Warning: Permanently added '3.80.124.161' (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-aarch64 --chroot fedora-rawhide-aarch64


Version: 0.73
PID: 35364
Logging PID: 35365
Task:
{'allow_user_ssh': False,
 'appstream': False,
 'background': False,
 'build_id': 8070929,
 'buildroot_pkgs': [],
 'chroot': 'fedora-rawhide-aarch64',
 '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-aarch64/',
            '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-aarch64',
 '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-h2cy18qe/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-h2cy18qe/samtools', '--depth', '500', '--no-single-branch', '--recursive']
cwd: .
rc: 0
stdout: 
stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-h2cy18qe/samtools'...

Running: git checkout 2234957ff21a1fd78b4fb0c2efdd7a750cf6ddef --

cmd: ['git', 'checkout', '2234957ff21a1fd78b4fb0c2efdd7a750cf6ddef', '--']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-h2cy18qe/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

cmd: ['copr-distgit-client', 'sources']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-h2cy18qe/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
/usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated
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  26.2M      0 --:--:-- --:--:-- --:--:-- 26.2M
INFO: Reading stdout from command: md5sum samtools-1.15.1.tar.bz2

Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-h2cy18qe/samtools/samtools.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-h2cy18qe/samtools --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1727357069.761619 -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-h2cy18qe/samtools/samtools.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-h2cy18qe/samtools --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1727357069.761619 -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-h2cy18qe/samtools/samtools.spec)  Config(fedora-rawhide-aarch64)
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-aarch64-bootstrap-1727357069.761619/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-aarch64-bootstrap-1727357069.761619/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/c61d04b00f3a194921c0189de421106de57372ce5a153e630de8a2adaa7428bb/merged
INFO: umounting image registry.fedoraproject.org/fedora:rawhide (/var/lib/containers/storage/overlay/c61d04b00f3a194921c0189de421106de57372ce5a153e630de8a2adaa7428bb/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-aarch64-1727357069.761619/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.aarch64
  rpm-sequoia-1.7.0-2.fc41.aarch64
  dnf5-5.2.6.2-1.fc42.aarch64
  dnf5-plugins-5.2.6.2-1.fc42.aarch64
Start: installing minimal buildroot with dnf5
Updating and loading repositories:
 fedora                                 100% | 119.0 KiB/s |   7.1 KiB |  00m00s
 Copr repository                        100% |  90.4 KiB/s |   1.5 KiB |  00m00s
 Copr repository                        100% |  41.4 MiB/s |   2.9 MiB |  00m00s
Repositories loaded.
Package                            Arch    Version                    Repository      Size
Installing group/module packages:
 bash                              aarch64 5.2.32-2.fc42              fedora       8.3 MiB
 bzip2                             aarch64 1.0.8-19.fc41              fedora     427.6 KiB
 coreutils                         aarch64 9.5-9.fc42                 fedora      20.8 MiB
 cpio                              aarch64 2.15-2.fc41                fedora       1.2 MiB
 diffutils                         aarch64 3.10-8.fc41                fedora       2.1 MiB
 fedora-release-common             noarch  42-0.3                     fedora      19.4 KiB
 findutils                         aarch64 1:4.10.0-4.fc41            fedora       2.1 MiB
 gawk                              aarch64 5.3.0-4.fc41               fedora       4.2 MiB
 glibc-minimal-langpack            aarch64 2.40.9000-5.fc42           copr_base    0.0   B
 grep                              aarch64 3.11-9.fc41                fedora       1.1 MiB
 gzip                              aarch64 1.13-2.fc41                fedora     488.9 KiB
 info                              aarch64 7.1.1-1.fc42               fedora     613.6 KiB
 patch                             aarch64 2.7.6-25.fc41              fedora     390.6 KiB
 redhat-rpm-config                 noarch  296-1.fc42                 fedora     186.6 KiB
 rpm-build                         aarch64 4.19.94-1.fc42             copr_base  525.9 KiB
 sed                               aarch64 4.9-3.fc41                 fedora       1.0 MiB
 shadow-utils                      aarch64 2:4.16.0-4.fc42            fedora       7.3 MiB
 tar                               aarch64 2:1.35-4.fc41              fedora       3.1 MiB
 unzip                             aarch64 6.0-64.fc41                fedora     726.7 KiB
 util-linux                        aarch64 2.40.2-8.fc42              fedora      16.9 MiB
 which                             aarch64 2.21-42.fc41               fedora     248.2 KiB
 xz                                aarch64 1:5.6.2-2.fc41             fedora       1.5 MiB
Installing dependencies:
 add-determinism                   aarch64 0.3.6-1.fc41               fedora       2.0 MiB
 alternatives                      aarch64 1.30-1.fc41                fedora     218.3 KiB
 ansible-srpm-macros               noarch  1-16.fc41                  fedora      35.7 KiB
 audit-libs                        aarch64 4.0.2-1.fc41               fedora     547.4 KiB
 authselect                        aarch64 1.5.0-7.fc41               fedora     309.5 KiB
 authselect-libs                   aarch64 1.5.0-7.fc41               fedora     931.9 KiB
 basesystem                        noarch  11-21.fc41                 fedora       0.0   B
 binutils                          aarch64 2.43.50-1.fc42             copr_base   32.7 MiB
 build-reproducibility-srpm-macros noarch  0.3.6-1.fc41               fedora     735.0   B
 bzip2-libs                        aarch64 1.0.8-19.fc41              fedora     200.7 KiB
 ca-certificates                   noarch  2024.2.69_v8.0.401-1.fc42  fedora       2.6 MiB
 coreutils-common                  aarch64 9.5-9.fc42                 fedora      11.2 MiB
 cracklib                          aarch64 2.9.11-6.fc42              copr_base  422.9 KiB
 crypto-policies                   noarch  20240828-1.git5f66e81.fc42 fedora     136.9 KiB
 curl                              aarch64 8.10.1-2.fc42              copr_base  453.3 KiB
 cyrus-sasl-lib                    aarch64 2.1.28-27.fc41             fedora       3.1 MiB
 debugedit                         aarch64 5.0-17.fc41                fedora     499.2 KiB
 dwz                               aarch64 0.15-7.fc41                fedora     386.8 KiB
 ed                                aarch64 1.20.2-2.fc41              fedora     282.8 KiB
 efi-srpm-macros                   noarch  5-12.fc41                  fedora      40.1 KiB
 elfutils                          aarch64 0.191-8.fc41               fedora       4.9 MiB
 elfutils-debuginfod-client        aarch64 0.191-8.fc41               fedora     396.9 KiB
 elfutils-default-yama-scope       noarch  0.191-8.fc41               fedora       1.8 KiB
 elfutils-libelf                   aarch64 0.191-8.fc41               fedora       1.3 MiB
 elfutils-libs                     aarch64 0.191-8.fc41               fedora     938.3 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                              aarch64 5.45-7.fc42                copr_base  139.5 KiB
 file-libs                         aarch64 5.45-7.fc42                copr_base   10.0 MiB
 filesystem                        aarch64 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                       aarch64 15.1-2.fc42                copr_base   12.9 MiB
 gdbm                              aarch64 1:1.23-7.fc41              fedora     928.5 KiB
 gdbm-libs                         aarch64 1:1.23-7.fc41              fedora     426.0 KiB
 ghc-srpm-macros                   noarch  1.9.2-1.fc42               fedora     779.0   B
 glibc                             aarch64 2.40.9000-5.fc42           copr_base    6.2 MiB
 glibc-common                      aarch64 2.40.9000-5.fc42           copr_base    1.3 MiB
 glibc-gconv-extra                 aarch64 2.40.9000-5.fc42           copr_base   18.6 MiB
 gmp                               aarch64 1:6.3.0-2.fc41             fedora     722.0 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                           aarch64 2.13.1-10.fc41             fedora     220.5 KiB
 kernel-srpm-macros                noarch  1.0-24.fc41                fedora       1.9 KiB
 keyutils-libs                     aarch64 1.6.3-4.fc41               fedora     226.4 KiB
 krb5-libs                         aarch64 1.21.3-2.fc41              fedora       3.3 MiB
 libacl                            aarch64 2.3.2-2.fc41               fedora     196.1 KiB
 libarchive                        aarch64 3.7.6-1.fc42               copr_base  910.8 KiB
 libattr                           aarch64 2.5.2-4.fc41               fedora     196.6 KiB
 libblkid                          aarch64 2.40.2-8.fc42              fedora     418.6 KiB
 libbrotli                         aarch64 1.1.0-5.fc41               fedora       1.1 MiB
 libcap                            aarch64 2.70-4.fc41                fedora       1.4 MiB
 libcap-ng                         aarch64 0.8.5-3.fc41               fedora     417.2 KiB
 libcom_err                        aarch64 1.47.1-3.fc41              fedora     239.3 KiB
 libcurl                           aarch64 8.10.1-2.fc42              copr_base  794.4 KiB
 libeconf                          aarch64 0.6.2-3.fc41               fedora     206.1 KiB
 libevent                          aarch64 2.1.12-14.fc41             fedora       1.5 MiB
 libfdisk                          aarch64 2.40.2-8.fc42              fedora     482.9 KiB
 libffi                            aarch64 3.4.6-3.fc42               fedora     282.4 KiB
 libgcc                            aarch64 14.2.1-3.fc42              fedora     350.2 KiB
 libgomp                           aarch64 14.2.1-3.fc42              fedora     567.3 KiB
 libidn2                           aarch64 2.3.7-2.fc41               fedora     457.2 KiB
 libmount                          aarch64 2.40.2-8.fc42              fedora     483.9 KiB
 libnghttp2                        aarch64 1.63.0-1.fc42              copr_base  198.2 KiB
 libnsl2                           aarch64 2.0.1-2.fc41               fedora     222.0 KiB
 libpkgconf                        aarch64 2.3.0-1.fc42               fedora     198.1 KiB
 libpsl                            aarch64 0.21.5-4.fc41              fedora     196.6 KiB
 libpwquality                      aarch64 1.4.5-11.fc41              fedora       1.1 MiB
 libselinux                        aarch64 3.7-6.fc42                 fedora     265.1 KiB
 libsemanage                       aarch64 3.7-3.fc42                 fedora     361.6 KiB
 libsepol                          aarch64 3.7-3.fc42                 fedora     873.9 KiB
 libsmartcols                      aarch64 2.40.2-8.fc42              fedora     288.5 KiB
 libssh                            aarch64 0.11.1-1.fc42              copr_base  585.5 KiB
 libssh-config                     noarch  0.11.1-1.fc42              copr_base  277.0   B
 libstdc++                         aarch64 14.2.1-3.fc42              fedora       2.8 MiB
 libtasn1                          aarch64 4.19.0-9.fc41              fedora     283.8 KiB
 libtirpc                          aarch64 1.3.5-0.fc41               fedora     274.8 KiB
 libtool-ltdl                      aarch64 2.4.7-12.fc41              fedora     222.2 KiB
 libunistring                      aarch64 1.1-8.fc41                 fedora       1.8 MiB
 libuuid                           aarch64 2.40.2-8.fc42              fedora     197.5 KiB
 libverto                          aarch64 0.3.2-9.fc41               fedora     197.5 KiB
 libxcrypt                         aarch64 4.4.36-7.fc41              fedora     399.0 KiB
 libxml2                           aarch64 2.12.8-2.fc42              copr_base    1.9 MiB
 libzstd                           aarch64 1.5.6-2.fc41               fedora     796.0 KiB
 lua-libs                          aarch64 5.4.6-6.fc41               fedora     393.1 KiB
 lua-srpm-macros                   noarch  1-14.fc41                  fedora       1.3 KiB
 lz4-libs                          aarch64 1.10.0-1.fc41              fedora     261.6 KiB
 mpfr                              aarch64 4.2.1-5.fc41               fedora     818.9 KiB
 ncurses-base                      noarch  6.5-2.20240629.fc41        fedora     326.3 KiB
 ncurses-libs                      aarch64 6.5-2.20240629.fc41        fedora       2.2 MiB
 ocaml-srpm-macros                 noarch  10-3.fc41                  fedora       1.9 KiB
 openblas-srpm-macros              noarch  2-18.fc41                  fedora     112.0   B
 openldap                          aarch64 2.6.8-5.fc41               fedora     952.3 KiB
 openssl-libs                      aarch64 1:3.2.2-9.fc42             copr_base    6.4 MiB
 p11-kit                           aarch64 0.25.5-3.fc41              fedora       2.6 MiB
 p11-kit-trust                     aarch64 0.25.5-3.fc41              fedora     655.6 KiB
 package-notes-srpm-macros         noarch  0.5-12.fc41                fedora       1.6 KiB
 pam                               aarch64 1.6.1-6.fc42               fedora      11.0 MiB
 pam-libs                          aarch64 1.6.1-6.fc42               fedora     607.3 KiB
 pcre2                             aarch64 10.44-1.fc41.1             fedora     905.5 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                           aarch64 2.3.0-1.fc42               fedora     240.6 KiB
 pkgconf-m4                        noarch  2.3.0-1.fc42               fedora      14.4 KiB
 pkgconf-pkg-config                aarch64 2.3.0-1.fc42               fedora     990.0   B
 popt                              aarch64 1.19-7.fc41                fedora     272.9 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                          aarch64 8.2-11.fc42                fedora     753.3 KiB
 rpm                               aarch64 4.19.94-1.fc42             copr_base    3.3 MiB
 rpm-build-libs                    aarch64 4.19.94-1.fc42             copr_base  198.7 KiB
 rpm-libs                          aarch64 4.19.94-1.fc42             copr_base  734.0 KiB
 rpm-sequoia                       aarch64 1.7.0-2.fc41               fedora       2.3 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                       aarch64 3.46.0-4.fc41              fedora       1.6 MiB
 systemd-libs                      aarch64 256.5-1.fc42               fedora       2.5 MiB
 util-linux-core                   aarch64 2.40.2-8.fc42              fedora       6.2 MiB
 xxhash-libs                       aarch64 0.8.2-3.fc41               fedora     212.3 KiB
 xz-libs                           aarch64 1:5.6.2-2.fc41             fedora     266.4 KiB
 zig-srpm-macros                   noarch  1-3.fc41                   fedora       1.1 KiB
 zip                               aarch64 3.0-41.fc41                fedora       1.1 MiB
 zlib-ng-compat                    aarch64 2.2.2-1.fc42               copr_base  197.6 KiB
 zstd                              aarch64 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 52 MiB. Need to download 0 B.
After this operation, 264 MiB extra will be used (install 264 MiB, remove 0 B).
[1/1] tar-2:1.35-4.fc41.aarch64         100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
--------------------------------------------------------------------------------
[1/1] Total                             100% |   0.0   B/s |   0.0   B |  00m00s
[1/2] bzip2-0:1.0.8-19.fc41.aarch64     100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
--------------------------------------------------------------------------------
[2/2] Total                             100% |   0.0   B/s |   0.0   B |  00m00s
[1/3] redhat-rpm-config-0:296-1.fc42.no 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[3/3] Total                             100% |   0.0   B/s |   0.0   B |  00m00s
[1/4] unzip-0:6.0-64.fc41.aarch64       100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[4/4] Total                             100% |   0.0   B/s |   0.0   B |  00m00s
[1/5] cpio-0:2.15-2.fc41.aarch64        100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[5/5] Total                             100% |   0.0   B/s |   0.0   B |  00m00s
[1/6] which-0:2.21-42.fc41.aarch64      100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[6/6] Total                             100% |   0.0   B/s |   0.0   B |  00m00s
[1/7] bash-0:5.2.32-2.fc42.aarch64      100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[7/7] Total                             100% |   0.0   B/s |   0.0   B |  00m00s
[1/8] coreutils-0:9.5-9.fc42.aarch64    100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[8/8] Total                             100% |   0.0   B/s |   0.0   B |  00m00s
[1/9] grep-0:3.11-9.fc41.aarch64        100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[9/9] Total                             100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/10] patch-0:2.7.6-25.fc41.aarch64   100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[10/10] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/11] sed-0:4.9-3.fc41.aarch64        100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[11/11] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/12] shadow-utils-2:4.16.0-4.fc42.aa 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[12/12] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/13] util-linux-0:2.40.2-8.fc42.aarc 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[13/13] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/14] diffutils-0:3.10-8.fc41.aarch64 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[14/14] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/15] fedora-release-common-0:42-0.3. 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[15/15] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/16] findutils-1:4.10.0-4.fc41.aarch 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[16/16] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/17] gawk-0:5.3.0-4.fc41.aarch64     100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[17/17] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/18] gzip-0:1.13-2.fc41.aarch64      100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[18/18] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/19] info-0:7.1.1-1.fc42.aarch64     100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[19/19] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/20] xz-1:5.6.2-2.fc41.aarch64       100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[20/20] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/21] rpm-build-0:4.19.94-1.fc42.aarc 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[21/21] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/22] glibc-minimal-langpack-0:2.40.9 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[22/22] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/23] libacl-0:2.3.2-2.fc41.aarch64   100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[23/23] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/24] libselinux-0:3.7-6.fc42.aarch64 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[24/24] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/25] bzip2-libs-0:1.0.8-19.fc41.aarc 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[25/25] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/26] ansible-srpm-macros-0:1-16.fc41 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[26/26] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/27] build-reproducibility-srpm-macr 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[27/27] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/28] dwz-0:0.15-7.fc41.aarch64       100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[28/28] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/29] efi-srpm-macros-0:5-12.fc41.noa 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[29/29] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/30] fonts-srpm-macros-1:2.0.5-17.fc 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[30/30] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/31] forge-srpm-macros-0:0.3.2-1.fc4 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[31/31] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/32] fpc-srpm-macros-0:1.3-13.fc41.n 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[32/32] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/33] ghc-srpm-macros-0:1.9.2-1.fc42. 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[33/33] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/34] gnat-srpm-macros-0:6-6.fc41.noa 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[34/34] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/35] go-srpm-macros-0:3.6.0-3.fc41.n 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[35/35] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/36] kernel-srpm-macros-0:1.0-24.fc4 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[36/36] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/37] lua-srpm-macros-0:1-14.fc41.noa 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[37/37] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/38] ocaml-srpm-macros-0:10-3.fc41.n 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[38/38] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/39] openblas-srpm-macros-0:2-18.fc4 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[39/39] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/40] package-notes-srpm-macros-0:0.5 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[40/40] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/41] perl-srpm-macros-0:1-56.fc41.no 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[41/41] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/42] pyproject-srpm-macros-0:1.15.0- 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[42/42] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/43] python-srpm-macros-0:3.13-3.fc4 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[43/43] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/44] qt5-srpm-macros-0:5.15.15-1.fc4 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[44/44] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/45] qt6-srpm-macros-0:6.7.2-3.fc41. 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[45/45] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/46] rust-srpm-macros-0:26.3-3.fc42. 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[46/46] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/47] zig-srpm-macros-0:1-3.fc41.noar 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[47/47] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/48] zip-0:3.0-41.fc41.aarch64       100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[48/48] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/49] filesystem-0:3.18-29.fc42.aarch 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[49/49] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/50] ncurses-libs-0:6.5-2.20240629.f 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[50/50] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/51] coreutils-common-0:9.5-9.fc42.a 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[51/51] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/52] gmp-1:6.3.0-2.fc41.aarch64      100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[52/52] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/53] libattr-0:2.5.2-4.fc41.aarch64  100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[53/53] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/54] libcap-0:2.70-4.fc41.aarch64    100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[54/54] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/55] systemd-libs-0:256.5-1.fc42.aar 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[55/55] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/56] pcre2-0:10.44-1.fc41.1.aarch64  100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[56/56] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/57] ed-0:1.20.2-2.fc41.aarch64      100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[57/57] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/58] audit-libs-0:4.0.2-1.fc41.aarch 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[58/58] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/59] libeconf-0:0.6.2-3.fc41.aarch64 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[59/59] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/60] libsemanage-0:3.7-3.fc42.aarch6 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[60/60] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/61] libxcrypt-0:4.4.36-7.fc41.aarch 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[61/61] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/62] pam-libs-0:1.6.1-6.fc42.aarch64 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[62/62] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/63] setup-0:2.15.0-5.fc41.noarch    100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[63/63] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/64] authselect-libs-0:1.5.0-7.fc41. 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[64/64] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/65] libblkid-0:2.40.2-8.fc42.aarch6 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[65/65] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/66] libcap-ng-0:0.8.5-3.fc41.aarch6 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[66/66] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/67] libfdisk-0:2.40.2-8.fc42.aarch6 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[67/67] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/68] libmount-0:2.40.2-8.fc42.aarch6 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[68/68] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/69] libsmartcols-0:2.40.2-8.fc42.aa 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[69/69] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/70] libuuid-0:2.40.2-8.fc42.aarch64 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[70/70] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/71] pam-0:1.6.1-6.fc42.aarch64      100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[71/71] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/72] readline-0:8.2-11.fc42.aarch64  100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[72/72] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/73] util-linux-core-0:2.40.2-8.fc42 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[73/73] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/74] fedora-repos-0:42-0.2.noarch    100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[74/74] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/75] mpfr-0:4.2.1-5.fc41.aarch64     100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[75/75] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/76] xz-libs-1:5.6.2-2.fc41.aarch64  100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[76/76] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/77] debugedit-0:5.0-17.fc41.aarch64 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[77/77] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/78] elfutils-0:0.191-8.fc41.aarch64 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[78/78] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/79] elfutils-libelf-0:0.191-8.fc41. 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[79/79] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/80] pkgconf-pkg-config-0:2.3.0-1.fc 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[80/80] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/81] popt-0:1.19-7.fc41.aarch64      100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[81/81] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/82] zstd-0:1.5.6-2.fc41.aarch64     100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[82/82] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/83] glibc-0:2.40.9000-5.fc42.aarch6 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[83/83] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/84] glibc-common-0:2.40.9000-5.fc42 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[84/84] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/85] libsepol-0:3.7-3.fc42.aarch64   100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[85/85] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/86] add-determinism-0:0.3.6-1.fc41. 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[86/86] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/87] ncurses-base-0:6.5-2.20240629.f 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[87/87] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/88] libgcc-0:14.2.1-3.fc42.aarch64  100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[88/88] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/89] pcre2-syntax-0:10.44-1.fc41.1.n 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[89/89] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/90] authselect-0:1.5.0-7.fc41.aarch 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[90/90] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/91] gdbm-1:1.23-7.fc41.aarch64      100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[91/91] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/92] gdbm-libs-1:1.23-7.fc41.aarch64 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[92/92] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/93] libnsl2-0:2.0.1-2.fc41.aarch64  100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[93/93] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/94] libpwquality-0:1.4.5-11.fc41.aa 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[94/94] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/95] libtirpc-0:1.3.5-0.fc41.aarch64 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[95/95] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/96] fedora-gpg-keys-0:42-0.2.noarch 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[96/96] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/97] fedora-repos-rawhide-0:42-0.2.n 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[97/97] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/98] elfutils-libs-0:0.191-8.fc41.aa 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[98/98] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/99] elfutils-debuginfod-client-0:0. 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[99/99] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
[  1/100] libstdc++-0:14.2.1-3.fc42.aar 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[100/100] Total                         100% |   0.0   B/s |   0.0   B |  00m00s
[  1/101] libzstd-0:1.5.6-2.fc41.aarch6 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[101/101] Total                         100% |   0.0   B/s |   0.0   B |  00m00s
[  1/102] pkgconf-0:2.3.0-1.fc42.aarch6 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[102/102] Total                         100% |   0.0   B/s |   0.0   B |  00m00s
[  1/103] pkgconf-m4-0:2.3.0-1.fc42.noa 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[103/103] Total                         100% |   0.0   B/s |   0.0   B |  00m00s
[  1/104] lz4-libs-0:1.10.0-1.fc41.aarc 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[104/104] Total                         100% |   0.0   B/s |   0.0   B |  00m00s
[  1/105] glibc-gconv-extra-0:2.40.9000 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[105/105] Total                         100% |   0.0   B/s |   0.0   B |  00m00s
[  1/106] basesystem-0:11-21.fc41.noarc 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[106/106] Total                         100% |   0.0   B/s |   0.0   B |  00m00s
[  1/107] krb5-libs-0:1.21.3-2.fc41.aar 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[107/107] Total                         100% |   0.0   B/s |   0.0   B |  00m00s
[  1/108] libcom_err-0:1.47.1-3.fc41.aa 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[108/108] Total                         100% |   0.0   B/s |   0.0   B |  00m00s
[  1/109] elfutils-default-yama-scope-0 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[109/109] Total                         100% |   0.0   B/s |   0.0   B |  00m00s
[  1/110] libpkgconf-0:2.3.0-1.fc42.aar 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[110/110] Total                         100% |   0.0   B/s |   0.0   B |  00m00s
[  1/111] crypto-policies-0:20240828-1. 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[111/111] Total                         100% |   0.0   B/s |   0.0   B |  00m00s
[  1/112] keyutils-libs-0:1.6.3-4.fc41. 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[112/112] Total                         100% |   0.0   B/s |   0.0   B |  00m00s
[  1/113] libverto-0:0.3.2-9.fc41.aarch 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[113/113] Total                         100% |   0.0   B/s |   0.0   B |  00m00s
[  1/114] binutils-0:2.43.50-1.fc42.aar 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[114/114] Total                         100% |   0.0   B/s |   0.0   B |  00m00s
[  1/115] alternatives-0:1.30-1.fc41.aa 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[115/115] Total                         100% |   0.0   B/s |   0.0   B |  00m00s
[  1/116] jansson-0:2.13.1-10.fc41.aarc 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[116/116] Total                         100% |   0.0   B/s |   0.0   B |  00m00s
[  1/117] file-0:5.45-7.fc42.aarch64    100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[117/117] Total                         100% |   0.0   B/s |   0.0   B |  00m00s
[  1/118] file-libs-0:5.45-7.fc42.aarch 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[118/118] Total                         100% |   0.0   B/s |   0.0   B |  00m00s
[  1/119] libarchive-0:3.7.6-1.fc42.aar 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[119/119] Total                         100% |   0.0   B/s |   0.0   B |  00m00s
[  1/120] rpm-0:4.19.94-1.fc42.aarch64  100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[120/120] Total                         100% |   0.0   B/s |   0.0   B |  00m00s
[  1/121] rpm-build-libs-0:4.19.94-1.fc 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[121/121] Total                         100% |   0.0   B/s |   0.0   B |  00m00s
[  1/122] libgomp-0:14.2.1-3.fc42.aarch 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[122/122] Total                         100% |   0.0   B/s |   0.0   B |  00m00s
[  1/123] lua-libs-0:5.4.6-6.fc41.aarch 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[123/123] Total                         100% |   0.0   B/s |   0.0   B |  00m00s
[  1/124] rpm-libs-0:4.19.94-1.fc42.aar 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[124/124] Total                         100% |   0.0   B/s |   0.0   B |  00m00s
[  1/125] rpm-sequoia-0:1.7.0-2.fc41.aa 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[125/125] Total                         100% |   0.0   B/s |   0.0   B |  00m00s
[  1/126] sqlite-libs-0:3.46.0-4.fc41.a 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[126/126] Total                         100% |   0.0   B/s |   0.0   B |  00m00s
[  1/127] curl-0:8.10.1-2.fc42.aarch64  100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[127/127] Total                         100% |   0.0   B/s |   0.0   B |  00m00s
[  1/128] libxml2-0:2.12.8-2.fc42.aarch 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[128/128] Total                         100% |   0.0   B/s |   0.0   B |  00m00s
[  1/129] openssl-libs-1:3.2.2-9.fc42.a 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[129/129] Total                         100% |   0.0   B/s |   0.0   B |  00m00s
[  1/130] ca-certificates-0:2024.2.69_v 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[130/130] Total                         100% |   0.0   B/s |   0.0   B |  00m00s
[  1/131] libffi-0:3.4.6-3.fc42.aarch64 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[131/131] Total                         100% |   0.0   B/s |   0.0   B |  00m00s
[  1/132] p11-kit-0:0.25.5-3.fc41.aarch 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[132/132] Total                         100% |   0.0   B/s |   0.0   B |  00m00s
[  1/133] p11-kit-trust-0:0.25.5-3.fc41 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[133/133] Total                         100% |   0.0   B/s |   0.0   B |  00m00s
[  1/134] libtasn1-0:4.19.0-9.fc41.aarc 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[134/134] Total                         100% |   0.0   B/s |   0.0   B |  00m00s
[  1/135] zlib-ng-compat-0:2.2.2-1.fc42 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[135/135] Total                         100% |   0.0   B/s |   0.0   B |  00m00s
[  1/136] cracklib-0:2.9.11-6.fc42.aarc 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[136/136] Total                         100% |   0.0   B/s |   0.0   B |  00m00s
[  1/137] gdb-minimal-0:15.1-2.fc42.aar 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[137/137] Total                         100% |   0.0   B/s |   0.0   B |  00m00s
[  1/138] xxhash-libs-0:0.8.2-3.fc41.aa 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[138/138] Total                         100% |   0.0   B/s |   0.0   B |  00m00s
[  1/139] libcurl-0:8.10.1-2.fc42.aarch 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[139/139] Total                         100% |   0.0   B/s |   0.0   B |  00m00s
[  1/140] libbrotli-0:1.1.0-5.fc41.aarc 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[140/140] Total                         100% |   0.0   B/s |   0.0   B |  00m00s
[  1/141] libidn2-0:2.3.7-2.fc41.aarch6 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[141/141] Total                         100% |   0.0   B/s |   0.0   B |  00m00s
[  1/142] libpsl-0:0.21.5-4.fc41.aarch6 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[142/142] Total                         100% |   0.0   B/s |   0.0   B |  00m00s
[  1/143] openldap-0:2.6.8-5.fc41.aarch 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[143/143] Total                         100% |   0.0   B/s |   0.0   B |  00m00s
[  1/144] libunistring-0:1.1-8.fc41.aar 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[144/144] Total                         100% |   0.0   B/s |   0.0   B |  00m00s
[  1/145] publicsuffix-list-dafsa-0:202 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[145/145] Total                         100% |   0.0   B/s |   0.0   B |  00m00s
[  1/146] cyrus-sasl-lib-0:2.1.28-27.fc 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[146/146] Total                         100% |   0.0   B/s |   0.0   B |  00m00s
[  1/147] libevent-0:2.1.12-14.fc41.aar 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[147/147] Total                         100% |   0.0   B/s |   0.0   B |  00m00s
[  1/148] libtool-ltdl-0:2.4.7-12.fc41. 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[148/148] Total                         100% |   0.0   B/s |   0.0   B |  00m00s
[  1/149] fedora-release-0:42-0.3.noarc 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[149/149] Total                         100% |   0.0   B/s |   0.0   B |  00m00s
[  1/150] fedora-release-identity-basic 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[150/150] Total                         100% |   0.0   B/s |   0.0   B |  00m00s
[  1/151] libnghttp2-0:1.63.0-1.fc42.aa 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[151/151] Total                         100% |   0.0   B/s |   0.0   B |  00m00s
[  1/152] libssh-0:0.11.1-1.fc42.aarch6 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[152/152] Total                         100% |   0.0   B/s |   0.0   B |  00m00s
[  1/153] libssh-config-0:0.11.1-1.fc42 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[153/153] Total                         100% |   0.0   B/s |   0.0   B |  00m00s
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% | 683.0   B/s | 153.0   B |  00m00s
[  2/155] Prepare transaction           100% |   2.5 KiB/s | 153.0   B |  00m00s
[  3/155] Installing libgcc-0:14.2.1-3. 100% | 171.8 MiB/s | 351.9 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% | 929.7 KiB/s | 952.0   B |  00m00s
[  6/155] Installing fedora-gpg-keys-0: 100% |  33.6 MiB/s | 172.2 KiB |  00m00s
[  7/155] Installing fedora-repos-rawhi 100% |   0.0   B/s |   2.4 KiB |  00m00s
[  8/155] Installing fedora-repos-0:42- 100% |   0.0   B/s |   5.7 KiB |  00m00s
[  9/155] Installing fedora-release-com 100% |  23.1 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% |  44.3 MiB/s | 726.1 KiB |  00m00s
[ 12/155] Installing filesystem-0:3.18- 100% |   2.3 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% |  57.2 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% | 321.2 MiB/s |   2.2 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
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% | 206.7 MiB/s |   6.2 MiB |  00m00s
[ 21/155] Installing bash-0:5.2.32-2.fc 100% | 319.7 MiB/s |   8.3 MiB |  00m00s
[ 22/155] Installing glibc-common-0:2.4 100% | 188.5 MiB/s |   1.3 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% | 346.2 MiB/s |  18.7 MiB |  00m00s
[ 24/155] Installing zlib-ng-compat-0:2 100% | 193.8 MiB/s | 198.5 KiB |  00m00s
[ 25/155] Installing bzip2-libs-0:1.0.8 100% | 197.1 MiB/s | 201.9 KiB |  00m00s
[ 26/155] Installing xz-libs-1:5.6.2-2. 100% | 261.2 MiB/s | 267.5 KiB |  00m00s
[ 27/155] Installing libuuid-0:2.40.2-8 100% | 194.0 MiB/s | 198.6 KiB |  00m00s
[ 28/155] Installing readline-0:8.2-11. 100% | 245.9 MiB/s | 755.5 KiB |  00m00s
[ 29/155] Installing popt-0:1.19-7.fc41 100% |  91.0 MiB/s | 279.5 KiB |  00m00s
[ 30/155] Installing libblkid-0:2.40.2- 100% | 409.9 MiB/s | 419.7 KiB |  00m00s
[ 31/155] Installing gmp-1:6.3.0-2.fc41 100% | 235.8 MiB/s | 724.2 KiB |  00m00s
[ 32/155] Installing libattr-0:2.5.2-4. 100% | 192.9 MiB/s | 197.5 KiB |  00m00s
[ 33/155] Installing libacl-0:2.3.2-2.f 100% | 192.3 MiB/s | 196.9 KiB |  00m00s
[ 34/155] Installing libxcrypt-0:4.4.36 100% | 196.1 MiB/s | 401.7 KiB |  00m00s
[ 35/155] Installing libstdc++-0:14.2.1 100% | 308.2 MiB/s |   2.8 MiB |  00m00s
[ 36/155] Installing libzstd-0:1.5.6-2. 100% | 259.5 MiB/s | 797.3 KiB |  00m00s
[ 37/155] Installing elfutils-libelf-0: 100% | 328.5 MiB/s |   1.3 MiB |  00m00s
[ 38/155] Installing libeconf-0:0.6.2-3 100% | 202.9 MiB/s | 207.8 KiB |  00m00s
[ 39/155] Installing gdbm-libs-1:1.23-7 100% | 417.7 MiB/s | 427.7 KiB |  00m00s
[ 40/155] Installing dwz-0:0.15-7.fc41. 100% | 189.5 MiB/s | 388.1 KiB |  00m00s
[ 41/155] Installing mpfr-0:4.2.1-5.fc4 100% | 267.1 MiB/s | 820.5 KiB |  00m00s
[ 42/155] Installing gawk-0:5.3.0-4.fc4 100% | 387.6 MiB/s |   4.3 MiB |  00m00s
[ 43/155] Installing unzip-0:6.0-64.fc4 100% | 356.5 MiB/s | 730.2 KiB |  00m00s
[ 44/155] Installing file-libs-0:5.45-7 100% | 586.0 MiB/s |  10.0 MiB |  00m00s
[ 45/155] Installing file-0:5.45-7.fc42 100% |  19.7 MiB/s | 140.9 KiB |  00m00s
[ 46/155] Installing crypto-policies-0: 100% |  22.8 MiB/s | 163.2 KiB |  00m00s
[ 47/155] Installing pcre2-0:10.44-1.fc 100% | 295.2 MiB/s | 906.9 KiB |  00m00s
[ 48/155] Installing grep-0:3.11-9.fc41 100% | 156.7 MiB/s |   1.1 MiB |  00m00s
[ 49/155] Installing xz-1:5.6.2-2.fc41. 100% | 185.3 MiB/s |   1.5 MiB |  00m00s
[ 50/155] Installing libcap-ng-0:0.8.5- 100% | 409.3 MiB/s | 419.1 KiB |  00m00s
[ 51/155] Installing audit-libs-0:4.0.2 100% | 268.3 MiB/s | 549.6 KiB |  00m00s
[ 52/155] Installing pam-libs-0:1.6.1-6 100% | 297.6 MiB/s | 609.5 KiB |  00m00s
[ 53/155] Installing libcap-0:2.70-4.fc 100% | 344.0 MiB/s |   1.4 MiB |  00m00s
[ 54/155] Installing systemd-libs-0:256 100% | 315.1 MiB/s |   2.5 MiB |  00m00s
[ 55/155] Installing libsmartcols-0:2.4 100% | 282.9 MiB/s | 289.7 KiB |  00m00s
[ 56/155] Installing libsepol-0:3.7-3.f 100% | 284.8 MiB/s | 874.9 KiB |  00m00s
[ 57/155] Installing libselinux-0:3.7-6 100% | 260.1 MiB/s | 266.3 KiB |  00m00s
[ 58/155] Installing sed-0:4.9-3.fc41.a 100% | 164.3 MiB/s |   1.0 MiB |  00m00s
[ 59/155] Installing findutils-1:4.10.0 100% | 263.5 MiB/s |   2.1 MiB |  00m00s
[ 60/155] Installing libmount-0:2.40.2- 100% | 236.8 MiB/s | 485.1 KiB |  00m00s
[ 61/155] Installing lz4-libs-0:1.10.0- 100% | 256.5 MiB/s | 262.7 KiB |  00m00s
[ 62/155] Installing libcom_err-0:1.47. 100% | 234.8 MiB/s | 240.4 KiB |  00m00s
[ 63/155] Installing alternatives-0:1.3 100% | 214.7 MiB/s | 219.9 KiB |  00m00s
[ 64/155] Installing lua-libs-0:5.4.6-6 100% | 192.5 MiB/s | 394.3 KiB |  00m00s
[ 65/155] Installing libffi-0:3.4.6-3.f 100% | 277.2 MiB/s | 283.8 KiB |  00m00s
[ 66/155] Installing libtasn1-0:4.19.0- 100% | 139.4 MiB/s | 285.6 KiB |  00m00s
[ 67/155] Installing p11-kit-0:0.25.5-3 100% | 220.5 MiB/s |   2.6 MiB |  00m00s
[ 68/155] Installing libunistring-0:1.1 100% | 301.5 MiB/s |   1.8 MiB |  00m00s
[ 69/155] Installing libidn2-0:2.3.7-2. 100% | 113.1 MiB/s | 463.1 KiB |  00m00s
[ 70/155] Installing libpsl-0:0.21.5-4. 100% | 193.1 MiB/s | 197.7 KiB |  00m00s
[ 71/155] Installing p11-kit-trust-0:0. 100% |  80.2 MiB/s | 657.4 KiB |  00m00s
[ 72/155] Installing zstd-0:1.5.6-2.fc4 100% | 281.8 MiB/s |   1.7 MiB |  00m00s
[ 73/155] Installing util-linux-core-0: 100% | 413.5 MiB/s |   6.2 MiB |  00m00s
[ 74/155] Installing tar-2:1.35-4.fc41. 100% | 278.8 MiB/s |   3.1 MiB |  00m00s
[ 75/155] Installing libsemanage-0:3.7- 100% | 118.3 MiB/s | 363.3 KiB |  00m00s
[ 76/155] Installing shadow-utils-2:4.1 100% | 253.4 MiB/s |   7.3 MiB |  00m00s
[ 77/155] Installing zip-0:3.0-41.fc41. 100% | 281.0 MiB/s |   1.1 MiB |  00m00s
[ 78/155] Installing gdbm-1:1.23-7.fc41 100% | 227.9 MiB/s | 933.4 KiB |  00m00s
[ 79/155] Installing cyrus-sasl-lib-0:2 100% | 345.2 MiB/s |   3.1 MiB |  00m00s
[ 80/155] Installing libfdisk-0:2.40.2- 100% | 236.3 MiB/s | 483.9 KiB |  00m00s
[ 81/155] Installing libxml2-0:2.12.8-2 100% | 315.3 MiB/s |   1.9 MiB |  00m00s
[ 82/155] Installing bzip2-0:1.0.8-19.f 100% | 211.0 MiB/s | 432.2 KiB |  00m00s
[ 83/155] Installing add-determinism-0: 100% | 338.9 MiB/s |   2.0 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% | 311.7 MiB/s |   1.6 MiB |  00m00s
[ 86/155] Installing ed-0:1.20.2-2.fc41 100% | 278.5 MiB/s | 285.1 KiB |  00m00s
[ 87/155] Installing patch-0:2.7.6-25.f 100% | 191.5 MiB/s | 392.1 KiB |  00m00s
[ 88/155] Installing elfutils-default-y 100% | 408.6 KiB/s |   2.0 KiB |  00m00s
[ 89/155] Installing elfutils-libs-0:0. 100% | 229.5 MiB/s | 940.2 KiB |  00m00s
[ 90/155] Installing cpio-0:2.15-2.fc41 100% | 203.4 MiB/s |   1.2 MiB |  00m00s
[ 91/155] Installing diffutils-0:3.10-8 100% | 263.7 MiB/s |   2.1 MiB |  00m00s
[ 92/155] Installing libpkgconf-0:2.3.0 100% | 194.6 MiB/s | 199.2 KiB |  00m00s
[ 93/155] Installing pkgconf-0:2.3.0-1. 100% | 118.7 MiB/s | 243.1 KiB |  00m00s
[ 94/155] Installing pkgconf-pkg-config 100% |   0.0   B/s |   1.8 KiB |  00m00s
[ 95/155] Installing keyutils-libs-0:1. 100% | 222.5 MiB/s | 227.9 KiB |  00m00s
[ 96/155] Installing libverto-0:0.3.2-9 100% | 194.7 MiB/s | 199.3 KiB |  00m00s
[ 97/155] Installing jansson-0:2.13.1-1 100% | 216.7 MiB/s | 221.9 KiB |  00m00s
[ 98/155] Installing libgomp-0:14.2.1-3 100% | 277.7 MiB/s | 568.7 KiB |  00m00s
[ 99/155] Installing xxhash-libs-0:0.8. 100% | 208.7 MiB/s | 213.7 KiB |  00m00s
[100/155] Installing libbrotli-0:1.1.0- 100% | 285.2 MiB/s |   1.1 MiB |  00m00s
[101/155] Installing libtool-ltdl-0:2.4 100% | 218.1 MiB/s | 223.4 KiB |  00m00s
[102/155] Installing libnghttp2-0:1.63. 100% |  97.3 MiB/s | 199.3 KiB |  00m00s
[103/155] Installing coreutils-common-0 100% | 310.8 MiB/s |  11.2 MiB |  00m00s
[104/155] Installing openssl-libs-1:3.2 100% | 336.7 MiB/s |   6.4 MiB |  00m00s
[105/155] Installing coreutils-0:9.5-9. 100% | 472.8 MiB/s |  20.8 MiB |  00m00s
[106/155] Installing ca-certificates-0: 100% |   1.5 MiB/s |   2.4 MiB |  00m02s
[107/155] Installing krb5-libs-0:1.21.3 100% | 278.8 MiB/s |   3.3 MiB |  00m00s
[108/155] Installing libarchive-0:3.7.6 100% | 222.8 MiB/s | 912.8 KiB |  00m00s
[109/155] Installing libtirpc-0:1.3.5-0 100% | 135.0 MiB/s | 276.5 KiB |  00m00s
[110/155] Installing gzip-0:1.13-2.fc41 100% | 160.9 MiB/s | 494.4 KiB |  00m00s
[111/155] Installing authselect-libs-0: 100% | 132.1 MiB/s | 946.8 KiB |  00m00s
[112/155] Installing cracklib-0:2.9.11- 100% |  84.8 MiB/s | 434.2 KiB |  00m00s
[113/155] Installing libpwquality-0:1.4 100% | 158.2 MiB/s |   1.1 MiB |  00m00s
[114/155] Installing libnsl2-0:2.0.1-2. 100% | 109.0 MiB/s | 223.2 KiB |  00m00s
[115/155] Installing pam-0:1.6.1-6.fc42 100% | 380.6 MiB/s |  11.0 MiB |  00m00s
[116/155] Installing libssh-0:0.11.1-1. 100% | 191.3 MiB/s | 587.6 KiB |  00m00s
[117/155] Installing rpm-sequoia-0:1.7. 100% | 328.2 MiB/s |   2.3 MiB |  00m00s
[118/155] Installing rpm-libs-0:4.19.94 100% | 239.4 MiB/s | 735.5 KiB |  00m00s
[119/155] Installing rpm-build-libs-0:4 100% | 194.7 MiB/s | 199.4 KiB |  00m00s
[120/155] Installing libevent-0:2.1.12- 100% | 380.8 MiB/s |   1.5 MiB |  00m00s
[121/155] Installing openldap-0:2.6.8-5 100% | 233.4 MiB/s | 956.1 KiB |  00m00s
[122/155] Installing libcurl-0:8.10.1-2 100% | 258.9 MiB/s | 795.5 KiB |  00m00s
[123/155] Installing elfutils-debuginfo 100% | 194.8 MiB/s | 398.9 KiB |  00m00s
[124/155] Installing elfutils-0:0.191-8 100% | 450.4 MiB/s |   5.0 MiB |  00m00s
[125/155] Installing binutils-0:2.43.50 100% | 376.3 MiB/s |  32.7 MiB |  00m00s
[126/155] Installing gdb-minimal-0:15.1 100% | 349.1 MiB/s |  12.9 MiB |  00m00s
[127/155] Installing debugedit-0:5.0-17 100% | 245.1 MiB/s | 502.0 KiB |  00m00s
[128/155] Installing curl-0:8.10.1-2.fc 100% |  44.5 MiB/s | 455.8 KiB |  00m00s
[129/155] Installing rpm-0:4.19.94-1.fc 100% | 130.1 MiB/s |   2.7 MiB |  00m00s
[130/155] Installing efi-srpm-macros-0: 100% |  40.2 MiB/s |  41.2 KiB |  00m00s
[131/155] Installing lua-srpm-macros-0: 100% |   0.0   B/s |   1.9 KiB |  00m00s
[132/155] Installing zig-srpm-macros-0: 100% |   0.0   B/s |   1.7 KiB |  00m00s
[133/155] Installing rust-srpm-macros-0 100% |   0.0   B/s |   5.6 KiB |  00m00s
[134/155] Installing qt6-srpm-macros-0: 100% |   0.0   B/s | 732.0   B |  00m00s
[135/155] Installing qt5-srpm-macros-0: 100% |   0.0   B/s | 776.0   B |  00m00s
[136/155] Installing perl-srpm-macros-0 100% |   0.0   B/s |   1.1 KiB |  00m00s
[137/155] Installing package-notes-srpm 100% |   0.0   B/s |   2.0 KiB |  00m00s
[138/155] Installing openblas-srpm-macr 100% |   0.0   B/s | 392.0   B |  00m00s
[139/155] Installing ocaml-srpm-macros- 100% |   0.0   B/s |   2.2 KiB |  00m00s
[140/155] Installing kernel-srpm-macros 100% |   0.0   B/s |   2.3 KiB |  00m00s
[141/155] Installing gnat-srpm-macros-0 100% |   0.0   B/s |   1.3 KiB |  00m00s
[142/155] Installing ghc-srpm-macros-0: 100% |   0.0   B/s |   1.0 KiB |  00m00s
[143/155] Installing fpc-srpm-macros-0: 100% |   0.0   B/s | 420.0   B |  00m00s
[144/155] Installing ansible-srpm-macro 100% |   0.0   B/s |  36.2 KiB |  00m00s
[145/155] Installing fonts-srpm-macros- 100% |  55.7 MiB/s |  57.0 KiB |  00m00s
[146/155] Installing forge-srpm-macros- 100% |  39.4 MiB/s |  40.4 KiB |  00m00s
[147/155] Installing go-srpm-macros-0:3 100% |  60.5 MiB/s |  62.0 KiB |  00m00s
[148/155] Installing python-srpm-macros 100% |  50.9 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% | 174.0 MiB/s | 534.5 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% | 385.3 MiB/s |  17.0 MiB |  00m00s
[153/155] Installing authselect-0:1.5.0 100% | 102.2 MiB/s | 313.9 KiB |  00m00s
[154/155] Installing which-0:2.21-42.fc 100% | 244.5 MiB/s | 250.4 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% | 291.0 KiB/s | 614.1 KiB |  00m02s
Warning: skipped PGP checks for 22 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.aarch64
alternatives-1.30-1.fc41.aarch64
ansible-srpm-macros-1-16.fc41.noarch
audit-libs-4.0.2-1.fc41.aarch64
authselect-1.5.0-7.fc41.aarch64
authselect-libs-1.5.0-7.fc41.aarch64
basesystem-11-21.fc41.noarch
bash-5.2.32-2.fc42.aarch64
binutils-2.43.50-1.fc42.aarch64
build-reproducibility-srpm-macros-0.3.6-1.fc41.noarch
bzip2-1.0.8-19.fc41.aarch64
bzip2-libs-1.0.8-19.fc41.aarch64
ca-certificates-2024.2.69_v8.0.401-1.fc42.noarch
coreutils-9.5-9.fc42.aarch64
coreutils-common-9.5-9.fc42.aarch64
cpio-2.15-2.fc41.aarch64
cracklib-2.9.11-6.fc42.aarch64
crypto-policies-20240828-1.git5f66e81.fc42.noarch
curl-8.10.1-2.fc42.aarch64
cyrus-sasl-lib-2.1.28-27.fc41.aarch64
debugedit-5.0-17.fc41.aarch64
diffutils-3.10-8.fc41.aarch64
dwz-0.15-7.fc41.aarch64
ed-1.20.2-2.fc41.aarch64
efi-srpm-macros-5-12.fc41.noarch
elfutils-0.191-8.fc41.aarch64
elfutils-debuginfod-client-0.191-8.fc41.aarch64
elfutils-default-yama-scope-0.191-8.fc41.noarch
elfutils-libelf-0.191-8.fc41.aarch64
elfutils-libs-0.191-8.fc41.aarch64
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.aarch64
file-libs-5.45-7.fc42.aarch64
filesystem-3.18-29.fc42.aarch64
findutils-4.10.0-4.fc41.aarch64
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.aarch64
gdb-minimal-15.1-2.fc42.aarch64
gdbm-1.23-7.fc41.aarch64
gdbm-libs-1.23-7.fc41.aarch64
ghc-srpm-macros-1.9.2-1.fc42.noarch
glibc-2.40.9000-5.fc42.aarch64
glibc-common-2.40.9000-5.fc42.aarch64
glibc-gconv-extra-2.40.9000-5.fc42.aarch64
glibc-minimal-langpack-2.40.9000-5.fc42.aarch64
gmp-6.3.0-2.fc41.aarch64
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.aarch64
gzip-1.13-2.fc41.aarch64
info-7.1.1-1.fc42.aarch64
jansson-2.13.1-10.fc41.aarch64
kernel-srpm-macros-1.0-24.fc41.noarch
keyutils-libs-1.6.3-4.fc41.aarch64
krb5-libs-1.21.3-2.fc41.aarch64
libacl-2.3.2-2.fc41.aarch64
libarchive-3.7.6-1.fc42.aarch64
libattr-2.5.2-4.fc41.aarch64
libblkid-2.40.2-8.fc42.aarch64
libbrotli-1.1.0-5.fc41.aarch64
libcap-2.70-4.fc41.aarch64
libcap-ng-0.8.5-3.fc41.aarch64
libcom_err-1.47.1-3.fc41.aarch64
libcurl-8.10.1-2.fc42.aarch64
libeconf-0.6.2-3.fc41.aarch64
libevent-2.1.12-14.fc41.aarch64
libfdisk-2.40.2-8.fc42.aarch64
libffi-3.4.6-3.fc42.aarch64
libgcc-14.2.1-3.fc42.aarch64
libgomp-14.2.1-3.fc42.aarch64
libidn2-2.3.7-2.fc41.aarch64
libmount-2.40.2-8.fc42.aarch64
libnghttp2-1.63.0-1.fc42.aarch64
libnsl2-2.0.1-2.fc41.aarch64
libpkgconf-2.3.0-1.fc42.aarch64
libpsl-0.21.5-4.fc41.aarch64
libpwquality-1.4.5-11.fc41.aarch64
libselinux-3.7-6.fc42.aarch64
libsemanage-3.7-3.fc42.aarch64
libsepol-3.7-3.fc42.aarch64
libsmartcols-2.40.2-8.fc42.aarch64
libssh-0.11.1-1.fc42.aarch64
libssh-config-0.11.1-1.fc42.noarch
libstdc++-14.2.1-3.fc42.aarch64
libtasn1-4.19.0-9.fc41.aarch64
libtirpc-1.3.5-0.fc41.aarch64
libtool-ltdl-2.4.7-12.fc41.aarch64
libunistring-1.1-8.fc41.aarch64
libuuid-2.40.2-8.fc42.aarch64
libverto-0.3.2-9.fc41.aarch64
libxcrypt-4.4.36-7.fc41.aarch64
libxml2-2.12.8-2.fc42.aarch64
libzstd-1.5.6-2.fc41.aarch64
lua-libs-5.4.6-6.fc41.aarch64
lua-srpm-macros-1-14.fc41.noarch
lz4-libs-1.10.0-1.fc41.aarch64
mpfr-4.2.1-5.fc41.aarch64
ncurses-base-6.5-2.20240629.fc41.noarch
ncurses-libs-6.5-2.20240629.fc41.aarch64
ocaml-srpm-macros-10-3.fc41.noarch
openblas-srpm-macros-2-18.fc41.noarch
openldap-2.6.8-5.fc41.aarch64
openssl-libs-3.2.2-9.fc42.aarch64
p11-kit-0.25.5-3.fc41.aarch64
p11-kit-trust-0.25.5-3.fc41.aarch64
package-notes-srpm-macros-0.5-12.fc41.noarch
pam-1.6.1-6.fc42.aarch64
pam-libs-1.6.1-6.fc42.aarch64
patch-2.7.6-25.fc41.aarch64
pcre2-10.44-1.fc41.1.aarch64
pcre2-syntax-10.44-1.fc41.1.noarch
perl-srpm-macros-1-56.fc41.noarch
pkgconf-2.3.0-1.fc42.aarch64
pkgconf-m4-2.3.0-1.fc42.noarch
pkgconf-pkg-config-2.3.0-1.fc42.aarch64
popt-1.19-7.fc41.aarch64
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.aarch64
redhat-rpm-config-296-1.fc42.noarch
rpm-4.19.94-1.fc42.aarch64
rpm-build-4.19.94-1.fc42.aarch64
rpm-build-libs-4.19.94-1.fc42.aarch64
rpm-libs-4.19.94-1.fc42.aarch64
rpm-sequoia-1.7.0-2.fc41.aarch64
rust-srpm-macros-26.3-3.fc42.noarch
sed-4.9-3.fc41.aarch64
setup-2.15.0-5.fc41.noarch
shadow-utils-4.16.0-4.fc42.aarch64
sqlite-libs-3.46.0-4.fc41.aarch64
systemd-libs-256.5-1.fc42.aarch64
tar-1.35-4.fc41.aarch64
unzip-6.0-64.fc41.aarch64
util-linux-2.40.2-8.fc42.aarch64
util-linux-core-2.40.2-8.fc42.aarch64
which-2.21-42.fc41.aarch64
xxhash-libs-0.8.2-3.fc41.aarch64
xz-5.6.2-2.fc41.aarch64
xz-libs-5.6.2-2.fc41.aarch64
zig-srpm-macros-1-3.fc41.noarch
zip-3.0-41.fc41.aarch64
zlib-ng-compat-2.2.2-1.fc42.aarch64
zstd-1.5.6-2.fc41.aarch64
Start: buildsrpm
Start: rpmbuild -bs
Building target platforms: aarch64
Building for target aarch64
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-aarch64-1727357069.761619/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-aarch64-1727357069.761619/root/var/log/dnf5.log
Finish: buildsrpm
INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-h2cy18qe/samtools/samtools.spec) Config(child) 0 minutes 14 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-aarch64)
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-aarch64-bootstrap-1727357069.761619/root.
INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-aarch64-bootstrap-1727357069.761619/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-aarch64-1727357069.761619/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.aarch64
  rpm-sequoia-1.7.0-2.fc41.aarch64
  dnf5-5.2.6.2-1.fc42.aarch64
  dnf5-plugins-5.2.6.2-1.fc42.aarch64
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: aarch64
Building for target aarch64
setting SOURCE_DATE_EPOCH=1721433600
Wrote: /builddir/build/SRPMS/samtools-1.15.1-5.fc42.src.rpm
Updating and loading repositories:
 Copr repository                        100% | 109.7 KiB/s |   1.5 KiB |  00m00s
 fedora                                 100% |  32.6 KiB/s |   7.1 KiB |  00m00s
Repositories loaded.
Package                 Arch    Version              Repository      Size
Installing:
 gcc                    aarch64 14.2.1-3.fc42        fedora      93.8 MiB
 htslib-devel           aarch64 1.15.1-7.fc42        copr_base  411.0 KiB
 htslib-tools           aarch64 1.15.1-7.fc42        copr_base    2.4 MiB
 make                   aarch64 1:4.4.1-8.fc41       fedora       1.8 MiB
 ncurses-devel          aarch64 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       aarch64 4:5.40.0-511.fc41    fedora     302.3 KiB
 perl-lib               aarch64 0.65-511.fc41        fedora       8.5 KiB
 zlib-ng-compat-devel   aarch64 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     aarch64 12.70-1.fc42         fedora       1.1 MiB
 cmake-filesystem       aarch64 3.28.3-7.fc41        fedora       0.0   B
 cpp                    aarch64 14.2.1-3.fc42        fedora      31.8 MiB
 gcc-plugin-annobin     aarch64 14.2.1-3.fc42        fedora     197.1 KiB
 glibc-devel            aarch64 2.40.9000-5.fc42     copr_base    2.2 MiB
 groff-base             aarch64 1.23.0-7.fc41        fedora       5.2 MiB
 htslib                 aarch64 1.15.1-7.fc42        copr_base    1.2 MiB
 kernel-headers         aarch64 6.11.0-63.fc42       fedora       6.3 MiB
 libasan                aarch64 14.2.1-3.fc42        fedora       1.6 MiB
 libatomic              aarch64 14.2.1-3.fc42        fedora     196.9 KiB
 libmpc                 aarch64 1.3.1-6.fc41         fedora     280.8 KiB
 libubsan               aarch64 14.2.1-3.fc42        fedora     539.3 KiB
 libxcrypt-devel        aarch64 4.4.36-7.fc41        fedora      30.3 KiB
 ncurses                aarch64 6.5-2.20240629.fc41  fedora       1.7 MiB
 ncurses-c++-libs       aarch64 6.5-2.20240629.fc41  fedora     393.7 KiB
 perl-AutoLoader        noarch  5.74-511.fc41        fedora      20.5 KiB
 perl-B                 aarch64 1.89-511.fc41        fedora     606.1 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       aarch64 2.189-512.fc41       fedora     263.8 KiB
 perl-Digest            noarch  1.20-511.fc41        fedora      35.3 KiB
 perl-Digest-MD5        aarch64 2.59-5.fc41          fedora     231.9 KiB
 perl-DynaLoader        aarch64 1.56-511.fc41        fedora      32.1 KiB
 perl-Encode            aarch64 4:3.21-511.fc41      fedora       5.9 MiB
 perl-Errno             aarch64 1.38-511.fc41        fedora       8.4 KiB
 perl-Exporter          noarch  5.78-511.fc41        fedora      54.3 KiB
 perl-Fcntl             aarch64 1.18-511.fc41        fedora     221.1 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                aarch64 1.55-511.fc41        fedora     319.2 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       aarch64 3.16-511.fc41        fedora     222.2 KiB
 perl-Mozilla-CA        noarch  20240730-1.fc41      fedora       9.8 KiB
 perl-Net-SSLeay        aarch64 1.94-7.fc41          fedora       1.4 MiB
 perl-POSIX             aarch64 2.20-511.fc41        fedora     327.3 KiB
 perl-PathTools         aarch64 3.91-511.fc41        fedora     352.1 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 aarch64 5:1.66-1.fc42        fedora     278.7 KiB
 perl-SelectSaver       noarch  1.02-511.fc41        fedora       2.2 KiB
 perl-Socket            aarch64 4:2.038-511.fc41     fedora     272.1 KiB
 perl-Storable          aarch64 1:3.32-511.fc41      fedora     372.5 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              aarch64 4:5.40.0-511.fc41    fedora      10.9 MiB
 perl-locale            noarch  1.12-511.fc41        fedora       6.5 KiB
 perl-mro               aarch64 1.29-511.fc41        fedora     209.7 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:        82 packages

Total size of inbound packages is 59 MiB. Need to download 10 MiB.
After this operation, 178 MiB extra will be used (install 178 MiB, remove 0 B).
[1/1] gcc-0:14.2.1-3.fc42.aarch64       100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
--------------------------------------------------------------------------------
[1/1] Total                             100% |   0.0   B/s |   0.0   B |  00m00s
[1/2] make-1:4.4.1-8.fc41.aarch64       100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
--------------------------------------------------------------------------------
[2/2] Total                             100% |   0.0   B/s |   0.0   B |  00m00s
[ 1/10] zlib-ng-compat-devel-0:2.2.2-1. 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[ 2/11] cpp-0:14.2.1-3.fc42.aarch64     100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[ 3/12] libasan-0:14.2.1-3.fc42.aarch64 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[ 4/13] libatomic-0:14.2.1-3.fc42.aarch 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[ 5/14] libmpc-0:1.3.1-6.fc41.aarch64   100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[ 6/15] libubsan-0:14.2.1-3.fc42.aarch6 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[ 7/28] cmake-filesystem-0:3.28.3-7.fc4 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[ 8/77] glibc-devel-0:2.40.9000-5.fc42. 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[ 9/78] kernel-headers-0:6.11.0-63.fc42 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[10/79] libxcrypt-devel-0:4.4.36-7.fc41 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[11/80] annobin-plugin-gcc-0:12.70-1.fc 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[12/81] gcc-plugin-annobin-0:14.2.1-3.f 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[13/82] annobin-docs-0:12.70-1.fc42.noa 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[14/82] perl-FindBin-0:1.54-511.fc41.no 100% |   1.1 MiB/s |  14.2 KiB |  00m00s
[15/82] perl-Getopt-Long-1:2.58-2.fc41. 100% |   4.5 MiB/s |  63.9 KiB |  00m00s
[16/82] perl-lib-0:0.65-511.fc41.aarch6 100% |   4.8 MiB/s |  14.9 KiB |  00m00s
[17/82] ncurses-devel-0:6.5-2.20240629. 100% |  27.8 MiB/s | 569.9 KiB |  00m00s
[18/82] perl-interpreter-4:5.40.0-511.f 100% |  11.8 MiB/s |  72.4 KiB |  00m00s
[19/82] ncurses-c++-libs-0:6.5-2.202406 100% |  18.4 MiB/s |  37.7 KiB |  00m00s
[20/82] perl-Carp-0:1.54-511.fc41.noarc 100% |  28.2 MiB/s |  28.9 KiB |  00m00s
[21/82] perl-Exporter-0:5.78-511.fc41.n 100% |  15.1 MiB/s |  30.9 KiB |  00m00s
[22/82] perl-File-Basename-0:2.86-511.f 100% |   8.4 MiB/s |  17.1 KiB |  00m00s
[23/82] perl-PathTools-0:3.91-511.fc41. 100% |  28.5 MiB/s |  87.5 KiB |  00m00s
[24/82] perl-libs-4:5.40.0-511.fc41.aar 100% | 152.6 MiB/s |   2.3 MiB |  00m00s
[25/82] perl-Pod-Usage-4:2.03-511.fc41. 100% |  13.0 MiB/s |  40.0 KiB |  00m00s
[26/82] perl-Text-ParseWords-0:3.31-511 100% |  16.2 MiB/s |  16.6 KiB |  00m00s
[27/82] perl-base-0:2.27-511.fc41.noarc 100% |  15.8 MiB/s |  16.2 KiB |  00m00s
[28/82] perl-constant-0:1.33-512.fc41.n 100% |  11.2 MiB/s |  23.0 KiB |  00m00s
[29/82] perl-overload-0:1.37-511.fc41.n 100% |   7.4 MiB/s |  45.5 KiB |  00m00s
[30/82] htslib-devel-0:1.15.1-7.fc42.aa 100% | 434.2 KiB/s |  99.4 KiB |  00m00s
[31/82] perl-Errno-0:1.38-511.fc41.aarc 100% |  14.5 MiB/s |  14.9 KiB |  00m00s
[32/82] perl-Scalar-List-Utils-5:1.66-1 100% |  17.4 MiB/s |  71.3 KiB |  00m00s
[33/82] perl-DynaLoader-0:1.56-511.fc41 100% |  12.7 MiB/s |  26.0 KiB |  00m00s
[34/82] perl-Encode-4:3.21-511.fc41.aar 100% | 208.2 MiB/s |   1.0 MiB |  00m00s
[35/82] htslib-0:1.15.1-7.fc42.aarch64  100% |   2.3 MiB/s | 484.9 KiB |  00m00s
[36/82] htslib-tools-0:1.15.1-7.fc42.aa 100% |   2.2 MiB/s | 551.3 KiB |  00m00s
[37/82] perl-Pod-Perldoc-0:3.28.01-512. 100% |   8.4 MiB/s |  86.1 KiB |  00m00s
[38/82] perl-podlators-1:6.0.2-2.fc41.n 100% |  41.9 MiB/s | 128.8 KiB |  00m00s
[39/82] perl-overloading-0:0.02-511.fc4 100% |   4.2 MiB/s |  12.9 KiB |  00m00s
[40/82] perl-vars-0:1.05-511.fc41.noarc 100% |   6.3 MiB/s |  13.0 KiB |  00m00s
[41/82] perl-mro-0:1.29-511.fc41.aarch6 100% |   4.8 MiB/s |  29.6 KiB |  00m00s
[42/82] perl-MIME-Base64-0:3.16-511.fc4 100% |  14.8 MiB/s |  30.2 KiB |  00m00s
[43/82] perl-Getopt-Std-0:1.14-511.fc41 100% |   5.1 MiB/s |  15.6 KiB |  00m00s
[44/82] perl-parent-1:0.242-1.fc42.noar 100% |  14.6 MiB/s |  15.0 KiB |  00m00s
[45/82] perl-Storable-1:3.32-511.fc41.a 100% |  23.8 MiB/s |  97.4 KiB |  00m00s
[46/82] perl-File-Temp-1:0.231.100-511. 100% |  19.2 MiB/s |  59.1 KiB |  00m00s
[47/82] perl-Fcntl-0:1.18-511.fc41.aarc 100% |   4.9 MiB/s |  30.0 KiB |  00m00s
[48/82] groff-base-0:1.23.0-7.fc41.aarc 100% | 119.5 MiB/s |   1.1 MiB |  00m00s
[49/82] perl-HTTP-Tiny-0:0.088-512.fc41 100% |  18.2 MiB/s |  55.8 KiB |  00m00s
[50/82] perl-IO-0:1.55-511.fc41.aarch64 100% |  20.0 MiB/s |  82.0 KiB |  00m00s
[51/82] perl-IPC-Open3-0:1.22-511.fc41. 100% |   7.1 MiB/s |  21.8 KiB |  00m00s
[52/82] perl-Pod-Simple-1:3.45-511.fc41 100% |  53.5 MiB/s | 219.0 KiB |  00m00s
[53/82] perl-Symbol-0:1.09-511.fc41.noa 100% |   6.9 MiB/s |  14.2 KiB |  00m00s
[54/82] perl-POSIX-0:2.20-511.fc41.aarc 100% |  31.6 MiB/s |  97.0 KiB |  00m00s
[55/82] perl-Term-ANSIColor-0:5.01-512. 100% |  15.5 MiB/s |  47.7 KiB |  00m00s
[56/82] perl-File-Path-0:2.18-511.fc41. 100% |  34.4 MiB/s |  35.3 KiB |  00m00s
[57/82] perl-Term-Cap-0:1.18-511.fc41.n 100% |   5.4 MiB/s |  22.1 KiB |  00m00s
[58/82] perl-Mozilla-CA-0:20240730-1.fc 100% |   7.0 MiB/s |  14.3 KiB |  00m00s
[59/82] perl-IO-Socket-SSL-0:2.089-1.fc 100% |  32.3 MiB/s | 231.2 KiB |  00m00s
[60/82] perl-Net-SSLeay-0:1.94-7.fc41.a 100% |  52.4 MiB/s | 375.4 KiB |  00m00s
[61/82] perl-Socket-4:2.038-511.fc41.aa 100% |   9.0 MiB/s |  55.5 KiB |  00m00s
[62/82] perl-File-stat-0:1.14-511.fc41. 100% |   8.3 MiB/s |  17.0 KiB |  00m00s
[63/82] perl-SelectSaver-0:1.02-511.fc4 100% |   1.9 MiB/s |  11.7 KiB |  00m00s
[64/82] perl-Time-Local-2:1.350-511.fc4 100% |   3.4 MiB/s |  34.5 KiB |  00m00s
[65/82] perl-Pod-Escapes-1:1.07-511.fc4 100% |   3.9 MiB/s |  19.8 KiB |  00m00s
[66/82] perl-Text-Tabs+Wrap-0:2024.001- 100% |  10.7 MiB/s |  21.9 KiB |  00m00s
[67/82] perl-locale-0:1.12-511.fc41.noa 100% |  13.3 MiB/s |  13.6 KiB |  00m00s
[68/82] perl-if-0:0.61.000-511.fc41.noa 100% |   6.8 MiB/s |  14.0 KiB |  00m00s
[69/82] perl-IO-Socket-IP-0:0.42-512.fc 100% |  20.4 MiB/s |  41.8 KiB |  00m00s
[70/82] ncurses-0:6.5-2.20240629.fc41.a 100% |  82.5 MiB/s | 422.6 KiB |  00m00s
[71/82] perl-AutoLoader-0:5.74-511.fc41 100% |  10.4 MiB/s |  21.2 KiB |  00m00s
[72/82] perl-URI-0:5.29-1.fc42.noarch   100% |  26.9 MiB/s | 137.7 KiB |  00m00s
[73/82] perl-Class-Struct-0:0.68-511.fc 100% |   7.2 MiB/s |  22.0 KiB |  00m00s
[74/82] perl-MIME-Base32-0:1.303-21.fc4 100% |  10.0 MiB/s |  20.5 KiB |  00m00s
[75/82] perl-libnet-0:3.15-512.fc41.noa 100% |  62.7 MiB/s | 128.5 KiB |  00m00s
[76/82] perl-B-0:1.89-511.fc41.aarch64  100% |  57.7 MiB/s | 177.2 KiB |  00m00s
[77/82] perl-Data-Dumper-0:2.189-512.fc 100% |   9.0 MiB/s |  55.1 KiB |  00m00s
[78/82] perl-Digest-MD5-0:2.59-5.fc41.a 100% |  35.2 MiB/s |  36.1 KiB |  00m00s
[79/82] perl-Digest-0:1.20-511.fc41.noa 100% |  24.3 MiB/s |  24.9 KiB |  00m00s
[80/82] perl-FileHandle-0:2.05-511.fc41 100% |   7.5 MiB/s |  15.5 KiB |  00m00s
--------------------------------------------------------------------------------
[82/82] Total                           100% |   0.0   B/s |   0.0   B |  00m00s
Running transaction
[ 1/84] Verify package files            100% | 394.0   B/s |  82.0   B |  00m00s
[ 2/84] Prepare transaction             100% |   1.8 KiB/s |  82.0   B |  00m00s
[ 3/84] Installing htslib-0:1.15.1-7.fc 100% | 206.0 MiB/s |   1.2 MiB |  00m00s
[ 4/84] Installing libmpc-0:1.3.1-6.fc4 100% | 275.7 MiB/s | 282.3 KiB |  00m00s
[ 5/84] Installing cpp-0:14.2.1-3.fc42. 100% | 338.2 MiB/s |  31.8 MiB |  00m00s
[ 6/84] Installing annobin-docs-0:12.70 100% |  32.2 MiB/s |  98.8 KiB |  00m00s
[ 7/84] Installing kernel-headers-0:6.1 100% | 153.1 MiB/s |   6.4 MiB |  00m00s
[ 8/84] Installing libxcrypt-devel-0:4. 100% |  15.9 MiB/s |  32.6 KiB |  00m00s
[ 9/84] Installing glibc-devel-0:2.40.9 100% | 120.5 MiB/s |   2.3 MiB |  00m00s
[10/84] Installing ncurses-0:6.5-2.2024 100% | 140.8 MiB/s |   1.7 MiB |  00m00s
[11/84] Installing groff-base-0:1.23.0- 100% | 200.0 MiB/s |   5.2 MiB |  00m00s
[12/84] Installing perl-Digest-0:1.20-5 100% |  36.2 MiB/s |  37.1 KiB |  00m00s
[13/84] Installing perl-B-0:1.89-511.fc 100% | 198.4 MiB/s | 609.4 KiB |  00m00s
[14/84] Installing perl-FileHandle-0:2. 100% |   0.0   B/s |   9.8 KiB |  00m00s
[15/84] Installing perl-Digest-MD5-0:2. 100% | 228.3 MiB/s | 233.8 KiB |  00m00s
[16/84] Installing perl-MIME-Base32-0:1 100% |  31.4 MiB/s |  32.2 KiB |  00m00s
[17/84] Installing perl-Data-Dumper-0:2 100% | 259.4 MiB/s | 265.7 KiB |  00m00s
[18/84] Installing perl-libnet-0:3.15-5 100% | 143.9 MiB/s | 294.7 KiB |  00m00s
[19/84] Installing perl-AutoLoader-0:5. 100% |   0.0   B/s |  20.9 KiB |  00m00s
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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
[84/84] Installing htslib-tools-0:1.15. 100% |  16.3 MiB/s |   2.4 MiB |  00m00s
Warning: skipped PGP checks for 5 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: aarch64
Building for target aarch64
setting SOURCE_DATE_EPOCH=1721433600
Executing(%mkbuilddir): /bin/sh -e /var/tmp/rpm-tmp.wat9AQ
+ 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.7ptWA2
+ 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.8vfHeN
+ 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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' ./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 13:24:52.440147094 +0000
@@ -1697,7 +1697,7 @@
 #ifdef __cplusplus
 extern "C"
 #endif
-char $2 ();
+__attribute__ ((used)) char $2 ();
 /* The GNU C library defines this for functions which it implements
     to always fail with ENOSYS.  Some functions are actually named
     something starting with __ and the normal name is an alias.  */
+ /usr/bin/sed --in-place=.backup '1{$!N;$!N};$!N;s/int x = 1;\nint y = 0;\nint z;\nint nan;/volatile int x = 1; volatile int y = 0; volatile int z, nan;/;P;D' ./htslib-1.15.1/configure
+ diff -u ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure
+ mv ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure
+ /usr/bin/sed --in-place=.backup 's#^lt_cv_sys_global_symbol_to_cdecl=.*#lt_cv_sys_global_symbol_to_cdecl="sed -n -e '\''s/^T .* \\(.*\\)$/extern int \\1();/p'\'' -e '\''s/^$symcode* .* \\(.*\\)$/extern char \\1;/p'\''"#' ./htslib-1.15.1/configure
+ diff -u ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure
+ mv ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure
+ for file in $(find . -type f -name configure -print)
+ /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\) = /__attribute__ ((used)) char (*f) () = /g' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\);/__attribute__ ((used)) char (*f) ();/g' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ /usr/bin/sed -r --in-place=.backup 's/^char \$2 \(\);/__attribute__ ((used)) char \$2 ();/g' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ /usr/bin/sed --in-place=.backup '1{$!N;$!N};$!N;s/int x = 1;\nint y = 0;\nint z;\nint nan;/volatile int x = 1; volatile int y = 0; volatile int z, nan;/;P;D' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ /usr/bin/sed --in-place=.backup 's#^lt_cv_sys_global_symbol_to_cdecl=.*#lt_cv_sys_global_symbol_to_cdecl="sed -n -e '\''s/^T .* \\(.*\\)$/extern int \\1();/p'\'' -e '\''s/^$symcode* .* \\(.*\\)$/extern char \\1;/p'\''"#' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ '[' 1 = 1 ']'
+++ dirname ./configure
++ find . -name config.guess -o -name config.sub
+ '[' 1 = 1 ']'
+ '[' x '!=' 'x-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' ']'
++ find . -name ltmain.sh
++ grep -q runstatedir=DIR ./configure
++ echo --runstatedir=/run
+ ./configure --build=aarch64-redhat-linux --host=aarch64-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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 aarch64-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 -j4 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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
ar -rcs libst.a sam_opts.o sam_utils.o bedidx.o
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o bamtk.o bamtk.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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -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 -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 -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -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_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 misc/ace2sam misc/ace2sam.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/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/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 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/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 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.rae7GF
+ 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -j4 --strict-build-id -m -i --build-id-seed 1.15.1-5.fc42 --unique-debug-suffix -1.15.1-5.fc42.aarch64 --unique-debug-src-base samtools-1.15.1-5.fc42.aarch64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -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.aarch64
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 -j4
+ /usr/lib/rpm/redhat/brp-python-hardlink
+ /usr/bin/add-determinism --brp -j4 /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.wCkOrr
+ 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 (0x0000ffff9a0a0000)
+ 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/A4jDGOpiGv/bgzip.dat.gz
.. ok

bgzip -c -b 979200 -s 6 /tmp/A4jDGOpiGv/bgzip.dat.gz
.. ok

bgzip -c -b 652804 -s 6 /tmp/A4jDGOpiGv/bgzip.dat.gz
.. ok

/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools faidx /tmp/A4jDGOpiGv/faidx.fa 3:11-13 | grep -v '^>'
.. ok

/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools faidx /tmp/A4jDGOpiGv/faidx.fa.gz 3:11-13 | grep -v '^>'
.. ok

/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools faidx /tmp/A4jDGOpiGv/faidx.fa 2:998-1003 | grep -v '^>'
.. ok

/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools faidx /tmp/A4jDGOpiGv/faidx.fa.gz 2:998-1003 | grep -v '^>'
.. ok

/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools faidx /tmp/A4jDGOpiGv/faidx.fa 1:100-104 | grep -v '^>'
.. ok

/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools faidx /tmp/A4jDGOpiGv/faidx.fa.gz 1:100-104 | grep -v '^>'
.. ok

/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools faidx /tmp/A4jDGOpiGv/faidx.fa 1:99998-100007 | grep -v '^>'
.. ok

/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools faidx /tmp/A4jDGOpiGv/faidx.fa.gz 1:99998-100007 | grep -v '^>'
.. ok

/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fqidx /tmp/A4jDGOpiGv/fqidx.fq 3:11-13
.. ok

.. ok

/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fqidx /tmp/A4jDGOpiGv/fqidx.fq.gz 3:11-13
.. ok

.. ok

/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fqidx /tmp/A4jDGOpiGv/fqidx.fq 2:998-1003
.. ok

.. ok

/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fqidx /tmp/A4jDGOpiGv/fqidx.fq.gz 2:998-1003
.. ok

.. ok

/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fqidx /tmp/A4jDGOpiGv/fqidx.fq 1:100-104
.. ok

.. ok

/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fqidx /tmp/A4jDGOpiGv/fqidx.fq.gz 1:100-104
.. ok

.. ok

/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fqidx /tmp/A4jDGOpiGv/fqidx.fq 1:99998-100007
.. ok

.. ok

/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools fqidx /tmp/A4jDGOpiGv/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/A4jDGOpiGv/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/A4jDGOpiGv/large_chrom.bam ref2
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools view /tmp/A4jDGOpiGv/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/A4jDGOpiGv/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/A4jDGOpiGv/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/A4jDGOpiGv/auto_indexed.csi && cat /tmp/A4jDGOpiGv/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/A4jDGOpiGv/auto_indexed.crai && cat /tmp/A4jDGOpiGv/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/A4jDGOpiGv/auto_indexed.csi && cat /tmp/A4jDGOpiGv/auto_indexed.csi
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools view -@ 2 /tmp/A4jDGOpiGv/large_chrom.bam ref2
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools view -@ 2 /tmp/A4jDGOpiGv/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/A4jDGOpiGv/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/A4jDGOpiGv/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/A4jDGOpiGv/auto_indexed.csi && cat /tmp/A4jDGOpiGv/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/A4jDGOpiGv/auto_indexed.crai && cat /tmp/A4jDGOpiGv/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/A4jDGOpiGv/auto_indexed.csi && cat /tmp/A4jDGOpiGv/auto_indexed.csi
.. ok

test_mpileup:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools mpileup -b /tmp/A4jDGOpiGv/mpileup.bam.list -f /tmp/A4jDGOpiGv/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/A4jDGOpiGv/mpileup.cram.list -f /tmp/A4jDGOpiGv/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/A4jDGOpiGv/mpileup.bam.urllist -f /tmp/A4jDGOpiGv/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/A4jDGOpiGv/mpileup.cram.urllist -f /tmp/A4jDGOpiGv/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/A4jDGOpiGv/mpileup.ref.fa.gz -r17:1050-1060 /tmp/A4jDGOpiGv/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/A4jDGOpiGv/mpileup.ref.fa.gz -r17:1050-1060 /tmp/A4jDGOpiGv/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/A4jDGOpiGv/view.001.fogn (SAM input)     .. ok

	50: Count -R /tmp/A4jDGOpiGv/view.001.fogn (SAM input)      .. ok

	51: Filter -R /tmp/A4jDGOpiGv/view.001.fogn (BAM input)     .. ok

	52: Count -R /tmp/A4jDGOpiGv/view.001.fogn (BAM input)      .. ok

	53: Filter -R /tmp/A4jDGOpiGv/view.001.fogn (CRAM input)    .. ok

	54: Count -R /tmp/A4jDGOpiGv/view.001.fogn (CRAM input)     .. ok

	55: Filter -R /tmp/A4jDGOpiGv/view.001.fogn -r grp2 (SAM input).. ok

	56: Count -R /tmp/A4jDGOpiGv/view.001.fogn -r grp2 (SAM input).. ok

	57: Filter -R /tmp/A4jDGOpiGv/view.001.fogn -r grp2 (BAM input).. ok

	58: Count -R /tmp/A4jDGOpiGv/view.001.fogn -r grp2 (BAM input).. ok

	59: Filter -R /tmp/A4jDGOpiGv/view.001.fogn -r grp2 (CRAM input).. ok

	60: Count -R /tmp/A4jDGOpiGv/view.001.fogn -r grp2 (CRAM input).. ok

	61: Filter -r grp2 -R /tmp/A4jDGOpiGv/view.001.fogn (SAM input).. ok

	62: Count -r grp2 -R /tmp/A4jDGOpiGv/view.001.fogn (SAM input).. ok

	63: Filter -r grp2 -R /tmp/A4jDGOpiGv/view.001.fogn (BAM input).. ok

	64: Count -r grp2 -R /tmp/A4jDGOpiGv/view.001.fogn (BAM input).. ok

	65: Filter -r grp2 -R /tmp/A4jDGOpiGv/view.001.fogn (CRAM input).. ok

	66: Count -r grp2 -R /tmp/A4jDGOpiGv/view.001.fogn (CRAM input).. ok

	67: Filter -N /tmp/A4jDGOpiGv/view.001.forn (SAM input)     .. ok

	68: Count -N /tmp/A4jDGOpiGv/view.001.forn (SAM input)      .. ok

	69: Filter -N /tmp/A4jDGOpiGv/view.001.forn (BAM input)     .. ok

	70: Count -N /tmp/A4jDGOpiGv/view.001.forn (BAM input)      .. ok

	71: Filter -N /tmp/A4jDGOpiGv/view.001.forn (CRAM input)    .. ok

	72: Count -N /tmp/A4jDGOpiGv/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/A4jDGOpiGv/view.001.fobc (SAM input)  .. ok

	86: Count -D BC:/tmp/A4jDGOpiGv/view.001.fobc (SAM input)   .. ok

	87: Filter -D BC:/tmp/A4jDGOpiGv/view.001.fobc (BAM input)  .. ok

	88: Count -D BC:/tmp/A4jDGOpiGv/view.001.fobc (BAM input)   .. ok

	89: Filter -D BC:/tmp/A4jDGOpiGv/view.001.fobc (CRAM input) .. ok

	90: Count -D BC:/tmp/A4jDGOpiGv/view.001.fobc (CRAM input)  .. ok

	91: Filter -D BC:/tmp/A4jDGOpiGv/view.001.fobc -d BC:TGCA (SAM input).. ok

	92: Count -D BC:/tmp/A4jDGOpiGv/view.001.fobc -d BC:TGCA (SAM input).. ok

	93: Filter -D BC:/tmp/A4jDGOpiGv/view.001.fobc -d BC:TGCA (BAM input).. ok

	94: Count -D BC:/tmp/A4jDGOpiGv/view.001.fobc -d BC:TGCA (BAM input).. ok

	95: Filter -D BC:/tmp/A4jDGOpiGv/view.001.fobc -d BC:TGCA (CRAM input).. ok

	96: Count -D BC:/tmp/A4jDGOpiGv/view.001.fobc -d BC:TGCA (CRAM input).. ok

	97: Filter -d BC:TGCA -D BC:/tmp/A4jDGOpiGv/view.001.fobc (SAM input).. ok

	98: Count -d BC:TGCA -D BC:/tmp/A4jDGOpiGv/view.001.fobc (SAM input).. ok

	99: Filter -d BC:TGCA -D BC:/tmp/A4jDGOpiGv/view.001.fobc (BAM input).. ok

	100: Count -d BC:TGCA -D BC:/tmp/A4jDGOpiGv/view.001.fobc (BAM input).. ok

	101: Filter -d BC:TGCA -D BC:/tmp/A4jDGOpiGv/view.001.fobc (CRAM input).. ok

	102: Count -d BC:TGCA -D BC:/tmp/A4jDGOpiGv/view.001.fobc (CRAM input).. ok

	103: Filter -D RG:/tmp/A4jDGOpiGv/view.001.fogn (SAM input) .. ok

	104: Count -D RG:/tmp/A4jDGOpiGv/view.001.fogn (SAM input)  .. ok

	105: Filter -D RG:/tmp/A4jDGOpiGv/view.001.fogn (BAM input) .. ok

	106: Count -D RG:/tmp/A4jDGOpiGv/view.001.fogn (BAM input)  .. ok

	107: Filter -D RG:/tmp/A4jDGOpiGv/view.001.fogn (CRAM input).. ok

	108: Count -D RG:/tmp/A4jDGOpiGv/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/A4jDGOpiGv/view.test115.sam -h -d TGCA /tmp/A4jDGOpiGv/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/A4jDGOpiGv/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/A4jDGOpiGv/view.test117.sam -h -d TGCA /tmp/A4jDGOpiGv/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/A4jDGOpiGv/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/A4jDGOpiGv/view.test119.sam -h -d TGCA /tmp/A4jDGOpiGv/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/A4jDGOpiGv/view.test006.cram --no-PG


.. expected failure

	121: Filter -D BClong:/tmp/A4jDGOpiGv/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/A4jDGOpiGv/view.001.fobc"
	Failed command:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools view -o /tmp/A4jDGOpiGv/view.test121.sam -h -D BClong:/tmp/A4jDGOpiGv/view.001.fobc /tmp/A4jDGOpiGv/view.001.sam --no-PG


.. expected failure

	122: Count -D BClong:/tmp/A4jDGOpiGv/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/A4jDGOpiGv/view.001.fobc"
	Failed command:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools view -c -D BClong:/tmp/A4jDGOpiGv/view.001.fobc /tmp/A4jDGOpiGv/view.001.sam --no-PG


.. expected failure

	123: Filter -D BClong:/tmp/A4jDGOpiGv/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/A4jDGOpiGv/view.001.fobc"
	Failed command:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools view -o /tmp/A4jDGOpiGv/view.test123.sam -h -D BClong:/tmp/A4jDGOpiGv/view.001.fobc /tmp/A4jDGOpiGv/view.test001.bam --no-PG


.. expected failure

	124: Count -D BClong:/tmp/A4jDGOpiGv/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/A4jDGOpiGv/view.001.fobc"
	Failed command:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools view -c -D BClong:/tmp/A4jDGOpiGv/view.001.fobc /tmp/A4jDGOpiGv/view.test001.bam --no-PG


.. expected failure

	125: Filter -D BClong:/tmp/A4jDGOpiGv/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/A4jDGOpiGv/view.001.fobc"
	Failed command:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools view -o /tmp/A4jDGOpiGv/view.test125.sam -h -D BClong:/tmp/A4jDGOpiGv/view.001.fobc /tmp/A4jDGOpiGv/view.test006.cram --no-PG


.. expected failure

	126: Count -D BClong:/tmp/A4jDGOpiGv/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/A4jDGOpiGv/view.001.fobc"
	Failed command:
	/builddir/build/BUILD/samtools-1.15.1-build/samtools-1.15.1/samtools view -c -D BClong:/tmp/A4jDGOpiGv/view.001.fobc /tmp/A4jDGOpiGv/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/A4jDGOpiGv/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/A4jDGOpiGv/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/A4jDGOpiGv/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/A4jDGOpiGv/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/A4jDGOpiGv/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/A4jDGOpiGv/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/A4jDGOpiGv/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/A4jDGOpiGv/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/A4jDGOpiGv/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/A4jDGOpiGv/bam2fq.discard.s.fq -0 /tmp/A4jDGOpiGv/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/A4jDGOpiGv/bam2fq.discard.s.fq -0 /tmp/A4jDGOpiGv/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/0hN6yL7teb - /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/A4jDGOpiGv/merge.tag.1.bam /tmp/A4jDGOpiGv/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/A4jDGOpiGv/merge.tag.3.bam /tmp/A4jDGOpiGv/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/A4jDGOpiGv/merge.bed.1.bam /tmp/A4jDGOpiGv/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/EhV3gLf2YZ - /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/A4jDGOpiGv/merge.tag.1.bam /tmp/A4jDGOpiGv/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/A4jDGOpiGv/merge.tag.3.bam /tmp/A4jDGOpiGv/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/A4jDGOpiGv/merge.bed.1.bam /tmp/A4jDGOpiGv/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/A4jDGOpiGv/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/A4jDGOpiGv/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/A4jDGOpiGv/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/A4jDGOpiGv/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/A4jDGOpiGv/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/A4jDGOpiGv/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/A4jDGOpiGv/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/A4jDGOpiGv/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/A4jDGOpiGv/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/A4jDGOpiGv/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.aarch64
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.g07kP2
+ 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.W31zxw
+ 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(aarch-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 ld-linux-aarch64.so.1()(64bit) ld-linux-aarch64.so.1(GLIBC_2.17)(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.17)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_ABI_DT_RELR)(64bit) libhts.so.3()(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.17)(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.aarch64
Provides: samtools-debugsource = 1.15.1-5.fc42 samtools-debugsource(aarch-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.aarch64
Provides: debuginfo(build-id) = 054eedd9ce3732fcfd28e95f233694bacb7c38d5 debuginfo(build-id) = 105d9e454f5e49b737b87686f621418fae261af7 debuginfo(build-id) = 58be6a7c6bfc3786330a1319920c2b001cc84981 debuginfo(build-id) = a849aaa8f1e80c54569b87473453ad43d5d1d516 debuginfo(build-id) = bf99e9f9e6b1bd7f74b0f5d26ebf065274215749 debuginfo(build-id) = ccbd29035a8409df181ac38ab99dd92cbac16920 debuginfo(build-id) = dae5119fde8a08b69794aa281203030752cb25ed samtools-debuginfo = 1.15.1-5.fc42 samtools-debuginfo(aarch-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(aarch-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.aarch64.rpm
Wrote: /builddir/build/RPMS/samtools-debugsource-1.15.1-5.fc42.aarch64.rpm
Wrote: /builddir/build/RPMS/samtools-debuginfo-1.15.1-5.fc42.aarch64.rpm
Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.80ATtL
+ 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-aarch64-1727357069.761619/root/var/log/dnf5.log
INFO: Done(/var/lib/copr-rpmbuild/results/samtools-1.15.1-5.fc42.src.rpm) Config(child) 0 minutes 46 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": "src"
        },
        {
            "name": "samtools-debugsource",
            "epoch": null,
            "version": "1.15.1",
            "release": "5.fc42",
            "arch": "aarch64"
        },
        {
            "name": "samtools-debuginfo",
            "epoch": null,
            "version": "1.15.1",
            "release": "5.fc42",
            "arch": "aarch64"
        },
        {
            "name": "samtools",
            "epoch": null,
            "version": "1.15.1",
            "release": "5.fc42",
            "arch": "aarch64"
        }
    ]
}
RPMResults finished