-base-1.22.4-10.fc37.x86_64 6/69 Installing : perl-Text-Tabs+Wrap-2021.0814-489.fc37.noarch 7/69 Installing : perl-if-0.61.000-492.fc38.noarch 8/69 Installing : perl-Time-Local-2:1.300-489.fc37.noarch 9/69 Installing : perl-File-Path-2.18-489.fc37.noarch 10/69 Installing : perl-Pod-Escapes-1:1.07-489.fc37.noarch 11/69 Installing : perl-Class-Struct-0.66-492.fc38.noarch 12/69 Installing : perl-POSIX-2.03-492.fc38.x86_64 13/69 Installing : perl-Term-ANSIColor-5.01-490.fc37.noarch 14/69 Installing : perl-IPC-Open3-1.22-492.fc38.noarch 15/69 Installing : perl-HTTP-Tiny-0.082-1.fc37.noarch 16/69 Installing : perl-subs-1.04-492.fc38.noarch 17/69 Installing : perl-File-Temp-1:0.231.100-489.fc37.noarch 18/69 Installing : perl-Term-Cap-1.17-489.fc37.noarch 19/69 Installing : perl-Pod-Simple-1:3.43-490.fc37.noarch 20/69 Installing : perl-Socket-4:2.036-1.fc38.x86_64 21/69 Installing : perl-SelectSaver-1.02-492.fc38.noarch 22/69 Installing : perl-Symbol-1.09-492.fc38.noarch 23/69 Installing : perl-File-stat-1.12-492.fc38.noarch 24/69 Installing : perl-podlators-1:4.14-489.fc37.noarch 25/69 Installing : perl-Pod-Perldoc-3.28.01-490.fc37.noarch 26/69 Installing : perl-Fcntl-1.15-492.fc38.x86_64 27/69 Installing : perl-Text-ParseWords-3.31-489.fc37.noarch 28/69 Installing : perl-mro-1.26-492.fc38.x86_64 29/69 Installing : perl-IO-1.50-492.fc38.x86_64 30/69 Installing : perl-overloading-0.02-492.fc38.noarch 31/69 Installing : perl-Pod-Usage-4:2.03-3.fc37.noarch 32/69 Installing : perl-Errno-1.36-492.fc38.x86_64 33/69 Installing : perl-File-Basename-2.85-492.fc38.noarch 34/69 Installing : perl-Getopt-Std-1.13-492.fc38.noarch 35/69 Installing : perl-MIME-Base64-3.16-489.fc37.x86_64 36/69 Installing : perl-Scalar-List-Utils-5:1.63-489.fc38.x86_64 37/69 Installing : perl-constant-1.33-490.fc37.noarch 38/69 Installing : perl-Storable-1:3.26-489.fc37.x86_64 39/69 Installing : perl-overload-1.35-492.fc38.noarch 40/69 Installing : perl-parent-1:0.238-489.fc37.noarch 41/69 Installing : perl-vars-1.05-492.fc38.noarch 42/69 Installing : perl-Getopt-Long-1:2.52-489.fc37.noarch 43/69 Installing : perl-Carp-1.52-489.fc37.noarch 44/69 Installing : perl-Exporter-5.77-489.fc37.noarch 45/69 Installing : perl-PathTools-3.84-489.fc37.x86_64 46/69 Installing : perl-DynaLoader-1.52-492.fc38.x86_64 47/69 Installing : perl-Encode-4:3.19-492.fc38.x86_64 48/69 Installing : perl-libs-4:5.36.0-492.fc38.x86_64 49/69 Installing : perl-interpreter-4:5.36.0-492.fc38.x86_64 50/69 Installing : perl-Data-Dumper-2.184-490.fc37.x86_64 51/69 Installing : perl-B-1.83-492.fc38.x86_64 52/69 Installing : glibc-headers-x86-2.36.9000-11.fc38.noarch 53/69 Installing : libxcrypt-devel-4.4.30-1.fc38.x86_64 54/69 Installing : glibc-devel-2.36.9000-11.fc38.x86_64 55/69 Installing : gc-8.2.2-1.fc38.x86_64 56/69 Installing : guile22-2.2.7-6.fc37.x86_64 57/69 Installing : make-1:4.4-1.fc38.x86_64 58/69 Installing : gcc-12.2.1-2.fc38.x86_64 59/69 Running scriptlet: gcc-12.2.1-2.fc38.x86_64 59/69 Installing : annobin-docs-10.91-1.fc38.noarch 60/69 Installing : annobin-plugin-gcc-10.91-1.fc38.x86_64 61/69 Running scriptlet: annobin-plugin-gcc-10.91-1.fc38.x86_64 61/69 Installing : gcc-plugin-annobin-12.2.1-2.fc38.x86_64 62/69 Installing : perl-FindBin-1.53-492.fc38.noarch 63/69 Installing : perl-lib-0.65-492.fc38.x86_64 64/69 Installing : zlib-devel-1.2.12-5.fc38.x86_64 65/69 Installing : xz-devel-5.2.7-1.fc38.x86_64 66/69 Installing : openssl-devel-1:3.0.5-6.fc38.x86_64 67/69 Installing : libcurl-devel-7.86.0-2.fc38.x86_64 68/69 Installing : bzip2-devel-1.0.8-12.fc38.x86_64 69/69 Running scriptlet: bzip2-devel-1.0.8-12.fc38.x86_64 69/69 Verifying : bzip2-devel-1.0.8-12.fc38.x86_64 1/69 Verifying : make-1:4.4-1.fc38.x86_64 2/69 Verifying : annobin-docs-10.91-1.fc38.noarch 3/69 Verifying : annobin-plugin-gcc-10.91-1.fc38.x86_64 4/69 Verifying : cpp-12.2.1-2.fc38.x86_64 5/69 Verifying : gc-8.2.2-1.fc38.x86_64 6/69 Verifying : gcc-12.2.1-2.fc38.x86_64 7/69 Verifying : gcc-plugin-annobin-12.2.1-2.fc38.x86_64 8/69 Verifying : glibc-devel-2.36.9000-11.fc38.x86_64 9/69 Verifying : glibc-headers-x86-2.36.9000-11.fc38.noarch 10/69 Verifying : groff-base-1.22.4-10.fc37.x86_64 11/69 Verifying : guile22-2.2.7-6.fc37.x86_64 12/69 Verifying : kernel-headers-6.1.0-0.rc2.git0.1.fc38.x86_64 13/69 Verifying : libcurl-devel-7.86.0-2.fc38.x86_64 14/69 Verifying : libmpc-1.2.1-5.fc37.x86_64 15/69 Verifying : libtool-ltdl-2.4.7-2.fc37.x86_64 16/69 Verifying : libxcrypt-devel-4.4.30-1.fc38.x86_64 17/69 Verifying : ncurses-6.3-3.20220501.fc37.x86_64 18/69 Verifying : openssl-devel-1:3.0.5-6.fc38.x86_64 19/69 Verifying : perl-B-1.83-492.fc38.x86_64 20/69 Verifying : perl-Carp-1.52-489.fc37.noarch 21/69 Verifying : perl-Class-Struct-0.66-492.fc38.noarch 22/69 Verifying : perl-Data-Dumper-2.184-490.fc37.x86_64 23/69 Verifying : perl-DynaLoader-1.52-492.fc38.x86_64 24/69 Verifying : perl-Encode-4:3.19-492.fc38.x86_64 25/69 Verifying : perl-Errno-1.36-492.fc38.x86_64 26/69 Verifying : perl-Exporter-5.77-489.fc37.noarch 27/69 Verifying : perl-Fcntl-1.15-492.fc38.x86_64 28/69 Verifying : perl-File-Basename-2.85-492.fc38.noarch 29/69 Verifying : perl-File-Path-2.18-489.fc37.noarch 30/69 Verifying : perl-File-Temp-1:0.231.100-489.fc37.noarch 31/69 Verifying : perl-File-stat-1.12-492.fc38.noarch 32/69 Verifying : perl-FindBin-1.53-492.fc38.noarch 33/69 Verifying : perl-Getopt-Long-1:2.52-489.fc37.noarch 34/69 Verifying : perl-Getopt-Std-1.13-492.fc38.noarch 35/69 Verifying : perl-HTTP-Tiny-0.082-1.fc37.noarch 36/69 Verifying : perl-IO-1.50-492.fc38.x86_64 37/69 Verifying : perl-IPC-Open3-1.22-492.fc38.noarch 38/69 Verifying : perl-MIME-Base64-3.16-489.fc37.x86_64 39/69 Verifying : perl-POSIX-2.03-492.fc38.x86_64 40/69 Verifying : perl-PathTools-3.84-489.fc37.x86_64 41/69 Verifying : perl-Pod-Escapes-1:1.07-489.fc37.noarch 42/69 Verifying : perl-Pod-Perldoc-3.28.01-490.fc37.noarch 43/69 Verifying : perl-Pod-Simple-1:3.43-490.fc37.noarch 44/69 Verifying : perl-Pod-Usage-4:2.03-3.fc37.noarch 45/69 Verifying : perl-Scalar-List-Utils-5:1.63-489.fc38.x86_64 46/69 Verifying : perl-SelectSaver-1.02-492.fc38.noarch 47/69 Verifying : perl-Socket-4:2.036-1.fc38.x86_64 48/69 Verifying : perl-Storable-1:3.26-489.fc37.x86_64 49/69 Verifying : perl-Symbol-1.09-492.fc38.noarch 50/69 Verifying : perl-Term-ANSIColor-5.01-490.fc37.noarch 51/69 Verifying : perl-Term-Cap-1.17-489.fc37.noarch 52/69 Verifying : perl-Text-ParseWords-3.31-489.fc37.noarch 53/69 Verifying : perl-Text-Tabs+Wrap-2021.0814-489.fc37.noarch 54/69 Verifying : perl-Time-Local-2:1.300-489.fc37.noarch 55/69 Verifying : perl-constant-1.33-490.fc37.noarch 56/69 Verifying : perl-if-0.61.000-492.fc38.noarch 57/69 Verifying : perl-interpreter-4:5.36.0-492.fc38.x86_64 58/69 Verifying : perl-lib-0.65-492.fc38.x86_64 59/69 Verifying : perl-libs-4:5.36.0-492.fc38.x86_64 60/69 Verifying : perl-mro-1.26-492.fc38.x86_64 61/69 Verifying : perl-overload-1.35-492.fc38.noarch 62/69 Verifying : perl-overloading-0.02-492.fc38.noarch 63/69 Verifying : perl-parent-1:0.238-489.fc37.noarch 64/69 Verifying : perl-podlators-1:4.14-489.fc37.noarch 65/69 Verifying : perl-subs-1.04-492.fc38.noarch 66/69 Verifying : perl-vars-1.05-492.fc38.noarch 67/69 Verifying : xz-devel-5.2.7-1.fc38.x86_64 68/69 Verifying : zlib-devel-1.2.12-5.fc38.x86_64 69/69 Installed: annobin-docs-10.91-1.fc38.noarch annobin-plugin-gcc-10.91-1.fc38.x86_64 bzip2-devel-1.0.8-12.fc38.x86_64 cpp-12.2.1-2.fc38.x86_64 gc-8.2.2-1.fc38.x86_64 gcc-12.2.1-2.fc38.x86_64 gcc-plugin-annobin-12.2.1-2.fc38.x86_64 glibc-devel-2.36.9000-11.fc38.x86_64 glibc-headers-x86-2.36.9000-11.fc38.noarch groff-base-1.22.4-10.fc37.x86_64 guile22-2.2.7-6.fc37.x86_64 kernel-headers-6.1.0-0.rc2.git0.1.fc38.x86_64 libcurl-devel-7.86.0-2.fc38.x86_64 libmpc-1.2.1-5.fc37.x86_64 libtool-ltdl-2.4.7-2.fc37.x86_64 libxcrypt-devel-4.4.30-1.fc38.x86_64 make-1:4.4-1.fc38.x86_64 ncurses-6.3-3.20220501.fc37.x86_64 openssl-devel-1:3.0.5-6.fc38.x86_64 perl-B-1.83-492.fc38.x86_64 perl-Carp-1.52-489.fc37.noarch perl-Class-Struct-0.66-492.fc38.noarch perl-Data-Dumper-2.184-490.fc37.x86_64 perl-DynaLoader-1.52-492.fc38.x86_64 perl-Encode-4:3.19-492.fc38.x86_64 perl-Errno-1.36-492.fc38.x86_64 perl-Exporter-5.77-489.fc37.noarch perl-Fcntl-1.15-492.fc38.x86_64 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-1:2.52-489.fc37.noarch perl-Getopt-Std-1.13-492.fc38.noarch perl-HTTP-Tiny-0.082-1.fc37.noarch perl-IO-1.50-492.fc38.x86_64 perl-IPC-Open3-1.22-492.fc38.noarch perl-MIME-Base64-3.16-489.fc37.x86_64 perl-POSIX-2.03-492.fc38.x86_64 perl-PathTools-3.84-489.fc37.x86_64 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.x86_64 perl-SelectSaver-1.02-492.fc38.noarch perl-Socket-4:2.036-1.fc38.x86_64 perl-Storable-1:3.26-489.fc37.x86_64 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.x86_64 perl-lib-0.65-492.fc38.x86_64 perl-libs-4:5.36.0-492.fc38.x86_64 perl-mro-1.26-492.fc38.x86_64 perl-overload-1.35-492.fc38.noarch perl-overloading-0.02-492.fc38.noarch perl-parent-1:0.238-489.fc37.noarch perl-podlators-1:4.14-489.fc37.noarch perl-subs-1.04-492.fc38.noarch perl-vars-1.05-492.fc38.noarch xz-devel-5.2.7-1.fc38.x86_64 zlib-devel-1.2.12-5.fc38.x86_64 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: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1660521600 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.wskJXt + 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.2iF1xc + 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FCFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FCFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -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 2022-11-05 05:59:13.098079292 +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* .* \\(.*\\)$/extern char \\1;/p'\''"#' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + '[' 1 = 1 ']' +++ dirname ./configure ++ find . -name config.guess -o -name config.sub + '[' 1 = 1 ']' + '[' x '!=' 'x-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' ']' ++ find . -name ltmain.sh ++ grep -q runstatedir=DIR ./configure ++ echo --runstatedir=/run + ./configure --build=x86_64-redhat-linux-gnu --host=x86_64-redhat-linux-gnu --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/libexec --localstatedir=/var --runstatedir=/run --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info 'CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' 'LDFLAGS=-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes' --prefix=/usr --libdir=/usr/lib64 --enable-plugins '--with-plugin-path=/usr/local/libexec/htslib:$(plugindir)' --enable-gcs --enable-libcurl --enable-s3 configure: WARNING: unrecognized options: --disable-dependency-tracking checking for x86_64-redhat-linux-gnu-gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for x86_64-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 x86_64-redhat-linux-gnu-pkg-config... /usr/bin/x86_64-redhat-linux-gnu-pkg-config checking pkg-config is at least version 0.9.0... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking shared library type for x86_64-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o kfunc.o kfunc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o kstring.o kstring.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o bcf_sr_sort.o bcf_sr_sort.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o errmod.o errmod.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o bgzf.o bgzf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o hfile.o hfile.c echo '#define HTS_VERSION_TEXT "1.15.1"' > version.h echo '#define HTS_CC "gcc"' > config_vars.h echo '#define HTS_CPPFLAGS ""' >> config_vars.h echo '#define HTS_CFLAGS "-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden"' >> config_vars.h echo '#define HTS_LDFLAGS "-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o hts_expr.o hts_expr.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o hts_os.o hts_os.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o md5.o md5.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o header.o header.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o multipart.o multipart.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o probaln.o probaln.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o realn.o realn.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o region.o region.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o regidx.o regidx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o synced_bcf_reader.o synced_bcf_reader.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o vcf_sweep.o vcf_sweep.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o tbx.o tbx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o textutils.o textutils.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o thread_pool.o thread_pool.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o sam.o sam.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o vcfutils.o vcfutils.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o vcf.o vcf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o cram/cram_codecs.o cram/cram_codecs.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o cram/cram_decode.o cram/cram_decode.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o cram/cram_external.o cram/cram_external.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o cram/cram_encode.o cram/cram_encode.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o cram/cram_index.o cram/cram_index.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o cram/cram_stats.o cram/cram_stats.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o cram/mFILE.o cram/mFILE.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o cram/open_trace_file.o cram/open_trace_file.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o cram/string_alloc.o cram/string_alloc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o cram/cram_io.o cram/cram_io.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -DPLUGINPATH=\"/usr/local/libexec/htslib:/usr/libexec/htslib\" -c -o plugin.o plugin.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o kfunc.pico kfunc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o kstring.pico kstring.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o bcf_sr_sort.pico bcf_sr_sort.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o errmod.pico errmod.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o bgzf.pico bgzf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o faidx.pico faidx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o hfile.pico hfile.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o header.pico header.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o hts_expr.pico hts_expr.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o hts_os.pico hts_os.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o md5.pico md5.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o multipart.pico multipart.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o probaln.pico probaln.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o realn.pico realn.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o regidx.pico regidx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o hts.pico hts.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o region.pico region.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o synced_bcf_reader.pico synced_bcf_reader.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o vcf_sweep.pico vcf_sweep.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o tbx.pico tbx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o textutils.pico textutils.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o thread_pool.pico thread_pool.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o sam.pico sam.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o vcfutils.pico vcfutils.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o vcf.pico vcf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o cram/cram_codecs.pico cram/cram_codecs.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o cram/cram_decode.pico cram/cram_decode.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o cram/cram_external.pico cram/cram_external.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o cram/cram_index.pico cram/cram_index.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o cram/cram_encode.pico cram/cram_encode.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o cram/cram_stats.pico cram/cram_stats.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o cram/mFILE.pico cram/mFILE.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o cram/open_trace_file.pico cram/open_trace_file.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o cram/pooled_alloc.pico cram/pooled_alloc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o cram/string_alloc.pico cram/string_alloc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/arith_dynamic.pico htscodecs/htscodecs/arith_dynamic.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o cram/cram_io.pico cram/cram_io.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/htscodecs.pico htscodecs/htscodecs/htscodecs.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/pack.pico htscodecs/htscodecs/pack.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/fqzcomp_qual.pico htscodecs/htscodecs/fqzcomp_qual.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rANS_static.pico htscodecs/htscodecs/rANS_static.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rle.pico htscodecs/htscodecs/rle.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rANS_static4x16pr.pico htscodecs/htscodecs/rANS_static4x16pr.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -DPLUGINPATH=\"/usr/local/libexec/htslib:/usr/libexec/htslib\" -fpic -c -o plugin.pico plugin.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o bgzip.o bgzip.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/tokenise_name3.pico htscodecs/htscodecs/tokenise_name3.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o htsfile.o htsfile.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o tabix.o tabix.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o hfile_gcs.pico hfile_gcs.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o hfile_libcurl.pico hfile_libcurl.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o hfile_s3_write.pico hfile_s3_write.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -fpic -c -o hfile_s3.pico hfile_s3.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o test/fieldarith.o test/fieldarith.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o test/hts_endian.o test/hts_endian.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o test/hfile.o test/hfile.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o test/pileup.o test/pileup.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o test/plugins-dlhts.o test/plugins-dlhts.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o test/pileup_mod.o test/pileup_mod.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o test/test_bgzf.o test/test_bgzf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o test/test_expr.o test/test_expr.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o test/test_kfunc.o test/test_kfunc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o test/test_kstring.o test/test_kstring.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o test/sam.o test/sam.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o test/test_mod.o test/test_mod.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o test/test_realn.o test/test_realn.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o test/test-regidx.o test/test-regidx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o test/test_str2int.o test/test_str2int.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o test/test_index.o test/test_index.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o test/test_view.o test/test_view.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o test/test-vcf-api.o test/test-vcf-api.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o test/test-bcf-sr.o test/test-bcf-sr.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o test/fuzz/hts_open_fuzzer.o test/fuzz/hts_open_fuzzer.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o test/test-bcf-translate.o test/test-bcf-translate.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o test/test-parse-reg.o test/test-parse-reg.c sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' htslib.pc.tmp > htslib_static.mk sed -e 's#@-includedir@#'`pwd`'#g;s#@-libdir@#'`pwd`'#g' htslib.pc.tmp > htslib-uninstalled.pc gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o test/test_introspection.o test/test_introspection.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -c -o hts.o hts.c gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -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_write.so hfile_s3_write.pico libhts.so -llzma -lbz2 -lz -lm -lcrypto -lcurl -lpthread gcc -shared -Wl,-E -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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 -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_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_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_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-translate test/test-bcf-translate.o libhts.a -lz -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test-parse-reg test/test-parse-reg.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test_introspection test/test_introspection.o libhts.a -llzma -lbz2 -lz -lm -lpthread + sed -i -E '/^(Libs|Requires)\.private:/d' htslib.pc.tmp + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.7ISIwo + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.x86_64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.x86_64 ++ dirname /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.x86_64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.x86_64 + 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FCFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -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.x86_64 'INSTALL=/usr/bin/install -p' mkdir -p -m 755 /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.x86_64/usr/bin /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.x86_64/usr/include /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.x86_64/usr/include/htslib /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.x86_64/usr/lib64 /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.x86_64/usr/share/man/man1 /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.x86_64/usr/share/man/man5 /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.x86_64/usr/share/man/man7 /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.x86_64/usr/lib64/pkgconfig if test -n "/usr/libexec/htslib"; then mkdir -p -m 755 /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.x86_64/usr/libexec/htslib; fi /usr/bin/install -p -m 644 libhts.so /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.x86_64/usr/lib64/libhts.so.1.15.1 ln -sf libhts.so.1.15.1 /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.x86_64/usr/lib64/libhts.so ln -sf libhts.so.1.15.1 /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.x86_64/usr/lib64/libhts.so.3 sed -e 's#@-includedir@#/usr/include#g;s#@-libdir@#/usr/lib64#g;s#@-PACKAGE_VERSION@#1.15.1#g' htslib.pc.tmp > /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.x86_64/usr/lib64/pkgconfig/htslib.pc chmod 644 /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.x86_64/usr/lib64/pkgconfig/htslib.pc /usr/bin/install -p bgzip htsfile tabix /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.x86_64/usr/bin if test -n "hfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so"; then /usr/bin/install -p hfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.x86_64/usr/libexec/htslib; fi /usr/bin/install -p -m 644 htslib/*.h /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.x86_64/usr/include/htslib /usr/bin/install -p -m 644 libhts.a /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.x86_64/usr/lib64/libhts.a /usr/bin/install -p -m 644 bgzip.1 htsfile.1 tabix.1 /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.x86_64/usr/share/man/man1 /usr/bin/install -p -m 644 faidx.5 sam.5 vcf.5 /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.x86_64/usr/share/man/man5 /usr/bin/install -p -m 644 htslib-s3-plugin.7 /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.x86_64/usr/share/man/man7 + pushd /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.x86_64//usr/lib64 ~/build/BUILDROOT/htslib-1.15.1-1.fc38.x86_64/usr/lib64 ~/build/BUILD/htslib-1.15.1 + chmod 755 libhts.so.1.15.1 + popd ~/build/BUILD/htslib-1.15.1 + find /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.x86_64 -name '*.la' -delete + rm -f /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.x86_64//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.x86_64 --unique-debug-src-base htslib-1.15.1-1.fc38.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/htslib-1.15.1 extracting debug info from /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.x86_64/usr/bin/bgzip extracting debug info from /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.x86_64/usr/bin/htsfile extracting debug info from /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.x86_64/usr/bin/tabix extracting debug info from /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.x86_64/usr/lib64/libhts.so.1.15.1 extracting debug info from /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.x86_64/usr/libexec/htslib/hfile_gcs.so extracting debug info from /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.x86_64/usr/libexec/htslib/hfile_libcurl.so extracting debug info from /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.x86_64/usr/libexec/htslib/hfile_s3.so extracting debug info from /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.x86_64/usr/libexec/htslib/hfile_s3_write.so original debug info size: 11948kB, size after compression: 11228kB /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.Zxa5iE + 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FCFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -Ihtscodecs -D_POSIX_C_SOURCE=200112L -c -o htscodecs/tests/rANS_static_test.o htscodecs/tests/rANS_static_test.c gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -Ihtscodecs -D_POSIX_C_SOURCE=200112L -c -o htscodecs/tests/rANS_static4x16pr_test.o htscodecs/tests/rANS_static4x16pr_test.c gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -Ihtscodecs -D_POSIX_C_SOURCE=200112L -c -o htscodecs/tests/arith_dynamic_test.o htscodecs/tests/arith_dynamic_test.c gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -Ihtscodecs -D_POSIX_C_SOURCE=200112L -c -o htscodecs/tests/tokenise_name3_test.o htscodecs/tests/tokenise_name3_test.c gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -Ihtscodecs -D_POSIX_C_SOURCE=200112L -c -o htscodecs/tests/fqzcomp_qual_test.o htscodecs/tests/fqzcomp_qual_test.c gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fvisibility=hidden -I. -Ihtscodecs -D_POSIX_C_SOURCE=200112L -c -o htscodecs/tests/varint_test.o htscodecs/tests/varint_test.c gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -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/uiKAFPBh2p/index.bam.csi /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/uiKAFPBh2p/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/uiKAFPBh2p/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -b -m 0 -x /tmp/uiKAFPBh2p/index.bam.bai /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/uiKAFPBh2p/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -b /tmp/uiKAFPBh2p/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -z -m 14 -x /tmp/uiKAFPBh2p/index.sam.gz.csi /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/uiKAFPBh2p/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/uiKAFPBh2p/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -z -m 0 -x /tmp/uiKAFPBh2p/index.sam.gz.bai /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/uiKAFPBh2p/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -b /tmp/uiKAFPBh2p/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -z -m 14 -x /tmp/uiKAFPBh2p/index.sam.gz.csi /builddir/build/BUILD/htslib-1.15.1/test/index_dos.sam > /tmp/uiKAFPBh2p/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/uiKAFPBh2p/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -z -m 0 -x /tmp/uiKAFPBh2p/index.sam.gz.bai /builddir/build/BUILD/htslib-1.15.1/test/index_dos.sam > /tmp/uiKAFPBh2p/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -b /tmp/uiKAFPBh2p/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -C -x /tmp/uiKAFPBh2p/index.cram.crai /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/uiKAFPBh2p/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index /tmp/uiKAFPBh2p/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -b -m 14 -x /tmp/uiKAFPBh2p/index.bcf.csi /builddir/build/BUILD/htslib-1.15.1/test/index.vcf > /tmp/uiKAFPBh2p/index.bcf .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/uiKAFPBh2p/index.bcf .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -z -m 14 -x /tmp/uiKAFPBh2p/index.vcf.gz.csi /builddir/build/BUILD/htslib-1.15.1/test/index.vcf > /tmp/uiKAFPBh2p/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/uiKAFPBh2p/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -z -m 0 -x /tmp/uiKAFPBh2p/index.vcf.gz.tbi /builddir/build/BUILD/htslib-1.15.1/test/index.vcf > /tmp/uiKAFPBh2p/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -t /tmp/uiKAFPBh2p/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/tabix /tmp/uiKAFPBh2p/index.vcf.gz##idx##/tmp/uiKAFPBh2p/index.vcf.gz.tbi 1:10000060-10000060 .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view /tmp/uiKAFPBh2p/index2.bam 1:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view /tmp/uiKAFPBh2p/index2.bam 1:2000000-2000000 .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view /tmp/uiKAFPBh2p/index2.bam 2:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view /tmp/uiKAFPBh2p/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/uiKAFPBh2p/index.bam.csi /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/uiKAFPBh2p/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/uiKAFPBh2p/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -b -m 0 -x /tmp/uiKAFPBh2p/index.bam.bai /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/uiKAFPBh2p/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -b /tmp/uiKAFPBh2p/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -z -m 14 -x /tmp/uiKAFPBh2p/index.sam.gz.csi /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/uiKAFPBh2p/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/uiKAFPBh2p/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -z -m 0 -x /tmp/uiKAFPBh2p/index.sam.gz.bai /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/uiKAFPBh2p/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -b /tmp/uiKAFPBh2p/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -z -m 14 -x /tmp/uiKAFPBh2p/index.sam.gz.csi /builddir/build/BUILD/htslib-1.15.1/test/index_dos.sam > /tmp/uiKAFPBh2p/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/uiKAFPBh2p/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -z -m 0 -x /tmp/uiKAFPBh2p/index.sam.gz.bai /builddir/build/BUILD/htslib-1.15.1/test/index_dos.sam > /tmp/uiKAFPBh2p/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -b /tmp/uiKAFPBh2p/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -C -x /tmp/uiKAFPBh2p/index.cram.crai /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/uiKAFPBh2p/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index /tmp/uiKAFPBh2p/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -b -m 14 -x /tmp/uiKAFPBh2p/index.bcf.csi /builddir/build/BUILD/htslib-1.15.1/test/index.vcf > /tmp/uiKAFPBh2p/index.bcf .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/uiKAFPBh2p/index.bcf .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -z -m 14 -x /tmp/uiKAFPBh2p/index.vcf.gz.csi /builddir/build/BUILD/htslib-1.15.1/test/index.vcf > /tmp/uiKAFPBh2p/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/uiKAFPBh2p/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -z -m 0 -x /tmp/uiKAFPBh2p/index.vcf.gz.tbi /builddir/build/BUILD/htslib-1.15.1/test/index.vcf > /tmp/uiKAFPBh2p/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -t /tmp/uiKAFPBh2p/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/tabix /tmp/uiKAFPBh2p/index.vcf.gz##idx##/tmp/uiKAFPBh2p/index.vcf.gz.tbi 1:10000060-10000060 .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view /tmp/uiKAFPBh2p/index2.bam 1:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view /tmp/uiKAFPBh2p/index2.bam 1:2000000-2000000 .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view /tmp/uiKAFPBh2p/index2.bam 2:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view /tmp/uiKAFPBh2p/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/uiKAFPBh2p/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/uiKAFPBh2p/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/uiKAFPBh2p/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/uiKAFPBh2p -s 1412275574 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/uiKAFPBh2p -s 28210461 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/uiKAFPBh2p -s 1494885301 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/uiKAFPBh2p -s 1542797537 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/uiKAFPBh2p -s 236862342 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/uiKAFPBh2p -s 321759424 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/uiKAFPBh2p -s 994982441 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/uiKAFPBh2p -s 932798597 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/uiKAFPBh2p -s 180943485 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/uiKAFPBh2p -s 693580248 .. 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/uiKAFPBh2p/headernul0.bam .. ok test_convert_padded_header: /builddir/build/BUILD/htslib-1.15.1/test/test_view -t ce.fa -C /tmp/uiKAFPBh2p/headernul1.bam .. ok test_convert_padded_header: /builddir/build/BUILD/htslib-1.15.1/test/test_view -t ce.fa -C /tmp/uiKAFPBh2p/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.x86_64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.zluinm + umask 022 + cd /builddir/build/BUILD + cd htslib-1.15.1 + DOCDIR=/builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.x86_64/usr/share/doc/htslib + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.x86_64/usr/share/doc/htslib + cp -pr NEWS /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.x86_64/usr/share/doc/htslib + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.QEYRwL + umask 022 + cd /builddir/build/BUILD + cd htslib-1.15.1 + LICENSEDIR=/builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.x86_64/usr/share/licenses/htslib + export LC_ALL=C + LC_ALL=C + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.x86_64/usr/share/licenses/htslib + cp -pr LICENSE /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.x86_64/usr/share/licenses/htslib + RPM_EC=0 ++ jobs -p + exit 0 Provides: htslib = 1.15.1-1.fc38 htslib(x86-64) = 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_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.2)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.7)(64bit) libcrypto.so.3()(64bit) libcrypto.so.3(OPENSSL_3.0.0)(64bit) libcurl.so.4()(64bit) libhts.so.3()(64bit) liblzma.so.5()(64bit) liblzma.so.5(XZ_5.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.23)(64bit) libm.so.6(GLIBC_2.29)(64bit) libz.so.1()(64bit) rtld(GNU_HASH) Processing files: htslib-devel-1.15.1-1.fc38.x86_64 Provides: htslib-devel = 1.15.1-1.fc38 htslib-devel(x86-64) = 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.x86_64 Provides: htslib-tools = 1.15.1-1.fc38 htslib-tools(x86-64) = 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_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.2)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.7)(64bit) liblzma.so.5()(64bit) liblzma.so.5(XZ_5.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.29)(64bit) libz.so.1()(64bit) rtld(GNU_HASH) Processing files: htslib-debugsource-1.15.1-1.fc38.x86_64 Provides: htslib-debugsource = 1.15.1-1.fc38 htslib-debugsource(x86-64) = 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.x86_64 Provides: debuginfo(build-id) = 022db4381a177c393765075175dbef75980d9059 debuginfo(build-id) = 3e1888980b72d0989e990f870f0cfe64a31f2466 debuginfo(build-id) = 3ebee6b9621ce0e57071dd767a27ec8212b77c02 debuginfo(build-id) = 4e78a3ae97f17824bc88bd0fdce8f351ea914bc7 debuginfo(build-id) = a0acecbe284f36132dfd8b09fd0fd14634b4f6f1 htslib-debuginfo = 1.15.1-1.fc38 htslib-debuginfo(x86-64) = 1.15.1-1.fc38 libhts.so.1.15.1-1.15.1-1.fc38.x86_64.debug()(64bit) Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: htslib-debugsource(x86-64) = 1.15.1-1.fc38 Processing files: htslib-tools-debuginfo-1.15.1-1.fc38.x86_64 Provides: debuginfo(build-id) = 18a262285c6da36a98879f86288d418b6e2f1b33 debuginfo(build-id) = 286186164c1e89da70078bcd6343ed93440f45c3 debuginfo(build-id) = ad7958541078635a47ea5b7561b5d0dccdcc47f9 htslib-tools-debuginfo = 1.15.1-1.fc38 htslib-tools-debuginfo(x86-64) = 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(x86-64) = 1.15.1-1.fc38 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.x86_64 Wrote: /builddir/build/RPMS/htslib-debuginfo-1.15.1-1.fc38.x86_64.rpm Wrote: /builddir/build/RPMS/htslib-debugsource-1.15.1-1.fc38.x86_64.rpm Wrote: /builddir/build/RPMS/htslib-tools-debuginfo-1.15.1-1.fc38.x86_64.rpm Wrote: /builddir/build/RPMS/htslib-1.15.1-1.fc38.x86_64.rpm Wrote: /builddir/build/RPMS/htslib-devel-1.15.1-1.fc38.x86_64.rpm Wrote: /builddir/build/RPMS/htslib-tools-1.15.1-1.fc38.x86_64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.fW9s00 + umask 022 + cd /builddir/build/BUILD + cd htslib-1.15.1 + /usr/bin/rm -rf /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.x86_64 + RPM_EC=0 ++ jobs -p + exit 0 Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.HAo53H + 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-x86_64-1667627884.349232/root/var/log/dnf.rpm.log /var/lib/mock/fedora-rawhide-x86_64-1667627884.349232/root/var/log/dnf.librepo.log /var/lib/mock/fedora-rawhide-x86_64-1667627884.349232/root/var/log/dnf.log INFO: Done(/var/lib/copr-rpmbuild/results/htslib-1.15.1-1.fc38.src.rpm) Config(child) 4 minutes 57 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