Warning: Permanently added '2620:52:3:1:dead:beef:cafe:c113' (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/6868888-amazonlinux-2023-x86_64 --chroot amazonlinux-2023-x86_64


Version: 0.70
PID: 7156
Logging PID: 7157
Task:
{'appstream': False,
 'background': False,
 'build_id': 6868888,
 'buildroot_pkgs': [],
 'chroot': 'amazonlinux-2023-x86_64',
 'enable_net': False,
 'fedora_review': False,
 'git_hash': '0392ffcf610a37f721b5e82445dac25a42cacab3',
 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/trawets/random-al2023-pkg-builds/samtools',
 'isolation': 'default',
 'memory_reqs': 2048,
 'package_name': 'samtools',
 'package_version': '1.15.1-3',
 'project_dirname': 'random-al2023-pkg-builds',
 'project_name': 'random-al2023-pkg-builds',
 'project_owner': 'trawets',
 'repo_priority': None,
 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/trawets/random-al2023-pkg-builds/amazonlinux-2023-x86_64/',
            'id': 'copr_base',
            'name': 'Copr repository',
            'priority': None}],
 'sandbox': 'trawets/random-al2023-pkg-builds--trawets',
 'source_json': {},
 'source_type': None,
 'submitter': 'trawets',
 'tags': [],
 'task_id': '6868888-amazonlinux-2023-x86_64',
 'timeout': 18000,
 'uses_devel_repo': False,
 'with_opts': [],
 'without_opts': []}

Running: git clone https://copr-dist-git.fedorainfracloud.org/git/trawets/random-al2023-pkg-builds/samtools /var/lib/copr-rpmbuild/workspace/workdir-_59crliw/samtools --depth 500 --no-single-branch --recursive

cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/trawets/random-al2023-pkg-builds/samtools', '/var/lib/copr-rpmbuild/workspace/workdir-_59crliw/samtools', '--depth', '500', '--no-single-branch', '--recursive']
cwd: .
rc: 0
stdout: 
stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-_59crliw/samtools'...

Running: git checkout 0392ffcf610a37f721b5e82445dac25a42cacab3 --

cmd: ['git', 'checkout', '0392ffcf610a37f721b5e82445dac25a42cacab3', '--']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-_59crliw/samtools
rc: 0
stdout: 
stderr: Note: switching to '0392ffcf610a37f721b5e82445dac25a42cacab3'.

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 0392ffc automatic import of samtools

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

cmd: ['copr-distgit-client', 'sources']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-_59crliw/samtools
rc: 0
stdout: 
stderr: INFO: Reading stdout from command: git rev-parse --abbrev-ref HEAD
INFO: Reading stdout from command: git rev-parse HEAD
INFO: Reading sources specification file: sources
INFO: Downloading samtools-1.15.1.tar.bz2
INFO: Reading stdout from command: curl --help all
INFO: Calling: curl -H Pragma: -o samtools-1.15.1.tar.bz2 --location --connect-timeout 60 --retry 3 --retry-delay 10 --remote-time --show-error --fail --retry-all-errors https://copr-dist-git.fedorainfracloud.org/repo/pkgs/trawets/random-al2023-pkg-builds/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  45.0M      0 --:--:-- --:--:-- --:--:-- 45.2M
INFO: Reading stdout from command: md5sum samtools-1.15.1.tar.bz2

Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-_59crliw/samtools/samtools.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-_59crliw/samtools --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1704591447.340321 -r /var/lib/copr-rpmbuild/results/configs/child.cfg
INFO: mock.py version 5.4 starting (python version = 3.11.3, NVR = mock-5.4-1.fc38), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-_59crliw/samtools/samtools.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-_59crliw/samtools --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1704591447.340321 -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-_59crliw/samtools/samtools.spec)  Config(amazonlinux-2023-x86_64)
Start: clean chroot
Finish: clean chroot
Mock Version: 5.4
INFO: Mock Version: 5.4
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/amazonlinux-2023-x86_64-bootstrap-1704591447.340321/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: public.ecr.aws/amazonlinux/amazonlinux:2023
INFO: Pulling image: public.ecr.aws/amazonlinux/amazonlinux:2023
INFO: Copy content of container public.ecr.aws/amazonlinux/amazonlinux:2023 to /var/lib/mock/amazonlinux-2023-x86_64-bootstrap-1704591447.340321/root
INFO: Checking that public.ecr.aws/amazonlinux/amazonlinux:2023 image matches host's architecture
INFO: mounting public.ecr.aws/amazonlinux/amazonlinux:2023 with podman image mount
INFO: image public.ecr.aws/amazonlinux/amazonlinux:2023 as /var/lib/containers/storage/overlay/feb47202015b991620a1d091d4c0e3cf93925009c823acb869c0ac54078b50fd/merged
INFO: umounting image public.ecr.aws/amazonlinux/amazonlinux:2023 (/var/lib/containers/storage/overlay/feb47202015b991620a1d091d4c0e3cf93925009c823acb869c0ac54078b50fd/merged) with podman image umount
INFO: Package manager dnf detected and used (fallback)
INFO: Bootstrap image not marked ready
Start(bootstrap): installing dnf tooling
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Copr repository                                 1.3 MB/s | 166 kB     00:00    
Amazon Linux 2023 repository - x86_64            27 MB/s |  22 MB     00:00    
Package python3-dnf-4.12.0-2.amzn2023.0.4.noarch is already installed.
Dependencies resolved.
================================================================================
 Package                   Arch    Version                   Repository    Size
================================================================================
Installing:
 python3-dnf-plugins-core  noarch  4.1.0-1.amzn2023.0.3      amazonlinux  219 k
Installing dependencies:
 dbus-libs                 x86_64  1:1.12.28-1.amzn2023.0.1  amazonlinux  153 k
 python3-dateutil          noarch  1:2.8.1-3.amzn2023.0.2    amazonlinux  289 k
 python3-dbus              x86_64  1.2.18-1.amzn2023.0.2     amazonlinux  134 k
 python3-distro            noarch  1.5.0-5.amzn2023.0.2      amazonlinux   36 k
 python3-setuptools        noarch  59.6.0-2.amzn2023.0.4     amazonlinux  940 k
 python3-six               noarch  1.15.0-5.amzn2023.0.2     amazonlinux   36 k
 systemd-libs              x86_64  252.16-1.amzn2023.0.1     amazonlinux  627 k

Transaction Summary
================================================================================
Install  8 Packages

Total download size: 2.4 M
Installed size: 11 M
Downloading Packages:
(1/8): dbus-libs-1.12.28-1.amzn2023.0.1.x86_64. 2.1 MB/s | 153 kB     00:00    
(2/8): python3-dbus-1.2.18-1.amzn2023.0.2.x86_6 1.7 MB/s | 134 kB     00:00    
(3/8): systemd-libs-252.16-1.amzn2023.0.1.x86_6 6.5 MB/s | 627 kB     00:00    
(4/8): python3-six-1.15.0-5.amzn2023.0.2.noarch 1.5 MB/s |  36 kB     00:00    
(5/8): python3-dateutil-2.8.1-3.amzn2023.0.2.no 8.0 MB/s | 289 kB     00:00    
(6/8): python3-distro-1.5.0-5.amzn2023.0.2.noar 1.7 MB/s |  36 kB     00:00    
(7/8): python3-setuptools-59.6.0-2.amzn2023.0.4  23 MB/s | 940 kB     00:00    
(8/8): python3-dnf-plugins-core-4.1.0-1.amzn202 8.6 MB/s | 219 kB     00:00    
--------------------------------------------------------------------------------
Total                                           5.2 MB/s | 2.4 MB     00:00     
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
  Preparing        :                                                        1/1 
  Installing       : python3-setuptools-59.6.0-2.amzn2023.0.4.noarch        1/8 
  Installing       : python3-distro-1.5.0-5.amzn2023.0.2.noarch             2/8 
  Installing       : python3-six-1.15.0-5.amzn2023.0.2.noarch               3/8 
  Installing       : python3-dateutil-1:2.8.1-3.amzn2023.0.2.noarch         4/8 
  Installing       : systemd-libs-252.16-1.amzn2023.0.1.x86_64              5/8 
  Installing       : dbus-libs-1:1.12.28-1.amzn2023.0.1.x86_64              6/8 
  Installing       : python3-dbus-1.2.18-1.amzn2023.0.2.x86_64              7/8 
  Installing       : python3-dnf-plugins-core-4.1.0-1.amzn2023.0.3.noarch   8/8 
  Running scriptlet: python3-dnf-plugins-core-4.1.0-1.amzn2023.0.3.noarch   8/8 
  Verifying        : python3-dbus-1.2.18-1.amzn2023.0.2.x86_64              1/8 
  Verifying        : dbus-libs-1:1.12.28-1.amzn2023.0.1.x86_64              2/8 
  Verifying        : systemd-libs-252.16-1.amzn2023.0.1.x86_64              3/8 
  Verifying        : python3-six-1.15.0-5.amzn2023.0.2.noarch               4/8 
  Verifying        : python3-dateutil-1:2.8.1-3.amzn2023.0.2.noarch         5/8 
  Verifying        : python3-setuptools-59.6.0-2.amzn2023.0.4.noarch        6/8 
  Verifying        : python3-distro-1.5.0-5.amzn2023.0.2.noarch             7/8 
  Verifying        : python3-dnf-plugins-core-4.1.0-1.amzn2023.0.3.noarch   8/8 

Installed:
  dbus-libs-1:1.12.28-1.amzn2023.0.1.x86_64                                     
  python3-dateutil-1:2.8.1-3.amzn2023.0.2.noarch                                
  python3-dbus-1.2.18-1.amzn2023.0.2.x86_64                                     
  python3-distro-1.5.0-5.amzn2023.0.2.noarch                                    
  python3-dnf-plugins-core-4.1.0-1.amzn2023.0.3.noarch                          
  python3-setuptools-59.6.0-2.amzn2023.0.4.noarch                               
  python3-six-1.15.0-5.amzn2023.0.2.noarch                                      
  systemd-libs-252.16-1.amzn2023.0.1.x86_64                                     

Complete!
Finish(bootstrap): installing dnf tooling
Start(bootstrap): creating root cache
Finish(bootstrap): creating root cache
Finish(bootstrap): chroot init
Start: chroot init
INFO: mounting tmpfs at /var/lib/mock/amazonlinux-2023-x86_64-1704591447.340321/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 dnf detected and used (direct choice)
INFO: Buildroot is handled by package management downloaded with a bootstrap image:
  rpm-4.16.1.3-12.amzn2023.0.6.x86_64
  python3-dnf-4.12.0-2.amzn2023.0.4.noarch
  python3-dnf-plugins-core-4.1.0-1.amzn2023.0.3.noarch
  yum-4.12.0-2.amzn2023.0.4.noarch
Start: installing minimal buildroot with dnf
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Copr repository                                  33 kB/s | 1.5 kB     00:00    
Copr repository                                 1.5 MB/s | 166 kB     00:00    
Amazon Linux 2023 repository - x86_64           9.6 kB/s | 3.6 kB     00:00    
Dependencies resolved.
============================================================================================
 Package                       Arch    Version                            Repository    Size
============================================================================================
Installing:
 amazon-rpm-config             noarch  228-3.amzn2023.0.2                 amazonlinux   74 k
 bash                          x86_64  5.2.15-1.amzn2023.0.2              amazonlinux  1.8 M
 bzip2                         x86_64  1.0.8-6.amzn2023.0.2               amazonlinux   53 k
 coreutils                     x86_64  8.32-30.amzn2023.0.3               amazonlinux  1.1 M
 cpio                          x86_64  2.13-13.amzn2023.0.2               amazonlinux  272 k
 diffutils                     x86_64  3.8-1.amzn2023.0.2                 amazonlinux  370 k
 findutils                     x86_64  1:4.8.0-2.amzn2023.0.2             amazonlinux  539 k
 gawk                          x86_64  5.1.0-3.amzn2023.0.3               amazonlinux  1.0 M
 glibc-minimal-langpack        x86_64  2.34-52.amzn2023.0.7               amazonlinux   33 k
 grep                          x86_64  3.8-1.amzn2023.0.4                 amazonlinux  283 k
 gzip                          x86_64  1.12-1.amzn2023.0.1                amazonlinux  160 k
 info                          x86_64  6.7-10.amzn2023.0.2                amazonlinux  227 k
 patch                         x86_64  2.7.6-14.amzn2023.0.2              amazonlinux  129 k
 rpm-build                     x86_64  4.16.1.3-12.amzn2023.0.6           amazonlinux   92 k
 sed                           x86_64  4.8-7.amzn2023.0.2                 amazonlinux  297 k
 system-release                noarch  2023.3.20231218-0.amzn2023         amazonlinux   27 k
 tar                           x86_64  2:1.34-1.amzn2023.0.3              amazonlinux  879 k
 unzip                         x86_64  6.0-57.amzn2023.0.2                amazonlinux  182 k
 util-linux                    x86_64  2.37.4-1.amzn2023.0.3              amazonlinux  2.2 M
 which                         x86_64  2.21-26.amzn2023.0.2               amazonlinux   42 k
 xz                            x86_64  5.2.5-9.amzn2023.0.2               amazonlinux  215 k
Installing dependencies:
 alternatives                  x86_64  1.15-2.amzn2023.0.2                amazonlinux   36 k
 amazon-linux-repo-cdn         noarch  2023.3.20231218-0.amzn2023         amazonlinux   16 k
 audit-libs                    x86_64  3.0.6-1.amzn2023.0.2               amazonlinux  116 k
 basesystem                    noarch  11-11.amzn2023.0.2                 amazonlinux  7.8 k
 binutils                      x86_64  2.39-6.amzn2023.0.10               amazonlinux  4.4 M
 bzip2-libs                    x86_64  1.0.8-6.amzn2023.0.2               amazonlinux   43 k
 ca-certificates               noarch  2023.2.62-1.0.amzn2023.0.1         amazonlinux  739 k
 coreutils-common              x86_64  8.32-30.amzn2023.0.3               amazonlinux  2.0 M
 cracklib                      x86_64  2.9.6-27.amzn2023.0.2              amazonlinux   82 k
 crypto-policies               noarch  20220428-1.gitdfb10ea.amzn2023.0.2 amazonlinux   60 k
 curl                          x86_64  8.3.0-1.amzn2023.0.2               amazonlinux  355 k
 cyrus-sasl-lib                x86_64  2.1.27-18.amzn2023.0.3             amazonlinux  786 k
 dwz                           x86_64  0.14-6.amzn2023.0.2                amazonlinux  129 k
 ed                            x86_64  1.14.2-10.amzn2023.0.2             amazonlinux   75 k
 efi-srpm-macros               noarch  5-4.amzn2023.0.5                   amazonlinux   23 k
 elfutils                      x86_64  0.188-3.amzn2023.0.2               amazonlinux  525 k
 elfutils-debuginfod-client    x86_64  0.188-3.amzn2023.0.2               amazonlinux   41 k
 elfutils-default-yama-scope   noarch  0.188-3.amzn2023.0.2               amazonlinux   17 k
 elfutils-libelf               x86_64  0.188-3.amzn2023.0.2               amazonlinux  199 k
 elfutils-libs                 x86_64  0.188-3.amzn2023.0.2               amazonlinux  258 k
 file                          x86_64  5.39-7.amzn2023.0.4                amazonlinux   49 k
 file-libs                     x86_64  5.39-7.amzn2023.0.4                amazonlinux  588 k
 filesystem                    x86_64  3.14-5.amzn2023.0.3                amazonlinux   22 k
 fonts-srpm-macros             noarch  1:2.0.5-12.amzn2023.0.2            amazonlinux   27 k
 gdb-minimal                   x86_64  12.1-5.amzn2023.0.3                amazonlinux  4.0 M
 gdbm-libs                     x86_64  1:1.19-2.amzn2023.0.2              amazonlinux   53 k
 ghc-srpm-macros               noarch  1.5.0-4.amzn2023.0.2               amazonlinux  8.5 k
 glibc                         x86_64  2.34-52.amzn2023.0.7               amazonlinux  1.9 M
 glibc-common                  x86_64  2.34-52.amzn2023.0.7               amazonlinux  304 k
 glibc-gconv-extra             x86_64  2.34-52.amzn2023.0.7               amazonlinux  1.5 M
 gmp                           x86_64  1:6.2.1-2.amzn2023.0.2             amazonlinux  324 k
 go-srpm-macros                noarch  3.3.1-1.amzn2023                   copr_base     28 k
 jansson                       x86_64  2.14-0.amzn2023                    amazonlinux   46 k
 kernel-srpm-macros            noarch  1.0-14.amzn2023.0.2                amazonlinux   10 k
 keyutils-libs                 x86_64  1.6.3-1.amzn2023                   amazonlinux   33 k
 krb5-libs                     x86_64  1.21-3.amzn2023.0.3                amazonlinux  760 k
 libacl                        x86_64  2.3.1-2.amzn2023.0.2               amazonlinux   24 k
 libarchive                    x86_64  3.5.3-2.amzn2023.0.3               amazonlinux  398 k
 libattr                       x86_64  2.5.1-3.amzn2023.0.2               amazonlinux   19 k
 libblkid                      x86_64  2.37.4-1.amzn2023.0.3              amazonlinux  107 k
 libbrotli                     x86_64  1.0.9-4.amzn2023.0.2               amazonlinux  315 k
 libcap                        x86_64  2.48-2.amzn2023.0.3                amazonlinux   67 k
 libcap-ng                     x86_64  0.8.2-4.amzn2023.0.2               amazonlinux   33 k
 libcom_err                    x86_64  1.46.5-2.amzn2023.0.2              amazonlinux   27 k
 libcurl                       x86_64  8.3.0-1.amzn2023.0.2               amazonlinux  344 k
 libdb                         x86_64  5.3.28-49.amzn2023.0.2             amazonlinux  756 k
 libeconf                      x86_64  0.4.0-1.amzn2023.0.3               amazonlinux   28 k
 libfdisk                      x86_64  2.37.4-1.amzn2023.0.3              amazonlinux  154 k
 libffi                        x86_64  3.4.4-1.amzn2023.0.1               amazonlinux   39 k
 libgcc                        x86_64  11.4.1-2.amzn2023.0.2              amazonlinux   93 k
 libgomp                       x86_64  11.4.1-2.amzn2023.0.2              amazonlinux  268 k
 libidn2                       x86_64  2.3.2-1.amzn2023.0.5               amazonlinux  104 k
 libmount                      x86_64  2.37.4-1.amzn2023.0.3              amazonlinux  133 k
 libnghttp2                    x86_64  1.57.0-1.amzn2023.0.1              amazonlinux   78 k
 libpkgconf                    x86_64  1.8.0-4.amzn2023.0.2               amazonlinux   37 k
 libpsl                        x86_64  0.21.1-3.amzn2023.0.2              amazonlinux   61 k
 libpwquality                  x86_64  1.4.4-6.amzn2023.0.2               amazonlinux  106 k
 libselinux                    x86_64  3.4-5.amzn2023.0.2                 amazonlinux   87 k
 libsemanage                   x86_64  3.4-5.amzn2023.0.2                 amazonlinux  121 k
 libsepol                      x86_64  3.4-3.amzn2023.0.3                 amazonlinux  320 k
 libsigsegv                    x86_64  2.13-2.amzn2023.0.2                amazonlinux   27 k
 libsmartcols                  x86_64  2.37.4-1.amzn2023.0.3              amazonlinux   63 k
 libssh                        x86_64  0.10.5-1.amzn2023.0.2              amazonlinux  215 k
 libssh-config                 noarch  0.10.5-1.amzn2023.0.2              amazonlinux   11 k
 libstdc++                     x86_64  11.4.1-2.amzn2023.0.2              amazonlinux  731 k
 libtasn1                      x86_64  4.19.0-1.amzn2023.0.4              amazonlinux   75 k
 libunistring                  x86_64  0.9.10-10.amzn2023.0.2             amazonlinux  499 k
 libutempter                   x86_64  1.2.1-4.amzn2023.0.2               amazonlinux   26 k
 libuuid                       x86_64  2.37.4-1.amzn2023.0.3              amazonlinux   27 k
 libverto                      x86_64  0.3.2-1.amzn2023.0.2               amazonlinux   22 k
 libxcrypt                     x86_64  4.4.33-7.amzn2023                  amazonlinux  121 k
 libxml2                       x86_64  2.10.4-1.amzn2023.0.6              amazonlinux  706 k
 libzstd                       x86_64  1.5.5-1.amzn2023.0.1               amazonlinux  309 k
 lua-libs                      x86_64  5.4.4-3.amzn2023.0.2               amazonlinux  217 k
 lua-srpm-macros               noarch  1-4.amzn2023.0.2                   amazonlinux  9.2 k
 lz4-libs                      x86_64  1.9.4-1.amzn2023.0.2               amazonlinux   81 k
 mpfr                          x86_64  4.1.0-7.amzn2023.0.2               amazonlinux  330 k
 ncurses-base                  noarch  6.2-4.20200222.amzn2023.0.4        amazonlinux   60 k
 ncurses-libs                  x86_64  6.2-4.20200222.amzn2023.0.4        amazonlinux  328 k
 ocaml-srpm-macros             noarch  6-6.amzn2023.0.2                   amazonlinux  8.8 k
 openblas-srpm-macros          noarch  2-9.amzn2023.0.2                   amazonlinux  8.2 k
 openldap                      x86_64  2.4.57-6.amzn2023.0.6              amazonlinux  257 k
 openssl-libs                  x86_64  1:3.0.8-1.amzn2023.0.10            amazonlinux  2.2 M
 p11-kit                       x86_64  0.24.1-2.amzn2023.0.3              amazonlinux  357 k
 p11-kit-trust                 x86_64  0.24.1-2.amzn2023.0.3              amazonlinux  138 k
 package-notes-srpm-macros     noarch  0.4-18.amzn2023.0.5                amazonlinux   13 k
 pam                           x86_64  1.5.1-8.amzn2023.0.3               amazonlinux  543 k
 pcre2                         x86_64  10.40-1.amzn2023.0.3               amazonlinux  236 k
 pcre2-syntax                  noarch  10.40-1.amzn2023.0.3               amazonlinux  142 k
 perl-srpm-macros              noarch  1-39.amzn2023.0.2                  amazonlinux  8.7 k
 pkgconf                       x86_64  1.8.0-4.amzn2023.0.2               amazonlinux   43 k
 pkgconf-m4                    noarch  1.8.0-4.amzn2023.0.2               amazonlinux   15 k
 pkgconf-pkg-config            x86_64  1.8.0-4.amzn2023.0.2               amazonlinux   11 k
 popt                          x86_64  1.18-6.amzn2023.0.2                amazonlinux   60 k
 publicsuffix-list-dafsa       noarch  20221208-60.amzn2023               amazonlinux   61 k
 python-srpm-macros            noarch  3.9-41.amzn2023.0.5                amazonlinux   22 k
 readline                      x86_64  8.1-2.amzn2023.0.2                 amazonlinux  212 k
 rpm                           x86_64  4.16.1.3-12.amzn2023.0.6           amazonlinux  486 k
 rpm-build-libs                x86_64  4.16.1.3-12.amzn2023.0.6           amazonlinux   90 k
 rpm-libs                      x86_64  4.16.1.3-12.amzn2023.0.6           amazonlinux  309 k
 rust-srpm-macros              noarch  21-42.amzn2023.0.2                 amazonlinux   10 k
 setup                         noarch  2.13.7-3.amzn2023.0.2              amazonlinux  141 k
 shadow-utils                  x86_64  2:4.9-12.amzn2023.0.4              amazonlinux  1.1 M
 sqlite-libs                   x86_64  3.40.0-1.amzn2023.0.3              amazonlinux  663 k
 systemd-libs                  x86_64  252.16-1.amzn2023.0.1              amazonlinux  627 k
 util-linux-core               x86_64  2.37.4-1.amzn2023.0.3              amazonlinux  433 k
 xxhash-libs                   x86_64  0.8.0-3.amzn2023.0.2               amazonlinux   40 k
 xz-libs                       x86_64  5.2.5-9.amzn2023.0.2               amazonlinux   93 k
 zip                           x86_64  3.0-28.amzn2023.0.2                amazonlinux  257 k
 zlib                          x86_64  1.2.11-33.amzn2023.0.5             amazonlinux   93 k
 zstd                          x86_64  1.5.5-1.amzn2023.0.1               amazonlinux  478 k

Transaction Summary
============================================================================================
Install  132 Packages

Total size: 46 M
Installed size: 165 M
Downloading Packages:
[SKIPPED] go-srpm-macros-3.3.1-1.amzn2023.noarch.rpm: Already downloaded       
[SKIPPED] bash-5.2.15-1.amzn2023.0.2.x86_64.rpm: Already downloaded            
[SKIPPED] pam-1.5.1-8.amzn2023.0.3.x86_64.rpm: Already downloaded              
[SKIPPED] libselinux-3.4-5.amzn2023.0.2.x86_64.rpm: Already downloaded         
[SKIPPED] diffutils-3.8-1.amzn2023.0.2.x86_64.rpm: Already downloaded          
[SKIPPED] libcurl-8.3.0-1.amzn2023.0.2.x86_64.rpm: Already downloaded          
[SKIPPED] libgomp-11.4.1-2.amzn2023.0.2.x86_64.rpm: Already downloaded         
[SKIPPED] bzip2-1.0.8-6.amzn2023.0.2.x86_64.rpm: Already downloaded            
[SKIPPED] elfutils-0.188-3.amzn2023.0.2.x86_64.rpm: Already downloaded         
[SKIPPED] libcap-2.48-2.amzn2023.0.3.x86_64.rpm: Already downloaded            
[SKIPPED] libtasn1-4.19.0-1.amzn2023.0.4.x86_64.rpm: Already downloaded        
[SKIPPED] sed-4.8-7.amzn2023.0.2.x86_64.rpm: Already downloaded                
[SKIPPED] binutils-2.39-6.amzn2023.0.10.x86_64.rpm: Already downloaded         
[SKIPPED] p11-kit-0.24.1-2.amzn2023.0.3.x86_64.rpm: Already downloaded         
[SKIPPED] findutils-4.8.0-2.amzn2023.0.2.x86_64.rpm: Already downloaded        
[SKIPPED] pkgconf-pkg-config-1.8.0-4.amzn2023.0.2.x86_64.rpm: Already downloaded
[SKIPPED] mpfr-4.1.0-7.amzn2023.0.2.x86_64.rpm: Already downloaded             
[SKIPPED] lz4-libs-1.9.4-1.amzn2023.0.2.x86_64.rpm: Already downloaded         
[SKIPPED] dwz-0.14-6.amzn2023.0.2.x86_64.rpm: Already downloaded               
[SKIPPED] zlib-1.2.11-33.amzn2023.0.5.x86_64.rpm: Already downloaded           
[SKIPPED] jansson-2.14-0.amzn2023.x86_64.rpm: Already downloaded               
[SKIPPED] patch-2.7.6-14.amzn2023.0.2.x86_64.rpm: Already downloaded           
[SKIPPED] xz-libs-5.2.5-9.amzn2023.0.2.x86_64.rpm: Already downloaded          
[SKIPPED] xz-5.2.5-9.amzn2023.0.2.x86_64.rpm: Already downloaded               
[SKIPPED] libxml2-2.10.4-1.amzn2023.0.6.x86_64.rpm: Already downloaded         
[SKIPPED] glibc-minimal-langpack-2.34-52.amzn2023.0.7.x86_64.rpm: Already downloaded
[SKIPPED] util-linux-2.37.4-1.amzn2023.0.3.x86_64.rpm: Already downloaded      
[SKIPPED] curl-8.3.0-1.amzn2023.0.2.x86_64.rpm: Already downloaded             
[SKIPPED] libdb-5.3.28-49.amzn2023.0.2.x86_64.rpm: Already downloaded          
[SKIPPED] lua-libs-5.4.4-3.amzn2023.0.2.x86_64.rpm: Already downloaded         
[SKIPPED] gdbm-libs-1.19-2.amzn2023.0.2.x86_64.rpm: Already downloaded         
[SKIPPED] libstdc++-11.4.1-2.amzn2023.0.2.x86_64.rpm: Already downloaded       
[SKIPPED] libxcrypt-4.4.33-7.amzn2023.x86_64.rpm: Already downloaded           
[SKIPPED] libacl-2.3.1-2.amzn2023.0.2.x86_64.rpm: Already downloaded           
[SKIPPED] glibc-common-2.34-52.amzn2023.0.7.x86_64.rpm: Already downloaded     
[SKIPPED] keyutils-libs-1.6.3-1.amzn2023.x86_64.rpm: Already downloaded        
[SKIPPED] libmount-2.37.4-1.amzn2023.0.3.x86_64.rpm: Already downloaded        
[SKIPPED] audit-libs-3.0.6-1.amzn2023.0.2.x86_64.rpm: Already downloaded       
[SKIPPED] rpm-build-libs-4.16.1.3-12.amzn2023.0.6.x86_64.rpm: Already downloaded
[SKIPPED] zstd-1.5.5-1.amzn2023.0.1.x86_64.rpm: Already downloaded             
[SKIPPED] alternatives-1.15-2.amzn2023.0.2.x86_64.rpm: Already downloaded      
[SKIPPED] sqlite-libs-3.40.0-1.amzn2023.0.3.x86_64.rpm: Already downloaded     
[SKIPPED] bzip2-libs-1.0.8-6.amzn2023.0.2.x86_64.rpm: Already downloaded       
[SKIPPED] rpm-build-4.16.1.3-12.amzn2023.0.6.x86_64.rpm: Already downloaded    
[SKIPPED] libffi-3.4.4-1.amzn2023.0.1.x86_64.rpm: Already downloaded           
[SKIPPED] krb5-libs-1.21-3.amzn2023.0.3.x86_64.rpm: Already downloaded         
[SKIPPED] libsepol-3.4-3.amzn2023.0.3.x86_64.rpm: Already downloaded           
[SKIPPED] glibc-2.34-52.amzn2023.0.7.x86_64.rpm: Already downloaded            
[SKIPPED] libidn2-2.3.2-1.amzn2023.0.5.x86_64.rpm: Already downloaded          
[SKIPPED] elfutils-libelf-0.188-3.amzn2023.0.2.x86_64.rpm: Already downloaded  
[SKIPPED] libcom_err-1.46.5-2.amzn2023.0.2.x86_64.rpm: Already downloaded      
[SKIPPED] cyrus-sasl-lib-2.1.27-18.amzn2023.0.3.x86_64.rpm: Already downloaded 
[SKIPPED] openssl-libs-3.0.8-1.amzn2023.0.10.x86_64.rpm: Already downloaded    
[SKIPPED] rpm-libs-4.16.1.3-12.amzn2023.0.6.x86_64.rpm: Already downloaded     
[SKIPPED] libattr-2.5.1-3.amzn2023.0.2.x86_64.rpm: Already downloaded          
[SKIPPED] shadow-utils-4.9-12.amzn2023.0.4.x86_64.rpm: Already downloaded      
[SKIPPED] grep-3.8-1.amzn2023.0.4.x86_64.rpm: Already downloaded               
[SKIPPED] libfdisk-2.37.4-1.amzn2023.0.3.x86_64.rpm: Already downloaded        
[SKIPPED] rpm-4.16.1.3-12.amzn2023.0.6.x86_64.rpm: Already downloaded          
[SKIPPED] filesystem-3.14-5.amzn2023.0.3.x86_64.rpm: Already downloaded        
[SKIPPED] libpwquality-1.4.4-6.amzn2023.0.2.x86_64.rpm: Already downloaded     
[SKIPPED] libuuid-2.37.4-1.amzn2023.0.3.x86_64.rpm: Already downloaded         
[SKIPPED] libpkgconf-1.8.0-4.amzn2023.0.2.x86_64.rpm: Already downloaded       
[SKIPPED] ed-1.14.2-10.amzn2023.0.2.x86_64.rpm: Already downloaded             
[SKIPPED] libgcc-11.4.1-2.amzn2023.0.2.x86_64.rpm: Already downloaded          
[SKIPPED] info-6.7-10.amzn2023.0.2.x86_64.rpm: Already downloaded              
[SKIPPED] libsemanage-3.4-5.amzn2023.0.2.x86_64.rpm: Already downloaded        
[SKIPPED] libblkid-2.37.4-1.amzn2023.0.3.x86_64.rpm: Already downloaded        
[SKIPPED] xxhash-libs-0.8.0-3.amzn2023.0.2.x86_64.rpm: Already downloaded      
[SKIPPED] gawk-5.1.0-3.amzn2023.0.3.x86_64.rpm: Already downloaded             
[SKIPPED] coreutils-8.32-30.amzn2023.0.3.x86_64.rpm: Already downloaded        
[SKIPPED] coreutils-common-8.32-30.amzn2023.0.3.x86_64.rpm: Already downloaded 
[SKIPPED] gzip-1.12-1.amzn2023.0.1.x86_64.rpm: Already downloaded              
[SKIPPED] libcap-ng-0.8.2-4.amzn2023.0.2.x86_64.rpm: Already downloaded        
[SKIPPED] libunistring-0.9.10-10.amzn2023.0.2.x86_64.rpm: Already downloaded   
[SKIPPED] tar-1.34-1.amzn2023.0.3.x86_64.rpm: Already downloaded               
[SKIPPED] gdb-minimal-12.1-5.amzn2023.0.3.x86_64.rpm: Already downloaded       
[SKIPPED] unzip-6.0-57.amzn2023.0.2.x86_64.rpm: Already downloaded             
[SKIPPED] libsigsegv-2.13-2.amzn2023.0.2.x86_64.rpm: Already downloaded        
[SKIPPED] libarchive-3.5.3-2.amzn2023.0.3.x86_64.rpm: Already downloaded       
[SKIPPED] which-2.21-26.amzn2023.0.2.x86_64.rpm: Already downloaded            
[SKIPPED] elfutils-debuginfod-client-0.188-3.amzn2023.0.2.x86_64.rpm: Already downloaded
[SKIPPED] cpio-2.13-13.amzn2023.0.2.x86_64.rpm: Already downloaded             
[SKIPPED] ncurses-libs-6.2-4.20200222.amzn2023.0.4.x86_64.rpm: Already downloaded
[SKIPPED] glibc-gconv-extra-2.34-52.amzn2023.0.7.x86_64.rpm: Already downloaded
[SKIPPED] libssh-0.10.5-1.amzn2023.0.2.x86_64.rpm: Already downloaded          
[SKIPPED] elfutils-libs-0.188-3.amzn2023.0.2.x86_64.rpm: Already downloaded    
[SKIPPED] readline-8.1-2.amzn2023.0.2.x86_64.rpm: Already downloaded           
[SKIPPED] libutempter-1.2.1-4.amzn2023.0.2.x86_64.rpm: Already downloaded      
[SKIPPED] util-linux-core-2.37.4-1.amzn2023.0.3.x86_64.rpm: Already downloaded 
[SKIPPED] cracklib-2.9.6-27.amzn2023.0.2.x86_64.rpm: Already downloaded        
[SKIPPED] libzstd-1.5.5-1.amzn2023.0.1.x86_64.rpm: Already downloaded          
[SKIPPED] zip-3.0-28.amzn2023.0.2.x86_64.rpm: Already downloaded               
[SKIPPED] p11-kit-trust-0.24.1-2.amzn2023.0.3.x86_64.rpm: Already downloaded   
[SKIPPED] libnghttp2-1.57.0-1.amzn2023.0.1.x86_64.rpm: Already downloaded      
[SKIPPED] libsmartcols-2.37.4-1.amzn2023.0.3.x86_64.rpm: Already downloaded    
[SKIPPED] gmp-6.2.1-2.amzn2023.0.2.x86_64.rpm: Already downloaded              
[SKIPPED] file-libs-5.39-7.amzn2023.0.4.x86_64.rpm: Already downloaded         
[SKIPPED] popt-1.18-6.amzn2023.0.2.x86_64.rpm: Already downloaded              
[SKIPPED] pcre2-10.40-1.amzn2023.0.3.x86_64.rpm: Already downloaded            
[SKIPPED] openldap-2.4.57-6.amzn2023.0.6.x86_64.rpm: Already downloaded        
[SKIPPED] file-5.39-7.amzn2023.0.4.x86_64.rpm: Already downloaded              
[SKIPPED] systemd-libs-252.16-1.amzn2023.0.1.x86_64.rpm: Already downloaded    
[SKIPPED] libpsl-0.21.1-3.amzn2023.0.2.x86_64.rpm: Already downloaded          
[SKIPPED] pkgconf-1.8.0-4.amzn2023.0.2.x86_64.rpm: Already downloaded          
[SKIPPED] libverto-0.3.2-1.amzn2023.0.2.x86_64.rpm: Already downloaded         
[SKIPPED] libeconf-0.4.0-1.amzn2023.0.3.x86_64.rpm: Already downloaded         
[SKIPPED] libbrotli-1.0.9-4.amzn2023.0.2.x86_64.rpm: Already downloaded        
[SKIPPED] efi-srpm-macros-5-4.amzn2023.0.5.noarch.rpm: Already downloaded      
[SKIPPED] ghc-srpm-macros-1.5.0-4.amzn2023.0.2.noarch.rpm: Already downloaded  
[SKIPPED] elfutils-default-yama-scope-0.188-3.amzn2023.0.2.noarch.rpm: Already downloaded
[SKIPPED] ncurses-base-6.2-4.20200222.amzn2023.0.4.noarch.rpm: Already downloaded
[SKIPPED] openblas-srpm-macros-2-9.amzn2023.0.2.noarch.rpm: Already downloaded 
[SKIPPED] publicsuffix-list-dafsa-20221208-60.amzn2023.noarch.rpm: Already downloaded
[SKIPPED] kernel-srpm-macros-1.0-14.amzn2023.0.2.noarch.rpm: Already downloaded
[SKIPPED] pcre2-syntax-10.40-1.amzn2023.0.3.noarch.rpm: Already downloaded     
[SKIPPED] ocaml-srpm-macros-6-6.amzn2023.0.2.noarch.rpm: Already downloaded    
[SKIPPED] basesystem-11-11.amzn2023.0.2.noarch.rpm: Already downloaded         
[SKIPPED] setup-2.13.7-3.amzn2023.0.2.noarch.rpm: Already downloaded           
[SKIPPED] libssh-config-0.10.5-1.amzn2023.0.2.noarch.rpm: Already downloaded   
[SKIPPED] amazon-rpm-config-228-3.amzn2023.0.2.noarch.rpm: Already downloaded  
[SKIPPED] ca-certificates-2023.2.62-1.0.amzn2023.0.1.noarch.rpm: Already downloaded
[SKIPPED] python-srpm-macros-3.9-41.amzn2023.0.5.noarch.rpm: Already downloaded
[SKIPPED] crypto-policies-20220428-1.gitdfb10ea.amzn2023.0.2.noarch.rpm: Already downloaded
[SKIPPED] fonts-srpm-macros-2.0.5-12.amzn2023.0.2.noarch.rpm: Already downloaded
[SKIPPED] package-notes-srpm-macros-0.4-18.amzn2023.0.5.noarch.rpm: Already downloaded
[SKIPPED] perl-srpm-macros-1-39.amzn2023.0.2.noarch.rpm: Already downloaded    
[SKIPPED] lua-srpm-macros-1-4.amzn2023.0.2.noarch.rpm: Already downloaded      
[SKIPPED] system-release-2023.3.20231218-0.amzn2023.noarch.rpm: Already downloaded
[SKIPPED] amazon-linux-repo-cdn-2023.3.20231218-0.amzn2023.noarch.rpm: Already downloaded
[SKIPPED] rust-srpm-macros-21-42.amzn2023.0.2.noarch.rpm: Already downloaded   
[SKIPPED] pkgconf-m4-1.8.0-4.amzn2023.0.2.noarch.rpm: Already downloaded       
Amazon Linux 2023 repository - x86_64           1.7 MB/s | 1.8 kB     00:00    
Importing GPG key 0xD832C631:
 Userid     : "Amazon Linux <amazon-linux@amazon.com>"
 Fingerprint: B21C 50FA 44A9 9720 EAA7 2F7F E951 904A D832 C631
 From       : /usr/share/distribution-gpg-keys/amazon-linux/RPM-GPG-KEY-amazon-linux-2023
Key imported successfully
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
  Running scriptlet: filesystem-3.14-5.amzn2023.0.3.x86_64                  1/1 
  Preparing        :                                                        1/1 
  Installing       : libgcc-11.4.1-2.amzn2023.0.2.x86_64                  1/132 
  Running scriptlet: libgcc-11.4.1-2.amzn2023.0.2.x86_64                  1/132 
  Installing       : crypto-policies-20220428-1.gitdfb10ea.amzn2023.0     2/132 
  Running scriptlet: crypto-policies-20220428-1.gitdfb10ea.amzn2023.0     2/132 
  Installing       : pkgconf-m4-1.8.0-4.amzn2023.0.2.noarch               3/132 
  Installing       : rust-srpm-macros-21-42.amzn2023.0.2.noarch           4/132 
  Installing       : perl-srpm-macros-1-39.amzn2023.0.2.noarch            5/132 
  Installing       : libssh-config-0.10.5-1.amzn2023.0.2.noarch           6/132 
  Installing       : ocaml-srpm-macros-6-6.amzn2023.0.2.noarch            7/132 
  Installing       : pcre2-syntax-10.40-1.amzn2023.0.3.noarch             8/132 
  Installing       : kernel-srpm-macros-1.0-14.amzn2023.0.2.noarch        9/132 
  Installing       : publicsuffix-list-dafsa-20221208-60.amzn2023.noa    10/132 
  Installing       : openblas-srpm-macros-2-9.amzn2023.0.2.noarch        11/132 
  Installing       : ncurses-base-6.2-4.20200222.amzn2023.0.4.noarch     12/132 
  Installing       : ncurses-libs-6.2-4.20200222.amzn2023.0.4.x86_64     13/132 
  Installing       : amazon-linux-repo-cdn-2023.3.20231218-0.amzn2023    14/132 
  Installing       : system-release-2023.3.20231218-0.amzn2023.noarch    15/132 
  Installing       : setup-2.13.7-3.amzn2023.0.2.noarch                  16/132 
warning: /etc/hosts created as /etc/hosts.rpmnew

  Running scriptlet: setup-2.13.7-3.amzn2023.0.2.noarch                  16/132 
  Installing       : filesystem-3.14-5.amzn2023.0.3.x86_64               17/132 
  Installing       : basesystem-11-11.amzn2023.0.2.noarch                18/132 
  Installing       : bash-5.2.15-1.amzn2023.0.2.x86_64                   19/132 
  Running scriptlet: bash-5.2.15-1.amzn2023.0.2.x86_64                   19/132 
  Installing       : glibc-minimal-langpack-2.34-52.amzn2023.0.7.x86_    20/132 
  Installing       : glibc-common-2.34-52.amzn2023.0.7.x86_64            21/132 
  Installing       : glibc-gconv-extra-2.34-52.amzn2023.0.7.x86_64       22/132 
  Running scriptlet: glibc-gconv-extra-2.34-52.amzn2023.0.7.x86_64       22/132 
  Running scriptlet: glibc-2.34-52.amzn2023.0.7.x86_64                   23/132 
  Installing       : glibc-2.34-52.amzn2023.0.7.x86_64                   23/132 
  Running scriptlet: glibc-2.34-52.amzn2023.0.7.x86_64                   23/132 
  Installing       : zlib-1.2.11-33.amzn2023.0.5.x86_64                  24/132 
  Installing       : xz-libs-5.2.5-9.amzn2023.0.2.x86_64                 25/132 
  Installing       : bzip2-libs-1.0.8-6.amzn2023.0.2.x86_64              26/132 
  Installing       : elfutils-libelf-0.188-3.amzn2023.0.2.x86_64         27/132 
  Installing       : libuuid-2.37.4-1.amzn2023.0.3.x86_64                28/132 
  Installing       : libcap-2.48-2.amzn2023.0.3.x86_64                   29/132 
  Installing       : libxcrypt-4.4.33-7.amzn2023.x86_64                  30/132 
  Installing       : libattr-2.5.1-3.amzn2023.0.2.x86_64                 31/132 
  Installing       : libacl-2.3.1-2.amzn2023.0.2.x86_64                  32/132 
  Installing       : libzstd-1.5.5-1.amzn2023.0.1.x86_64                 33/132 
  Installing       : gmp-1:6.2.1-2.amzn2023.0.2.x86_64                   34/132 
  Installing       : popt-1.18-6.amzn2023.0.2.x86_64                     35/132 
  Installing       : libstdc++-11.4.1-2.amzn2023.0.2.x86_64              36/132 
  Installing       : readline-8.1-2.amzn2023.0.2.x86_64                  37/132 
  Installing       : mpfr-4.1.0-7.amzn2023.0.2.x86_64                    38/132 
  Installing       : systemd-libs-252.16-1.amzn2023.0.1.x86_64           39/132 
  Installing       : unzip-6.0-57.amzn2023.0.2.x86_64                    40/132 
  Installing       : sqlite-libs-3.40.0-1.amzn2023.0.3.x86_64            41/132 
  Installing       : file-libs-5.39-7.amzn2023.0.4.x86_64                42/132 
  Installing       : file-5.39-7.amzn2023.0.4.x86_64                     43/132 
  Installing       : lz4-libs-1.9.4-1.amzn2023.0.2.x86_64                44/132 
  Installing       : lua-libs-5.4.4-3.amzn2023.0.2.x86_64                45/132 
  Installing       : alternatives-1.15-2.amzn2023.0.2.x86_64             46/132 
  Installing       : libsepol-3.4-3.amzn2023.0.3.x86_64                  47/132 
  Installing       : libcom_err-1.46.5-2.amzn2023.0.2.x86_64             48/132 
  Installing       : libcap-ng-0.8.2-4.amzn2023.0.2.x86_64               49/132 
  Installing       : audit-libs-3.0.6-1.amzn2023.0.2.x86_64              50/132 
  Installing       : libunistring-0.9.10-10.amzn2023.0.2.x86_64          51/132 
  Installing       : libidn2-2.3.2-1.amzn2023.0.5.x86_64                 52/132 
  Installing       : libsmartcols-2.37.4-1.amzn2023.0.3.x86_64           53/132 
  Installing       : pcre2-10.40-1.amzn2023.0.3.x86_64                   54/132 
  Installing       : libselinux-3.4-5.amzn2023.0.2.x86_64                55/132 
  Installing       : sed-4.8-7.amzn2023.0.2.x86_64                       56/132 
  Installing       : grep-3.8-1.amzn2023.0.4.x86_64                      57/132 
  Installing       : findutils-1:4.8.0-2.amzn2023.0.2.x86_64             58/132 
  Installing       : xz-5.2.5-9.amzn2023.0.2.x86_64                      59/132 
  Installing       : libsemanage-3.4-5.amzn2023.0.2.x86_64               60/132 
  Installing       : shadow-utils-2:4.9-12.amzn2023.0.4.x86_64           61/132 
  Running scriptlet: libutempter-1.2.1-4.amzn2023.0.2.x86_64             62/132 
  Installing       : libutempter-1.2.1-4.amzn2023.0.2.x86_64             62/132 
  Installing       : tar-2:1.34-1.amzn2023.0.3.x86_64                    63/132 
  Installing       : libpsl-0.21.1-3.amzn2023.0.2.x86_64                 64/132 
  Installing       : zstd-1.5.5-1.amzn2023.0.1.x86_64                    65/132 
  Installing       : zip-3.0-28.amzn2023.0.2.x86_64                      66/132 
  Installing       : dwz-0.14-6.amzn2023.0.2.x86_64                      67/132 
  Installing       : bzip2-1.0.8-6.amzn2023.0.2.x86_64                   68/132 
  Installing       : libxml2-2.10.4-1.amzn2023.0.6.x86_64                69/132 
  Installing       : info-6.7-10.amzn2023.0.2.x86_64                     70/132 
  Installing       : ed-1.14.2-10.amzn2023.0.2.x86_64                    71/132 
  Installing       : patch-2.7.6-14.amzn2023.0.2.x86_64                  72/132 
  Installing       : diffutils-3.8-1.amzn2023.0.2.x86_64                 73/132 
  Installing       : libgomp-11.4.1-2.amzn2023.0.2.x86_64                74/132 
  Installing       : libtasn1-4.19.0-1.amzn2023.0.4.x86_64               75/132 
  Installing       : jansson-2.14-0.amzn2023.x86_64                      76/132 
  Installing       : libdb-5.3.28-49.amzn2023.0.2.x86_64                 77/132 
  Installing       : gdbm-libs-1:1.19-2.amzn2023.0.2.x86_64              78/132 
  Installing       : keyutils-libs-1.6.3-1.amzn2023.x86_64               79/132 
  Installing       : libffi-3.4.4-1.amzn2023.0.1.x86_64                  80/132 
  Installing       : p11-kit-0.24.1-2.amzn2023.0.3.x86_64                81/132 
  Installing       : p11-kit-trust-0.24.1-2.amzn2023.0.3.x86_64          82/132 
  Running scriptlet: p11-kit-trust-0.24.1-2.amzn2023.0.3.x86_64          82/132 
  Installing       : libpkgconf-1.8.0-4.amzn2023.0.2.x86_64              83/132 
  Installing       : xxhash-libs-0.8.0-3.amzn2023.0.2.x86_64             84/132 
  Installing       : libsigsegv-2.13-2.amzn2023.0.2.x86_64               85/132 
  Installing       : gawk-5.1.0-3.amzn2023.0.3.x86_64                    86/132 
  Installing       : cpio-2.13-13.amzn2023.0.2.x86_64                    87/132 
  Installing       : libnghttp2-1.57.0-1.amzn2023.0.1.x86_64             88/132 
  Installing       : libverto-0.3.2-1.amzn2023.0.2.x86_64                89/132 
  Installing       : libeconf-0.4.0-1.amzn2023.0.3.x86_64                90/132 
  Installing       : libbrotli-1.0.9-4.amzn2023.0.2.x86_64               91/132 
  Installing       : elfutils-default-yama-scope-0.188-3.amzn2023.0.2    92/132 
  Running scriptlet: elfutils-default-yama-scope-0.188-3.amzn2023.0.2    92/132 
  Installing       : package-notes-srpm-macros-0.4-18.amzn2023.0.5.no    93/132 
  Installing       : ghc-srpm-macros-1.5.0-4.amzn2023.0.2.noarch         94/132 
  Installing       : coreutils-common-8.32-30.amzn2023.0.3.x86_64        95/132 
  Installing       : openssl-libs-1:3.0.8-1.amzn2023.0.10.x86_64         96/132 
  Installing       : coreutils-8.32-30.amzn2023.0.3.x86_64               97/132 
  Running scriptlet: ca-certificates-2023.2.62-1.0.amzn2023.0.1.noarc    98/132 
  Installing       : ca-certificates-2023.2.62-1.0.amzn2023.0.1.noarc    98/132 
  Running scriptlet: ca-certificates-2023.2.62-1.0.amzn2023.0.1.noarc    98/132 
  Installing       : libblkid-2.37.4-1.amzn2023.0.3.x86_64               99/132 
  Running scriptlet: libblkid-2.37.4-1.amzn2023.0.3.x86_64               99/132 
  Installing       : krb5-libs-1.21-3.amzn2023.0.3.x86_64               100/132 
  Installing       : libmount-2.37.4-1.amzn2023.0.3.x86_64              101/132 
  Installing       : gzip-1.12-1.amzn2023.0.1.x86_64                    102/132 
  Installing       : cracklib-2.9.6-27.amzn2023.0.2.x86_64              103/132 
  Installing       : libpwquality-1.4.4-6.amzn2023.0.2.x86_64           104/132 
  Installing       : pam-1.5.1-8.amzn2023.0.3.x86_64                    105/132 
  Installing       : util-linux-core-2.37.4-1.amzn2023.0.3.x86_64       106/132 
  Running scriptlet: util-linux-core-2.37.4-1.amzn2023.0.3.x86_64       106/132 
  Installing       : cyrus-sasl-lib-2.1.27-18.amzn2023.0.3.x86_64       107/132 
  Installing       : openldap-2.4.57-6.amzn2023.0.6.x86_64              108/132 
  Installing       : libssh-0.10.5-1.amzn2023.0.2.x86_64                109/132 
  Installing       : libcurl-8.3.0-1.amzn2023.0.2.x86_64                110/132 
  Installing       : elfutils-libs-0.188-3.amzn2023.0.2.x86_64          111/132 
  Installing       : elfutils-debuginfod-client-0.188-3.amzn2023.0.2.   112/132 
  Installing       : elfutils-0.188-3.amzn2023.0.2.x86_64               113/132 
  Installing       : binutils-2.39-6.amzn2023.0.10.x86_64               114/132 
  Running scriptlet: binutils-2.39-6.amzn2023.0.10.x86_64               114/132 
  Installing       : gdb-minimal-12.1-5.amzn2023.0.3.x86_64             115/132 
  Installing       : curl-8.3.0-1.amzn2023.0.2.x86_64                   116/132 
  Installing       : libfdisk-2.37.4-1.amzn2023.0.3.x86_64              117/132 
  Installing       : libarchive-3.5.3-2.amzn2023.0.3.x86_64             118/132 
  Installing       : rpm-libs-4.16.1.3-12.amzn2023.0.6.x86_64           119/132 
  Installing       : rpm-4.16.1.3-12.amzn2023.0.6.x86_64                120/132 
  Installing       : efi-srpm-macros-5-4.amzn2023.0.5.noarch            121/132 
  Installing       : lua-srpm-macros-1-4.amzn2023.0.2.noarch            122/132 
  Installing       : python-srpm-macros-3.9-41.amzn2023.0.5.noarch      123/132 
  Installing       : fonts-srpm-macros-1:2.0.5-12.amzn2023.0.2.noarch   124/132 
  Installing       : amazon-rpm-config-228-3.amzn2023.0.2.noarch        125/132 
  Running scriptlet: amazon-rpm-config-228-3.amzn2023.0.2.noarch        125/132 
  Installing       : go-srpm-macros-3.3.1-1.amzn2023.noarch             126/132 
  Installing       : pkgconf-1.8.0-4.amzn2023.0.2.x86_64                127/132 
  Installing       : pkgconf-pkg-config-1.8.0-4.amzn2023.0.2.x86_64     128/132 
  Installing       : rpm-build-libs-4.16.1.3-12.amzn2023.0.6.x86_64     129/132 
  Installing       : rpm-build-4.16.1.3-12.amzn2023.0.6.x86_64          130/132 
  Installing       : util-linux-2.37.4-1.amzn2023.0.3.x86_64            131/132 
  Running scriptlet: util-linux-2.37.4-1.amzn2023.0.3.x86_64            131/132 
  Installing       : which-2.21-26.amzn2023.0.2.x86_64                  132/132 
  Running scriptlet: filesystem-3.14-5.amzn2023.0.3.x86_64              132/132 
  Running scriptlet: ca-certificates-2023.2.62-1.0.amzn2023.0.1.noarc   132/132 
  Running scriptlet: pam-1.5.1-8.amzn2023.0.3.x86_64                    132/132 
  Running scriptlet: rpm-4.16.1.3-12.amzn2023.0.6.x86_64                132/132 
  Running scriptlet: which-2.21-26.amzn2023.0.2.x86_64                  132/132 
  Verifying        : go-srpm-macros-3.3.1-1.amzn2023.noarch               1/132 
  Verifying        : bash-5.2.15-1.amzn2023.0.2.x86_64                    2/132 
  Verifying        : pam-1.5.1-8.amzn2023.0.3.x86_64                      3/132 
  Verifying        : libselinux-3.4-5.amzn2023.0.2.x86_64                 4/132 
  Verifying        : diffutils-3.8-1.amzn2023.0.2.x86_64                  5/132 
  Verifying        : libcurl-8.3.0-1.amzn2023.0.2.x86_64                  6/132 
  Verifying        : libgomp-11.4.1-2.amzn2023.0.2.x86_64                 7/132 
  Verifying        : bzip2-1.0.8-6.amzn2023.0.2.x86_64                    8/132 
  Verifying        : elfutils-0.188-3.amzn2023.0.2.x86_64                 9/132 
  Verifying        : libcap-2.48-2.amzn2023.0.3.x86_64                   10/132 
  Verifying        : libtasn1-4.19.0-1.amzn2023.0.4.x86_64               11/132 
  Verifying        : sed-4.8-7.amzn2023.0.2.x86_64                       12/132 
  Verifying        : binutils-2.39-6.amzn2023.0.10.x86_64                13/132 
  Verifying        : p11-kit-0.24.1-2.amzn2023.0.3.x86_64                14/132 
  Verifying        : findutils-1:4.8.0-2.amzn2023.0.2.x86_64             15/132 
  Verifying        : pkgconf-pkg-config-1.8.0-4.amzn2023.0.2.x86_64      16/132 
  Verifying        : mpfr-4.1.0-7.amzn2023.0.2.x86_64                    17/132 
  Verifying        : lz4-libs-1.9.4-1.amzn2023.0.2.x86_64                18/132 
  Verifying        : dwz-0.14-6.amzn2023.0.2.x86_64                      19/132 
  Verifying        : zlib-1.2.11-33.amzn2023.0.5.x86_64                  20/132 
  Verifying        : jansson-2.14-0.amzn2023.x86_64                      21/132 
  Verifying        : patch-2.7.6-14.amzn2023.0.2.x86_64                  22/132 
  Verifying        : xz-libs-5.2.5-9.amzn2023.0.2.x86_64                 23/132 
  Verifying        : xz-5.2.5-9.amzn2023.0.2.x86_64                      24/132 
  Verifying        : libxml2-2.10.4-1.amzn2023.0.6.x86_64                25/132 
  Verifying        : glibc-minimal-langpack-2.34-52.amzn2023.0.7.x86_    26/132 
  Verifying        : util-linux-2.37.4-1.amzn2023.0.3.x86_64             27/132 
  Verifying        : curl-8.3.0-1.amzn2023.0.2.x86_64                    28/132 
  Verifying        : libdb-5.3.28-49.amzn2023.0.2.x86_64                 29/132 
  Verifying        : lua-libs-5.4.4-3.amzn2023.0.2.x86_64                30/132 
  Verifying        : gdbm-libs-1:1.19-2.amzn2023.0.2.x86_64              31/132 
  Verifying        : libstdc++-11.4.1-2.amzn2023.0.2.x86_64              32/132 
  Verifying        : libxcrypt-4.4.33-7.amzn2023.x86_64                  33/132 
  Verifying        : libacl-2.3.1-2.amzn2023.0.2.x86_64                  34/132 
  Verifying        : glibc-common-2.34-52.amzn2023.0.7.x86_64            35/132 
  Verifying        : keyutils-libs-1.6.3-1.amzn2023.x86_64               36/132 
  Verifying        : libmount-2.37.4-1.amzn2023.0.3.x86_64               37/132 
  Verifying        : audit-libs-3.0.6-1.amzn2023.0.2.x86_64              38/132 
  Verifying        : rpm-build-libs-4.16.1.3-12.amzn2023.0.6.x86_64      39/132 
  Verifying        : zstd-1.5.5-1.amzn2023.0.1.x86_64                    40/132 
  Verifying        : alternatives-1.15-2.amzn2023.0.2.x86_64             41/132 
  Verifying        : sqlite-libs-3.40.0-1.amzn2023.0.3.x86_64            42/132 
  Verifying        : bzip2-libs-1.0.8-6.amzn2023.0.2.x86_64              43/132 
  Verifying        : rpm-build-4.16.1.3-12.amzn2023.0.6.x86_64           44/132 
  Verifying        : libffi-3.4.4-1.amzn2023.0.1.x86_64                  45/132 
  Verifying        : krb5-libs-1.21-3.amzn2023.0.3.x86_64                46/132 
  Verifying        : libsepol-3.4-3.amzn2023.0.3.x86_64                  47/132 
  Verifying        : glibc-2.34-52.amzn2023.0.7.x86_64                   48/132 
  Verifying        : libidn2-2.3.2-1.amzn2023.0.5.x86_64                 49/132 
  Verifying        : elfutils-libelf-0.188-3.amzn2023.0.2.x86_64         50/132 
  Verifying        : libcom_err-1.46.5-2.amzn2023.0.2.x86_64             51/132 
  Verifying        : cyrus-sasl-lib-2.1.27-18.amzn2023.0.3.x86_64        52/132 
  Verifying        : openssl-libs-1:3.0.8-1.amzn2023.0.10.x86_64         53/132 
  Verifying        : rpm-libs-4.16.1.3-12.amzn2023.0.6.x86_64            54/132 
  Verifying        : libattr-2.5.1-3.amzn2023.0.2.x86_64                 55/132 
  Verifying        : shadow-utils-2:4.9-12.amzn2023.0.4.x86_64           56/132 
  Verifying        : grep-3.8-1.amzn2023.0.4.x86_64                      57/132 
  Verifying        : libfdisk-2.37.4-1.amzn2023.0.3.x86_64               58/132 
  Verifying        : rpm-4.16.1.3-12.amzn2023.0.6.x86_64                 59/132 
  Verifying        : filesystem-3.14-5.amzn2023.0.3.x86_64               60/132 
  Verifying        : libpwquality-1.4.4-6.amzn2023.0.2.x86_64            61/132 
  Verifying        : libuuid-2.37.4-1.amzn2023.0.3.x86_64                62/132 
  Verifying        : libpkgconf-1.8.0-4.amzn2023.0.2.x86_64              63/132 
  Verifying        : ed-1.14.2-10.amzn2023.0.2.x86_64                    64/132 
  Verifying        : libgcc-11.4.1-2.amzn2023.0.2.x86_64                 65/132 
  Verifying        : info-6.7-10.amzn2023.0.2.x86_64                     66/132 
  Verifying        : libsemanage-3.4-5.amzn2023.0.2.x86_64               67/132 
  Verifying        : libblkid-2.37.4-1.amzn2023.0.3.x86_64               68/132 
  Verifying        : xxhash-libs-0.8.0-3.amzn2023.0.2.x86_64             69/132 
  Verifying        : gawk-5.1.0-3.amzn2023.0.3.x86_64                    70/132 
  Verifying        : coreutils-8.32-30.amzn2023.0.3.x86_64               71/132 
  Verifying        : coreutils-common-8.32-30.amzn2023.0.3.x86_64        72/132 
  Verifying        : gzip-1.12-1.amzn2023.0.1.x86_64                     73/132 
  Verifying        : libcap-ng-0.8.2-4.amzn2023.0.2.x86_64               74/132 
  Verifying        : libunistring-0.9.10-10.amzn2023.0.2.x86_64          75/132 
  Verifying        : tar-2:1.34-1.amzn2023.0.3.x86_64                    76/132 
  Verifying        : gdb-minimal-12.1-5.amzn2023.0.3.x86_64              77/132 
  Verifying        : unzip-6.0-57.amzn2023.0.2.x86_64                    78/132 
  Verifying        : libsigsegv-2.13-2.amzn2023.0.2.x86_64               79/132 
  Verifying        : libarchive-3.5.3-2.amzn2023.0.3.x86_64              80/132 
  Verifying        : which-2.21-26.amzn2023.0.2.x86_64                   81/132 
  Verifying        : elfutils-debuginfod-client-0.188-3.amzn2023.0.2.    82/132 
  Verifying        : cpio-2.13-13.amzn2023.0.2.x86_64                    83/132 
  Verifying        : ncurses-libs-6.2-4.20200222.amzn2023.0.4.x86_64     84/132 
  Verifying        : glibc-gconv-extra-2.34-52.amzn2023.0.7.x86_64       85/132 
  Verifying        : libssh-0.10.5-1.amzn2023.0.2.x86_64                 86/132 
  Verifying        : elfutils-libs-0.188-3.amzn2023.0.2.x86_64           87/132 
  Verifying        : readline-8.1-2.amzn2023.0.2.x86_64                  88/132 
  Verifying        : libutempter-1.2.1-4.amzn2023.0.2.x86_64             89/132 
  Verifying        : util-linux-core-2.37.4-1.amzn2023.0.3.x86_64        90/132 
  Verifying        : cracklib-2.9.6-27.amzn2023.0.2.x86_64               91/132 
  Verifying        : libzstd-1.5.5-1.amzn2023.0.1.x86_64                 92/132 
  Verifying        : zip-3.0-28.amzn2023.0.2.x86_64                      93/132 
  Verifying        : p11-kit-trust-0.24.1-2.amzn2023.0.3.x86_64          94/132 
  Verifying        : libnghttp2-1.57.0-1.amzn2023.0.1.x86_64             95/132 
  Verifying        : libsmartcols-2.37.4-1.amzn2023.0.3.x86_64           96/132 
  Verifying        : gmp-1:6.2.1-2.amzn2023.0.2.x86_64                   97/132 
  Verifying        : file-libs-5.39-7.amzn2023.0.4.x86_64                98/132 
  Verifying        : popt-1.18-6.amzn2023.0.2.x86_64                     99/132 
  Verifying        : pcre2-10.40-1.amzn2023.0.3.x86_64                  100/132 
  Verifying        : openldap-2.4.57-6.amzn2023.0.6.x86_64              101/132 
  Verifying        : file-5.39-7.amzn2023.0.4.x86_64                    102/132 
  Verifying        : systemd-libs-252.16-1.amzn2023.0.1.x86_64          103/132 
  Verifying        : libpsl-0.21.1-3.amzn2023.0.2.x86_64                104/132 
  Verifying        : pkgconf-1.8.0-4.amzn2023.0.2.x86_64                105/132 
  Verifying        : libverto-0.3.2-1.amzn2023.0.2.x86_64               106/132 
  Verifying        : libeconf-0.4.0-1.amzn2023.0.3.x86_64               107/132 
  Verifying        : libbrotli-1.0.9-4.amzn2023.0.2.x86_64              108/132 
  Verifying        : efi-srpm-macros-5-4.amzn2023.0.5.noarch            109/132 
  Verifying        : ghc-srpm-macros-1.5.0-4.amzn2023.0.2.noarch        110/132 
  Verifying        : elfutils-default-yama-scope-0.188-3.amzn2023.0.2   111/132 
  Verifying        : ncurses-base-6.2-4.20200222.amzn2023.0.4.noarch    112/132 
  Verifying        : openblas-srpm-macros-2-9.amzn2023.0.2.noarch       113/132 
  Verifying        : publicsuffix-list-dafsa-20221208-60.amzn2023.noa   114/132 
  Verifying        : kernel-srpm-macros-1.0-14.amzn2023.0.2.noarch      115/132 
  Verifying        : pcre2-syntax-10.40-1.amzn2023.0.3.noarch           116/132 
  Verifying        : ocaml-srpm-macros-6-6.amzn2023.0.2.noarch          117/132 
  Verifying        : basesystem-11-11.amzn2023.0.2.noarch               118/132 
  Verifying        : setup-2.13.7-3.amzn2023.0.2.noarch                 119/132 
  Verifying        : libssh-config-0.10.5-1.amzn2023.0.2.noarch         120/132 
  Verifying        : amazon-rpm-config-228-3.amzn2023.0.2.noarch        121/132 
  Verifying        : ca-certificates-2023.2.62-1.0.amzn2023.0.1.noarc   122/132 
  Verifying        : python-srpm-macros-3.9-41.amzn2023.0.5.noarch      123/132 
  Verifying        : crypto-policies-20220428-1.gitdfb10ea.amzn2023.0   124/132 
  Verifying        : fonts-srpm-macros-1:2.0.5-12.amzn2023.0.2.noarch   125/132 
  Verifying        : package-notes-srpm-macros-0.4-18.amzn2023.0.5.no   126/132 
  Verifying        : perl-srpm-macros-1-39.amzn2023.0.2.noarch          127/132 
  Verifying        : lua-srpm-macros-1-4.amzn2023.0.2.noarch            128/132 
  Verifying        : system-release-2023.3.20231218-0.amzn2023.noarch   129/132 
  Verifying        : amazon-linux-repo-cdn-2023.3.20231218-0.amzn2023   130/132 
  Verifying        : rust-srpm-macros-21-42.amzn2023.0.2.noarch         131/132 
  Verifying        : pkgconf-m4-1.8.0-4.amzn2023.0.2.noarch             132/132 

Installed:
  alternatives-1.15-2.amzn2023.0.2.x86_64                                       
  amazon-linux-repo-cdn-2023.3.20231218-0.amzn2023.noarch                       
  amazon-rpm-config-228-3.amzn2023.0.2.noarch                                   
  audit-libs-3.0.6-1.amzn2023.0.2.x86_64                                        
  basesystem-11-11.amzn2023.0.2.noarch                                          
  bash-5.2.15-1.amzn2023.0.2.x86_64                                             
  binutils-2.39-6.amzn2023.0.10.x86_64                                          
  bzip2-1.0.8-6.amzn2023.0.2.x86_64                                             
  bzip2-libs-1.0.8-6.amzn2023.0.2.x86_64                                        
  ca-certificates-2023.2.62-1.0.amzn2023.0.1.noarch                             
  coreutils-8.32-30.amzn2023.0.3.x86_64                                         
  coreutils-common-8.32-30.amzn2023.0.3.x86_64                                  
  cpio-2.13-13.amzn2023.0.2.x86_64                                              
  cracklib-2.9.6-27.amzn2023.0.2.x86_64                                         
  crypto-policies-20220428-1.gitdfb10ea.amzn2023.0.2.noarch                     
  curl-8.3.0-1.amzn2023.0.2.x86_64                                              
  cyrus-sasl-lib-2.1.27-18.amzn2023.0.3.x86_64                                  
  diffutils-3.8-1.amzn2023.0.2.x86_64                                           
  dwz-0.14-6.amzn2023.0.2.x86_64                                                
  ed-1.14.2-10.amzn2023.0.2.x86_64                                              
  efi-srpm-macros-5-4.amzn2023.0.5.noarch                                       
  elfutils-0.188-3.amzn2023.0.2.x86_64                                          
  elfutils-debuginfod-client-0.188-3.amzn2023.0.2.x86_64                        
  elfutils-default-yama-scope-0.188-3.amzn2023.0.2.noarch                       
  elfutils-libelf-0.188-3.amzn2023.0.2.x86_64                                   
  elfutils-libs-0.188-3.amzn2023.0.2.x86_64                                     
  file-5.39-7.amzn2023.0.4.x86_64                                               
  file-libs-5.39-7.amzn2023.0.4.x86_64                                          
  filesystem-3.14-5.amzn2023.0.3.x86_64                                         
  findutils-1:4.8.0-2.amzn2023.0.2.x86_64                                       
  fonts-srpm-macros-1:2.0.5-12.amzn2023.0.2.noarch                              
  gawk-5.1.0-3.amzn2023.0.3.x86_64                                              
  gdb-minimal-12.1-5.amzn2023.0.3.x86_64                                        
  gdbm-libs-1:1.19-2.amzn2023.0.2.x86_64                                        
  ghc-srpm-macros-1.5.0-4.amzn2023.0.2.noarch                                   
  glibc-2.34-52.amzn2023.0.7.x86_64                                             
  glibc-common-2.34-52.amzn2023.0.7.x86_64                                      
  glibc-gconv-extra-2.34-52.amzn2023.0.7.x86_64                                 
  glibc-minimal-langpack-2.34-52.amzn2023.0.7.x86_64                            
  gmp-1:6.2.1-2.amzn2023.0.2.x86_64                                             
  go-srpm-macros-3.3.1-1.amzn2023.noarch                                        
  grep-3.8-1.amzn2023.0.4.x86_64                                                
  gzip-1.12-1.amzn2023.0.1.x86_64                                               
  info-6.7-10.amzn2023.0.2.x86_64                                               
  jansson-2.14-0.amzn2023.x86_64                                                
  kernel-srpm-macros-1.0-14.amzn2023.0.2.noarch                                 
  keyutils-libs-1.6.3-1.amzn2023.x86_64                                         
  krb5-libs-1.21-3.amzn2023.0.3.x86_64                                          
  libacl-2.3.1-2.amzn2023.0.2.x86_64                                            
  libarchive-3.5.3-2.amzn2023.0.3.x86_64                                        
  libattr-2.5.1-3.amzn2023.0.2.x86_64                                           
  libblkid-2.37.4-1.amzn2023.0.3.x86_64                                         
  libbrotli-1.0.9-4.amzn2023.0.2.x86_64                                         
  libcap-2.48-2.amzn2023.0.3.x86_64                                             
  libcap-ng-0.8.2-4.amzn2023.0.2.x86_64                                         
  libcom_err-1.46.5-2.amzn2023.0.2.x86_64                                       
  libcurl-8.3.0-1.amzn2023.0.2.x86_64                                           
  libdb-5.3.28-49.amzn2023.0.2.x86_64                                           
  libeconf-0.4.0-1.amzn2023.0.3.x86_64                                          
  libfdisk-2.37.4-1.amzn2023.0.3.x86_64                                         
  libffi-3.4.4-1.amzn2023.0.1.x86_64                                            
  libgcc-11.4.1-2.amzn2023.0.2.x86_64                                           
  libgomp-11.4.1-2.amzn2023.0.2.x86_64                                          
  libidn2-2.3.2-1.amzn2023.0.5.x86_64                                           
  libmount-2.37.4-1.amzn2023.0.3.x86_64                                         
  libnghttp2-1.57.0-1.amzn2023.0.1.x86_64                                       
  libpkgconf-1.8.0-4.amzn2023.0.2.x86_64                                        
  libpsl-0.21.1-3.amzn2023.0.2.x86_64                                           
  libpwquality-1.4.4-6.amzn2023.0.2.x86_64                                      
  libselinux-3.4-5.amzn2023.0.2.x86_64                                          
  libsemanage-3.4-5.amzn2023.0.2.x86_64                                         
  libsepol-3.4-3.amzn2023.0.3.x86_64                                            
  libsigsegv-2.13-2.amzn2023.0.2.x86_64                                         
  libsmartcols-2.37.4-1.amzn2023.0.3.x86_64                                     
  libssh-0.10.5-1.amzn2023.0.2.x86_64                                           
  libssh-config-0.10.5-1.amzn2023.0.2.noarch                                    
  libstdc++-11.4.1-2.amzn2023.0.2.x86_64                                        
  libtasn1-4.19.0-1.amzn2023.0.4.x86_64                                         
  libunistring-0.9.10-10.amzn2023.0.2.x86_64                                    
  libutempter-1.2.1-4.amzn2023.0.2.x86_64                                       
  libuuid-2.37.4-1.amzn2023.0.3.x86_64                                          
  libverto-0.3.2-1.amzn2023.0.2.x86_64                                          
  libxcrypt-4.4.33-7.amzn2023.x86_64                                            
  libxml2-2.10.4-1.amzn2023.0.6.x86_64                                          
  libzstd-1.5.5-1.amzn2023.0.1.x86_64                                           
  lua-libs-5.4.4-3.amzn2023.0.2.x86_64                                          
  lua-srpm-macros-1-4.amzn2023.0.2.noarch                                       
  lz4-libs-1.9.4-1.amzn2023.0.2.x86_64                                          
  mpfr-4.1.0-7.amzn2023.0.2.x86_64                                              
  ncurses-base-6.2-4.20200222.amzn2023.0.4.noarch                               
  ncurses-libs-6.2-4.20200222.amzn2023.0.4.x86_64                               
  ocaml-srpm-macros-6-6.amzn2023.0.2.noarch                                     
  openblas-srpm-macros-2-9.amzn2023.0.2.noarch                                  
  openldap-2.4.57-6.amzn2023.0.6.x86_64                                         
  openssl-libs-1:3.0.8-1.amzn2023.0.10.x86_64                                   
  p11-kit-0.24.1-2.amzn2023.0.3.x86_64                                          
  p11-kit-trust-0.24.1-2.amzn2023.0.3.x86_64                                    
  package-notes-srpm-macros-0.4-18.amzn2023.0.5.noarch                          
  pam-1.5.1-8.amzn2023.0.3.x86_64                                               
  patch-2.7.6-14.amzn2023.0.2.x86_64                                            
  pcre2-10.40-1.amzn2023.0.3.x86_64                                             
  pcre2-syntax-10.40-1.amzn2023.0.3.noarch                                      
  perl-srpm-macros-1-39.amzn2023.0.2.noarch                                     
  pkgconf-1.8.0-4.amzn2023.0.2.x86_64                                           
  pkgconf-m4-1.8.0-4.amzn2023.0.2.noarch                                        
  pkgconf-pkg-config-1.8.0-4.amzn2023.0.2.x86_64                                
  popt-1.18-6.amzn2023.0.2.x86_64                                               
  publicsuffix-list-dafsa-20221208-60.amzn2023.noarch                           
  python-srpm-macros-3.9-41.amzn2023.0.5.noarch                                 
  readline-8.1-2.amzn2023.0.2.x86_64                                            
  rpm-4.16.1.3-12.amzn2023.0.6.x86_64                                           
  rpm-build-4.16.1.3-12.amzn2023.0.6.x86_64                                     
  rpm-build-libs-4.16.1.3-12.amzn2023.0.6.x86_64                                
  rpm-libs-4.16.1.3-12.amzn2023.0.6.x86_64                                      
  rust-srpm-macros-21-42.amzn2023.0.2.noarch                                    
  sed-4.8-7.amzn2023.0.2.x86_64                                                 
  setup-2.13.7-3.amzn2023.0.2.noarch                                            
  shadow-utils-2:4.9-12.amzn2023.0.4.x86_64                                     
  sqlite-libs-3.40.0-1.amzn2023.0.3.x86_64                                      
  system-release-2023.3.20231218-0.amzn2023.noarch                              
  systemd-libs-252.16-1.amzn2023.0.1.x86_64                                     
  tar-2:1.34-1.amzn2023.0.3.x86_64                                              
  unzip-6.0-57.amzn2023.0.2.x86_64                                              
  util-linux-2.37.4-1.amzn2023.0.3.x86_64                                       
  util-linux-core-2.37.4-1.amzn2023.0.3.x86_64                                  
  which-2.21-26.amzn2023.0.2.x86_64                                             
  xxhash-libs-0.8.0-3.amzn2023.0.2.x86_64                                       
  xz-5.2.5-9.amzn2023.0.2.x86_64                                                
  xz-libs-5.2.5-9.amzn2023.0.2.x86_64                                           
  zip-3.0-28.amzn2023.0.2.x86_64                                                
  zlib-1.2.11-33.amzn2023.0.5.x86_64                                            
  zstd-1.5.5-1.amzn2023.0.1.x86_64                                              

Complete!
Finish: installing minimal buildroot with dnf
Start: creating root cache
Finish: creating root cache
Finish: chroot init
INFO: Installed packages:
INFO: alternatives-1.15-2.amzn2023.0.2.x86_64
amazon-linux-repo-cdn-2023.3.20231218-0.amzn2023.noarch
amazon-rpm-config-228-3.amzn2023.0.2.noarch
audit-libs-3.0.6-1.amzn2023.0.2.x86_64
basesystem-11-11.amzn2023.0.2.noarch
bash-5.2.15-1.amzn2023.0.2.x86_64
binutils-2.39-6.amzn2023.0.10.x86_64
bzip2-1.0.8-6.amzn2023.0.2.x86_64
bzip2-libs-1.0.8-6.amzn2023.0.2.x86_64
ca-certificates-2023.2.62-1.0.amzn2023.0.1.noarch
coreutils-8.32-30.amzn2023.0.3.x86_64
coreutils-common-8.32-30.amzn2023.0.3.x86_64
cpio-2.13-13.amzn2023.0.2.x86_64
cracklib-2.9.6-27.amzn2023.0.2.x86_64
crypto-policies-20220428-1.gitdfb10ea.amzn2023.0.2.noarch
curl-8.3.0-1.amzn2023.0.2.x86_64
cyrus-sasl-lib-2.1.27-18.amzn2023.0.3.x86_64
diffutils-3.8-1.amzn2023.0.2.x86_64
dwz-0.14-6.amzn2023.0.2.x86_64
ed-1.14.2-10.amzn2023.0.2.x86_64
efi-srpm-macros-5-4.amzn2023.0.5.noarch
elfutils-0.188-3.amzn2023.0.2.x86_64
elfutils-debuginfod-client-0.188-3.amzn2023.0.2.x86_64
elfutils-default-yama-scope-0.188-3.amzn2023.0.2.noarch
elfutils-libelf-0.188-3.amzn2023.0.2.x86_64
elfutils-libs-0.188-3.amzn2023.0.2.x86_64
file-5.39-7.amzn2023.0.4.x86_64
file-libs-5.39-7.amzn2023.0.4.x86_64
filesystem-3.14-5.amzn2023.0.3.x86_64
findutils-4.8.0-2.amzn2023.0.2.x86_64
fonts-srpm-macros-2.0.5-12.amzn2023.0.2.noarch
gawk-5.1.0-3.amzn2023.0.3.x86_64
gdb-minimal-12.1-5.amzn2023.0.3.x86_64
gdbm-libs-1.19-2.amzn2023.0.2.x86_64
ghc-srpm-macros-1.5.0-4.amzn2023.0.2.noarch
glibc-2.34-52.amzn2023.0.7.x86_64
glibc-common-2.34-52.amzn2023.0.7.x86_64
glibc-gconv-extra-2.34-52.amzn2023.0.7.x86_64
glibc-minimal-langpack-2.34-52.amzn2023.0.7.x86_64
gmp-6.2.1-2.amzn2023.0.2.x86_64
go-srpm-macros-3.3.1-1.amzn2023.noarch
gpg-pubkey-d832c631-6515c85e
grep-3.8-1.amzn2023.0.4.x86_64
gzip-1.12-1.amzn2023.0.1.x86_64
info-6.7-10.amzn2023.0.2.x86_64
jansson-2.14-0.amzn2023.x86_64
kernel-srpm-macros-1.0-14.amzn2023.0.2.noarch
keyutils-libs-1.6.3-1.amzn2023.x86_64
krb5-libs-1.21-3.amzn2023.0.3.x86_64
libacl-2.3.1-2.amzn2023.0.2.x86_64
libarchive-3.5.3-2.amzn2023.0.3.x86_64
libattr-2.5.1-3.amzn2023.0.2.x86_64
libblkid-2.37.4-1.amzn2023.0.3.x86_64
libbrotli-1.0.9-4.amzn2023.0.2.x86_64
libcap-2.48-2.amzn2023.0.3.x86_64
libcap-ng-0.8.2-4.amzn2023.0.2.x86_64
libcom_err-1.46.5-2.amzn2023.0.2.x86_64
libcurl-8.3.0-1.amzn2023.0.2.x86_64
libdb-5.3.28-49.amzn2023.0.2.x86_64
libeconf-0.4.0-1.amzn2023.0.3.x86_64
libfdisk-2.37.4-1.amzn2023.0.3.x86_64
libffi-3.4.4-1.amzn2023.0.1.x86_64
libgcc-11.4.1-2.amzn2023.0.2.x86_64
libgomp-11.4.1-2.amzn2023.0.2.x86_64
libidn2-2.3.2-1.amzn2023.0.5.x86_64
libmount-2.37.4-1.amzn2023.0.3.x86_64
libnghttp2-1.57.0-1.amzn2023.0.1.x86_64
libpkgconf-1.8.0-4.amzn2023.0.2.x86_64
libpsl-0.21.1-3.amzn2023.0.2.x86_64
libpwquality-1.4.4-6.amzn2023.0.2.x86_64
libselinux-3.4-5.amzn2023.0.2.x86_64
libsemanage-3.4-5.amzn2023.0.2.x86_64
libsepol-3.4-3.amzn2023.0.3.x86_64
libsigsegv-2.13-2.amzn2023.0.2.x86_64
libsmartcols-2.37.4-1.amzn2023.0.3.x86_64
libssh-0.10.5-1.amzn2023.0.2.x86_64
libssh-config-0.10.5-1.amzn2023.0.2.noarch
libstdc++-11.4.1-2.amzn2023.0.2.x86_64
libtasn1-4.19.0-1.amzn2023.0.4.x86_64
libunistring-0.9.10-10.amzn2023.0.2.x86_64
libutempter-1.2.1-4.amzn2023.0.2.x86_64
libuuid-2.37.4-1.amzn2023.0.3.x86_64
libverto-0.3.2-1.amzn2023.0.2.x86_64
libxcrypt-4.4.33-7.amzn2023.x86_64
libxml2-2.10.4-1.amzn2023.0.6.x86_64
libzstd-1.5.5-1.amzn2023.0.1.x86_64
lua-libs-5.4.4-3.amzn2023.0.2.x86_64
lua-srpm-macros-1-4.amzn2023.0.2.noarch
lz4-libs-1.9.4-1.amzn2023.0.2.x86_64
mpfr-4.1.0-7.amzn2023.0.2.x86_64
ncurses-base-6.2-4.20200222.amzn2023.0.4.noarch
ncurses-libs-6.2-4.20200222.amzn2023.0.4.x86_64
ocaml-srpm-macros-6-6.amzn2023.0.2.noarch
openblas-srpm-macros-2-9.amzn2023.0.2.noarch
openldap-2.4.57-6.amzn2023.0.6.x86_64
openssl-libs-3.0.8-1.amzn2023.0.10.x86_64
p11-kit-0.24.1-2.amzn2023.0.3.x86_64
p11-kit-trust-0.24.1-2.amzn2023.0.3.x86_64
package-notes-srpm-macros-0.4-18.amzn2023.0.5.noarch
pam-1.5.1-8.amzn2023.0.3.x86_64
patch-2.7.6-14.amzn2023.0.2.x86_64
pcre2-10.40-1.amzn2023.0.3.x86_64
pcre2-syntax-10.40-1.amzn2023.0.3.noarch
perl-srpm-macros-1-39.amzn2023.0.2.noarch
pkgconf-1.8.0-4.amzn2023.0.2.x86_64
pkgconf-m4-1.8.0-4.amzn2023.0.2.noarch
pkgconf-pkg-config-1.8.0-4.amzn2023.0.2.x86_64
popt-1.18-6.amzn2023.0.2.x86_64
publicsuffix-list-dafsa-20221208-60.amzn2023.noarch
python-srpm-macros-3.9-41.amzn2023.0.5.noarch
readline-8.1-2.amzn2023.0.2.x86_64
rpm-4.16.1.3-12.amzn2023.0.6.x86_64
rpm-build-4.16.1.3-12.amzn2023.0.6.x86_64
rpm-build-libs-4.16.1.3-12.amzn2023.0.6.x86_64
rpm-libs-4.16.1.3-12.amzn2023.0.6.x86_64
rust-srpm-macros-21-42.amzn2023.0.2.noarch
sed-4.8-7.amzn2023.0.2.x86_64
setup-2.13.7-3.amzn2023.0.2.noarch
shadow-utils-4.9-12.amzn2023.0.4.x86_64
sqlite-libs-3.40.0-1.amzn2023.0.3.x86_64
system-release-2023.3.20231218-0.amzn2023.noarch
systemd-libs-252.16-1.amzn2023.0.1.x86_64
tar-1.34-1.amzn2023.0.3.x86_64
unzip-6.0-57.amzn2023.0.2.x86_64
util-linux-2.37.4-1.amzn2023.0.3.x86_64
util-linux-core-2.37.4-1.amzn2023.0.3.x86_64
which-2.21-26.amzn2023.0.2.x86_64
xxhash-libs-0.8.0-3.amzn2023.0.2.x86_64
xz-5.2.5-9.amzn2023.0.2.x86_64
xz-libs-5.2.5-9.amzn2023.0.2.x86_64
zip-3.0-28.amzn2023.0.2.x86_64
zlib-1.2.11-33.amzn2023.0.5.x86_64
zstd-1.5.5-1.amzn2023.0.1.x86_64
Start: buildsrpm
Start: rpmbuild -bs
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1689984000
Wrote: /builddir/build/SRPMS/samtools-1.15.1-3.amzn2023.src.rpm
Finish: rpmbuild -bs
INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/amazonlinux-2023-x86_64-1704591447.340321/root/var/log/dnf.rpm.log
/var/lib/mock/amazonlinux-2023-x86_64-1704591447.340321/root/var/log/dnf.librepo.log
/var/lib/mock/amazonlinux-2023-x86_64-1704591447.340321/root/var/log/dnf.log
Finish: buildsrpm
INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-_59crliw/samtools/samtools.spec) Config(child) 0 minutes 23 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-1.15.1-3.amzn2023.src.rpm)  Config(amazonlinux-2023-x86_64)
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/amazonlinux-2023-x86_64-bootstrap-1704591447.340321/root.
INFO: reusing tmpfs at /var/lib/mock/amazonlinux-2023-x86_64-bootstrap-1704591447.340321/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/amazonlinux-2023-x86_64-1704591447.340321/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-4.16.1.3-12.amzn2023.0.6.x86_64
  python3-dnf-4.12.0-2.amzn2023.0.4.noarch
  python3-dnf-plugins-core-4.1.0-1.amzn2023.0.3.noarch
  yum-4.12.0-2.amzn2023.0.4.noarch
Finish: chroot init
Start: build phase for samtools-1.15.1-3.amzn2023.src.rpm
Start: build setup for samtools-1.15.1-3.amzn2023.src.rpm
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1689984000
Wrote: /builddir/build/SRPMS/samtools-1.15.1-3.amzn2023.src.rpm
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Copr repository                                  25 kB/s | 1.5 kB     00:00    
Copr repository                                 1.5 MB/s | 172 kB     00:00    
Amazon Linux 2023 repository - x86_64           9.8 kB/s | 3.6 kB     00:00    
Dependencies resolved.
================================================================================
 Package                Arch   Version                        Repository   Size
================================================================================
Installing:
 gcc                    x86_64 11.4.1-2.amzn2023.0.2          amazonlinux  32 M
 htslib-devel           x86_64 1.15.1-3.amzn2023              copr_base   100 k
 htslib-tools           x86_64 1.15.1-3.amzn2023              copr_base   540 k
 make                   x86_64 1:4.3-5.amzn2023.0.2           amazonlinux 534 k
 ncurses-devel          x86_64 6.2-4.20200222.amzn2023.0.4    amazonlinux 510 k
 perl-FindBin           noarch 1.51-477.amzn2023.0.6          amazonlinux  14 k
 perl-Getopt-Long       noarch 1:2.52-2.amzn2023.0.2          amazonlinux  60 k
 perl-interpreter       x86_64 4:5.32.1-477.amzn2023.0.6      amazonlinux  71 k
 perl-lib               x86_64 0.65-477.amzn2023.0.6          amazonlinux  15 k
 zlib-devel             x86_64 1.2.11-33.amzn2023.0.5         amazonlinux  45 k
Installing dependencies:
 annobin-docs           noarch 10.93-1.amzn2023.0.1           amazonlinux  92 k
 annobin-plugin-gcc     x86_64 10.93-1.amzn2023.0.1           amazonlinux 887 k
 cpp                    x86_64 11.4.1-2.amzn2023.0.2          amazonlinux  10 M
 gc                     x86_64 8.0.4-5.amzn2023.0.2           amazonlinux 105 k
 glibc-devel            x86_64 2.34-52.amzn2023.0.7           amazonlinux  45 k
 glibc-headers-x86      noarch 2.34-52.amzn2023.0.7           amazonlinux 446 k
 groff-base             x86_64 1.22.4-7.amzn2023.0.2          amazonlinux 1.0 M
 guile22                x86_64 2.2.7-2.amzn2023.0.3           amazonlinux 6.4 M
 htslib                 x86_64 1.15.1-3.amzn2023              copr_base   490 k
 kernel-headers         x86_64 6.1.66-91.160.amzn2023         amazonlinux 1.4 M
 libmpc                 x86_64 1.2.1-2.amzn2023.0.2           amazonlinux  62 k
 libtool-ltdl           x86_64 2.4.7-1.amzn2023.0.3           amazonlinux  38 k
 libxcrypt-devel        x86_64 4.4.33-7.amzn2023              amazonlinux  32 k
 ncurses                x86_64 6.2-4.20200222.amzn2023.0.4    amazonlinux 394 k
 ncurses-c++-libs       x86_64 6.2-4.20200222.amzn2023.0.4    amazonlinux  37 k
 perl-Carp              noarch 1.50-458.amzn2023.0.2          amazonlinux  29 k
 perl-Class-Struct      noarch 0.66-477.amzn2023.0.6          amazonlinux  22 k
 perl-DynaLoader        x86_64 1.47-477.amzn2023.0.6          amazonlinux  26 k
 perl-Encode            x86_64 4:3.15-462.amzn2023.0.2        amazonlinux 1.7 M
 perl-Errno             x86_64 1.30-477.amzn2023.0.6          amazonlinux  15 k
 perl-Exporter          noarch 5.74-459.amzn2023.0.2          amazonlinux  31 k
 perl-Fcntl             x86_64 1.13-477.amzn2023.0.6          amazonlinux  21 k
 perl-File-Basename     noarch 2.85-477.amzn2023.0.6          amazonlinux  18 k
 perl-File-Path         noarch 2.18-2.amzn2023.0.2            amazonlinux  36 k
 perl-File-Temp         noarch 1:0.231.100-2.amzn2023.0.2     amazonlinux  60 k
 perl-File-stat         noarch 1.09-477.amzn2023.0.6          amazonlinux  17 k
 perl-Getopt-Std        noarch 1.12-477.amzn2023.0.6          amazonlinux  16 k
 perl-HTTP-Tiny         noarch 0.078-1.amzn2023.0.3           amazonlinux  56 k
 perl-IO                x86_64 1.43-477.amzn2023.0.6          amazonlinux  87 k
 perl-IPC-Open3         noarch 1.21-477.amzn2023.0.6          amazonlinux  23 k
 perl-MIME-Base64       x86_64 3.16-2.amzn2023.0.2            amazonlinux  31 k
 perl-POSIX             x86_64 1.94-477.amzn2023.0.6          amazonlinux  97 k
 perl-PathTools         x86_64 3.78-459.amzn2023.0.2          amazonlinux  85 k
 perl-Pod-Escapes       noarch 1:1.07-458.amzn2023.0.2        amazonlinux  20 k
 perl-Pod-Perldoc       noarch 3.28.01-459.amzn2023.0.3       amazonlinux  84 k
 perl-Pod-Simple        noarch 1:3.42-2.amzn2023.0.2          amazonlinux 215 k
 perl-Pod-Usage         noarch 4:2.01-2.amzn2023.0.2          amazonlinux  41 k
 perl-Scalar-List-Utils x86_64 4:1.56-459.amzn2023.0.2        amazonlinux  71 k
 perl-SelectSaver       noarch 1.02-477.amzn2023.0.6          amazonlinux  12 k
 perl-Socket            x86_64 4:2.032-1.amzn2023.0.2         amazonlinux  55 k
 perl-Storable          x86_64 1:3.21-458.amzn2023.0.2        amazonlinux  96 k
 perl-Symbol            noarch 1.08-477.amzn2023.0.6          amazonlinux  15 k
 perl-Term-ANSIColor    noarch 5.01-459.amzn2023.0.2          amazonlinux  48 k
 perl-Term-Cap          noarch 1.17-458.amzn2023.0.2          amazonlinux  22 k
 perl-Text-ParseWords   noarch 3.30-458.amzn2023.0.2          amazonlinux  17 k
 perl-Text-Tabs+Wrap    noarch 2021.0726-1.amzn2023.0.1       amazonlinux  22 k
 perl-Time-Local        noarch 2:1.300-5.amzn2023.0.2         amazonlinux  34 k
 perl-constant          noarch 1.33-459.amzn2023.0.2          amazonlinux  23 k
 perl-if                noarch 0.60.800-477.amzn2023.0.6      amazonlinux  14 k
 perl-libs              x86_64 4:5.32.1-477.amzn2023.0.6      amazonlinux 2.0 M
 perl-mro               x86_64 1.23-477.amzn2023.0.6          amazonlinux  29 k
 perl-overload          noarch 1.31-477.amzn2023.0.6          amazonlinux  46 k
 perl-overloading       noarch 0.02-477.amzn2023.0.6          amazonlinux  13 k
 perl-parent            noarch 1:0.238-458.amzn2023.0.2       amazonlinux  14 k
 perl-podlators         noarch 1:4.14-458.amzn2023.0.2        amazonlinux 112 k
 perl-subs              noarch 1.03-477.amzn2023.0.6          amazonlinux  12 k
 perl-vars              noarch 1.05-477.amzn2023.0.6          amazonlinux  13 k

Transaction Summary
================================================================================
Install  67 Packages

Total download size: 61 M
Installed size: 199 M
Downloading Packages:
(1/67): htslib-devel-1.15.1-3.amzn2023.x86_64.r 983 kB/s | 100 kB     00:00    
(2/67): htslib-tools-1.15.1-3.amzn2023.x86_64.r 3.6 MB/s | 540 kB     00:00    
(3/67): htslib-1.15.1-3.amzn2023.x86_64.rpm     3.1 MB/s | 490 kB     00:00    
(4/67): ncurses-devel-6.2-4.20200222.amzn2023.0 4.0 MB/s | 510 kB     00:00    
(5/67): perl-MIME-Base64-3.16-2.amzn2023.0.2.x8 129 kB/s |  31 kB     00:00    
(6/67): annobin-plugin-gcc-10.93-1.amzn2023.0.1 8.4 MB/s | 887 kB     00:00    
(7/67): perl-IO-1.43-477.amzn2023.0.6.x86_64.rp 2.0 MB/s |  87 kB     00:00    
(8/67): perl-Encode-3.15-462.amzn2023.0.2.x86_6  22 MB/s | 1.7 MB     00:00    
(9/67): perl-Errno-1.30-477.amzn2023.0.6.x86_64 808 kB/s |  15 kB     00:00    
(10/67): libmpc-1.2.1-2.amzn2023.0.2.x86_64.rpm 2.0 MB/s |  62 kB     00:00    
(11/67): cpp-11.4.1-2.amzn2023.0.2.x86_64.rpm    28 MB/s |  10 MB     00:00    
(12/67): glibc-devel-2.34-52.amzn2023.0.7.x86_6 822 kB/s |  45 kB     00:00    
(13/67): perl-PathTools-3.78-459.amzn2023.0.2.x 1.9 MB/s |  85 kB     00:00    
(14/67): groff-base-1.22.4-7.amzn2023.0.2.x86_6  14 MB/s | 1.0 MB     00:00    
(15/67): ncurses-c++-libs-6.2-4.20200222.amzn20 684 kB/s |  37 kB     00:00    
(16/67): perl-POSIX-1.94-477.amzn2023.0.6.x86_6 1.5 MB/s |  97 kB     00:00    
(17/67): perl-Scalar-List-Utils-1.56-459.amzn20 1.0 MB/s |  71 kB     00:00    
(18/67): libxcrypt-devel-4.4.33-7.amzn2023.x86_ 344 kB/s |  32 kB     00:00    
(19/67): gc-8.0.4-5.amzn2023.0.2.x86_64.rpm     988 kB/s | 105 kB     00:00    
(20/67): perl-libs-5.32.1-477.amzn2023.0.6.x86_  16 MB/s | 2.0 MB     00:00    
(21/67): gcc-11.4.1-2.amzn2023.0.2.x86_64.rpm    62 MB/s |  32 MB     00:00    
(22/67): perl-Storable-3.21-458.amzn2023.0.2.x8 675 kB/s |  96 kB     00:00    
(23/67): zlib-devel-1.2.11-33.amzn2023.0.5.x86_ 836 kB/s |  45 kB     00:00    
(24/67): perl-lib-0.65-477.amzn2023.0.6.x86_64. 911 kB/s |  15 kB     00:00    
(25/67): libtool-ltdl-2.4.7-1.amzn2023.0.3.x86_ 1.9 MB/s |  38 kB     00:00    
(26/67): perl-interpreter-5.32.1-477.amzn2023.0 1.9 MB/s |  71 kB     00:00    
(27/67): kernel-headers-6.1.66-91.160.amzn2023.  22 MB/s | 1.4 MB     00:00    
(28/67): guile22-2.2.7-2.amzn2023.0.3.x86_64.rp  51 MB/s | 6.4 MB     00:00    
(29/67): ncurses-6.2-4.20200222.amzn2023.0.4.x8 5.6 MB/s | 394 kB     00:00    
(30/67): perl-mro-1.23-477.amzn2023.0.6.x86_64. 627 kB/s |  29 kB     00:00    
(31/67): perl-DynaLoader-1.47-477.amzn2023.0.6. 1.9 MB/s |  26 kB     00:00    
(32/67): perl-Socket-2.032-1.amzn2023.0.2.x86_6 3.4 MB/s |  55 kB     00:00    
(33/67): make-4.3-5.amzn2023.0.2.x86_64.rpm      22 MB/s | 534 kB     00:00    
(34/67): perl-podlators-4.14-458.amzn2023.0.2.n 5.3 MB/s | 112 kB     00:00    
(35/67): perl-Fcntl-1.13-477.amzn2023.0.6.x86_6 929 kB/s |  21 kB     00:00    
(36/67): perl-Carp-1.50-458.amzn2023.0.2.noarch 2.0 MB/s |  29 kB     00:00    
(37/67): perl-parent-0.238-458.amzn2023.0.2.noa 1.1 MB/s |  14 kB     00:00    
(38/67): perl-Time-Local-1.300-5.amzn2023.0.2.n 2.5 MB/s |  34 kB     00:00    
(39/67): perl-constant-1.33-459.amzn2023.0.2.no 1.7 MB/s |  23 kB     00:00    
(40/67): perl-Text-ParseWords-3.30-458.amzn2023 1.1 MB/s |  17 kB     00:00    
(41/67): perl-FindBin-1.51-477.amzn2023.0.6.noa 921 kB/s |  14 kB     00:00    
(42/67): perl-File-Temp-0.231.100-2.amzn2023.0. 3.3 MB/s |  60 kB     00:00    
(43/67): perl-if-0.60.800-477.amzn2023.0.6.noar 958 kB/s |  14 kB     00:00    
(44/67): perl-Term-ANSIColor-5.01-459.amzn2023. 2.7 MB/s |  48 kB     00:00    
(45/67): perl-Term-Cap-1.17-458.amzn2023.0.2.no 1.5 MB/s |  22 kB     00:00    
(46/67): perl-Text-Tabs+Wrap-2021.0726-1.amzn20 1.7 MB/s |  22 kB     00:00    
(47/67): perl-overloading-0.02-477.amzn2023.0.6 989 kB/s |  13 kB     00:00    
(48/67): perl-Exporter-5.74-459.amzn2023.0.2.no 2.2 MB/s |  31 kB     00:00    
(49/67): perl-subs-1.03-477.amzn2023.0.6.noarch 1.0 MB/s |  12 kB     00:00    
(50/67): perl-File-Basename-2.85-477.amzn2023.0 1.2 MB/s |  18 kB     00:00    
(51/67): perl-File-stat-1.09-477.amzn2023.0.6.n 1.3 MB/s |  17 kB     00:00    
(52/67): perl-Pod-Simple-3.42-2.amzn2023.0.2.no  13 MB/s | 215 kB     00:00    
(53/67): perl-Getopt-Long-2.52-2.amzn2023.0.2.n 3.6 MB/s |  60 kB     00:00    
(54/67): perl-overload-1.31-477.amzn2023.0.6.no 3.1 MB/s |  46 kB     00:00    
(55/67): perl-IPC-Open3-1.21-477.amzn2023.0.6.n 1.2 MB/s |  23 kB     00:00    
(56/67): perl-Getopt-Std-1.12-477.amzn2023.0.6. 754 kB/s |  16 kB     00:00    
(57/67): glibc-headers-x86-2.34-52.amzn2023.0.7  20 MB/s | 446 kB     00:00    
(58/67): perl-HTTP-Tiny-0.078-1.amzn2023.0.3.no 3.8 MB/s |  56 kB     00:00    
(59/67): perl-Pod-Usage-2.01-2.amzn2023.0.2.noa 3.0 MB/s |  41 kB     00:00    
(60/67): perl-Pod-Perldoc-3.28.01-459.amzn2023. 3.9 MB/s |  84 kB     00:00    
(61/67): perl-Symbol-1.08-477.amzn2023.0.6.noar 1.1 MB/s |  15 kB     00:00    
(62/67): perl-SelectSaver-1.02-477.amzn2023.0.6 967 kB/s |  12 kB     00:00    
(63/67): perl-vars-1.05-477.amzn2023.0.6.noarch 1.0 MB/s |  13 kB     00:00    
(64/67): perl-Pod-Escapes-1.07-458.amzn2023.0.2 1.5 MB/s |  20 kB     00:00    
(65/67): annobin-docs-10.93-1.amzn2023.0.1.noar 5.1 MB/s |  92 kB     00:00    
(66/67): perl-File-Path-2.18-2.amzn2023.0.2.noa 2.5 MB/s |  36 kB     00:00    
(67/67): perl-Class-Struct-0.66-477.amzn2023.0. 1.7 MB/s |  22 kB     00:00    
--------------------------------------------------------------------------------
Total                                            44 MB/s |  61 MB     00:01     
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
  Preparing        :                                                        1/1 
  Installing       : libmpc-1.2.1-2.amzn2023.0.2.x86_64                    1/67 
  Installing       : htslib-1.15.1-3.amzn2023.x86_64                       2/67 
  Installing       : cpp-11.4.1-2.amzn2023.0.2.x86_64                      3/67 
  Installing       : annobin-docs-10.93-1.amzn2023.0.1.noarch              4/67 
  Installing       : glibc-headers-x86-2.34-52.amzn2023.0.7.noarch         5/67 
  Installing       : ncurses-6.2-4.20200222.amzn2023.0.4.x86_64            6/67 
  Installing       : kernel-headers-6.1.66-91.160.amzn2023.x86_64          7/67 
  Installing       : libxcrypt-devel-4.4.33-7.amzn2023.x86_64              8/67 
  Installing       : glibc-devel-2.34-52.amzn2023.0.7.x86_64               9/67 
  Installing       : libtool-ltdl-2.4.7-1.amzn2023.0.3.x86_64             10/67 
  Installing       : gc-8.0.4-5.amzn2023.0.2.x86_64                       11/67 
  Installing       : guile22-2.2.7-2.amzn2023.0.3.x86_64                  12/67 
  Installing       : make-1:4.3-5.amzn2023.0.2.x86_64                     13/67 
  Installing       : gcc-11.4.1-2.amzn2023.0.2.x86_64                     14/67 
  Running scriptlet: gcc-11.4.1-2.amzn2023.0.2.x86_64                     14/67 
  Installing       : ncurses-c++-libs-6.2-4.20200222.amzn2023.0.4.x86_6   15/67 
  Running scriptlet: groff-base-1.22.4-7.amzn2023.0.2.x86_64              16/67 
  Installing       : groff-base-1.22.4-7.amzn2023.0.2.x86_64              16/67 
  Running scriptlet: groff-base-1.22.4-7.amzn2023.0.2.x86_64              16/67 
  Installing       : perl-if-0.60.800-477.amzn2023.0.6.noarch             17/67 
  Installing       : perl-Text-Tabs+Wrap-2021.0726-1.amzn2023.0.1.noarc   18/67 
  Installing       : perl-Time-Local-2:1.300-5.amzn2023.0.2.noarch        19/67 
  Installing       : perl-Pod-Escapes-1:1.07-458.amzn2023.0.2.noarch      20/67 
  Installing       : perl-File-Path-2.18-2.amzn2023.0.2.noarch            21/67 
  Installing       : perl-POSIX-1.94-477.amzn2023.0.6.x86_64              22/67 
  Installing       : perl-Term-ANSIColor-5.01-459.amzn2023.0.2.noarch     23/67 
  Installing       : perl-subs-1.03-477.amzn2023.0.6.noarch               24/67 
  Installing       : perl-Term-Cap-1.17-458.amzn2023.0.2.noarch           25/67 
  Installing       : perl-File-Temp-1:0.231.100-2.amzn2023.0.2.noarch     26/67 
  Installing       : perl-IPC-Open3-1.21-477.amzn2023.0.6.noarch          27/67 
  Installing       : perl-Class-Struct-0.66-477.amzn2023.0.6.noarch       28/67 
  Installing       : perl-Pod-Simple-1:3.42-2.amzn2023.0.2.noarch         29/67 
  Installing       : perl-HTTP-Tiny-0.078-1.amzn2023.0.3.noarch           30/67 
  Installing       : perl-Socket-4:2.032-1.amzn2023.0.2.x86_64            31/67 
  Installing       : perl-Symbol-1.08-477.amzn2023.0.6.noarch             32/67 
  Installing       : perl-SelectSaver-1.02-477.amzn2023.0.6.noarch        33/67 
  Installing       : perl-File-stat-1.09-477.amzn2023.0.6.noarch          34/67 
  Installing       : perl-podlators-1:4.14-458.amzn2023.0.2.noarch        35/67 
  Installing       : perl-Pod-Perldoc-3.28.01-459.amzn2023.0.3.noarch     36/67 
  Installing       : perl-mro-1.23-477.amzn2023.0.6.x86_64                37/67 
  Installing       : perl-Fcntl-1.13-477.amzn2023.0.6.x86_64              38/67 
  Installing       : perl-overloading-0.02-477.amzn2023.0.6.noarch        39/67 
  Installing       : perl-Text-ParseWords-3.30-458.amzn2023.0.2.noarch    40/67 
  Installing       : perl-IO-1.43-477.amzn2023.0.6.x86_64                 41/67 
  Installing       : perl-Pod-Usage-4:2.01-2.amzn2023.0.2.noarch          42/67 
  Installing       : perl-parent-1:0.238-458.amzn2023.0.2.noarch          43/67 
  Installing       : perl-Errno-1.30-477.amzn2023.0.6.x86_64              44/67 
  Installing       : perl-Scalar-List-Utils-4:1.56-459.amzn2023.0.2.x86   45/67 
  Installing       : perl-constant-1.33-459.amzn2023.0.2.noarch           46/67 
  Installing       : perl-File-Basename-2.85-477.amzn2023.0.6.noarch      47/67 
  Installing       : perl-overload-1.31-477.amzn2023.0.6.noarch           48/67 
  Installing       : perl-Getopt-Std-1.12-477.amzn2023.0.6.noarch         49/67 
  Installing       : perl-vars-1.05-477.amzn2023.0.6.noarch               50/67 
  Installing       : perl-Storable-1:3.21-458.amzn2023.0.2.x86_64         51/67 
  Installing       : perl-Getopt-Long-1:2.52-2.amzn2023.0.2.noarch        52/67 
  Installing       : perl-MIME-Base64-3.16-2.amzn2023.0.2.x86_64          53/67 
  Installing       : perl-DynaLoader-1.47-477.amzn2023.0.6.x86_64         54/67 
  Installing       : perl-PathTools-3.78-459.amzn2023.0.2.x86_64          55/67 
  Installing       : perl-Carp-1.50-458.amzn2023.0.2.noarch               56/67 
  Installing       : perl-Exporter-5.74-459.amzn2023.0.2.noarch           57/67 
  Installing       : perl-Encode-4:3.15-462.amzn2023.0.2.x86_64           58/67 
  Installing       : perl-libs-4:5.32.1-477.amzn2023.0.6.x86_64           59/67 
  Installing       : perl-interpreter-4:5.32.1-477.amzn2023.0.6.x86_64    60/67 
  Installing       : perl-lib-0.65-477.amzn2023.0.6.x86_64                61/67 
  Installing       : perl-FindBin-1.51-477.amzn2023.0.6.noarch            62/67 
  Installing       : ncurses-devel-6.2-4.20200222.amzn2023.0.4.x86_64     63/67 
  Installing       : annobin-plugin-gcc-10.93-1.amzn2023.0.1.x86_64       64/67 
  Running scriptlet: annobin-plugin-gcc-10.93-1.amzn2023.0.1.x86_64       64/67 
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Installed:
  annobin-docs-10.93-1.amzn2023.0.1.noarch                                      
  annobin-plugin-gcc-10.93-1.amzn2023.0.1.x86_64                                
  cpp-11.4.1-2.amzn2023.0.2.x86_64                                              
  gc-8.0.4-5.amzn2023.0.2.x86_64                                                
  gcc-11.4.1-2.amzn2023.0.2.x86_64                                              
  glibc-devel-2.34-52.amzn2023.0.7.x86_64                                       
  glibc-headers-x86-2.34-52.amzn2023.0.7.noarch                                 
  groff-base-1.22.4-7.amzn2023.0.2.x86_64                                       
  guile22-2.2.7-2.amzn2023.0.3.x86_64                                           
  htslib-1.15.1-3.amzn2023.x86_64                                               
  htslib-devel-1.15.1-3.amzn2023.x86_64                                         
  htslib-tools-1.15.1-3.amzn2023.x86_64                                         
  kernel-headers-6.1.66-91.160.amzn2023.x86_64                                  
  libmpc-1.2.1-2.amzn2023.0.2.x86_64                                            
  libtool-ltdl-2.4.7-1.amzn2023.0.3.x86_64                                      
  libxcrypt-devel-4.4.33-7.amzn2023.x86_64                                      
  make-1:4.3-5.amzn2023.0.2.x86_64                                              
  ncurses-6.2-4.20200222.amzn2023.0.4.x86_64                                    
  ncurses-c++-libs-6.2-4.20200222.amzn2023.0.4.x86_64                           
  ncurses-devel-6.2-4.20200222.amzn2023.0.4.x86_64                              
  perl-Carp-1.50-458.amzn2023.0.2.noarch                                        
  perl-Class-Struct-0.66-477.amzn2023.0.6.noarch                                
  perl-DynaLoader-1.47-477.amzn2023.0.6.x86_64                                  
  perl-Encode-4:3.15-462.amzn2023.0.2.x86_64                                    
  perl-Errno-1.30-477.amzn2023.0.6.x86_64                                       
  perl-Exporter-5.74-459.amzn2023.0.2.noarch                                    
  perl-Fcntl-1.13-477.amzn2023.0.6.x86_64                                       
  perl-File-Basename-2.85-477.amzn2023.0.6.noarch                               
  perl-File-Path-2.18-2.amzn2023.0.2.noarch                                     
  perl-File-Temp-1:0.231.100-2.amzn2023.0.2.noarch                              
  perl-File-stat-1.09-477.amzn2023.0.6.noarch                                   
  perl-FindBin-1.51-477.amzn2023.0.6.noarch                                     
  perl-Getopt-Long-1:2.52-2.amzn2023.0.2.noarch                                 
  perl-Getopt-Std-1.12-477.amzn2023.0.6.noarch                                  
  perl-HTTP-Tiny-0.078-1.amzn2023.0.3.noarch                                    
  perl-IO-1.43-477.amzn2023.0.6.x86_64                                          
  perl-IPC-Open3-1.21-477.amzn2023.0.6.noarch                                   
  perl-MIME-Base64-3.16-2.amzn2023.0.2.x86_64                                   
  perl-POSIX-1.94-477.amzn2023.0.6.x86_64                                       
  perl-PathTools-3.78-459.amzn2023.0.2.x86_64                                   
  perl-Pod-Escapes-1:1.07-458.amzn2023.0.2.noarch                               
  perl-Pod-Perldoc-3.28.01-459.amzn2023.0.3.noarch                              
  perl-Pod-Simple-1:3.42-2.amzn2023.0.2.noarch                                  
  perl-Pod-Usage-4:2.01-2.amzn2023.0.2.noarch                                   
  perl-Scalar-List-Utils-4:1.56-459.amzn2023.0.2.x86_64                         
  perl-SelectSaver-1.02-477.amzn2023.0.6.noarch                                 
  perl-Socket-4:2.032-1.amzn2023.0.2.x86_64                                     
  perl-Storable-1:3.21-458.amzn2023.0.2.x86_64                                  
  perl-Symbol-1.08-477.amzn2023.0.6.noarch                                      
  perl-Term-ANSIColor-5.01-459.amzn2023.0.2.noarch                              
  perl-Term-Cap-1.17-458.amzn2023.0.2.noarch                                    
  perl-Text-ParseWords-3.30-458.amzn2023.0.2.noarch                             
  perl-Text-Tabs+Wrap-2021.0726-1.amzn2023.0.1.noarch                           
  perl-Time-Local-2:1.300-5.amzn2023.0.2.noarch                                 
  perl-constant-1.33-459.amzn2023.0.2.noarch                                    
  perl-if-0.60.800-477.amzn2023.0.6.noarch                                      
  perl-interpreter-4:5.32.1-477.amzn2023.0.6.x86_64                             
  perl-lib-0.65-477.amzn2023.0.6.x86_64                                         
  perl-libs-4:5.32.1-477.amzn2023.0.6.x86_64                                    
  perl-mro-1.23-477.amzn2023.0.6.x86_64                                         
  perl-overload-1.31-477.amzn2023.0.6.noarch                                    
  perl-overloading-0.02-477.amzn2023.0.6.noarch                                 
  perl-parent-1:0.238-458.amzn2023.0.2.noarch                                   
  perl-podlators-1:4.14-458.amzn2023.0.2.noarch                                 
  perl-subs-1.03-477.amzn2023.0.6.noarch                                        
  perl-vars-1.05-477.amzn2023.0.6.noarch                                        
  zlib-devel-1.2.11-33.amzn2023.0.5.x86_64                                      

Complete!
Finish: build setup for samtools-1.15.1-3.amzn2023.src.rpm
Start: rpmbuild samtools-1.15.1-3.amzn2023.src.rpm
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1689984000
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.nOj0W5
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf samtools-1.15.1
+ /usr/bin/bzip2 -dc /builddir/build/SOURCES/samtools-1.15.1.tar.bz2
+ /usr/bin/tar -xof -
+ 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.E7T4ow
+ umask 022
+ cd /builddir/build/BUILD
+ CFLAGS='-O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CFLAGS
+ CXXFLAGS='-O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules'
+ export FFLAGS
+ FCFLAGS='-O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules'
+ export FCFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-3.amzn2023.x86_64.ld'
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ '[' -f /usr/lib/rpm/generate-rpm-note.sh ']'
+ /usr/lib/rpm/generate-rpm-note.sh samtools 1.15.1-3.amzn2023 x86_64
+ cd samtools-1.15.1
+ CFLAGS='-O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CFLAGS
+ CXXFLAGS='-O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules'
+ export FFLAGS
+ FCFLAGS='-O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules'
+ export FCFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-3.amzn2023.x86_64.ld'
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ '[' '-flto=auto -ffat-lto-objectsx' '!=' x ']'
++ find . -type f -name configure -print
+ for file in $(find . -type f -name configure -print)
+ /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\) = /__attribute__ ((used)) char (*f) () = /g' ./htslib-1.15.1/configure
+ diff -u ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure
+ mv ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure
+ /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\);/__attribute__ ((used)) char (*f) ();/g' ./htslib-1.15.1/configure
+ diff -u ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure
+ mv ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure
+ /usr/bin/sed -r --in-place=.backup 's/^char \$2 \(\);/__attribute__ ((used)) char \$2 ();/g' ./htslib-1.15.1/configure
+ diff -u ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure
--- ./htslib-1.15.1/configure.backup	2022-04-07 15:42:52.000000000 +0000
+++ ./htslib-1.15.1/configure	2024-01-07 01:38:01.801322611 +0000
@@ -1697,7 +1697,7 @@
 #ifdef __cplusplus
 extern "C"
 #endif
-char $2 ();
+__attribute__ ((used)) char $2 ();
 /* The GNU C library defines this for functions which it implements
     to always fail with ENOSYS.  Some functions are actually named
     something starting with __ and the normal name is an alias.  */
+ /usr/bin/sed --in-place=.backup '1{$!N;$!N};$!N;s/int x = 1;\nint y = 0;\nint z;\nint nan;/volatile int x = 1; volatile int y = 0; volatile int z, nan;/;P;D' ./htslib-1.15.1/configure
+ diff -u ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure
+ mv ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure
+ /usr/bin/sed --in-place=.backup 's#^lt_cv_sys_global_symbol_to_cdecl=.*#lt_cv_sys_global_symbol_to_cdecl="sed -n -e '\''s/^T .* \\(.*\\)$/extern int \\1();/p'\'' -e '\''s/^$symcode* .* \\(.*\\)$/extern char \\1;/p'\''"#' ./htslib-1.15.1/configure
+ diff -u ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure
+ mv ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure
+ for file in $(find . -type f -name configure -print)
+ /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\) = /__attribute__ ((used)) char (*f) () = /g' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\);/__attribute__ ((used)) char (*f) ();/g' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ /usr/bin/sed -r --in-place=.backup 's/^char \$2 \(\);/__attribute__ ((used)) char \$2 ();/g' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ /usr/bin/sed --in-place=.backup '1{$!N;$!N};$!N;s/int x = 1;\nint y = 0;\nint z;\nint nan;/volatile int x = 1; volatile int y = 0; volatile int z, nan;/;P;D' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ /usr/bin/sed --in-place=.backup 's#^lt_cv_sys_global_symbol_to_cdecl=.*#lt_cv_sys_global_symbol_to_cdecl="sed -n -e '\''s/^T .* \\(.*\\)$/extern int \\1();/p'\'' -e '\''s/^$symcode* .* \\(.*\\)$/extern char \\1;/p'\''"#' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ '[' 1 = 1 ']'
+++ dirname ./configure
++ find . -name config.guess -o -name config.sub
+ '[' 1 = 1 ']'
+ '[' x '!=' 'x-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' ']'
++ find . -name ltmain.sh
+ ./configure --build=x86_64-amazon-linux-gnu --host=x86_64-amazon-linux-gnu --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/libexec --localstatedir=/var --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info 'CFLAGS=-O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' 'LDFLAGS=-Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-3.amzn2023.x86_64.ld' --prefix=/usr --with-htslib=system
checking for gawk... gawk
checking for x86_64-amazon-linux-gnu-gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for C compiler warning flags... -Wall
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for htslib/sam.h... yes
checking for hts_version in -lhts... yes
checking for NcursesW wide-character library... yes
checking for working ncursesw/curses.h... yes
checking for library containing cbreak... none required
checking for zlib.h... yes
checking for inflate in -lz... yes
checking for library containing regcomp... none required
configure: creating ./config.status
config.status: creating config.mk
config.status: creating config.h
+ /usr/bin/make -O -j2 V=1 VERBOSE=1
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o bam_aux.o bam_aux.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o bam.o bam.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o bam_index.o bam_index.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o bam_plcmd.o bam_plcmd.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o sam_view.o sam_view.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o bam_fastq.o bam_fastq.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o bam_cat.o bam_cat.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o bam_plbuf.o bam_plbuf.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o bam_md.o bam_md.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o bam_reheader.o bam_reheader.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o bam_rmdup.o bam_rmdup.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o bam_rmdupse.o bam_rmdupse.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o bam_mate.o bam_mate.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o bam_stat.o bam_stat.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o bam_color.o bam_color.c
echo '#define SAMTOOLS_VERSION "1.15.1"' > version.h
echo '#define SAMTOOLS_CC "gcc"' >> version.h
echo '#define SAMTOOLS_CPPFLAGS ""' >> version.h
echo '#define SAMTOOLS_CFLAGS "-O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection"' >> version.h
echo '#define SAMTOOLS_LDFLAGS "-Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-3.amzn2023.x86_64.ld"' >> version.h
echo '#define SAMTOOLS_HTSDIR ""' >> version.h
echo '#define SAMTOOLS_LIBS ""' >> version.h
echo '#define SAMTOOLS_CURSES_LIB "-lncursesw"' >> version.h
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o bam2bcf.o bam2bcf.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o sample.o sample.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o cut_target.o cut_target.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o bam_sort.o bam_sort.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o phase.o phase.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o coverage.o coverage.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o bam2depth.o bam2depth.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o bedcov.o bedcov.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o padding.o padding.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o faidx.o faidx.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o dict.o dict.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o bamshuf.o bamshuf.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o stats_isize.o stats_isize.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o bam_flags.o bam_flags.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o bam_split.o bam_split.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o bam_tview.o bam_tview.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o stats.o stats.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o bam_tview_curses.o bam_tview_curses.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o bam_tview_html.o bam_tview_html.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o bam_lpileup.o bam_lpileup.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o bam_quickcheck.o bam_quickcheck.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o bam_addrprg.o bam_addrprg.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o tmp_file.o tmp_file.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o bam_ampliconclip.o bam_ampliconclip.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o bam_markdup.o bam_markdup.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o bam_import.o bam_import.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o bam_samples.o bam_samples.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o amplicon_stats.o amplicon_stats.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o consensus_pileup.o consensus_pileup.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o bam_consensus.o bam_consensus.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o sam_opts.o sam_opts.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o sam_utils.o sam_utils.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o bedidx.o bedidx.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o misc/ace2sam.o misc/ace2sam.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -DMAQ_LONGREADS -I.  -I./lz4  -c -o misc/maq2sam-long.o misc/maq2sam.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o misc/maq2sam-short.o misc/maq2sam.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o misc/md5fa.o misc/md5fa.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o misc/md5sum-lite.o misc/md5sum-lite.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o misc/wgsim.o misc/wgsim.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o lz4/lz4.o lz4/lz4.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o test/test.o test/test.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o test/split/test_count_rg.o test/split/test_count_rg.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o test/split/test_parse_args.o test/split/test_parse_args.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o test/vcf-miniview.o test/vcf-miniview.c
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o bamtk.o bamtk.c
ar -rcs libst.a sam_opts.o sam_utils.o bedidx.o
gcc  -L./lz4 -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-3.amzn2023.x86_64.ld -o misc/ace2sam misc/ace2sam.o -lhts -lz 
gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c
gcc -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-3.amzn2023.x86_64.ld -o misc/maq2sam-long misc/maq2sam-long.o -lz 
gcc -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-3.amzn2023.x86_64.ld -o misc/maq2sam-short misc/maq2sam-short.o -lz 
gcc  -L./lz4 -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-3.amzn2023.x86_64.ld -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz 
gcc  -L./lz4 -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-3.amzn2023.x86_64.ld -o misc/md5fa misc/md5fa.o -lhts -lz 
gcc  -L./lz4 -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-3.amzn2023.x86_64.ld -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o libst.a -lhts -lz  -lpthread
gcc  -L./lz4 -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-3.amzn2023.x86_64.ld -o misc/wgsim misc/wgsim.o -lm -lhts -lz 
gcc  -L./lz4 -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-3.amzn2023.x86_64.ld -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o test/test.o libst.a -lhts -lz  -lpthread
gcc  -L./lz4 -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-3.amzn2023.x86_64.ld -o test/split/test_count_rg test/split/test_count_rg.o test/test.o libst.a -lhts -lz  -lpthread
gcc  -L./lz4 -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-3.amzn2023.x86_64.ld -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o libst.a -lhts -lz  -lpthread
gcc  -L./lz4 -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-3.amzn2023.x86_64.ld -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o libst.a -lhts -lz  -lpthread
gcc  -L./lz4 -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-3.amzn2023.x86_64.ld -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o test/test.o libst.a -lhts -lz  -lpthread
gcc  -L./lz4 -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-3.amzn2023.x86_64.ld -o test/vcf-miniview test/vcf-miniview.o -lhts -lz  -lpthread
gcc  -L./lz4 -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-3.amzn2023.x86_64.ld -o test/split/test_parse_args test/split/test_parse_args.o test/test.o libst.a -lhts -lz  -lpthread
gcc  -L./lz4 -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-3.amzn2023.x86_64.ld -o samtools bam.o bam_aux.o bam_index.o bam_plcmd.o sam_view.o bam_fastq.o bam_cat.o bam_md.o bam_plbuf.o bam_reheader.o bam_sort.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o sample.o cut_target.o phase.o bam2depth.o coverage.o padding.o bedcov.o bamshuf.o faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o bam_quickcheck.o bam_addrprg.o bam_markdup.o tmp_file.o bam_ampliconclip.o amplicon_stats.o bam_import.o bam_samples.o bam_consensus.o consensus_pileup.o ./lz4/lz4.o libst.a -lhts -lncursesw -lm -lz  -lpthread
lto-wrapper: warning: using serial compilation of 8 LTRANS jobs
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.cTTCpN
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64 '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64
++ dirname /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64
+ CFLAGS='-O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CFLAGS
+ CXXFLAGS='-O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules'
+ export FFLAGS
+ FCFLAGS='-O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules'
+ export FCFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-3.amzn2023.x86_64.ld'
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd samtools-1.15.1
+ /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64 'INSTALL=/usr/bin/install -p'
mkdir -p -m 755 /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/share/man/man1
/usr/bin/install -p samtools /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin
/usr/bin/install -p misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin
/usr/bin/install -p misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl misc/fasta-sanitize.pl misc/interpolate_sam.pl misc/novo2sam.pl misc/plot-ampliconstats misc/plot-bamstats misc/psl2sam.pl misc/sam2vcf.pl misc/samtools.pl misc/seq_cache_populate.pl misc/soap2sam.pl misc/wgsim_eval.pl misc/zoom2sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin
/usr/bin/install -p -m 644 doc/samtools*.1 misc/wgsim.1 /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/share/man/man1
++ grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/ace2sam /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/blast2sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/bowtie2sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/export2sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/fasta-sanitize.pl /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/interpolate_sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/maq2sam-long /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/maq2sam-short /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/md5fa /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/md5sum-lite /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/novo2sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/plot-ampliconstats /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/plot-bamstats /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/psl2sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/sam2vcf.pl /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/samtools /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/samtools.pl /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/seq_cache_populate.pl /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/soap2sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/wgsim /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/wgsim_eval.pl /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/zoom2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/blast2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/bowtie2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/export2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/fasta-sanitize.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/interpolate_sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/novo2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/plot-ampliconstats
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/plot-bamstats
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/psl2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/sam2vcf.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/samtools.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/seq_cache_populate.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/soap2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/wgsim_eval.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/zoom2sam.pl
+ /usr/lib/rpm/find-debuginfo.sh -j2 --strict-build-id -m -i --build-id-seed 1.15.1-3.amzn2023 --unique-debug-suffix -1.15.1-3.amzn2023.x86_64 --unique-debug-src-base samtools-1.15.1-3.amzn2023.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/samtools-1.15.1
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/maq2sam-long
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/ace2sam
extracting debug info from /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/maq2sam-long
extracting debug info from /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/ace2sam
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/maq2sam-short
extracting debug info from /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/maq2sam-short
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/md5fa
extracting debug info from /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/md5fa
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/md5sum-lite
extracting debug info from /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/md5sum-lite
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/samtools
extracting debug info from /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/samtools
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/wgsim
extracting debug info from /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/bin/wgsim
original debug info size: 2036kB, size after compression: 1832kB
/usr/lib/rpm/sepdebugcrcfix: Updated 7 CRC32s, 0 CRC32s did match.
2442 blocks
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-ldconfig
+ /usr/lib/rpm/brp-compress
+ /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip
+ /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip
+ /usr/lib/rpm/check-rpaths
+ /usr/lib/rpm/redhat/brp-mangle-shebangs
+ /usr/lib/rpm/brp-python-bytecompile '' 0 1
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.mskPPB
+ umask 022
+ cd /builddir/build/BUILD
+ CFLAGS='-O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CFLAGS
+ CXXFLAGS='-O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules'
+ export FFLAGS
+ FCFLAGS='-O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules'
+ export FCFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/samtools-1.15.1/.package_note-samtools-1.15.1-3.amzn2023.x86_64.ld'
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ '[' -f /usr/lib/rpm/generate-rpm-note.sh ']'
+ /usr/lib/rpm/generate-rpm-note.sh samtools 1.15.1-3.amzn2023 x86_64
+ cd samtools-1.15.1
+ ldd samtools
+ grep -E '/lib(64)?/libhts\.so\.'
	libhts.so.3 => /lib64/libhts.so.3 (0x00007ffa81746000)
+ 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/kPWEewzuD6/bgzip.dat.gz
.. ok

bgzip -c -b 979200 -s 6 /tmp/kPWEewzuD6/bgzip.dat.gz
.. ok

bgzip -c -b 652804 -s 6 /tmp/kPWEewzuD6/bgzip.dat.gz
.. ok

/builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/kPWEewzuD6/faidx.fa 3:11-13 | grep -v '^>'
.. ok

/builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/kPWEewzuD6/faidx.fa.gz 3:11-13 | grep -v '^>'
.. ok

/builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/kPWEewzuD6/faidx.fa 2:998-1003 | grep -v '^>'
.. ok

/builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/kPWEewzuD6/faidx.fa.gz 2:998-1003 | grep -v '^>'
.. ok

/builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/kPWEewzuD6/faidx.fa 1:100-104 | grep -v '^>'
.. ok

/builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/kPWEewzuD6/faidx.fa.gz 1:100-104 | grep -v '^>'
.. ok

/builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/kPWEewzuD6/faidx.fa 1:99998-100007 | grep -v '^>'
.. ok

/builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/kPWEewzuD6/faidx.fa.gz 1:99998-100007 | grep -v '^>'
.. ok

/builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/kPWEewzuD6/fqidx.fq 3:11-13
.. ok

.. ok

/builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/kPWEewzuD6/fqidx.fq.gz 3:11-13
.. ok

.. ok

/builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/kPWEewzuD6/fqidx.fq 2:998-1003
.. ok

.. ok

/builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/kPWEewzuD6/fqidx.fq.gz 2:998-1003
.. ok

.. ok

/builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/kPWEewzuD6/fqidx.fq 1:100-104
.. ok

.. ok

/builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/kPWEewzuD6/fqidx.fq.gz 1:100-104
.. ok

.. ok

/builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/kPWEewzuD6/fqidx.fq 1:99998-100007
.. ok

.. ok

/builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/kPWEewzuD6/fqidx.fq.gz 1:99998-100007
.. ok

.. ok

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

test_dict:
	/builddir/build/BUILD/samtools-1.15.1/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/kPWEewzuD6/dict.fa.gz
.. ok

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

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

test_index:
	/builddir/build/BUILD/samtools-1.15.1/samtools view /tmp/kPWEewzuD6/large_chrom.bam ref2
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.15.1/samtools view /tmp/kPWEewzuD6/large_chrom.bam ref2:1-541556283
.. ok

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

test_index:
	/builddir/build/BUILD/samtools-1.15.1/samtools view -X /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_b.bam /tmp/kPWEewzuD6/test_input_1_b.bam.bai ref2
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.15.1/samtools merge -O sam - -X -cp -R ref2 /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_b.bam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam.bai /tmp/kPWEewzuD6/test_input_1_b.bam.bai
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.15.1/samtools index -c /builddir/build/BUILD/samtools-1.15.1/test/dat/auto_indexed.tmp.bam /tmp/kPWEewzuD6/auto_indexed.csi && cat /tmp/kPWEewzuD6/auto_indexed.csi
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.15.1/samtools index /builddir/build/BUILD/samtools-1.15.1/test/dat/auto_indexed.tmp.cram /tmp/kPWEewzuD6/auto_indexed.crai && cat /tmp/kPWEewzuD6/auto_indexed.crai
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.15.1/samtools index -c /builddir/build/BUILD/samtools-1.15.1/test/dat/auto_indexed.tmp.sam /tmp/kPWEewzuD6/auto_indexed.csi && cat /tmp/kPWEewzuD6/auto_indexed.csi
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.15.1/samtools view -@ 2 /tmp/kPWEewzuD6/large_chrom.bam ref2
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.15.1/samtools view -@ 2 /tmp/kPWEewzuD6/large_chrom.bam ref2:1-541556283
.. ok

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

test_index:
	/builddir/build/BUILD/samtools-1.15.1/samtools view -@ 2 -X /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_b.bam /tmp/kPWEewzuD6/test_input_1_b.bam.bai ref2
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.15.1/samtools merge -@ 2 -O sam - -X -cp -R ref2 /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_b.bam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam.bai /tmp/kPWEewzuD6/test_input_1_b.bam.bai
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.15.1/samtools index -@ 2 -c /builddir/build/BUILD/samtools-1.15.1/test/dat/auto_indexed.tmp.bam /tmp/kPWEewzuD6/auto_indexed.csi && cat /tmp/kPWEewzuD6/auto_indexed.csi
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.15.1/samtools index -@ 2 /builddir/build/BUILD/samtools-1.15.1/test/dat/auto_indexed.tmp.cram /tmp/kPWEewzuD6/auto_indexed.crai && cat /tmp/kPWEewzuD6/auto_indexed.crai
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.15.1/samtools index -@ 2 -c /builddir/build/BUILD/samtools-1.15.1/test/dat/auto_indexed.tmp.sam /tmp/kPWEewzuD6/auto_indexed.csi && cat /tmp/kPWEewzuD6/auto_indexed.csi
.. ok

test_mpileup:
	/builddir/build/BUILD/samtools-1.15.1/samtools mpileup -b /tmp/kPWEewzuD6/mpileup.bam.list -f /tmp/kPWEewzuD6/mpileup.ref.fa.gz -r17:100-150
.. ok

test_mpileup:
	/builddir/build/BUILD/samtools-1.15.1/samtools mpileup -b /tmp/kPWEewzuD6/mpileup.cram.list -f /tmp/kPWEewzuD6/mpileup.ref.fa.gz -r17:100-150
.. ok

test_mpileup:
	/builddir/build/BUILD/samtools-1.15.1/samtools mpileup -b /tmp/kPWEewzuD6/mpileup.bam.urllist -f /tmp/kPWEewzuD6/mpileup.ref.fa.gz -r17:100-150
.. ok

test_mpileup:
	/builddir/build/BUILD/samtools-1.15.1/samtools mpileup -b /tmp/kPWEewzuD6/mpileup.cram.urllist -f /tmp/kPWEewzuD6/mpileup.ref.fa.gz -r17:100-150
.. ok

test_mpileup:
	/builddir/build/BUILD/samtools-1.15.1/samtools mpileup -B --ff 0x14 -f /tmp/kPWEewzuD6/mpileup.ref.fa.gz -r17:1050-1060 /tmp/kPWEewzuD6/mpileup.1.bam | grep -v mpileup
.. ok

test_mpileup:
	/builddir/build/BUILD/samtools-1.15.1/samtools mpileup -B --ff 0x14 -f /tmp/kPWEewzuD6/mpileup.ref.fa.gz -r17:1050-1060 /tmp/kPWEewzuD6/mpileup.1.cram | grep -v mpileup
.. ok

test_mpileup:
	/builddir/build/BUILD/samtools-1.15.1/samtools mpileup /builddir/build/BUILD/samtools-1.15.1/test/mpileup/overlap.bam | grep 128814202
test/test.pl: no IO::Pty module or can't open pty; skipping usage tests
.. ok

test_usage:
	samtools
test_view:
	Generating test data file .................. done
	1: SAM -> BAM -> SAM                                        .. ok

	2: SAM -> uncompressed BAM                                  .. ok

	3: uncompressed BAM -> SAM and compare                      .. ok

	4: SAM -> fast compressed BAM                               .. ok

	5: fast compressed BAM -> SAM and compare                   .. ok

	6: SAM -> CRAM -> SAM (UR header tags)                      .. ok

	7: SAM -> CRAM -> SAM (M5 header tags)                      .. ok

	8: BAM -> CRAM with UR -> SAM                               .. ok

	9: SAM -> BAM (M5 header tags)                              .. ok

	10: SAM -> BAM -> CRAM -> SAM (M5 header tags)              .. ok

	11: CRAM -> BAM with UR                                     .. ok

	12: CRAM -> BAM with M5                                     .. ok

	13: SAM -> SAM via stdout                                   .. ok

	14: SAM -> BAM via stdout                                   .. ok

	15: SAM -> CRAM via stdout                                  .. ok

	16: SAM from stdin -> SAM                                   .. ok

	17: BAM from stdin -> SAM                                   .. ok

	18: CRAM from stdin -> SAM                                  .. ok

	19: samtools view -H (SAM input)                            .. ok

	20: samtools view -H (BAM input)                            .. ok

	21: samtools view -H (CRAM input)                           .. ok

	22: No headers (SAM input)                                  .. ok

	23: No headers (BAM input)                                  .. ok

	24: No headers (CRAM input)                                 .. ok

	25: Filter -f 128 (SAM input)                               .. ok

	26: Count -f 128 (SAM input)                                .. ok

	27: Filter -f 128 (BAM input)                               .. ok

	28: Count -f 128 (BAM input)                                .. ok

	29: Filter -f 128 (CRAM input)                              .. ok

	30: Count -f 128 (CRAM input)                               .. ok

	31: Filter -F 128 (SAM input)                               .. ok

	32: Count -F 128 (SAM input)                                .. ok

	33: Filter -F 128 (BAM input)                               .. ok

	34: Count -F 128 (BAM input)                                .. ok

	35: Filter -F 128 (CRAM input)                              .. ok

	36: Count -F 128 (CRAM input)                               .. ok

	37: Filter -F 128 -f 2 (SAM input)                          .. ok

	38: Count -F 128 -f 2 (SAM input)                           .. ok

	39: Filter -F 128 -f 2 (BAM input)                          .. ok

	40: Count -F 128 -f 2 (BAM input)                           .. ok

	41: Filter -F 128 -f 2 (CRAM input)                         .. ok

	42: Count -F 128 -f 2 (CRAM input)                          .. ok

	43: Filter -r grp2 (SAM input)                              .. ok

	44: Count -r grp2 (SAM input)                               .. ok

	45: Filter -r grp2 (BAM input)                              .. ok

	46: Count -r grp2 (BAM input)                               .. ok

	47: Filter -r grp2 (CRAM input)                             .. ok

	48: Count -r grp2 (CRAM input)                              .. ok

	49: Filter -R /tmp/kPWEewzuD6/view.001.fogn (SAM input)     .. ok

	50: Count -R /tmp/kPWEewzuD6/view.001.fogn (SAM input)      .. ok

	51: Filter -R /tmp/kPWEewzuD6/view.001.fogn (BAM input)     .. ok

	52: Count -R /tmp/kPWEewzuD6/view.001.fogn (BAM input)      .. ok

	53: Filter -R /tmp/kPWEewzuD6/view.001.fogn (CRAM input)    .. ok

	54: Count -R /tmp/kPWEewzuD6/view.001.fogn (CRAM input)     .. ok

	55: Filter -R /tmp/kPWEewzuD6/view.001.fogn -r grp2 (SAM input).. ok

	56: Count -R /tmp/kPWEewzuD6/view.001.fogn -r grp2 (SAM input).. ok

	57: Filter -R /tmp/kPWEewzuD6/view.001.fogn -r grp2 (BAM input).. ok

	58: Count -R /tmp/kPWEewzuD6/view.001.fogn -r grp2 (BAM input).. ok

	59: Filter -R /tmp/kPWEewzuD6/view.001.fogn -r grp2 (CRAM input).. ok

	60: Count -R /tmp/kPWEewzuD6/view.001.fogn -r grp2 (CRAM input).. ok

	61: Filter -r grp2 -R /tmp/kPWEewzuD6/view.001.fogn (SAM input).. ok

	62: Count -r grp2 -R /tmp/kPWEewzuD6/view.001.fogn (SAM input).. ok

	63: Filter -r grp2 -R /tmp/kPWEewzuD6/view.001.fogn (BAM input).. ok

	64: Count -r grp2 -R /tmp/kPWEewzuD6/view.001.fogn (BAM input).. ok

	65: Filter -r grp2 -R /tmp/kPWEewzuD6/view.001.fogn (CRAM input).. ok

	66: Count -r grp2 -R /tmp/kPWEewzuD6/view.001.fogn (CRAM input).. ok

	67: Filter -N /tmp/kPWEewzuD6/view.001.forn (SAM input)     .. ok

	68: Count -N /tmp/kPWEewzuD6/view.001.forn (SAM input)      .. ok

	69: Filter -N /tmp/kPWEewzuD6/view.001.forn (BAM input)     .. ok

	70: Count -N /tmp/kPWEewzuD6/view.001.forn (BAM input)      .. ok

	71: Filter -N /tmp/kPWEewzuD6/view.001.forn (CRAM input)    .. ok

	72: Count -N /tmp/kPWEewzuD6/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/kPWEewzuD6/view.001.fobc (SAM input)  .. ok

	86: Count -D BC:/tmp/kPWEewzuD6/view.001.fobc (SAM input)   .. ok

	87: Filter -D BC:/tmp/kPWEewzuD6/view.001.fobc (BAM input)  .. ok

	88: Count -D BC:/tmp/kPWEewzuD6/view.001.fobc (BAM input)   .. ok

	89: Filter -D BC:/tmp/kPWEewzuD6/view.001.fobc (CRAM input) .. ok

	90: Count -D BC:/tmp/kPWEewzuD6/view.001.fobc (CRAM input)  .. ok

	91: Filter -D BC:/tmp/kPWEewzuD6/view.001.fobc -d BC:TGCA (SAM input).. ok

	92: Count -D BC:/tmp/kPWEewzuD6/view.001.fobc -d BC:TGCA (SAM input).. ok

	93: Filter -D BC:/tmp/kPWEewzuD6/view.001.fobc -d BC:TGCA (BAM input).. ok

	94: Count -D BC:/tmp/kPWEewzuD6/view.001.fobc -d BC:TGCA (BAM input).. ok

	95: Filter -D BC:/tmp/kPWEewzuD6/view.001.fobc -d BC:TGCA (CRAM input).. ok

	96: Count -D BC:/tmp/kPWEewzuD6/view.001.fobc -d BC:TGCA (CRAM input).. ok

	97: Filter -d BC:TGCA -D BC:/tmp/kPWEewzuD6/view.001.fobc (SAM input).. ok

	98: Count -d BC:TGCA -D BC:/tmp/kPWEewzuD6/view.001.fobc (SAM input).. ok

	99: Filter -d BC:TGCA -D BC:/tmp/kPWEewzuD6/view.001.fobc (BAM input).. ok

	100: Count -d BC:TGCA -D BC:/tmp/kPWEewzuD6/view.001.fobc (BAM input).. ok

	101: Filter -d BC:TGCA -D BC:/tmp/kPWEewzuD6/view.001.fobc (CRAM input).. ok

	102: Count -d BC:TGCA -D BC:/tmp/kPWEewzuD6/view.001.fobc (CRAM input).. ok

	103: Filter -D RG:/tmp/kPWEewzuD6/view.001.fogn (SAM input) .. ok

	104: Count -D RG:/tmp/kPWEewzuD6/view.001.fogn (SAM input)  .. ok

	105: Filter -D RG:/tmp/kPWEewzuD6/view.001.fogn (BAM input) .. ok

	106: Count -D RG:/tmp/kPWEewzuD6/view.001.fogn (BAM input)  .. ok

	107: Filter -D RG:/tmp/kPWEewzuD6/view.001.fogn (CRAM input).. ok

	108: Count -D RG:/tmp/kPWEewzuD6/view.001.fogn (CRAM input) .. ok

	109: Filter -d NE:TGCA (SAM input)                          .. ok

	110: Count -d NE:TGCA (SAM input)                           .. ok

	111: Filter -d NE:TGCA (BAM input)                          .. ok

	112: Count -d NE:TGCA (BAM input)                           .. ok

	113: Filter -d NE:TGCA (CRAM input)                         .. ok

	114: Count -d NE:TGCA (CRAM input)                          .. ok

	115: Filter -d TGCA (SAM input)                             samtools view: Invalid "tag:value" option: "TGCA"
	Failed command:
	/builddir/build/BUILD/samtools-1.15.1/samtools view -o /tmp/kPWEewzuD6/view.test115.sam -h -d TGCA /tmp/kPWEewzuD6/view.001.sam --no-PG


.. expected failure

	116: Count -d TGCA (SAM input)                              samtools view: Invalid "tag:value" option: "TGCA"
	Failed command:
	/builddir/build/BUILD/samtools-1.15.1/samtools view -c -d TGCA /tmp/kPWEewzuD6/view.001.sam --no-PG


.. expected failure

	117: Filter -d TGCA (BAM input)                             samtools view: Invalid "tag:value" option: "TGCA"
	Failed command:
	/builddir/build/BUILD/samtools-1.15.1/samtools view -o /tmp/kPWEewzuD6/view.test117.sam -h -d TGCA /tmp/kPWEewzuD6/view.test001.bam --no-PG


.. expected failure

	118: Count -d TGCA (BAM input)                              samtools view: Invalid "tag:value" option: "TGCA"
	Failed command:
	/builddir/build/BUILD/samtools-1.15.1/samtools view -c -d TGCA /tmp/kPWEewzuD6/view.test001.bam --no-PG


.. expected failure

	119: Filter -d TGCA (CRAM input)                            samtools view: Invalid "tag:value" option: "TGCA"
	Failed command:
	/builddir/build/BUILD/samtools-1.15.1/samtools view -o /tmp/kPWEewzuD6/view.test119.sam -h -d TGCA /tmp/kPWEewzuD6/view.test006.cram --no-PG


.. expected failure

	120: Count -d TGCA (CRAM input)                             samtools view: Invalid "tag:value" option: "TGCA"
	Failed command:
	/builddir/build/BUILD/samtools-1.15.1/samtools view -c -d TGCA /tmp/kPWEewzuD6/view.test006.cram --no-PG


.. expected failure

	121: Filter -D BClong:/tmp/kPWEewzuD6/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/kPWEewzuD6/view.001.fobc"
	Failed command:
	/builddir/build/BUILD/samtools-1.15.1/samtools view -o /tmp/kPWEewzuD6/view.test121.sam -h -D BClong:/tmp/kPWEewzuD6/view.001.fobc /tmp/kPWEewzuD6/view.001.sam --no-PG


.. expected failure

	122: Count -D BClong:/tmp/kPWEewzuD6/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/kPWEewzuD6/view.001.fobc"
	Failed command:
	/builddir/build/BUILD/samtools-1.15.1/samtools view -c -D BClong:/tmp/kPWEewzuD6/view.001.fobc /tmp/kPWEewzuD6/view.001.sam --no-PG


.. expected failure

	123: Filter -D BClong:/tmp/kPWEewzuD6/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/kPWEewzuD6/view.001.fobc"
	Failed command:
	/builddir/build/BUILD/samtools-1.15.1/samtools view -o /tmp/kPWEewzuD6/view.test123.sam -h -D BClong:/tmp/kPWEewzuD6/view.001.fobc /tmp/kPWEewzuD6/view.test001.bam --no-PG


.. expected failure

	124: Count -D BClong:/tmp/kPWEewzuD6/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/kPWEewzuD6/view.001.fobc"
	Failed command:
	/builddir/build/BUILD/samtools-1.15.1/samtools view -c -D BClong:/tmp/kPWEewzuD6/view.001.fobc /tmp/kPWEewzuD6/view.test001.bam --no-PG


.. expected failure

	125: Filter -D BClong:/tmp/kPWEewzuD6/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/kPWEewzuD6/view.001.fobc"
	Failed command:
	/builddir/build/BUILD/samtools-1.15.1/samtools view -o /tmp/kPWEewzuD6/view.test125.sam -h -D BClong:/tmp/kPWEewzuD6/view.001.fobc /tmp/kPWEewzuD6/view.test006.cram --no-PG


.. expected failure

	126: Count -D BClong:/tmp/kPWEewzuD6/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/kPWEewzuD6/view.001.fobc"
	Failed command:
	/builddir/build/BUILD/samtools-1.15.1/samtools view -c -D BClong:/tmp/kPWEewzuD6/view.001.fobc /tmp/kPWEewzuD6/view.test006.cram --no-PG


.. expected failure

	127: Filter -d BC:ACGT -d RG:grp2 (SAM input)               samtools view: Different tag "BC" was specified before: "RG:grp2"
	Failed command:
	/builddir/build/BUILD/samtools-1.15.1/samtools view -o /tmp/kPWEewzuD6/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/kPWEewzuD6/view.001.sam --no-PG


.. expected failure

	128: Count -d BC:ACGT -d RG:grp2 (SAM input)                samtools view: Different tag "BC" was specified before: "RG:grp2"
	Failed command:
	/builddir/build/BUILD/samtools-1.15.1/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/kPWEewzuD6/view.001.sam --no-PG


.. expected failure

	129: Filter -d BC:ACGT -d RG:grp2 (BAM input)               samtools view: Different tag "BC" was specified before: "RG:grp2"
	Failed command:
	/builddir/build/BUILD/samtools-1.15.1/samtools view -o /tmp/kPWEewzuD6/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/kPWEewzuD6/view.test001.bam --no-PG


.. expected failure

	130: Count -d BC:ACGT -d RG:grp2 (BAM input)                samtools view: Different tag "BC" was specified before: "RG:grp2"
	Failed command:
	/builddir/build/BUILD/samtools-1.15.1/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/kPWEewzuD6/view.test001.bam --no-PG


.. expected failure

	131: Filter -d BC:ACGT -d RG:grp2 (CRAM input)              samtools view: Different tag "BC" was specified before: "RG:grp2"
	Failed command:
	/builddir/build/BUILD/samtools-1.15.1/samtools view -o /tmp/kPWEewzuD6/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/kPWEewzuD6/view.test006.cram --no-PG


.. expected failure

	132: Count -d BC:ACGT -d RG:grp2 (CRAM input)               samtools view: Different tag "BC" was specified before: "RG:grp2"
	Failed command:
	/builddir/build/BUILD/samtools-1.15.1/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/kPWEewzuD6/view.test006.cram --no-PG


.. expected failure

	133: Filter -d NM:13 (SAM input)                            .. ok

	134: Count -d NM:13 (SAM input)                             .. ok

	135: Filter -d NM:13 (BAM input)                            .. ok

	136: Count -d NM:13 (BAM input)                             .. ok

	137: Filter -d NM:13 (CRAM input)                           .. ok

	138: Count -d NM:13 (CRAM input)                            .. ok

	139: Filter -d ab:z (SAM input)                             .. ok

	140: Count -d ab:z (SAM input)                              .. ok

	141: Filter -d ab:z (BAM input)                             .. ok

	142: Count -d ab:z (BAM input)                              .. ok

	143: Filter -d ab:z (CRAM input)                            .. ok

	144: Count -d ab:z (CRAM input)                             .. ok

	145: Filter -l Library 2 (SAM input)                        .. ok

	146: Count -l Library 2 (SAM input)                         .. ok

	147: Filter -l Library 2 (BAM input)                        .. ok

	148: Count -l Library 2 (BAM input)                         .. ok

	149: Filter -l Library 2 (CRAM input)                       .. ok

	150: Count -l Library 2 (CRAM input)                        .. ok

	151: Filter -l Library 3 (SAM input)                        .. ok

	152: Count -l Library 3 (SAM input)                         .. ok

	153: Filter -l Library 3 (BAM input)                        .. ok

	154: Count -l Library 3 (BAM input)                         .. ok

	155: Filter -l Library 3 (CRAM input)                       .. ok

	156: Count -l Library 3 (CRAM input)                        .. ok

	157: Filter -q 50 (SAM input)                               .. ok

	158: Count -q 50 (SAM input)                                .. ok

	159: Filter -q 50 (BAM input)                               .. ok

	160: Count -q 50 (BAM input)                                .. ok

	161: Filter -q 50 (CRAM input)                              .. ok

	162: Count -q 50 (CRAM input)                               .. ok

	163: Filter -q 99 (SAM input)                               .. ok

	164: Count -q 99 (SAM input)                                .. ok

	165: Filter -q 99 (BAM input)                               .. ok

	166: Count -q 99 (BAM input)                                .. ok

	167: Filter -q 99 (CRAM input)                              .. ok

	168: Count -q 99 (CRAM input)                               .. ok

	169: Filter -q 100 (SAM input)                              .. ok

	170: Count -q 100 (SAM input)                               .. ok

	171: Filter -q 100 (BAM input)                              .. ok

	172: Count -q 100 (BAM input)                               .. ok

	173: Filter -q 100 (CRAM input)                             .. ok

	174: Count -q 100 (CRAM input)                              .. ok

	175: Filter -x fa (SAM input)                               .. ok

	176: Count -x fa (SAM input)                                .. ok

	177: Filter -x fa (BAM input)                               .. ok

	178: Count -x fa (BAM input)                                .. ok

	179: Filter -x fa (CRAM input)                              .. ok

	180: Count -x fa (CRAM input)                               .. ok

	181: Filter -x fa -x ha (SAM input)                         .. ok

	182: Count -x fa -x ha (SAM input)                          .. ok

	183: Filter -x fa -x ha (BAM input)                         .. ok

	184: Count -x fa -x ha (BAM input)                          .. ok

	185: Filter -x fa -x ha (CRAM input)                        .. ok

	186: Count -x fa -x ha (CRAM input)                         .. ok

	187: Filter -x fa,ha (SAM input)                            .. ok

	188: Count -x fa,ha (SAM input)                             .. ok

	189: Filter -x fa,ha (BAM input)                            .. ok

	190: Count -x fa,ha (BAM input)                             .. ok

	191: Filter -x fa,ha (CRAM input)                           .. ok

	192: Count -x fa,ha (CRAM input)                            .. ok

	193: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok

	194: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok

	195: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok

	196: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok

	197: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok

	198: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok

	199: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok

	200: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok

	201: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok

	202: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok

	203: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok

	204: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok

	205: Filter -x fa -r grp2 (SAM input)                       .. ok

	206: Count -x fa -r grp2 (SAM input)                        .. ok

	207: Filter -x fa -r grp2 (BAM input)                       .. ok

	208: Count -x fa -r grp2 (BAM input)                        .. ok

	209: Filter -x fa -r grp2 (CRAM input)                      .. ok

	210: Count -x fa -r grp2 (CRAM input)                       .. ok

	211: Filter -x RG -r grp2 (SAM input)                       .. ok

	212: Count -x RG -r grp2 (SAM input)                        .. ok

	213: Filter -x RG -r grp2 (BAM input)                       .. ok

	214: Count -x RG -r grp2 (BAM input)                        .. ok

	215: Filter -x RG -r grp2 (CRAM input)                      .. ok

	216: Count -x RG -r grp2 (CRAM input)                       .. ok

	217: Filter -m 10 (SAM input)                               .. ok

	218: Count -m 10 (SAM input)                                .. ok

	219: Filter -m 10 (BAM input)                               .. ok

	220: Count -m 10 (BAM input)                                .. ok

	221: Filter -m 10 (CRAM input)                              .. ok

	222: Count -m 10 (CRAM input)                               .. ok

	223: Filter -m 11 (SAM input)                               .. ok

	224: Count -m 11 (SAM input)                                .. ok

	225: Filter -m 11 (BAM input)                               .. ok

	226: Count -m 11 (BAM input)                                .. ok

	227: Filter -m 11 (CRAM input)                              .. ok

	228: Count -m 11 (CRAM input)                               .. ok

	229: Filter -m 15 (SAM input)                               .. ok

	230: Count -m 15 (SAM input)                                .. ok

	231: Filter -m 15 (BAM input)                               .. ok

	232: Count -m 15 (BAM input)                                .. ok

	233: Filter -m 15 (CRAM input)                              .. ok

	234: Count -m 15 (CRAM input)                               .. ok

	235: Filter -m 16 (SAM input)                               .. ok

	236: Count -m 16 (SAM input)                                .. ok

	237: Filter -m 16 (BAM input)                               .. ok

	238: Count -m 16 (BAM input)                                .. ok

	239: Filter -m 16 (CRAM input)                              .. ok

	240: Count -m 16 (CRAM input)                               .. ok

	241: Filter -e !(flag & 128) && (flag & 2) (SAM input)      .. ok

	242: Count -e !(flag & 128) && (flag & 2) (SAM input)       .. ok

	243: Filter -e !(flag & 128) && (flag & 2) (BAM input)      .. ok

	244: Count -e !(flag & 128) && (flag & 2) (BAM input)       .. ok

	245: Filter -e !(flag & 128) && (flag & 2) (CRAM input)     .. ok

	246: Count -e !(flag & 128) && (flag & 2) (CRAM input)      .. ok

	247: Filter -e [BC] (SAM input)                             .. ok

	248: Count -e [BC] (SAM input)                              .. ok

	249: Filter -e [BC] (BAM input)                             .. ok

	250: Count -e [BC] (BAM input)                              .. ok

	251: Filter -e [BC] (CRAM input)                            .. ok

	252: Count -e [BC] (CRAM input)                             .. ok

	253: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (SAM input).. ok

	254: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (SAM input).. ok

	255: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (BAM input).. ok

	256: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (BAM input).. ok

	257: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (CRAM input).. ok

	258: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (CRAM input).. ok

	259: Filter -e mapq >= 50 (SAM input)                       .. ok

	260: Count -e mapq >= 50 (SAM input)                        .. ok

	261: Filter -e mapq >= 50 (BAM input)                       .. ok

	262: Count -e mapq >= 50 (BAM input)                        .. ok

	263: Filter -e mapq >= 50 (CRAM input)                      .. ok

	264: Count -e mapq >= 50 (CRAM input)                       .. ok

	265: Filter -e mapq >= 99 (SAM input)                       .. ok

	266: Count -e mapq >= 99 (SAM input)                        .. ok

	267: Filter -e mapq >= 99 (BAM input)                       .. ok

	268: Count -e mapq >= 99 (BAM input)                        .. ok

	269: Filter -e mapq >= 99 (CRAM input)                      .. ok

	270: Count -e mapq >= 99 (CRAM input)                       .. ok

	271: Filter -e mapq >= 100 (SAM input)                      .. ok

	272: Count -e mapq >= 100 (SAM input)                       .. ok

	273: Filter -e mapq >= 100 (BAM input)                      .. ok

	274: Count -e mapq >= 100 (BAM input)                       .. ok

	275: Filter -e mapq >= 100 (CRAM input)                     .. ok

	276: Count -e mapq >= 100 (CRAM input)                      .. ok

	277: 1bp reads file SAM -> BAM -> SAM                       .. ok

	278: 1bp reads file SAM -> CRAM -> SAM                      .. ok

	278: Region  Z (BAM input)                                  .. ok

	279: Count  Z (BAM input)                                   .. ok

	280: Region  Z (CRAM input)                                 .. ok

	281: Count  Z (CRAM input)                                  .. ok

	282: Region  Z:30 (BAM input)                               .. ok

	283: Count  Z:30 (BAM input)                                .. ok

	284: Region  Z:30 (CRAM input)                              .. ok

	285: Count  Z:30 (CRAM input)                               .. ok

	286: Region  Z:20-40 (BAM input)                            .. ok

	287: Count  Z:20-40 (BAM input)                             .. ok

	288: Region  Z:20-40 (CRAM input)                           .. ok

	289: Count  Z:20-40 (CRAM input)                            .. ok

	290: Region  ref1 (BAM input)                               .. ok

	291: Count  ref1 (BAM input)                                .. ok

	292: Region  ref1 (CRAM input)                              .. ok

	293: Count  ref1 (CRAM input)                               .. ok

	294: Region  ref1:15 (BAM input)                            .. ok

	295: Count  ref1:15 (BAM input)                             .. ok

	296: Region  ref1:15 (CRAM input)                           .. ok

	297: Count  ref1:15 (CRAM input)                            .. ok

	298: Region  ref1:15-45 (BAM input)                         .. ok

	299: Count  ref1:15-45 (BAM input)                          .. ok

	300: Region  ref1:15-45 (CRAM input)                        .. ok

	301: Count  ref1:15-45 (CRAM input)                         .. ok

	302: Region  ref1:15-45 ref2 (BAM input)                    .. ok

	303: Count  ref1:15-45 ref2 (BAM input)                     .. ok

	304: Region  ref1:15-45 ref2 (CRAM input)                   .. ok

	305: Count  ref1:15-45 ref2 (CRAM input)                    .. ok

	306: Region  ref1:15-45 ref2:16 (BAM input)                 .. ok

	307: Count  ref1:15-45 ref2:16 (BAM input)                  .. ok

	308: Region  ref1:15-45 ref2:16 (CRAM input)                .. ok

	309: Count  ref1:15-45 ref2:16 (CRAM input)                 .. ok

	310: Region  ref1:15-45 ref2:16-31 (BAM input)              .. ok

	311: Count  ref1:15-45 ref2:16-31 (BAM input)               .. ok

	312: Region  ref1:15-45 ref2:16-31 (CRAM input)             .. ok

	313: Count  ref1:15-45 ref2:16-31 (CRAM input)              .. ok

	314: Region  ref1:15-15 ref1:45-45 (BAM input)              .. ok

	315: Count  ref1:15-15 ref1:45-45 (BAM input)               .. ok

	316: Region  ref1:15-15 ref1:45-45 (CRAM input)             .. ok

	317: Count  ref1:15-15 ref1:45-45 (CRAM input)              .. ok

	318: Region -f 128 ref1 (BAM input)                         .. ok

	319: Count -f 128 ref1 (BAM input)                          .. ok

	320: Region -f 128 ref1 (CRAM input)                        .. ok

	321: Count -f 128 ref1 (CRAM input)                         .. ok

	322: Region -q 50 ref1:15-45 (BAM input)                    .. ok

	323: Count -q 50 ref1:15-45 (BAM input)                     .. ok

	324: Region -q 50 ref1:15-45 (CRAM input)                   .. ok

	325: Count -q 50 ref1:15-45 (CRAM input)                    .. ok

	326: Region -r grp2 ref1:15-45 (BAM input)                  .. ok

	327: Count -r grp2 ref1:15-45 (BAM input)                   .. ok

	328: Region -r grp2 ref1:15-45 (CRAM input)                 .. ok

	329: Count -r grp2 ref1:15-45 (CRAM input)                  .. ok

	330: Region  * (BAM input)                                  .. ok

	331: Count  * (BAM input)                                   .. ok

	332: Region  * (CRAM input)                                 .. ok

	333: Count  * (CRAM input)                                  .. ok

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

	354: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z:30 (BAM input).. ok

	355: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z:30 (BAM input).. ok

	356: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z:30 (CRAM input).. ok

	357: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z:30 (CRAM input).. ok

	358: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok

	359: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok

	360: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok

	361: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok

	362: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok

	363: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok

	364: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok

	365: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok

	366: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok

	367: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok

	368: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok

	369: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok

	370: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed ref2 (BAM input).. ok

	371: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed ref2 (BAM input).. ok

	372: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed ref2 (CRAM input).. ok

	373: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed ref2 (CRAM input).. ok

	374: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok

	375: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok

	376: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok

	377: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok

	378: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -r grp1  (BAM input).. ok

	379: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -r grp1  (BAM input).. ok

	380: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -r grp1  (CRAM input).. ok

	381: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -r grp1  (CRAM input).. ok

	382: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -f 128  (BAM input).. ok

	383: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -f 128  (BAM input).. ok

	384: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -f 128  (CRAM input).. ok

	385: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -f 128  (CRAM input).. ok

	386: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -q 5  (BAM input).. ok

	387: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -q 5  (BAM input).. ok

	388: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -q 5  (CRAM input).. ok

	389: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -q 5  (CRAM input).. ok

	390: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok

	391: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok

	392: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok

	393: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok

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

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

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

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

	398: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok

	399: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok

	400: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -M --unmap ref1:11-30 (CRAM input).. ok

	401: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -M --unmap ref1:11-30 (CRAM input).. ok

	402: Make BAM with no M5/UR tags                            .. ok

	403: Add @SQ with -t (SAM -> SAM)                           .. ok

	404: Add @SQ with -T (SAM -> SAM)                           .. ok

	405: Add @SQ with -t (BAM -> SAM)                           .. ok

	406: Add @SQ with -T (BAM -> SAM)                           .. ok

	407: Add @SQ with -t (SAM -> BAM)                           .. ok

	408: Add @SQ with -T (SAM -> BAM)                           .. ok

	409: Add @SQ with -t (BAM -> BAM)                           .. ok

	410: Add @SQ with -T (BAM -> BAM)                           .. ok

	411: Add @SQ with -t (SAM -> CRAM)                          .. ok

	412: Add @SQ with -T (SAM -> CRAM)                          .. ok

	413: Add @SQ with -t (BAM -> CRAM)                          .. ok

	414: Add @SQ with -T (BAM -> CRAM)                          .. ok

	415: Make CRAM with no UR field                             .. ok

	416: Decoding CRAM with no UR field via -T                  .. ok

	417: CIGAR B-operator removal                               .. ok

	418: Big SAM -> BAM                                         .. ok

	419: Big SAM -> BAM (2 threads)                             .. ok

	420: Big SAM -> BAM (4 threads)                             .. ok

	421: Big SAM -> CRAM                                        .. ok

	422: Big SAM -> CRAM (2 threads)                            .. ok

	423: Big SAM -> CRAM (4 threads)                            .. ok

	424: Subsample 0.2 (SAM input) ............ ok

	425: Subsample 0.5 (SAM input) ............ ok

	426: Subsample 0.8 (SAM input) ............ ok

	427: Subsample 0.2 (BAM input) ............ ok

	428: Subsample 0.5 (BAM input) ............ ok

	429: Subsample 0.8 (BAM input) ............ ok

	430: Subsample 0.2 (CRAM input) ............ ok

	431: Subsample 0.5 (CRAM input) ............ ok

	432: Subsample 0.8 (CRAM input) ............ ok

	433: SAM add PG                                             .. ok

	434: Unset dup flag, remove dt and do tags                  .. ok

	435: Unmap dup flagged reads.                               .. ok

	436: Unmap dup flagged reads.                               .. ok

	437: fetch pairs                                            .. ok

	438: fetch pairs                                            .. ok

	439: fetch pairs                                            .. ok

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

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

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

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

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

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

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

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

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

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

test_cat:
	Generating test data file .................. done
	Generate BAM file #1                                        .. ok

	Generate CRAM file #1                                       .. ok

	Generating test data file .................. done
	Generate BAM file #2                                        .. ok

	Generate CRAM file #2                                       .. ok

	Generating test data file .................. done
	Generate BAM file #3                                        .. ok

	Generate CRAM file #3                                       .. ok

	Generating test data file .................. done
	Generate BAM file #4                                        .. ok

	Generate CRAM file #4                                       .. ok

	1: cat BAM files                                            .. ok

	2: cat recompressed BAM files                               .. ok

	3: cat CRAM files                                           .. ok

	4: cat BAM files to stdout                                  .. ok

	5: cat recompressed BAM files to stdout                     .. ok

	6: cat CRAM files to stdout                                 .. ok

	7: cat BAM files with new header                            .. ok

	8: cat recompressed BAM files with new header               .. ok

	9: cat CRAM files with new header                           .. ok

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

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

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

test_import:
	/builddir/build/BUILD/samtools-1.15.1/samtools import test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected | /builddir/build/BUILD/samtools-1.15.1/samtools fastq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.15.1/samtools import test/bam2fq/5.1.fq.expected test/bam2fq/5.2.fq.expected | /builddir/build/BUILD/samtools-1.15.1/samtools fastq -N -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.15.1/samtools import -i -1 test/bam2fq/12.1.fq.expected -2 test/bam2fq/12.2.fq.expected | /builddir/build/BUILD/samtools-1.15.1/samtools fastq -i --index-format 'i*i*' -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.15.1/samtools import --barcode-tag OX -i -1 test/bam2fq/12.1.fq.expected -2 test/bam2fq/12.2.fq.expected | /builddir/build/BUILD/samtools-1.15.1/samtools fastq --barcode-tag OX -i --index-format 'i*i*' -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.15.1/samtools import -T "" -1 test/bam2fq/6.1.fq.expected -2 test/bam2fq/6.2.fq.expected | /builddir/build/BUILD/samtools-1.15.1/samtools fastq -N -T RG,BC,QT -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.15.1/samtools import -T "*" -1 test/bam2fq/7.1.fq.expected -2 test/bam2fq/7.2.fq.expected | /builddir/build/BUILD/samtools-1.15.1/samtools fastq -N -T RG,BC,QT,MD,ia -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.15.1/samtools import test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -R rgid
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.15.1/samtools import test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -r ID:rgid
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.15.1/samtools import test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -r '@RG	ID:rgid'
.. ok

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

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

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

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

test_import:
	/builddir/build/BUILD/samtools-1.15.1/samtools import test/import/4.aux.fq -T XZ,XA,AA
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.15.1/samtools import --i1 test/import/5-i1.fq --i2  test/import/5-i2.fq --r1 test/import/5-r1.fq --r2 test/import/5-r2.fq
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.15.1/samtools import --i1 test/import/5-i1.fq --i2  test/import/5-i2.fq --r1 test/import/5-r1.fq --r2 test/import/5-r2.fq --barcode-tag OX --quality-tag BZ
.. ok

test_bam2fq:
	Generate BAM file                                           .. ok

	Generate CRAM file                                          .. ok

	1: fastq  (SAM input)                                       [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

	2: fastq -n (SAM input)                                     [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

	3: fastq  (BAM input)                                       [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

	4: fastq -n (BAM input)                                     [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

	5: fastq  (CRAM input)                                      [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

	6: fastq -n (CRAM input)                                    [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

test_bam2fq:
	/builddir/build/BUILD/samtools-1.15.1/samtools fastq  -N -s /tmp/kPWEewzuD6/bam2fq.discard.s.fq -0 /tmp/kPWEewzuD6/bam2fq.discard.0.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.001.sam
.. ok

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

test_bam2fq:
	/builddir/build/BUILD/samtools-1.15.1/samtools fastq  --index-format 'i8n1i8' --i1 /builddir/build/BUILD/samtools-1.15.1/test/i1.fq --i2 /builddir/build/BUILD/samtools-1.15.1/test/i2.fq -0 /builddir/build/BUILD/samtools-1.15.1/test/0.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.014.sam
.. ok

test_bam2fq:
	Generate BAM file (2 threads)                               .. ok

	Generate CRAM file (2 threads)                              .. ok

	1: fastq  (SAM input) (2 threads)                           [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

	2: fastq -n (SAM input) (2 threads)                         [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

	3: fastq  (BAM input) (2 threads)                           [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

	4: fastq -n (BAM input) (2 threads)                         [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

	5: fastq  (CRAM input) (2 threads)                          [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

	6: fastq -n (CRAM input) (2 threads)                        [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

test_bam2fq:
	/builddir/build/BUILD/samtools-1.15.1/samtools fastq -@ 2 -N -s /tmp/kPWEewzuD6/bam2fq.discard.s.fq -0 /tmp/kPWEewzuD6/bam2fq.discard.0.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.001.sam
.. ok

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

test_bam2fq:
	/builddir/build/BUILD/samtools-1.15.1/samtools fastq -@ 2 --index-format 'i8n1i8' --i1 /builddir/build/BUILD/samtools-1.15.1/test/i1.fq --i2 /builddir/build/BUILD/samtools-1.15.1/test/i2.fq -0 /builddir/build/BUILD/samtools-1.15.1/test/0.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.014.sam
.. ok

test_depad:
	Generate BAM file                                           .. ok

	depad  (SAM input)                                          .. ok

	depad -s (SAM input)                                        .. ok

	depad -u (SAM input)                                        .. ok

	depad -1 (SAM input)                                        .. ok

	depad  (BAM input)                                          .. ok

	depad -s (BAM input)                                        .. ok

	depad -u (BAM input)                                        .. ok

	depad -1 (BAM input)                                        .. ok

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

test_stats:
	/builddir/build/BUILD/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1/test/stat/1_map_cigar_large.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.15.1/samtools stats -r /builddir/build/BUILD/samtools-1.15.1/test/stat/test.fa /builddir/build/BUILD/samtools-1.15.1/test/stat/2_equal_cigar_full_seq.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1/test/stat/2_equal_cigar_full_seq_large.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.15.1/samtools stats -r /builddir/build/BUILD/samtools-1.15.1/test/stat/test.fa /builddir/build/BUILD/samtools-1.15.1/test/stat/3_map_cigar_equal_seq.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1/test/stat/3_map_cigar_equal_seq_large.sam | tail -n+4
.. ok

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

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

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

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

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

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

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

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

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

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

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

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

test_stats:
	/builddir/build/BUILD/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4
.. ok

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

test_stats:
	/builddir/build/BUILD/samtools-1.15.1/samtools stats -g 4 /builddir/build/BUILD/samtools-1.15.1/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4
.. ok

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

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

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

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

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

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

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

	/builddir/build/BUILD/samtools-1.15.1/test/stat/13.barcodes.fail.expected: No such file or directory
.. expected failure

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

	/builddir/build/BUILD/samtools-1.15.1/test/stat/13.barcodes.fail.expected: No such file or directory
.. expected failure

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

	/builddir/build/BUILD/samtools-1.15.1/test/stat/13.barcodes.fail.expected: No such file or directory
.. expected failure

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

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

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

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

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

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

test_merge:
	/builddir/build/BUILD/samtools-1.15.1/samtools merge -s 1 -O sam -b /tmp/W0UDoC7vah - /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam
.. ok

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

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

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

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

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

test_merge:
	/builddir/build/BUILD/samtools-1.15.1/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/kPWEewzuD6/merge.tag.1.bam /tmp/kPWEewzuD6/merge.tag.2.bam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.15.1/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/kPWEewzuD6/merge.tag.3.bam /tmp/kPWEewzuD6/merge.tag.4.bam
.. ok

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

test_merge:
	/builddir/build/BUILD/samtools-1.15.1/samtools merge --no-PG -O SAM -L /builddir/build/BUILD/samtools-1.15.1/test/merge/merge.bed - /tmp/kPWEewzuD6/merge.bed.1.bam /tmp/kPWEewzuD6/merge.bed.2.bam
.. ok

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

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

test_merge:
	/builddir/build/BUILD/samtools-1.15.1/samtools merge -@ 2 -s 1 -O sam -b /tmp/YiGIZBb7vz - /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam
.. ok

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

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

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

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

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

test_merge:
	/builddir/build/BUILD/samtools-1.15.1/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/kPWEewzuD6/merge.tag.1.bam /tmp/kPWEewzuD6/merge.tag.2.bam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.15.1/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/kPWEewzuD6/merge.tag.3.bam /tmp/kPWEewzuD6/merge.tag.4.bam
.. ok

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

test_merge:
	/builddir/build/BUILD/samtools-1.15.1/samtools merge -@ 2 --no-PG -O SAM -L /builddir/build/BUILD/samtools-1.15.1/test/merge/merge.bed - /tmp/kPWEewzuD6/merge.bed.1.bam /tmp/kPWEewzuD6/merge.bed.2.bam
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.15.1/samtools sort /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam /tmp/kPWEewzuD6/sortout
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.15.1/samtools sort -f /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam /tmp/kPWEewzuD6/sortout.bam
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.15.1/samtools sort -o /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam /tmp/kPWEewzuD6/sorttmp
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.15.1/samtools sort -m 10M /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam -O SAM -o -
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.15.1/samtools sort -n -m 10M /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam -O SAM -o -
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.15.1/samtools sort -t RG -m 10M /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam -O SAM -o -
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.15.1/samtools sort -n -t RG -m 10M /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam -O SAM -o -
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.15.1/samtools sort -t AS -m 10M /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_d.sam -O SAM -o -
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.15.1/samtools sort -t FI -m 10M /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_d.sam -O SAM -o -
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.15.1/samtools sort -@ 2 /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam /tmp/kPWEewzuD6/sortout
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.15.1/samtools sort -@ 2 -f /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam /tmp/kPWEewzuD6/sortout.bam
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.15.1/samtools sort -@ 2 -o /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam /tmp/kPWEewzuD6/sorttmp
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.15.1/samtools sort -@ 2 -m 10M /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam -O SAM -o -
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.15.1/samtools sort -@ 2 -n -m 10M /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam -O SAM -o -
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.15.1/samtools sort -@ 2 -t RG -m 10M /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam -O SAM -o -
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.15.1/samtools sort -@ 2 -n -t RG -m 10M /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam -O SAM -o -
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.15.1/samtools sort -@ 2 -t AS -m 10M /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_d.sam -O SAM -o -
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.15.1/samtools sort -@ 2 -t FI -m 10M /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_d.sam -O SAM -o -
.. ok

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

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

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

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

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

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

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

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

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

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

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

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

test_fixmate:
	/builddir/build/BUILD/samtools-1.15.1/samtools fixmate -O sam /builddir/build/BUILD/samtools-1.15.1/test/fixmate/1_coord_sort.sam -

	ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname.

.. expected failure

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

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

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

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

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

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

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

test_fixmate:
	/builddir/build/BUILD/samtools-1.15.1/samtools fixmate -@ 2 -O sam /builddir/build/BUILD/samtools-1.15.1/test/fixmate/1_coord_sort.sam -

	ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname.

.. expected failure

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

test_addrprg:
	/builddir/build/BUILD/samtools-1.15.1/samtools addreplacerg -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /builddir/build/BUILD/samtools-1.15.1/test/addrprg/1_fixup.sam
.. ok

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

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

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

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

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

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

test_addrprg:
	/builddir/build/BUILD/samtools-1.15.1/samtools addreplacerg -@ 2 -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /builddir/build/BUILD/samtools-1.15.1/test/addrprg/1_fixup.sam
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.15.1/samtools markdup -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/1_name_sort.sam -

	ERR: [markdup] error: queryname sorted, must be sorted by coordinate.

.. expected failure

test_markdup:
	/builddir/build/BUILD/samtools-1.15.1/samtools markdup -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/2_bad_order.sam -

	ERR: [markdup] error: not in coordinate sorted order.

.. expected failure

test_markdup:
	/builddir/build/BUILD/samtools-1.15.1/samtools markdup -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/3_missing_mc.sam -

	ERR: [markdup] error: no MC tag. Please run samtools fixmate on file first.
[markdup] error: unable to assign pair hash key.

.. expected failure

test_markdup:
	/builddir/build/BUILD/samtools-1.15.1/samtools markdup -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/4_missing_ms.sam -

	ERR: [markdup] error: no ms score tag. Please run samtools fixmate on file first.
[markdup] error: no ms score tag. Please run samtools fixmate on file first.

.. expected failure

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

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

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

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

test_markdup:
	/builddir/build/BUILD/samtools-1.15.1/samtools markdup -S -d 2500 --mode s -t --include-fails -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/9_optical_dup_qcfail.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.15.1/samtools markdup -S -d 2500 --mode s -t -O sam --no-PG -S /builddir/build/BUILD/samtools-1.15.1/test/markdup/10_optical_chain.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.15.1/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /builddir/build/BUILD/samtools-1.15.1/test/markdup/10_optical_chain.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.15.1/samtools markdup -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+):([[:print:]]+)' --coords-order xyt --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/11_optical_dup_regex.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.15.1/samtools markdup -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+)' --coords-order xy --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/11_optical_dup_regex.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.15.1/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/12_optical_chain_regex.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.15.1/samtools markdup -@ 2 -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/1_name_sort.sam -

	ERR: [markdup] error: queryname sorted, must be sorted by coordinate.

.. expected failure

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

	ERR: [markdup] error: not in coordinate sorted order.

.. expected failure

test_markdup:
	/builddir/build/BUILD/samtools-1.15.1/samtools markdup -@ 2 -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/3_missing_mc.sam -

	ERR: [markdup] error: no MC tag. Please run samtools fixmate on file first.
[markdup] error: unable to assign pair hash key.

.. expected failure

test_markdup:
	/builddir/build/BUILD/samtools-1.15.1/samtools markdup -@ 2 -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/4_missing_ms.sam -

	ERR: [markdup] error: no ms score tag. Please run samtools fixmate on file first.
[markdup] error: no ms score tag. Please run samtools fixmate on file first.

.. expected failure

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

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

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

test_markdup:
	/builddir/build/BUILD/samtools-1.15.1/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/8_optical_dup.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.15.1/samtools markdup -@ 2 -S -d 2500 --mode s -t --include-fails -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/9_optical_dup_qcfail.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.15.1/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --no-PG -S /builddir/build/BUILD/samtools-1.15.1/test/markdup/10_optical_chain.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.15.1/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /builddir/build/BUILD/samtools-1.15.1/test/markdup/10_optical_chain.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.15.1/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+):([[:print:]]+)' --coords-order xyt --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/11_optical_dup_regex.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.15.1/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+)' --coords-order xy --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/11_optical_dup_regex.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.15.1/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/12_optical_chain_regex.sam -
.. ok

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

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

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

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

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

test_large_positions:
	/builddir/build/BUILD/samtools-1.15.1/samtools view -h --no-PG /tmp/kPWEewzuD6/longref.sam.gz
.. ok

test_large_positions:
	/builddir/build/BUILD/samtools-1.15.1/samtools view -h --no-PG /tmp/kPWEewzuD6/longref.sam.gz CHROMOSOME_I:10000000114-10000000168
.. ok

test_large_positions:
	/builddir/build/BUILD/samtools-1.15.1/samtools view -h --no-PG -L /builddir/build/BUILD/samtools-1.15.1/test/large_pos/test.bed /tmp/kPWEewzuD6/longref.sam.gz
.. ok

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

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

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

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

test_large_positions:
	/builddir/build/BUILD/samtools-1.15.1/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/kPWEewzuD6/longref.sam.gz
.. ok

test_large_positions:
	/builddir/build/BUILD/samtools-1.15.1/samtools sort    -O sam --no-PG -n -m 10M test/large_pos/longref3.sam |
                     /builddir/build/BUILD/samtools-1.15.1/samtools fixmate -O sam --no-PG - - |
                     /builddir/build/BUILD/samtools-1.15.1/samtools sort    -O sam --no-PG -m 10M
.. ok

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

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

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

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.15.1/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.15.1/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/1_test_data.sam
.. ok

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

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

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

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

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

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

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.15.1/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.15.1/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/1_test_data.sam
.. ok

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

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

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

test_ampliconstats:
	/builddir/build/BUILD/samtools-1.15.1/samtools ampliconstats -@ 2 -S -t 50 -d 1,20,100 /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/1_hard_clipped.expected.sam /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/1_soft_clipped.expected.sam /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/1_soft_clipped_strand.expected.sam /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/2_both_clipped.expected.sam | egrep -v 'Samtools version|Command line'
.. ok

test_ampliconstats:
	/builddir/build/BUILD/samtools-1.15.1/samtools ampliconstats -@ 2 -c 0 /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/multi_ref.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconstats/mixed_clipped.sam | egrep -v 'Samtools version|Command line'
.. ok


Number of tests:
    total            .. 807
    passed           .. 776
    failed           .. 0
    expected failure .. 31
    unexpected pass  .. 0

test/merge/test_bam_translate test/merge/test_bam_translate.tmp
test/merge/test_rtrans_build
test/merge/test_trans_tbl_init
cd test/mpileup && AWK="gawk" ../regression.sh mpileup.reg

=== Testing mpileup.reg regressions ===

EXPECTED FAIL: Task failed, but expected to fail;
when running $samtools mpileup -ABQ0 -a -l xx.bed3 xx#depth3.bam

Expected   passes:   118
Unexpected passes:   0
Expected   failures: 1
Unexpected failures: 0
=> PASS
cd test/mpileup && AWK="gawk" ../regression.sh depth.reg

=== Testing depth.reg regressions ===

EXPECTED FAIL: Task failed, but expected to fail;
when running $samtools depth -a -b xx.bed3 xx#depth3.bam

Expected   passes:   47
Unexpected passes:   0
Expected   failures: 1
Unexpected failures: 0
=> PASS
cd test/consensus && AWK="gawk" ../regression.sh consensus.reg

=== Testing consensus.reg regressions ===

Expected   passes:   62
Unexpected passes:   0
Expected   failures: 0
Unexpected failures: 0
=> PASS
+ RPM_EC=0
++ jobs -p
+ exit 0
Processing files: samtools-1.15.1-3.amzn2023.x86_64
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.2VdErs
+ umask 022
+ cd /builddir/build/BUILD
+ cd samtools-1.15.1
+ DOCDIR=/builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/share/doc/samtools
+ export LC_ALL=C
+ LC_ALL=C
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/share/doc/samtools
+ cp -pr AUTHORS /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/share/doc/samtools
+ cp -pr ChangeLog.old /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/share/doc/samtools
+ cp -pr NEWS /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/share/doc/samtools
+ cp -pr examples/ /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/share/doc/samtools
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.cJm9eI
+ umask 022
+ cd /builddir/build/BUILD
+ cd samtools-1.15.1
+ LICENSEDIR=/builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/share/licenses/samtools
+ export LC_ALL=C
+ LC_ALL=C
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/share/licenses/samtools
+ cp -pr LICENSE /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64/usr/share/licenses/samtools
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: samtools = 1.15.1-3.amzn2023 samtools(x86-64) = 1.15.1-3.amzn2023
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: /usr/bin/perl libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.7)(64bit) libhts.so.3()(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.29)(64bit) libncursesw.so.6()(64bit) libtinfo.so.6()(64bit) libz.so.1()(64bit) rtld(GNU_HASH)
Processing files: samtools-debugsource-1.15.1-3.amzn2023.x86_64
Provides: samtools-debugsource = 1.15.1-3.amzn2023 samtools-debugsource(x86-64) = 1.15.1-3.amzn2023
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: samtools-debuginfo-1.15.1-3.amzn2023.x86_64
Provides: debuginfo(build-id) = 0ccf286d99175e1f311ffde12593133f05d7d655 debuginfo(build-id) = 1443bfca5495b2b3088f4099c21cfd29a0c1a81c debuginfo(build-id) = 8ced01969c7513bbae7ff5680a5ae098bc4c73c3 debuginfo(build-id) = 93e05eb825715679015854dc1bebcdcba2eac098 debuginfo(build-id) = a5ff72e991fc53205652218da7cd5a3a7996adff debuginfo(build-id) = b016840cc58875563895132ff3c7f10cd3be8d03 debuginfo(build-id) = ed9ae27514d5dc8d629a1f40da155bcc4005dcfc samtools-debuginfo = 1.15.1-3.amzn2023 samtools-debuginfo(x86-64) = 1.15.1-3.amzn2023
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: samtools-debugsource(x86-64) = 1.15.1-3.amzn2023
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64
Wrote: /builddir/build/RPMS/samtools-1.15.1-3.amzn2023.x86_64.rpm
Wrote: /builddir/build/RPMS/samtools-debuginfo-1.15.1-3.amzn2023.x86_64.rpm
Wrote: /builddir/build/RPMS/samtools-debugsource-1.15.1-3.amzn2023.x86_64.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.zXbJ51
+ umask 022
+ cd /builddir/build/BUILD
+ cd samtools-1.15.1
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/samtools-1.15.1-3.amzn2023.x86_64
+ RPM_EC=0
++ jobs -p
+ exit 0
Finish: rpmbuild samtools-1.15.1-3.amzn2023.src.rpm
Finish: build phase for samtools-1.15.1-3.amzn2023.src.rpm
INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/amazonlinux-2023-x86_64-1704591447.340321/root/var/log/dnf.rpm.log
/var/lib/mock/amazonlinux-2023-x86_64-1704591447.340321/root/var/log/dnf.librepo.log
/var/lib/mock/amazonlinux-2023-x86_64-1704591447.340321/root/var/log/dnf.log
INFO: Done(/var/lib/copr-rpmbuild/results/samtools-1.15.1-3.amzn2023.src.rpm) Config(child) 1 minutes 6 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-debuginfo",
            "epoch": null,
            "version": "1.15.1",
            "release": "3.amzn2023",
            "arch": "x86_64"
        },
        {
            "name": "samtools",
            "epoch": null,
            "version": "1.15.1",
            "release": "3.amzn2023",
            "arch": "x86_64"
        },
        {
            "name": "samtools-debugsource",
            "epoch": null,
            "version": "1.15.1",
            "release": "3.amzn2023",
            "arch": "x86_64"
        },
        {
            "name": "samtools",
            "epoch": null,
            "version": "1.15.1",
            "release": "3.amzn2023",
            "arch": "src"
        }
    ]
}
RPMResults finished