Warning: Permanently added '52.86.2.169' (ED25519) to the list of known hosts. Running: /usr/bin/copr-rpmbuild --verbose --drop-resultdir --build-id 4733910 --chroot fedora-rawhide-i386 --detached Version: 0.61 PID: 7440 Logging PID: 7441 Task: {'appstream': True, 'background': False, 'bootstrap': 'off', 'build_id': 4733910, 'buildroot_pkgs': [], 'chroot': 'fedora-rawhide-i386', '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-i386/', 'id': 'copr_base', 'name': 'Copr repository'}], 'sandbox': 'jaruga/staging--jaruga', 'source_json': {}, 'source_type': None, 'submitter': 'jaruga', 'tags': [], 'task_id': '4733910-fedora-rawhide-i386', '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-5cf8o246/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-5cf8o246/samtools', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-5cf8o246/samtools'... Running: git checkout 00e9239ef0d1f3ea39c07da84538bfbc7d86f9dd cmd: ['git', 'checkout', '00e9239ef0d1f3ea39c07da84538bfbc7d86f9dd'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-5cf8o246/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 cmd: ['copr-distgit-client', 'sources'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-5cf8o246/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 /usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated 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 133M 0 --:--:-- --:--:-- --:--:-- 135M 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-5cf8o246/samtools/samtools.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-5cf8o246/samtools --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1660573318.635731 -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-5cf8o246/samtools/samtools.spec) Config(fedora-rawhide-i686) Start: clean chroot Finish: clean chroot Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-i686-1660573318.635731/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 204 kB/s | 21 kB 00:00 local 41 MB/s | 60 MB 00:01 Dependencies resolved. ================================================================================ Package Arch Version Repo Size ================================================================================ Installing group/module packages: bash i686 5.1.16-3.fc37 local 1.7 M bzip2 i686 1.0.8-12.fc37 local 53 k coreutils i686 9.1-6.fc37 local 1.1 M cpio i686 2.13-13.fc37 local 274 k diffutils i686 3.8-3.fc37 local 375 k fedora-release noarch 38-0.2 local 12 k findutils i686 1:4.9.0-2.fc37 local 492 k gawk i686 5.1.1-4.fc37 local 1.0 M glibc-minimal-langpack i686 2.36-1.fc37 local 81 k grep i686 3.7-4.fc37 local 269 k gzip i686 1.12-2.fc37 local 157 k info i686 6.8-4.fc37 local 229 k make i686 1:4.3-11.fc37 local 540 k patch i686 2.7.6-17.fc37 local 137 k redhat-rpm-config noarch 227-1.fc37 local 73 k rpm-build i686 4.18.0-0.beta1.4.fc37 local 69 k sed i686 4.8-11.fc37 local 300 k shadow-utils i686 2:4.11.1-4.fc37 local 1.1 M tar i686 2:1.34-3.fc36 local 893 k unzip i686 6.0-58.fc37 local 178 k util-linux i686 2.38.1-1.fc37 local 2.3 M which i686 2.21-35.fc37 local 42 k xz i686 5.2.5-10.fc37 local 219 k Installing dependencies: alternatives i686 1.19-3.fc37 local 37 k ansible-srpm-macros noarch 1-6.fc37 local 7.5 k audit-libs i686 3.0.8-3.fc37 local 122 k authselect i686 1.4.0-3.fc37 local 141 k authselect-libs i686 1.4.0-3.fc37 local 238 k basesystem noarch 11-14.fc37 local 7.0 k binutils i686 2.39-1.fc38 local 5.8 M binutils-gold i686 2.39-1.fc38 local 842 k binutils-gprofng i686 2.39-1.fc38 local 3.3 M bzip2-libs i686 1.0.8-12.fc37 local 41 k ca-certificates noarch 2022.2.54-5.fc37 local 829 k coreutils-common i686 9.1-6.fc37 local 2.0 M cracklib i686 2.9.6-28.fc36 local 82 k crypto-policies noarch 20220815-1.gite4ed860.fc38 local 60 k curl i686 7.84.0-2.fc37 local 315 k cyrus-sasl-lib i686 2.1.28-7.fc37 local 857 k debugedit i686 5.0-5.fc37 local 78 k dwz i686 0.14-7.fc37 local 133 k ed i686 1.18-2.fc37 local 78 k efi-srpm-macros noarch 5-6.fc37 local 22 k elfutils i686 0.187-6.fc37 local 539 k elfutils-debuginfod-client i686 0.187-6.fc37 local 40 k elfutils-default-yama-scope noarch 0.187-6.fc37 local 17 k elfutils-libelf i686 0.187-6.fc37 local 203 k elfutils-libs i686 0.187-6.fc37 local 287 k fedora-gpg-keys noarch 38-0.2 local 115 k fedora-release-common noarch 38-0.2 local 22 k fedora-release-identity-basic noarch 38-0.2 local 12 k fedora-repos noarch 38-0.2 local 10 k fedora-repos-rawhide noarch 38-0.2 local 9.6 k file i686 5.42-4.fc37 local 49 k file-libs i686 5.42-4.fc37 local 684 k filesystem i686 3.18-2.fc37 local 1.1 M fonts-srpm-macros noarch 1:2.0.5-8.fc37 local 26 k fpc-srpm-macros noarch 1.3-6.fc37 local 7.7 k gc i686 8.0.6-4.fc37 local 105 k gdb-minimal i686 12.1-4.fc37 local 4.2 M gdbm-libs i686 1:1.23-2.fc37 local 60 k ghc-srpm-macros noarch 1.5.0-7.fc37 local 7.8 k glibc i686 2.36-1.fc37 local 1.9 M glibc-common i686 2.36-1.fc37 local 367 k glibc-gconv-extra i686 2.36-1.fc37 local 1.6 M gmp i686 1:6.2.1-3.fc37 local 305 k gnat-srpm-macros noarch 4-16.fc37 local 8.3 k go-srpm-macros noarch 3.1.0-4.fc37 local 27 k groff-base i686 1.22.4-10.fc37 local 1.0 M guile22 i686 2.2.7-6.fc37 local 6.5 M jansson i686 2.13.1-5.fc37 local 46 k kernel-srpm-macros noarch 1.0-15.fc37 local 9.4 k keyutils-libs i686 1.6.1-5.fc37 local 32 k krb5-libs i686 1.19.2-11.fc37.1 local 768 k libacl i686 2.3.1-4.fc37 local 25 k libarchive i686 3.6.1-2.fc37 local 443 k libattr i686 2.5.1-5.fc37 local 18 k libblkid i686 2.38.1-1.fc37 local 117 k libbrotli i686 1.0.9-9.fc37 local 317 k libcap i686 2.48-5.fc37 local 68 k libcap-ng i686 0.8.3-3.fc37 local 33 k libcom_err i686 1.46.5-3.fc37 local 26 k libcurl i686 7.84.0-2.fc37 local 332 k libdb i686 5.3.28-53.fc37 local 824 k libeconf i686 0.4.0-4.fc37 local 29 k libevent i686 2.1.12-7.fc37 local 279 k libfdisk i686 2.38.1-1.fc37 local 174 k libffi i686 3.4.2-9.fc37 local 36 k libgcc i686 12.1.1-4.fc38 local 116 k libgomp i686 12.1.1-4.fc38 local 300 k libidn2 i686 2.3.3-2.fc37 local 108 k libmount i686 2.38.1-1.fc37 local 141 k libnghttp2 i686 1.48.0-2.fc37 local 80 k libnsl2 i686 2.0.0-4.fc37 local 31 k libpkgconf i686 1.8.0-3.fc37 local 38 k libpsl i686 0.21.1-6.fc37 local 64 k libpwquality i686 1.4.4-11.fc37 local 106 k libselinux i686 3.4-5.fc37 local 91 k libsemanage i686 3.4-5.fc37 local 129 k libsepol i686 3.4-3.fc37 local 335 k libsigsegv i686 2.14-3.fc37 local 27 k libsmartcols i686 2.38.1-1.fc37 local 66 k libssh i686 0.9.6-5.fc37 local 216 k libssh-config noarch 0.9.6-5.fc37 local 7.8 k libstdc++ i686 12.1.1-4.fc38 local 850 k libtasn1 i686 4.18.0-3.fc37 local 76 k libtirpc i686 1.3.3-0.fc37 local 101 k libtool-ltdl i686 2.4.7-2.fc37 local 39 k libunistring i686 1.0-2.fc37 local 551 k libutempter i686 1.2.1-7.fc37 local 26 k libuuid i686 2.38.1-1.fc37 local 29 k libverto i686 0.3.2-4.fc37 local 21 k libxcrypt i686 4.4.28-3.fc38 local 123 k libxml2 i686 2.9.14-3.fc37 local 787 k libzstd i686 1.5.2-3.fc37 local 274 k lua-libs i686 5.4.4-4.fc37 local 243 k lua-srpm-macros noarch 1-7.fc37 local 8.8 k lz4-libs i686 1.9.3-5.fc37 local 72 k mpfr i686 4.1.0-10.fc37 local 371 k ncurses i686 6.3-3.20220501.fc37 local 406 k ncurses-base noarch 6.3-3.20220501.fc37 local 61 k ncurses-libs i686 6.3-3.20220501.fc37 local 347 k nim-srpm-macros noarch 3-7.fc37 local 8.4 k ocaml-srpm-macros noarch 7-2.fc37 local 13 k openblas-srpm-macros noarch 2-12.fc37 local 7.5 k openldap i686 2.6.2-5.fc38 local 273 k openssl-libs i686 1:3.0.5-2.fc37 local 2.1 M p11-kit i686 0.24.1-3.fc37 local 337 k p11-kit-trust i686 0.24.1-3.fc37 local 138 k package-notes-srpm-macros noarch 0.4-16.fc37 local 11 k pam i686 1.5.2-14.fc37 local 536 k pam-libs i686 1.5.2-14.fc37 local 61 k pcre i686 8.45-1.fc37.2 local 199 k pcre2 i686 10.40-1.fc37.1 local 234 k pcre2-syntax noarch 10.40-1.fc37.1 local 142 k perl-Carp noarch 1.52-489.fc37 local 29 k perl-Class-Struct noarch 0.66-491.fc37 local 26 k perl-DynaLoader i686 1.52-491.fc37 local 30 k perl-Encode i686 4:3.19-492.fc38 local 1.2 M perl-Errno i686 1.36-491.fc37 local 19 k perl-Exporter noarch 5.77-489.fc37 local 31 k perl-Fcntl i686 1.15-491.fc37 local 25 k perl-File-Basename noarch 2.85-491.fc37 local 22 k perl-File-Path noarch 2.18-489.fc37 local 35 k perl-File-Temp noarch 1:0.231.100-489.fc37 local 59 k perl-File-stat noarch 1.12-491.fc37 local 22 k perl-Getopt-Long noarch 1:2.52-489.fc37 local 60 k perl-Getopt-Std noarch 1.13-491.fc37 local 20 k perl-HTTP-Tiny noarch 0.082-1.fc37 local 55 k perl-IO i686 1.50-491.fc37 local 93 k perl-IPC-Open3 noarch 1.22-491.fc37 local 27 k perl-MIME-Base64 i686 3.16-489.fc37 local 31 k perl-POSIX i686 2.03-491.fc37 local 106 k perl-PathTools i686 3.84-489.fc37 local 85 k perl-Pod-Escapes noarch 1:1.07-489.fc37 local 20 k perl-Pod-Perldoc noarch 3.28.01-490.fc37 local 84 k perl-Pod-Simple noarch 1:3.43-490.fc37 local 215 k perl-Pod-Usage noarch 4:2.03-3.fc37 local 40 k perl-Scalar-List-Utils i686 5:1.63-489.fc38 local 76 k perl-SelectSaver noarch 1.02-491.fc37 local 16 k perl-Socket i686 4:2.035-2.fc37 local 56 k perl-Storable i686 1:3.26-489.fc37 local 99 k perl-Symbol noarch 1.09-491.fc37 local 19 k perl-Term-ANSIColor noarch 5.01-490.fc37 local 48 k perl-Term-Cap noarch 1.17-489.fc37 local 22 k perl-Text-ParseWords noarch 3.31-489.fc37 local 16 k perl-Text-Tabs+Wrap noarch 2021.0814-489.fc37 local 22 k perl-Time-Local noarch 2:1.300-489.fc37 local 33 k perl-constant noarch 1.33-490.fc37 local 23 k perl-if noarch 0.61.000-491.fc37 local 18 k perl-interpreter i686 4:5.36.0-491.fc37 local 77 k perl-libs i686 4:5.36.0-491.fc37 local 2.2 M perl-mro i686 1.26-491.fc37 local 34 k perl-overload noarch 1.35-491.fc37 local 50 k perl-overloading noarch 0.02-491.fc37 local 17 k perl-parent noarch 1:0.238-489.fc37 local 14 k perl-podlators noarch 1:4.14-489.fc37 local 112 k perl-srpm-macros noarch 1-46.fc37 local 8.3 k perl-subs noarch 1.04-491.fc37 local 16 k perl-vars noarch 1.05-491.fc37 local 17 k pkgconf i686 1.8.0-3.fc37 local 42 k pkgconf-m4 noarch 1.8.0-3.fc37 local 14 k pkgconf-pkg-config i686 1.8.0-3.fc37 local 10 k popt i686 1.19~rc1-3.fc37 local 61 k publicsuffix-list-dafsa noarch 20210518-5.fc37 local 58 k python-srpm-macros noarch 3.11-4.fc37 local 25 k qt5-srpm-macros noarch 5.15.5-2.fc37 local 8.1 k readline i686 8.1-7.fc37 local 217 k rpm i686 4.18.0-0.beta1.4.fc37 local 541 k rpm-build-libs i686 4.18.0-0.beta1.4.fc37 local 101 k rpm-libs i686 4.18.0-0.beta1.4.fc37 local 350 k rpmautospec-rpm-macros noarch 0.3.0-1.fc37 local 8.8 k rust-srpm-macros noarch 22-1.fc37 local 9.5 k setup noarch 2.14.1-2.fc37 local 143 k sqlite-libs i686 3.39.2-2.fc37 local 702 k systemd-libs i686 251.4-51.fc37 local 650 k tzdata noarch 2022b-1.fc38 local 432 k util-linux-core i686 2.38.1-1.fc37 local 468 k xxhash-libs i686 0.8.1-3.fc37 local 59 k xz-libs i686 5.2.5-10.fc37 local 99 k zip i686 3.0-33.fc37 local 264 k zlib i686 1.2.12-4.fc37 local 92 k zstd i686 1.5.2-3.fc37 local 418 k Installing Groups: build Transaction Summary ================================================================================ Install 203 Packages Total download size: 69 M Installed size: 250 M Downloading Packages: (1/203): ansible-srpm-macros-1-6.fc37.noarch.rp 256 kB/s | 7.5 kB 00:00 (2/203): alternatives-1.19-3.fc37.i686.rpm 1.1 MB/s | 37 kB 00:00 (3/203): audit-libs-3.0.8-3.fc37.i686.rpm 2.8 MB/s | 122 kB 00:00 (4/203): authselect-1.4.0-3.fc37.i686.rpm 11 MB/s | 141 kB 00:00 (5/203): basesystem-11-14.fc37.noarch.rpm 1.9 MB/s | 7.0 kB 00:00 (6/203): authselect-libs-1.4.0-3.fc37.i686.rpm 12 MB/s | 238 kB 00:00 (7/203): binutils-gold-2.39-1.fc38.i686.rpm 17 MB/s | 842 kB 00:00 (8/203): bash-5.1.16-3.fc37.i686.rpm 19 MB/s | 1.7 MB 00:00 (9/203): bzip2-1.0.8-12.fc37.i686.rpm 4.9 MB/s | 53 kB 00:00 (10/203): bzip2-libs-1.0.8-12.fc37.i686.rpm 7.8 MB/s | 41 kB 00:00 (11/203): ca-certificates-2022.2.54-5.fc37.noar 24 MB/s | 829 kB 00:00 (12/203): coreutils-9.1-6.fc37.i686.rpm 23 MB/s | 1.1 MB 00:00 (13/203): binutils-gprofng-2.39-1.fc38.i686.rpm 22 MB/s | 3.3 MB 00:00 (14/203): cpio-2.13-13.fc37.i686.rpm 16 MB/s | 274 kB 00:00 (15/203): cracklib-2.9.6-28.fc36.i686.rpm 6.0 MB/s | 82 kB 00:00 (16/203): crypto-policies-20220815-1.gite4ed860 9.2 MB/s | 60 kB 00:00 (17/203): binutils-2.39-1.fc38.i686.rpm 21 MB/s | 5.8 MB 00:00 (18/203): curl-7.84.0-2.fc37.i686.rpm 7.8 MB/s | 315 kB 00:00 (19/203): debugedit-5.0-5.fc37.i686.rpm 7.5 MB/s | 78 kB 00:00 (20/203): coreutils-common-9.1-6.fc37.i686.rpm 17 MB/s | 2.0 MB 00:00 (21/203): cyrus-sasl-lib-2.1.28-7.fc37.i686.rpm 19 MB/s | 857 kB 00:00 (22/203): diffutils-3.8-3.fc37.i686.rpm 14 MB/s | 375 kB 00:00 (23/203): dwz-0.14-7.fc37.i686.rpm 8.3 MB/s | 133 kB 00:00 (24/203): ed-1.18-2.fc37.i686.rpm 8.7 MB/s | 78 kB 00:00 (25/203): efi-srpm-macros-5-6.fc37.noarch.rpm 3.1 MB/s | 22 kB 00:00 (26/203): elfutils-debuginfod-client-0.187-6.fc 5.8 MB/s | 40 kB 00:00 (27/203): elfutils-default-yama-scope-0.187-6.f 2.4 MB/s | 17 kB 00:00 (28/203): elfutils-libelf-0.187-6.fc37.i686.rpm 18 MB/s | 203 kB 00:00 (29/203): elfutils-0.187-6.fc37.i686.rpm 19 MB/s | 539 kB 00:00 (30/203): fedora-gpg-keys-38-0.2.noarch.rpm 14 MB/s | 115 kB 00:00 (31/203): fedora-release-38-0.2.noarch.rpm 2.9 MB/s | 12 kB 00:00 (32/203): elfutils-libs-0.187-6.fc37.i686.rpm 12 MB/s | 287 kB 00:00 (33/203): fedora-release-common-38-0.2.noarch.r 4.5 MB/s | 22 kB 00:00 (34/203): fedora-release-identity-basic-38-0.2. 2.8 MB/s | 12 kB 00:00 (35/203): fedora-repos-38-0.2.noarch.rpm 2.3 MB/s | 10 kB 00:00 (36/203): fedora-repos-rawhide-38-0.2.noarch.rp 1.8 MB/s | 9.6 kB 00:00 (37/203): file-5.42-4.fc37.i686.rpm 6.7 MB/s | 49 kB 00:00 (38/203): file-libs-5.42-4.fc37.i686.rpm 22 MB/s | 684 kB 00:00 (39/203): findutils-4.9.0-2.fc37.i686.rpm 17 MB/s | 492 kB 00:00 (40/203): fonts-srpm-macros-2.0.5-8.fc37.noarch 4.7 MB/s | 26 kB 00:00 (41/203): fpc-srpm-macros-1.3-6.fc37.noarch.rpm 1.9 MB/s | 7.7 kB 00:00 (42/203): gc-8.0.6-4.fc37.i686.rpm 12 MB/s | 105 kB 00:00 (43/203): filesystem-3.18-2.fc37.i686.rpm 20 MB/s | 1.1 MB 00:00 (44/203): gdbm-libs-1.23-2.fc37.i686.rpm 3.6 MB/s | 60 kB 00:00 (45/203): ghc-srpm-macros-1.5.0-7.fc37.noarch.r 1.9 MB/s | 7.8 kB 00:00 (46/203): gawk-5.1.1-4.fc37.i686.rpm 22 MB/s | 1.0 MB 00:00 (47/203): glibc-common-2.36-1.fc37.i686.rpm 16 MB/s | 367 kB 00:00 (48/203): glibc-2.36-1.fc37.i686.rpm 21 MB/s | 1.9 MB 00:00 (49/203): glibc-minimal-langpack-2.36-1.fc37.i6 11 MB/s | 81 kB 00:00 (50/203): glibc-gconv-extra-2.36-1.fc37.i686.rp 20 MB/s | 1.6 MB 00:00 (51/203): gnat-srpm-macros-4-16.fc37.noarch.rpm 2.2 MB/s | 8.3 kB 00:00 (52/203): go-srpm-macros-3.1.0-4.fc37.noarch.rp 5.8 MB/s | 27 kB 00:00 (53/203): gmp-6.2.1-3.fc37.i686.rpm 15 MB/s | 305 kB 00:00 (54/203): grep-3.7-4.fc37.i686.rpm 19 MB/s | 269 kB 00:00 (55/203): gdb-minimal-12.1-4.fc37.i686.rpm 22 MB/s | 4.2 MB 00:00 (56/203): gzip-1.12-2.fc37.i686.rpm 12 MB/s | 157 kB 00:00 (57/203): groff-base-1.22.4-10.fc37.i686.rpm 15 MB/s | 1.0 MB 00:00 (58/203): info-6.8-4.fc37.i686.rpm 12 MB/s | 229 kB 00:00 (59/203): kernel-srpm-macros-1.0-15.fc37.noarch 1.8 MB/s | 9.4 kB 00:00 (60/203): jansson-2.13.1-5.fc37.i686.rpm 3.4 MB/s | 46 kB 00:00 (61/203): keyutils-libs-1.6.1-5.fc37.i686.rpm 4.0 MB/s | 32 kB 00:00 (62/203): libacl-2.3.1-4.fc37.i686.rpm 4.2 MB/s | 25 kB 00:00 (63/203): libarchive-3.6.1-2.fc37.i686.rpm 20 MB/s | 443 kB 00:00 (64/203): krb5-libs-1.19.2-11.fc37.1.i686.rpm 21 MB/s | 768 kB 00:00 (65/203): libattr-2.5.1-5.fc37.i686.rpm 3.0 MB/s | 18 kB 00:00 (66/203): libblkid-2.38.1-1.fc37.i686.rpm 9.8 MB/s | 117 kB 00:00 (67/203): libbrotli-1.0.9-9.fc37.i686.rpm 18 MB/s | 317 kB 00:00 (68/203): libcap-2.48-5.fc37.i686.rpm 8.3 MB/s | 68 kB 00:00 (69/203): libcap-ng-0.8.3-3.fc37.i686.rpm 6.7 MB/s | 33 kB 00:00 (70/203): libcom_err-1.46.5-3.fc37.i686.rpm 5.1 MB/s | 26 kB 00:00 (71/203): libcurl-7.84.0-2.fc37.i686.rpm 16 MB/s | 332 kB 00:00 (72/203): libeconf-0.4.0-4.fc37.i686.rpm 5.9 MB/s | 29 kB 00:00 (73/203): libdb-5.3.28-53.fc37.i686.rpm 21 MB/s | 824 kB 00:00 (74/203): libevent-2.1.12-7.fc37.i686.rpm 16 MB/s | 279 kB 00:00 (75/203): libffi-3.4.2-9.fc37.i686.rpm 7.2 MB/s | 36 kB 00:00 (76/203): libfdisk-2.38.1-1.fc37.i686.rpm 16 MB/s | 174 kB 00:00 (77/203): libgcc-12.1.1-4.fc38.i686.rpm 12 MB/s | 116 kB 00:00 (78/203): libidn2-2.3.3-2.fc37.i686.rpm 15 MB/s | 108 kB 00:00 (79/203): libgomp-12.1.1-4.fc38.i686.rpm 17 MB/s | 300 kB 00:00 (80/203): libmount-2.38.1-1.fc37.i686.rpm 14 MB/s | 141 kB 00:00 (81/203): libnghttp2-1.48.0-2.fc37.i686.rpm 9.2 MB/s | 80 kB 00:00 (82/203): libnsl2-2.0.0-4.fc37.i686.rpm 7.1 MB/s | 31 kB 00:00 (83/203): libpkgconf-1.8.0-3.fc37.i686.rpm 5.2 MB/s | 38 kB 00:00 (84/203): libpsl-0.21.1-6.fc37.i686.rpm 10 MB/s | 64 kB 00:00 (85/203): libselinux-3.4-5.fc37.i686.rpm 13 MB/s | 91 kB 00:00 (86/203): libpwquality-1.4.4-11.fc37.i686.rpm 9.9 MB/s | 106 kB 00:00 (87/203): libsemanage-3.4-5.fc37.i686.rpm 12 MB/s | 129 kB 00:00 (88/203): libsepol-3.4-3.fc37.i686.rpm 23 MB/s | 335 kB 00:00 (89/203): libsigsegv-2.14-3.fc37.i686.rpm 4.3 MB/s | 27 kB 00:00 (90/203): guile22-2.2.7-6.fc37.i686.rpm 24 MB/s | 6.5 MB 00:00 (91/203): libsmartcols-2.38.1-1.fc37.i686.rpm 2.0 MB/s | 66 kB 00:00 (92/203): libssh-config-0.9.6-5.fc37.noarch.rpm 1.9 MB/s | 7.8 kB 00:00 (93/203): libssh-0.9.6-5.fc37.i686.rpm 6.1 MB/s | 216 kB 00:00 (94/203): libtasn1-4.18.0-3.fc37.i686.rpm 10 MB/s | 76 kB 00:00 (95/203): libtirpc-1.3.3-0.fc37.i686.rpm 12 MB/s | 101 kB 00:00 (96/203): libtool-ltdl-2.4.7-2.fc37.i686.rpm 4.5 MB/s | 39 kB 00:00 (97/203): libutempter-1.2.1-7.fc37.i686.rpm 3.0 MB/s | 26 kB 00:00 (98/203): libstdc++-12.1.1-4.fc38.i686.rpm 23 MB/s | 850 kB 00:00 (99/203): libuuid-2.38.1-1.fc37.i686.rpm 3.4 MB/s | 29 kB 00:00 (100/203): libunistring-1.0-2.fc37.i686.rpm 18 MB/s | 551 kB 00:00 (101/203): libverto-0.3.2-4.fc37.i686.rpm 2.2 MB/s | 21 kB 00:00 (102/203): libxcrypt-4.4.28-3.fc38.i686.rpm 10 MB/s | 123 kB 00:00 (103/203): libzstd-1.5.2-3.fc37.i686.rpm 18 MB/s | 274 kB 00:00 (104/203): lua-libs-5.4.4-4.fc37.i686.rpm 17 MB/s | 243 kB 00:00 (105/203): lua-srpm-macros-1-7.fc37.noarch.rpm 1.4 MB/s | 8.8 kB 00:00 (106/203): lz4-libs-1.9.3-5.fc37.i686.rpm 11 MB/s | 72 kB 00:00 (107/203): libxml2-2.9.14-3.fc37.i686.rpm 21 MB/s | 787 kB 00:00 (108/203): make-4.3-11.fc37.i686.rpm 25 MB/s | 540 kB 00:00 (109/203): ncurses-base-6.3-3.20220501.fc37.noa 9.7 MB/s | 61 kB 00:00 (110/203): mpfr-4.1.0-10.fc37.i686.rpm 13 MB/s | 371 kB 00:00 (111/203): ncurses-6.3-3.20220501.fc37.i686.rpm 16 MB/s | 406 kB 00:00 (112/203): nim-srpm-macros-3-7.fc37.noarch.rpm 1.3 MB/s | 8.4 kB 00:00 (113/203): ncurses-libs-6.3-3.20220501.fc37.i68 23 MB/s | 347 kB 00:00 (114/203): openblas-srpm-macros-2-12.fc37.noarc 1.3 MB/s | 7.5 kB 00:00 (115/203): ocaml-srpm-macros-7-2.fc37.noarch.rp 1.4 MB/s | 13 kB 00:00 (116/203): openldap-2.6.2-5.fc38.i686.rpm 15 MB/s | 273 kB 00:00 (117/203): p11-kit-0.24.1-3.fc37.i686.rpm 14 MB/s | 337 kB 00:00 (118/203): p11-kit-trust-0.24.1-3.fc37.i686.rpm 12 MB/s | 138 kB 00:00 (119/203): package-notes-srpm-macros-0.4-16.fc3 2.9 MB/s | 11 kB 00:00 (120/203): pam-libs-1.5.2-14.fc37.i686.rpm 9.0 MB/s | 61 kB 00:00 (121/203): pam-1.5.2-14.fc37.i686.rpm 26 MB/s | 536 kB 00:00 (122/203): patch-2.7.6-17.fc37.i686.rpm 10 MB/s | 137 kB 00:00 (123/203): pcre-8.45-1.fc37.2.i686.rpm 19 MB/s | 199 kB 00:00 (124/203): pcre2-10.40-1.fc37.1.i686.rpm 20 MB/s | 234 kB 00:00 (125/203): pcre2-syntax-10.40-1.fc37.1.noarch.r 19 MB/s | 142 kB 00:00 (126/203): perl-Carp-1.52-489.fc37.noarch.rpm 3.7 MB/s | 29 kB 00:00 (127/203): openssl-libs-3.0.5-2.fc37.i686.rpm 26 MB/s | 2.1 MB 00:00 (128/203): perl-Class-Struct-0.66-491.fc37.noar 1.8 MB/s | 26 kB 00:00 (129/203): perl-DynaLoader-1.52-491.fc37.i686.r 2.8 MB/s | 30 kB 00:00 (130/203): perl-Exporter-5.77-489.fc37.noarch.r 4.6 MB/s | 31 kB 00:00 (131/203): perl-Errno-1.36-491.fc37.i686.rpm 2.3 MB/s | 19 kB 00:00 (132/203): perl-Fcntl-1.15-491.fc37.i686.rpm 4.3 MB/s | 25 kB 00:00 (133/203): perl-File-Basename-2.85-491.fc37.noa 3.6 MB/s | 22 kB 00:00 (134/203): perl-File-Temp-0.231.100-489.fc37.no 7.9 MB/s | 59 kB 00:00 (135/203): perl-File-Path-2.18-489.fc37.noarch. 3.3 MB/s | 35 kB 00:00 (136/203): perl-File-stat-1.12-491.fc37.noarch. 3.4 MB/s | 22 kB 00:00 (137/203): perl-Getopt-Long-2.52-489.fc37.noarc 6.2 MB/s | 60 kB 00:00 (138/203): perl-Getopt-Std-1.13-491.fc37.noarch 2.4 MB/s | 20 kB 00:00 (139/203): perl-HTTP-Tiny-0.082-1.fc37.noarch.r 6.8 MB/s | 55 kB 00:00 (140/203): perl-IO-1.50-491.fc37.i686.rpm 11 MB/s | 93 kB 00:00 (141/203): perl-IPC-Open3-1.22-491.fc37.noarch. 4.6 MB/s | 27 kB 00:00 (142/203): perl-MIME-Base64-3.16-489.fc37.i686. 3.1 MB/s | 31 kB 00:00 (143/203): perl-POSIX-2.03-491.fc37.i686.rpm 8.3 MB/s | 106 kB 00:00 (144/203): perl-Pod-Escapes-1.07-489.fc37.noarc 2.9 MB/s | 20 kB 00:00 (145/203): perl-Encode-3.19-492.fc38.i686.rpm 15 MB/s | 1.2 MB 00:00 (146/203): perl-PathTools-3.84-489.fc37.i686.rp 3.9 MB/s | 85 kB 00:00 (147/203): perl-Pod-Perldoc-3.28.01-490.fc37.no 7.4 MB/s | 84 kB 00:00 (148/203): perl-Pod-Simple-3.43-490.fc37.noarch 19 MB/s | 215 kB 00:00 (149/203): perl-Pod-Usage-2.03-3.fc37.noarch.rp 3.8 MB/s | 40 kB 00:00 (150/203): perl-Scalar-List-Utils-1.63-489.fc38 7.5 MB/s | 76 kB 00:00 (151/203): perl-SelectSaver-1.02-491.fc37.noarc 2.8 MB/s | 16 kB 00:00 (152/203): perl-Socket-2.035-2.fc37.i686.rpm 7.1 MB/s | 56 kB 00:00 (153/203): perl-Storable-3.26-489.fc37.i686.rpm 11 MB/s | 99 kB 00:00 (154/203): perl-Symbol-1.09-491.fc37.noarch.rpm 2.5 MB/s | 19 kB 00:00 (155/203): perl-Term-ANSIColor-5.01-490.fc37.no 6.2 MB/s | 48 kB 00:00 (156/203): perl-Text-ParseWords-3.31-489.fc37.n 2.9 MB/s | 16 kB 00:00 (157/203): perl-Term-Cap-1.17-489.fc37.noarch.r 2.2 MB/s | 22 kB 00:00 (158/203): perl-Time-Local-1.300-489.fc37.noarc 5.0 MB/s | 33 kB 00:00 (159/203): perl-Text-Tabs+Wrap-2021.0814-489.fc 2.0 MB/s | 22 kB 00:00 (160/203): perl-if-0.61.000-491.fc37.noarch.rpm 2.3 MB/s | 18 kB 00:00 (161/203): perl-constant-1.33-490.fc37.noarch.r 1.7 MB/s | 23 kB 00:00 (162/203): perl-interpreter-5.36.0-491.fc37.i68 7.6 MB/s | 77 kB 00:00 (163/203): perl-mro-1.26-491.fc37.i686.rpm 4.5 MB/s | 34 kB 00:00 (164/203): perl-overload-1.35-491.fc37.noarch.r 4.1 MB/s | 50 kB 00:00 (165/203): perl-overloading-0.02-491.fc37.noarc 2.0 MB/s | 17 kB 00:00 (166/203): perl-parent-0.238-489.fc37.noarch.rp 971 kB/s | 14 kB 00:00 (167/203): perl-podlators-4.14-489.fc37.noarch. 6.1 MB/s | 112 kB 00:00 (168/203): perl-srpm-macros-1-46.fc37.noarch.rp 883 kB/s | 8.3 kB 00:00 (169/203): perl-subs-1.04-491.fc37.noarch.rpm 2.3 MB/s | 16 kB 00:00 (170/203): perl-vars-1.05-491.fc37.noarch.rpm 3.3 MB/s | 17 kB 00:00 (171/203): pkgconf-1.8.0-3.fc37.i686.rpm 5.5 MB/s | 42 kB 00:00 (172/203): pkgconf-m4-1.8.0-3.fc37.noarch.rpm 2.2 MB/s | 14 kB 00:00 (173/203): pkgconf-pkg-config-1.8.0-3.fc37.i686 1.8 MB/s | 10 kB 00:00 (174/203): popt-1.19~rc1-3.fc37.i686.rpm 9.9 MB/s | 61 kB 00:00 (175/203): perl-libs-5.36.0-491.fc37.i686.rpm 30 MB/s | 2.2 MB 00:00 (176/203): python-srpm-macros-3.11-4.fc37.noarc 1.9 MB/s | 25 kB 00:00 (177/203): publicsuffix-list-dafsa-20210518-5.f 3.5 MB/s | 58 kB 00:00 (178/203): qt5-srpm-macros-5.15.5-2.fc37.noarch 1.9 MB/s | 8.1 kB 00:00 (179/203): redhat-rpm-config-227-1.fc37.noarch. 12 MB/s | 73 kB 00:00 (180/203): readline-8.1-7.fc37.i686.rpm 14 MB/s | 217 kB 00:00 (181/203): rpm-build-4.18.0-0.beta1.4.fc37.i686 5.8 MB/s | 69 kB 00:00 (182/203): rpm-build-libs-4.18.0-0.beta1.4.fc37 12 MB/s | 101 kB 00:00 (183/203): rpm-4.18.0-0.beta1.4.fc37.i686.rpm 20 MB/s | 541 kB 00:00 (184/203): rpmautospec-rpm-macros-0.3.0-1.fc37. 1.4 MB/s | 8.8 kB 00:00 (185/203): rust-srpm-macros-22-1.fc37.noarch.rp 2.5 MB/s | 9.5 kB 00:00 (186/203): sed-4.8-11.fc37.i686.rpm 23 MB/s | 300 kB 00:00 (187/203): setup-2.14.1-2.fc37.noarch.rpm 12 MB/s | 143 kB 00:00 (188/203): rpm-libs-4.18.0-0.beta1.4.fc37.i686. 9.5 MB/s | 350 kB 00:00 (189/203): sqlite-libs-3.39.2-2.fc37.i686.rpm 21 MB/s | 702 kB 00:00 (190/203): shadow-utils-4.11.1-4.fc37.i686.rpm 26 MB/s | 1.1 MB 00:00 (191/203): systemd-libs-251.4-51.fc37.i686.rpm 17 MB/s | 650 kB 00:00 (192/203): tzdata-2022b-1.fc38.noarch.rpm 19 MB/s | 432 kB 00:00 (193/203): unzip-6.0-58.fc37.i686.rpm 9.8 MB/s | 178 kB 00:00 (194/203): tar-1.34-3.fc36.i686.rpm 22 MB/s | 893 kB 00:00 (195/203): which-2.21-35.fc37.i686.rpm 4.2 MB/s | 42 kB 00:00 (196/203): util-linux-core-2.38.1-1.fc37.i686.r 20 MB/s | 468 kB 00:00 (197/203): xxhash-libs-0.8.1-3.fc37.i686.rpm 4.7 MB/s | 59 kB 00:00 (198/203): xz-libs-5.2.5-10.fc37.i686.rpm 9.5 MB/s | 99 kB 00:00 (199/203): xz-5.2.5-10.fc37.i686.rpm 9.3 MB/s | 219 kB 00:00 (200/203): zlib-1.2.12-4.fc37.i686.rpm 5.7 MB/s | 92 kB 00:00 (201/203): zip-3.0-33.fc37.i686.rpm 11 MB/s | 264 kB 00:00 (202/203): util-linux-2.38.1-1.fc37.i686.rpm 30 MB/s | 2.3 MB 00:00 (203/203): zstd-1.5.2-3.fc37.i686.rpm 15 MB/s | 418 kB 00:00 -------------------------------------------------------------------------------- Total 45 MB/s | 69 MB 00:01 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Running scriptlet: filesystem-3.18-2.fc37.i686 1/1 Preparing : 1/1 Installing : crypto-policies-20220815-1.gite4ed860.fc38.noarc 1/203 Running scriptlet: crypto-policies-20220815-1.gite4ed860.fc38.noarc 1/203 Installing : fedora-release-identity-basic-38-0.2.noarch 2/203 Installing : tzdata-2022b-1.fc38.noarch 3/203 Installing : rust-srpm-macros-22-1.fc37.noarch 4/203 Installing : qt5-srpm-macros-5.15.5-2.fc37.noarch 5/203 Installing : publicsuffix-list-dafsa-20210518-5.fc37.noarch 6/203 Installing : pkgconf-m4-1.8.0-3.fc37.noarch 7/203 Installing : perl-srpm-macros-1-46.fc37.noarch 8/203 Installing : pcre2-syntax-10.40-1.fc37.1.noarch 9/203 Installing : openblas-srpm-macros-2-12.fc37.noarch 10/203 Installing : ocaml-srpm-macros-7-2.fc37.noarch 11/203 Installing : nim-srpm-macros-3-7.fc37.noarch 12/203 Installing : ncurses-base-6.3-3.20220501.fc37.noarch 13/203 Installing : libssh-config-0.9.6-5.fc37.noarch 14/203 Installing : kernel-srpm-macros-1.0-15.fc37.noarch 15/203 Installing : gnat-srpm-macros-4-16.fc37.noarch 16/203 Installing : ghc-srpm-macros-1.5.0-7.fc37.noarch 17/203 Installing : fpc-srpm-macros-1.3-6.fc37.noarch 18/203 Installing : fedora-gpg-keys-38-0.2.noarch 19/203 Installing : fedora-release-38-0.2.noarch 20/203 Installing : fedora-release-common-38-0.2.noarch 21/203 Installing : fedora-repos-rawhide-38-0.2.noarch 22/203 Installing : fedora-repos-38-0.2.noarch 23/203 Installing : setup-2.14.1-2.fc37.noarch 24/203 warning: /etc/hosts created as /etc/hosts.rpmnew Running scriptlet: setup-2.14.1-2.fc37.noarch 24/203 Installing : filesystem-3.18-2.fc37.i686 25/203 Installing : basesystem-11-14.fc37.noarch 26/203 Installing : coreutils-common-9.1-6.fc37.i686 27/203 Installing : ansible-srpm-macros-1-6.fc37.noarch 28/203 Installing : libgcc-12.1.1-4.fc38.i686 29/203 Running scriptlet: libgcc-12.1.1-4.fc38.i686 29/203 Installing : glibc-gconv-extra-2.36-1.fc37.i686 30/203 Running scriptlet: glibc-gconv-extra-2.36-1.fc37.i686 30/203 Installing : glibc-minimal-langpack-2.36-1.fc37.i686 31/203 Installing : glibc-common-2.36-1.fc37.i686 32/203 Running scriptlet: glibc-2.36-1.fc37.i686 33/203 Installing : glibc-2.36-1.fc37.i686 33/203 Running scriptlet: glibc-2.36-1.fc37.i686 33/203 Installing : ncurses-libs-6.3-3.20220501.fc37.i686 34/203 Installing : bash-5.1.16-3.fc37.i686 35/203 Running scriptlet: bash-5.1.16-3.fc37.i686 35/203 Installing : zlib-1.2.12-4.fc37.i686 36/203 Installing : xz-libs-5.2.5-10.fc37.i686 37/203 Installing : bzip2-libs-1.0.8-12.fc37.i686 38/203 Installing : libstdc++-12.1.1-4.fc38.i686 39/203 Installing : elfutils-libelf-0.187-6.fc37.i686 40/203 Installing : libxcrypt-4.4.28-3.fc38.i686 41/203 Installing : readline-8.1-7.fc37.i686 42/203 Installing : gmp-1:6.2.1-3.fc37.i686 43/203 Installing : libuuid-2.38.1-1.fc37.i686 44/203 Installing : libzstd-1.5.2-3.fc37.i686 45/203 Installing : popt-1.19~rc1-3.fc37.i686 46/203 Installing : libblkid-2.38.1-1.fc37.i686 47/203 Installing : libattr-2.5.1-5.fc37.i686 48/203 Installing : libacl-2.3.1-4.fc37.i686 49/203 Installing : libcap-2.48-5.fc37.i686 50/203 Installing : libunistring-1.0-2.fc37.i686 51/203 Installing : lz4-libs-1.9.3-5.fc37.i686 52/203 Installing : systemd-libs-251.4-51.fc37.i686 53/203 Installing : libidn2-2.3.3-2.fc37.i686 54/203 Installing : mpfr-4.1.0-10.fc37.i686 55/203 Installing : dwz-0.14-7.fc37.i686 56/203 Installing : unzip-6.0-58.fc37.i686 57/203 Installing : file-libs-5.42-4.fc37.i686 58/203 Installing : file-5.42-4.fc37.i686 59/203 Installing : sqlite-libs-3.39.2-2.fc37.i686 60/203 Installing : alternatives-1.19-3.fc37.i686 61/203 Installing : libcap-ng-0.8.3-3.fc37.i686 62/203 Installing : audit-libs-3.0.8-3.fc37.i686 63/203 Installing : libcom_err-1.46.5-3.fc37.i686 64/203 Installing : libeconf-0.4.0-4.fc37.i686 65/203 Installing : pam-libs-1.5.2-14.fc37.i686 66/203 Installing : libffi-3.4.2-9.fc37.i686 67/203 Installing : p11-kit-0.24.1-3.fc37.i686 68/203 Installing : libsepol-3.4-3.fc37.i686 69/203 Installing : libsmartcols-2.38.1-1.fc37.i686 70/203 Installing : lua-libs-5.4.4-4.fc37.i686 71/203 Installing : elfutils-default-yama-scope-0.187-6.fc37.noarch 72/203 Running scriptlet: elfutils-default-yama-scope-0.187-6.fc37.noarch 72/203 Installing : package-notes-srpm-macros-0.4-16.fc37.noarch 73/203 Installing : zip-3.0-33.fc37.i686 74/203 Installing : libpsl-0.21.1-6.fc37.i686 75/203 Installing : zstd-1.5.2-3.fc37.i686 76/203 Installing : libfdisk-2.38.1-1.fc37.i686 77/203 Installing : gc-8.0.6-4.fc37.i686 78/203 Running scriptlet: groff-base-1.22.4-10.fc37.i686 79/203 Installing : groff-base-1.22.4-10.fc37.i686 79/203 Running scriptlet: groff-base-1.22.4-10.fc37.i686 79/203 Installing : bzip2-1.0.8-12.fc37.i686 80/203 Installing : libxml2-2.9.14-3.fc37.i686 81/203 Installing : ed-1.18-2.fc37.i686 82/203 Installing : ncurses-6.3-3.20220501.fc37.i686 83/203 Installing : perl-Text-Tabs+Wrap-2021.0814-489.fc37.noarch 84/203 Installing : perl-if-0.61.000-491.fc37.noarch 85/203 Installing : perl-Time-Local-2:1.300-489.fc37.noarch 86/203 Installing : perl-File-Path-2.18-489.fc37.noarch 87/203 Installing : perl-Pod-Escapes-1:1.07-489.fc37.noarch 88/203 Installing : perl-Class-Struct-0.66-491.fc37.noarch 89/203 Installing : perl-POSIX-2.03-491.fc37.i686 90/203 Installing : perl-Term-ANSIColor-5.01-490.fc37.noarch 91/203 Installing : perl-IPC-Open3-1.22-491.fc37.noarch 92/203 Installing : perl-HTTP-Tiny-0.082-1.fc37.noarch 93/203 Installing : perl-subs-1.04-491.fc37.noarch 94/203 Installing : perl-File-Temp-1:0.231.100-489.fc37.noarch 95/203 Installing : perl-Term-Cap-1.17-489.fc37.noarch 96/203 Installing : perl-Pod-Simple-1:3.43-490.fc37.noarch 97/203 Installing : perl-Socket-4:2.035-2.fc37.i686 98/203 Installing : perl-SelectSaver-1.02-491.fc37.noarch 99/203 Installing : perl-Symbol-1.09-491.fc37.noarch 100/203 Installing : perl-File-stat-1.12-491.fc37.noarch 101/203 Installing : perl-Pod-Perldoc-3.28.01-490.fc37.noarch 102/203 Installing : perl-podlators-1:4.14-489.fc37.noarch 103/203 Installing : perl-Fcntl-1.15-491.fc37.i686 104/203 Installing : perl-Text-ParseWords-3.31-489.fc37.noarch 105/203 Installing : perl-IO-1.50-491.fc37.i686 106/203 Installing : perl-overloading-0.02-491.fc37.noarch 107/203 Installing : perl-Pod-Usage-4:2.03-3.fc37.noarch 108/203 Installing : perl-mro-1.26-491.fc37.i686 109/203 Installing : perl-Errno-1.36-491.fc37.i686 110/203 Installing : perl-File-Basename-2.85-491.fc37.noarch 111/203 Installing : perl-Getopt-Std-1.13-491.fc37.noarch 112/203 Installing : perl-MIME-Base64-3.16-489.fc37.i686 113/203 Installing : perl-Scalar-List-Utils-5:1.63-489.fc38.i686 114/203 Installing : perl-Storable-1:3.26-489.fc37.i686 115/203 Installing : perl-constant-1.33-490.fc37.noarch 116/203 Installing : perl-parent-1:0.238-489.fc37.noarch 117/203 Installing : perl-vars-1.05-491.fc37.noarch 118/203 Installing : perl-Getopt-Long-1:2.52-489.fc37.noarch 119/203 Installing : perl-overload-1.35-491.fc37.noarch 120/203 Installing : perl-Carp-1.52-489.fc37.noarch 121/203 Installing : perl-Exporter-5.77-489.fc37.noarch 122/203 Installing : perl-PathTools-3.84-489.fc37.i686 123/203 Installing : perl-DynaLoader-1.52-491.fc37.i686 124/203 Installing : perl-Encode-4:3.19-492.fc38.i686 125/203 Installing : perl-libs-4:5.36.0-491.fc37.i686 126/203 Installing : perl-interpreter-4:5.36.0-491.fc37.i686 127/203 Installing : cpio-2.13-13.fc37.i686 128/203 Installing : diffutils-3.8-3.fc37.i686 129/203 Installing : gdbm-libs-1:1.23-2.fc37.i686 130/203 Installing : cyrus-sasl-lib-2.1.28-7.fc37.i686 131/203 Installing : jansson-2.13.1-5.fc37.i686 132/203 Installing : keyutils-libs-1.6.1-5.fc37.i686 133/203 Installing : libbrotli-1.0.9-9.fc37.i686 134/203 Installing : libdb-5.3.28-53.fc37.i686 135/203 Installing : libgomp-12.1.1-4.fc38.i686 136/203 Installing : libnghttp2-1.48.0-2.fc37.i686 137/203 Installing : libpkgconf-1.8.0-3.fc37.i686 138/203 Installing : pkgconf-1.8.0-3.fc37.i686 139/203 Installing : pkgconf-pkg-config-1.8.0-3.fc37.i686 140/203 Installing : libsigsegv-2.14-3.fc37.i686 141/203 Installing : gawk-5.1.1-4.fc37.i686 142/203 Installing : libtasn1-4.18.0-3.fc37.i686 143/203 Installing : p11-kit-trust-0.24.1-3.fc37.i686 144/203 Running scriptlet: p11-kit-trust-0.24.1-3.fc37.i686 144/203 Installing : libtool-ltdl-2.4.7-2.fc37.i686 145/203 Installing : libverto-0.3.2-4.fc37.i686 146/203 Installing : pcre-8.45-1.fc37.2.i686 147/203 Installing : grep-3.7-4.fc37.i686 148/203 Installing : xz-5.2.5-10.fc37.i686 149/203 Installing : pcre2-10.40-1.fc37.1.i686 150/203 Installing : libselinux-3.4-5.fc37.i686 151/203 Installing : sed-4.8-11.fc37.i686 152/203 Installing : findutils-1:4.9.0-2.fc37.i686 153/203 Installing : libmount-2.38.1-1.fc37.i686 154/203 Installing : openssl-libs-1:3.0.5-2.fc37.i686 155/203 Installing : coreutils-9.1-6.fc37.i686 156/203 Running scriptlet: ca-certificates-2022.2.54-5.fc37.noarch 157/203 Installing : ca-certificates-2022.2.54-5.fc37.noarch 157/203 Running scriptlet: ca-certificates-2022.2.54-5.fc37.noarch 157/203 Installing : krb5-libs-1.19.2-11.fc37.1.i686 158/203 Installing : libtirpc-1.3.3-0.fc37.i686 159/203 Running scriptlet: authselect-libs-1.4.0-3.fc37.i686 160/203 Installing : authselect-libs-1.4.0-3.fc37.i686 160/203 Installing : gzip-1.12-2.fc37.i686 161/203 Installing : cracklib-2.9.6-28.fc36.i686 162/203 Installing : libpwquality-1.4.4-11.fc37.i686 163/203 Installing : authselect-1.4.0-3.fc37.i686 164/203 Installing : libnsl2-2.0.0-4.fc37.i686 165/203 Installing : pam-1.5.2-14.fc37.i686 166/203 Installing : libssh-0.9.6-5.fc37.i686 167/203 Installing : guile22-2.2.7-6.fc37.i686 168/203 Installing : libarchive-3.6.1-2.fc37.i686 169/203 Installing : libevent-2.1.12-7.fc37.i686 170/203 Installing : openldap-2.6.2-5.fc38.i686 171/203 Installing : libcurl-7.84.0-2.fc37.i686 172/203 Installing : elfutils-libs-0.187-6.fc37.i686 173/203 Installing : elfutils-debuginfod-client-0.187-6.fc37.i686 174/203 Installing : binutils-gold-2.39-1.fc38.i686 175/203 Installing : binutils-gprofng-2.39-1.fc38.i686 176/203 Installing : binutils-2.39-1.fc38.i686 177/203 Running scriptlet: binutils-2.39-1.fc38.i686 177/203 Installing : elfutils-0.187-6.fc37.i686 178/203 Installing : curl-7.84.0-2.fc37.i686 179/203 Running scriptlet: rpm-4.18.0-0.beta1.4.fc37.i686 180/203 Installing : rpm-4.18.0-0.beta1.4.fc37.i686 180/203 Installing : rpm-libs-4.18.0-0.beta1.4.fc37.i686 181/203 Installing : efi-srpm-macros-5-6.fc37.noarch 182/203 Installing : lua-srpm-macros-1-7.fc37.noarch 183/203 Installing : rpmautospec-rpm-macros-0.3.0-1.fc37.noarch 184/203 Installing : fonts-srpm-macros-1:2.0.5-8.fc37.noarch 185/203 Installing : go-srpm-macros-3.1.0-4.fc37.noarch 186/203 Installing : python-srpm-macros-3.11-4.fc37.noarch 187/203 Installing : redhat-rpm-config-227-1.fc37.noarch 188/203 Installing : rpm-build-libs-4.18.0-0.beta1.4.fc37.i686 189/203 Installing : util-linux-core-2.38.1-1.fc37.i686 190/203 Installing : libsemanage-3.4-5.fc37.i686 191/203 Installing : shadow-utils-2:4.11.1-4.fc37.i686 192/203 Running scriptlet: libutempter-1.2.1-7.fc37.i686 193/203 Installing : libutempter-1.2.1-7.fc37.i686 193/203 Installing : patch-2.7.6-17.fc37.i686 194/203 Installing : tar-2:1.34-3.fc36.i686 195/203 Installing : xxhash-libs-0.8.1-3.fc37.i686 196/203 Installing : gdb-minimal-12.1-4.fc37.i686 197/203 Installing : debugedit-5.0-5.fc37.i686 198/203 Installing : rpm-build-4.18.0-0.beta1.4.fc37.i686 199/203 Installing : util-linux-2.38.1-1.fc37.i686 200/203 Installing : make-1:4.3-11.fc37.i686 201/203 Installing : which-2.21-35.fc37.i686 202/203 Installing : info-6.8-4.fc37.i686 203/203 Running scriptlet: filesystem-3.18-2.fc37.i686 203/203 Running scriptlet: ca-certificates-2022.2.54-5.fc37.noarch 203/203 Running scriptlet: authselect-libs-1.4.0-3.fc37.i686 203/203 Running scriptlet: rpm-4.18.0-0.beta1.4.fc37.i686 203/203 Running scriptlet: info-6.8-4.fc37.i686 203/203 Verifying : alternatives-1.19-3.fc37.i686 1/203 Verifying : ansible-srpm-macros-1-6.fc37.noarch 2/203 Verifying : audit-libs-3.0.8-3.fc37.i686 3/203 Verifying : authselect-1.4.0-3.fc37.i686 4/203 Verifying : authselect-libs-1.4.0-3.fc37.i686 5/203 Verifying : basesystem-11-14.fc37.noarch 6/203 Verifying : bash-5.1.16-3.fc37.i686 7/203 Verifying : binutils-2.39-1.fc38.i686 8/203 Verifying : binutils-gold-2.39-1.fc38.i686 9/203 Verifying : binutils-gprofng-2.39-1.fc38.i686 10/203 Verifying : bzip2-1.0.8-12.fc37.i686 11/203 Verifying : bzip2-libs-1.0.8-12.fc37.i686 12/203 Verifying : ca-certificates-2022.2.54-5.fc37.noarch 13/203 Verifying : coreutils-9.1-6.fc37.i686 14/203 Verifying : coreutils-common-9.1-6.fc37.i686 15/203 Verifying : cpio-2.13-13.fc37.i686 16/203 Verifying : cracklib-2.9.6-28.fc36.i686 17/203 Verifying : crypto-policies-20220815-1.gite4ed860.fc38.noarc 18/203 Verifying : curl-7.84.0-2.fc37.i686 19/203 Verifying : cyrus-sasl-lib-2.1.28-7.fc37.i686 20/203 Verifying : debugedit-5.0-5.fc37.i686 21/203 Verifying : diffutils-3.8-3.fc37.i686 22/203 Verifying : dwz-0.14-7.fc37.i686 23/203 Verifying : ed-1.18-2.fc37.i686 24/203 Verifying : efi-srpm-macros-5-6.fc37.noarch 25/203 Verifying : elfutils-0.187-6.fc37.i686 26/203 Verifying : elfutils-debuginfod-client-0.187-6.fc37.i686 27/203 Verifying : elfutils-default-yama-scope-0.187-6.fc37.noarch 28/203 Verifying : elfutils-libelf-0.187-6.fc37.i686 29/203 Verifying : elfutils-libs-0.187-6.fc37.i686 30/203 Verifying : fedora-gpg-keys-38-0.2.noarch 31/203 Verifying : fedora-release-38-0.2.noarch 32/203 Verifying : fedora-release-common-38-0.2.noarch 33/203 Verifying : fedora-release-identity-basic-38-0.2.noarch 34/203 Verifying : fedora-repos-38-0.2.noarch 35/203 Verifying : fedora-repos-rawhide-38-0.2.noarch 36/203 Verifying : file-5.42-4.fc37.i686 37/203 Verifying : file-libs-5.42-4.fc37.i686 38/203 Verifying : filesystem-3.18-2.fc37.i686 39/203 Verifying : findutils-1:4.9.0-2.fc37.i686 40/203 Verifying : fonts-srpm-macros-1:2.0.5-8.fc37.noarch 41/203 Verifying : fpc-srpm-macros-1.3-6.fc37.noarch 42/203 Verifying : gawk-5.1.1-4.fc37.i686 43/203 Verifying : gc-8.0.6-4.fc37.i686 44/203 Verifying : gdb-minimal-12.1-4.fc37.i686 45/203 Verifying : gdbm-libs-1:1.23-2.fc37.i686 46/203 Verifying : ghc-srpm-macros-1.5.0-7.fc37.noarch 47/203 Verifying : glibc-2.36-1.fc37.i686 48/203 Verifying : glibc-common-2.36-1.fc37.i686 49/203 Verifying : glibc-gconv-extra-2.36-1.fc37.i686 50/203 Verifying : glibc-minimal-langpack-2.36-1.fc37.i686 51/203 Verifying : gmp-1:6.2.1-3.fc37.i686 52/203 Verifying : gnat-srpm-macros-4-16.fc37.noarch 53/203 Verifying : go-srpm-macros-3.1.0-4.fc37.noarch 54/203 Verifying : grep-3.7-4.fc37.i686 55/203 Verifying : groff-base-1.22.4-10.fc37.i686 56/203 Verifying : guile22-2.2.7-6.fc37.i686 57/203 Verifying : gzip-1.12-2.fc37.i686 58/203 Verifying : info-6.8-4.fc37.i686 59/203 Verifying : jansson-2.13.1-5.fc37.i686 60/203 Verifying : kernel-srpm-macros-1.0-15.fc37.noarch 61/203 Verifying : keyutils-libs-1.6.1-5.fc37.i686 62/203 Verifying : krb5-libs-1.19.2-11.fc37.1.i686 63/203 Verifying : libacl-2.3.1-4.fc37.i686 64/203 Verifying : libarchive-3.6.1-2.fc37.i686 65/203 Verifying : libattr-2.5.1-5.fc37.i686 66/203 Verifying : libblkid-2.38.1-1.fc37.i686 67/203 Verifying : libbrotli-1.0.9-9.fc37.i686 68/203 Verifying : libcap-2.48-5.fc37.i686 69/203 Verifying : libcap-ng-0.8.3-3.fc37.i686 70/203 Verifying : libcom_err-1.46.5-3.fc37.i686 71/203 Verifying : libcurl-7.84.0-2.fc37.i686 72/203 Verifying : libdb-5.3.28-53.fc37.i686 73/203 Verifying : libeconf-0.4.0-4.fc37.i686 74/203 Verifying : libevent-2.1.12-7.fc37.i686 75/203 Verifying : libfdisk-2.38.1-1.fc37.i686 76/203 Verifying : libffi-3.4.2-9.fc37.i686 77/203 Verifying : libgcc-12.1.1-4.fc38.i686 78/203 Verifying : libgomp-12.1.1-4.fc38.i686 79/203 Verifying : libidn2-2.3.3-2.fc37.i686 80/203 Verifying : libmount-2.38.1-1.fc37.i686 81/203 Verifying : libnghttp2-1.48.0-2.fc37.i686 82/203 Verifying : libnsl2-2.0.0-4.fc37.i686 83/203 Verifying : libpkgconf-1.8.0-3.fc37.i686 84/203 Verifying : libpsl-0.21.1-6.fc37.i686 85/203 Verifying : libpwquality-1.4.4-11.fc37.i686 86/203 Verifying : libselinux-3.4-5.fc37.i686 87/203 Verifying : libsemanage-3.4-5.fc37.i686 88/203 Verifying : libsepol-3.4-3.fc37.i686 89/203 Verifying : libsigsegv-2.14-3.fc37.i686 90/203 Verifying : libsmartcols-2.38.1-1.fc37.i686 91/203 Verifying : libssh-0.9.6-5.fc37.i686 92/203 Verifying : libssh-config-0.9.6-5.fc37.noarch 93/203 Verifying : libstdc++-12.1.1-4.fc38.i686 94/203 Verifying : libtasn1-4.18.0-3.fc37.i686 95/203 Verifying : libtirpc-1.3.3-0.fc37.i686 96/203 Verifying : libtool-ltdl-2.4.7-2.fc37.i686 97/203 Verifying : libunistring-1.0-2.fc37.i686 98/203 Verifying : libutempter-1.2.1-7.fc37.i686 99/203 Verifying : libuuid-2.38.1-1.fc37.i686 100/203 Verifying : libverto-0.3.2-4.fc37.i686 101/203 Verifying : libxcrypt-4.4.28-3.fc38.i686 102/203 Verifying : libxml2-2.9.14-3.fc37.i686 103/203 Verifying : libzstd-1.5.2-3.fc37.i686 104/203 Verifying : lua-libs-5.4.4-4.fc37.i686 105/203 Verifying : lua-srpm-macros-1-7.fc37.noarch 106/203 Verifying : lz4-libs-1.9.3-5.fc37.i686 107/203 Verifying : make-1:4.3-11.fc37.i686 108/203 Verifying : mpfr-4.1.0-10.fc37.i686 109/203 Verifying : ncurses-6.3-3.20220501.fc37.i686 110/203 Verifying : ncurses-base-6.3-3.20220501.fc37.noarch 111/203 Verifying : ncurses-libs-6.3-3.20220501.fc37.i686 112/203 Verifying : nim-srpm-macros-3-7.fc37.noarch 113/203 Verifying : ocaml-srpm-macros-7-2.fc37.noarch 114/203 Verifying : openblas-srpm-macros-2-12.fc37.noarch 115/203 Verifying : openldap-2.6.2-5.fc38.i686 116/203 Verifying : openssl-libs-1:3.0.5-2.fc37.i686 117/203 Verifying : p11-kit-0.24.1-3.fc37.i686 118/203 Verifying : p11-kit-trust-0.24.1-3.fc37.i686 119/203 Verifying : package-notes-srpm-macros-0.4-16.fc37.noarch 120/203 Verifying : pam-1.5.2-14.fc37.i686 121/203 Verifying : pam-libs-1.5.2-14.fc37.i686 122/203 Verifying : patch-2.7.6-17.fc37.i686 123/203 Verifying : pcre-8.45-1.fc37.2.i686 124/203 Verifying : pcre2-10.40-1.fc37.1.i686 125/203 Verifying : pcre2-syntax-10.40-1.fc37.1.noarch 126/203 Verifying : perl-Carp-1.52-489.fc37.noarch 127/203 Verifying : perl-Class-Struct-0.66-491.fc37.noarch 128/203 Verifying : perl-DynaLoader-1.52-491.fc37.i686 129/203 Verifying : perl-Encode-4:3.19-492.fc38.i686 130/203 Verifying : perl-Errno-1.36-491.fc37.i686 131/203 Verifying : perl-Exporter-5.77-489.fc37.noarch 132/203 Verifying : perl-Fcntl-1.15-491.fc37.i686 133/203 Verifying : perl-File-Basename-2.85-491.fc37.noarch 134/203 Verifying : perl-File-Path-2.18-489.fc37.noarch 135/203 Verifying : perl-File-Temp-1:0.231.100-489.fc37.noarch 136/203 Verifying : perl-File-stat-1.12-491.fc37.noarch 137/203 Verifying : perl-Getopt-Long-1:2.52-489.fc37.noarch 138/203 Verifying : perl-Getopt-Std-1.13-491.fc37.noarch 139/203 Verifying : perl-HTTP-Tiny-0.082-1.fc37.noarch 140/203 Verifying : perl-IO-1.50-491.fc37.i686 141/203 Verifying : perl-IPC-Open3-1.22-491.fc37.noarch 142/203 Verifying : perl-MIME-Base64-3.16-489.fc37.i686 143/203 Verifying : perl-POSIX-2.03-491.fc37.i686 144/203 Verifying : perl-PathTools-3.84-489.fc37.i686 145/203 Verifying : perl-Pod-Escapes-1:1.07-489.fc37.noarch 146/203 Verifying : perl-Pod-Perldoc-3.28.01-490.fc37.noarch 147/203 Verifying : perl-Pod-Simple-1:3.43-490.fc37.noarch 148/203 Verifying : perl-Pod-Usage-4:2.03-3.fc37.noarch 149/203 Verifying : perl-Scalar-List-Utils-5:1.63-489.fc38.i686 150/203 Verifying : perl-SelectSaver-1.02-491.fc37.noarch 151/203 Verifying : perl-Socket-4:2.035-2.fc37.i686 152/203 Verifying : perl-Storable-1:3.26-489.fc37.i686 153/203 Verifying : perl-Symbol-1.09-491.fc37.noarch 154/203 Verifying : perl-Term-ANSIColor-5.01-490.fc37.noarch 155/203 Verifying : perl-Term-Cap-1.17-489.fc37.noarch 156/203 Verifying : perl-Text-ParseWords-3.31-489.fc37.noarch 157/203 Verifying : perl-Text-Tabs+Wrap-2021.0814-489.fc37.noarch 158/203 Verifying : perl-Time-Local-2:1.300-489.fc37.noarch 159/203 Verifying : perl-constant-1.33-490.fc37.noarch 160/203 Verifying : perl-if-0.61.000-491.fc37.noarch 161/203 Verifying : perl-interpreter-4:5.36.0-491.fc37.i686 162/203 Verifying : perl-libs-4:5.36.0-491.fc37.i686 163/203 Verifying : perl-mro-1.26-491.fc37.i686 164/203 Verifying : perl-overload-1.35-491.fc37.noarch 165/203 Verifying : perl-overloading-0.02-491.fc37.noarch 166/203 Verifying : perl-parent-1:0.238-489.fc37.noarch 167/203 Verifying : perl-podlators-1:4.14-489.fc37.noarch 168/203 Verifying : perl-srpm-macros-1-46.fc37.noarch 169/203 Verifying : perl-subs-1.04-491.fc37.noarch 170/203 Verifying : perl-vars-1.05-491.fc37.noarch 171/203 Verifying : pkgconf-1.8.0-3.fc37.i686 172/203 Verifying : pkgconf-m4-1.8.0-3.fc37.noarch 173/203 Verifying : pkgconf-pkg-config-1.8.0-3.fc37.i686 174/203 Verifying : popt-1.19~rc1-3.fc37.i686 175/203 Verifying : publicsuffix-list-dafsa-20210518-5.fc37.noarch 176/203 Verifying : python-srpm-macros-3.11-4.fc37.noarch 177/203 Verifying : qt5-srpm-macros-5.15.5-2.fc37.noarch 178/203 Verifying : readline-8.1-7.fc37.i686 179/203 Verifying : redhat-rpm-config-227-1.fc37.noarch 180/203 Verifying : rpm-4.18.0-0.beta1.4.fc37.i686 181/203 Verifying : rpm-build-4.18.0-0.beta1.4.fc37.i686 182/203 Verifying : rpm-build-libs-4.18.0-0.beta1.4.fc37.i686 183/203 Verifying : rpm-libs-4.18.0-0.beta1.4.fc37.i686 184/203 Verifying : rpmautospec-rpm-macros-0.3.0-1.fc37.noarch 185/203 Verifying : rust-srpm-macros-22-1.fc37.noarch 186/203 Verifying : sed-4.8-11.fc37.i686 187/203 Verifying : setup-2.14.1-2.fc37.noarch 188/203 Verifying : shadow-utils-2:4.11.1-4.fc37.i686 189/203 Verifying : sqlite-libs-3.39.2-2.fc37.i686 190/203 Verifying : systemd-libs-251.4-51.fc37.i686 191/203 Verifying : tar-2:1.34-3.fc36.i686 192/203 Verifying : tzdata-2022b-1.fc38.noarch 193/203 Verifying : unzip-6.0-58.fc37.i686 194/203 Verifying : util-linux-2.38.1-1.fc37.i686 195/203 Verifying : util-linux-core-2.38.1-1.fc37.i686 196/203 Verifying : which-2.21-35.fc37.i686 197/203 Verifying : xxhash-libs-0.8.1-3.fc37.i686 198/203 Verifying : xz-5.2.5-10.fc37.i686 199/203 Verifying : xz-libs-5.2.5-10.fc37.i686 200/203 Verifying : zip-3.0-33.fc37.i686 201/203 Verifying : zlib-1.2.12-4.fc37.i686 202/203 Verifying : zstd-1.5.2-3.fc37.i686 203/203 Installed products updated. Installed: alternatives-1.19-3.fc37.i686 ansible-srpm-macros-1-6.fc37.noarch audit-libs-3.0.8-3.fc37.i686 authselect-1.4.0-3.fc37.i686 authselect-libs-1.4.0-3.fc37.i686 basesystem-11-14.fc37.noarch bash-5.1.16-3.fc37.i686 binutils-2.39-1.fc38.i686 binutils-gold-2.39-1.fc38.i686 binutils-gprofng-2.39-1.fc38.i686 bzip2-1.0.8-12.fc37.i686 bzip2-libs-1.0.8-12.fc37.i686 ca-certificates-2022.2.54-5.fc37.noarch coreutils-9.1-6.fc37.i686 coreutils-common-9.1-6.fc37.i686 cpio-2.13-13.fc37.i686 cracklib-2.9.6-28.fc36.i686 crypto-policies-20220815-1.gite4ed860.fc38.noarch curl-7.84.0-2.fc37.i686 cyrus-sasl-lib-2.1.28-7.fc37.i686 debugedit-5.0-5.fc37.i686 diffutils-3.8-3.fc37.i686 dwz-0.14-7.fc37.i686 ed-1.18-2.fc37.i686 efi-srpm-macros-5-6.fc37.noarch elfutils-0.187-6.fc37.i686 elfutils-debuginfod-client-0.187-6.fc37.i686 elfutils-default-yama-scope-0.187-6.fc37.noarch elfutils-libelf-0.187-6.fc37.i686 elfutils-libs-0.187-6.fc37.i686 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.i686 file-libs-5.42-4.fc37.i686 filesystem-3.18-2.fc37.i686 findutils-1:4.9.0-2.fc37.i686 fonts-srpm-macros-1:2.0.5-8.fc37.noarch fpc-srpm-macros-1.3-6.fc37.noarch gawk-5.1.1-4.fc37.i686 gc-8.0.6-4.fc37.i686 gdb-minimal-12.1-4.fc37.i686 gdbm-libs-1:1.23-2.fc37.i686 ghc-srpm-macros-1.5.0-7.fc37.noarch glibc-2.36-1.fc37.i686 glibc-common-2.36-1.fc37.i686 glibc-gconv-extra-2.36-1.fc37.i686 glibc-minimal-langpack-2.36-1.fc37.i686 gmp-1:6.2.1-3.fc37.i686 gnat-srpm-macros-4-16.fc37.noarch go-srpm-macros-3.1.0-4.fc37.noarch grep-3.7-4.fc37.i686 groff-base-1.22.4-10.fc37.i686 guile22-2.2.7-6.fc37.i686 gzip-1.12-2.fc37.i686 info-6.8-4.fc37.i686 jansson-2.13.1-5.fc37.i686 kernel-srpm-macros-1.0-15.fc37.noarch keyutils-libs-1.6.1-5.fc37.i686 krb5-libs-1.19.2-11.fc37.1.i686 libacl-2.3.1-4.fc37.i686 libarchive-3.6.1-2.fc37.i686 libattr-2.5.1-5.fc37.i686 libblkid-2.38.1-1.fc37.i686 libbrotli-1.0.9-9.fc37.i686 libcap-2.48-5.fc37.i686 libcap-ng-0.8.3-3.fc37.i686 libcom_err-1.46.5-3.fc37.i686 libcurl-7.84.0-2.fc37.i686 libdb-5.3.28-53.fc37.i686 libeconf-0.4.0-4.fc37.i686 libevent-2.1.12-7.fc37.i686 libfdisk-2.38.1-1.fc37.i686 libffi-3.4.2-9.fc37.i686 libgcc-12.1.1-4.fc38.i686 libgomp-12.1.1-4.fc38.i686 libidn2-2.3.3-2.fc37.i686 libmount-2.38.1-1.fc37.i686 libnghttp2-1.48.0-2.fc37.i686 libnsl2-2.0.0-4.fc37.i686 libpkgconf-1.8.0-3.fc37.i686 libpsl-0.21.1-6.fc37.i686 libpwquality-1.4.4-11.fc37.i686 libselinux-3.4-5.fc37.i686 libsemanage-3.4-5.fc37.i686 libsepol-3.4-3.fc37.i686 libsigsegv-2.14-3.fc37.i686 libsmartcols-2.38.1-1.fc37.i686 libssh-0.9.6-5.fc37.i686 libssh-config-0.9.6-5.fc37.noarch libstdc++-12.1.1-4.fc38.i686 libtasn1-4.18.0-3.fc37.i686 libtirpc-1.3.3-0.fc37.i686 libtool-ltdl-2.4.7-2.fc37.i686 libunistring-1.0-2.fc37.i686 libutempter-1.2.1-7.fc37.i686 libuuid-2.38.1-1.fc37.i686 libverto-0.3.2-4.fc37.i686 libxcrypt-4.4.28-3.fc38.i686 libxml2-2.9.14-3.fc37.i686 libzstd-1.5.2-3.fc37.i686 lua-libs-5.4.4-4.fc37.i686 lua-srpm-macros-1-7.fc37.noarch lz4-libs-1.9.3-5.fc37.i686 make-1:4.3-11.fc37.i686 mpfr-4.1.0-10.fc37.i686 ncurses-6.3-3.20220501.fc37.i686 ncurses-base-6.3-3.20220501.fc37.noarch ncurses-libs-6.3-3.20220501.fc37.i686 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.i686 openssl-libs-1:3.0.5-2.fc37.i686 p11-kit-0.24.1-3.fc37.i686 p11-kit-trust-0.24.1-3.fc37.i686 package-notes-srpm-macros-0.4-16.fc37.noarch pam-1.5.2-14.fc37.i686 pam-libs-1.5.2-14.fc37.i686 patch-2.7.6-17.fc37.i686 pcre-8.45-1.fc37.2.i686 pcre2-10.40-1.fc37.1.i686 pcre2-syntax-10.40-1.fc37.1.noarch perl-Carp-1.52-489.fc37.noarch perl-Class-Struct-0.66-491.fc37.noarch perl-DynaLoader-1.52-491.fc37.i686 perl-Encode-4:3.19-492.fc38.i686 perl-Errno-1.36-491.fc37.i686 perl-Exporter-5.77-489.fc37.noarch perl-Fcntl-1.15-491.fc37.i686 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-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.i686 perl-IPC-Open3-1.22-491.fc37.noarch perl-MIME-Base64-3.16-489.fc37.i686 perl-POSIX-2.03-491.fc37.i686 perl-PathTools-3.84-489.fc37.i686 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.i686 perl-SelectSaver-1.02-491.fc37.noarch perl-Socket-4:2.035-2.fc37.i686 perl-Storable-1:3.26-489.fc37.i686 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.i686 perl-libs-4:5.36.0-491.fc37.i686 perl-mro-1.26-491.fc37.i686 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-srpm-macros-1-46.fc37.noarch perl-subs-1.04-491.fc37.noarch perl-vars-1.05-491.fc37.noarch pkgconf-1.8.0-3.fc37.i686 pkgconf-m4-1.8.0-3.fc37.noarch pkgconf-pkg-config-1.8.0-3.fc37.i686 popt-1.19~rc1-3.fc37.i686 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.i686 redhat-rpm-config-227-1.fc37.noarch rpm-4.18.0-0.beta1.4.fc37.i686 rpm-build-4.18.0-0.beta1.4.fc37.i686 rpm-build-libs-4.18.0-0.beta1.4.fc37.i686 rpm-libs-4.18.0-0.beta1.4.fc37.i686 rpmautospec-rpm-macros-0.3.0-1.fc37.noarch rust-srpm-macros-22-1.fc37.noarch sed-4.8-11.fc37.i686 setup-2.14.1-2.fc37.noarch shadow-utils-2:4.11.1-4.fc37.i686 sqlite-libs-3.39.2-2.fc37.i686 systemd-libs-251.4-51.fc37.i686 tar-2:1.34-3.fc36.i686 tzdata-2022b-1.fc38.noarch unzip-6.0-58.fc37.i686 util-linux-2.38.1-1.fc37.i686 util-linux-core-2.38.1-1.fc37.i686 which-2.21-35.fc37.i686 xxhash-libs-0.8.1-3.fc37.i686 xz-5.2.5-10.fc37.i686 xz-libs-5.2.5-10.fc37.i686 zip-3.0-33.fc37.i686 zlib-1.2.12-4.fc37.i686 zstd-1.5.2-3.fc37.i686 Complete! Finish: dnf install Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: xxhash-libs-0.8.1-3.fc37.i686 gmp-6.2.1-3.fc37.i686 authselect-libs-1.4.0-3.fc37.i686 perl-vars-1.05-491.fc37.noarch libssh-0.9.6-5.fc37.i686 ansible-srpm-macros-1-6.fc37.noarch rpm-build-4.18.0-0.beta1.4.fc37.i686 ocaml-srpm-macros-7-2.fc37.noarch openssl-libs-3.0.5-2.fc37.i686 pcre2-syntax-10.40-1.fc37.1.noarch util-linux-2.38.1-1.fc37.i686 fedora-release-common-38-0.2.noarch fpc-srpm-macros-1.3-6.fc37.noarch libblkid-2.38.1-1.fc37.i686 perl-PathTools-3.84-489.fc37.i686 gc-8.0.6-4.fc37.i686 libxml2-2.9.14-3.fc37.i686 file-5.42-4.fc37.i686 binutils-gprofng-2.39-1.fc38.i686 audit-libs-3.0.8-3.fc37.i686 libattr-2.5.1-5.fc37.i686 ed-1.18-2.fc37.i686 lz4-libs-1.9.3-5.fc37.i686 libunistring-1.0-2.fc37.i686 gzip-1.12-2.fc37.i686 libevent-2.1.12-7.fc37.i686 libeconf-0.4.0-4.fc37.i686 perl-File-Path-2.18-489.fc37.noarch perl-Time-Local-1.300-489.fc37.noarch perl-Exporter-5.77-489.fc37.noarch libacl-2.3.1-4.fc37.i686 p11-kit-0.24.1-3.fc37.i686 ncurses-6.3-3.20220501.fc37.i686 pcre-8.45-1.fc37.2.i686 sqlite-libs-3.39.2-2.fc37.i686 perl-Term-ANSIColor-5.01-490.fc37.noarch which-2.21-35.fc37.i686 crypto-policies-20220815-1.gite4ed860.fc38.noarch python-srpm-macros-3.11-4.fc37.noarch setup-2.14.1-2.fc37.noarch krb5-libs-1.19.2-11.fc37.1.i686 guile22-2.2.7-6.fc37.i686 perl-podlators-4.14-489.fc37.noarch libcurl-7.84.0-2.fc37.i686 libselinux-3.4-5.fc37.i686 fedora-repos-38-0.2.noarch systemd-libs-251.4-51.fc37.i686 perl-IO-1.50-491.fc37.i686 make-4.3-11.fc37.i686 pcre2-10.40-1.fc37.1.i686 perl-Text-ParseWords-3.31-489.fc37.noarch libarchive-3.6.1-2.fc37.i686 perl-SelectSaver-1.02-491.fc37.noarch gdbm-libs-1.23-2.fc37.i686 perl-IPC-Open3-1.22-491.fc37.noarch rpm-build-libs-4.18.0-0.beta1.4.fc37.i686 libmount-2.38.1-1.fc37.i686 coreutils-9.1-6.fc37.i686 ncurses-libs-6.3-3.20220501.fc37.i686 bzip2-1.0.8-12.fc37.i686 perl-HTTP-Tiny-0.082-1.fc37.noarch elfutils-default-yama-scope-0.187-6.fc37.noarch perl-MIME-Base64-3.16-489.fc37.i686 fonts-srpm-macros-2.0.5-8.fc37.noarch debugedit-5.0-5.fc37.i686 binutils-gold-2.39-1.fc38.i686 libpwquality-1.4.4-11.fc37.i686 perl-Getopt-Std-1.13-491.fc37.noarch perl-POSIX-2.03-491.fc37.i686 ca-certificates-2022.2.54-5.fc37.noarch alternatives-1.19-3.fc37.i686 bash-5.1.16-3.fc37.i686 libsigsegv-2.14-3.fc37.i686 libtirpc-1.3.3-0.fc37.i686 patch-2.7.6-17.fc37.i686 perl-Getopt-Long-2.52-489.fc37.noarch bzip2-libs-1.0.8-12.fc37.i686 perl-Carp-1.52-489.fc37.noarch fedora-release-identity-basic-38-0.2.noarch tar-1.34-3.fc36.i686 glibc-2.36-1.fc37.i686 perl-Errno-1.36-491.fc37.i686 cyrus-sasl-lib-2.1.28-7.fc37.i686 pkgconf-pkg-config-1.8.0-3.fc37.i686 perl-Pod-Escapes-1.07-489.fc37.noarch keyutils-libs-1.6.1-5.fc37.i686 openblas-srpm-macros-2-12.fc37.noarch gdb-minimal-12.1-4.fc37.i686 ncurses-base-6.3-3.20220501.fc37.noarch perl-Symbol-1.09-491.fc37.noarch perl-libs-5.36.0-491.fc37.i686 coreutils-common-9.1-6.fc37.i686 elfutils-0.187-6.fc37.i686 perl-DynaLoader-1.52-491.fc37.i686 groff-base-1.22.4-10.fc37.i686 perl-srpm-macros-1-46.fc37.noarch perl-overload-1.35-491.fc37.noarch libffi-3.4.2-9.fc37.i686 readline-8.1-7.fc37.i686 libidn2-2.3.3-2.fc37.i686 fedora-repos-rawhide-38-0.2.noarch perl-Pod-Simple-3.43-490.fc37.noarch libnghttp2-1.48.0-2.fc37.i686 perl-Pod-Usage-2.03-3.fc37.noarch popt-1.19~rc1-3.fc37.i686 openldap-2.6.2-5.fc38.i686 perl-File-Basename-2.85-491.fc37.noarch cpio-2.13-13.fc37.i686 redhat-rpm-config-227-1.fc37.noarch info-6.8-4.fc37.i686 glibc-common-2.36-1.fc37.i686 libcap-ng-0.8.3-3.fc37.i686 ghc-srpm-macros-1.5.0-7.fc37.noarch perl-Term-Cap-1.17-489.fc37.noarch libsemanage-3.4-5.fc37.i686 unzip-6.0-58.fc37.i686 elfutils-debuginfod-client-0.187-6.fc37.i686 gawk-5.1.1-4.fc37.i686 fedora-gpg-keys-38-0.2.noarch xz-libs-5.2.5-10.fc37.i686 libsmartcols-2.38.1-1.fc37.i686 fedora-release-38-0.2.noarch libverto-0.3.2-4.fc37.i686 pkgconf-m4-1.8.0-3.fc37.noarch diffutils-3.8-3.fc37.i686 dwz-0.14-7.fc37.i686 sed-4.8-11.fc37.i686 perl-constant-1.33-490.fc37.noarch libnsl2-2.0.0-4.fc37.i686 libsepol-3.4-3.fc37.i686 perl-Socket-2.035-2.fc37.i686 perl-Storable-3.26-489.fc37.i686 perl-interpreter-5.36.0-491.fc37.i686 p11-kit-trust-0.24.1-3.fc37.i686 efi-srpm-macros-5-6.fc37.noarch go-srpm-macros-3.1.0-4.fc37.noarch perl-File-Temp-0.231.100-489.fc37.noarch shadow-utils-4.11.1-4.fc37.i686 perl-File-stat-1.12-491.fc37.noarch filesystem-3.18-2.fc37.i686 perl-Class-Struct-0.66-491.fc37.noarch lua-srpm-macros-1-7.fc37.noarch zstd-1.5.2-3.fc37.i686 grep-3.7-4.fc37.i686 gnat-srpm-macros-4-16.fc37.noarch binutils-2.39-1.fc38.i686 zip-3.0-33.fc37.i686 jansson-2.13.1-5.fc37.i686 libtool-ltdl-2.4.7-2.fc37.i686 libutempter-1.2.1-7.fc37.i686 libuuid-2.38.1-1.fc37.i686 zlib-1.2.12-4.fc37.i686 libzstd-1.5.2-3.fc37.i686 libpsl-0.21.1-6.fc37.i686 libcap-2.48-5.fc37.i686 libdb-5.3.28-53.fc37.i686 pam-1.5.2-14.fc37.i686 rust-srpm-macros-22-1.fc37.noarch util-linux-core-2.38.1-1.fc37.i686 basesystem-11-14.fc37.noarch findutils-4.9.0-2.fc37.i686 curl-7.84.0-2.fc37.i686 elfutils-libelf-0.187-6.fc37.i686 perl-overloading-0.02-491.fc37.noarch mpfr-4.1.0-10.fc37.i686 perl-parent-0.238-489.fc37.noarch perl-Fcntl-1.15-491.fc37.i686 qt5-srpm-macros-5.15.5-2.fc37.noarch perl-Scalar-List-Utils-1.63-489.fc38.i686 perl-subs-1.04-491.fc37.noarch rpm-4.18.0-0.beta1.4.fc37.i686 cracklib-2.9.6-28.fc36.i686 libgcc-12.1.1-4.fc38.i686 libxcrypt-4.4.28-3.fc38.i686 perl-if-0.61.000-491.fc37.noarch nim-srpm-macros-3-7.fc37.noarch tzdata-2022b-1.fc38.noarch libfdisk-2.38.1-1.fc37.i686 libtasn1-4.18.0-3.fc37.i686 authselect-1.4.0-3.fc37.i686 perl-mro-1.26-491.fc37.i686 pam-libs-1.5.2-14.fc37.i686 lua-libs-5.4.4-4.fc37.i686 libbrotli-1.0.9-9.fc37.i686 rpmautospec-rpm-macros-0.3.0-1.fc37.noarch kernel-srpm-macros-1.0-15.fc37.noarch libcom_err-1.46.5-3.fc37.i686 package-notes-srpm-macros-0.4-16.fc37.noarch perl-Pod-Perldoc-3.28.01-490.fc37.noarch publicsuffix-list-dafsa-20210518-5.fc37.noarch perl-Text-Tabs+Wrap-2021.0814-489.fc37.noarch libssh-config-0.9.6-5.fc37.noarch perl-Encode-3.19-492.fc38.i686 libpkgconf-1.8.0-3.fc37.i686 libstdc++-12.1.1-4.fc38.i686 rpm-libs-4.18.0-0.beta1.4.fc37.i686 glibc-gconv-extra-2.36-1.fc37.i686 file-libs-5.42-4.fc37.i686 elfutils-libs-0.187-6.fc37.i686 libgomp-12.1.1-4.fc38.i686 pkgconf-1.8.0-3.fc37.i686 xz-5.2.5-10.fc37.i686 glibc-minimal-langpack-2.36-1.fc37.i686 Start: buildsrpm Start: rpmbuild -bs Building target platforms: i686 Building for target i686 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-i686-1660573318.635731/root/var/log/dnf.rpm.log /var/lib/mock/fedora-rawhide-i686-1660573318.635731/root/var/log/dnf.librepo.log /var/lib/mock/fedora-rawhide-i686-1660573318.635731/root/var/log/dnf.log Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-5cf8o246/samtools/samtools.spec) Config(child) 0 minutes 49 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 1660573318.635731 -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-i686) Start: clean chroot Finish: clean chroot Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-i686-1660573318.635731/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 147 kB/s | 3.3 kB 00:00 local 170 kB/s | 3.8 kB 00:00 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: i686 Building for target i686 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 106 kB/s | 3.3 kB 00:00 local 146 kB/s | 3.8 kB 00:00 Package make-1:4.3-11.fc37.i686 is already installed. Package perl-Getopt-Long-1:2.52-489.fc37.noarch is already installed. Package perl-interpreter-4:5.36.0-491.fc37.i686 is already installed. Dependencies resolved. ================================================================================ Package Arch Version Repository Size ================================================================================ Installing: gcc i686 12.1.1-4.fc38 local 33 M htslib-devel i686 1.15.1-1.fc38 copr_base 100 k htslib-tools i686 1.15.1-1.fc38 copr_base 578 k ncurses-devel i686 6.3-3.20220501.fc37 local 520 k perl-FindBin noarch 1.53-491.fc37 local 18 k perl-lib i686 0.65-491.fc37 local 19 k zlib-devel i686 1.2.12-4.fc37 local 44 k Installing dependencies: annobin-docs noarch 10.81-1.fc38 local 91 k annobin-plugin-gcc i686 10.81-1.fc38 local 883 k cpp i686 12.1.1-4.fc38 local 11 M gcc-plugin-annobin i686 12.1.1-4.fc38 local 51 k glibc-devel i686 2.36-1.fc37 local 92 k glibc-headers-x86 noarch 2.36-1.fc37 local 499 k htslib i686 1.15.1-1.fc38 copr_base 528 k kernel-headers i686 6.0.0-0.rc1.git0.1.fc38 local 1.4 M libasan i686 12.1.1-4.fc38 local 463 k libatomic i686 12.1.1-4.fc38 local 38 k libmpc i686 1.2.1-5.fc37 local 65 k libubsan i686 12.1.1-4.fc38 local 218 k libxcrypt-devel i686 4.4.28-3.fc38 local 28 k ncurses-c++-libs i686 6.3-3.20220501.fc37 local 39 k Transaction Summary ================================================================================ Install 21 Packages Total download size: 49 M Installed size: 136 M Downloading Packages: (1/21): htslib-devel-1.15.1-1.fc38.i686.rpm 2.5 MB/s | 100 kB 00:00 (2/21): htslib-tools-1.15.1-1.fc38.i686.rpm 13 MB/s | 578 kB 00:00 (3/21): htslib-1.15.1-1.fc38.i686.rpm 9.5 MB/s | 528 kB 00:00 (4/21): annobin-docs-10.81-1.fc38.noarch.rpm 1.8 MB/s | 91 kB 00:00 (5/21): annobin-plugin-gcc-10.81-1.fc38.i686.rp 10 MB/s | 883 kB 00:00 (6/21): gcc-plugin-annobin-12.1.1-4.fc38.i686.r 4.9 MB/s | 51 kB 00:00 (7/21): glibc-devel-2.36-1.fc37.i686.rpm 1.6 MB/s | 92 kB 00:00 (8/21): glibc-headers-x86-2.36-1.fc37.noarch.rp 15 MB/s | 499 kB 00:00 (9/21): kernel-headers-6.0.0-0.rc1.git0.1.fc38. 20 MB/s | 1.4 MB 00:00 (10/21): libasan-12.1.1-4.fc38.i686.rpm 14 MB/s | 463 kB 00:00 (11/21): libatomic-12.1.1-4.fc38.i686.rpm 2.4 MB/s | 38 kB 00:00 (12/21): libmpc-1.2.1-5.fc37.i686.rpm 3.9 MB/s | 65 kB 00:00 (13/21): libubsan-12.1.1-4.fc38.i686.rpm 8.9 MB/s | 218 kB 00:00 (14/21): cpp-12.1.1-4.fc38.i686.rpm 27 MB/s | 11 MB 00:00 (15/21): libxcrypt-devel-4.4.28-3.fc38.i686.rpm 517 kB/s | 28 kB 00:00 (16/21): ncurses-c++-libs-6.3-3.20220501.fc37.i 4.5 MB/s | 39 kB 00:00 (17/21): perl-FindBin-1.53-491.fc37.noarch.rpm 2.6 MB/s | 18 kB 00:00 (18/21): perl-lib-0.65-491.fc37.i686.rpm 1.5 MB/s | 19 kB 00:00 (19/21): ncurses-devel-6.3-3.20220501.fc37.i686 13 MB/s | 520 kB 00:00 (20/21): zlib-devel-1.2.12-4.fc37.i686.rpm 3.0 MB/s | 44 kB 00:00 (21/21): gcc-12.1.1-4.fc38.i686.rpm 20 MB/s | 33 MB 00:01 -------------------------------------------------------------------------------- Total 28 MB/s | 49 MB 00:01 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Installing : libmpc-1.2.1-5.fc37.i686 1/21 Installing : htslib-1.15.1-1.fc38.i686 2/21 Installing : kernel-headers-6.0.0-0.rc1.git0.1.fc38.i686 3/21 Installing : glibc-headers-x86-2.36-1.fc37.noarch 4/21 Installing : libxcrypt-devel-4.4.28-3.fc38.i686 5/21 Installing : glibc-devel-2.36-1.fc37.i686 6/21 Installing : annobin-docs-10.81-1.fc38.noarch 7/21 Installing : cpp-12.1.1-4.fc38.i686 8/21 Installing : ncurses-c++-libs-6.3-3.20220501.fc37.i686 9/21 Installing : libubsan-12.1.1-4.fc38.i686 10/21 Installing : libatomic-12.1.1-4.fc38.i686 11/21 Installing : libasan-12.1.1-4.fc38.i686 12/21 Installing : ncurses-devel-6.3-3.20220501.fc37.i686 13/21 Installing : htslib-devel-1.15.1-1.fc38.i686 14/21 Installing : zlib-devel-1.2.12-4.fc37.i686 15/21 Installing : perl-lib-0.65-491.fc37.i686 16/21 Installing : perl-FindBin-1.53-491.fc37.noarch 17/21 Installing : gcc-12.1.1-4.fc38.i686 18/21 Running scriptlet: gcc-12.1.1-4.fc38.i686 18/21 Installing : annobin-plugin-gcc-10.81-1.fc38.i686 19/21 Running scriptlet: annobin-plugin-gcc-10.81-1.fc38.i686 19/21 Installing : gcc-plugin-annobin-12.1.1-4.fc38.i686 20/21 Installing : htslib-tools-1.15.1-1.fc38.i686 21/21 Running scriptlet: htslib-tools-1.15.1-1.fc38.i686 21/21 Verifying : htslib-1.15.1-1.fc38.i686 1/21 Verifying : htslib-devel-1.15.1-1.fc38.i686 2/21 Verifying : htslib-tools-1.15.1-1.fc38.i686 3/21 Verifying : annobin-docs-10.81-1.fc38.noarch 4/21 Verifying : annobin-plugin-gcc-10.81-1.fc38.i686 5/21 Verifying : cpp-12.1.1-4.fc38.i686 6/21 Verifying : gcc-12.1.1-4.fc38.i686 7/21 Verifying : gcc-plugin-annobin-12.1.1-4.fc38.i686 8/21 Verifying : glibc-devel-2.36-1.fc37.i686 9/21 Verifying : glibc-headers-x86-2.36-1.fc37.noarch 10/21 Verifying : kernel-headers-6.0.0-0.rc1.git0.1.fc38.i686 11/21 Verifying : libasan-12.1.1-4.fc38.i686 12/21 Verifying : libatomic-12.1.1-4.fc38.i686 13/21 Verifying : libmpc-1.2.1-5.fc37.i686 14/21 Verifying : libubsan-12.1.1-4.fc38.i686 15/21 Verifying : libxcrypt-devel-4.4.28-3.fc38.i686 16/21 Verifying : ncurses-c++-libs-6.3-3.20220501.fc37.i686 17/21 Verifying : ncurses-devel-6.3-3.20220501.fc37.i686 18/21 Verifying : perl-FindBin-1.53-491.fc37.noarch 19/21 Verifying : perl-lib-0.65-491.fc37.i686 20/21 Verifying : zlib-devel-1.2.12-4.fc37.i686 21/21 Installed products updated. Installed: annobin-docs-10.81-1.fc38.noarch annobin-plugin-gcc-10.81-1.fc38.i686 cpp-12.1.1-4.fc38.i686 gcc-12.1.1-4.fc38.i686 gcc-plugin-annobin-12.1.1-4.fc38.i686 glibc-devel-2.36-1.fc37.i686 glibc-headers-x86-2.36-1.fc37.noarch htslib-1.15.1-1.fc38.i686 htslib-devel-1.15.1-1.fc38.i686 htslib-tools-1.15.1-1.fc38.i686 kernel-headers-6.0.0-0.rc1.git0.1.fc38.i686 libasan-12.1.1-4.fc38.i686 libatomic-12.1.1-4.fc38.i686 libmpc-1.2.1-5.fc37.i686 libubsan-12.1.1-4.fc38.i686 libxcrypt-devel-4.4.28-3.fc38.i686 ncurses-c++-libs-6.3-3.20220501.fc37.i686 ncurses-devel-6.3-3.20220501.fc37.i686 perl-FindBin-1.53-491.fc37.noarch perl-lib-0.65-491.fc37.i686 zlib-devel-1.2.12-4.fc37.i686 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: i686 Building for target i686 setting SOURCE_DATE_EPOCH=1660521600 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.CC9uiJ + 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.BZRIFu + 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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/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.i386.ld' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib: + 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 i386 + 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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/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.i386.ld' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib: + 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 14:23:03.708107922 +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=i686-redhat-linux-gnu --host=i686-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/lib --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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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.i386.ld' --prefix=/usr --with-htslib=system checking for gawk... gawk checking for i686-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... 64 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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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.i386.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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 [2147483648, 4294967294] exceeds maximum object size 2147483647 [-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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -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.i386.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.i386.ld -o misc/maq2sam-long misc/maq2sam-long.o -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.i386.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.i386.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.i386.ld -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -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.i386.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.i386.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.i386.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.i386.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.i386.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.i386.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.i386.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.i386.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.i386.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.i386.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 [2147483648, 4294967294] exceeds maximum object size 2147483647 [-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.rLKLab + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386 ++ dirname /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386 + 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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/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.i386.ld' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib: + 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.i386 'INSTALL=/usr/bin/install -p' mkdir -p -m 755 /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/share/man/man1 /usr/bin/install -p samtools /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/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.i386/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.i386/usr/bin /usr/bin/install -p -m 644 doc/samtools*.1 misc/wgsim.1 /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/share/man/man1 ++ grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin/ace2sam /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin/blast2sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin/bowtie2sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin/export2sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin/fasta-sanitize.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin/interpolate_sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin/maq2sam-long /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin/maq2sam-short /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin/md5fa /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin/md5sum-lite /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin/novo2sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin/plot-ampliconstats /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin/plot-bamstats /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin/psl2sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin/sam2vcf.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin/samtools /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin/samtools.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin/seq_cache_populate.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin/soap2sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin/wgsim /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin/wgsim_eval.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin/zoom2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin/blast2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin/bowtie2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin/export2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin/fasta-sanitize.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin/interpolate_sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin/novo2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin/plot-ampliconstats + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin/plot-bamstats + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin/psl2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin/sam2vcf.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin/samtools.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin/seq_cache_populate.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin/soap2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin/wgsim_eval.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/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.i386 --unique-debug-src-base samtools-1.15.1-1.fc38.i386 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/samtools-1.15.1 extracting debug info from /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin/ace2sam extracting debug info from /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin/maq2sam-long extracting debug info from /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin/maq2sam-short extracting debug info from /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin/md5fa extracting debug info from /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin/samtools extracting debug info from /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin/md5sum-lite extracting debug info from /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/bin/wgsim original debug info size: 1844kB, size after compression: 1656kB /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.OmlKAM + 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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/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.i386.ld' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib: + 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 i386 + cd samtools-1.15.1 + grep -E '/lib(64)?/libhts\.so\.' + ldd samtools libhts.so.3 => /lib/libhts.so.3 (0xf7d84000) + 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/T1bk_ezKPY/bgzip.dat.gz .. ok bgzip -c -b 979200 -s 6 /tmp/T1bk_ezKPY/bgzip.dat.gz .. ok bgzip -c -b 652804 -s 6 /tmp/T1bk_ezKPY/bgzip.dat.gz .. ok /builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/T1bk_ezKPY/faidx.fa 3:11-13 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/T1bk_ezKPY/faidx.fa.gz 3:11-13 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/T1bk_ezKPY/faidx.fa 2:998-1003 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/T1bk_ezKPY/faidx.fa.gz 2:998-1003 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/T1bk_ezKPY/faidx.fa 1:100-104 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/T1bk_ezKPY/faidx.fa.gz 1:100-104 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/T1bk_ezKPY/faidx.fa 1:99998-100007 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/T1bk_ezKPY/faidx.fa.gz 1:99998-100007 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/T1bk_ezKPY/fqidx.fq 3:11-13 .. ok .. ok /builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/T1bk_ezKPY/fqidx.fq.gz 3:11-13 .. ok .. ok /builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/T1bk_ezKPY/fqidx.fq 2:998-1003 .. ok .. ok /builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/T1bk_ezKPY/fqidx.fq.gz 2:998-1003 .. ok .. ok /builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/T1bk_ezKPY/fqidx.fq 1:100-104 .. ok .. ok /builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/T1bk_ezKPY/fqidx.fq.gz 1:100-104 .. ok .. ok /builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/T1bk_ezKPY/fqidx.fq 1:99998-100007 .. ok .. ok /builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/T1bk_ezKPY/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/T1bk_ezKPY/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/T1bk_ezKPY/large_chrom.bam ref2 .. ok test_index: /builddir/build/BUILD/samtools-1.15.1/samtools view /tmp/T1bk_ezKPY/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/T1bk_ezKPY/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/T1bk_ezKPY/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/T1bk_ezKPY/auto_indexed.csi && cat /tmp/T1bk_ezKPY/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/T1bk_ezKPY/auto_indexed.crai && cat /tmp/T1bk_ezKPY/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/T1bk_ezKPY/auto_indexed.csi && cat /tmp/T1bk_ezKPY/auto_indexed.csi .. ok test_index: /builddir/build/BUILD/samtools-1.15.1/samtools view -@ 2 /tmp/T1bk_ezKPY/large_chrom.bam ref2 .. ok test_index: /builddir/build/BUILD/samtools-1.15.1/samtools view -@ 2 /tmp/T1bk_ezKPY/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/T1bk_ezKPY/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/T1bk_ezKPY/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/T1bk_ezKPY/auto_indexed.csi && cat /tmp/T1bk_ezKPY/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/T1bk_ezKPY/auto_indexed.crai && cat /tmp/T1bk_ezKPY/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/T1bk_ezKPY/auto_indexed.csi && cat /tmp/T1bk_ezKPY/auto_indexed.csi .. ok test_mpileup: /builddir/build/BUILD/samtools-1.15.1/samtools mpileup -b /tmp/T1bk_ezKPY/mpileup.bam.list -f /tmp/T1bk_ezKPY/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /builddir/build/BUILD/samtools-1.15.1/samtools mpileup -b /tmp/T1bk_ezKPY/mpileup.cram.list -f /tmp/T1bk_ezKPY/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /builddir/build/BUILD/samtools-1.15.1/samtools mpileup -b /tmp/T1bk_ezKPY/mpileup.bam.urllist -f /tmp/T1bk_ezKPY/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /builddir/build/BUILD/samtools-1.15.1/samtools mpileup -b /tmp/T1bk_ezKPY/mpileup.cram.urllist -f /tmp/T1bk_ezKPY/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /builddir/build/BUILD/samtools-1.15.1/samtools mpileup -B --ff 0x14 -f /tmp/T1bk_ezKPY/mpileup.ref.fa.gz -r17:1050-1060 /tmp/T1bk_ezKPY/mpileup.1.bam | grep -v mpileup .. ok test_mpileup: /builddir/build/BUILD/samtools-1.15.1/samtools mpileup -B --ff 0x14 -f /tmp/T1bk_ezKPY/mpileup.ref.fa.gz -r17:1050-1060 /tmp/T1bk_ezKPY/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/T1bk_ezKPY/view.001.fogn (SAM input) .. ok 50: Count -R /tmp/T1bk_ezKPY/view.001.fogn (SAM input) .. ok 51: Filter -R /tmp/T1bk_ezKPY/view.001.fogn (BAM input) .. ok 52: Count -R /tmp/T1bk_ezKPY/view.001.fogn (BAM input) .. ok 53: Filter -R /tmp/T1bk_ezKPY/view.001.fogn (CRAM input) .. ok 54: Count -R /tmp/T1bk_ezKPY/view.001.fogn (CRAM input) .. ok 55: Filter -R /tmp/T1bk_ezKPY/view.001.fogn -r grp2 (SAM input).. ok 56: Count -R /tmp/T1bk_ezKPY/view.001.fogn -r grp2 (SAM input).. ok 57: Filter -R /tmp/T1bk_ezKPY/view.001.fogn -r grp2 (BAM input).. ok 58: Count -R /tmp/T1bk_ezKPY/view.001.fogn -r grp2 (BAM input).. ok 59: Filter -R /tmp/T1bk_ezKPY/view.001.fogn -r grp2 (CRAM input).. ok 60: Count -R /tmp/T1bk_ezKPY/view.001.fogn -r grp2 (CRAM input).. ok 61: Filter -r grp2 -R /tmp/T1bk_ezKPY/view.001.fogn (SAM input).. ok 62: Count -r grp2 -R /tmp/T1bk_ezKPY/view.001.fogn (SAM input).. ok 63: Filter -r grp2 -R /tmp/T1bk_ezKPY/view.001.fogn (BAM input).. ok 64: Count -r grp2 -R /tmp/T1bk_ezKPY/view.001.fogn (BAM input).. ok 65: Filter -r grp2 -R /tmp/T1bk_ezKPY/view.001.fogn (CRAM input).. ok 66: Count -r grp2 -R /tmp/T1bk_ezKPY/view.001.fogn (CRAM input).. ok 67: Filter -N /tmp/T1bk_ezKPY/view.001.forn (SAM input) .. ok 68: Count -N /tmp/T1bk_ezKPY/view.001.forn (SAM input) .. ok 69: Filter -N /tmp/T1bk_ezKPY/view.001.forn (BAM input) .. ok 70: Count -N /tmp/T1bk_ezKPY/view.001.forn (BAM input) .. ok 71: Filter -N /tmp/T1bk_ezKPY/view.001.forn (CRAM input) .. ok 72: Count -N /tmp/T1bk_ezKPY/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/T1bk_ezKPY/view.001.fobc (SAM input) .. ok 86: Count -D BC:/tmp/T1bk_ezKPY/view.001.fobc (SAM input) .. ok 87: Filter -D BC:/tmp/T1bk_ezKPY/view.001.fobc (BAM input) .. ok 88: Count -D BC:/tmp/T1bk_ezKPY/view.001.fobc (BAM input) .. ok 89: Filter -D BC:/tmp/T1bk_ezKPY/view.001.fobc (CRAM input) .. ok 90: Count -D BC:/tmp/T1bk_ezKPY/view.001.fobc (CRAM input) .. ok 91: Filter -D BC:/tmp/T1bk_ezKPY/view.001.fobc -d BC:TGCA (SAM input).. ok 92: Count -D BC:/tmp/T1bk_ezKPY/view.001.fobc -d BC:TGCA (SAM input).. ok 93: Filter -D BC:/tmp/T1bk_ezKPY/view.001.fobc -d BC:TGCA (BAM input).. ok 94: Count -D BC:/tmp/T1bk_ezKPY/view.001.fobc -d BC:TGCA (BAM input).. ok 95: Filter -D BC:/tmp/T1bk_ezKPY/view.001.fobc -d BC:TGCA (CRAM input).. ok 96: Count -D BC:/tmp/T1bk_ezKPY/view.001.fobc -d BC:TGCA (CRAM input).. ok 97: Filter -d BC:TGCA -D BC:/tmp/T1bk_ezKPY/view.001.fobc (SAM input).. ok 98: Count -d BC:TGCA -D BC:/tmp/T1bk_ezKPY/view.001.fobc (SAM input).. ok 99: Filter -d BC:TGCA -D BC:/tmp/T1bk_ezKPY/view.001.fobc (BAM input).. ok 100: Count -d BC:TGCA -D BC:/tmp/T1bk_ezKPY/view.001.fobc (BAM input).. ok 101: Filter -d BC:TGCA -D BC:/tmp/T1bk_ezKPY/view.001.fobc (CRAM input).. ok 102: Count -d BC:TGCA -D BC:/tmp/T1bk_ezKPY/view.001.fobc (CRAM input).. ok 103: Filter -D RG:/tmp/T1bk_ezKPY/view.001.fogn (SAM input) .. ok 104: Count -D RG:/tmp/T1bk_ezKPY/view.001.fogn (SAM input) .. ok 105: Filter -D RG:/tmp/T1bk_ezKPY/view.001.fogn (BAM input) .. ok 106: Count -D RG:/tmp/T1bk_ezKPY/view.001.fogn (BAM input) .. ok 107: Filter -D RG:/tmp/T1bk_ezKPY/view.001.fogn (CRAM input).. ok 108: Count -D RG:/tmp/T1bk_ezKPY/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/T1bk_ezKPY/view.test115.sam -h -d TGCA /tmp/T1bk_ezKPY/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/T1bk_ezKPY/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/T1bk_ezKPY/view.test117.sam -h -d TGCA /tmp/T1bk_ezKPY/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/T1bk_ezKPY/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/T1bk_ezKPY/view.test119.sam -h -d TGCA /tmp/T1bk_ezKPY/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/T1bk_ezKPY/view.test006.cram --no-PG .. expected failure 121: Filter -D BClong:/tmp/T1bk_ezKPY/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/T1bk_ezKPY/view.001.fobc" Failed command: /builddir/build/BUILD/samtools-1.15.1/samtools view -o /tmp/T1bk_ezKPY/view.test121.sam -h -D BClong:/tmp/T1bk_ezKPY/view.001.fobc /tmp/T1bk_ezKPY/view.001.sam --no-PG .. expected failure 122: Count -D BClong:/tmp/T1bk_ezKPY/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/T1bk_ezKPY/view.001.fobc" Failed command: /builddir/build/BUILD/samtools-1.15.1/samtools view -c -D BClong:/tmp/T1bk_ezKPY/view.001.fobc /tmp/T1bk_ezKPY/view.001.sam --no-PG .. expected failure 123: Filter -D BClong:/tmp/T1bk_ezKPY/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/T1bk_ezKPY/view.001.fobc" Failed command: /builddir/build/BUILD/samtools-1.15.1/samtools view -o /tmp/T1bk_ezKPY/view.test123.sam -h -D BClong:/tmp/T1bk_ezKPY/view.001.fobc /tmp/T1bk_ezKPY/view.test001.bam --no-PG .. expected failure 124: Count -D BClong:/tmp/T1bk_ezKPY/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/T1bk_ezKPY/view.001.fobc" Failed command: /builddir/build/BUILD/samtools-1.15.1/samtools view -c -D BClong:/tmp/T1bk_ezKPY/view.001.fobc /tmp/T1bk_ezKPY/view.test001.bam --no-PG .. expected failure 125: Filter -D BClong:/tmp/T1bk_ezKPY/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/T1bk_ezKPY/view.001.fobc" Failed command: /builddir/build/BUILD/samtools-1.15.1/samtools view -o /tmp/T1bk_ezKPY/view.test125.sam -h -D BClong:/tmp/T1bk_ezKPY/view.001.fobc /tmp/T1bk_ezKPY/view.test006.cram --no-PG .. expected failure 126: Count -D BClong:/tmp/T1bk_ezKPY/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/T1bk_ezKPY/view.001.fobc" Failed command: /builddir/build/BUILD/samtools-1.15.1/samtools view -c -D BClong:/tmp/T1bk_ezKPY/view.001.fobc /tmp/T1bk_ezKPY/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/T1bk_ezKPY/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/T1bk_ezKPY/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/T1bk_ezKPY/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/T1bk_ezKPY/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/T1bk_ezKPY/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/T1bk_ezKPY/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/T1bk_ezKPY/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/T1bk_ezKPY/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/T1bk_ezKPY/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/T1bk_ezKPY/bam2fq.discard.s.fq -0 /tmp/T1bk_ezKPY/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/T1bk_ezKPY/bam2fq.discard.s.fq -0 /tmp/T1bk_ezKPY/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/TwML3WLswp - /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/T1bk_ezKPY/merge.tag.1.bam /tmp/T1bk_ezKPY/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/T1bk_ezKPY/merge.tag.3.bam /tmp/T1bk_ezKPY/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/T1bk_ezKPY/merge.bed.1.bam /tmp/T1bk_ezKPY/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/zQzYKUZgoE - /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/T1bk_ezKPY/merge.tag.1.bam /tmp/T1bk_ezKPY/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/T1bk_ezKPY/merge.tag.3.bam /tmp/T1bk_ezKPY/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/T1bk_ezKPY/merge.bed.1.bam /tmp/T1bk_ezKPY/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/T1bk_ezKPY/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/T1bk_ezKPY/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/T1bk_ezKPY/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/T1bk_ezKPY/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/T1bk_ezKPY/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/T1bk_ezKPY/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/T1bk_ezKPY/longref.sam.gz .. ok test_large_positions: /builddir/build/BUILD/samtools-1.15.1/samtools view -h --no-PG /tmp/T1bk_ezKPY/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/T1bk_ezKPY/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/T1bk_ezKPY/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.i686 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.Fx8vMa + umask 022 + cd /builddir/build/BUILD + cd samtools-1.15.1 + DOCDIR=/builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/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.i386/usr/share/doc/samtools + cp -pr AUTHORS /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/share/doc/samtools + cp -pr ChangeLog.old /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/share/doc/samtools + cp -pr NEWS /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/share/doc/samtools + cp -pr examples/ /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/share/doc/samtools + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.nksHG1 + umask 022 + cd /builddir/build/BUILD + cd samtools-1.15.1 + LICENSEDIR=/builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/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.i386/usr/share/licenses/samtools + cp -pr LICENSE /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386/usr/share/licenses/samtools + RPM_EC=0 ++ jobs -p + exit 0 Provides: samtools = 1.15.1-1.fc38 samtools(x86-32) = 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 libc.so.6(GLIBC_2.0) libc.so.6(GLIBC_2.1) libc.so.6(GLIBC_2.1.3) libc.so.6(GLIBC_2.2) libc.so.6(GLIBC_2.3) libc.so.6(GLIBC_2.3.4) libc.so.6(GLIBC_2.33) libc.so.6(GLIBC_2.34) libc.so.6(GLIBC_2.4) libc.so.6(GLIBC_2.7) libhts.so.3 libm.so.6 libm.so.6(GLIBC_2.0) libm.so.6(GLIBC_2.1) libm.so.6(GLIBC_2.29) libncursesw.so.6 libtinfo.so.6 libz.so.1 libz.so.1(ZLIB_1.2.3.3) rtld(GNU_HASH) Processing files: samtools-debugsource-1.15.1-1.fc38.i686 Provides: samtools-debugsource = 1.15.1-1.fc38 samtools-debugsource(x86-32) = 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.i686 Provides: debuginfo(build-id) = 4d3bf1611a22c351cbba086c1078427c884c1572 debuginfo(build-id) = 62c3154c9034f1334c1292c3cfe8595690296b15 debuginfo(build-id) = 6c56fd34c6d18148d89c1b60729a758003d3dc35 debuginfo(build-id) = 7a9a69be0a2cb056e1404da655ec6d936afcae0f debuginfo(build-id) = 91059efddb7e0f07680156bed0043ff70f071724 debuginfo(build-id) = 9ab5507550c784a344d3aebe40f474fbacb20e78 debuginfo(build-id) = b7459cd30097ada1879d84210dd3bea7e19d9fa4 samtools-debuginfo = 1.15.1-1.fc38 samtools-debuginfo(x86-32) = 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(x86-32) = 1.15.1-1.fc38 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386 Wrote: /builddir/build/RPMS/samtools-1.15.1-1.fc38.i686.rpm Wrote: /builddir/build/RPMS/samtools-debuginfo-1.15.1-1.fc38.i686.rpm Wrote: /builddir/build/RPMS/samtools-debugsource-1.15.1-1.fc38.i686.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.HV1GJZ + umask 022 + cd /builddir/build/BUILD + cd samtools-1.15.1 + /usr/bin/rm -rf /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.i386 + RPM_EC=0 ++ jobs -p + exit 0 Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.oNnB8r + 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-i686-1660573318.635731/root/var/log/dnf.rpm.log /var/lib/mock/fedora-rawhide-i686-1660573318.635731/root/var/log/dnf.librepo.log /var/lib/mock/fedora-rawhide-i686-1660573318.635731/root/var/log/dnf.log INFO: Done(/var/lib/copr-rpmbuild/results/samtools-1.15.1-1.fc38.src.rpm) Config(child) 2 minutes 4 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