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 4733910 --chroot fedora-rawhide-x86_64 --detached Version: 0.61 PID: 5288 Logging PID: 5289 Task: {'appstream': True, 'background': False, 'bootstrap': 'off', 'build_id': 4733910, 'buildroot_pkgs': [], 'chroot': 'fedora-rawhide-x86_64', 'enable_net': False, 'fedora_review': False, 'git_hash': '00e9239ef0d1f3ea39c07da84538bfbc7d86f9dd', 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/jaruga/staging/samtools', 'isolation': 'default', 'memory_reqs': 2048, 'package_name': 'samtools', 'package_version': '1.15.1-1.fc38', 'project_dirname': 'staging', 'project_name': 'staging', 'project_owner': 'jaruga', 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/jaruga/staging/fedora-rawhide-x86_64/', 'id': 'copr_base', 'name': 'Copr repository'}], 'sandbox': 'jaruga/staging--jaruga', 'source_json': {}, 'source_type': None, 'submitter': 'jaruga', 'tags': [], 'task_id': '4733910-fedora-rawhide-x86_64', 'timeout': 18000, 'uses_devel_repo': False, 'with_opts': [], 'without_opts': []} Running: git clone https://copr-dist-git.fedorainfracloud.org/git/jaruga/staging/samtools /var/lib/copr-rpmbuild/workspace/workdir-6n_9c0b8/samtools --depth 500 --no-single-branch --recursive cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/jaruga/staging/samtools', '/var/lib/copr-rpmbuild/workspace/workdir-6n_9c0b8/samtools', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-6n_9c0b8/samtools'... Running: git checkout 00e9239ef0d1f3ea39c07da84538bfbc7d86f9dd cmd: ['git', 'checkout', '00e9239ef0d1f3ea39c07da84538bfbc7d86f9dd'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-6n_9c0b8/samtools rc: 0 stdout: stderr: Note: switching to '00e9239ef0d1f3ea39c07da84538bfbc7d86f9dd'. 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 00e9239 automatic import of samtools 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-6n_9c0b8/samtools 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 samtools-1.15.1.tar.bz2 INFO: Calling: curl -H Pragma: -o samtools-1.15.1.tar.bz2 --location --remote-time --show-error --fail https://copr-dist-git.fedorainfracloud.org/repo/pkgs/jaruga/staging/samtools/samtools-1.15.1.tar.bz2/md5/b71d1aa1de9749773b1a04bf54281ca0/samtools-1.15.1.tar.bz2 % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 7648k 100 7648k 0 0 47.8M 0 --:--:-- --:--:-- --:--:-- 48.1M INFO: Reading stdout from command: md5sum samtools-1.15.1.tar.bz2 Running (timeout=18000): unbuffer mock --buildsrpm --spec /var/lib/copr-rpmbuild/workspace/workdir-6n_9c0b8/samtools/samtools.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-6n_9c0b8/samtools --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1660573317.563253 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 3.1 starting (python version = 3.10.4, NVR = mock-3.1-1.fc35)... 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-6n_9c0b8/samtools/samtools.spec) Config(fedora-rawhide-x86_64) Start: clean chroot Finish: clean chroot Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-1660573317.563253/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: 3.1 INFO: Mock Version: 3.1 Start: 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 127 kB/s | 23 kB 00:00 fedora 9.5 MB/s | 65 MB 00:06 Dependencies resolved. ================================================================================ Package Arch Version Repo Size ================================================================================ Installing group/module packages: bash x86_64 5.1.16-3.fc37 fedora 1.7 M bzip2 x86_64 1.0.8-12.fc37 fedora 52 k coreutils x86_64 9.1-6.fc37 fedora 1.1 M cpio x86_64 2.13-13.fc37 fedora 277 k diffutils x86_64 3.8-3.fc37 fedora 378 k fedora-release-common noarch 38-0.2 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 2.36-1.fc37 fedora 81 k grep x86_64 3.7-4.fc37 fedora 273 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 227-1.fc37 fedora 80 k rpm-build x86_64 4.18.0-0.beta1.4.fc37 fedora 76 k sed x86_64 4.8-11.fc37 fedora 306 k shadow-utils x86_64 2:4.11.1-4.fc37 fedora 1.1 M tar x86_64 2:1.34-3.fc36 fedora 886 k unzip x86_64 6.0-58.fc37 fedora 182 k util-linux x86_64 2.38.1-1.fc37 fedora 2.3 M which x86_64 2.21-35.fc37 fedora 41 k xz x86_64 5.2.5-10.fc37 fedora 223 k Installing dependencies: alternatives x86_64 1.19-3.fc37 fedora 36 k ansible-srpm-macros noarch 1-6.fc37 fedora 7.5 k audit-libs x86_64 3.0.8-3.fc37 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 2.38-24.fc38 fedora 5.4 M binutils-gold x86_64 2.38-24.fc38 fedora 777 k bzip2-libs x86_64 1.0.8-12.fc37 fedora 41 k ca-certificates noarch 2022.2.54-5.fc37 fedora 829 k coreutils-common x86_64 9.1-6.fc37 fedora 2.0 M cracklib x86_64 2.9.6-28.fc36 fedora 92 k crypto-policies noarch 20220802-1.gita99dfd2.fc37 fedora 86 k curl x86_64 7.84.0-2.fc37 fedora 313 k cyrus-sasl-lib x86_64 2.1.28-7.fc37 fedora 792 k debugedit x86_64 5.0-5.fc37 fedora 77 k dwz x86_64 0.14-7.fc37 fedora 129 k ed x86_64 1.18-2.fc37 fedora 78 k efi-srpm-macros noarch 5-6.fc37 fedora 22 k elfutils x86_64 0.187-6.fc37 fedora 528 k elfutils-debuginfod-client x86_64 0.187-6.fc37 fedora 39 k elfutils-default-yama-scope noarch 0.187-6.fc37 fedora 17 k elfutils-libelf x86_64 0.187-6.fc37 fedora 197 k elfutils-libs x86_64 0.187-6.fc37 fedora 257 k fedora-gpg-keys noarch 38-0.2 fedora 125 k fedora-release noarch 38-0.2 fedora 12 k fedora-release-identity-basic noarch 38-0.2 fedora 12 k fedora-repos noarch 38-0.2 fedora 10 k fedora-repos-rawhide noarch 38-0.2 fedora 9.6 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 1:2.0.5-8.fc37 fedora 26 k fpc-srpm-macros noarch 1.3-6.fc37 fedora 7.7 k gdb-minimal x86_64 12.1-4.fc37 fedora 3.9 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 2.36-1.fc37 fedora 2.1 M glibc-common x86_64 2.36-1.fc37 fedora 359 k glibc-gconv-extra x86_64 2.36-1.fc37 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 3.1.0-4.fc37 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 2.38.1-1.fc37 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 7.84.0-2.fc37 fedora 306 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 2.38.1-1.fc37 fedora 160 k libffi x86_64 3.4.2-9.fc37 fedora 37 k libgcc x86_64 12.1.1-4.fc38 fedora 106 k libgomp x86_64 12.1.1-4.fc38 fedora 293 k libidn2 x86_64 2.3.3-2.fc37 fedora 113 k libmount x86_64 2.38.1-1.fc37 fedora 135 k libnghttp2 x86_64 1.48.0-2.fc37 fedora 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 2.38.1-1.fc37 fedora 64 k libssh x86_64 0.9.6-5.fc37 fedora 203 k libssh-config noarch 0.9.6-5.fc37 fedora 7.8 k libstdc++ x86_64 12.1.1-4.fc38 fedora 798 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 2.38.1-1.fc37 fedora 28 k libverto x86_64 0.3.2-4.fc37 fedora 21 k libxcrypt x86_64 4.4.28-3.fc38 fedora 117 k libxml2 x86_64 2.9.14-3.fc37 fedora 752 k libzstd x86_64 1.5.2-3.fc37 fedora 294 k lua-libs x86_64 5.4.4-4.fc37 fedora 217 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 2.6.2-5.fc38 fedora 254 k openssl-libs x86_64 1:3.0.5-2.fc37 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 0.4-16.fc37 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 pcre x86_64 8.45-1.fc37.2 fedora 202 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~rc1-3.fc37 fedora 65 k publicsuffix-list-dafsa noarch 20210518-5.fc37 fedora 58 k python-srpm-macros noarch 3.11-4.fc37 fedora 25 k qt5-srpm-macros noarch 5.15.5-2.fc37 fedora 8.1 k readline x86_64 8.1-7.fc37 fedora 211 k rpm x86_64 4.18.0-0.beta1.4.fc37 fedora 570 k rpm-build-libs x86_64 4.18.0-0.beta1.4.fc37 fedora 93 k rpm-libs x86_64 4.18.0-0.beta1.4.fc37 fedora 319 k rpmautospec-rpm-macros noarch 0.3.0-1.fc37 fedora 8.8 k rust-srpm-macros noarch 22-1.fc37 fedora 9.5 k setup noarch 2.14.1-2.fc37 fedora 149 k sqlite-libs x86_64 3.39.2-2.fc37 fedora 657 k systemd-libs x86_64 251.4-51.fc37 fedora 620 k tzdata noarch 2022a-4.fc37 fedora 719 k util-linux-core x86_64 2.38.1-1.fc37 fedora 470 k xxhash-libs x86_64 0.8.1-3.fc37 fedora 41 k xz-libs x86_64 5.2.5-10.fc37 fedora 92 k zip x86_64 3.0-33.fc37 fedora 259 k zlib x86_64 1.2.12-4.fc37 fedora 94 k zstd x86_64 1.5.2-3.fc37 fedora 447 k Installing Groups: Buildsystem building group Transaction Summary ================================================================================ Install 152 Packages Total download size: 51 M Installed size: 177 M Downloading Packages: (1/152): ansible-srpm-macros-1-6.fc37.noarch.rp 120 kB/s | 7.5 kB 00:00 (2/152): alternatives-1.19-3.fc37.x86_64.rpm 398 kB/s | 36 kB 00:00 (3/152): audit-libs-3.0.8-3.fc37.x86_64.rpm 783 kB/s | 116 kB 00:00 (4/152): basesystem-11-14.fc37.noarch.rpm 246 kB/s | 7.0 kB 00:00 (5/152): authselect-libs-1.4.0-3.fc37.x86_64.rp 2.7 MB/s | 248 kB 00:00 (6/152): authselect-1.4.0-3.fc37.x86_64.rpm 1.1 MB/s | 144 kB 00:00 (7/152): binutils-gold-2.38-24.fc38.x86_64.rpm 3.4 MB/s | 777 kB 00:00 (8/152): bzip2-1.0.8-12.fc37.x86_64.rpm 1.8 MB/s | 52 kB 00:00 (9/152): bzip2-libs-1.0.8-12.fc37.x86_64.rpm 1.4 MB/s | 41 kB 00:00 (10/152): bash-5.1.16-3.fc37.x86_64.rpm 4.1 MB/s | 1.7 MB 00:00 (11/152): ca-certificates-2022.2.54-5.fc37.noar 4.7 MB/s | 829 kB 00:00 (12/152): coreutils-9.1-6.fc37.x86_64.rpm 4.4 MB/s | 1.1 MB 00:00 (13/152): cpio-2.13-13.fc37.x86_64.rpm 3.5 MB/s | 277 kB 00:00 (14/152): cracklib-2.9.6-28.fc36.x86_64.rpm 2.1 MB/s | 92 kB 00:00 (15/152): crypto-policies-20220802-1.gita99dfd2 2.7 MB/s | 86 kB 00:00 (16/152): coreutils-common-9.1-6.fc37.x86_64.rp 5.1 MB/s | 2.0 MB 00:00 (17/152): curl-7.84.0-2.fc37.x86_64.rpm 4.9 MB/s | 313 kB 00:00 (18/152): debugedit-5.0-5.fc37.x86_64.rpm 2.2 MB/s | 77 kB 00:00 (19/152): binutils-2.38-24.fc38.x86_64.rpm 5.8 MB/s | 5.4 MB 00:00 (20/152): diffutils-3.8-3.fc37.x86_64.rpm 4.9 MB/s | 378 kB 00:00 (21/152): dwz-0.14-7.fc37.x86_64.rpm 3.5 MB/s | 129 kB 00:00 (22/152): cyrus-sasl-lib-2.1.28-7.fc37.x86_64.r 6.6 MB/s | 792 kB 00:00 (23/152): ed-1.18-2.fc37.x86_64.rpm 2.8 MB/s | 78 kB 00:00 (24/152): efi-srpm-macros-5-6.fc37.noarch.rpm 839 kB/s | 22 kB 00:00 (25/152): elfutils-debuginfod-client-0.187-6.fc 1.4 MB/s | 39 kB 00:00 (26/152): elfutils-default-yama-scope-0.187-6.f 573 kB/s | 17 kB 00:00 (27/152): elfutils-libelf-0.187-6.fc37.x86_64.r 6.7 MB/s | 197 kB 00:00 (28/152): elfutils-libs-0.187-6.fc37.x86_64.rpm 8.4 MB/s | 257 kB 00:00 (29/152): elfutils-0.187-6.fc37.x86_64.rpm 6.2 MB/s | 528 kB 00:00 (30/152): fedora-gpg-keys-38-0.2.noarch.rpm 4.3 MB/s | 125 kB 00:00 (31/152): fedora-release-38-0.2.noarch.rpm 437 kB/s | 12 kB 00:00 (32/152): fedora-release-common-38-0.2.noarch.r 832 kB/s | 22 kB 00:00 (33/152): fedora-release-identity-basic-38-0.2. 458 kB/s | 12 kB 00:00 (34/152): fedora-repos-38-0.2.noarch.rpm 384 kB/s | 10 kB 00:00 (35/152): fedora-repos-rawhide-38-0.2.noarch.rp 367 kB/s | 9.6 kB 00:00 (36/152): file-5.42-4.fc37.x86_64.rpm 1.8 MB/s | 49 kB 00:00 (37/152): file-libs-5.42-4.fc37.x86_64.rpm 7.9 MB/s | 676 kB 00:00 (38/152): findutils-4.9.0-2.fc37.x86_64.rpm 6.0 MB/s | 492 kB 00:00 (39/152): fonts-srpm-macros-2.0.5-8.fc37.noarch 989 kB/s | 26 kB 00:00 (40/152): filesystem-3.18-2.fc37.x86_64.rpm 8.5 MB/s | 1.1 MB 00:00 (41/152): fpc-srpm-macros-1.3-6.fc37.noarch.rpm 247 kB/s | 7.7 kB 00:00 (42/152): gdbm-libs-1.23-2.fc37.x86_64.rpm 2.0 MB/s | 56 kB 00:00 (43/152): ghc-srpm-macros-1.5.0-7.fc37.noarch.r 297 kB/s | 7.8 kB 00:00 (44/152): gawk-5.1.1-4.fc37.x86_64.rpm 9.5 MB/s | 1.0 MB 00:00 (45/152): glibc-common-2.36-1.fc37.x86_64.rpm 11 MB/s | 359 kB 00:00 (46/152): glibc-gconv-extra-2.36-1.fc37.x86_64. 12 MB/s | 1.6 MB 00:00 (47/152): glibc-minimal-langpack-2.36-1.fc37.x8 2.9 MB/s | 81 kB 00:00 (48/152): glibc-2.36-1.fc37.x86_64.rpm 8.8 MB/s | 2.1 MB 00:00 (49/152): gdb-minimal-12.1-4.fc37.x86_64.rpm 13 MB/s | 3.9 MB 00:00 (50/152): gmp-6.2.1-3.fc37.x86_64.rpm 10 MB/s | 315 kB 00:00 (51/152): gnat-srpm-macros-4-16.fc37.noarch.rpm 313 kB/s | 8.3 kB 00:00 (52/152): go-srpm-macros-3.1.0-4.fc37.noarch.rp 1.0 MB/s | 27 kB 00:00 (53/152): grep-3.7-4.fc37.x86_64.rpm 9.2 MB/s | 273 kB 00:00 (54/152): gzip-1.12-2.fc37.x86_64.rpm 5.1 MB/s | 166 kB 00:00 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(142/152): tar-1.34-3.fc36.x86_64.rpm 13 MB/s | 886 kB 00:00 (143/152): tzdata-2022a-4.fc37.noarch.rpm 9.9 MB/s | 719 kB 00:00 (144/152): util-linux-core-2.38.1-1.fc37.x86_64 10 MB/s | 470 kB 00:00 (145/152): which-2.21-35.fc37.x86_64.rpm 948 kB/s | 41 kB 00:00 (146/152): xxhash-libs-0.8.1-3.fc37.x86_64.rpm 998 kB/s | 41 kB 00:00 (147/152): xz-5.2.5-10.fc37.x86_64.rpm 5.2 MB/s | 223 kB 00:00 (148/152): xz-libs-5.2.5-10.fc37.x86_64.rpm 2.0 MB/s | 92 kB 00:00 (149/152): zip-3.0-33.fc37.x86_64.rpm 6.0 MB/s | 259 kB 00:00 (150/152): zlib-1.2.12-4.fc37.x86_64.rpm 2.8 MB/s | 94 kB 00:00 (151/152): zstd-1.5.2-3.fc37.x86_64.rpm 11 MB/s | 447 kB 00:00 (152/152): util-linux-2.38.1-1.fc37.x86_64.rpm 10 MB/s | 2.3 MB 00:00 -------------------------------------------------------------------------------- Total 16 MB/s | 51 MB 00:03 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-12.1.1-4.fc38.x86_64 1/152 Running scriptlet: libgcc-12.1.1-4.fc38.x86_64 1/152 Installing : crypto-policies-20220802-1.gita99dfd2.fc37.noarc 2/152 Running scriptlet: crypto-policies-20220802-1.gita99dfd2.fc37.noarc 2/152 Installing : fedora-release-identity-basic-38-0.2.noarch 3/152 Installing : tzdata-2022a-4.fc37.noarch 4/152 Installing : rust-srpm-macros-22-1.fc37.noarch 5/152 Installing : qt5-srpm-macros-5.15.5-2.fc37.noarch 6/152 Installing : publicsuffix-list-dafsa-20210518-5.fc37.noarch 7/152 Installing : pkgconf-m4-1.8.0-3.fc37.noarch 8/152 Installing : perl-srpm-macros-1-46.fc37.noarch 9/152 Installing : pcre2-syntax-10.40-1.fc37.1.noarch 10/152 Installing : openblas-srpm-macros-2-12.fc37.noarch 11/152 Installing : ocaml-srpm-macros-7-2.fc37.noarch 12/152 Installing : nim-srpm-macros-3-7.fc37.noarch 13/152 Installing : ncurses-base-6.3-3.20220501.fc37.noarch 14/152 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libmount-2.38.1-1.fc37.x86_64 104/152 Installing : util-linux-core-2.38.1-1.fc37.x86_64 105/152 Installing : libsemanage-3.4-5.fc37.x86_64 106/152 Installing : shadow-utils-2:4.11.1-4.fc37.x86_64 107/152 Running scriptlet: libutempter-1.2.1-7.fc37.x86_64 108/152 Installing : libutempter-1.2.1-7.fc37.x86_64 108/152 Installing : patch-2.7.6-17.fc37.x86_64 109/152 Installing : tar-2:1.34-3.fc36.x86_64 110/152 Installing : xxhash-libs-0.8.1-3.fc37.x86_64 111/152 Installing : coreutils-common-9.1-6.fc37.x86_64 112/152 Installing : openssl-libs-1:3.0.5-2.fc37.x86_64 113/152 Installing : coreutils-9.1-6.fc37.x86_64 114/152 Running scriptlet: ca-certificates-2022.2.54-5.fc37.noarch 115/152 Installing : ca-certificates-2022.2.54-5.fc37.noarch 115/152 Running scriptlet: ca-certificates-2022.2.54-5.fc37.noarch 115/152 Installing : krb5-libs-1.19.2-11.fc37.1.x86_64 116/152 Installing : libtirpc-1.3.3-0.fc37.x86_64 117/152 Running scriptlet: authselect-libs-1.4.0-3.fc37.x86_64 118/152 Installing : authselect-libs-1.4.0-3.fc37.x86_64 118/152 Installing : gzip-1.12-2.fc37.x86_64 119/152 Installing : cracklib-2.9.6-28.fc36.x86_64 120/152 Installing : libpwquality-1.4.4-11.fc37.x86_64 121/152 Installing : authselect-1.4.0-3.fc37.x86_64 122/152 Installing : libnsl2-2.0.0-4.fc37.x86_64 123/152 Installing : pam-1.5.2-14.fc37.x86_64 124/152 Installing : libssh-0.9.6-5.fc37.x86_64 125/152 Installing : libarchive-3.6.1-2.fc37.x86_64 126/152 Installing : libevent-2.1.12-7.fc37.x86_64 127/152 Installing : openldap-2.6.2-5.fc38.x86_64 128/152 Installing : libcurl-7.84.0-2.fc37.x86_64 129/152 Installing : elfutils-libs-0.187-6.fc37.x86_64 130/152 Installing : elfutils-debuginfod-client-0.187-6.fc37.x86_64 131/152 Installing : binutils-gold-2.38-24.fc38.x86_64 132/152 Installing : binutils-2.38-24.fc38.x86_64 133/152 Running scriptlet: binutils-2.38-24.fc38.x86_64 133/152 Installing : elfutils-0.187-6.fc37.x86_64 134/152 Installing : gdb-minimal-12.1-4.fc37.x86_64 135/152 Installing : debugedit-5.0-5.fc37.x86_64 136/152 Installing : curl-7.84.0-2.fc37.x86_64 137/152 Running scriptlet: rpm-4.18.0-0.beta1.4.fc37.x86_64 138/152 Installing : rpm-4.18.0-0.beta1.4.fc37.x86_64 138/152 Installing : rpm-libs-4.18.0-0.beta1.4.fc37.x86_64 139/152 Installing : rpm-build-libs-4.18.0-0.beta1.4.fc37.x86_64 140/152 Installing : efi-srpm-macros-5-6.fc37.noarch 141/152 Installing : lua-srpm-macros-1-7.fc37.noarch 142/152 Installing : rpmautospec-rpm-macros-0.3.0-1.fc37.noarch 143/152 Installing : ansible-srpm-macros-1-6.fc37.noarch 144/152 Installing : fonts-srpm-macros-1:2.0.5-8.fc37.noarch 145/152 Installing : go-srpm-macros-3.1.0-4.fc37.noarch 146/152 Installing : python-srpm-macros-3.11-4.fc37.noarch 147/152 Installing : redhat-rpm-config-227-1.fc37.noarch 148/152 Installing : rpm-build-4.18.0-0.beta1.4.fc37.x86_64 149/152 Installing : util-linux-2.38.1-1.fc37.x86_64 150/152 Installing : which-2.21-35.fc37.x86_64 151/152 Installing : info-6.8-4.fc37.x86_64 152/152 Running scriptlet: filesystem-3.18-2.fc37.x86_64 152/152 Running scriptlet: ca-certificates-2022.2.54-5.fc37.noarch 152/152 Running scriptlet: authselect-libs-1.4.0-3.fc37.x86_64 152/152 Running scriptlet: rpm-4.18.0-0.beta1.4.fc37.x86_64 152/152 Running scriptlet: info-6.8-4.fc37.x86_64 152/152 Verifying : alternatives-1.19-3.fc37.x86_64 1/152 Verifying : ansible-srpm-macros-1-6.fc37.noarch 2/152 Verifying : audit-libs-3.0.8-3.fc37.x86_64 3/152 Verifying : authselect-1.4.0-3.fc37.x86_64 4/152 Verifying : authselect-libs-1.4.0-3.fc37.x86_64 5/152 Verifying : basesystem-11-14.fc37.noarch 6/152 Verifying : bash-5.1.16-3.fc37.x86_64 7/152 Verifying : binutils-2.38-24.fc38.x86_64 8/152 Verifying : binutils-gold-2.38-24.fc38.x86_64 9/152 Verifying : bzip2-1.0.8-12.fc37.x86_64 10/152 Verifying : bzip2-libs-1.0.8-12.fc37.x86_64 11/152 Verifying : ca-certificates-2022.2.54-5.fc37.noarch 12/152 Verifying : coreutils-9.1-6.fc37.x86_64 13/152 Verifying : coreutils-common-9.1-6.fc37.x86_64 14/152 Verifying : cpio-2.13-13.fc37.x86_64 15/152 Verifying : cracklib-2.9.6-28.fc36.x86_64 16/152 Verifying : crypto-policies-20220802-1.gita99dfd2.fc37.noarc 17/152 Verifying : curl-7.84.0-2.fc37.x86_64 18/152 Verifying : cyrus-sasl-lib-2.1.28-7.fc37.x86_64 19/152 Verifying : debugedit-5.0-5.fc37.x86_64 20/152 Verifying : diffutils-3.8-3.fc37.x86_64 21/152 Verifying : dwz-0.14-7.fc37.x86_64 22/152 Verifying : ed-1.18-2.fc37.x86_64 23/152 Verifying : efi-srpm-macros-5-6.fc37.noarch 24/152 Verifying : elfutils-0.187-6.fc37.x86_64 25/152 Verifying : elfutils-debuginfod-client-0.187-6.fc37.x86_64 26/152 Verifying : elfutils-default-yama-scope-0.187-6.fc37.noarch 27/152 Verifying : elfutils-libelf-0.187-6.fc37.x86_64 28/152 Verifying : elfutils-libs-0.187-6.fc37.x86_64 29/152 Verifying : fedora-gpg-keys-38-0.2.noarch 30/152 Verifying : fedora-release-38-0.2.noarch 31/152 Verifying : fedora-release-common-38-0.2.noarch 32/152 Verifying : fedora-release-identity-basic-38-0.2.noarch 33/152 Verifying : fedora-repos-38-0.2.noarch 34/152 Verifying : fedora-repos-rawhide-38-0.2.noarch 35/152 Verifying : file-5.42-4.fc37.x86_64 36/152 Verifying : file-libs-5.42-4.fc37.x86_64 37/152 Verifying : filesystem-3.18-2.fc37.x86_64 38/152 Verifying : findutils-1:4.9.0-2.fc37.x86_64 39/152 Verifying : fonts-srpm-macros-1:2.0.5-8.fc37.noarch 40/152 Verifying : fpc-srpm-macros-1.3-6.fc37.noarch 41/152 Verifying : gawk-5.1.1-4.fc37.x86_64 42/152 Verifying : gdb-minimal-12.1-4.fc37.x86_64 43/152 Verifying : gdbm-libs-1:1.23-2.fc37.x86_64 44/152 Verifying : ghc-srpm-macros-1.5.0-7.fc37.noarch 45/152 Verifying : glibc-2.36-1.fc37.x86_64 46/152 Verifying : glibc-common-2.36-1.fc37.x86_64 47/152 Verifying : glibc-gconv-extra-2.36-1.fc37.x86_64 48/152 Verifying : glibc-minimal-langpack-2.36-1.fc37.x86_64 49/152 Verifying : gmp-1:6.2.1-3.fc37.x86_64 50/152 Verifying : gnat-srpm-macros-4-16.fc37.noarch 51/152 Verifying : go-srpm-macros-3.1.0-4.fc37.noarch 52/152 Verifying : grep-3.7-4.fc37.x86_64 53/152 Verifying : gzip-1.12-2.fc37.x86_64 54/152 Verifying : info-6.8-4.fc37.x86_64 55/152 Verifying : jansson-2.13.1-5.fc37.x86_64 56/152 Verifying : kernel-srpm-macros-1.0-15.fc37.noarch 57/152 Verifying : keyutils-libs-1.6.1-5.fc37.x86_64 58/152 Verifying : krb5-libs-1.19.2-11.fc37.1.x86_64 59/152 Verifying : libacl-2.3.1-4.fc37.x86_64 60/152 Verifying : libarchive-3.6.1-2.fc37.x86_64 61/152 Verifying : libattr-2.5.1-5.fc37.x86_64 62/152 Verifying : libblkid-2.38.1-1.fc37.x86_64 63/152 Verifying : libbrotli-1.0.9-9.fc37.x86_64 64/152 Verifying : libcap-2.48-5.fc37.x86_64 65/152 Verifying : libcap-ng-0.8.3-3.fc37.x86_64 66/152 Verifying : libcom_err-1.46.5-3.fc37.x86_64 67/152 Verifying : libcurl-7.84.0-2.fc37.x86_64 68/152 Verifying : libdb-5.3.28-53.fc37.x86_64 69/152 Verifying : libeconf-0.4.0-4.fc37.x86_64 70/152 Verifying : libevent-2.1.12-7.fc37.x86_64 71/152 Verifying : libfdisk-2.38.1-1.fc37.x86_64 72/152 Verifying : libffi-3.4.2-9.fc37.x86_64 73/152 Verifying : libgcc-12.1.1-4.fc38.x86_64 74/152 Verifying : libgomp-12.1.1-4.fc38.x86_64 75/152 Verifying : libidn2-2.3.3-2.fc37.x86_64 76/152 Verifying : libmount-2.38.1-1.fc37.x86_64 77/152 Verifying : libnghttp2-1.48.0-2.fc37.x86_64 78/152 Verifying : libnsl2-2.0.0-4.fc37.x86_64 79/152 Verifying : libpkgconf-1.8.0-3.fc37.x86_64 80/152 Verifying : libpsl-0.21.1-6.fc37.x86_64 81/152 Verifying : libpwquality-1.4.4-11.fc37.x86_64 82/152 Verifying : libselinux-3.4-5.fc37.x86_64 83/152 Verifying : libsemanage-3.4-5.fc37.x86_64 84/152 Verifying : libsepol-3.4-3.fc37.x86_64 85/152 Verifying : libsigsegv-2.14-3.fc37.x86_64 86/152 Verifying : libsmartcols-2.38.1-1.fc37.x86_64 87/152 Verifying : libssh-0.9.6-5.fc37.x86_64 88/152 Verifying : libssh-config-0.9.6-5.fc37.noarch 89/152 Verifying : libstdc++-12.1.1-4.fc38.x86_64 90/152 Verifying : libtasn1-4.18.0-3.fc37.x86_64 91/152 Verifying : libtirpc-1.3.3-0.fc37.x86_64 92/152 Verifying : libunistring-1.0-2.fc37.x86_64 93/152 Verifying : libutempter-1.2.1-7.fc37.x86_64 94/152 Verifying : libuuid-2.38.1-1.fc37.x86_64 95/152 Verifying : libverto-0.3.2-4.fc37.x86_64 96/152 Verifying : libxcrypt-4.4.28-3.fc38.x86_64 97/152 Verifying : libxml2-2.9.14-3.fc37.x86_64 98/152 Verifying : libzstd-1.5.2-3.fc37.x86_64 99/152 Verifying : lua-libs-5.4.4-4.fc37.x86_64 100/152 Verifying : lua-srpm-macros-1-7.fc37.noarch 101/152 Verifying : lz4-libs-1.9.3-5.fc37.x86_64 102/152 Verifying : mpfr-4.1.0-10.fc37.x86_64 103/152 Verifying : ncurses-base-6.3-3.20220501.fc37.noarch 104/152 Verifying : ncurses-libs-6.3-3.20220501.fc37.x86_64 105/152 Verifying : nim-srpm-macros-3-7.fc37.noarch 106/152 Verifying : ocaml-srpm-macros-7-2.fc37.noarch 107/152 Verifying : openblas-srpm-macros-2-12.fc37.noarch 108/152 Verifying : openldap-2.6.2-5.fc38.x86_64 109/152 Verifying : openssl-libs-1:3.0.5-2.fc37.x86_64 110/152 Verifying : p11-kit-0.24.1-3.fc37.x86_64 111/152 Verifying : p11-kit-trust-0.24.1-3.fc37.x86_64 112/152 Verifying : package-notes-srpm-macros-0.4-16.fc37.noarch 113/152 Verifying : pam-1.5.2-14.fc37.x86_64 114/152 Verifying : pam-libs-1.5.2-14.fc37.x86_64 115/152 Verifying : patch-2.7.6-17.fc37.x86_64 116/152 Verifying : pcre-8.45-1.fc37.2.x86_64 117/152 Verifying : pcre2-10.40-1.fc37.1.x86_64 118/152 Verifying : pcre2-syntax-10.40-1.fc37.1.noarch 119/152 Verifying : perl-srpm-macros-1-46.fc37.noarch 120/152 Verifying : pkgconf-1.8.0-3.fc37.x86_64 121/152 Verifying : pkgconf-m4-1.8.0-3.fc37.noarch 122/152 Verifying : pkgconf-pkg-config-1.8.0-3.fc37.x86_64 123/152 Verifying : popt-1.19~rc1-3.fc37.x86_64 124/152 Verifying : publicsuffix-list-dafsa-20210518-5.fc37.noarch 125/152 Verifying : python-srpm-macros-3.11-4.fc37.noarch 126/152 Verifying : qt5-srpm-macros-5.15.5-2.fc37.noarch 127/152 Verifying : readline-8.1-7.fc37.x86_64 128/152 Verifying : redhat-rpm-config-227-1.fc37.noarch 129/152 Verifying : rpm-4.18.0-0.beta1.4.fc37.x86_64 130/152 Verifying : rpm-build-4.18.0-0.beta1.4.fc37.x86_64 131/152 Verifying : rpm-build-libs-4.18.0-0.beta1.4.fc37.x86_64 132/152 Verifying : rpm-libs-4.18.0-0.beta1.4.fc37.x86_64 133/152 Verifying : rpmautospec-rpm-macros-0.3.0-1.fc37.noarch 134/152 Verifying : rust-srpm-macros-22-1.fc37.noarch 135/152 Verifying : sed-4.8-11.fc37.x86_64 136/152 Verifying : setup-2.14.1-2.fc37.noarch 137/152 Verifying : shadow-utils-2:4.11.1-4.fc37.x86_64 138/152 Verifying : sqlite-libs-3.39.2-2.fc37.x86_64 139/152 Verifying : systemd-libs-251.4-51.fc37.x86_64 140/152 Verifying : tar-2:1.34-3.fc36.x86_64 141/152 Verifying : tzdata-2022a-4.fc37.noarch 142/152 Verifying : unzip-6.0-58.fc37.x86_64 143/152 Verifying : util-linux-2.38.1-1.fc37.x86_64 144/152 Verifying : util-linux-core-2.38.1-1.fc37.x86_64 145/152 Verifying : which-2.21-35.fc37.x86_64 146/152 Verifying : xxhash-libs-0.8.1-3.fc37.x86_64 147/152 Verifying : xz-5.2.5-10.fc37.x86_64 148/152 Verifying : xz-libs-5.2.5-10.fc37.x86_64 149/152 Verifying : zip-3.0-33.fc37.x86_64 150/152 Verifying : zlib-1.2.12-4.fc37.x86_64 151/152 Verifying : zstd-1.5.2-3.fc37.x86_64 152/152 Installed products updated. Installed: alternatives-1.19-3.fc37.x86_64 ansible-srpm-macros-1-6.fc37.noarch audit-libs-3.0.8-3.fc37.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-5.1.16-3.fc37.x86_64 binutils-2.38-24.fc38.x86_64 binutils-gold-2.38-24.fc38.x86_64 bzip2-1.0.8-12.fc37.x86_64 bzip2-libs-1.0.8-12.fc37.x86_64 ca-certificates-2022.2.54-5.fc37.noarch coreutils-9.1-6.fc37.x86_64 coreutils-common-9.1-6.fc37.x86_64 cpio-2.13-13.fc37.x86_64 cracklib-2.9.6-28.fc36.x86_64 crypto-policies-20220802-1.gita99dfd2.fc37.noarch curl-7.84.0-2.fc37.x86_64 cyrus-sasl-lib-2.1.28-7.fc37.x86_64 debugedit-5.0-5.fc37.x86_64 diffutils-3.8-3.fc37.x86_64 dwz-0.14-7.fc37.x86_64 ed-1.18-2.fc37.x86_64 efi-srpm-macros-5-6.fc37.noarch elfutils-0.187-6.fc37.x86_64 elfutils-debuginfod-client-0.187-6.fc37.x86_64 elfutils-default-yama-scope-0.187-6.fc37.noarch elfutils-libelf-0.187-6.fc37.x86_64 elfutils-libs-0.187-6.fc37.x86_64 fedora-gpg-keys-38-0.2.noarch fedora-release-38-0.2.noarch fedora-release-common-38-0.2.noarch fedora-release-identity-basic-38-0.2.noarch fedora-repos-38-0.2.noarch fedora-repos-rawhide-38-0.2.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-1:2.0.5-8.fc37.noarch fpc-srpm-macros-1.3-6.fc37.noarch gawk-5.1.1-4.fc37.x86_64 gdb-minimal-12.1-4.fc37.x86_64 gdbm-libs-1:1.23-2.fc37.x86_64 ghc-srpm-macros-1.5.0-7.fc37.noarch glibc-2.36-1.fc37.x86_64 glibc-common-2.36-1.fc37.x86_64 glibc-gconv-extra-2.36-1.fc37.x86_64 glibc-minimal-langpack-2.36-1.fc37.x86_64 gmp-1:6.2.1-3.fc37.x86_64 gnat-srpm-macros-4-16.fc37.noarch go-srpm-macros-3.1.0-4.fc37.noarch grep-3.7-4.fc37.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-2.38.1-1.fc37.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-7.84.0-2.fc37.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-2.38.1-1.fc37.x86_64 libffi-3.4.2-9.fc37.x86_64 libgcc-12.1.1-4.fc38.x86_64 libgomp-12.1.1-4.fc38.x86_64 libidn2-2.3.3-2.fc37.x86_64 libmount-2.38.1-1.fc37.x86_64 libnghttp2-1.48.0-2.fc37.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-2.38.1-1.fc37.x86_64 libssh-0.9.6-5.fc37.x86_64 libssh-config-0.9.6-5.fc37.noarch libstdc++-12.1.1-4.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-2.38.1-1.fc37.x86_64 libverto-0.3.2-4.fc37.x86_64 libxcrypt-4.4.28-3.fc38.x86_64 libxml2-2.9.14-3.fc37.x86_64 libzstd-1.5.2-3.fc37.x86_64 lua-libs-5.4.4-4.fc37.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-2.6.2-5.fc38.x86_64 openssl-libs-1:3.0.5-2.fc37.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-0.4-16.fc37.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 pcre-8.45-1.fc37.2.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~rc1-3.fc37.x86_64 publicsuffix-list-dafsa-20210518-5.fc37.noarch python-srpm-macros-3.11-4.fc37.noarch qt5-srpm-macros-5.15.5-2.fc37.noarch readline-8.1-7.fc37.x86_64 redhat-rpm-config-227-1.fc37.noarch rpm-4.18.0-0.beta1.4.fc37.x86_64 rpm-build-4.18.0-0.beta1.4.fc37.x86_64 rpm-build-libs-4.18.0-0.beta1.4.fc37.x86_64 rpm-libs-4.18.0-0.beta1.4.fc37.x86_64 rpmautospec-rpm-macros-0.3.0-1.fc37.noarch rust-srpm-macros-22-1.fc37.noarch sed-4.8-11.fc37.x86_64 setup-2.14.1-2.fc37.noarch shadow-utils-2:4.11.1-4.fc37.x86_64 sqlite-libs-3.39.2-2.fc37.x86_64 systemd-libs-251.4-51.fc37.x86_64 tar-2:1.34-3.fc36.x86_64 tzdata-2022a-4.fc37.noarch unzip-6.0-58.fc37.x86_64 util-linux-2.38.1-1.fc37.x86_64 util-linux-core-2.38.1-1.fc37.x86_64 which-2.21-35.fc37.x86_64 xxhash-libs-0.8.1-3.fc37.x86_64 xz-5.2.5-10.fc37.x86_64 xz-libs-5.2.5-10.fc37.x86_64 zip-3.0-33.fc37.x86_64 zlib-1.2.12-4.fc37.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: p11-kit-trust-0.24.1-3.fc37.x86_64 libmount-2.38.1-1.fc37.x86_64 tzdata-2022a-4.fc37.noarch audit-libs-3.0.8-3.fc37.x86_64 libsmartcols-2.38.1-1.fc37.x86_64 libutempter-1.2.1-7.fc37.x86_64 bzip2-1.0.8-12.fc37.x86_64 libacl-2.3.1-4.fc37.x86_64 libffi-3.4.2-9.fc37.x86_64 pkgconf-m4-1.8.0-3.fc37.noarch openldap-2.6.2-5.fc38.x86_64 openssl-libs-3.0.5-2.fc37.x86_64 fonts-srpm-macros-2.0.5-8.fc37.noarch nim-srpm-macros-3-7.fc37.noarch xz-libs-5.2.5-10.fc37.x86_64 libsemanage-3.4-5.fc37.x86_64 mpfr-4.1.0-10.fc37.x86_64 libtasn1-4.18.0-3.fc37.x86_64 fedora-repos-rawhide-38-0.2.noarch popt-1.19~rc1-3.fc37.x86_64 authselect-1.4.0-3.fc37.x86_64 ncurses-base-6.3-3.20220501.fc37.noarch libevent-2.1.12-7.fc37.x86_64 coreutils-common-9.1-6.fc37.x86_64 rpm-4.18.0-0.beta1.4.fc37.x86_64 patch-2.7.6-17.fc37.x86_64 libgomp-12.1.1-4.fc38.x86_64 sed-4.8-11.fc37.x86_64 libzstd-1.5.2-3.fc37.x86_64 fedora-release-38-0.2.noarch pkgconf-1.8.0-3.fc37.x86_64 glibc-minimal-langpack-2.36-1.fc37.x86_64 grep-3.7-4.fc37.x86_64 pcre2-10.40-1.fc37.1.x86_64 lua-srpm-macros-1-7.fc37.noarch shadow-utils-4.11.1-4.fc37.x86_64 libcap-2.48-5.fc37.x86_64 ed-1.18-2.fc37.x86_64 pam-1.5.2-14.fc37.x86_64 coreutils-9.1-6.fc37.x86_64 libnghttp2-1.48.0-2.fc37.x86_64 bash-5.1.16-3.fc37.x86_64 which-2.21-35.fc37.x86_64 gnat-srpm-macros-4-16.fc37.noarch zlib-1.2.12-4.fc37.x86_64 gmp-6.2.1-3.fc37.x86_64 qt5-srpm-macros-5.15.5-2.fc37.noarch setup-2.14.1-2.fc37.noarch file-5.42-4.fc37.x86_64 cpio-2.13-13.fc37.x86_64 rpm-libs-4.18.0-0.beta1.4.fc37.x86_64 kernel-srpm-macros-1.0-15.fc37.noarch unzip-6.0-58.fc37.x86_64 libcap-ng-0.8.3-3.fc37.x86_64 rpmautospec-rpm-macros-0.3.0-1.fc37.noarch crypto-policies-20220802-1.gita99dfd2.fc37.noarch ghc-srpm-macros-1.5.0-7.fc37.noarch libeconf-0.4.0-4.fc37.x86_64 gdb-minimal-12.1-4.fc37.x86_64 libpsl-0.21.1-6.fc37.x86_64 readline-8.1-7.fc37.x86_64 cracklib-2.9.6-28.fc36.x86_64 fedora-gpg-keys-38-0.2.noarch pkgconf-pkg-config-1.8.0-3.fc37.x86_64 libselinux-3.4-5.fc37.x86_64 bzip2-libs-1.0.8-12.fc37.x86_64 pam-libs-1.5.2-14.fc37.x86_64 libattr-2.5.1-5.fc37.x86_64 jansson-2.13.1-5.fc37.x86_64 xz-5.2.5-10.fc37.x86_64 libgcc-12.1.1-4.fc38.x86_64 libssh-config-0.9.6-5.fc37.noarch openblas-srpm-macros-2-12.fc37.noarch xxhash-libs-0.8.1-3.fc37.x86_64 elfutils-libelf-0.187-6.fc37.x86_64 ca-certificates-2022.2.54-5.fc37.noarch rpm-build-4.18.0-0.beta1.4.fc37.x86_64 libcom_err-1.46.5-3.fc37.x86_64 glibc-common-2.36-1.fc37.x86_64 libfdisk-2.38.1-1.fc37.x86_64 file-libs-5.42-4.fc37.x86_64 zip-3.0-33.fc37.x86_64 systemd-libs-251.4-51.fc37.x86_64 elfutils-default-yama-scope-0.187-6.fc37.noarch curl-7.84.0-2.fc37.x86_64 rpm-build-libs-4.18.0-0.beta1.4.fc37.x86_64 ansible-srpm-macros-1-6.fc37.noarch gpg-pubkey-eb10b464-6202d9c6 keyutils-libs-1.6.1-5.fc37.x86_64 zstd-1.5.2-3.fc37.x86_64 cyrus-sasl-lib-2.1.28-7.fc37.x86_64 libarchive-3.6.1-2.fc37.x86_64 libpkgconf-1.8.0-3.fc37.x86_64 tar-1.34-3.fc36.x86_64 ocaml-srpm-macros-7-2.fc37.noarch glibc-gconv-extra-2.36-1.fc37.x86_64 pcre-8.45-1.fc37.2.x86_64 authselect-libs-1.4.0-3.fc37.x86_64 libpwquality-1.4.4-11.fc37.x86_64 fedora-release-common-38-0.2.noarch libtirpc-1.3.3-0.fc37.x86_64 fedora-repos-38-0.2.noarch libunistring-1.0-2.fc37.x86_64 sqlite-libs-3.39.2-2.fc37.x86_64 info-6.8-4.fc37.x86_64 fedora-release-identity-basic-38-0.2.noarch libssh-0.9.6-5.fc37.x86_64 python-srpm-macros-3.11-4.fc37.noarch diffutils-3.8-3.fc37.x86_64 go-srpm-macros-3.1.0-4.fc37.noarch findutils-4.9.0-2.fc37.x86_64 libcurl-7.84.0-2.fc37.x86_64 gdbm-libs-1.23-2.fc37.x86_64 filesystem-3.18-2.fc37.x86_64 alternatives-1.19-3.fc37.x86_64 libsepol-3.4-3.fc37.x86_64 lz4-libs-1.9.3-5.fc37.x86_64 publicsuffix-list-dafsa-20210518-5.fc37.noarch pcre2-syntax-10.40-1.fc37.1.noarch package-notes-srpm-macros-0.4-16.fc37.noarch elfutils-libs-0.187-6.fc37.x86_64 p11-kit-0.24.1-3.fc37.x86_64 krb5-libs-1.19.2-11.fc37.1.x86_64 elfutils-debuginfod-client-0.187-6.fc37.x86_64 glibc-2.36-1.fc37.x86_64 debugedit-5.0-5.fc37.x86_64 dwz-0.14-7.fc37.x86_64 lua-libs-5.4.4-4.fc37.x86_64 libstdc++-12.1.1-4.fc38.x86_64 libuuid-2.38.1-1.fc37.x86_64 libidn2-2.3.3-2.fc37.x86_64 binutils-gold-2.38-24.fc38.x86_64 libxml2-2.9.14-3.fc37.x86_64 perl-srpm-macros-1-46.fc37.noarch gzip-1.12-2.fc37.x86_64 libbrotli-1.0.9-9.fc37.x86_64 libdb-5.3.28-53.fc37.x86_64 gpg-pubkey-5323552a-6112bcdc libblkid-2.38.1-1.fc37.x86_64 libxcrypt-4.4.28-3.fc38.x86_64 redhat-rpm-config-227-1.fc37.noarch ncurses-libs-6.3-3.20220501.fc37.x86_64 elfutils-0.187-6.fc37.x86_64 basesystem-11-14.fc37.noarch util-linux-core-2.38.1-1.fc37.x86_64 fpc-srpm-macros-1.3-6.fc37.noarch rust-srpm-macros-22-1.fc37.noarch gawk-5.1.1-4.fc37.x86_64 libverto-0.3.2-4.fc37.x86_64 efi-srpm-macros-5-6.fc37.noarch libsigsegv-2.14-3.fc37.x86_64 binutils-2.38-24.fc38.x86_64 libnsl2-2.0.0-4.fc37.x86_64 util-linux-2.38.1-1.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/samtools-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_64-1660573317.563253/root/var/log/dnf.rpm.log /var/lib/mock/fedora-rawhide-x86_64-1660573317.563253/root/var/log/dnf.librepo.log /var/lib/mock/fedora-rawhide-x86_64-1660573317.563253/root/var/log/dnf.log Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-6n_9c0b8/samtools/samtools.spec) Config(child) 0 minutes 42 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot Finish: run Running (timeout=18000): unbuffer mock --rebuild /var/lib/copr-rpmbuild/results/samtools-1.15.1-1.fc38.src.rpm --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1660573317.563253 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 3.1 starting (python version = 3.10.4, NVR = mock-3.1-1.fc35)... 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/samtools-1.15.1-1.fc38.src.rpm) Config(fedora-rawhide-x86_64) Start: clean chroot Finish: clean chroot Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-1660573317.563253/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: 3.1 INFO: Mock Version: 3.1 Start: dnf update 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 44 kB/s | 3.3 kB 00:00 fedora 700 kB/s | 18 kB 00:00 fedora 461 kB/s | 1.7 MB 00:03 Dependencies resolved. Nothing to do. Complete! Finish: dnf update Finish: chroot init Start: build phase for samtools-1.15.1-1.fc38.src.rpm Start: build setup for samtools-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/samtools-1.15.1-1.fc38.src.rpm No matches found for the following disable plugin patterns: local, spacewalk, versionlock Updating Subscription Management repositories. Unable to read consumer identity This system is not registered with an entitlement server. You can use subscription-manager to register. Copr repository 71 kB/s | 3.3 kB 00:00 fedora 684 kB/s | 18 kB 00:00 fedora 2.0 MB/s | 3.3 MB 00:01 Dependencies resolved. ================================================================================ Package Arch Version Repository Size ================================================================================ Installing: gcc x86_64 12.1.1-4.fc38 fedora 33 M htslib-devel x86_64 1.15.1-1.fc38 copr_base 100 k htslib-tools x86_64 1.15.1-1.fc38 copr_base 533 k make x86_64 1:4.3-11.fc37 fedora 542 k ncurses-devel x86_64 6.3-3.20220501.fc37 fedora 547 k perl-FindBin noarch 1.53-491.fc37 fedora 18 k perl-Getopt-Long noarch 1:2.52-489.fc37 fedora 60 k perl-interpreter x86_64 4:5.36.0-491.fc37 fedora 76 k perl-lib x86_64 0.65-491.fc37 fedora 19 k zlib-devel x86_64 1.2.12-4.fc37 fedora 44 k Installing dependencies: annobin-docs noarch 10.81-1.fc38 fedora 91 k annobin-plugin-gcc x86_64 10.81-1.fc38 fedora 882 k cpp x86_64 12.1.1-4.fc38 fedora 11 M gc x86_64 8.0.6-4.fc37 fedora 103 k gcc-plugin-annobin x86_64 12.1.1-4.fc38 fedora 50 k glibc-devel x86_64 2.36-1.fc37 fedora 96 k glibc-headers-x86 noarch 2.36-1.fc37 fedora 574 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 htslib x86_64 1.15.1-1.fc38 copr_base 487 k kernel-headers x86_64 5.19.0-1.fc37 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 4.4.28-3.fc38 fedora 28 k ncurses x86_64 6.3-3.20220501.fc37 fedora 409 k ncurses-c++-libs x86_64 6.3-3.20220501.fc37 fedora 37 k perl-Carp noarch 1.52-489.fc37 fedora 29 k perl-Class-Struct noarch 0.66-491.fc37 fedora 26 k perl-DynaLoader x86_64 1.52-491.fc37 fedora 30 k perl-Encode x86_64 4:3.19-491.fc37 fedora 1.7 M perl-Errno x86_64 1.36-491.fc37 fedora 19 k perl-Exporter noarch 5.77-489.fc37 fedora 31 k perl-Fcntl x86_64 1.15-491.fc37 fedora 25 k perl-File-Basename noarch 2.85-491.fc37 fedora 22 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 1.12-491.fc37 fedora 22 k perl-Getopt-Std noarch 1.13-491.fc37 fedora 20 k perl-HTTP-Tiny noarch 0.082-1.fc37 fedora 55 k perl-IO x86_64 1.50-491.fc37 fedora 96 k perl-IPC-Open3 noarch 1.22-491.fc37 fedora 27 k perl-MIME-Base64 x86_64 3.16-489.fc37 fedora 30 k perl-POSIX x86_64 2.03-491.fc37 fedora 102 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 1.02-491.fc37 fedora 16 k perl-Socket x86_64 4:2.035-2.fc37 fedora 55 k perl-Storable x86_64 1:3.26-489.fc37 fedora 97 k perl-Symbol noarch 1.09-491.fc37 fedora 19 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 0.61.000-491.fc37 fedora 18 k perl-libs x86_64 4:5.36.0-491.fc37 fedora 2.2 M perl-mro x86_64 1.26-491.fc37 fedora 33 k perl-overload noarch 1.35-491.fc37 fedora 50 k perl-overloading noarch 0.02-491.fc37 fedora 17 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 1.04-491.fc37 fedora 16 k perl-vars noarch 1.05-491.fc37 fedora 17 k Transaction Summary ================================================================================ Install 68 Packages Total download size: 63 M Installed size: 208 M Downloading Packages: (1/68): htslib-devel-1.15.1-1.fc38.x86_64.rpm 1.7 MB/s | 100 kB 00:00 (2/68): htslib-1.15.1-1.fc38.x86_64.rpm 6.7 MB/s | 487 kB 00:00 (3/68): htslib-tools-1.15.1-1.fc38.x86_64.rpm 6.4 MB/s | 533 kB 00:00 (4/68): annobin-docs-10.81-1.fc38.noarch.rpm 418 kB/s | 91 kB 00:00 (5/68): gc-8.0.6-4.fc37.x86_64.rpm 875 kB/s | 103 kB 00:00 (6/68): annobin-plugin-gcc-10.81-1.fc38.x86_64. 2.5 MB/s | 882 kB 00:00 (7/68): gcc-plugin-annobin-12.1.1-4.fc38.x86_64 738 kB/s | 50 kB 00:00 (8/68): glibc-devel-2.36-1.fc37.x86_64.rpm 1.0 MB/s | 96 kB 00:00 (9/68): cpp-12.1.1-4.fc38.x86_64.rpm 19 MB/s | 11 MB 00:00 (10/68): glibc-headers-x86-2.36-1.fc37.noarch.r 4.2 MB/s | 574 kB 00:00 (11/68): groff-base-1.22.4-10.fc37.x86_64.rpm 10 MB/s | 1.1 MB 00:00 (12/68): kernel-headers-5.19.0-1.fc37.x86_64.rp 15 MB/s | 1.5 MB 00:00 (13/68): libmpc-1.2.1-5.fc37.x86_64.rpm 993 kB/s | 61 kB 00:00 (14/68): libtool-ltdl-2.4.7-2.fc37.x86_64.rpm 495 kB/s | 37 kB 00:00 (15/68): libxcrypt-devel-4.4.28-3.fc38.x86_64.r 512 kB/s | 28 kB 00:00 (16/68): guile22-2.2.7-6.fc37.x86_64.rpm 15 MB/s | 6.5 MB 00:00 (17/68): make-4.3-11.fc37.x86_64.rpm 5.3 MB/s | 542 kB 00:00 (18/68): ncurses-c++-libs-6.3-3.20220501.fc37.x 438 kB/s | 37 kB 00:00 (19/68): ncurses-6.3-3.20220501.fc37.x86_64.rpm 4.0 MB/s | 409 kB 00:00 (20/68): perl-Carp-1.52-489.fc37.noarch.rpm 362 kB/s | 29 kB 00:00 (21/68): ncurses-devel-6.3-3.20220501.fc37.x86_ 3.9 MB/s | 547 kB 00:00 (22/68): perl-Class-Struct-0.66-491.fc37.noarch 270 kB/s | 26 kB 00:00 (23/68): perl-DynaLoader-1.52-491.fc37.x86_64.r 500 kB/s | 30 kB 00:00 (24/68): perl-Errno-1.36-491.fc37.x86_64.rpm 407 kB/s | 19 kB 00:00 (25/68): perl-Exporter-5.77-489.fc37.noarch.rpm 630 kB/s | 31 kB 00:00 (26/68): perl-Fcntl-1.15-491.fc37.x86_64.rpm 625 kB/s | 25 kB 00:00 (27/68): perl-Encode-3.19-491.fc37.x86_64.rpm 9.9 MB/s | 1.7 MB 00:00 (28/68): perl-File-Basename-2.85-491.fc37.noarc 641 kB/s | 22 kB 00:00 (29/68): perl-File-Path-2.18-489.fc37.noarch.rp 801 kB/s | 35 kB 00:00 (30/68): perl-File-Temp-0.231.100-489.fc37.noar 1.3 MB/s | 59 kB 00:00 (31/68): perl-File-stat-1.12-491.fc37.noarch.rp 524 kB/s | 22 kB 00:00 (32/68): perl-FindBin-1.53-491.fc37.noarch.rpm 463 kB/s | 18 kB 00:00 (33/68): perl-Getopt-Long-2.52-489.fc37.noarch. 839 kB/s | 60 kB 00:00 (34/68): perl-Getopt-Std-1.13-491.fc37.noarch.r 294 kB/s | 20 kB 00:00 (35/68): perl-HTTP-Tiny-0.082-1.fc37.noarch.rpm 1.2 MB/s | 55 kB 00:00 (36/68): perl-IO-1.50-491.fc37.x86_64.rpm 1.9 MB/s | 96 kB 00:00 (37/68): perl-IPC-Open3-1.22-491.fc37.noarch.rp 668 kB/s | 27 kB 00:00 (38/68): perl-MIME-Base64-3.16-489.fc37.x86_64. 656 kB/s | 30 kB 00:00 (39/68): perl-POSIX-2.03-491.fc37.x86_64.rpm 1.8 MB/s | 102 kB 00:00 (40/68): perl-PathTools-3.84-489.fc37.x86_64.rp 1.7 MB/s | 89 kB 00:00 (41/68): perl-Pod-Escapes-1.07-489.fc37.noarch. 424 kB/s | 20 kB 00:00 (42/68): perl-Pod-Perldoc-3.28.01-490.fc37.noar 1.8 MB/s | 90 kB 00:00 (43/68): perl-Pod-Usage-2.03-3.fc37.noarch.rpm 729 kB/s | 40 kB 00:00 (44/68): perl-Pod-Simple-3.43-490.fc37.noarch.r 3.3 MB/s | 225 kB 00:00 (45/68): perl-Scalar-List-Utils-1.63-489.fc38.x 1.4 MB/s | 72 kB 00:00 (46/68): perl-SelectSaver-1.02-491.fc37.noarch. 274 kB/s | 16 kB 00:00 (47/68): perl-Socket-2.035-2.fc37.x86_64.rpm 1.2 MB/s | 55 kB 00:00 (48/68): perl-Storable-3.26-489.fc37.x86_64.rpm 2.0 MB/s | 97 kB 00:00 (49/68): perl-Symbol-1.09-491.fc37.noarch.rpm 405 kB/s | 19 kB 00:00 (50/68): perl-Term-ANSIColor-5.01-490.fc37.noar 1.2 MB/s | 48 kB 00:00 (51/68): perl-Term-Cap-1.17-489.fc37.noarch.rpm 657 kB/s | 22 kB 00:00 (52/68): perl-Text-ParseWords-3.31-489.fc37.noa 452 kB/s | 16 kB 00:00 (53/68): perl-Text-Tabs+Wrap-2021.0814-489.fc37 458 kB/s | 22 kB 00:00 (54/68): perl-Time-Local-1.300-489.fc37.noarch. 817 kB/s | 33 kB 00:00 (55/68): gcc-12.1.1-4.fc38.x86_64.rpm 18 MB/s | 33 MB 00:01 (56/68): perl-constant-1.33-490.fc37.noarch.rpm 463 kB/s | 23 kB 00:00 (57/68): perl-if-0.61.000-491.fc37.noarch.rpm 413 kB/s | 18 kB 00:00 (58/68): perl-interpreter-5.36.0-491.fc37.x86_6 1.9 MB/s | 76 kB 00:00 (59/68): perl-lib-0.65-491.fc37.x86_64.rpm 471 kB/s | 19 kB 00:00 (60/68): perl-overload-1.35-491.fc37.noarch.rpm 821 kB/s | 50 kB 00:00 (61/68): perl-mro-1.26-491.fc37.x86_64.rpm 382 kB/s | 33 kB 00:00 (62/68): perl-overloading-0.02-491.fc37.noarch. 507 kB/s | 17 kB 00:00 (63/68): perl-libs-5.36.0-491.fc37.x86_64.rpm 15 MB/s | 2.2 MB 00:00 (64/68): perl-parent-0.238-489.fc37.noarch.rpm 345 kB/s | 14 kB 00:00 (65/68): perl-podlators-4.14-489.fc37.noarch.rp 2.3 MB/s | 116 kB 00:00 (66/68): perl-subs-1.04-491.fc37.noarch.rpm 330 kB/s | 16 kB 00:00 (67/68): perl-vars-1.05-491.fc37.noarch.rpm 485 kB/s | 17 kB 00:00 (68/68): zlib-devel-1.2.12-4.fc37.x86_64.rpm 815 kB/s | 44 kB 00:00 -------------------------------------------------------------------------------- Total 25 MB/s | 63 MB 00:02 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 1/68 Installing : htslib-1.15.1-1.fc38.x86_64 2/68 Installing : cpp-12.1.1-4.fc38.x86_64 3/68 Installing : ncurses-c++-libs-6.3-3.20220501.fc37.x86_64 4/68 Installing : ncurses-6.3-3.20220501.fc37.x86_64 5/68 Installing : libtool-ltdl-2.4.7-2.fc37.x86_64 6/68 Installing : kernel-headers-5.19.0-1.fc37.x86_64 7/68 Running scriptlet: groff-base-1.22.4-10.fc37.x86_64 8/68 Installing : groff-base-1.22.4-10.fc37.x86_64 8/68 Running scriptlet: groff-base-1.22.4-10.fc37.x86_64 8/68 Installing : perl-Text-Tabs+Wrap-2021.0814-489.fc37.noarch 9/68 Installing : perl-if-0.61.000-491.fc37.noarch 10/68 Installing : perl-Time-Local-2:1.300-489.fc37.noarch 11/68 Installing : perl-File-Path-2.18-489.fc37.noarch 12/68 Installing : perl-Pod-Escapes-1:1.07-489.fc37.noarch 13/68 Installing : perl-Class-Struct-0.66-491.fc37.noarch 14/68 Installing : perl-POSIX-2.03-491.fc37.x86_64 15/68 Installing : perl-Term-ANSIColor-5.01-490.fc37.noarch 16/68 Installing : perl-IPC-Open3-1.22-491.fc37.noarch 17/68 Installing : perl-HTTP-Tiny-0.082-1.fc37.noarch 18/68 Installing : perl-subs-1.04-491.fc37.noarch 19/68 Installing : perl-File-Temp-1:0.231.100-489.fc37.noarch 20/68 Installing : perl-Term-Cap-1.17-489.fc37.noarch 21/68 Installing : perl-Pod-Simple-1:3.43-490.fc37.noarch 22/68 Installing : perl-Socket-4:2.035-2.fc37.x86_64 23/68 Installing : perl-SelectSaver-1.02-491.fc37.noarch 24/68 Installing : perl-Symbol-1.09-491.fc37.noarch 25/68 Installing : perl-File-stat-1.12-491.fc37.noarch 26/68 Installing : perl-podlators-1:4.14-489.fc37.noarch 27/68 Installing : perl-Pod-Perldoc-3.28.01-490.fc37.noarch 28/68 Installing : perl-Fcntl-1.15-491.fc37.x86_64 29/68 Installing : perl-Text-ParseWords-3.31-489.fc37.noarch 30/68 Installing : perl-mro-1.26-491.fc37.x86_64 31/68 Installing : perl-IO-1.50-491.fc37.x86_64 32/68 Installing : perl-overloading-0.02-491.fc37.noarch 33/68 Installing : perl-Pod-Usage-4:2.03-3.fc37.noarch 34/68 Installing : perl-Errno-1.36-491.fc37.x86_64 35/68 Installing : perl-File-Basename-2.85-491.fc37.noarch 36/68 Installing : perl-Getopt-Std-1.13-491.fc37.noarch 37/68 Installing : perl-MIME-Base64-3.16-489.fc37.x86_64 38/68 Installing : perl-Scalar-List-Utils-5:1.63-489.fc38.x86_64 39/68 Installing : perl-constant-1.33-490.fc37.noarch 40/68 Installing : perl-Storable-1:3.26-489.fc37.x86_64 41/68 Installing : perl-overload-1.35-491.fc37.noarch 42/68 Installing : perl-parent-1:0.238-489.fc37.noarch 43/68 Installing : perl-vars-1.05-491.fc37.noarch 44/68 Installing : perl-Getopt-Long-1:2.52-489.fc37.noarch 45/68 Installing : perl-Carp-1.52-489.fc37.noarch 46/68 Installing : perl-Exporter-5.77-489.fc37.noarch 47/68 Installing : perl-PathTools-3.84-489.fc37.x86_64 48/68 Installing : perl-DynaLoader-1.52-491.fc37.x86_64 49/68 Installing : perl-Encode-4:3.19-491.fc37.x86_64 50/68 Installing : perl-libs-4:5.36.0-491.fc37.x86_64 51/68 Installing : perl-interpreter-4:5.36.0-491.fc37.x86_64 52/68 Installing : glibc-headers-x86-2.36-1.fc37.noarch 53/68 Installing : libxcrypt-devel-4.4.28-3.fc38.x86_64 54/68 Installing : glibc-devel-2.36-1.fc37.x86_64 55/68 Installing : gc-8.0.6-4.fc37.x86_64 56/68 Installing : guile22-2.2.7-6.fc37.x86_64 57/68 Installing : make-1:4.3-11.fc37.x86_64 58/68 Installing : gcc-12.1.1-4.fc38.x86_64 59/68 Running scriptlet: gcc-12.1.1-4.fc38.x86_64 59/68 Installing : annobin-docs-10.81-1.fc38.noarch 60/68 Installing : annobin-plugin-gcc-10.81-1.fc38.x86_64 61/68 Running scriptlet: annobin-plugin-gcc-10.81-1.fc38.x86_64 61/68 Installing : gcc-plugin-annobin-12.1.1-4.fc38.x86_64 62/68 Installing : perl-FindBin-1.53-491.fc37.noarch 63/68 Installing : perl-lib-0.65-491.fc37.x86_64 64/68 Installing : ncurses-devel-6.3-3.20220501.fc37.x86_64 65/68 Installing : htslib-devel-1.15.1-1.fc38.x86_64 66/68 Installing : htslib-tools-1.15.1-1.fc38.x86_64 67/68 Installing : zlib-devel-1.2.12-4.fc37.x86_64 68/68 Running scriptlet: zlib-devel-1.2.12-4.fc37.x86_64 68/68 Verifying : htslib-1.15.1-1.fc38.x86_64 1/68 Verifying : htslib-devel-1.15.1-1.fc38.x86_64 2/68 Verifying : htslib-tools-1.15.1-1.fc38.x86_64 3/68 Verifying : annobin-docs-10.81-1.fc38.noarch 4/68 Verifying : annobin-plugin-gcc-10.81-1.fc38.x86_64 5/68 Verifying : cpp-12.1.1-4.fc38.x86_64 6/68 Verifying : gc-8.0.6-4.fc37.x86_64 7/68 Verifying : gcc-12.1.1-4.fc38.x86_64 8/68 Verifying : gcc-plugin-annobin-12.1.1-4.fc38.x86_64 9/68 Verifying : glibc-devel-2.36-1.fc37.x86_64 10/68 Verifying : glibc-headers-x86-2.36-1.fc37.noarch 11/68 Verifying : groff-base-1.22.4-10.fc37.x86_64 12/68 Verifying : guile22-2.2.7-6.fc37.x86_64 13/68 Verifying : kernel-headers-5.19.0-1.fc37.x86_64 14/68 Verifying : libmpc-1.2.1-5.fc37.x86_64 15/68 Verifying : libtool-ltdl-2.4.7-2.fc37.x86_64 16/68 Verifying : libxcrypt-devel-4.4.28-3.fc38.x86_64 17/68 Verifying : make-1:4.3-11.fc37.x86_64 18/68 Verifying : ncurses-6.3-3.20220501.fc37.x86_64 19/68 Verifying : ncurses-c++-libs-6.3-3.20220501.fc37.x86_64 20/68 Verifying : ncurses-devel-6.3-3.20220501.fc37.x86_64 21/68 Verifying : perl-Carp-1.52-489.fc37.noarch 22/68 Verifying : perl-Class-Struct-0.66-491.fc37.noarch 23/68 Verifying : perl-DynaLoader-1.52-491.fc37.x86_64 24/68 Verifying : perl-Encode-4:3.19-491.fc37.x86_64 25/68 Verifying : perl-Errno-1.36-491.fc37.x86_64 26/68 Verifying : perl-Exporter-5.77-489.fc37.noarch 27/68 Verifying : perl-Fcntl-1.15-491.fc37.x86_64 28/68 Verifying : perl-File-Basename-2.85-491.fc37.noarch 29/68 Verifying : perl-File-Path-2.18-489.fc37.noarch 30/68 Verifying : perl-File-Temp-1:0.231.100-489.fc37.noarch 31/68 Verifying : perl-File-stat-1.12-491.fc37.noarch 32/68 Verifying : perl-FindBin-1.53-491.fc37.noarch 33/68 Verifying : perl-Getopt-Long-1:2.52-489.fc37.noarch 34/68 Verifying : perl-Getopt-Std-1.13-491.fc37.noarch 35/68 Verifying : perl-HTTP-Tiny-0.082-1.fc37.noarch 36/68 Verifying : perl-IO-1.50-491.fc37.x86_64 37/68 Verifying : perl-IPC-Open3-1.22-491.fc37.noarch 38/68 Verifying : perl-MIME-Base64-3.16-489.fc37.x86_64 39/68 Verifying : perl-POSIX-2.03-491.fc37.x86_64 40/68 Verifying : perl-PathTools-3.84-489.fc37.x86_64 41/68 Verifying : perl-Pod-Escapes-1:1.07-489.fc37.noarch 42/68 Verifying : perl-Pod-Perldoc-3.28.01-490.fc37.noarch 43/68 Verifying : perl-Pod-Simple-1:3.43-490.fc37.noarch 44/68 Verifying : perl-Pod-Usage-4:2.03-3.fc37.noarch 45/68 Verifying : perl-Scalar-List-Utils-5:1.63-489.fc38.x86_64 46/68 Verifying : perl-SelectSaver-1.02-491.fc37.noarch 47/68 Verifying : perl-Socket-4:2.035-2.fc37.x86_64 48/68 Verifying : perl-Storable-1:3.26-489.fc37.x86_64 49/68 Verifying : perl-Symbol-1.09-491.fc37.noarch 50/68 Verifying : perl-Term-ANSIColor-5.01-490.fc37.noarch 51/68 Verifying : perl-Term-Cap-1.17-489.fc37.noarch 52/68 Verifying : perl-Text-ParseWords-3.31-489.fc37.noarch 53/68 Verifying : perl-Text-Tabs+Wrap-2021.0814-489.fc37.noarch 54/68 Verifying : perl-Time-Local-2:1.300-489.fc37.noarch 55/68 Verifying : perl-constant-1.33-490.fc37.noarch 56/68 Verifying : perl-if-0.61.000-491.fc37.noarch 57/68 Verifying : perl-interpreter-4:5.36.0-491.fc37.x86_64 58/68 Verifying : perl-lib-0.65-491.fc37.x86_64 59/68 Verifying : perl-libs-4:5.36.0-491.fc37.x86_64 60/68 Verifying : perl-mro-1.26-491.fc37.x86_64 61/68 Verifying : perl-overload-1.35-491.fc37.noarch 62/68 Verifying : perl-overloading-0.02-491.fc37.noarch 63/68 Verifying : perl-parent-1:0.238-489.fc37.noarch 64/68 Verifying : perl-podlators-1:4.14-489.fc37.noarch 65/68 Verifying : perl-subs-1.04-491.fc37.noarch 66/68 Verifying : perl-vars-1.05-491.fc37.noarch 67/68 Verifying : zlib-devel-1.2.12-4.fc37.x86_64 68/68 Installed products updated. Installed: annobin-docs-10.81-1.fc38.noarch annobin-plugin-gcc-10.81-1.fc38.x86_64 cpp-12.1.1-4.fc38.x86_64 gc-8.0.6-4.fc37.x86_64 gcc-12.1.1-4.fc38.x86_64 gcc-plugin-annobin-12.1.1-4.fc38.x86_64 glibc-devel-2.36-1.fc37.x86_64 glibc-headers-x86-2.36-1.fc37.noarch groff-base-1.22.4-10.fc37.x86_64 guile22-2.2.7-6.fc37.x86_64 htslib-1.15.1-1.fc38.x86_64 htslib-devel-1.15.1-1.fc38.x86_64 htslib-tools-1.15.1-1.fc38.x86_64 kernel-headers-5.19.0-1.fc37.x86_64 libmpc-1.2.1-5.fc37.x86_64 libtool-ltdl-2.4.7-2.fc37.x86_64 libxcrypt-devel-4.4.28-3.fc38.x86_64 make-1:4.3-11.fc37.x86_64 ncurses-6.3-3.20220501.fc37.x86_64 ncurses-c++-libs-6.3-3.20220501.fc37.x86_64 ncurses-devel-6.3-3.20220501.fc37.x86_64 perl-Carp-1.52-489.fc37.noarch perl-Class-Struct-0.66-491.fc37.noarch perl-DynaLoader-1.52-491.fc37.x86_64 perl-Encode-4:3.19-491.fc37.x86_64 perl-Errno-1.36-491.fc37.x86_64 perl-Exporter-5.77-489.fc37.noarch perl-Fcntl-1.15-491.fc37.x86_64 perl-File-Basename-2.85-491.fc37.noarch perl-File-Path-2.18-489.fc37.noarch perl-File-Temp-1:0.231.100-489.fc37.noarch perl-File-stat-1.12-491.fc37.noarch perl-FindBin-1.53-491.fc37.noarch perl-Getopt-Long-1:2.52-489.fc37.noarch perl-Getopt-Std-1.13-491.fc37.noarch perl-HTTP-Tiny-0.082-1.fc37.noarch perl-IO-1.50-491.fc37.x86_64 perl-IPC-Open3-1.22-491.fc37.noarch perl-MIME-Base64-3.16-489.fc37.x86_64 perl-POSIX-2.03-491.fc37.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-1.02-491.fc37.noarch perl-Socket-4:2.035-2.fc37.x86_64 perl-Storable-1:3.26-489.fc37.x86_64 perl-Symbol-1.09-491.fc37.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-0.61.000-491.fc37.noarch perl-interpreter-4:5.36.0-491.fc37.x86_64 perl-lib-0.65-491.fc37.x86_64 perl-libs-4:5.36.0-491.fc37.x86_64 perl-mro-1.26-491.fc37.x86_64 perl-overload-1.35-491.fc37.noarch perl-overloading-0.02-491.fc37.noarch perl-parent-1:0.238-489.fc37.noarch perl-podlators-1:4.14-489.fc37.noarch perl-subs-1.04-491.fc37.noarch perl-vars-1.05-491.fc37.noarch zlib-devel-1.2.12-4.fc37.x86_64 Complete! Finish: build setup for samtools-1.15.1-1.fc38.src.rpm Start: rpmbuild samtools-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.D5qpUE + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf samtools-1.15.1 + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/samtools-1.15.1.tar.bz2 + STATUS=0 + '[' 0 -ne 0 ']' + cd samtools-1.15.1 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + rm -f INSTALL + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.Le1HzF + 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 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-1.fc38.x86_64.ld' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + '[' -f /usr/lib/rpm/generate-rpm-note.sh ']' + /usr/lib/rpm/generate-rpm-note.sh samtools 1.15.1-1.fc38 x86_64 + cd samtools-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 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-1.fc38.x86_64.ld' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + '[' '-flto=auto -ffat-lto-objectsx' '!=' x ']' ++ find . -type f -name configure -print + for file in $(find . -type f -name configure -print) + /usr/bin/sed -r --in-place=.backup 's/^char $\*f$  = /__attribute__ ((used)) char (*f) () = /g' ./htslib-1.15.1/configure + diff -u ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure + mv ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure + /usr/bin/sed -r --in-place=.backup 's/^char $\*f$ ;/__attribute__ ((used)) char (*f) ();/g' ./htslib-1.15.1/configure + diff -u ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure + mv ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure + /usr/bin/sed -r --in-place=.backup 's/^char \$2 ;/__attribute__ ((used)) char \$2 ();/g' ./htslib-1.15.1/configure + diff -u ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure --- ./htslib-1.15.1/configure.backup 2022-04-07 15:42:52.000000000 +0000 +++ ./htslib-1.15.1/configure 2022-08-15 14:23:17.946600441 +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' ./htslib-1.15.1/configure + diff -u ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure + mv ./htslib-1.15.1/configure.backup ./htslib-1.15.1/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'\''"#' ./htslib-1.15.1/configure + diff -u ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure + mv ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure + for file in $(find . -type f -name configure -print) + /usr/bin/sed -r --in-place=.backup 's/^char $\*f$  = /__attribute__ ((used)) char (*f) () = /g' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed -r --in-place=.backup 's/^char $\*f$ ;/__attribute__ ((used)) char (*f) ();/g' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed -r --in-place=.backup 's/^char \$2 ;/__attribute__ ((used)) char \$2 ();/g' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed --in-place=.backup '1{$!N;$!N};$!N;s/int x = 1;\nint y = 0;\nint z;\nint nan;/volatile int x = 1; volatile int y = 0; volatile int z, nan;/;P;D' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed --in-place=.backup 's#^lt_cv_sys_global_symbol_to_cdecl=.*#lt_cv_sys_global_symbol_to_cdecl="sed -n -e '\''s/^T .* \$.*\$$/extern int \\1();/p'\'' -e '\''s/^$symcode* .* \$.*\$$/extern char \\1;/p'\''"#' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + '[' 1 = 1 ']' +++ dirname ./configure ++ find . -name config.guess -o -name config.sub + '[' 1 = 1 ']' + '[' x '!=' 'x-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' ']' ++ find . -name ltmain.sh + ./configure --build=x86_64-redhat-linux-gnu --host=x86_64-redhat-linux-gnu --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/libexec --localstatedir=/var --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info 'CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' 'LDFLAGS=-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-1.fc38.x86_64.ld' --prefix=/usr --with-htslib=system checking for gawk... gawk 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 grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for htslib/sam.h... yes checking for hts_version in -lhts... yes checking for NcursesW wide-character library... yes checking for working ncursesw/curses.h... yes checking for library containing cbreak... none required checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating config.h + /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 -I. -I./lz4 -c -o bam_aux.o bam_aux.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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. -I./lz4 -c -o bam.o bam.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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. -I./lz4 -c -o bam_index.o bam_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 -I. -I./lz4 -c -o bam_plcmd.o bam_plcmd.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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. -I./lz4 -c -o sam_view.o sam_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 -I. -I./lz4 -c -o bam_fastq.o bam_fastq.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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. -I./lz4 -c -o bam_cat.o bam_cat.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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. -I./lz4 -c -o bam_plbuf.o bam_plbuf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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. -I./lz4 -c -o bam_md.o bam_md.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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. -I./lz4 -c -o bam_reheader.o bam_reheader.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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. -I./lz4 -c -o bam_rmdup.o bam_rmdup.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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. -I./lz4 -c -o bam_rmdupse.o bam_rmdupse.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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. -I./lz4 -c -o bam_mate.o bam_mate.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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. -I./lz4 -c -o bam_stat.o bam_stat.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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. -I./lz4 -c -o bam_color.o bam_color.c echo '#define SAMTOOLS_VERSION "1.15.1"' > version.h echo '#define SAMTOOLS_CC "gcc"' >> version.h echo '#define SAMTOOLS_CPPFLAGS ""' >> version.h echo '#define SAMTOOLS_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"' >> version.h echo '#define SAMTOOLS_LDFLAGS "-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-1.fc38.x86_64.ld"' >> version.h echo '#define SAMTOOLS_HTSDIR ""' >> version.h echo '#define SAMTOOLS_LIBS ""' >> version.h echo '#define SAMTOOLS_CURSES_LIB "-lncursesw"' >> version.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 -I. -I./lz4 -c -o bam2bcf.o bam2bcf.c bam2bcf.c: In function 'bcf_call_glfgen': bam2bcf.c:81:33: warning: argument 2 range [18446744071562067968, 18446744073709551614] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 81 | bca->bases = (uint16_t*)realloc(bca->bases, 2 * bca->max_bases); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/htslib/kstring.h:30, from /usr/include/htslib/hts.h:37, from bam2bcf.c:30: /usr/include/stdlib.h:564:14: note: in a call to allocation function 'realloc' declared here 564 | extern void *realloc (void *__ptr, size_t __size) | ^~~~~~~ gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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. -I./lz4 -c -o sample.o sample.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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. -I./lz4 -c -o cut_target.o cut_target.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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. -I./lz4 -c -o bam_sort.o bam_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 -I. -I./lz4 -c -o phase.o phase.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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. -I./lz4 -c -o bam2depth.o bam2depth.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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. -I./lz4 -c -o coverage.o coverage.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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. -I./lz4 -c -o bedcov.o bedcov.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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. -I./lz4 -c -o padding.o padding.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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. -I./lz4 -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 -I. -I./lz4 -c -o dict.o dict.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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. -I./lz4 -c -o bamshuf.o bamshuf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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. -I./lz4 -c -o stats_isize.o stats_isize.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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. -I./lz4 -c -o bam_flags.o bam_flags.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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. -I./lz4 -c -o bam_split.o bam_split.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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. -I./lz4 -c -o bam_tview.o bam_tview.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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. -I./lz4 -c -o stats.o 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 -I. -I./lz4 -c -o bam_tview_curses.o bam_tview_curses.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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. -I./lz4 -c -o bam_tview_html.o bam_tview_html.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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. -I./lz4 -c -o bam_quickcheck.o bam_quickcheck.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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. -I./lz4 -c -o bam_lpileup.o bam_lpileup.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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. -I./lz4 -c -o bam_addrprg.o bam_addrprg.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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. -I./lz4 -c -o tmp_file.o tmp_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 -I. -I./lz4 -c -o bam_ampliconclip.o bam_ampliconclip.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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. -I./lz4 -c -o bam_markdup.o bam_markdup.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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. -I./lz4 -c -o bam_import.o bam_import.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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. -I./lz4 -c -o bam_samples.o bam_samples.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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. -I./lz4 -c -o amplicon_stats.o amplicon_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 -I. -I./lz4 -c -o consensus_pileup.o consensus_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 -I. -I./lz4 -c -o bam_consensus.o bam_consensus.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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. -I./lz4 -c -o sam_opts.o sam_opts.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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. -I./lz4 -c -o sam_utils.o sam_utils.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -I./lz4 -c -o bedidx.o bedidx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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. -I./lz4 -c -o misc/ace2sam.o misc/ace2sam.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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 -DMAQ_LONGREADS -I. -I./lz4 -c -o misc/maq2sam-long.o misc/maq2sam.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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. -I./lz4 -c -o misc/maq2sam-short.o misc/maq2sam.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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. -I./lz4 -c -o lz4/lz4.o lz4/lz4.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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. -I./lz4 -c -o misc/md5sum-lite.o misc/md5sum-lite.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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. -I./lz4 -c -o misc/md5fa.o misc/md5fa.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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. -I./lz4 -c -o misc/wgsim.o misc/wgsim.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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. -I./lz4 -c -o test/test.o test/test.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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. -I./lz4 -c -o test/merge/test_bam_translate.o test/merge/test_bam_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 -I. -I./lz4 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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. -I./lz4 -c -o test/split/test_count_rg.o test/split/test_count_rg.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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. -I./lz4 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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. -I./lz4 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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. -I./lz4 -c -o test/split/test_parse_args.o test/split/test_parse_args.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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. -I./lz4 -c -o test/vcf-miniview.o test/vcf-miniview.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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. -I./lz4 -c -o bamtk.o bamtk.c ar -rcs libst.a sam_opts.o sam_utils.o bedidx.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -I./lz4 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-1.fc38.x86_64.ld -o misc/maq2sam-long misc/maq2sam-long.o -lz gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-1.fc38.x86_64.ld -o misc/ace2sam misc/ace2sam.o -lhts -lz gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-1.fc38.x86_64.ld -o misc/maq2sam-short misc/maq2sam-short.o -lz gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-1.fc38.x86_64.ld -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-1.fc38.x86_64.ld -o misc/md5fa misc/md5fa.o -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-1.fc38.x86_64.ld -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-1.fc38.x86_64.ld -o misc/wgsim misc/wgsim.o -lm -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-1.fc38.x86_64.ld -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-1.fc38.x86_64.ld -o test/split/test_count_rg test/split/test_count_rg.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-1.fc38.x86_64.ld -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-1.fc38.x86_64.ld -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-1.fc38.x86_64.ld -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-1.fc38.x86_64.ld -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-1.fc38.x86_64.ld -o test/split/test_parse_args test/split/test_parse_args.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-1.fc38.x86_64.ld -o samtools bam.o bam_aux.o bam_index.o bam_plcmd.o sam_view.o bam_fastq.o bam_cat.o bam_md.o bam_plbuf.o bam_reheader.o bam_sort.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o sample.o cut_target.o phase.o bam2depth.o coverage.o padding.o bedcov.o bamshuf.o faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o bam_quickcheck.o bam_addrprg.o bam_markdup.o tmp_file.o bam_ampliconclip.o amplicon_stats.o bam_import.o bam_samples.o bam_consensus.o consensus_pileup.o ./lz4/lz4.o libst.a -lhts -lncursesw -lm -lz -lpthread In function 'bcf_call_glfgen', inlined from 'tv_pl_func' at bam_tview.c:196:9: bam2bcf.c:81:33: warning: argument 2 range [18446744071562067968, 18446744073709551614] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 81 | bca->bases = (uint16_t*)realloc(bca->bases, 2 * bca->max_bases); | ^ /usr/include/stdlib.h: In function 'tv_pl_func': /usr/include/stdlib.h:564:14: note: in a call to allocation function 'realloc' declared here 564 | extern void *realloc (void *__ptr, size_t __size) | ^ + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.zxf9Gv + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64 ++ dirname /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/samtools-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 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-1.fc38.x86_64.ld' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd samtools-1.15.1 + /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64 'INSTALL=/usr/bin/install -p' mkdir -p -m 755 /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/share/man/man1 /usr/bin/install -p samtools /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin /usr/bin/install -p misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin /usr/bin/install -p misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl misc/fasta-sanitize.pl misc/interpolate_sam.pl misc/novo2sam.pl misc/plot-ampliconstats misc/plot-bamstats misc/psl2sam.pl misc/sam2vcf.pl misc/samtools.pl misc/seq_cache_populate.pl misc/soap2sam.pl misc/wgsim_eval.pl misc/zoom2sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin /usr/bin/install -p -m 644 doc/samtools*.1 misc/wgsim.1 /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/share/man/man1 ++ grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/ace2sam /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/blast2sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/bowtie2sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/export2sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/fasta-sanitize.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/interpolate_sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/maq2sam-long /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/maq2sam-short /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/md5fa /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/md5sum-lite /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/novo2sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/plot-ampliconstats /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/plot-bamstats /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/psl2sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/sam2vcf.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/samtools /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/samtools.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/seq_cache_populate.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/soap2sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/wgsim /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/wgsim_eval.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/zoom2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/blast2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/bowtie2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/export2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/fasta-sanitize.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/interpolate_sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/novo2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/plot-ampliconstats + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/plot-bamstats + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/psl2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/sam2vcf.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/samtools.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/seq_cache_populate.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/soap2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/wgsim_eval.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/zoom2sam.pl + /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 samtools-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/samtools-1.15.1 extracting debug info from /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/ace2sam extracting debug info from /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/maq2sam-long extracting debug info from /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/maq2sam-short extracting debug info from /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/md5fa extracting debug info from /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/md5sum-lite extracting debug info from /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/samtools extracting debug info from /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/wgsim original debug info size: 2036kB, size after compression: 1832kB /usr/bin/sepdebugcrcfix: Updated 7 CRC32s, 0 CRC32s did match. 2442 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.mlkydV + 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 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-1.fc38.x86_64.ld' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + '[' -f /usr/lib/rpm/generate-rpm-note.sh ']' + /usr/lib/rpm/generate-rpm-note.sh samtools 1.15.1-1.fc38 x86_64 + cd samtools-1.15.1 + ldd samtools + grep -E '/lib(64)?/libhts\.so\.' libhts.so.3 => /lib64/libhts.so.3 (0x00007faf9a515000) + make test test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args REF_PATH=: test/test.pl --exec bgzip= ${TEST_OPTS:-} bgzip -c -b 65272 -s 5 /tmp/qdLMY7TwIk/bgzip.dat.gz .. ok bgzip -c -b 979200 -s 6 /tmp/qdLMY7TwIk/bgzip.dat.gz .. ok bgzip -c -b 652804 -s 6 /tmp/qdLMY7TwIk/bgzip.dat.gz .. ok /builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/qdLMY7TwIk/faidx.fa 3:11-13 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/qdLMY7TwIk/faidx.fa.gz 3:11-13 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/qdLMY7TwIk/faidx.fa 2:998-1003 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/qdLMY7TwIk/faidx.fa.gz 2:998-1003 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/qdLMY7TwIk/faidx.fa 1:100-104 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/qdLMY7TwIk/faidx.fa.gz 1:100-104 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/qdLMY7TwIk/faidx.fa 1:99998-100007 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/qdLMY7TwIk/faidx.fa.gz 1:99998-100007 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/qdLMY7TwIk/fqidx.fq 3:11-13 .. ok .. ok /builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/qdLMY7TwIk/fqidx.fq.gz 3:11-13 .. ok .. ok /builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/qdLMY7TwIk/fqidx.fq 2:998-1003 .. ok .. ok /builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/qdLMY7TwIk/fqidx.fq.gz 2:998-1003 .. ok .. ok /builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/qdLMY7TwIk/fqidx.fq 1:100-104 .. ok .. ok /builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/qdLMY7TwIk/fqidx.fq.gz 1:100-104 .. ok .. ok /builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/qdLMY7TwIk/fqidx.fq 1:99998-100007 .. ok .. ok /builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/qdLMY7TwIk/fqidx.fq.gz 1:99998-100007 .. ok .. ok test_dict: /builddir/build/BUILD/samtools-1.15.1/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /builddir/build/BUILD/samtools-1.15.1/test/dat/dict.fa .. ok test_dict: /builddir/build/BUILD/samtools-1.15.1/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/qdLMY7TwIk/dict.fa.gz .. ok test_dict: cat /builddir/build/BUILD/samtools-1.15.1/test/dat/dict.fa | /builddir/build/BUILD/samtools-1.15.1/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz .. ok test_dict: /builddir/build/BUILD/samtools-1.15.1/samtools dict -AH < /builddir/build/BUILD/samtools-1.15.1/test/dat/dict.alias.fa .. ok test_index: /builddir/build/BUILD/samtools-1.15.1/samtools view /tmp/qdLMY7TwIk/large_chrom.bam ref2 .. ok test_index: /builddir/build/BUILD/samtools-1.15.1/samtools view /tmp/qdLMY7TwIk/large_chrom.bam ref2:1-541556283 .. ok test_index: /builddir/build/BUILD/samtools-1.15.1/samtools index /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam && cat /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam.bai .. ok test_index: /builddir/build/BUILD/samtools-1.15.1/samtools view -X /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_b.bam /tmp/qdLMY7TwIk/test_input_1_b.bam.bai ref2 .. ok test_index: /builddir/build/BUILD/samtools-1.15.1/samtools merge -O sam - -X -cp -R ref2 /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_b.bam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam.bai /tmp/qdLMY7TwIk/test_input_1_b.bam.bai .. ok test_index: /builddir/build/BUILD/samtools-1.15.1/samtools index -c /builddir/build/BUILD/samtools-1.15.1/test/dat/auto_indexed.tmp.bam /tmp/qdLMY7TwIk/auto_indexed.csi && cat /tmp/qdLMY7TwIk/auto_indexed.csi .. ok test_index: /builddir/build/BUILD/samtools-1.15.1/samtools index /builddir/build/BUILD/samtools-1.15.1/test/dat/auto_indexed.tmp.cram /tmp/qdLMY7TwIk/auto_indexed.crai && cat /tmp/qdLMY7TwIk/auto_indexed.crai .. ok test_index: /builddir/build/BUILD/samtools-1.15.1/samtools index -c /builddir/build/BUILD/samtools-1.15.1/test/dat/auto_indexed.tmp.sam /tmp/qdLMY7TwIk/auto_indexed.csi && cat /tmp/qdLMY7TwIk/auto_indexed.csi .. ok test_index: /builddir/build/BUILD/samtools-1.15.1/samtools view -@ 2 /tmp/qdLMY7TwIk/large_chrom.bam ref2 .. ok test_index: /builddir/build/BUILD/samtools-1.15.1/samtools view -@ 2 /tmp/qdLMY7TwIk/large_chrom.bam ref2:1-541556283 .. ok test_index: /builddir/build/BUILD/samtools-1.15.1/samtools index -@ 2 /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam && cat /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam.bai .. ok test_index: /builddir/build/BUILD/samtools-1.15.1/samtools view -@ 2 -X /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_b.bam /tmp/qdLMY7TwIk/test_input_1_b.bam.bai ref2 .. ok test_index: /builddir/build/BUILD/samtools-1.15.1/samtools merge -@ 2 -O sam - -X -cp -R ref2 /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_b.bam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam.bai /tmp/qdLMY7TwIk/test_input_1_b.bam.bai .. ok test_index: /builddir/build/BUILD/samtools-1.15.1/samtools index -@ 2 -c /builddir/build/BUILD/samtools-1.15.1/test/dat/auto_indexed.tmp.bam /tmp/qdLMY7TwIk/auto_indexed.csi && cat /tmp/qdLMY7TwIk/auto_indexed.csi .. ok test_index: /builddir/build/BUILD/samtools-1.15.1/samtools index -@ 2 /builddir/build/BUILD/samtools-1.15.1/test/dat/auto_indexed.tmp.cram /tmp/qdLMY7TwIk/auto_indexed.crai && cat /tmp/qdLMY7TwIk/auto_indexed.crai .. ok test_index: /builddir/build/BUILD/samtools-1.15.1/samtools index -@ 2 -c /builddir/build/BUILD/samtools-1.15.1/test/dat/auto_indexed.tmp.sam /tmp/qdLMY7TwIk/auto_indexed.csi && cat /tmp/qdLMY7TwIk/auto_indexed.csi .. ok test_mpileup: /builddir/build/BUILD/samtools-1.15.1/samtools mpileup -b /tmp/qdLMY7TwIk/mpileup.bam.list -f /tmp/qdLMY7TwIk/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /builddir/build/BUILD/samtools-1.15.1/samtools mpileup -b /tmp/qdLMY7TwIk/mpileup.cram.list -f /tmp/qdLMY7TwIk/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /builddir/build/BUILD/samtools-1.15.1/samtools mpileup -b /tmp/qdLMY7TwIk/mpileup.bam.urllist -f /tmp/qdLMY7TwIk/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /builddir/build/BUILD/samtools-1.15.1/samtools mpileup -b /tmp/qdLMY7TwIk/mpileup.cram.urllist -f /tmp/qdLMY7TwIk/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /builddir/build/BUILD/samtools-1.15.1/samtools mpileup -B --ff 0x14 -f /tmp/qdLMY7TwIk/mpileup.ref.fa.gz -r17:1050-1060 /tmp/qdLMY7TwIk/mpileup.1.bam | grep -v mpileup .. ok test_mpileup: /builddir/build/BUILD/samtools-1.15.1/samtools mpileup -B --ff 0x14 -f /tmp/qdLMY7TwIk/mpileup.ref.fa.gz -r17:1050-1060 /tmp/qdLMY7TwIk/mpileup.1.cram | grep -v mpileup .. ok test_mpileup: /builddir/build/BUILD/samtools-1.15.1/samtools mpileup /builddir/build/BUILD/samtools-1.15.1/test/mpileup/overlap.bam | grep 128814202 test/test.pl: no IO::Pty module or can't open pty; skipping usage tests .. ok test_usage: samtools test_view: Generating test data file .................. done 1: SAM -> BAM -> SAM .. ok 2: SAM -> uncompressed BAM .. ok 3: uncompressed BAM -> SAM and compare .. ok 4: SAM -> fast compressed BAM .. ok 5: fast compressed BAM -> SAM and compare .. ok 6: SAM -> CRAM -> SAM (UR header tags) .. ok 7: SAM -> CRAM -> SAM (M5 header tags) .. ok 8: BAM -> CRAM with UR -> SAM .. ok 9: SAM -> BAM (M5 header tags) .. ok 10: SAM -> BAM -> CRAM -> SAM (M5 header tags) .. ok 11: CRAM -> BAM with UR .. ok 12: CRAM -> BAM with M5 .. ok 13: SAM -> SAM via stdout .. ok 14: SAM -> BAM via stdout .. ok 15: SAM -> CRAM via stdout .. ok 16: SAM from stdin -> SAM .. ok 17: BAM from stdin -> SAM .. ok 18: CRAM from stdin -> SAM .. ok 19: samtools view -H (SAM input) .. ok 20: samtools view -H (BAM input) .. ok 21: samtools view -H (CRAM input) .. ok 22: No headers (SAM input) .. ok 23: No headers (BAM input) .. ok 24: No headers (CRAM input) .. ok 25: Filter -f 128 (SAM input) .. ok 26: Count -f 128 (SAM input) .. ok 27: Filter -f 128 (BAM input) .. ok 28: Count -f 128 (BAM input) .. ok 29: Filter -f 128 (CRAM input) .. ok 30: Count -f 128 (CRAM input) .. ok 31: Filter -F 128 (SAM input) .. ok 32: Count -F 128 (SAM input) .. ok 33: Filter -F 128 (BAM input) .. ok 34: Count -F 128 (BAM input) .. ok 35: Filter -F 128 (CRAM input) .. ok 36: Count -F 128 (CRAM input) .. ok 37: Filter -F 128 -f 2 (SAM input) .. ok 38: Count -F 128 -f 2 (SAM input) .. ok 39: Filter -F 128 -f 2 (BAM input) .. ok 40: Count -F 128 -f 2 (BAM input) .. ok 41: Filter -F 128 -f 2 (CRAM input) .. ok 42: Count -F 128 -f 2 (CRAM input) .. ok 43: Filter -r grp2 (SAM input) .. ok 44: Count -r grp2 (SAM input) .. ok 45: Filter -r grp2 (BAM input) .. ok 46: Count -r grp2 (BAM input) .. ok 47: Filter -r grp2 (CRAM input) .. ok 48: Count -r grp2 (CRAM input) .. ok 49: Filter -R /tmp/qdLMY7TwIk/view.001.fogn (SAM input) .. ok 50: Count -R /tmp/qdLMY7TwIk/view.001.fogn (SAM input) .. ok 51: Filter -R /tmp/qdLMY7TwIk/view.001.fogn (BAM input) .. ok 52: Count -R /tmp/qdLMY7TwIk/view.001.fogn (BAM input) .. ok 53: Filter -R /tmp/qdLMY7TwIk/view.001.fogn (CRAM input) .. ok 54: Count -R /tmp/qdLMY7TwIk/view.001.fogn (CRAM input) .. ok 55: Filter -R /tmp/qdLMY7TwIk/view.001.fogn -r grp2 (SAM input).. ok 56: Count -R /tmp/qdLMY7TwIk/view.001.fogn -r grp2 (SAM input).. ok 57: Filter -R /tmp/qdLMY7TwIk/view.001.fogn -r grp2 (BAM input).. ok 58: Count -R /tmp/qdLMY7TwIk/view.001.fogn -r grp2 (BAM input).. ok 59: Filter -R /tmp/qdLMY7TwIk/view.001.fogn -r grp2 (CRAM input).. ok 60: Count -R /tmp/qdLMY7TwIk/view.001.fogn -r grp2 (CRAM input).. ok 61: Filter -r grp2 -R /tmp/qdLMY7TwIk/view.001.fogn (SAM input).. ok 62: Count -r grp2 -R /tmp/qdLMY7TwIk/view.001.fogn (SAM input).. ok 63: Filter -r grp2 -R /tmp/qdLMY7TwIk/view.001.fogn (BAM input).. ok 64: Count -r grp2 -R /tmp/qdLMY7TwIk/view.001.fogn (BAM input).. ok 65: Filter -r grp2 -R /tmp/qdLMY7TwIk/view.001.fogn (CRAM input).. ok 66: Count -r grp2 -R /tmp/qdLMY7TwIk/view.001.fogn (CRAM input).. ok 67: Filter -N /tmp/qdLMY7TwIk/view.001.forn (SAM input) .. ok 68: Count -N /tmp/qdLMY7TwIk/view.001.forn (SAM input) .. ok 69: Filter -N /tmp/qdLMY7TwIk/view.001.forn (BAM input) .. ok 70: Count -N /tmp/qdLMY7TwIk/view.001.forn (BAM input) .. ok 71: Filter -N /tmp/qdLMY7TwIk/view.001.forn (CRAM input) .. ok 72: Count -N /tmp/qdLMY7TwIk/view.001.forn (CRAM input) .. ok 73: Filter -d BC (SAM input) .. ok 74: Count -d BC (SAM input) .. ok 75: Filter -d BC (BAM input) .. ok 76: Count -d BC (BAM input) .. ok 77: Filter -d BC (CRAM input) .. ok 78: Count -d BC (CRAM input) .. ok 79: Filter -d BC:TGCA (SAM input) .. ok 80: Count -d BC:TGCA (SAM input) .. ok 81: Filter -d BC:TGCA (BAM input) .. ok 82: Count -d BC:TGCA (BAM input) .. ok 83: Filter -d BC:TGCA (CRAM input) .. ok 84: Count -d BC:TGCA (CRAM input) .. ok 85: Filter -D BC:/tmp/qdLMY7TwIk/view.001.fobc (SAM input) .. ok 86: Count -D BC:/tmp/qdLMY7TwIk/view.001.fobc (SAM input) .. ok 87: Filter -D BC:/tmp/qdLMY7TwIk/view.001.fobc (BAM input) .. ok 88: Count -D BC:/tmp/qdLMY7TwIk/view.001.fobc (BAM input) .. ok 89: Filter -D BC:/tmp/qdLMY7TwIk/view.001.fobc (CRAM input) .. ok 90: Count -D BC:/tmp/qdLMY7TwIk/view.001.fobc (CRAM input) .. ok 91: Filter -D BC:/tmp/qdLMY7TwIk/view.001.fobc -d BC:TGCA (SAM input).. ok 92: Count -D BC:/tmp/qdLMY7TwIk/view.001.fobc -d BC:TGCA (SAM input).. ok 93: Filter -D BC:/tmp/qdLMY7TwIk/view.001.fobc -d BC:TGCA (BAM input).. ok 94: Count -D BC:/tmp/qdLMY7TwIk/view.001.fobc -d BC:TGCA (BAM input).. ok 95: Filter -D BC:/tmp/qdLMY7TwIk/view.001.fobc -d BC:TGCA (CRAM input).. ok 96: Count -D BC:/tmp/qdLMY7TwIk/view.001.fobc -d BC:TGCA (CRAM input).. ok 97: Filter -d BC:TGCA -D BC:/tmp/qdLMY7TwIk/view.001.fobc (SAM input).. ok 98: Count -d BC:TGCA -D BC:/tmp/qdLMY7TwIk/view.001.fobc (SAM input).. ok 99: Filter -d BC:TGCA -D BC:/tmp/qdLMY7TwIk/view.001.fobc (BAM input).. ok 100: Count -d BC:TGCA -D BC:/tmp/qdLMY7TwIk/view.001.fobc (BAM input).. ok 101: Filter -d BC:TGCA -D BC:/tmp/qdLMY7TwIk/view.001.fobc (CRAM input).. ok 102: Count -d BC:TGCA -D BC:/tmp/qdLMY7TwIk/view.001.fobc (CRAM input).. ok 103: Filter -D RG:/tmp/qdLMY7TwIk/view.001.fogn (SAM input) .. ok 104: Count -D RG:/tmp/qdLMY7TwIk/view.001.fogn (SAM input) .. ok 105: Filter -D RG:/tmp/qdLMY7TwIk/view.001.fogn (BAM input) .. ok 106: Count -D RG:/tmp/qdLMY7TwIk/view.001.fogn (BAM input) .. ok 107: Filter -D RG:/tmp/qdLMY7TwIk/view.001.fogn (CRAM input).. ok 108: Count -D RG:/tmp/qdLMY7TwIk/view.001.fogn (CRAM input) .. ok 109: Filter -d NE:TGCA (SAM input) .. ok 110: Count -d NE:TGCA (SAM input) .. ok 111: Filter -d NE:TGCA (BAM input) .. ok 112: Count -d NE:TGCA (BAM input) .. ok 113: Filter -d NE:TGCA (CRAM input) .. ok 114: Count -d NE:TGCA (CRAM input) .. ok 115: Filter -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /builddir/build/BUILD/samtools-1.15.1/samtools view -o /tmp/qdLMY7TwIk/view.test115.sam -h -d TGCA /tmp/qdLMY7TwIk/view.001.sam --no-PG .. expected failure 116: Count -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /builddir/build/BUILD/samtools-1.15.1/samtools view -c -d TGCA /tmp/qdLMY7TwIk/view.001.sam --no-PG .. expected failure 117: Filter -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /builddir/build/BUILD/samtools-1.15.1/samtools view -o /tmp/qdLMY7TwIk/view.test117.sam -h -d TGCA /tmp/qdLMY7TwIk/view.test001.bam --no-PG .. expected failure 118: Count -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /builddir/build/BUILD/samtools-1.15.1/samtools view -c -d TGCA /tmp/qdLMY7TwIk/view.test001.bam --no-PG .. expected failure 119: Filter -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /builddir/build/BUILD/samtools-1.15.1/samtools view -o /tmp/qdLMY7TwIk/view.test119.sam -h -d TGCA /tmp/qdLMY7TwIk/view.test006.cram --no-PG .. expected failure 120: Count -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /builddir/build/BUILD/samtools-1.15.1/samtools view -c -d TGCA /tmp/qdLMY7TwIk/view.test006.cram --no-PG .. expected failure 121: Filter -D BClong:/tmp/qdLMY7TwIk/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/qdLMY7TwIk/view.001.fobc" Failed command: /builddir/build/BUILD/samtools-1.15.1/samtools view -o /tmp/qdLMY7TwIk/view.test121.sam -h -D BClong:/tmp/qdLMY7TwIk/view.001.fobc /tmp/qdLMY7TwIk/view.001.sam --no-PG .. expected failure 122: Count -D BClong:/tmp/qdLMY7TwIk/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/qdLMY7TwIk/view.001.fobc" Failed command: /builddir/build/BUILD/samtools-1.15.1/samtools view -c -D BClong:/tmp/qdLMY7TwIk/view.001.fobc /tmp/qdLMY7TwIk/view.001.sam --no-PG .. expected failure 123: Filter -D BClong:/tmp/qdLMY7TwIk/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/qdLMY7TwIk/view.001.fobc" Failed command: /builddir/build/BUILD/samtools-1.15.1/samtools view -o /tmp/qdLMY7TwIk/view.test123.sam -h -D BClong:/tmp/qdLMY7TwIk/view.001.fobc /tmp/qdLMY7TwIk/view.test001.bam --no-PG .. expected failure 124: Count -D BClong:/tmp/qdLMY7TwIk/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/qdLMY7TwIk/view.001.fobc" Failed command: /builddir/build/BUILD/samtools-1.15.1/samtools view -c -D BClong:/tmp/qdLMY7TwIk/view.001.fobc /tmp/qdLMY7TwIk/view.test001.bam --no-PG .. expected failure 125: Filter -D BClong:/tmp/qdLMY7TwIk/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/qdLMY7TwIk/view.001.fobc" Failed command: /builddir/build/BUILD/samtools-1.15.1/samtools view -o /tmp/qdLMY7TwIk/view.test125.sam -h -D BClong:/tmp/qdLMY7TwIk/view.001.fobc /tmp/qdLMY7TwIk/view.test006.cram --no-PG .. expected failure 126: Count -D BClong:/tmp/qdLMY7TwIk/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/qdLMY7TwIk/view.001.fobc" Failed command: /builddir/build/BUILD/samtools-1.15.1/samtools view -c -D BClong:/tmp/qdLMY7TwIk/view.001.fobc /tmp/qdLMY7TwIk/view.test006.cram --no-PG .. expected failure 127: Filter -d BC:ACGT -d RG:grp2 (SAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /builddir/build/BUILD/samtools-1.15.1/samtools view -o /tmp/qdLMY7TwIk/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/qdLMY7TwIk/view.001.sam --no-PG .. expected failure 128: Count -d BC:ACGT -d RG:grp2 (SAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /builddir/build/BUILD/samtools-1.15.1/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/qdLMY7TwIk/view.001.sam --no-PG .. expected failure 129: Filter -d BC:ACGT -d RG:grp2 (BAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /builddir/build/BUILD/samtools-1.15.1/samtools view -o /tmp/qdLMY7TwIk/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/qdLMY7TwIk/view.test001.bam --no-PG .. expected failure 130: Count -d BC:ACGT -d RG:grp2 (BAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /builddir/build/BUILD/samtools-1.15.1/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/qdLMY7TwIk/view.test001.bam --no-PG .. expected failure 131: Filter -d BC:ACGT -d RG:grp2 (CRAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /builddir/build/BUILD/samtools-1.15.1/samtools view -o /tmp/qdLMY7TwIk/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/qdLMY7TwIk/view.test006.cram --no-PG .. expected failure 132: Count -d BC:ACGT -d RG:grp2 (CRAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /builddir/build/BUILD/samtools-1.15.1/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/qdLMY7TwIk/view.test006.cram --no-PG .. expected failure 133: Filter -d NM:13 (SAM input) .. ok 134: Count -d NM:13 (SAM input) .. ok 135: Filter -d NM:13 (BAM input) .. ok 136: Count -d NM:13 (BAM input) .. ok 137: Filter -d NM:13 (CRAM input) .. ok 138: Count -d NM:13 (CRAM input) .. ok 139: Filter -d ab:z (SAM input) .. ok 140: Count -d ab:z (SAM input) .. ok 141: Filter -d ab:z (BAM input) .. ok 142: Count -d ab:z (BAM input) .. ok 143: Filter -d ab:z (CRAM input) .. ok 144: Count -d ab:z (CRAM input) .. ok 145: Filter -l Library 2 (SAM input) .. ok 146: Count -l Library 2 (SAM input) .. ok 147: Filter -l Library 2 (BAM input) .. ok 148: Count -l Library 2 (BAM input) .. ok 149: Filter -l Library 2 (CRAM input) .. ok 150: Count -l Library 2 (CRAM input) .. ok 151: Filter -l Library 3 (SAM input) .. ok 152: Count -l Library 3 (SAM input) .. ok 153: Filter -l Library 3 (BAM input) .. ok 154: Count -l Library 3 (BAM input) .. ok 155: Filter -l Library 3 (CRAM input) .. ok 156: Count -l Library 3 (CRAM input) .. ok 157: Filter -q 50 (SAM input) .. ok 158: Count -q 50 (SAM input) .. ok 159: Filter -q 50 (BAM input) .. ok 160: Count -q 50 (BAM input) .. ok 161: Filter -q 50 (CRAM input) .. ok 162: Count -q 50 (CRAM input) .. ok 163: Filter -q 99 (SAM input) .. ok 164: Count -q 99 (SAM input) .. ok 165: Filter -q 99 (BAM input) .. ok 166: Count -q 99 (BAM input) .. ok 167: Filter -q 99 (CRAM input) .. ok 168: Count -q 99 (CRAM input) .. ok 169: Filter -q 100 (SAM input) .. ok 170: Count -q 100 (SAM input) .. ok 171: Filter -q 100 (BAM input) .. ok 172: Count -q 100 (BAM input) .. ok 173: Filter -q 100 (CRAM input) .. ok 174: Count -q 100 (CRAM input) .. ok 175: Filter -x fa (SAM input) .. ok 176: Count -x fa (SAM input) .. ok 177: Filter -x fa (BAM input) .. ok 178: Count -x fa (BAM input) .. ok 179: Filter -x fa (CRAM input) .. ok 180: Count -x fa (CRAM input) .. ok 181: Filter -x fa -x ha (SAM input) .. ok 182: Count -x fa -x ha (SAM input) .. ok 183: Filter -x fa -x ha (BAM input) .. ok 184: Count -x fa -x ha (BAM input) .. ok 185: Filter -x fa -x ha (CRAM input) .. ok 186: Count -x fa -x ha (CRAM input) .. ok 187: Filter -x fa,ha (SAM input) .. ok 188: Count -x fa,ha (SAM input) .. ok 189: Filter -x fa,ha (BAM input) .. ok 190: Count -x fa,ha (BAM input) .. ok 191: Filter -x fa,ha (CRAM input) .. ok 192: Count -x fa,ha (CRAM input) .. ok 193: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok 194: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok 195: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok 196: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok 197: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok 198: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok 199: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok 200: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok 201: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok 202: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok 203: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok 204: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok 205: Filter -x fa -r grp2 (SAM input) .. ok 206: Count -x fa -r grp2 (SAM input) .. ok 207: Filter -x fa -r grp2 (BAM input) .. ok 208: Count -x fa -r grp2 (BAM input) .. ok 209: Filter -x fa -r grp2 (CRAM input) .. ok 210: Count -x fa -r grp2 (CRAM input) .. ok 211: Filter -x RG -r grp2 (SAM input) .. ok 212: Count -x RG -r grp2 (SAM input) .. ok 213: Filter -x RG -r grp2 (BAM input) .. ok 214: Count -x RG -r grp2 (BAM input) .. ok 215: Filter -x RG -r grp2 (CRAM input) .. ok 216: Count -x RG -r grp2 (CRAM input) .. ok 217: Filter -m 10 (SAM input) .. ok 218: Count -m 10 (SAM input) .. ok 219: Filter -m 10 (BAM input) .. ok 220: Count -m 10 (BAM input) .. ok 221: Filter -m 10 (CRAM input) .. ok 222: Count -m 10 (CRAM input) .. ok 223: Filter -m 11 (SAM input) .. ok 224: Count -m 11 (SAM input) .. ok 225: Filter -m 11 (BAM input) .. ok 226: Count -m 11 (BAM input) .. ok 227: Filter -m 11 (CRAM input) .. ok 228: Count -m 11 (CRAM input) .. ok 229: Filter -m 15 (SAM input) .. ok 230: Count -m 15 (SAM input) .. ok 231: Filter -m 15 (BAM input) .. ok 232: Count -m 15 (BAM input) .. ok 233: Filter -m 15 (CRAM input) .. ok 234: Count -m 15 (CRAM input) .. ok 235: Filter -m 16 (SAM input) .. ok 236: Count -m 16 (SAM input) .. ok 237: Filter -m 16 (BAM input) .. ok 238: Count -m 16 (BAM input) .. ok 239: Filter -m 16 (CRAM input) .. ok 240: Count -m 16 (CRAM input) .. ok 241: Filter -e !(flag & 128) && (flag & 2) (SAM input) .. ok 242: Count -e !(flag & 128) && (flag & 2) (SAM input) .. ok 243: Filter -e !(flag & 128) && (flag & 2) (BAM input) .. ok 244: Count -e !(flag & 128) && (flag & 2) (BAM input) .. ok 245: Filter -e !(flag & 128) && (flag & 2) (CRAM input) .. ok 246: Count -e !(flag & 128) && (flag & 2) (CRAM input) .. ok 247: Filter -e [BC] (SAM input) .. ok 248: Count -e [BC] (SAM input) .. ok 249: Filter -e [BC] (BAM input) .. ok 250: Count -e [BC] (BAM input) .. ok 251: Filter -e [BC] (CRAM input) .. ok 252: Count -e [BC] (CRAM input) .. ok 253: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (SAM input).. ok 254: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (SAM input).. ok 255: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (BAM input).. ok 256: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (BAM input).. ok 257: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (CRAM input).. ok 258: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (CRAM input).. ok 259: Filter -e mapq >= 50 (SAM input) .. ok 260: Count -e mapq >= 50 (SAM input) .. ok 261: Filter -e mapq >= 50 (BAM input) .. ok 262: Count -e mapq >= 50 (BAM input) .. ok 263: Filter -e mapq >= 50 (CRAM input) .. ok 264: Count -e mapq >= 50 (CRAM input) .. ok 265: Filter -e mapq >= 99 (SAM input) .. ok 266: Count -e mapq >= 99 (SAM input) .. ok 267: Filter -e mapq >= 99 (BAM input) .. ok 268: Count -e mapq >= 99 (BAM input) .. ok 269: Filter -e mapq >= 99 (CRAM input) .. ok 270: Count -e mapq >= 99 (CRAM input) .. ok 271: Filter -e mapq >= 100 (SAM input) .. ok 272: Count -e mapq >= 100 (SAM input) .. ok 273: Filter -e mapq >= 100 (BAM input) .. ok 274: Count -e mapq >= 100 (BAM input) .. ok 275: Filter -e mapq >= 100 (CRAM input) .. ok 276: Count -e mapq >= 100 (CRAM input) .. ok 277: 1bp reads file SAM -> BAM -> SAM .. ok 278: 1bp reads file SAM -> CRAM -> SAM .. ok 278: Region Z (BAM input) .. ok 279: Count Z (BAM input) .. ok 280: Region Z (CRAM input) .. ok 281: Count Z (CRAM input) .. ok 282: Region Z:30 (BAM input) .. ok 283: Count Z:30 (BAM input) .. ok 284: Region Z:30 (CRAM input) .. ok 285: Count Z:30 (CRAM input) .. ok 286: Region Z:20-40 (BAM input) .. ok 287: Count Z:20-40 (BAM input) .. ok 288: Region Z:20-40 (CRAM input) .. ok 289: Count Z:20-40 (CRAM input) .. ok 290: Region ref1 (BAM input) .. ok 291: Count ref1 (BAM input) .. ok 292: Region ref1 (CRAM input) .. ok 293: Count ref1 (CRAM input) .. ok 294: Region ref1:15 (BAM input) .. ok 295: Count ref1:15 (BAM input) .. ok 296: Region ref1:15 (CRAM input) .. ok 297: Count ref1:15 (CRAM input) .. ok 298: Region ref1:15-45 (BAM input) .. ok 299: Count ref1:15-45 (BAM input) .. ok 300: Region ref1:15-45 (CRAM input) .. ok 301: Count ref1:15-45 (CRAM input) .. ok 302: Region ref1:15-45 ref2 (BAM input) .. ok 303: Count ref1:15-45 ref2 (BAM input) .. ok 304: Region ref1:15-45 ref2 (CRAM input) .. ok 305: Count ref1:15-45 ref2 (CRAM input) .. ok 306: Region ref1:15-45 ref2:16 (BAM input) .. ok 307: Count ref1:15-45 ref2:16 (BAM input) .. ok 308: Region ref1:15-45 ref2:16 (CRAM input) .. ok 309: Count ref1:15-45 ref2:16 (CRAM input) .. ok 310: Region ref1:15-45 ref2:16-31 (BAM input) .. ok 311: Count ref1:15-45 ref2:16-31 (BAM input) .. ok 312: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok 313: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok 314: Region ref1:15-15 ref1:45-45 (BAM input) .. ok 315: Count ref1:15-15 ref1:45-45 (BAM input) .. ok 316: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok 317: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok 318: Region -f 128 ref1 (BAM input) .. ok 319: Count -f 128 ref1 (BAM input) .. ok 320: Region -f 128 ref1 (CRAM input) .. ok 321: Count -f 128 ref1 (CRAM input) .. ok 322: Region -q 50 ref1:15-45 (BAM input) .. ok 323: Count -q 50 ref1:15-45 (BAM input) .. ok 324: Region -q 50 ref1:15-45 (CRAM input) .. ok 325: Count -q 50 ref1:15-45 (CRAM input) .. ok 326: Region -r grp2 ref1:15-45 (BAM input) .. ok 327: Count -r grp2 ref1:15-45 (BAM input) .. ok 328: Region -r grp2 ref1:15-45 (CRAM input) .. ok 329: Count -r grp2 ref1:15-45 (CRAM input) .. ok 330: Region * (BAM input) .. ok 331: Count * (BAM input) .. ok 332: Region * (CRAM input) .. ok 333: Count * (CRAM input) .. ok 334: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed (BAM input).. ok 335: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed (BAM input).. ok 336: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed (CRAM input).. ok 337: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed (CRAM input).. ok 338: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.02.bed (BAM input).. ok 339: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.02.bed (BAM input).. ok 340: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.02.bed (CRAM input).. ok 341: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.02.bed (CRAM input).. ok 342: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed (BAM input).. ok 343: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed (BAM input).. ok 344: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed (CRAM input).. ok 345: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed (CRAM input).. ok 346: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.02.bed (BAM input).. ok 347: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.02.bed (BAM input).. ok 348: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.02.bed (CRAM input).. ok 349: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.02.bed (CRAM input).. ok 350: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z (BAM input).. ok 351: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z (BAM input).. ok 352: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z (CRAM input).. ok 353: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z (CRAM input).. ok 354: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z:30 (BAM input).. ok 355: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z:30 (BAM input).. ok 356: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 357: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 358: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 359: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 360: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 361: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 362: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 363: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 364: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 365: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 366: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 367: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 368: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 369: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 370: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed ref2 (BAM input).. ok 371: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed ref2 (BAM input).. ok 372: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed ref2 (CRAM input).. ok 373: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed ref2 (CRAM input).. ok 374: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok 375: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok 376: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 377: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 378: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 379: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 380: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 381: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 382: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -f 128 (BAM input).. ok 383: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -f 128 (BAM input).. ok 384: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 385: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 386: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -q 5 (BAM input).. ok 387: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -q 5 (BAM input).. ok 388: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 389: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 390: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 391: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 392: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 393: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 394: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -M --unmap (BAM input).. ok 395: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -M --unmap (BAM input).. ok 396: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -M --unmap (CRAM input).. ok 397: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -M --unmap (CRAM input).. ok 398: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok 399: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok 400: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -M --unmap ref1:11-30 (CRAM input).. ok 401: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -M --unmap ref1:11-30 (CRAM input).. ok 402: Make BAM with no M5/UR tags .. ok 403: Add @SQ with -t (SAM -> SAM) .. ok 404: Add @SQ with -T (SAM -> SAM) .. ok 405: Add @SQ with -t (BAM -> SAM) .. ok 406: Add @SQ with -T (BAM -> SAM) .. ok 407: Add @SQ with -t (SAM -> BAM) .. ok 408: Add @SQ with -T (SAM -> BAM) .. ok 409: Add @SQ with -t (BAM -> BAM) .. ok 410: Add @SQ with -T (BAM -> BAM) .. ok 411: Add @SQ with -t (SAM -> CRAM) .. ok 412: Add @SQ with -T (SAM -> CRAM) .. ok 413: Add @SQ with -t (BAM -> CRAM) .. ok 414: Add @SQ with -T (BAM -> CRAM) .. ok 415: Make CRAM with no UR field .. ok 416: Decoding CRAM with no UR field via -T .. ok 417: CIGAR B-operator removal .. ok 418: Big SAM -> BAM .. ok 419: Big SAM -> BAM (2 threads) .. ok 420: Big SAM -> BAM (4 threads) .. ok 421: Big SAM -> CRAM .. ok 422: Big SAM -> CRAM (2 threads) .. ok 423: Big SAM -> CRAM (4 threads) .. ok 424: Subsample 0.2 (SAM input) ............ ok 425: Subsample 0.5 (SAM input) ............ ok 426: Subsample 0.8 (SAM input) ............ ok 427: Subsample 0.2 (BAM input) ............ ok 428: Subsample 0.5 (BAM input) ............ ok 429: Subsample 0.8 (BAM input) ............ ok 430: Subsample 0.2 (CRAM input) ............ ok 431: Subsample 0.5 (CRAM input) ............ ok 432: Subsample 0.8 (CRAM input) ............ ok 433: SAM add PG .. ok 434: Unset dup flag, remove dt and do tags .. ok 435: Unmap dup flagged reads. .. ok 436: Unmap dup flagged reads. .. ok 437: fetch pairs .. ok 438: fetch pairs .. ok 439: fetch pairs .. ok test_head: /builddir/build/BUILD/samtools-1.15.1/samtools head /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.sam .. ok test_head: /builddir/build/BUILD/samtools-1.15.1/samtools head -h 0 /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.sam .. ok test_head: /builddir/build/BUILD/samtools-1.15.1/samtools head -h 1 /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.sam .. ok test_head: /builddir/build/BUILD/samtools-1.15.1/samtools head -h 5 /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.sam .. ok test_head: /builddir/build/BUILD/samtools-1.15.1/samtools head -h 29 /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.sam .. ok test_head: /builddir/build/BUILD/samtools-1.15.1/samtools head -h 30 /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.sam .. ok test_head: /builddir/build/BUILD/samtools-1.15.1/samtools head -n 0 /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.sam .. ok test_head: /builddir/build/BUILD/samtools-1.15.1/samtools head -n 1 /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.sam .. ok test_head: /builddir/build/BUILD/samtools-1.15.1/samtools head -n 5 /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.sam .. ok test_head: /builddir/build/BUILD/samtools-1.15.1/samtools head -h 5 -n 5 < /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.sam .. ok test_cat: Generating test data file .................. done Generate BAM file #1 .. ok Generate CRAM file #1 .. ok Generating test data file .................. done Generate BAM file #2 .. ok Generate CRAM file #2 .. ok Generating test data file .................. done Generate BAM file #3 .. ok Generate CRAM file #3 .. ok Generating test data file .................. done Generate BAM file #4 .. ok Generate CRAM file #4 .. ok 1: cat BAM files .. ok 2: cat recompressed BAM files .. ok 3: cat CRAM files .. ok 4: cat BAM files to stdout .. ok 5: cat recompressed BAM files to stdout .. ok 6: cat CRAM files to stdout .. ok 7: cat BAM files with new header .. ok 8: cat recompressed BAM files with new header .. ok 9: cat CRAM files with new header .. ok test_import: /builddir/build/BUILD/samtools-1.15.1/samtools import -0 test/bam2fq/1.1.fq.expected | /builddir/build/BUILD/samtools-1.15.1/samtools fastq -0 /builddir/build/BUILD/samtools-1.15.1/test/0.fq .. ok test_import: /builddir/build/BUILD/samtools-1.15.1/samtools import -s test/bam2fq/1.1.fq.expected | /builddir/build/BUILD/samtools-1.15.1/samtools fastq -0 /builddir/build/BUILD/samtools-1.15.1/test/0.fq .. ok test_import: /builddir/build/BUILD/samtools-1.15.1/samtools import -s test/bam2fq/5.s.fq.expected | /builddir/build/BUILD/samtools-1.15.1/samtools fastq -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq .. ok test_import: /builddir/build/BUILD/samtools-1.15.1/samtools import test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected | /builddir/build/BUILD/samtools-1.15.1/samtools fastq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq .. ok test_import: /builddir/build/BUILD/samtools-1.15.1/samtools import test/bam2fq/5.1.fq.expected test/bam2fq/5.2.fq.expected | /builddir/build/BUILD/samtools-1.15.1/samtools fastq -N -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq .. ok test_import: /builddir/build/BUILD/samtools-1.15.1/samtools import -i -1 test/bam2fq/12.1.fq.expected -2 test/bam2fq/12.2.fq.expected | /builddir/build/BUILD/samtools-1.15.1/samtools fastq -i --index-format 'i*i*' -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq .. ok test_import: /builddir/build/BUILD/samtools-1.15.1/samtools import --barcode-tag OX -i -1 test/bam2fq/12.1.fq.expected -2 test/bam2fq/12.2.fq.expected | /builddir/build/BUILD/samtools-1.15.1/samtools fastq --barcode-tag OX -i --index-format 'i*i*' -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq .. ok test_import: /builddir/build/BUILD/samtools-1.15.1/samtools import -T "" -1 test/bam2fq/6.1.fq.expected -2 test/bam2fq/6.2.fq.expected | /builddir/build/BUILD/samtools-1.15.1/samtools fastq -N -T RG,BC,QT -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq .. ok test_import: /builddir/build/BUILD/samtools-1.15.1/samtools import -T "*" -1 test/bam2fq/7.1.fq.expected -2 test/bam2fq/7.2.fq.expected | /builddir/build/BUILD/samtools-1.15.1/samtools fastq -N -T RG,BC,QT,MD,ia -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq .. ok test_import: /builddir/build/BUILD/samtools-1.15.1/samtools import test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -R rgid .. ok test_import: /builddir/build/BUILD/samtools-1.15.1/samtools import test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -r ID:rgid .. ok test_import: /builddir/build/BUILD/samtools-1.15.1/samtools import test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -r '@RG ID:rgid' .. ok test_import: /builddir/build/BUILD/samtools-1.15.1/samtools import test/import/2.interleaved.fq -T "" .. ok test_import: /builddir/build/BUILD/samtools-1.15.1/samtools import test/import/3.interleaved.fq -i .. ok test_import: /builddir/build/BUILD/samtools-1.15.1/samtools import test/import/4.aux.fq -T "*" .. ok test_import: /builddir/build/BUILD/samtools-1.15.1/samtools import test/import/4.aux.fq -T "" .. ok test_import: /builddir/build/BUILD/samtools-1.15.1/samtools import test/import/4.aux.fq -T XZ,XA,AA .. ok test_import: /builddir/build/BUILD/samtools-1.15.1/samtools import --i1 test/import/5-i1.fq --i2 test/import/5-i2.fq --r1 test/import/5-r1.fq --r2 test/import/5-r2.fq .. ok test_import: /builddir/build/BUILD/samtools-1.15.1/samtools import --i1 test/import/5-i1.fq --i2 test/import/5-i2.fq --r1 test/import/5-r1.fq --r2 test/import/5-r2.fq --barcode-tag OX --quality-tag BZ .. ok test_bam2fq: Generate BAM file .. ok Generate CRAM file .. ok 1: fastq (SAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 2: fastq -n (SAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 3: fastq (BAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 4: fastq -n (BAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 5: fastq (CRAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 6: fastq -n (CRAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.002.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.003.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq --barcode-tag BC --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.15.1/test/bc.fq -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.004.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.15.1/test/bc.fq -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.004.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.15.1/test/bc.fq -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.010.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq --barcode-tag BC -N --index-format 'n*i*' --i1 /builddir/build/BUILD/samtools-1.15.1/test/bc_split.fq -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -N -t -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -N -t -T MD,ia -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq --barcode-tag BC -i --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.15.1/test/i.fq -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.004.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq --barcode-tag BC -i --index-format 'i*i*' --i1 /builddir/build/BUILD/samtools-1.15.1/test/i.fq -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -i --index-format 'i*i*' -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.703.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -N -1 /builddir/build/BUILD/samtools-1.15.1/test/o.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/o.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fasta -N -1 /builddir/build/BUILD/samtools-1.15.1/test/o.fa -2 /builddir/build/BUILD/samtools-1.15.1/test/o.fa /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -N -o /builddir/build/BUILD/samtools-1.15.1/test/o.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -N -s /tmp/qdLMY7TwIk/bam2fq.discard.s.fq -0 /tmp/qdLMY7TwIk/bam2fq.discard.0.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -T ba,bb,bc,bd,be,bf,bg /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.013.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq --index-format 'i8n1i8' --i1 /builddir/build/BUILD/samtools-1.15.1/test/i1.fq --i2 /builddir/build/BUILD/samtools-1.15.1/test/i2.fq -0 /builddir/build/BUILD/samtools-1.15.1/test/0.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.014.sam .. ok test_bam2fq: Generate BAM file (2 threads) .. ok Generate CRAM file (2 threads) .. ok 1: fastq (SAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 2: fastq -n (SAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 3: fastq (BAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 4: fastq -n (BAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 5: fastq (CRAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 6: fastq -n (CRAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -@ 2 -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -@ 2 -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -@ 2 -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.002.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -@ 2 -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.003.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -@ 2 --barcode-tag BC --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.15.1/test/bc.fq -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.004.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.15.1/test/bc.fq -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.004.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.15.1/test/bc.fq -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.010.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -@ 2 --barcode-tag BC -N --index-format 'n*i*' --i1 /builddir/build/BUILD/samtools-1.15.1/test/bc_split.fq -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -@ 2 -N -t -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -@ 2 -N -t -T MD,ia -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.15.1/test/i.fq -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.004.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'i*i*' --i1 /builddir/build/BUILD/samtools-1.15.1/test/i.fq -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -@ 2 -i --index-format 'i*i*' -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -@ 2 -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.703.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -@ 2 -N -1 /builddir/build/BUILD/samtools-1.15.1/test/o.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/o.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fasta -@ 2 -N -1 /builddir/build/BUILD/samtools-1.15.1/test/o.fa -2 /builddir/build/BUILD/samtools-1.15.1/test/o.fa /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -@ 2 -N -o /builddir/build/BUILD/samtools-1.15.1/test/o.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -@ 2 -N -s /tmp/qdLMY7TwIk/bam2fq.discard.s.fq -0 /tmp/qdLMY7TwIk/bam2fq.discard.0.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -@ 2 -T ba,bb,bc,bd,be,bf,bg /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.013.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.15.1/samtools fastq -@ 2 --index-format 'i8n1i8' --i1 /builddir/build/BUILD/samtools-1.15.1/test/i1.fq --i2 /builddir/build/BUILD/samtools-1.15.1/test/i2.fq -0 /builddir/build/BUILD/samtools-1.15.1/test/0.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.014.sam .. ok test_depad: Generate BAM file .. ok depad (SAM input) .. ok depad -s (SAM input) .. ok depad -u (SAM input) .. ok depad -1 (SAM input) .. ok depad (BAM input) .. ok depad -s (BAM input) .. ok depad -u (BAM input) .. ok depad -1 (BAM input) .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats -r /builddir/build/BUILD/samtools-1.15.1/test/stat/test.fa /builddir/build/BUILD/samtools-1.15.1/test/stat/1_map_cigar.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1/test/stat/1_map_cigar_large.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats -r /builddir/build/BUILD/samtools-1.15.1/test/stat/test.fa /builddir/build/BUILD/samtools-1.15.1/test/stat/2_equal_cigar_full_seq.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1/test/stat/2_equal_cigar_full_seq_large.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats -r /builddir/build/BUILD/samtools-1.15.1/test/stat/test.fa /builddir/build/BUILD/samtools-1.15.1/test/stat/3_map_cigar_equal_seq.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1/test/stat/3_map_cigar_equal_seq_large.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats -r /builddir/build/BUILD/samtools-1.15.1/test/stat/test.fa /builddir/build/BUILD/samtools-1.15.1/test/stat/4_X_cigar_full_seq.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1/test/stat/4_X_cigar_full_seq_large.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats -r /builddir/build/BUILD/samtools-1.15.1/test/stat/test.fa /builddir/build/BUILD/samtools-1.15.1/test/stat/5_insert_cigar.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1/test/stat/5_insert_cigar_large.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats -r /builddir/build/BUILD/samtools-1.15.1/test/stat/test.fa -i 0 /builddir/build/BUILD/samtools-1.15.1/test/stat/5_insert_cigar.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats -r /builddir/build/BUILD/samtools-1.15.1/test/stat/test.fa /builddir/build/BUILD/samtools-1.15.1/test/stat/7_supp.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1/test/stat/7_supp_large.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats -r /builddir/build/BUILD/samtools-1.15.1/test/stat/test.fa /builddir/build/BUILD/samtools-1.15.1/test/stat/8_secondary.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1/test/stat/8_secondary_large.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats -S RG -r /builddir/build/BUILD/samtools-1.15.1/test/stat/test.fa /builddir/build/BUILD/samtools-1.15.1/test/stat/1_map_cigar.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats -S RG -r /builddir/build/BUILD/samtools-1.15.1/test/stat/test.fa /builddir/build/BUILD/samtools-1.15.1/test/stat/10_map_cigar.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats -t /builddir/build/BUILD/samtools-1.15.1/test/stat/11.stats.targets /builddir/build/BUILD/samtools-1.15.1/test/stat/11_target.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats -g 4 -t /builddir/build/BUILD/samtools-1.15.1/test/stat/11.stats.targets /builddir/build/BUILD/samtools-1.15.1/test/stat/11_target.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats -g 4 /builddir/build/BUILD/samtools-1.15.1/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1/test/stat/12_overlaps.bam -t /builddir/build/BUILD/samtools-1.15.1/test/stat/12_3reads.bed | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1/test/stat/12_overlaps.bam -p -t /builddir/build/BUILD/samtools-1.15.1/test/stat/12_3reads.bed | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1/test/stat/12_overlaps.bam -t /builddir/build/BUILD/samtools-1.15.1/test/stat/12_2reads.bed | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1/test/stat/12_overlaps.bam -p -t /builddir/build/BUILD/samtools-1.15.1/test/stat/12_2reads.bed | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1/test/stat/13_barcodes_ok.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1/test/stat/13_barcodes_ok_ox_bz.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1/test/stat/13_barcodes_fail_bc_length.sam | tail -n+4 /builddir/build/BUILD/samtools-1.15.1/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1/test/stat/13_barcodes_fail_hyphen.sam | tail -n+4 /builddir/build/BUILD/samtools-1.15.1/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1/test/stat/13_barcodes_fail_qt_length.sam | tail -n+4 /builddir/build/BUILD/samtools-1.15.1/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats -I s1 /builddir/build/BUILD/samtools-1.15.1/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats -I grp2 /builddir/build/BUILD/samtools-1.15.1/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats -I grp3 /builddir/build/BUILD/samtools-1.15.1/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.15.1/samtools stats -I Sample /builddir/build/BUILD/samtools-1.15.1/test/stat/11_target.bam | tail -n+4 .. ok test_merge: /builddir/build/BUILD/samtools-1.15.1/samtools merge -s 1 -O sam - /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_c.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.15.1/samtools merge -s 1 -O sam - /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_b.bam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_c.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.15.1/samtools merge -s 1 -O sam -b /tmp/cW2BPPSMe1 - /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.15.1/samtools merge -s 1 -O sam - /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_b.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.15.1/samtools merge -r -s 1 -O sam - /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_c.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.15.1/samtools merge -cp -s 1 -O sam - /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_b.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.15.1/samtools merge -s 1 -O sam - /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a_regex.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_b_regex.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.15.1/samtools merge -o - -s 1 -O sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_c.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.15.1/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/qdLMY7TwIk/merge.tag.1.bam /tmp/qdLMY7TwIk/merge.tag.2.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.15.1/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/qdLMY7TwIk/merge.tag.3.bam /tmp/qdLMY7TwIk/merge.tag.4.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.15.1/samtools merge --no-PG -O SAM - /builddir/build/BUILD/samtools-1.15.1/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.15.1/samtools merge --no-PG -O SAM -L /builddir/build/BUILD/samtools-1.15.1/test/merge/merge.bed - /tmp/qdLMY7TwIk/merge.bed.1.bam /tmp/qdLMY7TwIk/merge.bed.2.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.15.1/samtools merge -@ 2 -s 1 -O sam - /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_c.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.15.1/samtools merge -@ 2 -s 1 -O sam - /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_b.bam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_c.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.15.1/samtools merge -@ 2 -s 1 -O sam -b /tmp/5hB4Tyez1g - /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.15.1/samtools merge -@ 2 -s 1 -O sam - /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_b.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.15.1/samtools merge -@ 2 -r -s 1 -O sam - /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_c.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.15.1/samtools merge -@ 2 -cp -s 1 -O sam - /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_b.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.15.1/samtools merge -@ 2 -s 1 -O sam - /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a_regex.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_b_regex.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.15.1/samtools merge -@ 2 -o - -s 1 -O sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_c.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.15.1/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/qdLMY7TwIk/merge.tag.1.bam /tmp/qdLMY7TwIk/merge.tag.2.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.15.1/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/qdLMY7TwIk/merge.tag.3.bam /tmp/qdLMY7TwIk/merge.tag.4.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.15.1/samtools merge -@ 2 --no-PG -O SAM - /builddir/build/BUILD/samtools-1.15.1/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.15.1/samtools merge -@ 2 --no-PG -O SAM -L /builddir/build/BUILD/samtools-1.15.1/test/merge/merge.bed - /tmp/qdLMY7TwIk/merge.bed.1.bam /tmp/qdLMY7TwIk/merge.bed.2.bam .. ok test_sort: /builddir/build/BUILD/samtools-1.15.1/samtools sort /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam /tmp/qdLMY7TwIk/sortout .. ok test_sort: /builddir/build/BUILD/samtools-1.15.1/samtools sort -f /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam /tmp/qdLMY7TwIk/sortout.bam .. ok test_sort: /builddir/build/BUILD/samtools-1.15.1/samtools sort -o /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam /tmp/qdLMY7TwIk/sorttmp .. ok test_sort: /builddir/build/BUILD/samtools-1.15.1/samtools sort -m 10M /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.15.1/samtools sort -n -m 10M /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.15.1/samtools sort -t RG -m 10M /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.15.1/samtools sort -n -t RG -m 10M /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.15.1/samtools sort -t AS -m 10M /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.15.1/samtools sort -t FI -m 10M /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.15.1/samtools sort -@ 2 /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam /tmp/qdLMY7TwIk/sortout .. ok test_sort: /builddir/build/BUILD/samtools-1.15.1/samtools sort -@ 2 -f /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam /tmp/qdLMY7TwIk/sortout.bam .. ok test_sort: /builddir/build/BUILD/samtools-1.15.1/samtools sort -@ 2 -o /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam /tmp/qdLMY7TwIk/sorttmp .. ok test_sort: /builddir/build/BUILD/samtools-1.15.1/samtools sort -@ 2 -m 10M /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.15.1/samtools sort -@ 2 -n -m 10M /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.15.1/samtools sort -@ 2 -t RG -m 10M /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.15.1/samtools sort -@ 2 -n -t RG -m 10M /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.15.1/samtools sort -@ 2 -t AS -m 10M /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.15.1/samtools sort -@ 2 -t FI -m 10M /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_collate: /builddir/build/BUILD/samtools-1.15.1/samtools collate --output-fmt=sam -O /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_d.sam .. ok test_collate: /builddir/build/BUILD/samtools-1.15.1/samtools collate -o /builddir/build/BUILD/samtools-1.15.1/test/collate/collate1.tmp.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_d.sam .. ok test_collate: /builddir/build/BUILD/samtools-1.15.1/samtools collate -o /builddir/build/BUILD/samtools-1.15.1/test/collate/collate2.tmp.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_d.sam /builddir/build/BUILD/samtools-1.15.1/test/collate/collate2.tmp .. ok test_collate: /builddir/build/BUILD/samtools-1.15.1/samtools collate --output-fmt=sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_d.sam /builddir/build/BUILD/samtools-1.15.1/test/collate/collate3.tmp .. ok test_collate: /builddir/build/BUILD/samtools-1.15.1/samtools collate --output-fmt=sam -f /builddir/build/BUILD/samtools-1.15.1/test/collate/fast_collate.sam -o /builddir/build/BUILD/samtools-1.15.1/test/collate/1_fast_collate.sam .. ok test_collate: /builddir/build/BUILD/samtools-1.15.1/samtools collate --output-fmt=sam -f -r 4 /builddir/build/BUILD/samtools-1.15.1/test/collate/fast_collate.sam -o /builddir/build/BUILD/samtools-1.15.1/test/collate/2_fast_collate_with_tmp.sam .. ok test_collate: /builddir/build/BUILD/samtools-1.15.1/samtools collate -@ 2 --output-fmt=sam -O /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_d.sam .. ok test_collate: /builddir/build/BUILD/samtools-1.15.1/samtools collate -@ 2 -o /builddir/build/BUILD/samtools-1.15.1/test/collate/collate1.tmp.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_d.sam .. ok test_collate: /builddir/build/BUILD/samtools-1.15.1/samtools collate -@ 2 -o /builddir/build/BUILD/samtools-1.15.1/test/collate/collate2.tmp.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_d.sam /builddir/build/BUILD/samtools-1.15.1/test/collate/collate2.tmp .. ok test_collate: /builddir/build/BUILD/samtools-1.15.1/samtools collate -@ 2 --output-fmt=sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_d.sam /builddir/build/BUILD/samtools-1.15.1/test/collate/collate3.tmp .. ok test_collate: /builddir/build/BUILD/samtools-1.15.1/samtools collate -@ 2 --output-fmt=sam -f /builddir/build/BUILD/samtools-1.15.1/test/collate/fast_collate.sam -o /builddir/build/BUILD/samtools-1.15.1/test/collate/1_fast_collate.sam .. ok test_collate: /builddir/build/BUILD/samtools-1.15.1/samtools collate -@ 2 --output-fmt=sam -f -r 4 /builddir/build/BUILD/samtools-1.15.1/test/collate/fast_collate.sam -o /builddir/build/BUILD/samtools-1.15.1/test/collate/2_fast_collate_with_tmp.sam .. ok test_fixmate: /builddir/build/BUILD/samtools-1.15.1/samtools fixmate -O sam /builddir/build/BUILD/samtools-1.15.1/test/fixmate/1_coord_sort.sam - ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname. .. expected failure test_fixmate: /builddir/build/BUILD/samtools-1.15.1/samtools fixmate -O sam /builddir/build/BUILD/samtools-1.15.1/test/fixmate/2_isize_overflow.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.15.1/samtools fixmate -O sam /builddir/build/BUILD/samtools-1.15.1/test/fixmate/3_reverse_read_pp_lt.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.15.1/samtools fixmate -O sam /builddir/build/BUILD/samtools-1.15.1/test/fixmate/4_reverse_read_pp_equal.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.15.1/samtools fixmate -cO sam /builddir/build/BUILD/samtools-1.15.1/test/fixmate/5_ct.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.15.1/samtools fixmate -cO sam /builddir/build/BUILD/samtools-1.15.1/test/fixmate/6_ct_replace.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.15.1/samtools fixmate -O sam /builddir/build/BUILD/samtools-1.15.1/test/fixmate/7_two_read_mapped.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.15.1/samtools fixmate -O sam /builddir/build/BUILD/samtools-1.15.1/test/fixmate/8_isize_overflow_64bit.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.15.1/samtools fixmate -@ 2 -O sam /builddir/build/BUILD/samtools-1.15.1/test/fixmate/1_coord_sort.sam - ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname. .. expected failure test_fixmate: /builddir/build/BUILD/samtools-1.15.1/samtools fixmate -@ 2 -O sam /builddir/build/BUILD/samtools-1.15.1/test/fixmate/2_isize_overflow.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.15.1/samtools fixmate -@ 2 -O sam /builddir/build/BUILD/samtools-1.15.1/test/fixmate/3_reverse_read_pp_lt.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.15.1/samtools fixmate -@ 2 -O sam /builddir/build/BUILD/samtools-1.15.1/test/fixmate/4_reverse_read_pp_equal.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.15.1/samtools fixmate -@ 2 -cO sam /builddir/build/BUILD/samtools-1.15.1/test/fixmate/5_ct.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.15.1/samtools fixmate -@ 2 -cO sam /builddir/build/BUILD/samtools-1.15.1/test/fixmate/6_ct_replace.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.15.1/samtools fixmate -@ 2 -O sam /builddir/build/BUILD/samtools-1.15.1/test/fixmate/7_two_read_mapped.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.15.1/samtools fixmate -@ 2 -O sam /builddir/build/BUILD/samtools-1.15.1/test/fixmate/8_isize_overflow_64bit.sam - .. ok /builddir/build/BUILD/samtools-1.15.1/samtools calmd -uAr /builddir/build/BUILD/samtools-1.15.1/test/dat/mpileup.1.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/mpileup.ref.fa .. ok /builddir/build/BUILD/samtools-1.15.1/samtools calmd -@ 2 -uAr /builddir/build/BUILD/samtools-1.15.1/test/dat/mpileup.1.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/mpileup.ref.fa .. ok test_idxstat: /builddir/build/BUILD/samtools-1.15.1/samtools idxstats /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam .. ok test_idxstat: /builddir/build/BUILD/samtools-1.15.1/samtools idxstats /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.cram .. ok test_idxstat: /builddir/build/BUILD/samtools-1.15.1/samtools idxstats /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.sam .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.15.1/samtools quickcheck /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/1.quickcheck.badeof.bam .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.15.1/samtools quickcheck /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/2.quickcheck.badheader.bam .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.15.1/samtools quickcheck /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/3.quickcheck.ok.bam .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.15.1/samtools quickcheck /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/4.quickcheck.ok.bam .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.15.1/samtools quickcheck /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/5.quickcheck.scramble30.truncated.cram .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.15.1/samtools quickcheck /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/6.quickcheck.cram21.ok.cram .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.15.1/samtools quickcheck /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/7.quickcheck.cram30.ok.cram .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.15.1/samtools quickcheck /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/8.quickcheck.cram21.truncated.cram .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.15.1/samtools quickcheck /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/9.quickcheck.cram30.truncated.cram .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.15.1/samtools quickcheck /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/10.quickcheck.notargets.bam .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.15.1/samtools quickcheck -v /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/1.quickcheck.badeof.bam /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/2.quickcheck.badheader.bam /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/3.quickcheck.ok.bam /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/4.quickcheck.ok.bam /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/5.quickcheck.scramble30.truncated.cram /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/6.quickcheck.cram21.ok.cram /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/7.quickcheck.cram30.ok.cram /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/8.quickcheck.cram21.truncated.cram /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/9.quickcheck.cram30.truncated.cram /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,' .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.15.1/samtools quickcheck -uv /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,' .. ok test_reheader: /builddir/build/BUILD/samtools-1.15.1/samtools reheader /builddir/build/BUILD/samtools-1.15.1/test/reheader/hdr.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.tmp.bam | /builddir/build/BUILD/samtools-1.15.1/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /builddir/build/BUILD/samtools-1.15.1/samtools reheader /builddir/build/BUILD/samtools-1.15.1/test/reheader/hdr.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.tmp.v21.cram | /builddir/build/BUILD/samtools-1.15.1/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /builddir/build/BUILD/samtools-1.15.1/samtools reheader /builddir/build/BUILD/samtools-1.15.1/test/reheader/hdr.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.tmp.v30.cram | /builddir/build/BUILD/samtools-1.15.1/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /builddir/build/BUILD/samtools-1.15.1/samtools reheader --in-place /builddir/build/BUILD/samtools-1.15.1/test/reheader/hdr.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.tmp.v21.cram && /builddir/build/BUILD/samtools-1.15.1/samtools view -h --no-PG /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.tmp.v21.cram | perl -pe 's/ VN:.*//' .. ok test_reheader: /builddir/build/BUILD/samtools-1.15.1/samtools reheader --in-place /builddir/build/BUILD/samtools-1.15.1/test/reheader/hdr.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.tmp.v30.cram && /builddir/build/BUILD/samtools-1.15.1/samtools view -h --no-PG /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.tmp.v30.cram | perl -pe 's/ VN:.*//' .. ok test_reheader: /builddir/build/BUILD/samtools-1.15.1/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.tmp.bam | /builddir/build/BUILD/samtools-1.15.1/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /builddir/build/BUILD/samtools-1.15.1/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.tmp.v30.cram | /builddir/build/BUILD/samtools-1.15.1/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_addrprg: /builddir/build/BUILD/samtools-1.15.1/samtools addreplacerg -O sam -m overwrite_all /builddir/build/BUILD/samtools-1.15.1/test/addrprg/1_fixup.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.15.1/samtools addreplacerg -O sam -m orphan_only /builddir/build/BUILD/samtools-1.15.1/test/addrprg/2_fixup_orphan.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.15.1/samtools addreplacerg -O sam -R '1#9' /builddir/build/BUILD/samtools-1.15.1/test/addrprg/1_fixup.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.15.1/samtools addreplacerg -O sam -r '@RG\tID:1#8\tCN:SC' /builddir/build/BUILD/samtools-1.15.1/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.15.1/samtools addreplacerg -O sam -m overwrite_all -R '1#8' /builddir/build/BUILD/samtools-1.15.1/test/addrprg/1_fixup.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.15.1/samtools addreplacerg -O sam -r 'ID:1#8' -r 'CN:SC' /builddir/build/BUILD/samtools-1.15.1/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.15.1/samtools addreplacerg -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /builddir/build/BUILD/samtools-1.15.1/test/addrprg/1_fixup.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.15.1/samtools addreplacerg -@ 2 -O sam -m overwrite_all /builddir/build/BUILD/samtools-1.15.1/test/addrprg/1_fixup.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.15.1/samtools addreplacerg -@ 2 -O sam -m orphan_only /builddir/build/BUILD/samtools-1.15.1/test/addrprg/2_fixup_orphan.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.15.1/samtools addreplacerg -@ 2 -O sam -R '1#9' /builddir/build/BUILD/samtools-1.15.1/test/addrprg/1_fixup.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.15.1/samtools addreplacerg -@ 2 -O sam -r '@RG\tID:1#8\tCN:SC' /builddir/build/BUILD/samtools-1.15.1/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.15.1/samtools addreplacerg -@ 2 -O sam -m overwrite_all -R '1#8' /builddir/build/BUILD/samtools-1.15.1/test/addrprg/1_fixup.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.15.1/samtools addreplacerg -@ 2 -O sam -r 'ID:1#8' -r 'CN:SC' /builddir/build/BUILD/samtools-1.15.1/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.15.1/samtools addreplacerg -@ 2 -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /builddir/build/BUILD/samtools-1.15.1/test/addrprg/1_fixup.sam .. ok test_markdup: /builddir/build/BUILD/samtools-1.15.1/samtools markdup -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/1_name_sort.sam - ERR: [markdup] error: queryname sorted, must be sorted by coordinate. .. expected failure test_markdup: /builddir/build/BUILD/samtools-1.15.1/samtools markdup -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/2_bad_order.sam - ERR: [markdup] error: not in coordinate sorted order. .. expected failure test_markdup: /builddir/build/BUILD/samtools-1.15.1/samtools markdup -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/3_missing_mc.sam - ERR: [markdup] error: no MC tag. Please run samtools fixmate on file first. [markdup] error: unable to assign pair hash key. .. expected failure test_markdup: /builddir/build/BUILD/samtools-1.15.1/samtools markdup -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/4_missing_ms.sam - ERR: [markdup] error: no ms score tag. Please run samtools fixmate on file first. [markdup] error: no ms score tag. Please run samtools fixmate on file first. .. expected failure test_markdup: /builddir/build/BUILD/samtools-1.15.1/samtools markdup -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/5_markdup.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.15.1/samtools markdup -O sam -r --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/6_remove_dups.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.15.1/samtools markdup -S -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/7_mark_supp_dup.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.15.1/samtools markdup -S -d 100 --mode s -t -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/8_optical_dup.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.15.1/samtools markdup -S -d 2500 --mode s -t --include-fails -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/9_optical_dup_qcfail.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.15.1/samtools markdup -S -d 2500 --mode s -t -O sam --no-PG -S /builddir/build/BUILD/samtools-1.15.1/test/markdup/10_optical_chain.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.15.1/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /builddir/build/BUILD/samtools-1.15.1/test/markdup/10_optical_chain.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.15.1/samtools markdup -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+):([[:print:]]+)' --coords-order xyt --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.15.1/samtools markdup -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+)' --coords-order xy --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.15.1/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/12_optical_chain_regex.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.15.1/samtools markdup -@ 2 -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/1_name_sort.sam - ERR: [markdup] error: queryname sorted, must be sorted by coordinate. .. expected failure test_markdup: /builddir/build/BUILD/samtools-1.15.1/samtools markdup -@ 2 -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/2_bad_order.sam - ERR: [markdup] error: not in coordinate sorted order. .. expected failure test_markdup: /builddir/build/BUILD/samtools-1.15.1/samtools markdup -@ 2 -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/3_missing_mc.sam - ERR: [markdup] error: no MC tag. Please run samtools fixmate on file first. [markdup] error: unable to assign pair hash key. .. expected failure test_markdup: /builddir/build/BUILD/samtools-1.15.1/samtools markdup -@ 2 -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/4_missing_ms.sam - ERR: [markdup] error: no ms score tag. Please run samtools fixmate on file first. [markdup] error: no ms score tag. Please run samtools fixmate on file first. .. expected failure test_markdup: /builddir/build/BUILD/samtools-1.15.1/samtools markdup -@ 2 -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/5_markdup.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.15.1/samtools markdup -@ 2 -O sam -r --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/6_remove_dups.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.15.1/samtools markdup -@ 2 -S -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/7_mark_supp_dup.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.15.1/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/8_optical_dup.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.15.1/samtools markdup -@ 2 -S -d 2500 --mode s -t --include-fails -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/9_optical_dup_qcfail.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.15.1/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --no-PG -S /builddir/build/BUILD/samtools-1.15.1/test/markdup/10_optical_chain.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.15.1/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /builddir/build/BUILD/samtools-1.15.1/test/markdup/10_optical_chain.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.15.1/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+):([[:print:]]+)' --coords-order xyt --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.15.1/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+)' --coords-order xy --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.15.1/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/12_optical_chain_regex.sam - .. ok test_bedcov: /builddir/build/BUILD/samtools-1.15.1/samtools bedcov /builddir/build/BUILD/samtools-1.15.1/test/bedcov/bedcov.bed /builddir/build/BUILD/samtools-1.15.1/test/bedcov/bedcov.bam .. ok test_bedcov: /builddir/build/BUILD/samtools-1.15.1/samtools bedcov -j /builddir/build/BUILD/samtools-1.15.1/test/bedcov/bedcov.bed /builddir/build/BUILD/samtools-1.15.1/test/bedcov/bedcov.bam .. ok test_bedcov: /builddir/build/BUILD/samtools-1.15.1/samtools bedcov -g512 -G2048 /builddir/build/BUILD/samtools-1.15.1/test/bedcov/bedcov_gG.bed /builddir/build/BUILD/samtools-1.15.1/test/bedcov/bedcov.bam .. ok test_split: /builddir/build/BUILD/samtools-1.15.1/samtools split --output-fmt sam -u /builddir/build/BUILD/samtools-1.15.1/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.15.1/test/split/split.tmp.%!.%. /builddir/build/BUILD/samtools-1.15.1/test/split/split.sam .. ok test_split: /builddir/build/BUILD/samtools-1.15.1/samtools split -@ 2 --output-fmt sam -u /builddir/build/BUILD/samtools-1.15.1/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.15.1/test/split/split.tmp.%!.%. /builddir/build/BUILD/samtools-1.15.1/test/split/split.sam .. ok test_large_positions: /builddir/build/BUILD/samtools-1.15.1/samtools view -h --no-PG /tmp/qdLMY7TwIk/longref.sam.gz .. ok test_large_positions: /builddir/build/BUILD/samtools-1.15.1/samtools view -h --no-PG /tmp/qdLMY7TwIk/longref.sam.gz CHROMOSOME_I:10000000114-10000000168 .. ok test_large_positions: /builddir/build/BUILD/samtools-1.15.1/samtools view -h --no-PG -L /builddir/build/BUILD/samtools-1.15.1/test/large_pos/test.bed /tmp/qdLMY7TwIk/longref.sam.gz .. ok test_large_positions: /builddir/build/BUILD/samtools-1.15.1/samtools sort -O sam --no-PG -m 10M /builddir/build/BUILD/samtools-1.15.1/test/large_pos/longref_name.sam .. ok test_large_positions: /builddir/build/BUILD/samtools-1.15.1/samtools merge -O sam --no-PG - /builddir/build/BUILD/samtools-1.15.1/test/large_pos/longref.sam /builddir/build/BUILD/samtools-1.15.1/test/large_pos/longref2.sam .. ok test_large_positions: /builddir/build/BUILD/samtools-1.15.1/samtools depth /builddir/build/BUILD/samtools-1.15.1/test/large_pos/longref.sam .. ok test_large_positions: /builddir/build/BUILD/samtools-1.15.1/samtools depth -b /builddir/build/BUILD/samtools-1.15.1/test/large_pos/test.bed /builddir/build/BUILD/samtools-1.15.1/test/large_pos/longref.sam .. ok test_large_positions: /builddir/build/BUILD/samtools-1.15.1/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/qdLMY7TwIk/longref.sam.gz .. ok test_large_positions: /builddir/build/BUILD/samtools-1.15.1/samtools sort -O sam --no-PG -n -m 10M test/large_pos/longref3.sam | /builddir/build/BUILD/samtools-1.15.1/samtools fixmate -O sam --no-PG - - | /builddir/build/BUILD/samtools-1.15.1/samtools sort -O sam --no-PG -m 10M .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.15.1/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam -b /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.15.1/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --hard-clip -b /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.15.1/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand -b /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.15.1/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.15.1/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.15.1/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --original -b /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.15.1/samtools ampliconclip --no-PG --output-fmt=sam -b /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.15.1/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/2_both_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.15.1/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam -b /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.15.1/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --hard-clip -b /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.15.1/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand -b /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.15.1/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.15.1/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.15.1/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --original -b /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.15.1/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam -b /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.15.1/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/2_both_test_data.sam .. ok test_ampliconstats: /builddir/build/BUILD/samtools-1.15.1/samtools ampliconstats -@ 2 -S -t 50 -d 1,20,100 /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/1_hard_clipped.expected.sam /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/1_soft_clipped.expected.sam /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/1_soft_clipped_strand.expected.sam /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/2_both_clipped.expected.sam | egrep -v 'Samtools version|Command line' .. ok test_ampliconstats: /builddir/build/BUILD/samtools-1.15.1/samtools ampliconstats -@ 2 -c 0 /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/multi_ref.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconstats/mixed_clipped.sam | egrep -v 'Samtools version|Command line' .. ok Number of tests: total .. 807 passed .. 776 failed .. 0 expected failure .. 31 unexpected pass .. 0 test/merge/test_bam_translate test/merge/test_bam_translate.tmp test/merge/test_rtrans_build test/merge/test_trans_tbl_init cd test/mpileup && AWK="gawk" ../regression.sh mpileup.reg === Testing mpileup.reg regressions === EXPECTED FAIL: Task failed, but expected to fail; when running $samtools mpileup -ABQ0 -a -l xx.bed3 xx#depth3.bam Expected passes: 118 Unexpected passes: 0 Expected failures: 1 Unexpected failures: 0 => PASS cd test/mpileup && AWK="gawk" ../regression.sh depth.reg === Testing depth.reg regressions === EXPECTED FAIL: Task failed, but expected to fail; when running $samtools depth -a -b xx.bed3 xx#depth3.bam Expected passes: 47 Unexpected passes: 0 Expected failures: 1 Unexpected failures: 0 => PASS cd test/consensus && AWK="gawk" ../regression.sh consensus.reg === Testing consensus.reg regressions === Expected passes: 62 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 => PASS + RPM_EC=0 ++ jobs -p + exit 0 Processing files: samtools-1.15.1-1.fc38.x86_64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.qX9Cmm + umask 022 + cd /builddir/build/BUILD + cd samtools-1.15.1 + DOCDIR=/builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/share/doc/samtools + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/share/doc/samtools + cp -pr AUTHORS /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/share/doc/samtools + cp -pr ChangeLog.old /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/share/doc/samtools + cp -pr NEWS /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/share/doc/samtools + cp -pr examples/ /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/share/doc/samtools + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.duZOo2 + umask 022 + cd /builddir/build/BUILD + cd samtools-1.15.1 + LICENSEDIR=/builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/share/licenses/samtools + export LC_ALL=C + LC_ALL=C + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/share/licenses/samtools + cp -pr LICENSE /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/share/licenses/samtools + RPM_EC=0 ++ jobs -p + exit 0 Provides: samtools = 1.15.1-1.fc38 samtools(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: /usr/bin/perl 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_2.3.4)(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) libhts.so.3()(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.29)(64bit) libncursesw.so.6()(64bit) libtinfo.so.6()(64bit) libz.so.1()(64bit) rtld(GNU_HASH) Processing files: samtools-debugsource-1.15.1-1.fc38.x86_64 Provides: samtools-debugsource = 1.15.1-1.fc38 samtools-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: samtools-debuginfo-1.15.1-1.fc38.x86_64 Provides: debuginfo(build-id) = 0a45b355cd935be7e23f6228310bcff3292b397d debuginfo(build-id) = 29580a9a74649fc4d5b446f6c9050aec25d82015 debuginfo(build-id) = 36f7518bf99a75c1ded43450783aa782f730112a debuginfo(build-id) = 5c052b00c03831a9ceba8156cea0af61b0922d72 debuginfo(build-id) = 5c7f6fb4c016d7d9e719b5fc2da256dc5df8881c debuginfo(build-id) = 5d5748db97df15addd20df900f9de5e2cc0db902 debuginfo(build-id) = fadd27168a24a7a148b70a69470ae51f245c6d7b samtools-debuginfo = 1.15.1-1.fc38 samtools-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: samtools-debugsource(x86-64) = 1.15.1-1.fc38 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64 Wrote: /builddir/build/RPMS/samtools-1.15.1-1.fc38.x86_64.rpm Wrote: /builddir/build/RPMS/samtools-debuginfo-1.15.1-1.fc38.x86_64.rpm Wrote: /builddir/build/RPMS/samtools-debugsource-1.15.1-1.fc38.x86_64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.JHyuQo + umask 022 + cd /builddir/build/BUILD + cd samtools-1.15.1 + /usr/bin/rm -rf /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64 + RPM_EC=0 ++ jobs -p + exit 0 Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.NL8maz + umask 022 + cd /builddir/build/BUILD + rm -rf samtools-1.15.1 samtools-1.15.1.gemspec + RPM_EC=0 ++ jobs -p + exit 0 Finish: rpmbuild samtools-1.15.1-1.fc38.src.rpm Finish: build phase for samtools-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_64-1660573317.563253/root/var/log/dnf.rpm.log /var/lib/mock/fedora-rawhide-x86_64-1660573317.563253/root/var/log/dnf.librepo.log /var/lib/mock/fedora-rawhide-x86_64-1660573317.563253/root/var/log/dnf.log INFO: Done(/var/lib/copr-rpmbuild/results/samtools-1.15.1-1.fc38.src.rpm) Config(child) 1 minutes 31 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