Warning: Permanently added '2620:52:3:1:dead:beef:cafe:c198' (ED25519) to the list of known hosts.

You can reproduce this build on your computer by running:

  sudo dnf install copr-rpmbuild
  /usr/bin/copr-rpmbuild --verbose --drop-resultdir --task-url https://copr.fedorainfracloud.org/backend/get-build-task/8070929-fedora-rawhide-x86_64 --chroot fedora-rawhide-x86_64


Version: 0.73
PID: 6803
Logging PID: 6804
Task:
{'allow_user_ssh': False,
 'appstream': False,
 'background': False,
 'build_id': 8070929,
 'buildroot_pkgs': [],
 'chroot': 'fedora-rawhide-x86_64',
 'enable_net': False,
 'fedora_review': False,
 'git_hash': '2234957ff21a1fd78b4fb0c2efdd7a750cf6ddef',
 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/ljavorsk/zlib-ng-rebase-fedora/samtools',
 'isolation': 'default',
 'memory_reqs': 2048,
 'package_name': 'samtools',
 'package_version': '1.15.1-5',
 'project_dirname': 'zlib-ng-rebase-fedora',
 'project_name': 'zlib-ng-rebase-fedora',
 'project_owner': 'ljavorsk',
 'repo_priority': None,
 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/ljavorsk/zlib-ng-rebase-fedora/fedora-rawhide-x86_64/',
            'id': 'copr_base',
            'name': 'Copr repository',
            'priority': None}],
 'sandbox': 'ljavorsk/zlib-ng-rebase-fedora--ljavorsk',
 'source_json': {},
 'source_type': None,
 'ssh_public_keys': None,
 'submitter': 'ljavorsk',
 'tags': [],
 'task_id': '8070929-fedora-rawhide-x86_64',
 'timeout': 18000,
 'uses_devel_repo': False,
 'with_opts': [],
 'without_opts': []}

Running: git clone https://copr-dist-git.fedorainfracloud.org/git/ljavorsk/zlib-ng-rebase-fedora/samtools /var/lib/copr-rpmbuild/workspace/workdir-owepyad1/samtools --depth 500 --no-single-branch --recursive

cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/ljavorsk/zlib-ng-rebase-fedora/samtools', '/var/lib/copr-rpmbuild/workspace/workdir-owepyad1/samtools', '--depth', '500', '--no-single-branch', '--recursive']
cwd: .
rc: 0
stdout: 
stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-owepyad1/samtools'...

Running: git checkout 2234957ff21a1fd78b4fb0c2efdd7a750cf6ddef --

cmd: ['git', 'checkout', '2234957ff21a1fd78b4fb0c2efdd7a750cf6ddef', '--']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-owepyad1/samtools
rc: 0
stdout: 
stderr: Note: switching to '2234957ff21a1fd78b4fb0c2efdd7a750cf6ddef'.

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 <new-branch-name>

Or undo this operation with:

  git switch -

Turn off this advice by setting config variable advice.detachedHead to false

HEAD is now at 2234957 automatic import of samtools

Running: copr-distgit-client sources
/usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated

cmd: ['copr-distgit-client', 'sources']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-owepyad1/samtools
rc: 0
stdout: 
stderr: INFO: Reading stdout from command: git rev-parse --abbrev-ref HEAD
INFO: Reading stdout from command: git rev-parse HEAD
INFO: Reading sources specification file: sources
INFO: Downloading samtools-1.15.1.tar.bz2
INFO: Reading stdout from command: curl --help all
INFO: Calling: curl -H Pragma: -o samtools-1.15.1.tar.bz2 --location --connect-timeout 60 --retry 3 --retry-delay 10 --remote-time --show-error --fail --retry-all-errors https://copr-dist-git.fedorainfracloud.org/repo/pkgs/ljavorsk/zlib-ng-rebase-fedora/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  22.4M      0 --:--:-- --:--:-- --:--:-- 22.5M
INFO: Reading stdout from command: md5sum samtools-1.15.1.tar.bz2

Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-owepyad1/samtools/samtools.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-owepyad1/samtools --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1727357827.031697 -r /var/lib/copr-rpmbuild/results/configs/child.cfg
INFO: mock.py version 5.6 starting (python version = 3.12.1, NVR = mock-5.6-1.fc39), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-owepyad1/samtools/samtools.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-owepyad1/samtools --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1727357827.031697 -r /var/lib/copr-rpmbuild/results/configs/child.cfg
Start(bootstrap): init plugins
INFO: tmpfs initialized
INFO: selinux enabled
INFO: chroot_scan: initialized
INFO: compress_logs: initialized
Finish(bootstrap): init plugins
Start: init plugins
INFO: tmpfs initialized
INFO: selinux enabled
INFO: chroot_scan: initialized
INFO: compress_logs: initialized
Finish: init plugins
INFO: Signal handler active
Start: run
INFO: Start(/var/lib/copr-rpmbuild/workspace/workdir-owepyad1/samtools/samtools.spec)  Config(fedora-rawhide-x86_64)
Start: clean chroot
Finish: clean chroot
Mock Version: 5.6
INFO: Mock Version: 5.6
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1727357827.031697/root.
INFO: calling preinit hooks
INFO: enabled root cache
INFO: enabled package manager cache
Start(bootstrap): cleaning package manager metadata
Finish(bootstrap): cleaning package manager metadata
INFO: Guessed host environment type: unknown
INFO: Using bootstrap image: registry.fedoraproject.org/fedora:rawhide
INFO: Pulling image: registry.fedoraproject.org/fedora:rawhide
INFO: Copy content of container registry.fedoraproject.org/fedora:rawhide to /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1727357827.031697/root
INFO: Checking that registry.fedoraproject.org/fedora:rawhide image matches host's architecture
INFO: mounting registry.fedoraproject.org/fedora:rawhide with podman image mount
INFO: image registry.fedoraproject.org/fedora:rawhide as /var/lib/containers/storage/overlay/05740a7305e959e54c4a8211936ece174c79e084adc69e0871f429f98696b9b3/merged
INFO: umounting image registry.fedoraproject.org/fedora:rawhide (/var/lib/containers/storage/overlay/05740a7305e959e54c4a8211936ece174c79e084adc69e0871f429f98696b9b3/merged) with podman image umount
INFO: Package manager dnf5 detected and used (fallback)
INFO: Not updating bootstrap chroot, bootstrap_image_ready=True
Start(bootstrap): creating root cache
Finish(bootstrap): creating root cache
Finish(bootstrap): chroot init
Start: chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-1727357827.031697/root.
INFO: calling preinit hooks
INFO: enabled root cache
INFO: enabled package manager cache
Start: cleaning package manager metadata
Finish: cleaning package manager metadata
INFO: enabled HW Info plugin
INFO: Package manager dnf5 detected and used (direct choice)
INFO: Buildroot is handled by package management downloaded with a bootstrap image:
  rpm-4.19.94-1.fc42.x86_64
  rpm-sequoia-1.7.0-2.fc41.x86_64
  dnf5-5.2.6.2-1.fc42.x86_64
  dnf5-plugins-5.2.6.2-1.fc42.x86_64
Start: installing minimal buildroot with dnf5
Updating and loading repositories:
 fedora                                 100% |  21.1 MiB/s |  21.8 MiB |  00m01s
 Copr repository                        100% |  20.6 MiB/s |   2.9 MiB |  00m00s
Repositories loaded.
Package                            Arch   Version                    Repository      Size
Installing group/module packages:
 bash                              x86_64 5.2.32-2.fc42              fedora       8.2 MiB
 bzip2                             x86_64 1.0.8-19.fc41              fedora      95.7 KiB
 coreutils                         x86_64 9.5-9.fc42                 fedora       5.7 MiB
 cpio                              x86_64 2.15-2.fc41                fedora       1.1 MiB
 diffutils                         x86_64 3.10-8.fc41                fedora       1.6 MiB
 fedora-release-common             noarch 42-0.3                     fedora      19.4 KiB
 findutils                         x86_64 1:4.10.0-4.fc41            fedora       1.8 MiB
 gawk                              x86_64 5.3.0-4.fc41               fedora       1.7 MiB
 glibc-minimal-langpack            x86_64 2.40.9000-5.fc42           copr_base    0.0   B
 grep                              x86_64 3.11-9.fc41                fedora       1.0 MiB
 gzip                              x86_64 1.13-2.fc41                fedora     389.0 KiB
 info                              x86_64 7.1.1-1.fc42               fedora     361.9 KiB
 patch                             x86_64 2.7.6-25.fc41              fedora     266.7 KiB
 redhat-rpm-config                 noarch 295-1.fc42                 fedora     186.6 KiB
 rpm-build                         x86_64 4.19.94-1.fc42             copr_base  194.2 KiB
 sed                               x86_64 4.9-3.fc41                 fedora     861.5 KiB
 shadow-utils                      x86_64 2:4.16.0-4.fc42            fedora       4.1 MiB
 tar                               x86_64 2:1.35-4.fc41              fedora       2.9 MiB
 unzip                             x86_64 6.0-64.fc41                fedora     386.8 KiB
 util-linux                        x86_64 2.40.2-8.fc42              fedora       3.7 MiB
 which                             x86_64 2.21-42.fc41               fedora      80.2 KiB
 xz                                x86_64 1:5.6.2-2.fc41             fedora       1.2 MiB
Installing dependencies:
 add-determinism                   x86_64 0.3.6-1.fc41               fedora       2.2 MiB
 alternatives                      x86_64 1.30-1.fc41                fedora      66.3 KiB
 ansible-srpm-macros               noarch 1-16.fc41                  fedora      35.7 KiB
 audit-libs                        x86_64 4.0.2-1.fc41               fedora     331.3 KiB
 authselect                        x86_64 1.5.0-7.fc41               fedora     153.5 KiB
 authselect-libs                   x86_64 1.5.0-7.fc41               fedora     818.3 KiB
 basesystem                        noarch 11-21.fc41                 fedora       0.0   B
 binutils                          x86_64 2.43.50-1.fc42             copr_base   27.5 MiB
 build-reproducibility-srpm-macros noarch 0.3.6-1.fc41               fedora     735.0   B
 bzip2-libs                        x86_64 1.0.8-19.fc41              fedora      80.7 KiB
 ca-certificates                   noarch 2024.2.69_v8.0.401-1.fc42  fedora       2.6 MiB
 coreutils-common                  x86_64 9.5-9.fc42                 fedora      11.2 MiB
 cracklib                          x86_64 2.9.11-6.fc42              copr_base  242.9 KiB
 crypto-policies                   noarch 20240828-1.git5f66e81.fc42 fedora     136.9 KiB
 curl                              x86_64 8.10.1-2.fc42              copr_base  453.3 KiB
 cyrus-sasl-lib                    x86_64 2.1.28-27.fc41             fedora       2.3 MiB
 debugedit                         x86_64 5.0-17.fc41                fedora     199.3 KiB
 dwz                               x86_64 0.15-7.fc41                fedora     290.9 KiB
 ed                                x86_64 1.20.2-2.fc41              fedora     146.9 KiB
 efi-srpm-macros                   noarch 5-12.fc41                  fedora      40.1 KiB
 elfutils                          x86_64 0.191-8.fc42               copr_base    2.6 MiB
 elfutils-debuginfod-client        x86_64 0.191-8.fc42               copr_base   64.9 KiB
 elfutils-default-yama-scope       noarch 0.191-8.fc42               copr_base    1.8 KiB
 elfutils-libelf                   x86_64 0.191-8.fc42               copr_base    1.2 MiB
 elfutils-libs                     x86_64 0.191-8.fc42               copr_base  655.0 KiB
 fedora-gpg-keys                   noarch 42-0.2                     fedora     126.4 KiB
 fedora-release                    noarch 42-0.3                     fedora       0.0   B
 fedora-release-identity-basic     noarch 42-0.3                     fedora     694.0   B
 fedora-repos                      noarch 42-0.2                     fedora       4.9 KiB
 fedora-repos-rawhide              noarch 42-0.2                     fedora       2.2 KiB
 file                              x86_64 5.45-7.fc42                copr_base  103.5 KiB
 file-libs                         x86_64 5.45-7.fc42                copr_base    9.9 MiB
 filesystem                        x86_64 3.18-29.fc42               fedora     106.0   B
 fonts-srpm-macros                 noarch 1:2.0.5-17.fc41            fedora      55.8 KiB
 forge-srpm-macros                 noarch 0.3.2-1.fc41               fedora      39.0 KiB
 fpc-srpm-macros                   noarch 1.3-13.fc41                fedora     144.0   B
 gdb-minimal                       x86_64 15.1-2.fc42                copr_base   13.0 MiB
 gdbm                              x86_64 1:1.23-7.fc41              fedora     460.9 KiB
 gdbm-libs                         x86_64 1:1.23-7.fc41              fedora     121.9 KiB
 ghc-srpm-macros                   noarch 1.9.2-1.fc42               fedora     779.0   B
 glibc                             x86_64 2.40.9000-5.fc42           copr_base    6.7 MiB
 glibc-common                      x86_64 2.40.9000-5.fc42           copr_base    1.0 MiB
 glibc-gconv-extra                 x86_64 2.40.9000-5.fc42           copr_base    8.1 MiB
 gmp                               x86_64 1:6.3.0-2.fc41             fedora     811.4 KiB
 gnat-srpm-macros                  noarch 6-6.fc41                   fedora       1.0 KiB
 go-srpm-macros                    noarch 3.6.0-3.fc41               fedora      60.8 KiB
 jansson                           x86_64 2.13.1-10.fc41             fedora      88.3 KiB
 kernel-srpm-macros                noarch 1.0-24.fc41                fedora       1.9 KiB
 keyutils-libs                     x86_64 1.6.3-4.fc41               fedora      54.4 KiB
 krb5-libs                         x86_64 1.21.3-2.fc41              fedora       2.3 MiB
 libacl                            x86_64 2.3.2-2.fc41               fedora      40.0 KiB
 libarchive                        x86_64 3.7.6-1.fc42               copr_base  934.8 KiB
 libattr                           x86_64 2.5.2-4.fc41               fedora      28.5 KiB
 libblkid                          x86_64 2.40.2-8.fc42              fedora     262.5 KiB
 libbrotli                         x86_64 1.1.0-5.fc41               fedora     837.6 KiB
 libcap                            x86_64 2.70-4.fc41                fedora     220.2 KiB
 libcap-ng                         x86_64 0.8.5-3.fc41               fedora      69.2 KiB
 libcom_err                        x86_64 1.47.1-3.fc41              fedora      67.2 KiB
 libcurl                           x86_64 8.10.1-2.fc42              copr_base  838.4 KiB
 libeconf                          x86_64 0.6.2-3.fc41               fedora      58.0 KiB
 libevent                          x86_64 2.1.12-14.fc41             fedora     895.7 KiB
 libfdisk                          x86_64 2.40.2-8.fc42              fedora     362.9 KiB
 libffi                            x86_64 3.4.6-3.fc42               fedora      86.4 KiB
 libgcc                            x86_64 14.2.1-3.fc42              fedora     274.6 KiB
 libgomp                           x86_64 14.2.1-3.fc42              fedora     523.8 KiB
 libidn2                           x86_64 2.3.7-2.fc41               fedora     329.1 KiB
 libmount                          x86_64 2.40.2-8.fc42              fedora     355.8 KiB
 libnghttp2                        x86_64 1.63.0-1.fc42              copr_base  174.5 KiB
 libnsl2                           x86_64 2.0.1-2.fc41               fedora      57.9 KiB
 libpkgconf                        x86_64 2.3.0-1.fc42               fedora      78.2 KiB
 libpsl                            x86_64 0.21.5-4.fc41              fedora      80.5 KiB
 libpwquality                      x86_64 1.4.5-11.fc41              fedora     417.8 KiB
 libselinux                        x86_64 3.7-6.fc42                 fedora     181.1 KiB
 libsemanage                       x86_64 3.7-3.fc42                 fedora     298.0 KiB
 libsepol                          x86_64 3.7-3.fc42                 fedora     818.0 KiB
 libsmartcols                      x86_64 2.40.2-8.fc42              fedora     180.4 KiB
 libssh                            x86_64 0.11.1-1.fc42              copr_base  569.6 KiB
 libssh-config                     noarch 0.11.1-1.fc42              copr_base  277.0   B
 libstdc++                         x86_64 14.2.1-3.fc42              fedora       2.8 MiB
 libtasn1                          x86_64 4.19.0-9.fc41              fedora     175.7 KiB
 libtirpc                          x86_64 1.3.5-0.fc41               fedora     202.7 KiB
 libtool-ltdl                      x86_64 2.4.7-12.fc41              fedora      66.2 KiB
 libunistring                      x86_64 1.1-8.fc41                 fedora       1.7 MiB
 libuuid                           x86_64 2.40.2-8.fc42              fedora      41.4 KiB
 libverto                          x86_64 0.3.2-9.fc41               fedora      29.5 KiB
 libxcrypt                         x86_64 4.4.36-7.fc41              fedora     266.8 KiB
 libxml2                           x86_64 2.12.8-2.fc42              copr_base    1.7 MiB
 libzstd                           x86_64 1.5.6-2.fc41               fedora     795.9 KiB
 lua-libs                          x86_64 5.4.6-6.fc41               fedora     285.0 KiB
 lua-srpm-macros                   noarch 1-14.fc41                  fedora       1.3 KiB
 lz4-libs                          x86_64 1.10.0-1.fc41              fedora     145.5 KiB
 mpfr                              x86_64 4.2.1-5.fc41               fedora     832.1 KiB
 ncurses-base                      noarch 6.5-2.20240629.fc41        fedora     326.3 KiB
 ncurses-libs                      x86_64 6.5-2.20240629.fc41        fedora     975.2 KiB
 ocaml-srpm-macros                 noarch 10-3.fc41                  fedora       1.9 KiB
 openblas-srpm-macros              noarch 2-18.fc41                  fedora     112.0   B
 openldap                          x86_64 2.6.8-5.fc41               fedora     644.2 KiB
 openssl-libs                      x86_64 1:3.2.2-9.fc42             copr_base    7.8 MiB
 p11-kit                           x86_64 0.25.5-3.fc41              fedora       2.2 MiB
 p11-kit-trust                     x86_64 0.25.5-3.fc41              fedora     391.4 KiB
 package-notes-srpm-macros         noarch 0.5-12.fc41                fedora       1.6 KiB
 pam                               x86_64 1.6.1-6.fc42               fedora       1.8 MiB
 pam-libs                          x86_64 1.6.1-6.fc42               fedora     139.0 KiB
 pcre2                             x86_64 10.44-1.fc41.1             fedora     653.5 KiB
 pcre2-syntax                      noarch 10.44-1.fc41.1             fedora     251.6 KiB
 perl-srpm-macros                  noarch 1-56.fc41                  fedora     861.0   B
 pkgconf                           x86_64 2.3.0-1.fc42               fedora      88.6 KiB
 pkgconf-m4                        noarch 2.3.0-1.fc42               fedora      14.4 KiB
 pkgconf-pkg-config                x86_64 2.3.0-1.fc42               fedora     989.0   B
 popt                              x86_64 1.19-7.fc41                fedora     136.9 KiB
 publicsuffix-list-dafsa           noarch 20240107-4.fc41            fedora      67.5 KiB
 pyproject-srpm-macros             noarch 1.15.0-1.fc42              fedora       1.9 KiB
 python-srpm-macros                noarch 3.13-3.fc41                fedora      51.0 KiB
 qt5-srpm-macros                   noarch 5.15.15-1.fc42             fedora     500.0   B
 qt6-srpm-macros                   noarch 6.7.2-3.fc41               fedora     456.0   B
 readline                          x86_64 8.2-11.fc42                fedora     493.1 KiB
 rpm                               x86_64 4.19.94-1.fc42             copr_base    3.1 MiB
 rpm-build-libs                    x86_64 4.19.94-1.fc42             copr_base  206.7 KiB
 rpm-libs                          x86_64 4.19.94-1.fc42             copr_base  726.1 KiB
 rpm-sequoia                       x86_64 1.7.0-2.fc41               fedora       2.4 MiB
 rust-srpm-macros                  noarch 26.3-3.fc42                fedora       4.8 KiB
 setup                             noarch 2.15.0-5.fc41              fedora     720.7 KiB
 sqlite-libs                       x86_64 3.46.0-4.fc41              fedora       1.4 MiB
 systemd-libs                      x86_64 256.5-1.fc42               fedora       2.0 MiB
 util-linux-core                   x86_64 2.40.2-8.fc42              fedora       1.5 MiB
 xxhash-libs                       x86_64 0.8.2-3.fc41               fedora      88.5 KiB
 xz-libs                           x86_64 1:5.6.2-2.fc41             fedora     214.4 KiB
 zig-srpm-macros                   noarch 1-3.fc41                   fedora       1.1 KiB
 zip                               x86_64 3.0-41.fc41                fedora     703.2 KiB
 zlib-ng-compat                    x86_64 2.2.2-1.fc42               copr_base  137.8 KiB
 zstd                              x86_64 1.5.6-2.fc41               fedora       1.7 MiB
Installing groups:
 Buildsystem building group                                                              

Transaction Summary:
 Installing:       153 packages

Total size of inbound packages is 53 MiB. Need to download 53 MiB.
After this operation, 180 MiB extra will be used (install 180 MiB, remove 0 B).
[  1/153] bzip2-0:1.0.8-19.fc41.x86_64  100% | 272.1 KiB/s |  52.5 KiB |  00m00s
[  2/153] coreutils-0:9.5-9.fc42.x86_64 100% |   3.5 MiB/s |   1.1 MiB |  00m00s
[  3/153] cpio-0:2.15-2.fc41.x86_64     100% |   2.2 MiB/s | 291.8 KiB |  00m00s
[  4/153] bash-0:5.2.32-2.fc42.x86_64   100% |   5.4 MiB/s |   1.8 MiB |  00m00s
[  5/153] fedora-release-common-0:42-0. 100% | 434.1 KiB/s |  23.0 KiB |  00m00s
[  6/153] findutils-1:4.10.0-4.fc41.x86 100% |   9.2 MiB/s | 548.6 KiB |  00m00s
[  7/153] diffutils-0:3.10-8.fc41.x86_6 100% |   4.9 MiB/s | 405.4 KiB |  00m00s
[  8/153] grep-0:3.11-9.fc41.x86_64     100% |   5.0 MiB/s | 299.8 KiB |  00m00s
[  9/153] gzip-0:1.13-2.fc41.x86_64     100% |   3.0 MiB/s | 170.2 KiB |  00m00s
[ 10/153] info-0:7.1.1-1.fc42.x86_64    100% |   3.2 MiB/s | 182.8 KiB |  00m00s
[ 11/153] patch-0:2.7.6-25.fc41.x86_64  100% |   2.4 MiB/s | 131.0 KiB |  00m00s
[ 12/153] redhat-rpm-config-0:295-1.fc4 100% |   1.5 MiB/s |  82.4 KiB |  00m00s
[ 13/153] sed-0:4.9-3.fc41.x86_64       100% |   5.5 MiB/s | 317.7 KiB |  00m00s
[ 14/153] tar-2:1.35-4.fc41.x86_64      100% |  13.3 MiB/s | 860.7 KiB |  00m00s
[ 15/153] unzip-0:6.0-64.fc41.x86_64    100% |   3.1 MiB/s | 184.9 KiB |  00m00s
[ 16/153] shadow-utils-2:4.16.0-4.fc42. 100% |  14.3 MiB/s |   1.3 MiB |  00m00s
[ 17/153] which-0:2.21-42.fc41.x86_64   100% | 784.1 KiB/s |  41.6 KiB |  00m00s
[ 18/153] xz-1:5.6.2-2.fc41.x86_64      100% |   7.8 MiB/s | 471.5 KiB |  00m00s
[ 19/153] gawk-0:5.3.0-4.fc41.x86_64    100% |  15.1 MiB/s |   1.1 MiB |  00m00s
[ 20/153] glibc-minimal-langpack-0:2.40 100% |   2.4 MiB/s | 121.1 KiB |  00m00s
[ 21/153] rpm-build-0:4.19.94-1.fc42.x8 100% |   1.7 MiB/s |  76.0 KiB |  00m00s
[ 22/153] ncurses-libs-0:6.5-2.20240629 100% |   1.7 MiB/s | 334.0 KiB |  00m00s
[ 23/153] bzip2-libs-0:1.0.8-19.fc41.x8 100% | 775.7 KiB/s |  41.1 KiB |  00m00s
[ 24/153] filesystem-0:3.18-29.fc42.x86 100% |   3.6 MiB/s |   1.1 MiB |  00m00s
[ 25/153] util-linux-0:2.40.2-8.fc42.x8 100% |   3.4 MiB/s |   1.2 MiB |  00m00s
[ 26/153] coreutils-common-0:9.5-9.fc42 100% |  18.9 MiB/s |   2.1 MiB |  00m00s
[ 27/153] gmp-1:6.3.0-2.fc41.x86_64     100% |   5.0 MiB/s | 318.0 KiB |  00m00s
[ 28/153] libacl-0:2.3.2-2.fc41.x86_64  100% | 453.7 KiB/s |  24.5 KiB |  00m00s
[ 29/153] libattr-0:2.5.2-4.fc41.x86_64 100% | 342.9 KiB/s |  18.2 KiB |  00m00s
[ 30/153] libcap-0:2.70-4.fc41.x86_64   100% |   1.6 MiB/s |  86.7 KiB |  00m00s
[ 31/153] libselinux-0:3.7-6.fc42.x86_6 100% |   1.6 MiB/s |  88.6 KiB |  00m00s
[ 32/153] systemd-libs-0:256.5-1.fc42.x 100% |  11.1 MiB/s | 730.4 KiB |  00m00s
[ 33/153] fedora-repos-0:42-0.2.noarch  100% | 160.8 KiB/s |   9.2 KiB |  00m00s
[ 34/153] pcre2-0:10.44-1.fc41.1.x86_64 100% |   4.2 MiB/s | 243.1 KiB |  00m00s
[ 35/153] ed-0:1.20.2-2.fc41.x86_64     100% |   1.5 MiB/s |  81.8 KiB |  00m00s
[ 36/153] ansible-srpm-macros-0:1-16.fc 100% | 384.7 KiB/s |  20.8 KiB |  00m00s
[ 37/153] build-reproducibility-srpm-ma 100% | 200.1 KiB/s |  10.6 KiB |  00m00s
[ 38/153] dwz-0:0.15-7.fc41.x86_64      100% |   2.5 MiB/s | 138.0 KiB |  00m00s
[ 39/153] efi-srpm-macros-0:5-12.fc41.n 100% | 414.4 KiB/s |  22.4 KiB |  00m00s
[ 40/153] fonts-srpm-macros-1:2.0.5-17. 100% | 508.8 KiB/s |  27.0 KiB |  00m00s
[ 41/153] forge-srpm-macros-0:0.3.2-1.f 100% | 371.7 KiB/s |  19.7 KiB |  00m00s
[ 42/153] fpc-srpm-macros-0:1.3-13.fc41 100% | 150.2 KiB/s |   8.0 KiB |  00m00s
[ 43/153] ghc-srpm-macros-0:1.9.2-1.fc4 100% | 172.0 KiB/s |   9.1 KiB |  00m00s
[ 44/153] gnat-srpm-macros-0:6-6.fc41.n 100% | 168.9 KiB/s |   9.0 KiB |  00m00s
[ 45/153] go-srpm-macros-0:3.6.0-3.fc41 100% | 527.4 KiB/s |  28.0 KiB |  00m00s
[ 46/153] kernel-srpm-macros-0:1.0-24.f 100% | 186.2 KiB/s |   9.9 KiB |  00m00s
[ 47/153] lua-srpm-macros-0:1-14.fc41.n 100% | 167.5 KiB/s |   8.9 KiB |  00m00s
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[ 50/153] package-notes-srpm-macros-0:0 100% | 185.5 KiB/s |   9.8 KiB |  00m00s
[ 51/153] perl-srpm-macros-0:1-56.fc41. 100% | 160.6 KiB/s |   8.5 KiB |  00m00s
[ 52/153] pyproject-srpm-macros-0:1.15. 100% | 255.7 KiB/s |  13.5 KiB |  00m00s
[ 53/153] qt5-srpm-macros-0:5.15.15-1.f 100% | 167.9 KiB/s |   8.9 KiB |  00m00s
[ 54/153] python-srpm-macros-0:3.13-3.f 100% | 423.6 KiB/s |  23.7 KiB |  00m00s
[ 55/153] qt6-srpm-macros-0:6.7.2-3.fc4 100% | 172.2 KiB/s |   9.1 KiB |  00m00s
[ 56/153] rust-srpm-macros-0:26.3-3.fc4 100% | 228.3 KiB/s |  12.1 KiB |  00m00s
[ 57/153] zig-srpm-macros-0:1-3.fc41.no 100% | 153.3 KiB/s |   8.1 KiB |  00m00s
[ 58/153] zip-0:3.0-41.fc41.x86_64      100% |   4.6 MiB/s | 264.8 KiB |  00m00s
[ 59/153] audit-libs-0:4.0.2-1.fc41.x86 100% |   2.3 MiB/s | 126.2 KiB |  00m00s
[ 60/153] libeconf-0:0.6.2-3.fc41.x86_6 100% | 595.9 KiB/s |  32.2 KiB |  00m00s
[ 61/153] libsemanage-0:3.7-3.fc42.x86_ 100% |   2.1 MiB/s | 117.2 KiB |  00m00s
[ 62/153] libxcrypt-0:4.4.36-7.fc41.x86 100% |   2.1 MiB/s | 118.5 KiB |  00m00s
[ 63/153] pam-libs-0:1.6.1-6.fc42.x86_6 100% |   1.0 MiB/s |  57.2 KiB |  00m00s
[ 64/153] setup-0:2.15.0-5.fc41.noarch  100% |   2.7 MiB/s | 154.4 KiB |  00m00s
[ 65/153] xz-libs-1:5.6.2-2.fc41.x86_64 100% |   2.0 MiB/s | 111.8 KiB |  00m00s
[ 66/153] mpfr-0:4.2.1-5.fc41.x86_64    100% |   5.9 MiB/s | 346.3 KiB |  00m00s
[ 67/153] readline-0:8.2-11.fc42.x86_64 100% |   3.7 MiB/s | 213.4 KiB |  00m00s
[ 68/153] glibc-common-0:2.40.9000-5.fc 100% |   9.6 MiB/s | 404.9 KiB |  00m00s
[ 69/153] glibc-0:2.40.9000-5.fc42.x86_ 100% |  40.7 MiB/s |   2.2 MiB |  00m00s
[ 70/153] debugedit-0:5.0-17.fc41.x86_6 100% |   1.4 MiB/s |  80.1 KiB |  00m00s
[ 71/153] popt-0:1.19-7.fc41.x86_64     100% |   1.2 MiB/s |  65.9 KiB |  00m00s
[ 72/153] zstd-0:1.5.6-2.fc41.x86_64    100% |   8.1 MiB/s | 481.5 KiB |  00m00s
[ 73/153] libblkid-0:2.40.2-8.fc42.x86_ 100% |   2.2 MiB/s | 125.0 KiB |  00m00s
[ 74/153] libcap-ng-0:0.8.5-3.fc41.x86_ 100% | 614.4 KiB/s |  32.6 KiB |  00m00s
[ 75/153] libfdisk-0:2.40.2-8.fc42.x86_ 100% |   2.8 MiB/s | 159.6 KiB |  00m00s
[ 76/153] libmount-0:2.40.2-8.fc42.x86_ 100% |   2.8 MiB/s | 156.1 KiB |  00m00s
[ 77/153] libsmartcols-0:2.40.2-8.fc42. 100% |   1.5 MiB/s |  83.9 KiB |  00m00s
[ 78/153] libuuid-0:2.40.2-8.fc42.x86_6 100% | 536.6 KiB/s |  29.0 KiB |  00m00s
[ 79/153] util-linux-core-0:2.40.2-8.fc 100% |   9.0 MiB/s | 537.3 KiB |  00m00s
[ 80/153] ncurses-base-0:6.5-2.20240629 100% |   1.6 MiB/s |  88.4 KiB |  00m00s
[ 81/153] libgcc-0:14.2.1-3.fc42.x86_64 100% |   2.4 MiB/s | 133.3 KiB |  00m00s
[ 82/153] libsepol-0:3.7-3.fc42.x86_64  100% |   6.0 MiB/s | 342.2 KiB |  00m00s
[ 83/153] fedora-gpg-keys-0:42-0.2.noar 100% |   2.4 MiB/s | 133.6 KiB |  00m00s
[ 84/153] fedora-repos-rawhide-0:42-0.2 100% | 164.9 KiB/s |   8.7 KiB |  00m00s
[ 85/153] pcre2-syntax-0:10.44-1.fc41.1 100% |   2.7 MiB/s | 149.9 KiB |  00m00s
[ 86/153] glibc-gconv-extra-0:2.40.9000 100% |  51.7 MiB/s |   1.7 MiB |  00m00s
[ 87/153] add-determinism-0:0.3.6-1.fc4 100% |  13.6 MiB/s | 851.8 KiB |  00m00s
[ 88/153] basesystem-0:11-21.fc41.noarc 100% | 136.5 KiB/s |   7.4 KiB |  00m00s
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[ 90/153] lz4-libs-0:1.10.0-1.fc41.x86_ 100% |   1.3 MiB/s |  70.7 KiB |  00m00s
[ 91/153] pam-0:1.6.1-6.fc42.x86_64     100% |   9.2 MiB/s | 554.2 KiB |  00m00s
[ 92/153] pkgconf-pkg-config-0:2.3.0-1. 100% | 185.4 KiB/s |  10.0 KiB |  00m00s
[ 93/153] authselect-libs-0:1.5.0-7.fc4 100% |   3.7 MiB/s | 218.1 KiB |  00m00s
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[ 95/153] gdbm-1:1.23-7.fc41.x86_64     100% |   2.7 MiB/s | 151.8 KiB |  00m00s
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[ 97/153] libnsl2-0:2.0.1-2.fc41.x86_64 100% | 558.7 KiB/s |  29.6 KiB |  00m00s
[ 98/153] libpwquality-0:1.4.5-11.fc41. 100% |   2.1 MiB/s | 119.1 KiB |  00m00s
[ 99/153] libtirpc-0:1.3.5-0.fc41.x86_6 100% |   1.7 MiB/s |  94.2 KiB |  00m00s
[100/153] pkgconf-0:2.3.0-1.fc42.x86_64 100% | 836.6 KiB/s |  45.2 KiB |  00m00s
[101/153] pkgconf-m4-0:2.3.0-1.fc42.noa 100% | 270.2 KiB/s |  14.3 KiB |  00m00s
[102/153] krb5-libs-0:1.21.3-2.fc41.x86 100% |  12.3 MiB/s | 757.4 KiB |  00m00s
[103/153] libcom_err-0:1.47.1-3.fc41.x8 100% | 489.1 KiB/s |  26.4 KiB |  00m00s
[104/153] libpkgconf-0:2.3.0-1.fc42.x86 100% | 726.2 KiB/s |  38.5 KiB |  00m00s
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[109/153] jansson-0:2.13.1-10.fc41.x86_ 100% | 822.8 KiB/s |  44.4 KiB |  00m00s
[110/153] binutils-0:2.43.50-1.fc42.x86 100% |  58.5 MiB/s |   6.4 MiB |  00m00s
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[115/153] file-0:5.45-7.fc42.x86_64     100% |   6.1 MiB/s |  49.6 KiB |  00m00s
[116/153] file-libs-0:5.45-7.fc42.x86_6 100% |  29.8 MiB/s | 763.2 KiB |  00m00s
[117/153] libarchive-0:3.7.6-1.fc42.x86 100% |  16.9 MiB/s | 414.3 KiB |  00m00s
[118/153] libzstd-0:1.5.6-2.fc41.x86_64 100% |   5.4 MiB/s | 310.3 KiB |  00m00s
[119/153] rpm-0:4.19.94-1.fc42.x86_64   100% |  22.1 MiB/s | 520.3 KiB |  00m00s
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[129/153] ca-certificates-0:2024.2.69_v 100% |  14.9 MiB/s | 944.3 KiB |  00m00s
[130/153] libffi-0:3.4.6-3.fc42.x86_64  100% | 754.6 KiB/s |  40.0 KiB |  00m00s
[131/153] p11-kit-0:0.25.5-3.fc41.x86_6 100% |   8.4 MiB/s | 490.9 KiB |  00m00s
[132/153] p11-kit-trust-0:0.25.5-3.fc41 100% |   2.3 MiB/s | 132.1 KiB |  00m00s
[133/153] zlib-ng-compat-0:2.2.2-1.fc42 100% |   4.7 MiB/s |  77.3 KiB |  00m00s
[134/153] elfutils-default-yama-scope-0 100% |   1.6 MiB/s |  12.9 KiB |  00m00s
[135/153] libtasn1-0:4.19.0-9.fc41.x86_ 100% |   1.4 MiB/s |  74.2 KiB |  00m00s
[136/153] cracklib-0:2.9.11-6.fc42.x86_ 100% |   5.0 MiB/s |  82.2 KiB |  00m00s
[137/153] xxhash-libs-0:0.8.2-3.fc41.x8 100% | 700.4 KiB/s |  37.1 KiB |  00m00s
[138/153] gdb-minimal-0:15.1-2.fc42.x86 100% |  41.1 MiB/s |   4.3 MiB |  00m00s
[139/153] libcurl-0:8.10.1-2.fc42.x86_6 100% |   3.7 MiB/s | 371.8 KiB |  00m00s
[140/153] libbrotli-0:1.1.0-5.fc41.x86_ 100% |   5.9 MiB/s | 340.5 KiB |  00m00s
[141/153] libidn2-0:2.3.7-2.fc41.x86_64 100% |   2.1 MiB/s | 118.4 KiB |  00m00s
[142/153] libpsl-0:0.21.5-4.fc41.x86_64 100% |   1.2 MiB/s |  64.1 KiB |  00m00s
[143/153] libunistring-0:1.1-8.fc41.x86 100% |   9.0 MiB/s | 544.8 KiB |  00m00s
[144/153] openldap-0:2.6.8-5.fc41.x86_6 100% |   2.3 MiB/s | 255.6 KiB |  00m00s
[145/153] publicsuffix-list-dafsa-0:202 100% |   1.0 MiB/s |  58.3 KiB |  00m00s
[146/153] libtool-ltdl-0:2.4.7-12.fc41. 100% | 624.4 KiB/s |  35.6 KiB |  00m00s
[147/153] libevent-0:2.1.12-14.fc41.x86 100% |   4.2 MiB/s | 257.5 KiB |  00m00s
[148/153] cyrus-sasl-lib-0:2.1.28-27.fc 100% |  12.3 MiB/s | 794.9 KiB |  00m00s
[149/153] libnghttp2-0:1.63.0-1.fc42.x8 100% |   4.5 MiB/s |  77.9 KiB |  00m00s
[150/153] libssh-0:0.11.1-1.fc42.x86_64 100% |  10.3 MiB/s | 232.3 KiB |  00m00s
[151/153] libssh-config-0:0.11.1-1.fc42 100% |   1.2 MiB/s |   9.9 KiB |  00m00s
[152/153] fedora-release-0:42-0.3.noarc 100% | 230.7 KiB/s |  12.2 KiB |  00m00s
[153/153] fedora-release-identity-basic 100% | 245.6 KiB/s |  13.0 KiB |  00m00s
--------------------------------------------------------------------------------
[153/153] Total                         100% |  16.3 MiB/s |  53.1 MiB |  00m03s
Running transaction
Importing PGP key 0x105EF944:
 UserID     : "Fedora (42) <fedora-42-primary@fedoraproject.org>"
 Fingerprint: B0F4950458F69E1150C6C5EDC8AC4916105EF944
 From       : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-42-primary
The key was successfully imported.
Importing PGP key 0x105EF944:
 UserID     : "Fedora (42) <fedora-42-primary@fedoraproject.org>"
 Fingerprint: B0F4950458F69E1150C6C5EDC8AC4916105EF944
 From       : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-42-primary
The key was successfully imported.
Importing PGP key 0xE99D6AD1:
 UserID     : "Fedora (41) <fedora-41-primary@fedoraproject.org>"
 Fingerprint: 466CF2D8B60BC3057AA9453ED0622462E99D6AD1
 From       : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-41-primary
The key was successfully imported.
Importing PGP key 0x31645531:
 UserID     : "Fedora (43) <fedora-43-primary@fedoraproject.org>"
 Fingerprint: C6E7F081CF80E13146676E88829B606631645531
 From       : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-43-primary
The key was successfully imported.
[  1/155] Verify package files          100% | 698.0   B/s | 153.0   B |  00m00s
[  2/155] Prepare transaction           100% |   1.8 KiB/s | 153.0   B |  00m00s
[  3/155] Installing libgcc-0:14.2.1-3. 100% | 134.9 MiB/s | 276.3 KiB |  00m00s
[  4/155] Installing libssh-config-0:0. 100% |   0.0   B/s | 816.0   B |  00m00s
[  5/155] Installing fedora-release-ide 100% |   0.0   B/s | 952.0   B |  00m00s
[  6/155] Installing fedora-repos-rawhi 100% |   2.4 MiB/s |   2.4 KiB |  00m00s
[  7/155] Installing fedora-gpg-keys-0: 100% |  18.7 MiB/s | 172.2 KiB |  00m00s
[  8/155] Installing fedora-repos-0:42- 100% |   5.6 MiB/s |   5.7 KiB |  00m00s
[  9/155] Installing fedora-release-com 100% |  11.6 MiB/s |  23.7 KiB |  00m00s
[ 10/155] Installing fedora-release-0:4 100% |   0.0   B/s | 124.0   B |  00m00s
[ 11/155] Installing setup-0:2.15.0-5.f 100% |  47.3 MiB/s | 726.1 KiB |  00m00s
[ 12/155] Installing filesystem-0:3.18- 100% |   1.6 MiB/s | 212.6 KiB |  00m00s
[ 13/155] Installing basesystem-0:11-21 100% |   0.0   B/s | 124.0   B |  00m00s
[ 14/155] Installing publicsuffix-list- 100% |  66.7 MiB/s |  68.3 KiB |  00m00s
[ 15/155] Installing pkgconf-m4-0:2.3.0 100% |   0.0   B/s |  14.8 KiB |  00m00s
[ 16/155] Installing pcre2-syntax-0:10. 100% | 124.1 MiB/s | 254.1 KiB |  00m00s
[ 17/155] Installing ncurses-base-0:6.5 100% |  38.2 MiB/s | 351.7 KiB |  00m00s
[ 18/155] Installing glibc-minimal-lang 100% |   0.0   B/s | 124.0   B |  00m00s
[ 19/155] Installing ncurses-libs-0:6.5 100% | 137.0 MiB/s | 981.8 KiB |  00m00s
warning: posix.fork(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead
warning: posix.wait(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead
warning: posix.exec(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead
warning: posix.fork(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead
warning: posix.wait(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead
warning: posix.exec(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead
[ 20/155] Installing glibc-0:2.40.9000- 100% | 134.1 MiB/s |   6.7 MiB |  00m00s
[ 21/155] Installing bash-0:5.2.32-2.fc 100% | 247.6 MiB/s |   8.2 MiB |  00m00s
[ 22/155] Installing glibc-common-0:2.4 100% | 131.3 MiB/s |   1.1 MiB |  00m00s
warning: posix.fork(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead
warning: posix.wait(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead
warning: posix.exec(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead
[ 23/155] Installing glibc-gconv-extra- 100% | 130.4 MiB/s |   8.2 MiB |  00m00s
[ 24/155] Installing zlib-ng-compat-0:2 100% | 135.4 MiB/s | 138.7 KiB |  00m00s
[ 25/155] Installing bzip2-libs-0:1.0.8 100% |  79.9 MiB/s |  81.8 KiB |  00m00s
[ 26/155] Installing xz-libs-1:5.6.2-2. 100% | 210.4 MiB/s | 215.5 KiB |  00m00s
[ 27/155] Installing readline-0:8.2-11. 100% | 161.2 MiB/s | 495.3 KiB |  00m00s
[ 28/155] Installing popt-0:1.19-7.fc41 100% |  35.0 MiB/s | 143.5 KiB |  00m00s
[ 29/155] Installing libuuid-0:2.40.2-8 100% |  41.5 MiB/s |  42.5 KiB |  00m00s
[ 30/155] Installing libblkid-0:2.40.2- 100% | 128.7 MiB/s | 263.6 KiB |  00m00s
[ 31/155] Installing gmp-1:6.3.0-2.fc41 100% | 198.6 MiB/s | 813.7 KiB |  00m00s
[ 32/155] Installing libattr-0:2.5.2-4. 100% |  28.8 MiB/s |  29.5 KiB |  00m00s
[ 33/155] Installing libacl-0:2.3.2-2.f 100% |  39.8 MiB/s |  40.7 KiB |  00m00s
[ 34/155] Installing libxcrypt-0:4.4.36 100% | 131.6 MiB/s | 269.5 KiB |  00m00s
[ 35/155] Installing libstdc++-0:14.2.1 100% | 252.2 MiB/s |   2.8 MiB |  00m00s
[ 36/155] Installing libzstd-0:1.5.6-2. 100% | 259.5 MiB/s | 797.2 KiB |  00m00s
[ 37/155] Installing elfutils-libelf-0: 100% | 292.4 MiB/s |   1.2 MiB |  00m00s
[ 38/155] Installing libeconf-0:0.6.2-3 100% |  58.3 MiB/s |  59.7 KiB |  00m00s
[ 39/155] Installing gdbm-libs-1:1.23-7 100% | 120.7 MiB/s | 123.6 KiB |  00m00s
[ 40/155] Installing dwz-0:0.15-7.fc41. 100% | 142.7 MiB/s | 292.3 KiB |  00m00s
[ 41/155] Installing mpfr-0:4.2.1-5.fc4 100% | 203.5 MiB/s | 833.7 KiB |  00m00s
[ 42/155] Installing gawk-0:5.3.0-4.fc4 100% | 173.2 MiB/s |   1.7 MiB |  00m00s
[ 43/155] Installing unzip-0:6.0-64.fc4 100% | 127.0 MiB/s | 390.3 KiB |  00m00s
[ 44/155] Installing file-libs-0:5.45-7 100% | 431.9 MiB/s |   9.9 MiB |  00m00s
[ 45/155] Installing file-0:5.45-7.fc42 100% |   8.5 MiB/s | 105.0 KiB |  00m00s
[ 46/155] Installing crypto-policies-0: 100% |  14.5 MiB/s | 163.2 KiB |  00m00s
[ 47/155] Installing pcre2-0:10.44-1.fc 100% | 213.2 MiB/s | 654.9 KiB |  00m00s
[ 48/155] Installing grep-0:3.11-9.fc41 100% | 111.5 MiB/s |   1.0 MiB |  00m00s
[ 49/155] Installing xz-1:5.6.2-2.fc41. 100% | 120.5 MiB/s |   1.2 MiB |  00m00s
[ 50/155] Installing libcap-ng-0:0.8.5- 100% |  69.4 MiB/s |  71.0 KiB |  00m00s
[ 51/155] Installing audit-libs-0:4.0.2 100% | 162.8 MiB/s | 333.4 KiB |  00m00s
[ 52/155] Installing pam-libs-0:1.6.1-6 100% |  69.0 MiB/s | 141.3 KiB |  00m00s
[ 53/155] Installing libcap-0:2.70-4.fc 100% |  73.3 MiB/s | 225.2 KiB |  00m00s
[ 54/155] Installing systemd-libs-0:256 100% | 254.2 MiB/s |   2.0 MiB |  00m00s
[ 55/155] Installing libsmartcols-0:2.4 100% |  88.6 MiB/s | 181.4 KiB |  00m00s
[ 56/155] Installing libsepol-0:3.7-3.f 100% | 266.6 MiB/s | 819.0 KiB |  00m00s
[ 57/155] Installing libselinux-0:3.7-6 100% |  89.0 MiB/s | 182.3 KiB |  00m00s
[ 58/155] Installing sed-0:4.9-3.fc41.x 100% | 106.2 MiB/s | 869.7 KiB |  00m00s
[ 59/155] Installing findutils-1:4.10.0 100% | 168.9 MiB/s |   1.9 MiB |  00m00s
[ 60/155] Installing libmount-0:2.40.2- 100% | 174.3 MiB/s | 356.9 KiB |  00m00s
[ 61/155] Installing lz4-libs-0:1.10.0- 100% | 143.1 MiB/s | 146.6 KiB |  00m00s
[ 62/155] Installing libcom_err-0:1.47. 100% |  66.7 MiB/s |  68.3 KiB |  00m00s
[ 63/155] Installing alternatives-0:1.3 100% |  66.3 MiB/s |  67.9 KiB |  00m00s
[ 64/155] Installing lua-libs-0:5.4.6-6 100% | 139.8 MiB/s | 286.2 KiB |  00m00s
[ 65/155] Installing libffi-0:3.4.6-3.f 100% |  85.7 MiB/s |  87.8 KiB |  00m00s
[ 66/155] Installing libtasn1-0:4.19.0- 100% |  86.7 MiB/s | 177.5 KiB |  00m00s
[ 67/155] Installing p11-kit-0:0.25.5-3 100% | 147.2 MiB/s |   2.2 MiB |  00m00s
[ 68/155] Installing libunistring-0:1.1 100% | 288.5 MiB/s |   1.7 MiB |  00m00s
[ 69/155] Installing libidn2-0:2.3.7-2. 100% |  65.4 MiB/s | 335.1 KiB |  00m00s
[ 70/155] Installing libpsl-0:0.21.5-4. 100% |  79.7 MiB/s |  81.7 KiB |  00m00s
[ 71/155] Installing p11-kit-trust-0:0. 100% |  27.4 MiB/s | 393.1 KiB |  00m00s
[ 72/155] Installing zstd-0:1.5.6-2.fc4 100% | 241.6 MiB/s |   1.7 MiB |  00m00s
[ 73/155] Installing util-linux-core-0: 100% | 138.9 MiB/s |   1.5 MiB |  00m00s
[ 74/155] Installing tar-2:1.35-4.fc41. 100% | 211.3 MiB/s |   3.0 MiB |  00m00s
[ 75/155] Installing libsemanage-0:3.7- 100% |  97.6 MiB/s | 299.8 KiB |  00m00s
[ 76/155] Installing shadow-utils-2:4.1 100% | 121.9 MiB/s |   4.1 MiB |  00m00s
[ 77/155] Installing zip-0:3.0-41.fc41. 100% | 172.6 MiB/s | 707.1 KiB |  00m00s
[ 78/155] Installing gdbm-1:1.23-7.fc41 100% | 113.7 MiB/s | 465.8 KiB |  00m00s
[ 79/155] Installing cyrus-sasl-lib-0:2 100% | 256.2 MiB/s |   2.3 MiB |  00m00s
[ 80/155] Installing libfdisk-0:2.40.2- 100% | 177.7 MiB/s | 364.0 KiB |  00m00s
[ 81/155] Installing libxml2-0:2.12.8-2 100% | 245.1 MiB/s |   1.7 MiB |  00m00s
[ 82/155] Installing bzip2-0:1.0.8-19.f 100% |  48.9 MiB/s | 100.2 KiB |  00m00s
[ 83/155] Installing add-determinism-0: 100% | 280.7 MiB/s |   2.2 MiB |  00m00s
[ 84/155] Installing build-reproducibil 100% |   0.0   B/s |   1.0 KiB |  00m00s
[ 85/155] Installing sqlite-libs-0:3.46 100% | 238.2 MiB/s |   1.4 MiB |  00m00s
[ 86/155] Installing ed-0:1.20.2-2.fc41 100% |  72.8 MiB/s | 149.2 KiB |  00m00s
[ 87/155] Installing patch-0:2.7.6-25.f 100% | 131.0 MiB/s | 268.2 KiB |  00m00s
[ 88/155] Installing elfutils-default-y 100% | 204.3 KiB/s |   2.0 KiB |  00m00s
[ 89/155] Installing elfutils-libs-0:0. 100% | 160.4 MiB/s | 656.9 KiB |  00m00s
[ 90/155] Installing cpio-0:2.15-2.fc41 100% | 157.1 MiB/s |   1.1 MiB |  00m00s
[ 91/155] Installing diffutils-0:3.10-8 100% | 159.0 MiB/s |   1.6 MiB |  00m00s
[ 92/155] Installing libpkgconf-0:2.3.0 100% |  77.5 MiB/s |  79.3 KiB |  00m00s
[ 93/155] Installing pkgconf-0:2.3.0-1. 100% |  44.5 MiB/s |  91.1 KiB |  00m00s
[ 94/155] Installing pkgconf-pkg-config 100% |   1.7 MiB/s |   1.8 KiB |  00m00s
[ 95/155] Installing keyutils-libs-0:1. 100% |  54.5 MiB/s |  55.8 KiB |  00m00s
[ 96/155] Installing libverto-0:0.3.2-9 100% |  30.5 MiB/s |  31.3 KiB |  00m00s
[ 97/155] Installing jansson-0:2.13.1-1 100% |  87.6 MiB/s |  89.7 KiB |  00m00s
[ 98/155] Installing libgomp-0:14.2.1-3 100% | 256.5 MiB/s | 525.2 KiB |  00m00s
[ 99/155] Installing xxhash-libs-0:0.8. 100% |  87.8 MiB/s |  89.9 KiB |  00m00s
[100/155] Installing libbrotli-0:1.1.0- 100% | 205.0 MiB/s | 839.9 KiB |  00m00s
[101/155] Installing libtool-ltdl-0:2.4 100% |  65.7 MiB/s |  67.3 KiB |  00m00s
[102/155] Installing libnghttp2-0:1.63. 100% | 171.5 MiB/s | 175.6 KiB |  00m00s
[103/155] Installing rust-srpm-macros-0 100% |   0.0   B/s |   5.6 KiB |  00m00s
[104/155] Installing qt6-srpm-macros-0: 100% |   0.0   B/s | 732.0   B |  00m00s
[105/155] Installing qt5-srpm-macros-0: 100% |   0.0   B/s | 776.0   B |  00m00s
[106/155] Installing perl-srpm-macros-0 100% |   0.0   B/s |   1.1 KiB |  00m00s
[107/155] Installing package-notes-srpm 100% |   2.0 MiB/s |   2.0 KiB |  00m00s
[108/155] Installing openblas-srpm-macr 100% |   0.0   B/s | 392.0   B |  00m00s
[109/155] Installing ocaml-srpm-macros- 100% |   0.0   B/s |   2.2 KiB |  00m00s
[110/155] Installing kernel-srpm-macros 100% |   0.0   B/s |   2.3 KiB |  00m00s
[111/155] Installing gnat-srpm-macros-0 100% |   0.0   B/s |   1.3 KiB |  00m00s
[112/155] Installing ghc-srpm-macros-0: 100% |   0.0   B/s |   1.0 KiB |  00m00s
[113/155] Installing fpc-srpm-macros-0: 100% |   0.0   B/s | 420.0   B |  00m00s
[114/155] Installing ansible-srpm-macro 100% |  35.4 MiB/s |  36.2 KiB |  00m00s
[115/155] Installing coreutils-common-0 100% | 243.3 MiB/s |  11.2 MiB |  00m00s
[116/155] Installing openssl-libs-1:3.2 100% | 301.2 MiB/s |   7.8 MiB |  00m00s
[117/155] Installing coreutils-0:9.5-9. 100% | 146.6 MiB/s |   5.7 MiB |  00m00s
[118/155] Installing ca-certificates-0: 100% |   1.1 MiB/s |   2.4 MiB |  00m02s
[119/155] Installing krb5-libs-0:1.21.3 100% | 176.9 MiB/s |   2.3 MiB |  00m00s
[120/155] Installing libarchive-0:3.7.6 100% | 183.0 MiB/s | 936.7 KiB |  00m00s
[121/155] Installing libtirpc-0:1.3.5-0 100% |  99.8 MiB/s | 204.5 KiB |  00m00s
[122/155] Installing gzip-0:1.13-2.fc41 100% |  96.3 MiB/s | 394.6 KiB |  00m00s
[123/155] Installing authselect-libs-0: 100% |  90.4 MiB/s | 833.2 KiB |  00m00s
[124/155] Installing cracklib-0:2.9.11- 100% |  31.0 MiB/s | 254.3 KiB |  00m00s
[125/155] Installing libpwquality-0:1.4 100% |  52.5 MiB/s | 430.1 KiB |  00m00s
[126/155] Installing libnsl2-0:2.0.1-2. 100% |  28.8 MiB/s |  59.1 KiB |  00m00s
[127/155] Installing pam-0:1.6.1-6.fc42 100% |  78.2 MiB/s |   1.9 MiB |  00m00s
[128/155] Installing libssh-0:0.11.1-1. 100% | 139.6 MiB/s | 571.7 KiB |  00m00s
[129/155] Installing rpm-sequoia-0:1.7. 100% | 263.0 MiB/s |   2.4 MiB |  00m00s
[130/155] Installing rpm-libs-0:4.19.94 100% | 177.6 MiB/s | 727.6 KiB |  00m00s
[131/155] Installing rpm-build-libs-0:4 100% | 101.3 MiB/s | 207.5 KiB |  00m00s
[132/155] Installing libevent-0:2.1.12- 100% | 219.6 MiB/s | 899.5 KiB |  00m00s
[133/155] Installing openldap-0:2.6.8-5 100% | 158.2 MiB/s | 648.0 KiB |  00m00s
[134/155] Installing libcurl-0:8.10.1-2 100% | 205.0 MiB/s | 839.5 KiB |  00m00s
[135/155] Installing elfutils-debuginfo 100% |  32.7 MiB/s |  66.9 KiB |  00m00s
[136/155] Installing binutils-0:2.43.50 100% | 246.0 MiB/s |  27.6 MiB |  00m00s
[137/155] Installing elfutils-0:0.191-8 100% | 216.5 MiB/s |   2.6 MiB |  00m00s
[138/155] Installing gdb-minimal-0:15.1 100% | 295.3 MiB/s |  13.0 MiB |  00m00s
[139/155] Installing debugedit-0:5.0-17 100% |  98.6 MiB/s | 202.0 KiB |  00m00s
[140/155] Installing curl-0:8.10.1-2.fc 100% |  22.3 MiB/s | 455.8 KiB |  00m00s
[141/155] Installing rpm-0:4.19.94-1.fc 100% |  89.5 MiB/s |   2.5 MiB |  00m00s
[142/155] Installing efi-srpm-macros-0: 100% |  40.2 MiB/s |  41.2 KiB |  00m00s
[143/155] Installing lua-srpm-macros-0: 100% |   1.9 MiB/s |   1.9 KiB |  00m00s
[144/155] Installing zig-srpm-macros-0: 100% |   0.0   B/s |   1.7 KiB |  00m00s
[145/155] Installing fonts-srpm-macros- 100% |  55.7 MiB/s |  57.0 KiB |  00m00s
[146/155] Installing forge-srpm-macros- 100% |  19.7 MiB/s |  40.4 KiB |  00m00s
[147/155] Installing go-srpm-macros-0:3 100% |  30.3 MiB/s |  62.0 KiB |  00m00s
[148/155] Installing python-srpm-macros 100% |  25.5 MiB/s |  52.2 KiB |  00m00s
[149/155] Installing redhat-rpm-config- 100% |  62.9 MiB/s | 193.2 KiB |  00m00s
[150/155] Installing rpm-build-0:4.19.9 100% |  49.5 MiB/s | 202.9 KiB |  00m00s
[151/155] Installing pyproject-srpm-mac 100% |   1.2 MiB/s |   2.5 KiB |  00m00s
[152/155] Installing util-linux-0:2.40. 100% |  90.6 MiB/s |   3.7 MiB |  00m00s
[153/155] Installing authselect-0:1.5.0 100% |  38.6 MiB/s | 157.9 KiB |  00m00s
[154/155] Installing which-0:2.21-42.fc 100% |  40.2 MiB/s |  82.4 KiB |  00m00s
warning: posix.fork(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead
warning: posix.wait(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead
warning: posix.exec(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead
[155/155] Installing info-0:7.1.1-1.fc4 100% | 127.1 KiB/s | 362.3 KiB |  00m03s
Warning: skipped PGP checks for 27 packages from repository: copr_base
Complete!
Finish: installing minimal buildroot with dnf5
Start: creating root cache
Finish: creating root cache
Finish: chroot init
INFO: Installed packages:
INFO: add-determinism-0.3.6-1.fc41.x86_64
alternatives-1.30-1.fc41.x86_64
ansible-srpm-macros-1-16.fc41.noarch
audit-libs-4.0.2-1.fc41.x86_64
authselect-1.5.0-7.fc41.x86_64
authselect-libs-1.5.0-7.fc41.x86_64
basesystem-11-21.fc41.noarch
bash-5.2.32-2.fc42.x86_64
binutils-2.43.50-1.fc42.x86_64
build-reproducibility-srpm-macros-0.3.6-1.fc41.noarch
bzip2-1.0.8-19.fc41.x86_64
bzip2-libs-1.0.8-19.fc41.x86_64
ca-certificates-2024.2.69_v8.0.401-1.fc42.noarch
coreutils-9.5-9.fc42.x86_64
coreutils-common-9.5-9.fc42.x86_64
cpio-2.15-2.fc41.x86_64
cracklib-2.9.11-6.fc42.x86_64
crypto-policies-20240828-1.git5f66e81.fc42.noarch
curl-8.10.1-2.fc42.x86_64
cyrus-sasl-lib-2.1.28-27.fc41.x86_64
debugedit-5.0-17.fc41.x86_64
diffutils-3.10-8.fc41.x86_64
dwz-0.15-7.fc41.x86_64
ed-1.20.2-2.fc41.x86_64
efi-srpm-macros-5-12.fc41.noarch
elfutils-0.191-8.fc42.x86_64
elfutils-debuginfod-client-0.191-8.fc42.x86_64
elfutils-default-yama-scope-0.191-8.fc42.noarch
elfutils-libelf-0.191-8.fc42.x86_64
elfutils-libs-0.191-8.fc42.x86_64
fedora-gpg-keys-42-0.2.noarch
fedora-release-42-0.3.noarch
fedora-release-common-42-0.3.noarch
fedora-release-identity-basic-42-0.3.noarch
fedora-repos-42-0.2.noarch
fedora-repos-rawhide-42-0.2.noarch
file-5.45-7.fc42.x86_64
file-libs-5.45-7.fc42.x86_64
filesystem-3.18-29.fc42.x86_64
findutils-4.10.0-4.fc41.x86_64
fonts-srpm-macros-2.0.5-17.fc41.noarch
forge-srpm-macros-0.3.2-1.fc41.noarch
fpc-srpm-macros-1.3-13.fc41.noarch
gawk-5.3.0-4.fc41.x86_64
gdb-minimal-15.1-2.fc42.x86_64
gdbm-1.23-7.fc41.x86_64
gdbm-libs-1.23-7.fc41.x86_64
ghc-srpm-macros-1.9.2-1.fc42.noarch
glibc-2.40.9000-5.fc42.x86_64
glibc-common-2.40.9000-5.fc42.x86_64
glibc-gconv-extra-2.40.9000-5.fc42.x86_64
glibc-minimal-langpack-2.40.9000-5.fc42.x86_64
gmp-6.3.0-2.fc41.x86_64
gnat-srpm-macros-6-6.fc41.noarch
go-srpm-macros-3.6.0-3.fc41.noarch
gpg-pubkey-105ef944-65ca83d1
gpg-pubkey-31645531-66b6dccf
gpg-pubkey-e99d6ad1-64d2612c
grep-3.11-9.fc41.x86_64
gzip-1.13-2.fc41.x86_64
info-7.1.1-1.fc42.x86_64
jansson-2.13.1-10.fc41.x86_64
kernel-srpm-macros-1.0-24.fc41.noarch
keyutils-libs-1.6.3-4.fc41.x86_64
krb5-libs-1.21.3-2.fc41.x86_64
libacl-2.3.2-2.fc41.x86_64
libarchive-3.7.6-1.fc42.x86_64
libattr-2.5.2-4.fc41.x86_64
libblkid-2.40.2-8.fc42.x86_64
libbrotli-1.1.0-5.fc41.x86_64
libcap-2.70-4.fc41.x86_64
libcap-ng-0.8.5-3.fc41.x86_64
libcom_err-1.47.1-3.fc41.x86_64
libcurl-8.10.1-2.fc42.x86_64
libeconf-0.6.2-3.fc41.x86_64
libevent-2.1.12-14.fc41.x86_64
libfdisk-2.40.2-8.fc42.x86_64
libffi-3.4.6-3.fc42.x86_64
libgcc-14.2.1-3.fc42.x86_64
libgomp-14.2.1-3.fc42.x86_64
libidn2-2.3.7-2.fc41.x86_64
libmount-2.40.2-8.fc42.x86_64
libnghttp2-1.63.0-1.fc42.x86_64
libnsl2-2.0.1-2.fc41.x86_64
libpkgconf-2.3.0-1.fc42.x86_64
libpsl-0.21.5-4.fc41.x86_64
libpwquality-1.4.5-11.fc41.x86_64
libselinux-3.7-6.fc42.x86_64
libsemanage-3.7-3.fc42.x86_64
libsepol-3.7-3.fc42.x86_64
libsmartcols-2.40.2-8.fc42.x86_64
libssh-0.11.1-1.fc42.x86_64
libssh-config-0.11.1-1.fc42.noarch
libstdc++-14.2.1-3.fc42.x86_64
libtasn1-4.19.0-9.fc41.x86_64
libtirpc-1.3.5-0.fc41.x86_64
libtool-ltdl-2.4.7-12.fc41.x86_64
libunistring-1.1-8.fc41.x86_64
libuuid-2.40.2-8.fc42.x86_64
libverto-0.3.2-9.fc41.x86_64
libxcrypt-4.4.36-7.fc41.x86_64
libxml2-2.12.8-2.fc42.x86_64
libzstd-1.5.6-2.fc41.x86_64
lua-libs-5.4.6-6.fc41.x86_64
lua-srpm-macros-1-14.fc41.noarch
lz4-libs-1.10.0-1.fc41.x86_64
mpfr-4.2.1-5.fc41.x86_64
ncurses-base-6.5-2.20240629.fc41.noarch
ncurses-libs-6.5-2.20240629.fc41.x86_64
ocaml-srpm-macros-10-3.fc41.noarch
openblas-srpm-macros-2-18.fc41.noarch
openldap-2.6.8-5.fc41.x86_64
openssl-libs-3.2.2-9.fc42.x86_64
p11-kit-0.25.5-3.fc41.x86_64
p11-kit-trust-0.25.5-3.fc41.x86_64
package-notes-srpm-macros-0.5-12.fc41.noarch
pam-1.6.1-6.fc42.x86_64
pam-libs-1.6.1-6.fc42.x86_64
patch-2.7.6-25.fc41.x86_64
pcre2-10.44-1.fc41.1.x86_64
pcre2-syntax-10.44-1.fc41.1.noarch
perl-srpm-macros-1-56.fc41.noarch
pkgconf-2.3.0-1.fc42.x86_64
pkgconf-m4-2.3.0-1.fc42.noarch
pkgconf-pkg-config-2.3.0-1.fc42.x86_64
popt-1.19-7.fc41.x86_64
publicsuffix-list-dafsa-20240107-4.fc41.noarch
pyproject-srpm-macros-1.15.0-1.fc42.noarch
python-srpm-macros-3.13-3.fc41.noarch
qt5-srpm-macros-5.15.15-1.fc42.noarch
qt6-srpm-macros-6.7.2-3.fc41.noarch
readline-8.2-11.fc42.x86_64
redhat-rpm-config-295-1.fc42.noarch
rpm-4.19.94-1.fc42.x86_64
rpm-build-4.19.94-1.fc42.x86_64
rpm-build-libs-4.19.94-1.fc42.x86_64
rpm-libs-4.19.94-1.fc42.x86_64
rpm-sequoia-1.7.0-2.fc41.x86_64
rust-srpm-macros-26.3-3.fc42.noarch
sed-4.9-3.fc41.x86_64
setup-2.15.0-5.fc41.noarch
shadow-utils-4.16.0-4.fc42.x86_64
sqlite-libs-3.46.0-4.fc41.x86_64
systemd-libs-256.5-1.fc42.x86_64
tar-1.35-4.fc41.x86_64
unzip-6.0-64.fc41.x86_64
util-linux-2.40.2-8.fc42.x86_64
util-linux-core-2.40.2-8.fc42.x86_64
which-2.21-42.fc41.x86_64
xxhash-libs-0.8.2-3.fc41.x86_64
xz-5.6.2-2.fc41.x86_64
xz-libs-5.6.2-2.fc41.x86_64
zig-srpm-macros-1-3.fc41.noarch
zip-3.0-41.fc41.x86_64
zlib-ng-compat-2.2.2-1.fc42.x86_64
zstd-1.5.6-2.fc41.x86_64
Start: buildsrpm
Start: rpmbuild -bs
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1721433600
Wrote: /builddir/build/SRPMS/samtools-1.15.1-5.fc42.src.rpm
Finish: rpmbuild -bs
cp: preserving permissions for ‘/var/lib/copr-rpmbuild/results/chroot_scan/var/lib/mock/fedora-rawhide-x86_64-1727357827.031697/root/var/log’: No such file or directory
INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/fedora-rawhide-x86_64-1727357827.031697/root/var/log/dnf5.log
Finish: buildsrpm
INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-owepyad1/samtools/samtools.spec) Config(child) 0 minutes 34 seconds
INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results
INFO: Cleaning up build root ('cleanup_on_success=True')
Start: clean chroot
INFO: unmounting tmpfs.
Finish: clean chroot
INFO: Start(/var/lib/copr-rpmbuild/results/samtools-1.15.1-5.fc42.src.rpm)  Config(fedora-rawhide-x86_64)
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1727357827.031697/root.
INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1727357827.031697/root.
INFO: calling preinit hooks
INFO: enabled root cache
INFO: enabled package manager cache
Start(bootstrap): cleaning package manager metadata
Finish(bootstrap): cleaning package manager metadata
Finish(bootstrap): chroot init
Start: chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-1727357827.031697/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
INFO: Buildroot is handled by package management downloaded with a bootstrap image:
  rpm-4.19.94-1.fc42.x86_64
  rpm-sequoia-1.7.0-2.fc41.x86_64
  dnf5-5.2.6.2-1.fc42.x86_64
  dnf5-plugins-5.2.6.2-1.fc42.x86_64
Finish: chroot init
Start: build phase for samtools-1.15.1-5.fc42.src.rpm
Start: build setup for samtools-1.15.1-5.fc42.src.rpm
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1721433600
Wrote: /builddir/build/SRPMS/samtools-1.15.1-5.fc42.src.rpm
Updating and loading repositories:
 fedora                                 100% | 245.3 KiB/s |   7.1 KiB |  00m00s
 Copr repository                        100% |  45.2 KiB/s |   1.5 KiB |  00m00s
 fedora                                 100% |   1.0 MiB/s | 456.1 KiB |  00m00s
 Copr repository                        100% |  20.4 MiB/s |   2.9 MiB |  00m00s
Repositories loaded.
Package                 Arch   Version              Repository      Size
Installing:
 gcc                    x86_64 14.2.1-3.fc42        fedora     104.4 MiB
 htslib-devel           x86_64 1.15.1-7.fc42        copr_base  411.0 KiB
 htslib-tools           x86_64 1.15.1-7.fc42        copr_base    2.4 MiB
 make                   x86_64 1:4.4.1-8.fc41       fedora       1.8 MiB
 ncurses-devel          x86_64 6.5-2.20240629.fc41  fedora     870.1 KiB
 perl-FindBin           noarch 1.54-511.fc41        fedora       6.7 KiB
 perl-Getopt-Long       noarch 1:2.58-2.fc41        fedora     144.5 KiB
 perl-interpreter       x86_64 4:5.40.0-511.fc41    fedora     122.3 KiB
 perl-lib               x86_64 0.65-511.fc41        fedora       8.5 KiB
 zlib-ng-compat-devel   x86_64 2.2.2-1.fc42         copr_base  106.8 KiB
Installing dependencies:
 annobin-docs           noarch 12.70-1.fc42         fedora      97.7 KiB
 annobin-plugin-gcc     x86_64 12.70-1.fc42         fedora     985.6 KiB
 cmake-filesystem       x86_64 3.28.3-7.fc41        fedora       0.0   B
 cpp                    x86_64 14.2.1-3.fc42        fedora      35.0 MiB
 gcc-plugin-annobin     x86_64 14.2.1-3.fc42        fedora      61.1 KiB
 glibc-devel            x86_64 2.40.9000-5.fc42     copr_base   37.8 KiB
 glibc-headers-x86      noarch 2.40.9000-5.fc42     copr_base    2.2 MiB
 groff-base             x86_64 1.23.0-7.fc41        fedora       3.8 MiB
 htslib                 x86_64 1.15.1-7.fc42        copr_base    1.1 MiB
 kernel-headers         x86_64 6.11.0-63.fc42       fedora       6.4 MiB
 libmpc                 x86_64 1.3.1-6.fc41         fedora     164.7 KiB
 libxcrypt-devel        x86_64 4.4.36-7.fc41        fedora      30.3 KiB
 ncurses                x86_64 6.5-2.20240629.fc41  fedora     627.3 KiB
 ncurses-c++-libs       x86_64 6.5-2.20240629.fc41  fedora     161.7 KiB
 perl-AutoLoader        noarch 5.74-511.fc41        fedora      20.5 KiB
 perl-B                 x86_64 1.89-511.fc41        fedora     498.0 KiB
 perl-Carp              noarch 1.54-511.fc41        fedora      46.6 KiB
 perl-Class-Struct      noarch 0.68-511.fc41        fedora      25.4 KiB
 perl-Data-Dumper       x86_64 2.189-512.fc41       fedora     111.7 KiB
 perl-Digest            noarch 1.20-511.fc41        fedora      35.3 KiB
 perl-Digest-MD5        x86_64 2.59-5.fc41          fedora      59.8 KiB
 perl-DynaLoader        x86_64 1.56-511.fc41        fedora      32.1 KiB
 perl-Encode            x86_64 4:3.21-511.fc41      fedora       4.7 MiB
 perl-Errno             x86_64 1.38-511.fc41        fedora       8.4 KiB
 perl-Exporter          noarch 5.78-511.fc41        fedora      54.3 KiB
 perl-Fcntl             x86_64 1.18-511.fc41        fedora      49.0 KiB
 perl-File-Basename     noarch 2.86-511.fc41        fedora      14.0 KiB
 perl-File-Path         noarch 2.18-511.fc41        fedora      63.5 KiB
 perl-File-Temp         noarch 1:0.231.100-511.fc41 fedora     162.3 KiB
 perl-File-stat         noarch 1.14-511.fc41        fedora      12.5 KiB
 perl-FileHandle        noarch 2.05-511.fc41        fedora       9.3 KiB
 perl-Getopt-Std        noarch 1.14-511.fc41        fedora      11.2 KiB
 perl-HTTP-Tiny         noarch 0.088-512.fc41       fedora     152.2 KiB
 perl-IO                x86_64 1.55-511.fc41        fedora     151.1 KiB
 perl-IO-Socket-IP      noarch 0.42-512.fc41        fedora      98.7 KiB
 perl-IO-Socket-SSL     noarch 2.089-1.fc42         fedora     703.3 KiB
 perl-IPC-Open3         noarch 1.22-511.fc41        fedora      22.5 KiB
 perl-MIME-Base32       noarch 1.303-21.fc41        fedora      30.7 KiB
 perl-MIME-Base64       x86_64 3.16-511.fc41        fedora      46.1 KiB
 perl-Mozilla-CA        noarch 20240730-1.fc41      fedora       9.8 KiB
 perl-Net-SSLeay        x86_64 1.94-7.fc41          fedora       1.3 MiB
 perl-POSIX             x86_64 2.20-511.fc41        fedora     235.1 KiB
 perl-PathTools         x86_64 3.91-511.fc41        fedora     180.0 KiB
 perl-Pod-Escapes       noarch 1:1.07-511.fc41      fedora      24.9 KiB
 perl-Pod-Perldoc       noarch 3.28.01-512.fc41     fedora     163.7 KiB
 perl-Pod-Simple        noarch 1:3.45-511.fc41      fedora     560.9 KiB
 perl-Pod-Usage         noarch 4:2.03-511.fc41      fedora      84.8 KiB
 perl-Scalar-List-Utils x86_64 5:1.66-1.fc42        fedora     146.6 KiB
 perl-SelectSaver       noarch 1.02-511.fc41        fedora       2.2 KiB
 perl-Socket            x86_64 4:2.038-511.fc41     fedora     124.0 KiB
 perl-Storable          x86_64 1:3.32-511.fc41      fedora     232.4 KiB
 perl-Symbol            noarch 1.09-511.fc41        fedora       6.8 KiB
 perl-Term-ANSIColor    noarch 5.01-512.fc41        fedora      97.5 KiB
 perl-Term-Cap          noarch 1.18-511.fc41        fedora      29.3 KiB
 perl-Text-ParseWords   noarch 3.31-511.fc41        fedora      13.6 KiB
 perl-Text-Tabs+Wrap    noarch 2024.001-511.fc41    fedora      22.6 KiB
 perl-Time-Local        noarch 2:1.350-511.fc41     fedora      69.0 KiB
 perl-URI               noarch 5.29-1.fc42          fedora     251.9 KiB
 perl-base              noarch 2.27-511.fc41        fedora      12.5 KiB
 perl-constant          noarch 1.33-512.fc41        fedora      26.2 KiB
 perl-if                noarch 0.61.000-511.fc41    fedora       5.8 KiB
 perl-libnet            noarch 3.15-512.fc41        fedora     289.4 KiB
 perl-libs              x86_64 4:5.40.0-511.fc41    fedora       9.9 MiB
 perl-locale            noarch 1.12-511.fc41        fedora       6.5 KiB
 perl-mro               x86_64 1.29-511.fc41        fedora      45.6 KiB
 perl-overload          noarch 1.37-511.fc41        fedora      71.5 KiB
 perl-overloading       noarch 0.02-511.fc41        fedora       4.8 KiB
 perl-parent            noarch 1:0.242-1.fc42       fedora      10.0 KiB
 perl-podlators         noarch 1:6.0.2-2.fc41       fedora     317.5 KiB
 perl-vars              noarch 1.05-511.fc41        fedora       3.9 KiB

Transaction Summary:
 Installing:        80 packages

Total size of inbound packages is 63 MiB. Need to download 63 MiB.
After this operation, 182 MiB extra will be used (install 182 MiB, remove 0 B).
[ 1/80] perl-FindBin-0:1.54-511.fc41.no 100% | 159.3 KiB/s |  14.2 KiB |  00m00s
[ 2/80] perl-Getopt-Long-1:2.58-2.fc41. 100% |   1.2 MiB/s |  63.9 KiB |  00m00s
[ 3/80] make-1:4.4.1-8.fc41.x86_64      100% |   3.4 MiB/s | 586.1 KiB |  00m00s
[ 4/80] perl-lib-0:0.65-511.fc41.x86_64 100% | 298.1 KiB/s |  14.9 KiB |  00m00s
[ 5/80] perl-interpreter-4:5.40.0-511.f 100% | 443.6 KiB/s |  72.3 KiB |  00m00s
[ 6/80] htslib-devel-0:1.15.1-7.fc42.x8 100% | 347.7 KiB/s |  99.5 KiB |  00m00s
[ 7/80] htslib-tools-0:1.15.1-7.fc42.x8 100% |   2.1 MiB/s | 554.5 KiB |  00m00s
[ 8/80] zlib-ng-compat-devel-0:2.2.2-1. 100% |   3.4 MiB/s |  38.7 KiB |  00m00s
[ 9/80] ncurses-devel-0:6.5-2.20240629. 100% |   2.3 MiB/s | 569.9 KiB |  00m00s
[10/80] gcc-0:14.2.1-3.fc42.x86_64      100% |  47.1 MiB/s |  37.0 MiB |  00m01s
[11/80] perl-Carp-0:1.54-511.fc41.noarc 100% | 577.8 KiB/s |  28.9 KiB |  00m00s
[12/80] libmpc-0:1.3.1-6.fc41.x86_64    100% | 629.4 KiB/s |  71.1 KiB |  00m00s
[13/80] perl-Exporter-0:5.78-511.fc41.n 100% | 736.0 KiB/s |  30.9 KiB |  00m00s
[14/80] perl-File-Basename-0:2.86-511.f 100% | 407.7 KiB/s |  17.1 KiB |  00m00s
[15/80] perl-Pod-Usage-4:2.03-511.fc41. 100% |   1.0 MiB/s |  40.0 KiB |  00m00s
[16/80] cpp-0:14.2.1-3.fc42.x86_64      100% |  34.3 MiB/s |  11.9 MiB |  00m00s
[17/80] perl-PathTools-0:3.91-511.fc41. 100% |   1.1 MiB/s |  87.4 KiB |  00m00s
[18/80] perl-Text-ParseWords-0:3.31-511 100% | 460.4 KiB/s |  16.6 KiB |  00m00s
[19/80] perl-base-0:2.27-511.fc41.noarc 100% |   1.1 MiB/s |  16.2 KiB |  00m00s
[20/80] perl-constant-0:1.33-512.fc41.n 100% |   1.5 MiB/s |  23.0 KiB |  00m00s
[21/80] perl-overload-0:1.37-511.fc41.n 100% |   3.0 MiB/s |  45.5 KiB |  00m00s
[22/80] ncurses-c++-libs-0:6.5-2.202406 100% |   2.5 MiB/s |  37.8 KiB |  00m00s
[23/80] perl-libs-4:5.40.0-511.fc41.x86 100% |  37.0 MiB/s |   2.3 MiB |  00m00s
[24/80] cmake-filesystem-0:3.28.3-7.fc4 100% | 388.2 KiB/s |  18.2 KiB |  00m00s
[25/80] perl-Errno-0:1.38-511.fc41.x86_ 100% | 994.4 KiB/s |  14.9 KiB |  00m00s
[26/80] perl-Scalar-List-Utils-5:1.66-1 100% |   2.4 MiB/s |  72.2 KiB |  00m00s
[27/80] htslib-0:1.15.1-7.fc42.x86_64   100% |   4.6 MiB/s | 496.8 KiB |  00m00s
[28/80] perl-Pod-Perldoc-0:3.28.01-512. 100% |   2.8 MiB/s |  86.1 KiB |  00m00s
[29/80] perl-mro-0:1.29-511.fc41.x86_64 100% |   1.9 MiB/s |  29.9 KiB |  00m00s
[30/80] perl-podlators-1:6.0.2-2.fc41.n 100% |   4.1 MiB/s | 128.8 KiB |  00m00s
[31/80] perl-overloading-0:0.02-511.fc4 100% | 857.7 KiB/s |  12.9 KiB |  00m00s
[32/80] perl-DynaLoader-0:1.56-511.fc41 100% |   1.7 MiB/s |  26.0 KiB |  00m00s
[33/80] perl-Fcntl-0:1.18-511.fc41.x86_ 100% |   1.9 MiB/s |  29.8 KiB |  00m00s
[34/80] perl-File-Temp-1:0.231.100-511. 100% |   3.8 MiB/s |  59.1 KiB |  00m00s
[35/80] groff-base-0:1.23.0-7.fc41.x86_ 100% |  27.5 MiB/s |   1.1 MiB |  00m00s
[36/80] perl-HTTP-Tiny-0:0.088-512.fc41 100% |   1.9 MiB/s |  55.8 KiB |  00m00s
[37/80] perl-IPC-Open3-0:1.22-511.fc41. 100% |   1.4 MiB/s |  21.8 KiB |  00m00s
[38/80] perl-IO-0:1.55-511.fc41.x86_64  100% |   2.7 MiB/s |  81.9 KiB |  00m00s
[39/80] perl-Symbol-0:1.09-511.fc41.noa 100% | 943.8 KiB/s |  14.2 KiB |  00m00s
[40/80] perl-Pod-Simple-1:3.45-511.fc41 100% |   6.7 MiB/s | 219.0 KiB |  00m00s
[41/80] perl-parent-1:0.242-1.fc42.noar 100% | 879.9 KiB/s |  15.0 KiB |  00m00s
[42/80] perl-vars-0:1.05-511.fc41.noarc 100% | 863.8 KiB/s |  13.0 KiB |  00m00s
[43/80] perl-Term-ANSIColor-0:5.01-512. 100% |   3.1 MiB/s |  47.7 KiB |  00m00s
[44/80] perl-Term-Cap-0:1.18-511.fc41.n 100% |   1.4 MiB/s |  22.1 KiB |  00m00s
[45/80] perl-POSIX-0:2.20-511.fc41.x86_ 100% |   3.2 MiB/s |  97.0 KiB |  00m00s
[46/80] perl-File-Path-0:2.18-511.fc41. 100% |   2.3 MiB/s |  35.3 KiB |  00m00s
[47/80] perl-MIME-Base64-0:3.16-511.fc4 100% |   1.8 MiB/s |  29.9 KiB |  00m00s
[48/80] perl-Mozilla-CA-0:20240730-1.fc 100% | 891.1 KiB/s |  14.3 KiB |  00m00s
[49/80] perl-IO-Socket-SSL-0:2.089-1.fc 100% |   6.8 MiB/s | 231.2 KiB |  00m00s
[50/80] perl-Socket-4:2.038-511.fc41.x8 100% |   3.3 MiB/s |  54.8 KiB |  00m00s
[51/80] perl-Time-Local-2:1.350-511.fc4 100% |   2.1 MiB/s |  34.5 KiB |  00m00s
[52/80] perl-Net-SSLeay-0:1.94-7.fc41.x 100% |  10.5 MiB/s | 375.7 KiB |  00m00s
[53/80] perl-File-stat-0:1.14-511.fc41. 100% | 607.4 KiB/s |  17.0 KiB |  00m00s
[54/80] perl-SelectSaver-0:1.02-511.fc4 100% | 730.3 KiB/s |  11.7 KiB |  00m00s
[55/80] perl-Pod-Escapes-1:1.07-511.fc4 100% |   1.2 MiB/s |  19.8 KiB |  00m00s
[56/80] perl-Text-Tabs+Wrap-0:2024.001- 100% |   1.3 MiB/s |  21.9 KiB |  00m00s
[57/80] perl-if-0:0.61.000-511.fc41.noa 100% | 821.3 KiB/s |  14.0 KiB |  00m00s
[58/80] perl-locale-0:1.12-511.fc41.noa 100% | 798.8 KiB/s |  13.6 KiB |  00m00s
[59/80] perl-IO-Socket-IP-0:0.42-512.fc 100% |   2.3 MiB/s |  41.8 KiB |  00m00s
[60/80] ncurses-0:6.5-2.20240629.fc41.x 100% |  11.2 MiB/s | 423.8 KiB |  00m00s
[61/80] perl-AutoLoader-0:5.74-511.fc41 100% |   1.1 MiB/s |  21.2 KiB |  00m00s
[62/80] perl-URI-0:5.29-1.fc42.noarch   100% |   4.3 MiB/s | 137.7 KiB |  00m00s
[63/80] perl-Class-Struct-0:0.68-511.fc 100% |   1.4 MiB/s |  22.0 KiB |  00m00s
[64/80] perl-Data-Dumper-0:2.189-512.fc 100% |   3.7 MiB/s |  56.3 KiB |  00m00s
[65/80] perl-MIME-Base32-0:1.303-21.fc4 100% |   1.3 MiB/s |  20.5 KiB |  00m00s
[66/80] perl-Digest-MD5-0:2.59-5.fc41.x 100% |   2.3 MiB/s |  36.0 KiB |  00m00s
[67/80] perl-libnet-0:3.15-512.fc41.noa 100% |   4.2 MiB/s | 128.5 KiB |  00m00s
[68/80] perl-B-0:1.89-511.fc41.x86_64   100% |   5.6 MiB/s | 176.3 KiB |  00m00s
[69/80] perl-FileHandle-0:2.05-511.fc41 100% |   1.0 MiB/s |  15.5 KiB |  00m00s
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[71/80] perl-Getopt-Std-0:1.14-511.fc41 100% |   1.0 MiB/s |  15.6 KiB |  00m00s
[72/80] glibc-devel-0:2.40.9000-5.fc42. 100% |   7.2 MiB/s | 131.8 KiB |  00m00s
[73/80] perl-Encode-4:3.21-511.fc41.x86 100% |  25.7 MiB/s |   1.1 MiB |  00m00s
[74/80] perl-Storable-1:3.32-511.fc41.x 100% |   3.2 MiB/s |  98.4 KiB |  00m00s
[75/80] libxcrypt-devel-0:4.4.36-7.fc41 100% |   1.9 MiB/s |  28.9 KiB |  00m00s
[76/80] glibc-headers-x86-0:2.40.9000-5 100% |  21.6 MiB/s | 552.8 KiB |  00m00s
[77/80] kernel-headers-0:6.11.0-63.fc42 100% |  31.9 MiB/s |   1.6 MiB |  00m00s
[78/80] annobin-plugin-gcc-0:12.70-1.fc 100% |  16.4 MiB/s | 971.7 KiB |  00m00s
[79/80] gcc-plugin-annobin-0:14.2.1-3.f 100% |   1.3 MiB/s |  55.2 KiB |  00m00s
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--------------------------------------------------------------------------------
[80/80] Total                           100% |  40.7 MiB/s |  62.8 MiB |  00m02s
Running transaction
[ 1/82] Verify package files            100% | 375.0   B/s |  80.0   B |  00m00s
[ 2/82] Prepare transaction             100% |   1.4 KiB/s |  80.0   B |  00m00s
[ 3/82] Installing htslib-0:1.15.1-7.fc 100% | 156.5 MiB/s |   1.1 MiB |  00m00s
[ 4/82] Installing libmpc-0:1.3.1-6.fc4 100% |  81.1 MiB/s | 166.2 KiB |  00m00s
[ 5/82] Installing cpp-0:14.2.1-3.fc42. 100% | 277.8 MiB/s |  35.0 MiB |  00m00s
[ 6/82] Installing annobin-docs-0:12.70 100% |  32.2 MiB/s |  98.8 KiB |  00m00s
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[ 8/82] Installing glibc-headers-x86-0: 100% |  88.0 MiB/s |   2.3 MiB |  00m00s
[ 9/82] Installing libxcrypt-devel-0:4. 100% |  15.9 MiB/s |  32.6 KiB |  00m00s
[10/82] Installing glibc-devel-0:2.40.9 100% |  20.3 MiB/s |  41.5 KiB |  00m00s
[11/82] Installing ncurses-0:6.5-2.2024 100% |  34.4 MiB/s | 633.9 KiB |  00m00s
[12/82] Installing groff-base-0:1.23.0- 100% | 107.6 MiB/s |   3.9 MiB |  00m00s
[13/82] Installing perl-Digest-0:1.20-5 100% |  36.2 MiB/s |  37.1 KiB |  00m00s
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[16/82] Installing perl-Digest-MD5-0:2. 100% |  60.2 MiB/s |  61.7 KiB |  00m00s
[17/82] Installing perl-MIME-Base32-0:1 100% |  31.4 MiB/s |  32.2 KiB |  00m00s
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[19/82] Installing perl-libnet-0:3.15-5 100% |  95.9 MiB/s | 294.7 KiB |  00m00s
[20/82] Installing perl-AutoLoader-0:5. 100% |   0.0   B/s |  20.9 KiB |  00m00s
[21/82] Installing perl-IO-Socket-IP-0: 100% |  49.1 MiB/s | 100.5 KiB |  00m00s
[22/82] Installing perl-URI-0:5.29-1.fc 100% |  51.5 MiB/s | 263.8 KiB |  00m00s
[23/82] Installing perl-File-Path-0:2.1 100% |  63.0 MiB/s |  64.5 KiB |  00m00s
[24/82] Installing perl-Mozilla-CA-0:20 100% |  10.6 MiB/s |  10.8 KiB |  00m00s
[25/82] Installing perl-Time-Local-2:1. 100% |  68.9 MiB/s |  70.6 KiB |  00m00s
[26/82] Installing perl-Pod-Escapes-1:1 100% |  25.3 MiB/s |  25.9 KiB |  00m00s
[27/82] Installing perl-Text-Tabs+Wrap- 100% |  23.3 MiB/s |  23.9 KiB |  00m00s
[28/82] Installing perl-if-0:0.61.000-5 100% |   0.0   B/s |   6.2 KiB |  00m00s
[29/82] Installing perl-locale-0:1.12-5 100% |   6.7 MiB/s |   6.9 KiB |  00m00s
[30/82] Installing perl-Net-SSLeay-0:1. 100% | 151.4 MiB/s |   1.4 MiB |  00m00s
[31/82] Installing perl-IO-Socket-SSL-0 100% | 172.7 MiB/s | 707.4 KiB |  00m00s
[32/82] Installing perl-Term-ANSIColor- 100% |  48.4 MiB/s |  99.2 KiB |  00m00s
[33/82] Installing perl-Term-Cap-0:1.18 100% |  29.9 MiB/s |  30.6 KiB |  00m00s
[34/82] Installing perl-POSIX-0:2.20-51 100% | 115.4 MiB/s | 236.4 KiB |  00m00s
[35/82] Installing perl-File-Temp-1:0.2 100% | 160.2 MiB/s | 164.1 KiB |  00m00s
[36/82] Installing perl-IPC-Open3-0:1.2 100% |  22.7 MiB/s |  23.3 KiB |  00m00s
[37/82] Installing perl-Class-Struct-0: 100% |  25.3 MiB/s |  25.9 KiB |  00m00s
[38/82] Installing perl-Pod-Simple-1:3. 100% | 139.3 MiB/s | 570.5 KiB |  00m00s
[39/82] Installing perl-HTTP-Tiny-0:0.0 100% | 150.6 MiB/s | 154.2 KiB |  00m00s
[40/82] Installing perl-Symbol-0:1.09-5 100% |   0.0   B/s |   7.2 KiB |  00m00s
[41/82] Installing perl-Socket-4:2.038- 100% |  61.6 MiB/s | 126.1 KiB |  00m00s
[42/82] Installing perl-SelectSaver-0:1 100% |   0.0   B/s |   2.6 KiB |  00m00s
[43/82] Installing perl-File-stat-0:1.1 100% |  12.7 MiB/s |  13.1 KiB |  00m00s
[44/82] Installing perl-podlators-1:6.0 100% | 104.6 MiB/s | 321.4 KiB |  00m00s
[45/82] Installing perl-Pod-Perldoc-0:3 100% |  82.6 MiB/s | 169.3 KiB |  00m00s
[46/82] Installing perl-Text-ParseWords 100% |  14.2 MiB/s |  14.6 KiB |  00m00s
[47/82] Installing perl-base-0:2.27-511 100% |   0.0   B/s |  12.9 KiB |  00m00s
[48/82] Installing perl-mro-0:1.29-511. 100% |  45.6 MiB/s |  46.7 KiB |  00m00s
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[50/82] Installing perl-Fcntl-0:1.18-51 100% |  48.9 MiB/s |  50.1 KiB |  00m00s
[51/82] Installing perl-IO-0:1.55-511.f 100% |  75.8 MiB/s | 155.3 KiB |  00m00s
[52/82] Installing perl-Pod-Usage-4:2.0 100% |  84.3 MiB/s |  86.3 KiB |  00m00s
[53/82] Installing perl-File-Basename-0 100% |   0.0   B/s |  14.6 KiB |  00m00s
[54/82] Installing perl-constant-0:1.33 100% |  26.7 MiB/s |  27.4 KiB |  00m00s
[55/82] Installing perl-Errno-0:1.38-51 100% |   0.0   B/s |   8.8 KiB |  00m00s
[56/82] Installing perl-Scalar-List-Uti 100% |  73.2 MiB/s | 149.9 KiB |  00m00s
[57/82] Installing perl-overload-0:1.37 100% |  70.3 MiB/s |  71.9 KiB |  00m00s
[58/82] Installing perl-parent-1:0.242- 100% |   0.0   B/s |  10.7 KiB |  00m00s
[59/82] Installing perl-vars-0:1.05-511 100% |   0.0   B/s |   4.3 KiB |  00m00s
[60/82] Installing perl-MIME-Base64-0:3 100% |  23.6 MiB/s |  48.4 KiB |  00m00s
[61/82] Installing perl-Getopt-Std-0:1. 100% |   0.0   B/s |  11.7 KiB |  00m00s
[62/82] Installing perl-Storable-1:3.32 100% | 114.3 MiB/s | 234.0 KiB |  00m00s
[63/82] Installing perl-Getopt-Long-1:2 100% |  71.9 MiB/s | 147.2 KiB |  00m00s
[64/82] Installing perl-Carp-0:1.54-511 100% |  46.6 MiB/s |  47.7 KiB |  00m00s
[65/82] Installing perl-Exporter-0:5.78 100% |  54.3 MiB/s |  55.6 KiB |  00m00s
[66/82] Installing perl-PathTools-0:3.9 100% |  90.1 MiB/s | 184.6 KiB |  00m00s
[67/82] Installing perl-DynaLoader-0:1. 100% |  31.7 MiB/s |  32.5 KiB |  00m00s
[68/82] Installing perl-Encode-4:3.21-5 100% | 224.7 MiB/s |   4.7 MiB |  00m00s
[69/82] Installing perl-libs-4:5.40.0-5 100% | 150.9 MiB/s |  10.0 MiB |  00m00s
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[71/82] Installing cmake-filesystem-0:3 100% |   3.5 MiB/s |   7.1 KiB |  00m00s
[72/82] Installing ncurses-c++-libs-0:6 100% | 159.1 MiB/s | 162.9 KiB |  00m00s
[73/82] Installing make-1:4.4.1-8.fc41. 100% | 180.0 MiB/s |   1.8 MiB |  00m00s
[74/82] Installing gcc-0:14.2.1-3.fc42. 100% | 304.4 MiB/s | 104.4 MiB |  00m00s
[75/82] Installing annobin-plugin-gcc-0 100% |  38.6 MiB/s | 987.3 KiB |  00m00s
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[78/82] Installing zlib-ng-compat-devel 100% | 105.8 MiB/s | 108.3 KiB |  00m00s
[79/82] Installing perl-FindBin-0:1.54- 100% |   7.0 MiB/s |   7.1 KiB |  00m00s
[80/82] Installing perl-lib-0:0.65-511. 100% |   0.0   B/s |   8.9 KiB |  00m00s
[81/82] Installing htslib-devel-0:1.15. 100% | 135.2 MiB/s | 415.5 KiB |  00m00s
warning: posix.fork(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead
warning: posix.wait(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead
warning: posix.exec(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead
[82/82] Installing htslib-tools-0:1.15. 100% |  12.4 MiB/s |   2.4 MiB |  00m00s
Warning: skipped PGP checks for 6 packages from repository: copr_base
Complete!
Finish: build setup for samtools-1.15.1-5.fc42.src.rpm
Start: rpmbuild samtools-1.15.1-5.fc42.src.rpm
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1721433600
Executing(%mkbuilddir): /bin/sh -e /var/tmp/rpm-tmp.g6EU8Y
+ umask 022
+ cd /builddir/build/BUILD/samtools-1.15.1-build
+ test -d /builddir/build/BUILD/samtools-1.15.1-build
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w /builddir/build/BUILD/samtools-1.15.1-build
+ /usr/bin/rm -rf /builddir/build/BUILD/samtools-1.15.1-build
+ /usr/bin/mkdir -p /builddir/build/BUILD/samtools-1.15.1-build
+ /usr/bin/mkdir -p /builddir/build/BUILD/samtools-1.15.1-build/SPECPARTS
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.dJIJk8
+ umask 022
+ cd /builddir/build/BUILD/samtools-1.15.1-build
+ cd /builddir/build/BUILD/samtools-1.15.1-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.pu363v
+ umask 022
+ cd /builddir/build/BUILD/samtools-1.15.1-build
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd samtools-1.15.1
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ '[' '-flto=auto -ffat-lto-objectsx' '!=' x ']'
++ find . -type f -name configure -print
+ for file in $(find . -type f -name configure -print)
+ /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\) = /__attribute__ ((used)) char (*f) () = /g' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\);/__attribute__ ((used)) char (*f) ();/g' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ /usr/bin/sed -r --in-place=.backup 's/^char \$2 \(\);/__attribute__ ((used)) char \$2 ();/g' ./configure
+ diff -u ./configure.backup ./configure
+ 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
+ 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	2024-09-26 13:37:54.122920950 +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
+ '[' 1 = 1 ']'
+++ dirname ./configure
++ find . -name config.guess -o -name config.sub
+ '[' 1 = 1 ']'
+ '[' x '!=' 'x-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' ']'
++ find . -name ltmain.sh
++ grep -q runstatedir=DIR ./configure
++ echo --runstatedir=/run
+ ./configure --build=x86_64-redhat-linux --host=x86_64-redhat-linux --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/libexec --localstatedir=/var --runstatedir=/run --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info 'CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer' 'LDFLAGS=-Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' --prefix=/usr --with-htslib=system
checking for gawk... gawk
checking for x86_64-redhat-linux-gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for C compiler warning flags... -Wall
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for htslib/sam.h... yes
checking for hts_version in -lhts... yes
checking for NcursesW wide-character library... yes
checking for working ncursesw/curses.h... yes
checking for library containing cbreak... none required
checking for zlib.h... yes
checking for inflate in -lz... yes
checking for library containing regcomp... none required
configure: creating ./config.status
config.status: creating config.mk
config.status: creating config.h
+ /usr/bin/make -O -j2 V=1 VERBOSE=1
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o bam.o bam.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer"' >> version.h
echo '#define SAMTOOLS_LDFLAGS "-Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes "' >> 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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o bam2bcf.o bam2bcf.c
bam2bcf.c: In function ‘bcf_call_glfgen’:
bam2bcf.c:81:33: warning: argument 2 range [18446744071562067968, 18446744073709551614] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
   81 |         bca->bases = (uint16_t*)realloc(bca->bases, 2 * bca->max_bases);
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/htslib/kstring.h:30,
                 from /usr/include/htslib/hts.h:37,
                 from bam2bcf.c:30:
/usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here
  683 | extern void *realloc (void *__ptr, size_t __size)
      |              ^~~~~~~
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o sample.o sample.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o phase.o phase.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o bam2depth.o bam2depth.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o coverage.o coverage.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o padding.o padding.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o bedcov.o bedcov.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o faidx.o faidx.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o dict.o dict.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o bamshuf.o bamshuf.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o bam_tview_curses.o bam_tview_curses.c
bam_tview_curses.c: In function ‘tv_win_help’:
bam_tview_curses.c:333:14: warning: ‘base’ is used uninitialized [-Wuninitialized]
  333 |     tview_t* base=(tview_t*)base;
      |              ^~~~
bam_tview_curses.c:333:14: note: ‘base’ was declared here
  333 |     tview_t* base=(tview_t*)base;
      |              ^~~~
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o stats.o stats.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o bedidx.o bedidx.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -o misc/ace2sam misc/ace2sam.o -lhts -lz 
gcc -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -o misc/maq2sam-long misc/maq2sam-long.o -lz 
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c
gcc -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -o misc/maq2sam-short misc/maq2sam-short.o -lz 
gcc  -L./lz4 -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz 
gcc  -L./lz4 -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -o misc/md5fa misc/md5fa.o -lhts -lz 
gcc  -L./lz4 -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -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,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -o misc/wgsim misc/wgsim.o -lm -lhts -lz 
gcc  -L./lz4 -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -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,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -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,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -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,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -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,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -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,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -o test/vcf-miniview test/vcf-miniview.o -lhts -lz  -lpthread
gcc  -L./lz4 -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -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,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -o samtools bam.o bam_aux.o bam_index.o bam_plcmd.o sam_view.o bam_fastq.o bam_cat.o bam_md.o bam_plbuf.o bam_reheader.o bam_sort.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o sample.o cut_target.o phase.o bam2depth.o coverage.o padding.o bedcov.o bamshuf.o faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o bam_quickcheck.o bam_addrprg.o bam_markdup.o tmp_file.o bam_ampliconclip.o amplicon_stats.o bam_import.o bam_samples.o bam_consensus.o consensus_pileup.o ./lz4/lz4.o libst.a -lhts -lncursesw -lm -lz  -lpthread
In function ‘bcf_call_glfgen’,
    inlined from ‘tv_pl_func’ at bam_tview.c:196:9:
bam2bcf.c:81:33: warning: argument 2 range [18446744071562067968, 18446744073709551614] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
   81 |         bca->bases = (uint16_t*)realloc(bca->bases, 2 * bca->max_bases);
      |                                 ^
/usr/include/stdlib.h: In function ‘tv_pl_func’:
/usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here
  683 | extern void *realloc (void *__ptr, size_t __size)
      |              ^
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.rqQwwb
+ umask 022
+ cd /builddir/build/BUILD/samtools-1.15.1-build
+ '[' /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT '!=' / ']'
+ rm -rf /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT
++ dirname /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT
+ mkdir -p /builddir/build/BUILD/samtools-1.15.1-build
+ mkdir /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd samtools-1.15.1
+ /usr/bin/make install DESTDIR=/builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT 'INSTALL=/usr/bin/install -p'
mkdir -p -m 755 /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/bin /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/bin /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/share/man/man1
/usr/bin/install -p samtools /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/bin
/usr/bin/install -p misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/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/BUILD/samtools-1.15.1-build/BUILDROOT/usr/bin
/usr/bin/install -p -m 644 doc/samtools*.1 misc/wgsim.1 /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/share/man/man1
++ grep -l '^#!/usr/bin/env perl' /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/bin/ace2sam /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/bin/blast2sam.pl /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/bin/bowtie2sam.pl /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/bin/export2sam.pl /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/bin/fasta-sanitize.pl /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/bin/interpolate_sam.pl /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/bin/maq2sam-long /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/bin/maq2sam-short /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/bin/md5fa /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/bin/md5sum-lite /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/bin/novo2sam.pl /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/bin/plot-ampliconstats /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/bin/plot-bamstats /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/bin/psl2sam.pl /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/bin/sam2vcf.pl /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/bin/samtools /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/bin/samtools.pl /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/bin/seq_cache_populate.pl /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/bin/soap2sam.pl /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/bin/wgsim /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/bin/wgsim_eval.pl /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/bin/zoom2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/bin/blast2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/bin/bowtie2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/bin/export2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/bin/fasta-sanitize.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/bin/interpolate_sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/bin/novo2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/bin/plot-ampliconstats
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/bin/plot-bamstats
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/bin/psl2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/bin/sam2vcf.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/bin/samtools.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/bin/seq_cache_populate.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/bin/soap2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/bin/wgsim_eval.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/bin/zoom2sam.pl
+ /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 1.15.1-5.fc42 --unique-debug-suffix -1.15.1-5.fc42.x86_64 --unique-debug-src-base samtools-1.15.1-5.fc42.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1
find-debuginfo: starting
Extracting debug info from 7 files
DWARF-compressing 7 files
sepdebugcrcfix: Updated 7 CRC32s, 0 CRC32s did match.
Creating .debug symlinks for symlinks to ELF files
Copying sources found by 'debugedit -l' to /usr/src/debug/samtools-1.15.1-5.fc42.x86_64
2442 blocks
find-debuginfo: done
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-ldconfig
+ /usr/lib/rpm/brp-compress
+ /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip
+ /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip
+ /usr/lib/rpm/check-rpaths
+ /usr/lib/rpm/redhat/brp-mangle-shebangs
+ /usr/lib/rpm/brp-remove-la-files
+ env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j2
+ /usr/lib/rpm/redhat/brp-python-hardlink
+ /usr/bin/add-determinism --brp -j2 /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT
Scanned 16 directories and 138 files,
               processed 0 inodes,
               0 modified (0 replaced + 0 rewritten),
               0 unsupported format, 0 errors
Reading /builddir/build/BUILD/samtools-1.15.1-build/SPECPARTS/rpm-debuginfo.specpart
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.4MwDCM
+ umask 022
+ cd /builddir/build/BUILD/samtools-1.15.1-build
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd samtools-1.15.1
+ ldd samtools
+ grep -E '/lib(64)?/libhts\.so\.'
	libhts.so.3 => /lib64/libhts.so.3 (0x00007f8b19218000)
+ 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/Jpr20lL5nU/bgzip.dat.gz
.. ok

bgzip -c -b 979200 -s 6 /tmp/Jpr20lL5nU/bgzip.dat.gz
.. ok

bgzip -c -b 652804 -s 6 /tmp/Jpr20lL5nU/bgzip.dat.gz
.. ok

/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools faidx /tmp/Jpr20lL5nU/faidx.fa 3:11-13 | grep -v '^>'
.. ok

/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools faidx /tmp/Jpr20lL5nU/faidx.fa.gz 3:11-13 | grep -v '^>'
.. ok

/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools faidx /tmp/Jpr20lL5nU/faidx.fa 2:998-1003 | grep -v '^>'
.. ok

/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools faidx /tmp/Jpr20lL5nU/faidx.fa.gz 2:998-1003 | grep -v '^>'
.. ok

/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools faidx /tmp/Jpr20lL5nU/faidx.fa 1:100-104 | grep -v '^>'
.. ok

/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools faidx /tmp/Jpr20lL5nU/faidx.fa.gz 1:100-104 | grep -v '^>'
.. ok

/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools faidx /tmp/Jpr20lL5nU/faidx.fa 1:99998-100007 | grep -v '^>'
.. ok

/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools faidx /tmp/Jpr20lL5nU/faidx.fa.gz 1:99998-100007 | grep -v '^>'
.. ok

/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fqidx /tmp/Jpr20lL5nU/fqidx.fq 3:11-13
.. ok

.. ok

/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fqidx /tmp/Jpr20lL5nU/fqidx.fq.gz 3:11-13
.. ok

.. ok

/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fqidx /tmp/Jpr20lL5nU/fqidx.fq 2:998-1003
.. ok

.. ok

/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fqidx /tmp/Jpr20lL5nU/fqidx.fq.gz 2:998-1003
.. ok

.. ok

/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fqidx /tmp/Jpr20lL5nU/fqidx.fq 1:100-104
.. ok

.. ok

/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fqidx /tmp/Jpr20lL5nU/fqidx.fq.gz 1:100-104
.. ok

.. ok

/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fqidx /tmp/Jpr20lL5nU/fqidx.fq 1:99998-100007
.. ok

.. ok

/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fqidx /tmp/Jpr20lL5nU/fqidx.fq.gz 1:99998-100007
.. ok

.. ok

test_dict:
	/builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/test/dat/dict.fa
.. ok

test_dict:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/Jpr20lL5nU/dict.fa.gz
.. ok

test_dict:
	cat /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/dict.fa | /builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/samtools dict -AH < /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/dict.alias.fa
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools view /tmp/Jpr20lL5nU/large_chrom.bam ref2
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools view /tmp/Jpr20lL5nU/large_chrom.bam ref2:1-541556283
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools index /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_a.bam && cat /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_a.bam.bai
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools view -X /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_b.bam /tmp/Jpr20lL5nU/test_input_1_b.bam.bai ref2
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools merge -O sam - -X -cp -R ref2 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_b.bam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_a.bam.bai /tmp/Jpr20lL5nU/test_input_1_b.bam.bai
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools index -c /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/auto_indexed.tmp.bam /tmp/Jpr20lL5nU/auto_indexed.csi && cat /tmp/Jpr20lL5nU/auto_indexed.csi
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools index /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/auto_indexed.tmp.cram /tmp/Jpr20lL5nU/auto_indexed.crai && cat /tmp/Jpr20lL5nU/auto_indexed.crai
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools index -c /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/auto_indexed.tmp.sam /tmp/Jpr20lL5nU/auto_indexed.csi && cat /tmp/Jpr20lL5nU/auto_indexed.csi
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools view -@ 2 /tmp/Jpr20lL5nU/large_chrom.bam ref2
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools view -@ 2 /tmp/Jpr20lL5nU/large_chrom.bam ref2:1-541556283
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools index -@ 2 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_a.bam && cat /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_a.bam.bai
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools view -@ 2 -X /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_b.bam /tmp/Jpr20lL5nU/test_input_1_b.bam.bai ref2
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools merge -@ 2 -O sam - -X -cp -R ref2 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_b.bam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_a.bam.bai /tmp/Jpr20lL5nU/test_input_1_b.bam.bai
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools index -@ 2 -c /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/auto_indexed.tmp.bam /tmp/Jpr20lL5nU/auto_indexed.csi && cat /tmp/Jpr20lL5nU/auto_indexed.csi
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools index -@ 2 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/auto_indexed.tmp.cram /tmp/Jpr20lL5nU/auto_indexed.crai && cat /tmp/Jpr20lL5nU/auto_indexed.crai
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools index -@ 2 -c /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/auto_indexed.tmp.sam /tmp/Jpr20lL5nU/auto_indexed.csi && cat /tmp/Jpr20lL5nU/auto_indexed.csi
.. ok

test_mpileup:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools mpileup -b /tmp/Jpr20lL5nU/mpileup.bam.list -f /tmp/Jpr20lL5nU/mpileup.ref.fa.gz -r17:100-150
.. ok

test_mpileup:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools mpileup -b /tmp/Jpr20lL5nU/mpileup.cram.list -f /tmp/Jpr20lL5nU/mpileup.ref.fa.gz -r17:100-150
.. ok

test_mpileup:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools mpileup -b /tmp/Jpr20lL5nU/mpileup.bam.urllist -f /tmp/Jpr20lL5nU/mpileup.ref.fa.gz -r17:100-150
.. ok

test_mpileup:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools mpileup -b /tmp/Jpr20lL5nU/mpileup.cram.urllist -f /tmp/Jpr20lL5nU/mpileup.ref.fa.gz -r17:100-150
.. ok

test_mpileup:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools mpileup -B --ff 0x14 -f /tmp/Jpr20lL5nU/mpileup.ref.fa.gz -r17:1050-1060 /tmp/Jpr20lL5nU/mpileup.1.bam | grep -v mpileup
.. ok

test_mpileup:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools mpileup -B --ff 0x14 -f /tmp/Jpr20lL5nU/mpileup.ref.fa.gz -r17:1050-1060 /tmp/Jpr20lL5nU/mpileup.1.cram | grep -v mpileup
.. ok

test_mpileup:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools mpileup /builddir/build/BUILD/samtools-1.15.1-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/Jpr20lL5nU/view.001.fogn (SAM input)     .. ok

	50: Count -R /tmp/Jpr20lL5nU/view.001.fogn (SAM input)      .. ok

	51: Filter -R /tmp/Jpr20lL5nU/view.001.fogn (BAM input)     .. ok

	52: Count -R /tmp/Jpr20lL5nU/view.001.fogn (BAM input)      .. ok

	53: Filter -R /tmp/Jpr20lL5nU/view.001.fogn (CRAM input)    .. ok

	54: Count -R /tmp/Jpr20lL5nU/view.001.fogn (CRAM input)     .. ok

	55: Filter -R /tmp/Jpr20lL5nU/view.001.fogn -r grp2 (SAM input).. ok

	56: Count -R /tmp/Jpr20lL5nU/view.001.fogn -r grp2 (SAM input).. ok

	57: Filter -R /tmp/Jpr20lL5nU/view.001.fogn -r grp2 (BAM input).. ok

	58: Count -R /tmp/Jpr20lL5nU/view.001.fogn -r grp2 (BAM input).. ok

	59: Filter -R /tmp/Jpr20lL5nU/view.001.fogn -r grp2 (CRAM input).. ok

	60: Count -R /tmp/Jpr20lL5nU/view.001.fogn -r grp2 (CRAM input).. ok

	61: Filter -r grp2 -R /tmp/Jpr20lL5nU/view.001.fogn (SAM input).. ok

	62: Count -r grp2 -R /tmp/Jpr20lL5nU/view.001.fogn (SAM input).. ok

	63: Filter -r grp2 -R /tmp/Jpr20lL5nU/view.001.fogn (BAM input).. ok

	64: Count -r grp2 -R /tmp/Jpr20lL5nU/view.001.fogn (BAM input).. ok

	65: Filter -r grp2 -R /tmp/Jpr20lL5nU/view.001.fogn (CRAM input).. ok

	66: Count -r grp2 -R /tmp/Jpr20lL5nU/view.001.fogn (CRAM input).. ok

	67: Filter -N /tmp/Jpr20lL5nU/view.001.forn (SAM input)     .. ok

	68: Count -N /tmp/Jpr20lL5nU/view.001.forn (SAM input)      .. ok

	69: Filter -N /tmp/Jpr20lL5nU/view.001.forn (BAM input)     .. ok

	70: Count -N /tmp/Jpr20lL5nU/view.001.forn (BAM input)      .. ok

	71: Filter -N /tmp/Jpr20lL5nU/view.001.forn (CRAM input)    .. ok

	72: Count -N /tmp/Jpr20lL5nU/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/Jpr20lL5nU/view.001.fobc (SAM input)  .. ok

	86: Count -D BC:/tmp/Jpr20lL5nU/view.001.fobc (SAM input)   .. ok

	87: Filter -D BC:/tmp/Jpr20lL5nU/view.001.fobc (BAM input)  .. ok

	88: Count -D BC:/tmp/Jpr20lL5nU/view.001.fobc (BAM input)   .. ok

	89: Filter -D BC:/tmp/Jpr20lL5nU/view.001.fobc (CRAM input) .. ok

	90: Count -D BC:/tmp/Jpr20lL5nU/view.001.fobc (CRAM input)  .. ok

	91: Filter -D BC:/tmp/Jpr20lL5nU/view.001.fobc -d BC:TGCA (SAM input).. ok

	92: Count -D BC:/tmp/Jpr20lL5nU/view.001.fobc -d BC:TGCA (SAM input).. ok

	93: Filter -D BC:/tmp/Jpr20lL5nU/view.001.fobc -d BC:TGCA (BAM input).. ok

	94: Count -D BC:/tmp/Jpr20lL5nU/view.001.fobc -d BC:TGCA (BAM input).. ok

	95: Filter -D BC:/tmp/Jpr20lL5nU/view.001.fobc -d BC:TGCA (CRAM input).. ok

	96: Count -D BC:/tmp/Jpr20lL5nU/view.001.fobc -d BC:TGCA (CRAM input).. ok

	97: Filter -d BC:TGCA -D BC:/tmp/Jpr20lL5nU/view.001.fobc (SAM input).. ok

	98: Count -d BC:TGCA -D BC:/tmp/Jpr20lL5nU/view.001.fobc (SAM input).. ok

	99: Filter -d BC:TGCA -D BC:/tmp/Jpr20lL5nU/view.001.fobc (BAM input).. ok

	100: Count -d BC:TGCA -D BC:/tmp/Jpr20lL5nU/view.001.fobc (BAM input).. ok

	101: Filter -d BC:TGCA -D BC:/tmp/Jpr20lL5nU/view.001.fobc (CRAM input).. ok

	102: Count -d BC:TGCA -D BC:/tmp/Jpr20lL5nU/view.001.fobc (CRAM input).. ok

	103: Filter -D RG:/tmp/Jpr20lL5nU/view.001.fogn (SAM input) .. ok

	104: Count -D RG:/tmp/Jpr20lL5nU/view.001.fogn (SAM input)  .. ok

	105: Filter -D RG:/tmp/Jpr20lL5nU/view.001.fogn (BAM input) .. ok

	106: Count -D RG:/tmp/Jpr20lL5nU/view.001.fogn (BAM input)  .. ok

	107: Filter -D RG:/tmp/Jpr20lL5nU/view.001.fogn (CRAM input).. ok

	108: Count -D RG:/tmp/Jpr20lL5nU/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-build/samtools-1.15.1/samtools view -o /tmp/Jpr20lL5nU/view.test115.sam -h -d TGCA /tmp/Jpr20lL5nU/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-build/samtools-1.15.1/samtools view -c -d TGCA /tmp/Jpr20lL5nU/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-build/samtools-1.15.1/samtools view -o /tmp/Jpr20lL5nU/view.test117.sam -h -d TGCA /tmp/Jpr20lL5nU/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-build/samtools-1.15.1/samtools view -c -d TGCA /tmp/Jpr20lL5nU/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-build/samtools-1.15.1/samtools view -o /tmp/Jpr20lL5nU/view.test119.sam -h -d TGCA /tmp/Jpr20lL5nU/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-build/samtools-1.15.1/samtools view -c -d TGCA /tmp/Jpr20lL5nU/view.test006.cram --no-PG


.. expected failure

	121: Filter -D BClong:/tmp/Jpr20lL5nU/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/Jpr20lL5nU/view.001.fobc"
	Failed command:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools view -o /tmp/Jpr20lL5nU/view.test121.sam -h -D BClong:/tmp/Jpr20lL5nU/view.001.fobc /tmp/Jpr20lL5nU/view.001.sam --no-PG


.. expected failure

	122: Count -D BClong:/tmp/Jpr20lL5nU/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/Jpr20lL5nU/view.001.fobc"
	Failed command:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools view -c -D BClong:/tmp/Jpr20lL5nU/view.001.fobc /tmp/Jpr20lL5nU/view.001.sam --no-PG


.. expected failure

	123: Filter -D BClong:/tmp/Jpr20lL5nU/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/Jpr20lL5nU/view.001.fobc"
	Failed command:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools view -o /tmp/Jpr20lL5nU/view.test123.sam -h -D BClong:/tmp/Jpr20lL5nU/view.001.fobc /tmp/Jpr20lL5nU/view.test001.bam --no-PG


.. expected failure

	124: Count -D BClong:/tmp/Jpr20lL5nU/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/Jpr20lL5nU/view.001.fobc"
	Failed command:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools view -c -D BClong:/tmp/Jpr20lL5nU/view.001.fobc /tmp/Jpr20lL5nU/view.test001.bam --no-PG


.. expected failure

	125: Filter -D BClong:/tmp/Jpr20lL5nU/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/Jpr20lL5nU/view.001.fobc"
	Failed command:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools view -o /tmp/Jpr20lL5nU/view.test125.sam -h -D BClong:/tmp/Jpr20lL5nU/view.001.fobc /tmp/Jpr20lL5nU/view.test006.cram --no-PG


.. expected failure

	126: Count -D BClong:/tmp/Jpr20lL5nU/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/Jpr20lL5nU/view.001.fobc"
	Failed command:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools view -c -D BClong:/tmp/Jpr20lL5nU/view.001.fobc /tmp/Jpr20lL5nU/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-build/samtools-1.15.1/samtools view -o /tmp/Jpr20lL5nU/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/Jpr20lL5nU/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-build/samtools-1.15.1/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/Jpr20lL5nU/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-build/samtools-1.15.1/samtools view -o /tmp/Jpr20lL5nU/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/Jpr20lL5nU/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-build/samtools-1.15.1/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/Jpr20lL5nU/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-build/samtools-1.15.1/samtools view -o /tmp/Jpr20lL5nU/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/Jpr20lL5nU/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-build/samtools-1.15.1/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/Jpr20lL5nU/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-build/samtools-1.15.1/test/dat/view.002.01.bed  (BAM input).. ok

	335: Count -L /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/view.002.01.bed  (BAM input).. ok

	336: Region -L /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/view.002.01.bed  (CRAM input).. ok

	337: Count -L /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/view.002.01.bed  (CRAM input).. ok

	338: Region -L /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/view.002.02.bed  (BAM input).. ok

	339: Count -L /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/view.002.02.bed  (BAM input).. ok

	340: Region -L /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/view.002.02.bed  (CRAM input).. ok

	341: Count -L /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/view.002.02.bed  (CRAM input).. ok

	342: Region -L /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/view.001.01.bed  (BAM input).. ok

	343: Count -L /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/view.001.01.bed  (BAM input).. ok

	344: Region -L /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/view.001.01.bed  (CRAM input).. ok

	345: Count -L /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/view.001.01.bed  (CRAM input).. ok

	346: Region -L /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/view.001.02.bed  (BAM input).. ok

	347: Count -L /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/view.001.02.bed  (BAM input).. ok

	348: Region -L /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/view.001.02.bed  (CRAM input).. ok

	349: Count -L /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/view.001.02.bed  (CRAM input).. ok

	350: Region -L /builddir/build/BUILD/samtools-1.15.1-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-build/samtools-1.15.1/samtools head /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/view.001.sam
.. ok

test_head:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools head -h 0 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/view.001.sam
.. ok

test_head:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools head -h 1 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/view.001.sam
.. ok

test_head:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools head -h 5 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/view.001.sam
.. ok

test_head:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools head -h 29 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/view.001.sam
.. ok

test_head:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools head -h 30 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/view.001.sam
.. ok

test_head:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools head -n 0 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/view.001.sam
.. ok

test_head:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools head -n 1 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/view.001.sam
.. ok

test_head:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools head -n 5 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/view.001.sam
.. ok

test_head:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools head -h 5 -n 5 < /builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/samtools import -0 test/bam2fq/1.1.fq.expected  | /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fastq -0 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/0.fq
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools import -s test/bam2fq/1.1.fq.expected  | /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fastq -0 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/0.fq
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools import -s test/bam2fq/5.s.fq.expected  | /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fastq -s /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/s.fq
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/samtools fastq -1 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/2.fq
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/samtools fastq -N -1 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/2.fq
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/samtools fastq -i --index-format 'i*i*' -1 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/2.fq
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/samtools fastq --barcode-tag OX -i --index-format 'i*i*' -1 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/2.fq
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/samtools fastq -N -T RG,BC,QT -1 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/2.fq
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/samtools fastq -N -T RG,BC,QT,MD,ia -1 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/2.fq
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.15.1-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-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-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-build/samtools-1.15.1/samtools import test/import/2.interleaved.fq -T ""
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools import test/import/3.interleaved.fq -i
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools import test/import/4.aux.fq -T "*"
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools import test/import/4.aux.fq -T ""
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.15.1-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-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-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-build/samtools-1.15.1/samtools fastq  -1 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fastq  -s /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fastq  -s /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/bam2fq.002.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fastq  -s /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/bam2fq.003.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fastq  --barcode-tag BC --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/bc.fq -s /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/bam2fq.004.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fastq  --barcode-tag BC -O --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/bc.fq -s /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/bam2fq.004.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fastq  --barcode-tag BC -O --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/bc.fq -s /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/bam2fq.010.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fastq  --barcode-tag BC -N --index-format 'n*i*' --i1 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/bc_split.fq -s /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/bam2fq.005.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fastq  -N -t -s /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/bam2fq.005.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fastq  -N -t -T MD,ia -s /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/bam2fq.005.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fastq  --barcode-tag BC -i --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/i.fq -s /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/bam2fq.004.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fastq  --barcode-tag BC -i --index-format 'i*i*' --i1 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/i.fq -s /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/bam2fq.005.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fastq  -i --index-format 'i*i*' -s /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/bam2fq.005.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fastq  -1 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/bam2fq.703.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fastq  -N -1 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/o.fq -2 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/o.fq /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fasta  -N -1 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/o.fa -2 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/o.fa /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fastq  -N -o /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/o.fq /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fastq  -N -s /tmp/Jpr20lL5nU/bam2fq.discard.s.fq -0 /tmp/Jpr20lL5nU/bam2fq.discard.0.fq /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fastq  -T ba,bb,bc,bd,be,bf,bg /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/bam2fq.013.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fastq  --index-format 'i8n1i8' --i1 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/i1.fq --i2 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/i2.fq -0 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/0.fq /builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/samtools fastq -@ 2 -1 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fastq -@ 2 -s /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fastq -@ 2 -s /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/bam2fq.002.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fastq -@ 2 -s /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/bam2fq.003.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fastq -@ 2 --barcode-tag BC --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/bc.fq -s /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/bam2fq.004.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/bc.fq -s /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/bam2fq.004.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/bc.fq -s /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/bam2fq.010.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fastq -@ 2 --barcode-tag BC -N --index-format 'n*i*' --i1 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/bc_split.fq -s /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/bam2fq.005.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fastq -@ 2 -N -t -s /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/bam2fq.005.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fastq -@ 2 -N -t -T MD,ia -s /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/bam2fq.005.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/i.fq -s /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/bam2fq.004.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'i*i*' --i1 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/i.fq -s /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/bam2fq.005.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fastq -@ 2 -i --index-format 'i*i*' -s /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/bam2fq.005.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fastq -@ 2 -1 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/bam2fq.703.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fastq -@ 2 -N -1 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/o.fq -2 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/o.fq /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fasta -@ 2 -N -1 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/o.fa -2 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/o.fa /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fastq -@ 2 -N -o /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/o.fq /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fastq -@ 2 -N -s /tmp/Jpr20lL5nU/bam2fq.discard.s.fq -0 /tmp/Jpr20lL5nU/bam2fq.discard.0.fq /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fastq -@ 2 -T ba,bb,bc,bd,be,bf,bg /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/bam2fq.013.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fastq -@ 2 --index-format 'i8n1i8' --i1 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/i1.fq --i2 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/i2.fq -0 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/0.fq /builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/samtools stats -r /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/stat/test.fa /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/stat/1_map_cigar.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/samtools stats -r /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/stat/test.fa /builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/samtools stats -r /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/stat/test.fa /builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/samtools stats -r /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/stat/test.fa /builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/samtools stats -r /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/stat/test.fa /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/stat/5_insert_cigar.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/samtools stats -r /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/stat/test.fa -i 0 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/stat/5_insert_cigar.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools stats -r /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/stat/test.fa /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/stat/7_supp.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/stat/7_supp_large.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools stats -r /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/stat/test.fa /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/stat/8_secondary.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/stat/8_secondary_large.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools stats -S RG -r /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/stat/test.fa /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/stat/1_map_cigar.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools stats -S RG -r /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/stat/test.fa /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/stat/10_map_cigar.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools stats -t /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/stat/11.stats.targets /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/stat/11_target.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/samtools stats -g 4 -t /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/stat/11.stats.targets /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/stat/11_target.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools stats -g 4 /builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/stat/12_overlaps.bam -t /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/stat/12_3reads.bed | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/stat/12_overlaps.bam -p -t /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/stat/12_3reads.bed | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/stat/12_overlaps.bam -t /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/stat/12_2reads.bed | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/stat/12_overlaps.bam -p -t /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/stat/12_2reads.bed | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/stat/13_barcodes_ok.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/stat/13_barcodes_fail_bc_length.sam | tail -n+4

	/builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/stat/13_barcodes_fail_hyphen.sam | tail -n+4

	/builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/stat/13_barcodes_fail_qt_length.sam | tail -n+4

	/builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/samtools stats -I s1 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/stat/11_target.bam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools stats -I grp2 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/stat/11_target.bam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools stats -I grp3 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/stat/11_target.bam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools stats -I Sample /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/stat/11_target.bam | tail -n+4
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools merge -s 1 -O sam - /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_c.sam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools merge -s 1 -O sam - /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_b.bam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_c.bam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools merge -s 1 -O sam -b /tmp/Eehws_IZBs - /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_a.bam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools merge -s 1 -O sam - /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_b.bam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools merge -r -s 1 -O sam - /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_c.sam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools merge -cp -s 1 -O sam - /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_b.sam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools merge -s 1 -O sam - /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_a_regex.sam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_b_regex.sam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools merge -o - -s 1 -O sam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_c.sam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/Jpr20lL5nU/merge.tag.1.bam /tmp/Jpr20lL5nU/merge.tag.2.bam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/Jpr20lL5nU/merge.tag.3.bam /tmp/Jpr20lL5nU/merge.tag.4.bam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools merge --no-PG -O SAM - /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/merge/test_no_pg_rg_co.sam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools merge --no-PG -O SAM -L /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/merge/merge.bed - /tmp/Jpr20lL5nU/merge.bed.1.bam /tmp/Jpr20lL5nU/merge.bed.2.bam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools merge -@ 2 -s 1 -O sam - /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_c.sam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools merge -@ 2 -s 1 -O sam - /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_b.bam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_c.bam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools merge -@ 2 -s 1 -O sam -b /tmp/RYPjhFMsaQ - /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_a.bam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools merge -@ 2 -s 1 -O sam - /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_b.bam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools merge -@ 2 -r -s 1 -O sam - /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_c.sam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools merge -@ 2 -cp -s 1 -O sam - /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_b.sam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools merge -@ 2 -s 1 -O sam - /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_a_regex.sam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_b_regex.sam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools merge -@ 2 -o - -s 1 -O sam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_c.sam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/Jpr20lL5nU/merge.tag.1.bam /tmp/Jpr20lL5nU/merge.tag.2.bam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/Jpr20lL5nU/merge.tag.3.bam /tmp/Jpr20lL5nU/merge.tag.4.bam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools merge -@ 2 --no-PG -O SAM - /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/merge/test_no_pg_rg_co.sam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools merge -@ 2 --no-PG -O SAM -L /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/merge/merge.bed - /tmp/Jpr20lL5nU/merge.bed.1.bam /tmp/Jpr20lL5nU/merge.bed.2.bam
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools sort /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_a.bam /tmp/Jpr20lL5nU/sortout
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools sort -f /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_a.bam /tmp/Jpr20lL5nU/sortout.bam
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools sort -o /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_a.bam /tmp/Jpr20lL5nU/sorttmp
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools sort -m 10M /builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/samtools sort -n -m 10M /builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/samtools sort -t RG -m 10M /builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/samtools sort -n -t RG -m 10M /builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/samtools sort -t AS -m 10M /builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/samtools sort -t FI -m 10M /builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/samtools sort -@ 2 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_a.bam /tmp/Jpr20lL5nU/sortout
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools sort -@ 2 -f /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_a.bam /tmp/Jpr20lL5nU/sortout.bam
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools sort -@ 2 -o /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_a.bam /tmp/Jpr20lL5nU/sorttmp
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools sort -@ 2 -m 10M /builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/samtools sort -@ 2 -n -m 10M /builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/samtools sort -@ 2 -t RG -m 10M /builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/samtools sort -@ 2 -n -t RG -m 10M /builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/samtools sort -@ 2 -t AS -m 10M /builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/samtools sort -@ 2 -t FI -m 10M /builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/samtools collate --output-fmt=sam -O /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_d.sam
.. ok

test_collate:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools collate -o /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/collate/collate1.tmp.sam  /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_d.sam
.. ok

test_collate:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools collate -o /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/collate/collate2.tmp.sam  /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_d.sam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/collate/collate2.tmp
.. ok

test_collate:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools collate --output-fmt=sam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_d.sam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/collate/collate3.tmp
.. ok

test_collate:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools collate --output-fmt=sam -f /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/collate/fast_collate.sam -o /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/collate/1_fast_collate.sam
.. ok

test_collate:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools collate --output-fmt=sam -f -r 4 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/collate/fast_collate.sam -o /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/collate/2_fast_collate_with_tmp.sam
.. ok

test_collate:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools collate -@ 2 --output-fmt=sam -O /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_d.sam
.. ok

test_collate:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools collate -@ 2 -o /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/collate/collate1.tmp.sam  /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_d.sam
.. ok

test_collate:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools collate -@ 2 -o /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/collate/collate2.tmp.sam  /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_d.sam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/collate/collate2.tmp
.. ok

test_collate:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools collate -@ 2 --output-fmt=sam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_d.sam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/collate/collate3.tmp
.. ok

test_collate:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools collate -@ 2 --output-fmt=sam -f /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/collate/fast_collate.sam -o /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/collate/1_fast_collate.sam
.. ok

test_collate:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools collate -@ 2 --output-fmt=sam -f -r 4 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/collate/fast_collate.sam -o /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/collate/2_fast_collate_with_tmp.sam
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fixmate -O sam /builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/samtools fixmate -O sam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/fixmate/2_isize_overflow.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fixmate -O sam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/fixmate/3_reverse_read_pp_lt.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fixmate -O sam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/fixmate/4_reverse_read_pp_equal.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fixmate -cO sam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/fixmate/5_ct.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fixmate -cO sam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/fixmate/6_ct_replace.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fixmate -O sam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/fixmate/7_two_read_mapped.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fixmate -O sam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/fixmate/8_isize_overflow_64bit.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fixmate -@ 2 -O sam /builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/samtools fixmate -@ 2 -O sam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/fixmate/2_isize_overflow.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fixmate -@ 2 -O sam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/fixmate/3_reverse_read_pp_lt.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fixmate -@ 2 -O sam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/fixmate/4_reverse_read_pp_equal.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fixmate -@ 2 -cO sam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/fixmate/5_ct.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fixmate -@ 2 -cO sam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/fixmate/6_ct_replace.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fixmate -@ 2 -O sam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/fixmate/7_two_read_mapped.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fixmate -@ 2 -O sam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/fixmate/8_isize_overflow_64bit.sam -
.. ok

/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools calmd -uAr /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/mpileup.1.sam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/mpileup.ref.fa
.. ok

/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools calmd -@ 2 -uAr /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/mpileup.1.sam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/mpileup.ref.fa
.. ok

test_idxstat:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools idxstats /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_a.bam
.. ok

test_idxstat:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools idxstats /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_a.cram
.. ok

test_idxstat:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools idxstats /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/test_input_1_a.sam
.. ok

test_quickcheck:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools quickcheck /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/quickcheck/1.quickcheck.badeof.bam
.. ok

test_quickcheck:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools quickcheck /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/quickcheck/2.quickcheck.badheader.bam
.. ok

test_quickcheck:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools quickcheck /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/quickcheck/3.quickcheck.ok.bam
.. ok

test_quickcheck:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools quickcheck /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/quickcheck/4.quickcheck.ok.bam
.. ok

test_quickcheck:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools quickcheck /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/quickcheck/5.quickcheck.scramble30.truncated.cram
.. ok

test_quickcheck:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools quickcheck /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/quickcheck/6.quickcheck.cram21.ok.cram
.. ok

test_quickcheck:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools quickcheck /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/quickcheck/7.quickcheck.cram30.ok.cram
.. ok

test_quickcheck:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools quickcheck /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/quickcheck/8.quickcheck.cram21.truncated.cram
.. ok

test_quickcheck:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools quickcheck /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/quickcheck/9.quickcheck.cram30.truncated.cram
.. ok

test_quickcheck:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools quickcheck /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/quickcheck/10.quickcheck.notargets.bam
.. ok

test_quickcheck:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools quickcheck -v  /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/quickcheck/1.quickcheck.badeof.bam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/quickcheck/2.quickcheck.badheader.bam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/quickcheck/3.quickcheck.ok.bam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/quickcheck/4.quickcheck.ok.bam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/quickcheck/5.quickcheck.scramble30.truncated.cram /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/quickcheck/6.quickcheck.cram21.ok.cram /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/quickcheck/7.quickcheck.cram30.ok.cram /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/quickcheck/8.quickcheck.cram21.truncated.cram /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/quickcheck/9.quickcheck.cram30.truncated.cram /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,'
.. ok

test_quickcheck:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools quickcheck -uv /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,'
.. ok

test_reheader:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools reheader /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/reheader/hdr.sam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/view.001.tmp.bam | /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools view -h --no-PG | perl -pe 's/	VN:.*//'
.. ok

test_reheader:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools reheader /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/reheader/hdr.sam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/view.001.tmp.v21.cram | /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools view -h --no-PG | perl -pe 's/	VN:.*//'
.. ok

test_reheader:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools reheader /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/reheader/hdr.sam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/view.001.tmp.v30.cram | /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools view -h --no-PG | perl -pe 's/	VN:.*//'
.. ok

test_reheader:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools reheader --in-place /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/reheader/hdr.sam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/view.001.tmp.v21.cram && /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools view -h --no-PG /builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/samtools reheader --in-place /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/reheader/hdr.sam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/view.001.tmp.v30.cram && /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools view -h --no-PG /builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/view.001.tmp.bam | /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools view -h --no-PG | perl -pe 's/	VN:.*//'
.. ok

test_reheader:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/dat/view.001.tmp.v30.cram | /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools view -h --no-PG | perl -pe 's/	VN:.*//'
.. ok

test_addrprg:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools addreplacerg -O sam -m overwrite_all /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/addrprg/1_fixup.sam
.. ok

test_addrprg:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools addreplacerg -O sam -m orphan_only /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/addrprg/2_fixup_orphan.sam
.. ok

test_addrprg:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools addreplacerg -O sam -R '1#9' /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/addrprg/1_fixup.sam
.. ok

test_addrprg:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools addreplacerg -O sam -r '@RG\tID:1#8\tCN:SC' /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/addrprg/4_fixup_norg.sam
.. ok

test_addrprg:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools addreplacerg -O sam -m overwrite_all -R '1#8' /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/addrprg/1_fixup.sam
.. ok

test_addrprg:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools addreplacerg -O sam -r 'ID:1#8' -r 'CN:SC' /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/addrprg/4_fixup_norg.sam
.. ok

test_addrprg:
	/builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/test/addrprg/1_fixup.sam
.. ok

test_addrprg:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools addreplacerg -@ 2 -O sam -m overwrite_all /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/addrprg/1_fixup.sam
.. ok

test_addrprg:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools addreplacerg -@ 2 -O sam -m orphan_only /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/addrprg/2_fixup_orphan.sam
.. ok

test_addrprg:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools addreplacerg -@ 2 -O sam -R '1#9' /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/addrprg/1_fixup.sam
.. ok

test_addrprg:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools addreplacerg -@ 2 -O sam -r '@RG\tID:1#8\tCN:SC' /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/addrprg/4_fixup_norg.sam
.. ok

test_addrprg:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools addreplacerg -@ 2 -O sam -m overwrite_all -R '1#8' /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/addrprg/1_fixup.sam
.. ok

test_addrprg:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools addreplacerg -@ 2 -O sam -r 'ID:1#8' -r 'CN:SC' /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/addrprg/4_fixup_norg.sam
.. ok

test_addrprg:
	/builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/test/addrprg/1_fixup.sam
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools markdup -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/samtools markdup -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/samtools markdup -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/samtools markdup -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/samtools markdup -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/markdup/5_markdup.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools markdup -O sam -r --no-PG /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/markdup/6_remove_dups.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools markdup -S -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/markdup/7_mark_supp_dup.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools markdup -S -d 100 --mode s -t -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/markdup/8_optical_dup.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/test/markdup/9_optical_dup_qcfail.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/test/markdup/10_optical_chain.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/test/markdup/10_optical_chain.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/test/markdup/11_optical_dup_regex.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/test/markdup/11_optical_dup_regex.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/test/markdup/12_optical_chain_regex.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools markdup -@ 2 -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/samtools markdup -@ 2 -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/samtools markdup -@ 2 -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/samtools markdup -@ 2 -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/samtools markdup -@ 2 -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/markdup/5_markdup.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools markdup -@ 2 -O sam -r --no-PG /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/markdup/6_remove_dups.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools markdup -@ 2 -S -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/markdup/7_mark_supp_dup.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/test/markdup/8_optical_dup.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/test/markdup/9_optical_dup_qcfail.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/test/markdup/10_optical_chain.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/test/markdup/10_optical_chain.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/test/markdup/11_optical_dup_regex.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/test/markdup/11_optical_dup_regex.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/test/markdup/12_optical_chain_regex.sam -
.. ok

test_bedcov:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools bedcov /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/bedcov/bedcov.bed /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/bedcov/bedcov.bam
.. ok

test_bedcov:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools bedcov -j /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/bedcov/bedcov.bed /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/bedcov/bedcov.bam
.. ok

test_bedcov:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools bedcov -g512 -G2048 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/bedcov/bedcov_gG.bed /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/bedcov/bedcov.bam
.. ok

test_split:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools split  --output-fmt sam -u /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/split/split.tmp.%!.%. /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/split/split.sam
.. ok

test_split:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools split  -@ 2 --output-fmt sam -u /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/split/split.tmp.%!.%. /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/split/split.sam
.. ok

test_large_positions:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools view -h --no-PG /tmp/Jpr20lL5nU/longref.sam.gz
.. ok

test_large_positions:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools view -h --no-PG /tmp/Jpr20lL5nU/longref.sam.gz CHROMOSOME_I:10000000114-10000000168
.. ok

test_large_positions:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools view -h --no-PG -L /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/large_pos/test.bed /tmp/Jpr20lL5nU/longref.sam.gz
.. ok

test_large_positions:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools sort -O sam --no-PG -m 10M /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/large_pos/longref_name.sam
.. ok

test_large_positions:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools merge -O sam --no-PG - /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/large_pos/longref.sam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/large_pos/longref2.sam
.. ok

test_large_positions:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools depth /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/large_pos/longref.sam
.. ok

test_large_positions:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools depth -b /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/large_pos/test.bed /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/large_pos/longref.sam
.. ok

test_large_positions:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/Jpr20lL5nU/longref.sam.gz
.. ok

test_large_positions:
	/builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/samtools fixmate -O sam --no-PG - - |
                     /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools sort    -O sam --no-PG -m 10M
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam -b /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --hard-clip -b /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand -b /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools ampliconclip --no-PG  --keep-tag --output-fmt=sam --original -b /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools ampliconclip --no-PG --output-fmt=sam -b /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/ampliconclip/2_both_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam -b /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand -b /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools ampliconclip -@ 2 --no-PG  --keep-tag --output-fmt=sam --original -b /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam -b /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/ampliconclip/2_both_test_data.sam
.. ok

test_ampliconstats:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools ampliconstats -@ 2 -S -t 50 -d 1,20,100 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/ampliconclip/1_hard_clipped.expected.sam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/ampliconclip/1_soft_clipped.expected.sam /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/ampliconclip/1_soft_clipped_strand.expected.sam /builddir/build/BUILD/samtools-1.15.1-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-build/samtools-1.15.1/samtools ampliconstats -@ 2 -c 0 /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/test/ampliconclip/multi_ref.bed /builddir/build/BUILD/samtools-1.15.1-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-1.15.1-5.fc42.x86_64
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.PzMYzM
+ umask 022
+ cd /builddir/build/BUILD/samtools-1.15.1-build
+ cd samtools-1.15.1
+ DOCDIR=/builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/share/doc/samtools
+ export LC_ALL=C.UTF-8
+ LC_ALL=C.UTF-8
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/share/doc/samtools
+ cp -pr /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/AUTHORS /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/share/doc/samtools
+ cp -pr /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/ChangeLog.old /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/share/doc/samtools
+ cp -pr /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/NEWS /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/share/doc/samtools
+ cp -pr /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/examples /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/share/doc/samtools
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.nhLeuG
+ umask 022
+ cd /builddir/build/BUILD/samtools-1.15.1-build
+ cd samtools-1.15.1
+ LICENSEDIR=/builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/share/licenses/samtools
+ export LC_ALL=C.UTF-8
+ LC_ALL=C.UTF-8
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/share/licenses/samtools
+ cp -pr /builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/LICENSE /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT/usr/share/licenses/samtools
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: samtools = 1.15.1-5.fc42 samtools(x86-64) = 1.15.1-5.fc42
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: /usr/bin/perl libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.7)(64bit) libc.so.6(GLIBC_ABI_DT_RELR)(64bit) libhts.so.3()(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.29)(64bit) libncursesw.so.6()(64bit) libtinfo.so.6()(64bit) libz.so.1()(64bit) rtld(GNU_HASH)
Processing files: samtools-debugsource-1.15.1-5.fc42.x86_64
Provides: samtools-debugsource = 1.15.1-5.fc42 samtools-debugsource(x86-64) = 1.15.1-5.fc42
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: samtools-debuginfo-1.15.1-5.fc42.x86_64
Provides: debuginfo(build-id) = 2279c09943d2baad545922a8876f3a2e8b10ea7e debuginfo(build-id) = 28249aa3a4641e99c73246041fe1450bd1349ea5 debuginfo(build-id) = 377a62e08c90a0443510a8f2af5b1f6bbea5dccc debuginfo(build-id) = 577cc39dce3c7879b35112303a0075f94f8f49e9 debuginfo(build-id) = 6744ea3914466bc189b12851840611e27f8fbfe4 debuginfo(build-id) = b118d555e7c358bfeda5c567d07be64f0fd0cc9f debuginfo(build-id) = fc7b34a7575bc2552fc31803affbd4df133119a8 samtools-debuginfo = 1.15.1-5.fc42 samtools-debuginfo(x86-64) = 1.15.1-5.fc42
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: samtools-debugsource(x86-64) = 1.15.1-5.fc42
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILD/samtools-1.15.1-build/BUILDROOT
Wrote: /builddir/build/RPMS/samtools-1.15.1-5.fc42.x86_64.rpm
Wrote: /builddir/build/RPMS/samtools-debuginfo-1.15.1-5.fc42.x86_64.rpm
Wrote: /builddir/build/RPMS/samtools-debugsource-1.15.1-5.fc42.x86_64.rpm
Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.11TPb4
+ umask 022
+ cd /builddir/build/BUILD/samtools-1.15.1-build
+ test -d /builddir/build/BUILD/samtools-1.15.1-build
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w /builddir/build/BUILD/samtools-1.15.1-build
+ rm -rf /builddir/build/BUILD/samtools-1.15.1-build
+ RPM_EC=0
++ jobs -p
+ exit 0
Finish: rpmbuild samtools-1.15.1-5.fc42.src.rpm
Finish: build phase for samtools-1.15.1-5.fc42.src.rpm
INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/fedora-rawhide-x86_64-1727357827.031697/root/var/log/dnf5.log
INFO: Done(/var/lib/copr-rpmbuild/results/samtools-1.15.1-5.fc42.src.rpm) Config(child) 1 minutes 8 seconds
INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results
INFO: Cleaning up build root ('cleanup_on_success=True')
Start: clean chroot
INFO: unmounting tmpfs.
Finish: clean chroot
Finish: run
Running RPMResults tool
Package info:
{
    "packages": [
        {
            "name": "samtools",
            "epoch": null,
            "version": "1.15.1",
            "release": "5.fc42",
            "arch": "x86_64"
        },
        {
            "name": "samtools",
            "epoch": null,
            "version": "1.15.1",
            "release": "5.fc42",
            "arch": "src"
        },
        {
            "name": "samtools-debuginfo",
            "epoch": null,
            "version": "1.15.1",
            "release": "5.fc42",
            "arch": "x86_64"
        },
        {
            "name": "samtools-debugsource",
            "epoch": null,
            "version": "1.15.1",
            "release": "5.fc42",
            "arch": "x86_64"
        }
    ]
}
RPMResults finished