Warning: Permanently added '2620:52:3:1:dead:beef:cafe:c290' (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/6408261-fedora-rawhide-ppc64le --chroot fedora-rawhide-ppc64le
Version: 0.69
PID: 67336
Logging PID: 67337
Task:
{'appstream': False,
'background': True,
'build_id': 6408261,
'buildroot_pkgs': [],
'chroot': 'fedora-rawhide-ppc64le',
'enable_net': False,
'fedora_review': False,
'git_hash': '9a1c29996af7c4c77ddea2c5f9443e30fa48ef01',
'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/tuliom/zlib-ng-compat-mpb/samtools',
'isolation': 'default',
'memory_reqs': 2048,
'package_name': 'samtools',
'package_version': '1.15.1-3',
'project_dirname': 'zlib-ng-compat-mpb',
'project_name': 'zlib-ng-compat-mpb',
'project_owner': 'tuliom',
'repo_priority': None,
'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/tuliom/zlib-ng-compat-mpb/fedora-rawhide-ppc64le/',
'id': 'copr_base',
'name': 'Copr repository',
'priority': None}],
'sandbox': 'tuliom/zlib-ng-compat-mpb--tuliom',
'source_json': {},
'source_type': None,
'submitter': 'tuliom',
'tags': [],
'task_id': '6408261-fedora-rawhide-ppc64le',
'timeout': 115200,
'uses_devel_repo': False,
'with_opts': [],
'without_opts': []}
Running: git clone https://copr-dist-git.fedorainfracloud.org/git/tuliom/zlib-ng-compat-mpb/samtools /var/lib/copr-rpmbuild/workspace/workdir-xegk6rp2/samtools --depth 500 --no-single-branch --recursive
cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/tuliom/zlib-ng-compat-mpb/samtools', '/var/lib/copr-rpmbuild/workspace/workdir-xegk6rp2/samtools', '--depth', '500', '--no-single-branch', '--recursive']
cwd: .
rc: 0
stdout:
stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-xegk6rp2/samtools'...
Running: git checkout 9a1c29996af7c4c77ddea2c5f9443e30fa48ef01 --
cmd: ['git', 'checkout', '9a1c29996af7c4c77ddea2c5f9443e30fa48ef01', '--']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-xegk6rp2/samtools
rc: 0
stdout:
stderr: Note: switching to '9a1c29996af7c4c77ddea2c5f9443e30fa48ef01'.
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 9a1c299 automatic import of samtools
Running: copr-distgit-client sources
cmd: ['copr-distgit-client', 'sources']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-xegk6rp2/samtools
rc: 0
stdout:
/usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated
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/tuliom/zlib-ng-compat-mpb/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 25.5M 0 --:--:-- --:--:-- --:--:-- 25.6M
INFO: Reading stdout from command: md5sum samtools-1.15.1.tar.bz2
Running (timeout=115200): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-xegk6rp2/samtools/samtools.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-xegk6rp2/samtools --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1695069238.164412 -r /var/lib/copr-rpmbuild/results/configs/child.cfg
INFO: mock.py version 5.1.1 starting (python version = 3.11.3, NVR = mock-5.1.1-1.fc38)...
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-xegk6rp2/samtools/samtools.spec) Config(fedora-rawhide-ppc64le)
Start: clean chroot
Finish: clean chroot
Mock Version: 5.1.1
INFO: Mock Version: 5.1.1
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-ppc64le-bootstrap-1695069238.164412/root.
INFO: calling preinit hooks
INFO: enabled root cache
INFO: enabled package manager cache
Start(bootstrap): cleaning package manager metadata
Finish(bootstrap): cleaning package manager metadata
INFO: Guessed host environment type: unknown
INFO: Using bootstrap image: registry.fedoraproject.org/fedora:rawhide
INFO: Pulling image: registry.fedoraproject.org/fedora:rawhide
INFO: Copy content of container registry.fedoraproject.org/fedora:rawhide to /var/lib/mock/fedora-rawhide-ppc64le-bootstrap-1695069238.164412/root
INFO: Checking that registry.fedoraproject.org/fedora:rawhide image matches host's architecture
INFO: mounting registry.fedoraproject.org/fedora:rawhide with podman image mount
INFO: image registry.fedoraproject.org/fedora:rawhide as /var/lib/containers/storage/overlay/beb0de4744e4962ffb82970f219a3113083def0169e600824024dd4ef0391d1c/merged
INFO: umounting image registry.fedoraproject.org/fedora:rawhide (/var/lib/containers/storage/overlay/beb0de4744e4962ffb82970f219a3113083def0169e600824024dd4ef0391d1c/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 21 MB/s | 5.4 MB 00:00
fedora 14 MB/s | 67 MB 00:04
Last metadata expiration check: 0:00:02 ago on Mon Sep 18 20:34:09 2023.
Package python3-dnf-4.16.2-4.fc40.noarch is already installed.
Dependencies resolved.
================================================================================
Package Arch Version Repository Size
================================================================================
Installing:
python3-dnf-plugins-core noarch 4.4.2-1.fc39 fedora 293 k
Installing dependencies:
dbus-libs ppc64le 1:1.14.10-1.fc40 fedora 177 k
python3-dateutil noarch 1:2.8.2-10.fc39 fedora 355 k
python3-dbus ppc64le 1.3.2-4.fc39 fedora 161 k
python3-distro noarch 1.8.0-6.fc39 fedora 49 k
python3-six noarch 1.16.0-12.fc39 fedora 41 k
python3-systemd ppc64le 235-5.fc39 fedora 108 k
Transaction Summary
================================================================================
Install 7 Packages
Total download size: 1.2 M
Installed size: 4.8 M
Downloading Packages:
(1/7): python3-dbus-1.3.2-4.fc39.ppc64le.rpm 376 kB/s | 161 kB 00:00
(2/7): dbus-libs-1.14.10-1.fc40.ppc64le.rpm 402 kB/s | 177 kB 00:00
(3/7): python3-distro-1.8.0-6.fc39.noarch.rpm 547 kB/s | 49 kB 00:00
(4/7): python3-dateutil-2.8.2-10.fc39.noarch.rp 661 kB/s | 355 kB 00:00
(5/7): python3-six-1.16.0-12.fc39.noarch.rpm 473 kB/s | 41 kB 00:00
(6/7): python3-dnf-plugins-core-4.4.2-1.fc39.no 1.6 MB/s | 293 kB 00:00
(7/7): python3-systemd-235-5.fc39.ppc64le.rpm 1.1 MB/s | 108 kB 00:00
--------------------------------------------------------------------------------
Total 1.6 MB/s | 1.2 MB 00:00
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
Preparing : 1/1
Installing : python3-systemd-235-5.fc39.ppc64le 1/7
Installing : python3-six-1.16.0-12.fc39.noarch 2/7
Installing : python3-dateutil-1:2.8.2-10.fc39.noarch 3/7
Installing : python3-distro-1.8.0-6.fc39.noarch 4/7
Installing : dbus-libs-1:1.14.10-1.fc40.ppc64le 5/7
Installing : python3-dbus-1.3.2-4.fc39.ppc64le 6/7
Installing : python3-dnf-plugins-core-4.4.2-1.fc39.noarch 7/7
Running scriptlet: python3-dnf-plugins-core-4.4.2-1.fc39.noarch 7/7
Verifying : dbus-libs-1:1.14.10-1.fc40.ppc64le 1/7
Verifying : python3-dateutil-1:2.8.2-10.fc39.noarch 2/7
Verifying : python3-dbus-1.3.2-4.fc39.ppc64le 3/7
Verifying : python3-distro-1.8.0-6.fc39.noarch 4/7
Verifying : python3-dnf-plugins-core-4.4.2-1.fc39.noarch 5/7
Verifying : python3-six-1.16.0-12.fc39.noarch 6/7
Verifying : python3-systemd-235-5.fc39.ppc64le 7/7
Installed:
dbus-libs-1:1.14.10-1.fc40.ppc64le
python3-dateutil-1:2.8.2-10.fc39.noarch
python3-dbus-1.3.2-4.fc39.ppc64le
python3-distro-1.8.0-6.fc39.noarch
python3-dnf-plugins-core-4.4.2-1.fc39.noarch
python3-six-1.16.0-12.fc39.noarch
python3-systemd-235-5.fc39.ppc64le
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/fedora-rawhide-ppc64le-1695069238.164412/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)
Start: installing minimal buildroot with dnf
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Copr repository 18 kB/s | 1.5 kB 00:00
Copr repository 21 MB/s | 5.4 MB 00:00
fedora 73 kB/s | 6.1 kB 00:00
Dependencies resolved.
================================================================================
Package Arch Version Repo Size
================================================================================
Installing group/module packages:
bash ppc64le 5.2.15-5.fc39 fedora 1.9 M
bzip2 ppc64le 1.0.8-16.fc39 fedora 53 k
coreutils ppc64le 9.4-1.fc40 fedora 1.4 M
cpio ppc64le 2.14-4.fc39 fedora 286 k
diffutils ppc64le 3.10-3.fc39 fedora 408 k
fedora-release-common noarch 40-0.7 fedora 18 k
findutils ppc64le 1:4.9.0-6.fc40 fedora 540 k
gawk ppc64le 5.2.2-2.fc39 fedora 1.1 M
glibc-minimal-langpack ppc64le 2.38.9000-8.fc40 copr_base 73 k
grep ppc64le 3.11-5.fc40 fedora 308 k
gzip ppc64le 1.12-6.fc39 fedora 170 k
info ppc64le 7.0.3-3.fc39 fedora 200 k
patch ppc64le 2.7.6-22.fc39 fedora 137 k
redhat-rpm-config noarch 270-1.fc40 copr_base 74 k
rpm-build ppc64le 4.18.99-1.fc40 fedora 80 k
sed ppc64le 4.8-14.fc39 fedora 312 k
shadow-utils ppc64le 2:4.14.0-1.fc40 fedora 1.3 M
tar ppc64le 2:1.35-2.fc40 fedora 884 k
unzip ppc64le 6.0-62.fc39 fedora 190 k
util-linux ppc64le 2.39.2-1.fc40 copr_base 1.2 M
which ppc64le 2.21-40.fc39 fedora 43 k
xz ppc64le 5.4.4-1.fc39 fedora 559 k
Installing dependencies:
alternatives ppc64le 1.25-1.fc39 fedora 41 k
ansible-srpm-macros noarch 1-11.fc39 fedora 21 k
audit-libs ppc64le 3.1.2-4.fc40 fedora 132 k
authselect ppc64le 1.4.2-3.fc39 fedora 145 k
authselect-libs ppc64le 1.4.2-3.fc39 fedora 253 k
basesystem noarch 11-18.fc39 fedora 7.2 k
binutils ppc64le 2.41-5.fc40 fedora 6.4 M
binutils-gold ppc64le 2.41-5.fc40 fedora 1.1 M
bzip2-libs ppc64le 1.0.8-16.fc39 fedora 47 k
ca-certificates noarch 2023.2.60_v7.0.306-3.fc40 fedora 837 k
coreutils-common ppc64le 9.4-1.fc40 fedora 2.1 M
cracklib ppc64le 2.9.11-2.fc40 copr_base 86 k
crypto-policies noarch 20230731-1.git5ed06e0.fc39 fedora 99 k
curl ppc64le 8.3.0-1.fc40 copr_base 357 k
cyrus-sasl-lib ppc64le 2.1.28-11.fc40 copr_base 878 k
debugedit ppc64le 5.0-10.fc39 fedora 80 k
dwz ppc64le 0.15-3.fc39 fedora 147 k
ed ppc64le 1.19-4.fc39 fedora 81 k
efi-srpm-macros noarch 5-9.fc39 fedora 22 k
elfutils ppc64le 0.189-6.fc40 copr_base 563 k
elfutils-debuginfod-client ppc64le 0.189-6.fc40 copr_base 40 k
elfutils-default-yama-scope noarch 0.189-6.fc40 copr_base 14 k
elfutils-libelf ppc64le 0.189-6.fc40 copr_base 204 k
elfutils-libs ppc64le 0.189-6.fc40 copr_base 294 k
fedora-gpg-keys noarch 40-0.1 fedora 130 k
fedora-release noarch 40-0.7 fedora 8.0 k
fedora-release-identity-basic
noarch 40-0.7 fedora 8.8 k
fedora-repos noarch 40-0.1 fedora 9.4 k
fedora-repos-rawhide noarch 40-0.1 fedora 9.0 k
file ppc64le 5.45-1.fc40 copr_base 50 k
file-libs ppc64le 5.45-1.fc40 copr_base 775 k
filesystem ppc64le 3.18-6.fc39 fedora 1.1 M
fonts-srpm-macros noarch 1:2.0.5-12.fc39 fedora 26 k
forge-srpm-macros noarch 0.1.0-1.fc40 fedora 18 k
fpc-srpm-macros noarch 1.3-8.fc39 fedora 7.4 k
gdb-minimal ppc64le 13.2-8.fc40 fedora 4.2 M
gdbm-libs ppc64le 1:1.23-4.fc39 fedora 62 k
ghc-srpm-macros noarch 1.6.1-2.fc39 fedora 7.8 k
glibc ppc64le 2.38.9000-8.fc40 copr_base 2.2 M
glibc-common ppc64le 2.38.9000-8.fc40 copr_base 364 k
glibc-gconv-extra ppc64le 2.38.9000-8.fc40 copr_base 2.0 M
gmp ppc64le 1:6.2.1-5.fc39 fedora 304 k
gnat-srpm-macros noarch 6-3.fc39 fedora 8.8 k
go-srpm-macros noarch 3.2.0-7.fc40 fedora 27 k
jansson ppc64le 2.13.1-7.fc39 fedora 49 k
kernel-srpm-macros noarch 1.0-20.fc39 fedora 10 k
keyutils-libs ppc64le 1.6.1-7.fc39 fedora 32 k
krb5-libs ppc64le 1.21.2-1.fc40 fedora 850 k
libacl ppc64le 2.3.1-9.fc40 fedora 26 k
libarchive ppc64le 3.7.2-1.fc40 copr_base 477 k
libattr ppc64le 2.5.1-9.fc40 fedora 19 k
libblkid ppc64le 2.39.2-1.fc40 copr_base 134 k
libbrotli ppc64le 1.1.0-1.fc40 fedora 380 k
libcap ppc64le 2.48-7.fc39 fedora 73 k
libcap-ng ppc64le 0.8.3-8.fc40 fedora 33 k
libcom_err ppc64le 1.47.0-2.fc39 fedora 27 k
libcurl ppc64le 8.3.0-1.fc40 copr_base 380 k
libdb ppc64le 5.3.28-58.fc40 copr_base 831 k
libeconf ppc64le 0.5.2-1.fc40 fedora 34 k
libevent ppc64le 2.1.12-9.fc39 fedora 275 k
libfdisk ppc64le 2.39.2-1.fc40 copr_base 179 k
libffi ppc64le 3.4.4-4.fc39 fedora 38 k
libgcc ppc64le 13.2.1-1.fc39 fedora 104 k
libgomp ppc64le 13.2.1-1.fc39 fedora 332 k
libidn2 ppc64le 2.3.4-3.fc39 fedora 121 k
libmount ppc64le 2.39.2-1.fc40 copr_base 177 k
libnghttp2 ppc64le 1.56.0-1.fc40 copr_base 85 k
libnsl2 ppc64le 2.0.0-6.fc39 fedora 32 k
libpkgconf ppc64le 1.9.5-2.fc39 fedora 42 k
libpsl ppc64le 0.21.2-4.fc39 fedora 65 k
libpwquality ppc64le 1.4.5-6.fc39 fedora 123 k
librtas ppc64le 2.0.4-3.fc39 fedora 70 k
libselinux ppc64le 3.5-5.fc39 fedora 100 k
libsemanage ppc64le 3.5-4.fc39 fedora 131 k
libsepol ppc64le 3.5-2.fc39 fedora 356 k
libsigsegv ppc64le 2.14-5.fc39 fedora 28 k
libsmartcols ppc64le 2.39.2-1.fc40 copr_base 74 k
libssh ppc64le 0.10.5-2.fc40 copr_base 239 k
libssh-config noarch 0.10.5-2.fc40 copr_base 9.6 k
libstdc++ ppc64le 13.2.1-1.fc39 fedora 994 k
libtasn1 ppc64le 4.19.0-3.fc39 fedora 80 k
libtirpc ppc64le 1.3.3-1.rc2.fc39 fedora 108 k
libunistring ppc64le 1.1-5.fc40 fedora 578 k
libutempter ppc64le 1.2.1-10.fc39 fedora 27 k
libuuid ppc64le 2.39.2-1.fc40 copr_base 30 k
libverto ppc64le 0.3.2-6.fc39 fedora 22 k
libxcrypt ppc64le 4.4.36-2.fc39 fedora 132 k
libxml2 ppc64le 2.11.5-1.fc40 copr_base 778 k
libzstd ppc64le 1.5.5-4.fc40 copr_base 336 k
lua-libs ppc64le 5.4.6-3.fc39 fedora 149 k
lua-srpm-macros noarch 1-9.fc39 fedora 8.6 k
lz4-libs ppc64le 1.9.4-4.fc39 fedora 85 k
mpfr ppc64le 4.2.0-3.fc39 fedora 353 k
ncurses-base noarch 6.4-7.20230520.fc40 fedora 88 k
ncurses-libs ppc64le 6.4-7.20230520.fc40 fedora 380 k
ocaml-srpm-macros noarch 8-2.fc39 fedora 14 k
openblas-srpm-macros noarch 2-14.fc39 fedora 7.5 k
openldap ppc64le 2.6.6-1.fc39 fedora 287 k
openssl-libs ppc64le 1:3.1.1-4.fc40 copr_base 2.3 M
p11-kit ppc64le 0.25.0-2.fc39 fedora 500 k
p11-kit-trust ppc64le 0.25.0-2.fc39 fedora 156 k
package-notes-srpm-macros noarch 0.5-9.fc39 fedora 11 k
pam ppc64le 1.5.3-2.fc39 fedora 592 k
pam-libs ppc64le 1.5.3-2.fc39 fedora 64 k
pcre2 ppc64le 10.42-1.fc39.2 fedora 241 k
pcre2-syntax noarch 10.42-1.fc39.2 fedora 143 k
perl-srpm-macros noarch 1-51.fc39 fedora 8.0 k
pkgconf ppc64le 1.9.5-2.fc39 fedora 43 k
pkgconf-m4 noarch 1.9.5-2.fc39 fedora 14 k
pkgconf-pkg-config ppc64le 1.9.5-2.fc39 fedora 9.6 k
popt ppc64le 1.19-3.fc39 fedora 71 k
publicsuffix-list-dafsa noarch 20230812-1.fc40 fedora 57 k
pyproject-srpm-macros noarch 1.9.0-2.fc39 fedora 14 k
python-srpm-macros noarch 3.12-4.fc40 fedora 25 k
qt5-srpm-macros noarch 5.15.10-2.fc39 fedora 8.3 k
qt6-srpm-macros noarch 6.5.2-2.fc39 fedora 9.2 k
readline ppc64le 8.2-4.fc39 fedora 229 k
rpm ppc64le 4.18.99-1.fc40 fedora 537 k
rpm-build-libs ppc64le 4.18.99-1.fc40 fedora 103 k
rpm-libs ppc64le 4.18.99-1.fc40 fedora 356 k
rpm-sequoia ppc64le 1.5.0-1.fc40 fedora 1.7 M
rust-srpm-macros noarch 24-5.fc40 fedora 12 k
setup noarch 2.14.4-1.fc39 fedora 154 k
sqlite-libs ppc64le 3.43.1-1.fc40 fedora 798 k
systemd-libs ppc64le 254.1-2.fc40 fedora 733 k
tzdata noarch 2023c-3.fc40 fedora 718 k
util-linux-core ppc64le 2.39.2-1.fc40 copr_base 520 k
xxhash-libs ppc64le 0.8.2-1.fc39 fedora 37 k
xz-libs ppc64le 5.4.4-1.fc39 fedora 121 k
zip ppc64le 3.0-38.fc39 fedora 274 k
zlib-ng-compat ppc64le 2.1.3-3.fc40 copr_base 83 k
zstd ppc64le 1.5.5-4.fc40 copr_base 500 k
Installing Groups:
Buildsystem building group
Transaction Summary
================================================================================
Install 154 Packages
Total size: 57 M
Installed size: 327 M
Downloading Packages:
[SKIPPED] cracklib-2.9.11-2.fc40.ppc64le.rpm: Already downloaded
[SKIPPED] curl-8.3.0-1.fc40.ppc64le.rpm: Already downloaded
[SKIPPED] cyrus-sasl-lib-2.1.28-11.fc40.ppc64le.rpm: Already downloaded
[SKIPPED] elfutils-0.189-6.fc40.ppc64le.rpm: Already downloaded
[SKIPPED] elfutils-debuginfod-client-0.189-6.fc40.ppc64le.rpm: Already downloaded
[SKIPPED] elfutils-default-yama-scope-0.189-6.fc40.noarch.rpm: Already downloaded
[SKIPPED] elfutils-libelf-0.189-6.fc40.ppc64le.rpm: Already downloaded
[SKIPPED] elfutils-libs-0.189-6.fc40.ppc64le.rpm: Already downloaded
[SKIPPED] file-5.45-1.fc40.ppc64le.rpm: Already downloaded
[SKIPPED] file-libs-5.45-1.fc40.ppc64le.rpm: Already downloaded
[SKIPPED] glibc-2.38.9000-8.fc40.ppc64le.rpm: Already downloaded
[SKIPPED] glibc-common-2.38.9000-8.fc40.ppc64le.rpm: Already downloaded
[SKIPPED] glibc-gconv-extra-2.38.9000-8.fc40.ppc64le.rpm: Already downloaded
[SKIPPED] glibc-minimal-langpack-2.38.9000-8.fc40.ppc64le.rpm: Already downloaded
[SKIPPED] libarchive-3.7.2-1.fc40.ppc64le.rpm: Already downloaded
[SKIPPED] libblkid-2.39.2-1.fc40.ppc64le.rpm: Already downloaded
[SKIPPED] libcurl-8.3.0-1.fc40.ppc64le.rpm: Already downloaded
[SKIPPED] libdb-5.3.28-58.fc40.ppc64le.rpm: Already downloaded
[SKIPPED] libfdisk-2.39.2-1.fc40.ppc64le.rpm: Already downloaded
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fedora 1.6 MB/s | 1.6 kB 00:00
Importing GPG key 0xA15B79CC:
Userid : "Fedora (40) <fedora-40-primary@fedoraproject.org>"
Fingerprint: 115D F9AE F857 853E E844 5D0A 0727 707E A15B 79CC
From : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-40-primary
Key imported successfully
fedora 1.6 MB/s | 1.6 kB 00:00
GPG key at file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-40-primary (0xA15B79CC) is already installed
fedora 1.6 MB/s | 1.6 kB 00:00
Importing GPG key 0x18B8E74C:
Userid : "Fedora (39) <fedora-39-primary@fedoraproject.org>"
Fingerprint: E8F2 3996 F232 1864 0CB4 4CBE 75CF 5AC4 18B8 E74C
From : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-39-primary
Key imported successfully
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
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Installing : cracklib-2.9.11-2.fc40.ppc64le 120/154
Installing : libpwquality-1.4.5-6.fc39.ppc64le 121/154
Installing : authselect-1.4.2-3.fc39.ppc64le 122/154
Installing : libnsl2-2.0.0-6.fc39.ppc64le 123/154
Installing : pam-1.5.3-2.fc39.ppc64le 124/154
Installing : libarchive-3.7.2-1.fc40.ppc64le 125/154
Installing : libevent-2.1.12-9.fc39.ppc64le 126/154
Installing : openldap-2.6.6-1.fc39.ppc64le 127/154
Installing : rpm-sequoia-1.5.0-1.fc40.ppc64le 128/154
Installing : rpm-libs-4.18.99-1.fc40.ppc64le 129/154
Installing : ansible-srpm-macros-1-11.fc39.noarch 130/154
Installing : libssh-config-0.10.5-2.fc40.noarch 131/154
Installing : libssh-0.10.5-2.fc40.ppc64le 132/154
Installing : libcurl-8.3.0-1.fc40.ppc64le 133/154
Installing : elfutils-libs-0.189-6.fc40.ppc64le 134/154
Installing : elfutils-debuginfod-client-0.189-6.fc40.ppc64le 135/154
Installing : binutils-gold-2.41-5.fc40.ppc64le 136/154
Running scriptlet: binutils-gold-2.41-5.fc40.ppc64le 136/154
Installing : binutils-2.41-5.fc40.ppc64le 137/154
Running scriptlet: binutils-2.41-5.fc40.ppc64le 137/154
Installing : elfutils-0.189-6.fc40.ppc64le 138/154
Installing : gdb-minimal-13.2-8.fc40.ppc64le 139/154
Installing : debugedit-5.0-10.fc39.ppc64le 140/154
Installing : rpm-build-libs-4.18.99-1.fc40.ppc64le 141/154
Installing : curl-8.3.0-1.fc40.ppc64le 142/154
Running scriptlet: rpm-4.18.99-1.fc40.ppc64le 143/154
Installing : rpm-4.18.99-1.fc40.ppc64le 143/154
Installing : efi-srpm-macros-5-9.fc39.noarch 144/154
Installing : lua-srpm-macros-1-9.fc39.noarch 145/154
Installing : fonts-srpm-macros-1:2.0.5-12.fc39.noarch 146/154
Installing : forge-srpm-macros-0.1.0-1.fc40.noarch 147/154
Installing : go-srpm-macros-3.2.0-7.fc40.noarch 148/154
Installing : python-srpm-macros-3.12-4.fc40.noarch 149/154
Installing : redhat-rpm-config-270-1.fc40.noarch 150/154
Installing : rpm-build-4.18.99-1.fc40.ppc64le 151/154
Installing : util-linux-2.39.2-1.fc40.ppc64le 152/154
Installing : which-2.21-40.fc39.ppc64le 153/154
Installing : info-7.0.3-3.fc39.ppc64le 154/154
Running scriptlet: filesystem-3.18-6.fc39.ppc64le 154/154
Running scriptlet: ca-certificates-2023.2.60_v7.0.306-3.fc40.noarch 154/154
Running scriptlet: authselect-libs-1.4.2-3.fc39.ppc64le 154/154
Running scriptlet: rpm-4.18.99-1.fc40.ppc64le 154/154
Running scriptlet: info-7.0.3-3.fc39.ppc64le 154/154
Verifying : cracklib-2.9.11-2.fc40.ppc64le 1/154
Verifying : curl-8.3.0-1.fc40.ppc64le 2/154
Verifying : cyrus-sasl-lib-2.1.28-11.fc40.ppc64le 3/154
Verifying : elfutils-0.189-6.fc40.ppc64le 4/154
Verifying : elfutils-debuginfod-client-0.189-6.fc40.ppc64le 5/154
Verifying : elfutils-default-yama-scope-0.189-6.fc40.noarch 6/154
Verifying : elfutils-libelf-0.189-6.fc40.ppc64le 7/154
Verifying : elfutils-libs-0.189-6.fc40.ppc64le 8/154
Verifying : file-5.45-1.fc40.ppc64le 9/154
Verifying : file-libs-5.45-1.fc40.ppc64le 10/154
Verifying : glibc-2.38.9000-8.fc40.ppc64le 11/154
Verifying : glibc-common-2.38.9000-8.fc40.ppc64le 12/154
Verifying : glibc-gconv-extra-2.38.9000-8.fc40.ppc64le 13/154
Verifying : glibc-minimal-langpack-2.38.9000-8.fc40.ppc64le 14/154
Verifying : libarchive-3.7.2-1.fc40.ppc64le 15/154
Verifying : libblkid-2.39.2-1.fc40.ppc64le 16/154
Verifying : libcurl-8.3.0-1.fc40.ppc64le 17/154
Verifying : libdb-5.3.28-58.fc40.ppc64le 18/154
Verifying : libfdisk-2.39.2-1.fc40.ppc64le 19/154
Verifying : libmount-2.39.2-1.fc40.ppc64le 20/154
Verifying : libnghttp2-1.56.0-1.fc40.ppc64le 21/154
Verifying : libsmartcols-2.39.2-1.fc40.ppc64le 22/154
Verifying : libssh-0.10.5-2.fc40.ppc64le 23/154
Verifying : libssh-config-0.10.5-2.fc40.noarch 24/154
Verifying : libuuid-2.39.2-1.fc40.ppc64le 25/154
Verifying : libxml2-2.11.5-1.fc40.ppc64le 26/154
Verifying : libzstd-1.5.5-4.fc40.ppc64le 27/154
Verifying : openssl-libs-1:3.1.1-4.fc40.ppc64le 28/154
Verifying : redhat-rpm-config-270-1.fc40.noarch 29/154
Verifying : util-linux-2.39.2-1.fc40.ppc64le 30/154
Verifying : util-linux-core-2.39.2-1.fc40.ppc64le 31/154
Verifying : zlib-ng-compat-2.1.3-3.fc40.ppc64le 32/154
Verifying : zstd-1.5.5-4.fc40.ppc64le 33/154
Verifying : alternatives-1.25-1.fc39.ppc64le 34/154
Verifying : ansible-srpm-macros-1-11.fc39.noarch 35/154
Verifying : audit-libs-3.1.2-4.fc40.ppc64le 36/154
Verifying : authselect-1.4.2-3.fc39.ppc64le 37/154
Verifying : authselect-libs-1.4.2-3.fc39.ppc64le 38/154
Verifying : basesystem-11-18.fc39.noarch 39/154
Verifying : bash-5.2.15-5.fc39.ppc64le 40/154
Verifying : binutils-2.41-5.fc40.ppc64le 41/154
Verifying : binutils-gold-2.41-5.fc40.ppc64le 42/154
Verifying : bzip2-1.0.8-16.fc39.ppc64le 43/154
Verifying : bzip2-libs-1.0.8-16.fc39.ppc64le 44/154
Verifying : ca-certificates-2023.2.60_v7.0.306-3.fc40.noarch 45/154
Verifying : coreutils-9.4-1.fc40.ppc64le 46/154
Verifying : coreutils-common-9.4-1.fc40.ppc64le 47/154
Verifying : cpio-2.14-4.fc39.ppc64le 48/154
Verifying : crypto-policies-20230731-1.git5ed06e0.fc39.noarc 49/154
Verifying : debugedit-5.0-10.fc39.ppc64le 50/154
Verifying : diffutils-3.10-3.fc39.ppc64le 51/154
Verifying : dwz-0.15-3.fc39.ppc64le 52/154
Verifying : ed-1.19-4.fc39.ppc64le 53/154
Verifying : efi-srpm-macros-5-9.fc39.noarch 54/154
Verifying : fedora-gpg-keys-40-0.1.noarch 55/154
Verifying : fedora-release-40-0.7.noarch 56/154
Verifying : fedora-release-common-40-0.7.noarch 57/154
Verifying : fedora-release-identity-basic-40-0.7.noarch 58/154
Verifying : fedora-repos-40-0.1.noarch 59/154
Verifying : fedora-repos-rawhide-40-0.1.noarch 60/154
Verifying : filesystem-3.18-6.fc39.ppc64le 61/154
Verifying : findutils-1:4.9.0-6.fc40.ppc64le 62/154
Verifying : fonts-srpm-macros-1:2.0.5-12.fc39.noarch 63/154
Verifying : forge-srpm-macros-0.1.0-1.fc40.noarch 64/154
Verifying : fpc-srpm-macros-1.3-8.fc39.noarch 65/154
Verifying : gawk-5.2.2-2.fc39.ppc64le 66/154
Verifying : gdb-minimal-13.2-8.fc40.ppc64le 67/154
Verifying : gdbm-libs-1:1.23-4.fc39.ppc64le 68/154
Verifying : ghc-srpm-macros-1.6.1-2.fc39.noarch 69/154
Verifying : gmp-1:6.2.1-5.fc39.ppc64le 70/154
Verifying : gnat-srpm-macros-6-3.fc39.noarch 71/154
Verifying : go-srpm-macros-3.2.0-7.fc40.noarch 72/154
Verifying : grep-3.11-5.fc40.ppc64le 73/154
Verifying : gzip-1.12-6.fc39.ppc64le 74/154
Verifying : info-7.0.3-3.fc39.ppc64le 75/154
Verifying : jansson-2.13.1-7.fc39.ppc64le 76/154
Verifying : kernel-srpm-macros-1.0-20.fc39.noarch 77/154
Verifying : keyutils-libs-1.6.1-7.fc39.ppc64le 78/154
Verifying : krb5-libs-1.21.2-1.fc40.ppc64le 79/154
Verifying : libacl-2.3.1-9.fc40.ppc64le 80/154
Verifying : libattr-2.5.1-9.fc40.ppc64le 81/154
Verifying : libbrotli-1.1.0-1.fc40.ppc64le 82/154
Verifying : libcap-2.48-7.fc39.ppc64le 83/154
Verifying : libcap-ng-0.8.3-8.fc40.ppc64le 84/154
Verifying : libcom_err-1.47.0-2.fc39.ppc64le 85/154
Verifying : libeconf-0.5.2-1.fc40.ppc64le 86/154
Verifying : libevent-2.1.12-9.fc39.ppc64le 87/154
Verifying : libffi-3.4.4-4.fc39.ppc64le 88/154
Verifying : libgcc-13.2.1-1.fc39.ppc64le 89/154
Verifying : libgomp-13.2.1-1.fc39.ppc64le 90/154
Verifying : libidn2-2.3.4-3.fc39.ppc64le 91/154
Verifying : libnsl2-2.0.0-6.fc39.ppc64le 92/154
Verifying : libpkgconf-1.9.5-2.fc39.ppc64le 93/154
Verifying : libpsl-0.21.2-4.fc39.ppc64le 94/154
Verifying : libpwquality-1.4.5-6.fc39.ppc64le 95/154
Verifying : librtas-2.0.4-3.fc39.ppc64le 96/154
Verifying : libselinux-3.5-5.fc39.ppc64le 97/154
Verifying : libsemanage-3.5-4.fc39.ppc64le 98/154
Verifying : libsepol-3.5-2.fc39.ppc64le 99/154
Verifying : libsigsegv-2.14-5.fc39.ppc64le 100/154
Verifying : libstdc++-13.2.1-1.fc39.ppc64le 101/154
Verifying : libtasn1-4.19.0-3.fc39.ppc64le 102/154
Verifying : libtirpc-1.3.3-1.rc2.fc39.ppc64le 103/154
Verifying : libunistring-1.1-5.fc40.ppc64le 104/154
Verifying : libutempter-1.2.1-10.fc39.ppc64le 105/154
Verifying : libverto-0.3.2-6.fc39.ppc64le 106/154
Verifying : libxcrypt-4.4.36-2.fc39.ppc64le 107/154
Verifying : lua-libs-5.4.6-3.fc39.ppc64le 108/154
Verifying : lua-srpm-macros-1-9.fc39.noarch 109/154
Verifying : lz4-libs-1.9.4-4.fc39.ppc64le 110/154
Verifying : mpfr-4.2.0-3.fc39.ppc64le 111/154
Verifying : ncurses-base-6.4-7.20230520.fc40.noarch 112/154
Verifying : ncurses-libs-6.4-7.20230520.fc40.ppc64le 113/154
Verifying : ocaml-srpm-macros-8-2.fc39.noarch 114/154
Verifying : openblas-srpm-macros-2-14.fc39.noarch 115/154
Verifying : openldap-2.6.6-1.fc39.ppc64le 116/154
Verifying : p11-kit-0.25.0-2.fc39.ppc64le 117/154
Verifying : p11-kit-trust-0.25.0-2.fc39.ppc64le 118/154
Verifying : package-notes-srpm-macros-0.5-9.fc39.noarch 119/154
Verifying : pam-1.5.3-2.fc39.ppc64le 120/154
Verifying : pam-libs-1.5.3-2.fc39.ppc64le 121/154
Verifying : patch-2.7.6-22.fc39.ppc64le 122/154
Verifying : pcre2-10.42-1.fc39.2.ppc64le 123/154
Verifying : pcre2-syntax-10.42-1.fc39.2.noarch 124/154
Verifying : perl-srpm-macros-1-51.fc39.noarch 125/154
Verifying : pkgconf-1.9.5-2.fc39.ppc64le 126/154
Verifying : pkgconf-m4-1.9.5-2.fc39.noarch 127/154
Verifying : pkgconf-pkg-config-1.9.5-2.fc39.ppc64le 128/154
Verifying : popt-1.19-3.fc39.ppc64le 129/154
Verifying : publicsuffix-list-dafsa-20230812-1.fc40.noarch 130/154
Verifying : pyproject-srpm-macros-1.9.0-2.fc39.noarch 131/154
Verifying : python-srpm-macros-3.12-4.fc40.noarch 132/154
Verifying : qt5-srpm-macros-5.15.10-2.fc39.noarch 133/154
Verifying : qt6-srpm-macros-6.5.2-2.fc39.noarch 134/154
Verifying : readline-8.2-4.fc39.ppc64le 135/154
Verifying : rpm-4.18.99-1.fc40.ppc64le 136/154
Verifying : rpm-build-4.18.99-1.fc40.ppc64le 137/154
Verifying : rpm-build-libs-4.18.99-1.fc40.ppc64le 138/154
Verifying : rpm-libs-4.18.99-1.fc40.ppc64le 139/154
Verifying : rpm-sequoia-1.5.0-1.fc40.ppc64le 140/154
Verifying : rust-srpm-macros-24-5.fc40.noarch 141/154
Verifying : sed-4.8-14.fc39.ppc64le 142/154
Verifying : setup-2.14.4-1.fc39.noarch 143/154
Verifying : shadow-utils-2:4.14.0-1.fc40.ppc64le 144/154
Verifying : sqlite-libs-3.43.1-1.fc40.ppc64le 145/154
Verifying : systemd-libs-254.1-2.fc40.ppc64le 146/154
Verifying : tar-2:1.35-2.fc40.ppc64le 147/154
Verifying : tzdata-2023c-3.fc40.noarch 148/154
Verifying : unzip-6.0-62.fc39.ppc64le 149/154
Verifying : which-2.21-40.fc39.ppc64le 150/154
Verifying : xxhash-libs-0.8.2-1.fc39.ppc64le 151/154
Verifying : xz-5.4.4-1.fc39.ppc64le 152/154
Verifying : xz-libs-5.4.4-1.fc39.ppc64le 153/154
Verifying : zip-3.0-38.fc39.ppc64le 154/154
Installed:
alternatives-1.25-1.fc39.ppc64le
ansible-srpm-macros-1-11.fc39.noarch
audit-libs-3.1.2-4.fc40.ppc64le
authselect-1.4.2-3.fc39.ppc64le
authselect-libs-1.4.2-3.fc39.ppc64le
basesystem-11-18.fc39.noarch
bash-5.2.15-5.fc39.ppc64le
binutils-2.41-5.fc40.ppc64le
binutils-gold-2.41-5.fc40.ppc64le
bzip2-1.0.8-16.fc39.ppc64le
bzip2-libs-1.0.8-16.fc39.ppc64le
ca-certificates-2023.2.60_v7.0.306-3.fc40.noarch
coreutils-9.4-1.fc40.ppc64le
coreutils-common-9.4-1.fc40.ppc64le
cpio-2.14-4.fc39.ppc64le
cracklib-2.9.11-2.fc40.ppc64le
crypto-policies-20230731-1.git5ed06e0.fc39.noarch
curl-8.3.0-1.fc40.ppc64le
cyrus-sasl-lib-2.1.28-11.fc40.ppc64le
debugedit-5.0-10.fc39.ppc64le
diffutils-3.10-3.fc39.ppc64le
dwz-0.15-3.fc39.ppc64le
ed-1.19-4.fc39.ppc64le
efi-srpm-macros-5-9.fc39.noarch
elfutils-0.189-6.fc40.ppc64le
elfutils-debuginfod-client-0.189-6.fc40.ppc64le
elfutils-default-yama-scope-0.189-6.fc40.noarch
elfutils-libelf-0.189-6.fc40.ppc64le
elfutils-libs-0.189-6.fc40.ppc64le
fedora-gpg-keys-40-0.1.noarch
fedora-release-40-0.7.noarch
fedora-release-common-40-0.7.noarch
fedora-release-identity-basic-40-0.7.noarch
fedora-repos-40-0.1.noarch
fedora-repos-rawhide-40-0.1.noarch
file-5.45-1.fc40.ppc64le
file-libs-5.45-1.fc40.ppc64le
filesystem-3.18-6.fc39.ppc64le
findutils-1:4.9.0-6.fc40.ppc64le
fonts-srpm-macros-1:2.0.5-12.fc39.noarch
forge-srpm-macros-0.1.0-1.fc40.noarch
fpc-srpm-macros-1.3-8.fc39.noarch
gawk-5.2.2-2.fc39.ppc64le
gdb-minimal-13.2-8.fc40.ppc64le
gdbm-libs-1:1.23-4.fc39.ppc64le
ghc-srpm-macros-1.6.1-2.fc39.noarch
glibc-2.38.9000-8.fc40.ppc64le
glibc-common-2.38.9000-8.fc40.ppc64le
glibc-gconv-extra-2.38.9000-8.fc40.ppc64le
glibc-minimal-langpack-2.38.9000-8.fc40.ppc64le
gmp-1:6.2.1-5.fc39.ppc64le
gnat-srpm-macros-6-3.fc39.noarch
go-srpm-macros-3.2.0-7.fc40.noarch
grep-3.11-5.fc40.ppc64le
gzip-1.12-6.fc39.ppc64le
info-7.0.3-3.fc39.ppc64le
jansson-2.13.1-7.fc39.ppc64le
kernel-srpm-macros-1.0-20.fc39.noarch
keyutils-libs-1.6.1-7.fc39.ppc64le
krb5-libs-1.21.2-1.fc40.ppc64le
libacl-2.3.1-9.fc40.ppc64le
libarchive-3.7.2-1.fc40.ppc64le
libattr-2.5.1-9.fc40.ppc64le
libblkid-2.39.2-1.fc40.ppc64le
libbrotli-1.1.0-1.fc40.ppc64le
libcap-2.48-7.fc39.ppc64le
libcap-ng-0.8.3-8.fc40.ppc64le
libcom_err-1.47.0-2.fc39.ppc64le
libcurl-8.3.0-1.fc40.ppc64le
libdb-5.3.28-58.fc40.ppc64le
libeconf-0.5.2-1.fc40.ppc64le
libevent-2.1.12-9.fc39.ppc64le
libfdisk-2.39.2-1.fc40.ppc64le
libffi-3.4.4-4.fc39.ppc64le
libgcc-13.2.1-1.fc39.ppc64le
libgomp-13.2.1-1.fc39.ppc64le
libidn2-2.3.4-3.fc39.ppc64le
libmount-2.39.2-1.fc40.ppc64le
libnghttp2-1.56.0-1.fc40.ppc64le
libnsl2-2.0.0-6.fc39.ppc64le
libpkgconf-1.9.5-2.fc39.ppc64le
libpsl-0.21.2-4.fc39.ppc64le
libpwquality-1.4.5-6.fc39.ppc64le
librtas-2.0.4-3.fc39.ppc64le
libselinux-3.5-5.fc39.ppc64le
libsemanage-3.5-4.fc39.ppc64le
libsepol-3.5-2.fc39.ppc64le
libsigsegv-2.14-5.fc39.ppc64le
libsmartcols-2.39.2-1.fc40.ppc64le
libssh-0.10.5-2.fc40.ppc64le
libssh-config-0.10.5-2.fc40.noarch
libstdc++-13.2.1-1.fc39.ppc64le
libtasn1-4.19.0-3.fc39.ppc64le
libtirpc-1.3.3-1.rc2.fc39.ppc64le
libunistring-1.1-5.fc40.ppc64le
libutempter-1.2.1-10.fc39.ppc64le
libuuid-2.39.2-1.fc40.ppc64le
libverto-0.3.2-6.fc39.ppc64le
libxcrypt-4.4.36-2.fc39.ppc64le
libxml2-2.11.5-1.fc40.ppc64le
libzstd-1.5.5-4.fc40.ppc64le
lua-libs-5.4.6-3.fc39.ppc64le
lua-srpm-macros-1-9.fc39.noarch
lz4-libs-1.9.4-4.fc39.ppc64le
mpfr-4.2.0-3.fc39.ppc64le
ncurses-base-6.4-7.20230520.fc40.noarch
ncurses-libs-6.4-7.20230520.fc40.ppc64le
ocaml-srpm-macros-8-2.fc39.noarch
openblas-srpm-macros-2-14.fc39.noarch
openldap-2.6.6-1.fc39.ppc64le
openssl-libs-1:3.1.1-4.fc40.ppc64le
p11-kit-0.25.0-2.fc39.ppc64le
p11-kit-trust-0.25.0-2.fc39.ppc64le
package-notes-srpm-macros-0.5-9.fc39.noarch
pam-1.5.3-2.fc39.ppc64le
pam-libs-1.5.3-2.fc39.ppc64le
patch-2.7.6-22.fc39.ppc64le
pcre2-10.42-1.fc39.2.ppc64le
pcre2-syntax-10.42-1.fc39.2.noarch
perl-srpm-macros-1-51.fc39.noarch
pkgconf-1.9.5-2.fc39.ppc64le
pkgconf-m4-1.9.5-2.fc39.noarch
pkgconf-pkg-config-1.9.5-2.fc39.ppc64le
popt-1.19-3.fc39.ppc64le
publicsuffix-list-dafsa-20230812-1.fc40.noarch
pyproject-srpm-macros-1.9.0-2.fc39.noarch
python-srpm-macros-3.12-4.fc40.noarch
qt5-srpm-macros-5.15.10-2.fc39.noarch
qt6-srpm-macros-6.5.2-2.fc39.noarch
readline-8.2-4.fc39.ppc64le
redhat-rpm-config-270-1.fc40.noarch
rpm-4.18.99-1.fc40.ppc64le
rpm-build-4.18.99-1.fc40.ppc64le
rpm-build-libs-4.18.99-1.fc40.ppc64le
rpm-libs-4.18.99-1.fc40.ppc64le
rpm-sequoia-1.5.0-1.fc40.ppc64le
rust-srpm-macros-24-5.fc40.noarch
sed-4.8-14.fc39.ppc64le
setup-2.14.4-1.fc39.noarch
shadow-utils-2:4.14.0-1.fc40.ppc64le
sqlite-libs-3.43.1-1.fc40.ppc64le
systemd-libs-254.1-2.fc40.ppc64le
tar-2:1.35-2.fc40.ppc64le
tzdata-2023c-3.fc40.noarch
unzip-6.0-62.fc39.ppc64le
util-linux-2.39.2-1.fc40.ppc64le
util-linux-core-2.39.2-1.fc40.ppc64le
which-2.21-40.fc39.ppc64le
xxhash-libs-0.8.2-1.fc39.ppc64le
xz-5.4.4-1.fc39.ppc64le
xz-libs-5.4.4-1.fc39.ppc64le
zip-3.0-38.fc39.ppc64le
zlib-ng-compat-2.1.3-3.fc40.ppc64le
zstd-1.5.5-4.fc40.ppc64le
Complete!
Finish: installing minimal buildroot with dnf
Start: creating root cache
Finish: creating root cache
Finish: chroot init
INFO: Installed packages:
INFO: alternatives-1.25-1.fc39.ppc64le
ansible-srpm-macros-1-11.fc39.noarch
audit-libs-3.1.2-4.fc40.ppc64le
authselect-1.4.2-3.fc39.ppc64le
authselect-libs-1.4.2-3.fc39.ppc64le
basesystem-11-18.fc39.noarch
bash-5.2.15-5.fc39.ppc64le
binutils-2.41-5.fc40.ppc64le
binutils-gold-2.41-5.fc40.ppc64le
bzip2-1.0.8-16.fc39.ppc64le
bzip2-libs-1.0.8-16.fc39.ppc64le
ca-certificates-2023.2.60_v7.0.306-3.fc40.noarch
coreutils-9.4-1.fc40.ppc64le
coreutils-common-9.4-1.fc40.ppc64le
cpio-2.14-4.fc39.ppc64le
cracklib-2.9.11-2.fc40.ppc64le
crypto-policies-20230731-1.git5ed06e0.fc39.noarch
curl-8.3.0-1.fc40.ppc64le
cyrus-sasl-lib-2.1.28-11.fc40.ppc64le
debugedit-5.0-10.fc39.ppc64le
diffutils-3.10-3.fc39.ppc64le
dwz-0.15-3.fc39.ppc64le
ed-1.19-4.fc39.ppc64le
efi-srpm-macros-5-9.fc39.noarch
elfutils-0.189-6.fc40.ppc64le
elfutils-debuginfod-client-0.189-6.fc40.ppc64le
elfutils-default-yama-scope-0.189-6.fc40.noarch
elfutils-libelf-0.189-6.fc40.ppc64le
elfutils-libs-0.189-6.fc40.ppc64le
fedora-gpg-keys-40-0.1.noarch
fedora-release-40-0.7.noarch
fedora-release-common-40-0.7.noarch
fedora-release-identity-basic-40-0.7.noarch
fedora-repos-40-0.1.noarch
fedora-repos-rawhide-40-0.1.noarch
file-5.45-1.fc40.ppc64le
file-libs-5.45-1.fc40.ppc64le
filesystem-3.18-6.fc39.ppc64le
findutils-4.9.0-6.fc40.ppc64le
fonts-srpm-macros-2.0.5-12.fc39.noarch
forge-srpm-macros-0.1.0-1.fc40.noarch
fpc-srpm-macros-1.3-8.fc39.noarch
gawk-5.2.2-2.fc39.ppc64le
gdb-minimal-13.2-8.fc40.ppc64le
gdbm-libs-1.23-4.fc39.ppc64le
ghc-srpm-macros-1.6.1-2.fc39.noarch
glibc-2.38.9000-8.fc40.ppc64le
glibc-common-2.38.9000-8.fc40.ppc64le
glibc-gconv-extra-2.38.9000-8.fc40.ppc64le
glibc-minimal-langpack-2.38.9000-8.fc40.ppc64le
gmp-6.2.1-5.fc39.ppc64le
gnat-srpm-macros-6-3.fc39.noarch
go-srpm-macros-3.2.0-7.fc40.noarch
gpg-pubkey-18b8e74c-62f2920f
gpg-pubkey-a15b79cc-63d04c2c
grep-3.11-5.fc40.ppc64le
gzip-1.12-6.fc39.ppc64le
info-7.0.3-3.fc39.ppc64le
jansson-2.13.1-7.fc39.ppc64le
kernel-srpm-macros-1.0-20.fc39.noarch
keyutils-libs-1.6.1-7.fc39.ppc64le
krb5-libs-1.21.2-1.fc40.ppc64le
libacl-2.3.1-9.fc40.ppc64le
libarchive-3.7.2-1.fc40.ppc64le
libattr-2.5.1-9.fc40.ppc64le
libblkid-2.39.2-1.fc40.ppc64le
libbrotli-1.1.0-1.fc40.ppc64le
libcap-2.48-7.fc39.ppc64le
libcap-ng-0.8.3-8.fc40.ppc64le
libcom_err-1.47.0-2.fc39.ppc64le
libcurl-8.3.0-1.fc40.ppc64le
libdb-5.3.28-58.fc40.ppc64le
libeconf-0.5.2-1.fc40.ppc64le
libevent-2.1.12-9.fc39.ppc64le
libfdisk-2.39.2-1.fc40.ppc64le
libffi-3.4.4-4.fc39.ppc64le
libgcc-13.2.1-1.fc39.ppc64le
libgomp-13.2.1-1.fc39.ppc64le
libidn2-2.3.4-3.fc39.ppc64le
libmount-2.39.2-1.fc40.ppc64le
libnghttp2-1.56.0-1.fc40.ppc64le
libnsl2-2.0.0-6.fc39.ppc64le
libpkgconf-1.9.5-2.fc39.ppc64le
libpsl-0.21.2-4.fc39.ppc64le
libpwquality-1.4.5-6.fc39.ppc64le
librtas-2.0.4-3.fc39.ppc64le
libselinux-3.5-5.fc39.ppc64le
libsemanage-3.5-4.fc39.ppc64le
libsepol-3.5-2.fc39.ppc64le
libsigsegv-2.14-5.fc39.ppc64le
libsmartcols-2.39.2-1.fc40.ppc64le
libssh-0.10.5-2.fc40.ppc64le
libssh-config-0.10.5-2.fc40.noarch
libstdc++-13.2.1-1.fc39.ppc64le
libtasn1-4.19.0-3.fc39.ppc64le
libtirpc-1.3.3-1.rc2.fc39.ppc64le
libunistring-1.1-5.fc40.ppc64le
libutempter-1.2.1-10.fc39.ppc64le
libuuid-2.39.2-1.fc40.ppc64le
libverto-0.3.2-6.fc39.ppc64le
libxcrypt-4.4.36-2.fc39.ppc64le
libxml2-2.11.5-1.fc40.ppc64le
libzstd-1.5.5-4.fc40.ppc64le
lua-libs-5.4.6-3.fc39.ppc64le
lua-srpm-macros-1-9.fc39.noarch
lz4-libs-1.9.4-4.fc39.ppc64le
mpfr-4.2.0-3.fc39.ppc64le
ncurses-base-6.4-7.20230520.fc40.noarch
ncurses-libs-6.4-7.20230520.fc40.ppc64le
ocaml-srpm-macros-8-2.fc39.noarch
openblas-srpm-macros-2-14.fc39.noarch
openldap-2.6.6-1.fc39.ppc64le
openssl-libs-3.1.1-4.fc40.ppc64le
p11-kit-0.25.0-2.fc39.ppc64le
p11-kit-trust-0.25.0-2.fc39.ppc64le
package-notes-srpm-macros-0.5-9.fc39.noarch
pam-1.5.3-2.fc39.ppc64le
pam-libs-1.5.3-2.fc39.ppc64le
patch-2.7.6-22.fc39.ppc64le
pcre2-10.42-1.fc39.2.ppc64le
pcre2-syntax-10.42-1.fc39.2.noarch
perl-srpm-macros-1-51.fc39.noarch
pkgconf-1.9.5-2.fc39.ppc64le
pkgconf-m4-1.9.5-2.fc39.noarch
pkgconf-pkg-config-1.9.5-2.fc39.ppc64le
popt-1.19-3.fc39.ppc64le
publicsuffix-list-dafsa-20230812-1.fc40.noarch
pyproject-srpm-macros-1.9.0-2.fc39.noarch
python-srpm-macros-3.12-4.fc40.noarch
qt5-srpm-macros-5.15.10-2.fc39.noarch
qt6-srpm-macros-6.5.2-2.fc39.noarch
readline-8.2-4.fc39.ppc64le
redhat-rpm-config-270-1.fc40.noarch
rpm-4.18.99-1.fc40.ppc64le
rpm-build-4.18.99-1.fc40.ppc64le
rpm-build-libs-4.18.99-1.fc40.ppc64le
rpm-libs-4.18.99-1.fc40.ppc64le
rpm-sequoia-1.5.0-1.fc40.ppc64le
rust-srpm-macros-24-5.fc40.noarch
sed-4.8-14.fc39.ppc64le
setup-2.14.4-1.fc39.noarch
shadow-utils-4.14.0-1.fc40.ppc64le
sqlite-libs-3.43.1-1.fc40.ppc64le
systemd-libs-254.1-2.fc40.ppc64le
tar-1.35-2.fc40.ppc64le
tzdata-2023c-3.fc40.noarch
unzip-6.0-62.fc39.ppc64le
util-linux-2.39.2-1.fc40.ppc64le
util-linux-core-2.39.2-1.fc40.ppc64le
which-2.21-40.fc39.ppc64le
xxhash-libs-0.8.2-1.fc39.ppc64le
xz-5.4.4-1.fc39.ppc64le
xz-libs-5.4.4-1.fc39.ppc64le
zip-3.0-38.fc39.ppc64le
zlib-ng-compat-2.1.3-3.fc40.ppc64le
zstd-1.5.5-4.fc40.ppc64le
Start: buildsrpm
Start: rpmbuild -bs
Building target platforms: ppc64le
Building for target ppc64le
setting SOURCE_DATE_EPOCH=1689984000
Wrote: /builddir/build/SRPMS/samtools-1.15.1-3.fc40.src.rpm
Finish: rpmbuild -bs
INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/fedora-rawhide-ppc64le-1695069238.164412/root/var/log/dnf.rpm.log
/var/lib/mock/fedora-rawhide-ppc64le-1695069238.164412/root/var/log/dnf.librepo.log
/var/lib/mock/fedora-rawhide-ppc64le-1695069238.164412/root/var/log/dnf.log
Finish: buildsrpm
INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-xegk6rp2/samtools/samtools.spec) Config(child) 1 minutes 46 seconds
INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results
INFO: Cleaning up build root ('cleanup_on_success=True')
Start: clean chroot
INFO: unmounting tmpfs.
Finish: clean chroot
INFO: Start(/var/lib/copr-rpmbuild/results/samtools-1.15.1-3.fc40.src.rpm) Config(fedora-rawhide-ppc64le)
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-ppc64le-bootstrap-1695069238.164412/root.
INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-ppc64le-bootstrap-1695069238.164412/root.
INFO: calling preinit hooks
INFO: enabled root cache
INFO: enabled package manager cache
Start(bootstrap): cleaning package manager metadata
Finish(bootstrap): cleaning package manager metadata
Finish(bootstrap): chroot init
Start: chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-ppc64le-1695069238.164412/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
Finish: chroot init
INFO: Buildroot is handled by package management downloaded with a bootstrap image:
rpm-4.18.99-1.fc40.ppc64le
rpm-sequoia-1.5.0-1.fc40.ppc64le
python3-dnf-4.16.2-4.fc40.noarch
python3-dnf-plugins-core-4.4.2-1.fc39.noarch
yum-4.16.2-4.fc40.noarch
Start: build phase for samtools-1.15.1-3.fc40.src.rpm
Start: build setup for samtools-1.15.1-3.fc40.src.rpm
Building target platforms: ppc64le
Building for target ppc64le
setting SOURCE_DATE_EPOCH=1689984000
Wrote: /builddir/build/SRPMS/samtools-1.15.1-3.fc40.src.rpm
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Copr repository 18 kB/s | 1.5 kB 00:00
fedora 88 kB/s | 6.1 kB 00:00
Dependencies resolved.
================================================================================
Package Arch Version Repository Size
================================================================================
Installing:
gcc ppc64le 13.2.1-1.fc39 fedora 31 M
htslib-devel ppc64le 1.15.1-3.fc40 copr_base 100 k
htslib-tools ppc64le 1.15.1-3.fc40 copr_base 628 k
make ppc64le 1:4.4.1-2.fc39 fedora 604 k
ncurses-devel ppc64le 6.4-7.20230520.fc40 fedora 546 k
perl-FindBin noarch 1.53-500.fc39 fedora 14 k
perl-Getopt-Long noarch 1:2.54-500.fc39 fedora 60 k
perl-interpreter ppc64le 4:5.38.0-500.fc39 fedora 72 k
perl-lib ppc64le 0.65-500.fc39 fedora 15 k
zlib-ng-compat-devel ppc64le 2.1.3-3.fc40 copr_base 34 k
Installing dependencies:
annobin-docs noarch 12.26-1.fc40 fedora 94 k
annobin-plugin-gcc ppc64le 12.26-1.fc40 fedora 961 k
cpp ppc64le 13.2.1-1.fc39 fedora 9.8 M
gc ppc64le 8.2.2-4.fc39 fedora 122 k
gcc-plugin-annobin ppc64le 13.2.1-1.fc39 fedora 49 k
glibc-devel ppc64le 2.38.9000-8.fc40 copr_base 515 k
groff-base ppc64le 1.23.0-2.fc39 fedora 1.2 M
guile22 ppc64le 2.2.7-9.fc39 fedora 6.6 M
htslib ppc64le 1.15.1-3.fc40 copr_base 560 k
kernel-headers ppc64le 6.6.0-0.rc1.git0.1.fc40 fedora 1.5 M
libasan ppc64le 13.2.1-1.fc39 fedora 493 k
libatomic ppc64le 13.2.1-1.fc39 fedora 35 k
libmpc ppc64le 1.3.1-3.fc39 fedora 95 k
libtool-ltdl ppc64le 2.4.7-8.fc40 fedora 40 k
libubsan ppc64le 13.2.1-1.fc39 fedora 250 k
libxcrypt-devel ppc64le 4.4.36-2.fc39 fedora 30 k
ncurses ppc64le 6.4-7.20230520.fc40 fedora 424 k
ncurses-c++-libs ppc64le 6.4-7.20230520.fc40 fedora 39 k
perl-AutoLoader noarch 5.74-500.fc39 fedora 21 k
perl-B ppc64le 1.88-500.fc39 fedora 181 k
perl-Carp noarch 1.54-500.fc39 fedora 29 k
perl-Class-Struct noarch 0.68-500.fc39 fedora 22 k
perl-Data-Dumper ppc64le 2.188-501.fc39 fedora 57 k
perl-Digest noarch 1.20-500.fc39 fedora 25 k
perl-Digest-MD5 ppc64le 2.58-500.fc39 fedora 36 k
perl-DynaLoader ppc64le 1.54-500.fc39 fedora 26 k
perl-Encode ppc64le 4:3.19-500.fc39 fedora 1.7 M
perl-Errno ppc64le 1.37-500.fc39 fedora 15 k
perl-Exporter noarch 5.77-500.fc39 fedora 31 k
perl-Fcntl ppc64le 1.15-500.fc39 fedora 21 k
perl-File-Basename noarch 2.86-500.fc39 fedora 17 k
perl-File-Path noarch 2.18-500.fc39 fedora 35 k
perl-File-Temp noarch 1:0.231.100-500.fc39 fedora 58 k
perl-File-stat noarch 1.13-500.fc39 fedora 17 k
perl-FileHandle noarch 2.05-500.fc39 fedora 16 k
perl-Getopt-Std noarch 1.13-500.fc39 fedora 16 k
perl-HTTP-Tiny noarch 0.088-3.fc39 fedora 56 k
perl-IO ppc64le 1.52-500.fc39 fedora 83 k
perl-IO-Socket-IP noarch 0.42-1.fc39 fedora 42 k
perl-IO-Socket-SSL noarch 2.083-3.fc39 fedora 225 k
perl-IPC-Open3 noarch 1.22-500.fc39 fedora 22 k
perl-MIME-Base64 ppc64le 3.16-500.fc39 fedora 30 k
perl-Mozilla-CA noarch 20230821-1.fc40 fedora 13 k
perl-Net-SSLeay ppc64le 1.92-10.fc39 fedora 367 k
perl-POSIX ppc64le 2.13-500.fc39 fedora 117 k
perl-PathTools ppc64le 3.89-500.fc39 fedora 88 k
perl-Pod-Escapes noarch 1:1.07-501.fc40 fedora 19 k
perl-Pod-Perldoc noarch 3.28.01-501.fc39 fedora 86 k
perl-Pod-Simple noarch 1:3.45-4.fc39 fedora 218 k
perl-Pod-Usage noarch 4:2.03-500.fc39 fedora 39 k
perl-Scalar-List-Utils ppc64le 5:1.63-500.fc39 fedora 75 k
perl-SelectSaver noarch 1.02-500.fc39 fedora 12 k
perl-Socket ppc64le 4:2.037-3.fc39 fedora 56 k
perl-Storable ppc64le 1:3.32-500.fc39 fedora 103 k
perl-Symbol noarch 1.09-500.fc39 fedora 14 k
perl-Term-ANSIColor noarch 5.01-501.fc39 fedora 47 k
perl-Term-Cap noarch 1.18-500.fc39 fedora 22 k
perl-Text-ParseWords noarch 3.31-500.fc39 fedora 16 k
perl-Text-Tabs+Wrap noarch 2023.0511-3.fc39 fedora 22 k
perl-Time-Local noarch 2:1.350-3.fc39 fedora 34 k
perl-URI noarch 5.21-1.fc40 fedora 125 k
perl-base noarch 2.27-500.fc39 fedora 16 k
perl-constant noarch 1.33-501.fc39 fedora 22 k
perl-if noarch 0.61.000-500.fc39 fedora 14 k
perl-libnet noarch 3.15-501.fc39 fedora 129 k
perl-libs ppc64le 4:5.38.0-500.fc39 fedora 2.4 M
perl-locale noarch 1.10-500.fc39 fedora 14 k
perl-mro ppc64le 1.28-500.fc39 fedora 29 k
perl-overload noarch 1.37-500.fc39 fedora 46 k
perl-overloading noarch 0.02-500.fc39 fedora 13 k
perl-parent noarch 1:0.241-500.fc39 fedora 14 k
perl-podlators noarch 1:5.01-500.fc39 fedora 125 k
perl-vars noarch 1.05-500.fc39 fedora 13 k
Transaction Summary
================================================================================
Install 83 Packages
Total size: 62 M
Total download size: 1.8 M
Installed size: 224 M
Downloading Packages:
[SKIPPED] glibc-devel-2.38.9000-8.fc40.ppc64le.rpm: Already downloaded
[SKIPPED] zlib-ng-compat-devel-2.1.3-3.fc40.ppc64le.rpm: Already downloaded
[SKIPPED] annobin-docs-12.26-1.fc40.noarch.rpm: Already downloaded
[SKIPPED] annobin-plugin-gcc-12.26-1.fc40.ppc64le.rpm: Already downloaded
[SKIPPED] cpp-13.2.1-1.fc39.ppc64le.rpm: Already downloaded
[SKIPPED] gc-8.2.2-4.fc39.ppc64le.rpm: Already downloaded
[SKIPPED] gcc-13.2.1-1.fc39.ppc64le.rpm: Already downloaded
[SKIPPED] gcc-plugin-annobin-13.2.1-1.fc39.ppc64le.rpm: Already downloaded
[SKIPPED] groff-base-1.23.0-2.fc39.ppc64le.rpm: Already downloaded
[SKIPPED] guile22-2.2.7-9.fc39.ppc64le.rpm: Already downloaded
[SKIPPED] kernel-headers-6.6.0-0.rc1.git0.1.fc40.ppc64le.rpm: Already downloaded
[SKIPPED] libasan-13.2.1-1.fc39.ppc64le.rpm: Already downloaded
[SKIPPED] libatomic-13.2.1-1.fc39.ppc64le.rpm: Already downloaded
[SKIPPED] libmpc-1.3.1-3.fc39.ppc64le.rpm: Already downloaded
[SKIPPED] libtool-ltdl-2.4.7-8.fc40.ppc64le.rpm: Already downloaded
[SKIPPED] libubsan-13.2.1-1.fc39.ppc64le.rpm: Already downloaded
[SKIPPED] libxcrypt-devel-4.4.36-2.fc39.ppc64le.rpm: Already downloaded
[SKIPPED] make-4.4.1-2.fc39.ppc64le.rpm: Already downloaded
[SKIPPED] ncurses-6.4-7.20230520.fc40.ppc64le.rpm: Already downloaded
[SKIPPED] perl-AutoLoader-5.74-500.fc39.noarch.rpm: Already downloaded
[SKIPPED] perl-B-1.88-500.fc39.ppc64le.rpm: Already downloaded
[SKIPPED] perl-Carp-1.54-500.fc39.noarch.rpm: Already downloaded
[SKIPPED] perl-Class-Struct-0.68-500.fc39.noarch.rpm: Already downloaded
[SKIPPED] perl-Data-Dumper-2.188-501.fc39.ppc64le.rpm: Already downloaded
[SKIPPED] perl-Digest-1.20-500.fc39.noarch.rpm: Already downloaded
[SKIPPED] perl-Digest-MD5-2.58-500.fc39.ppc64le.rpm: Already downloaded
[SKIPPED] perl-DynaLoader-1.54-500.fc39.ppc64le.rpm: Already downloaded
[SKIPPED] perl-Encode-3.19-500.fc39.ppc64le.rpm: Already downloaded
[SKIPPED] perl-Errno-1.37-500.fc39.ppc64le.rpm: Already downloaded
[SKIPPED] perl-Exporter-5.77-500.fc39.noarch.rpm: Already downloaded
[SKIPPED] perl-Fcntl-1.15-500.fc39.ppc64le.rpm: Already downloaded
[SKIPPED] perl-File-Basename-2.86-500.fc39.noarch.rpm: Already downloaded
[SKIPPED] perl-File-Path-2.18-500.fc39.noarch.rpm: Already downloaded
[SKIPPED] perl-File-Temp-0.231.100-500.fc39.noarch.rpm: Already downloaded
[SKIPPED] perl-File-stat-1.13-500.fc39.noarch.rpm: Already downloaded
[SKIPPED] perl-FileHandle-2.05-500.fc39.noarch.rpm: Already downloaded
[SKIPPED] perl-FindBin-1.53-500.fc39.noarch.rpm: Already downloaded
[SKIPPED] perl-Getopt-Long-2.54-500.fc39.noarch.rpm: Already downloaded
[SKIPPED] perl-Getopt-Std-1.13-500.fc39.noarch.rpm: Already downloaded
[SKIPPED] perl-HTTP-Tiny-0.088-3.fc39.noarch.rpm: Already downloaded
[SKIPPED] perl-IO-1.52-500.fc39.ppc64le.rpm: Already downloaded
[SKIPPED] perl-IO-Socket-IP-0.42-1.fc39.noarch.rpm: Already downloaded
[SKIPPED] perl-IO-Socket-SSL-2.083-3.fc39.noarch.rpm: Already downloaded
[SKIPPED] perl-IPC-Open3-1.22-500.fc39.noarch.rpm: Already downloaded
[SKIPPED] perl-MIME-Base64-3.16-500.fc39.ppc64le.rpm: Already downloaded
[SKIPPED] perl-Mozilla-CA-20230821-1.fc40.noarch.rpm: Already downloaded
[SKIPPED] perl-Net-SSLeay-1.92-10.fc39.ppc64le.rpm: Already downloaded
[SKIPPED] perl-POSIX-2.13-500.fc39.ppc64le.rpm: Already downloaded
[SKIPPED] perl-PathTools-3.89-500.fc39.ppc64le.rpm: Already downloaded
[SKIPPED] perl-Pod-Escapes-1.07-501.fc40.noarch.rpm: Already downloaded
[SKIPPED] perl-Pod-Perldoc-3.28.01-501.fc39.noarch.rpm: Already downloaded
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[SKIPPED] perl-SelectSaver-1.02-500.fc39.noarch.rpm: Already downloaded
[SKIPPED] perl-Socket-2.037-3.fc39.ppc64le.rpm: Already downloaded
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[SKIPPED] perl-Symbol-1.09-500.fc39.noarch.rpm: Already downloaded
[SKIPPED] perl-Term-ANSIColor-5.01-501.fc39.noarch.rpm: Already downloaded
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[SKIPPED] perl-Text-ParseWords-3.31-500.fc39.noarch.rpm: Already downloaded
[SKIPPED] perl-Text-Tabs+Wrap-2023.0511-3.fc39.noarch.rpm: Already downloaded
[SKIPPED] perl-Time-Local-1.350-3.fc39.noarch.rpm: Already downloaded
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[SKIPPED] perl-overload-1.37-500.fc39.noarch.rpm: Already downloaded
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(79/83): htslib-devel-1.15.1-3.fc40.ppc64le.rpm 1.1 MB/s | 100 kB 00:00
(80/83): htslib-1.15.1-3.fc40.ppc64le.rpm 5.2 MB/s | 560 kB 00:00
(81/83): htslib-tools-1.15.1-3.fc40.ppc64le.rpm 5.3 MB/s | 628 kB 00:00
(82/83): ncurses-c++-libs-6.4-7.20230520.fc40.p 148 kB/s | 39 kB 00:00
(83/83): ncurses-devel-6.4-7.20230520.fc40.ppc6 976 kB/s | 546 kB 00:00
--------------------------------------------------------------------------------
Total 1.5 MB/s | 1.8 MB 00:01
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
Preparing : 1/1
Installing : libmpc-1.3.1-3.fc39.ppc64le 1/83
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Installing : cpp-13.2.1-1.fc39.ppc64le 3/83
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Installing : libxcrypt-devel-4.4.36-2.fc39.ppc64le 11/83
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Verifying : glibc-devel-2.38.9000-8.fc40.ppc64le 1/83
Verifying : htslib-1.15.1-3.fc40.ppc64le 2/83
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Verifying : gc-8.2.2-4.fc39.ppc64le 9/83
Verifying : gcc-13.2.1-1.fc39.ppc64le 10/83
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Verifying : groff-base-1.23.0-2.fc39.ppc64le 12/83
Verifying : guile22-2.2.7-9.fc39.ppc64le 13/83
Verifying : kernel-headers-6.6.0-0.rc1.git0.1.fc40.ppc64le 14/83
Verifying : libasan-13.2.1-1.fc39.ppc64le 15/83
Verifying : libatomic-13.2.1-1.fc39.ppc64le 16/83
Verifying : libmpc-1.3.1-3.fc39.ppc64le 17/83
Verifying : libtool-ltdl-2.4.7-8.fc40.ppc64le 18/83
Verifying : libubsan-13.2.1-1.fc39.ppc64le 19/83
Verifying : libxcrypt-devel-4.4.36-2.fc39.ppc64le 20/83
Verifying : make-1:4.4.1-2.fc39.ppc64le 21/83
Verifying : ncurses-6.4-7.20230520.fc40.ppc64le 22/83
Verifying : ncurses-c++-libs-6.4-7.20230520.fc40.ppc64le 23/83
Verifying : ncurses-devel-6.4-7.20230520.fc40.ppc64le 24/83
Verifying : perl-AutoLoader-5.74-500.fc39.noarch 25/83
Verifying : perl-B-1.88-500.fc39.ppc64le 26/83
Verifying : perl-Carp-1.54-500.fc39.noarch 27/83
Verifying : perl-Class-Struct-0.68-500.fc39.noarch 28/83
Verifying : perl-Data-Dumper-2.188-501.fc39.ppc64le 29/83
Verifying : perl-Digest-1.20-500.fc39.noarch 30/83
Verifying : perl-Digest-MD5-2.58-500.fc39.ppc64le 31/83
Verifying : perl-DynaLoader-1.54-500.fc39.ppc64le 32/83
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Verifying : perl-Exporter-5.77-500.fc39.noarch 35/83
Verifying : perl-Fcntl-1.15-500.fc39.ppc64le 36/83
Verifying : perl-File-Basename-2.86-500.fc39.noarch 37/83
Verifying : perl-File-Path-2.18-500.fc39.noarch 38/83
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Verifying : perl-File-stat-1.13-500.fc39.noarch 40/83
Verifying : perl-FileHandle-2.05-500.fc39.noarch 41/83
Verifying : perl-FindBin-1.53-500.fc39.noarch 42/83
Verifying : perl-Getopt-Long-1:2.54-500.fc39.noarch 43/83
Verifying : perl-Getopt-Std-1.13-500.fc39.noarch 44/83
Verifying : perl-HTTP-Tiny-0.088-3.fc39.noarch 45/83
Verifying : perl-IO-1.52-500.fc39.ppc64le 46/83
Verifying : perl-IO-Socket-IP-0.42-1.fc39.noarch 47/83
Verifying : perl-IO-Socket-SSL-2.083-3.fc39.noarch 48/83
Verifying : perl-IPC-Open3-1.22-500.fc39.noarch 49/83
Verifying : perl-MIME-Base64-3.16-500.fc39.ppc64le 50/83
Verifying : perl-Mozilla-CA-20230821-1.fc40.noarch 51/83
Verifying : perl-Net-SSLeay-1.92-10.fc39.ppc64le 52/83
Verifying : perl-POSIX-2.13-500.fc39.ppc64le 53/83
Verifying : perl-PathTools-3.89-500.fc39.ppc64le 54/83
Verifying : perl-Pod-Escapes-1:1.07-501.fc40.noarch 55/83
Verifying : perl-Pod-Perldoc-3.28.01-501.fc39.noarch 56/83
Verifying : perl-Pod-Simple-1:3.45-4.fc39.noarch 57/83
Verifying : perl-Pod-Usage-4:2.03-500.fc39.noarch 58/83
Verifying : perl-Scalar-List-Utils-5:1.63-500.fc39.ppc64le 59/83
Verifying : perl-SelectSaver-1.02-500.fc39.noarch 60/83
Verifying : perl-Socket-4:2.037-3.fc39.ppc64le 61/83
Verifying : perl-Storable-1:3.32-500.fc39.ppc64le 62/83
Verifying : perl-Symbol-1.09-500.fc39.noarch 63/83
Verifying : perl-Term-ANSIColor-5.01-501.fc39.noarch 64/83
Verifying : perl-Term-Cap-1.18-500.fc39.noarch 65/83
Verifying : perl-Text-ParseWords-3.31-500.fc39.noarch 66/83
Verifying : perl-Text-Tabs+Wrap-2023.0511-3.fc39.noarch 67/83
Verifying : perl-Time-Local-2:1.350-3.fc39.noarch 68/83
Verifying : perl-URI-5.21-1.fc40.noarch 69/83
Verifying : perl-base-2.27-500.fc39.noarch 70/83
Verifying : perl-constant-1.33-501.fc39.noarch 71/83
Verifying : perl-if-0.61.000-500.fc39.noarch 72/83
Verifying : perl-interpreter-4:5.38.0-500.fc39.ppc64le 73/83
Verifying : perl-lib-0.65-500.fc39.ppc64le 74/83
Verifying : perl-libnet-3.15-501.fc39.noarch 75/83
Verifying : perl-libs-4:5.38.0-500.fc39.ppc64le 76/83
Verifying : perl-locale-1.10-500.fc39.noarch 77/83
Verifying : perl-mro-1.28-500.fc39.ppc64le 78/83
Verifying : perl-overload-1.37-500.fc39.noarch 79/83
Verifying : perl-overloading-0.02-500.fc39.noarch 80/83
Verifying : perl-parent-1:0.241-500.fc39.noarch 81/83
Verifying : perl-podlators-1:5.01-500.fc39.noarch 82/83
Verifying : perl-vars-1.05-500.fc39.noarch 83/83
Installed:
annobin-docs-12.26-1.fc40.noarch
annobin-plugin-gcc-12.26-1.fc40.ppc64le
cpp-13.2.1-1.fc39.ppc64le
gc-8.2.2-4.fc39.ppc64le
gcc-13.2.1-1.fc39.ppc64le
gcc-plugin-annobin-13.2.1-1.fc39.ppc64le
glibc-devel-2.38.9000-8.fc40.ppc64le
groff-base-1.23.0-2.fc39.ppc64le
guile22-2.2.7-9.fc39.ppc64le
htslib-1.15.1-3.fc40.ppc64le
htslib-devel-1.15.1-3.fc40.ppc64le
htslib-tools-1.15.1-3.fc40.ppc64le
kernel-headers-6.6.0-0.rc1.git0.1.fc40.ppc64le
libasan-13.2.1-1.fc39.ppc64le
libatomic-13.2.1-1.fc39.ppc64le
libmpc-1.3.1-3.fc39.ppc64le
libtool-ltdl-2.4.7-8.fc40.ppc64le
libubsan-13.2.1-1.fc39.ppc64le
libxcrypt-devel-4.4.36-2.fc39.ppc64le
make-1:4.4.1-2.fc39.ppc64le
ncurses-6.4-7.20230520.fc40.ppc64le
ncurses-c++-libs-6.4-7.20230520.fc40.ppc64le
ncurses-devel-6.4-7.20230520.fc40.ppc64le
perl-AutoLoader-5.74-500.fc39.noarch
perl-B-1.88-500.fc39.ppc64le
perl-Carp-1.54-500.fc39.noarch
perl-Class-Struct-0.68-500.fc39.noarch
perl-Data-Dumper-2.188-501.fc39.ppc64le
perl-Digest-1.20-500.fc39.noarch
perl-Digest-MD5-2.58-500.fc39.ppc64le
perl-DynaLoader-1.54-500.fc39.ppc64le
perl-Encode-4:3.19-500.fc39.ppc64le
perl-Errno-1.37-500.fc39.ppc64le
perl-Exporter-5.77-500.fc39.noarch
perl-Fcntl-1.15-500.fc39.ppc64le
perl-File-Basename-2.86-500.fc39.noarch
perl-File-Path-2.18-500.fc39.noarch
perl-File-Temp-1:0.231.100-500.fc39.noarch
perl-File-stat-1.13-500.fc39.noarch
perl-FileHandle-2.05-500.fc39.noarch
perl-FindBin-1.53-500.fc39.noarch
perl-Getopt-Long-1:2.54-500.fc39.noarch
perl-Getopt-Std-1.13-500.fc39.noarch
perl-HTTP-Tiny-0.088-3.fc39.noarch
perl-IO-1.52-500.fc39.ppc64le
perl-IO-Socket-IP-0.42-1.fc39.noarch
perl-IO-Socket-SSL-2.083-3.fc39.noarch
perl-IPC-Open3-1.22-500.fc39.noarch
perl-MIME-Base64-3.16-500.fc39.ppc64le
perl-Mozilla-CA-20230821-1.fc40.noarch
perl-Net-SSLeay-1.92-10.fc39.ppc64le
perl-POSIX-2.13-500.fc39.ppc64le
perl-PathTools-3.89-500.fc39.ppc64le
perl-Pod-Escapes-1:1.07-501.fc40.noarch
perl-Pod-Perldoc-3.28.01-501.fc39.noarch
perl-Pod-Simple-1:3.45-4.fc39.noarch
perl-Pod-Usage-4:2.03-500.fc39.noarch
perl-Scalar-List-Utils-5:1.63-500.fc39.ppc64le
perl-SelectSaver-1.02-500.fc39.noarch
perl-Socket-4:2.037-3.fc39.ppc64le
perl-Storable-1:3.32-500.fc39.ppc64le
perl-Symbol-1.09-500.fc39.noarch
perl-Term-ANSIColor-5.01-501.fc39.noarch
perl-Term-Cap-1.18-500.fc39.noarch
perl-Text-ParseWords-3.31-500.fc39.noarch
perl-Text-Tabs+Wrap-2023.0511-3.fc39.noarch
perl-Time-Local-2:1.350-3.fc39.noarch
perl-URI-5.21-1.fc40.noarch
perl-base-2.27-500.fc39.noarch
perl-constant-1.33-501.fc39.noarch
perl-if-0.61.000-500.fc39.noarch
perl-interpreter-4:5.38.0-500.fc39.ppc64le
perl-lib-0.65-500.fc39.ppc64le
perl-libnet-3.15-501.fc39.noarch
perl-libs-4:5.38.0-500.fc39.ppc64le
perl-locale-1.10-500.fc39.noarch
perl-mro-1.28-500.fc39.ppc64le
perl-overload-1.37-500.fc39.noarch
perl-overloading-0.02-500.fc39.noarch
perl-parent-1:0.241-500.fc39.noarch
perl-podlators-1:5.01-500.fc39.noarch
perl-vars-1.05-500.fc39.noarch
zlib-ng-compat-devel-2.1.3-3.fc40.ppc64le
Complete!
Finish: build setup for samtools-1.15.1-3.fc40.src.rpm
Start: rpmbuild samtools-1.15.1-3.fc40.src.rpm
Building target platforms: ppc64le
Building for target ppc64le
setting SOURCE_DATE_EPOCH=1689984000
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.rBLIAE
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf samtools-1.15.1
+ /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/samtools-1.15.1.tar.bz2
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd samtools-1.15.1
+ rm -rf /builddir/build/BUILD/samtools-1.15.1-SPECPARTS
+ /usr/bin/mkdir -p /builddir/build/BUILD/samtools-1.15.1-SPECPARTS
+ /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.vYEapN
+ umask 022
+ cd /builddir/build/BUILD
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ 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 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd samtools-1.15.1
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ 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 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ '[' '-flto=auto -ffat-lto-objectsx' '!=' x ']'
++ find . -type f -name configure -print
+ for file in $(find . -type f -name configure -print)
+ /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\) = /__attribute__ ((used)) char (*f) () = /g' ./htslib-1.15.1/configure
+ diff -u ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure
+ mv ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure
+ /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\);/__attribute__ ((used)) char (*f) ();/g' ./htslib-1.15.1/configure
+ diff -u ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure
+ mv ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure
+ /usr/bin/sed -r --in-place=.backup 's/^char \$2 \(\);/__attribute__ ((used)) char \$2 ();/g' ./htslib-1.15.1/configure
+ diff -u ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure
--- ./htslib-1.15.1/configure.backup 2022-04-07 15:42:52.000000000 +0000
+++ ./htslib-1.15.1/configure 2023-09-18 20:36:18.033900806 +0000
@@ -1697,7 +1697,7 @@
#ifdef __cplusplus
extern "C"
#endif
-char $2 ();
+__attribute__ ((used)) char $2 ();
/* The GNU C library defines this for functions which it implements
to always fail with ENOSYS. Some functions are actually named
something starting with __ and the normal name is an alias. */
+ /usr/bin/sed --in-place=.backup '1{$!N;$!N};$!N;s/int x = 1;\nint y = 0;\nint z;\nint nan;/volatile int x = 1; volatile int y = 0; volatile int z, nan;/;P;D' ./htslib-1.15.1/configure
+ diff -u ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure
+ mv ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure
+ /usr/bin/sed --in-place=.backup 's#^lt_cv_sys_global_symbol_to_cdecl=.*#lt_cv_sys_global_symbol_to_cdecl="sed -n -e '\''s/^T .* \\(.*\\)$/extern int \\1();/p'\'' -e '\''s/^$symcode* .* \\(.*\\)$/extern char \\1;/p'\''"#' ./htslib-1.15.1/configure
+ diff -u ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure
+ mv ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure
+ for file in $(find . -type f -name configure -print)
+ /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\) = /__attribute__ ((used)) char (*f) () = /g' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\);/__attribute__ ((used)) char (*f) ();/g' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ /usr/bin/sed -r --in-place=.backup 's/^char \$2 \(\);/__attribute__ ((used)) char \$2 ();/g' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ /usr/bin/sed --in-place=.backup '1{$!N;$!N};$!N;s/int x = 1;\nint y = 0;\nint z;\nint nan;/volatile int x = 1; volatile int y = 0; volatile int z, nan;/;P;D' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ /usr/bin/sed --in-place=.backup 's#^lt_cv_sys_global_symbol_to_cdecl=.*#lt_cv_sys_global_symbol_to_cdecl="sed -n -e '\''s/^T .* \\(.*\\)$/extern int \\1();/p'\'' -e '\''s/^$symcode* .* \\(.*\\)$/extern char \\1;/p'\''"#' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ '[' 1 = 1 ']'
+++ dirname ./configure
++ find . -name config.guess -o -name config.sub
+ '[' 1 = 1 ']'
+ '[' x '!=' 'x-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' ']'
++ find . -name ltmain.sh
++ grep -q runstatedir=DIR ./configure
++ echo --runstatedir=/run
+ ./configure --build=ppc64le-redhat-linux --host=ppc64le-redhat-linux --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/libexec --localstatedir=/var --runstatedir=/run --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info 'CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-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 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' --prefix=/usr --with-htslib=system
checking for gawk... gawk
checking for ppc64le-redhat-linux-gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for C compiler warning flags... -Wall
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for htslib/sam.h... yes
checking for hts_version in -lhts... yes
checking for NcursesW wide-character library... yes
checking for working ncursesw/curses.h... yes
checking for library containing cbreak... none required
checking for zlib.h... yes
checking for inflate in -lz... yes
checking for library containing regcomp... none required
configure: creating ./config.status
config.status: creating config.mk
config.status: creating config.h
+ /usr/bin/make -O -j5 V=1 VERBOSE=1
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_aux.o bam_aux.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam.o bam.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_index.o bam_index.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_cat.o bam_cat.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_md.o bam_md.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_plbuf.o bam_plbuf.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_fastq.o bam_fastq.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_reheader.o bam_reheader.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_plcmd.o bam_plcmd.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_rmdup.o bam_rmdup.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_rmdupse.o bam_rmdupse.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_mate.o bam_mate.c
echo '#define SAMTOOLS_VERSION "1.15.1"' > version.h
echo '#define SAMTOOLS_CC "gcc"' >> version.h
echo '#define SAMTOOLS_CPPFLAGS ""' >> version.h
echo '#define SAMTOOLS_CFLAGS "-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-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 -specs=/usr/lib/rpm/redhat/redhat-package-notes "' >> version.h
echo '#define SAMTOOLS_HTSDIR ""' >> version.h
echo '#define SAMTOOLS_LIBS ""' >> version.h
echo '#define SAMTOOLS_CURSES_LIB "-lncursesw"' >> version.h
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_color.o bam_color.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam2bcf.o bam2bcf.c
bam2bcf.c: In function ‘bcf_call_glfgen’:
bam2bcf.c:81:33: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
81 | bca->bases = (uint16_t*)realloc(bca->bases, 2 * bca->max_bases);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/htslib/kstring.h:30,
from /usr/include/htslib/hts.h:37,
from bam2bcf.c:30:
/usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here
683 | extern void *realloc (void *__ptr, size_t __size)
| ^~~~~~~
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o sam_view.o sam_view.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_stat.o bam_stat.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o cut_target.o cut_target.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o sample.o sample.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o coverage.o coverage.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o padding.o padding.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam2depth.o bam2depth.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bedcov.o bedcov.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o faidx.o faidx.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o phase.o phase.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o dict.o dict.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_flags.o bam_flags.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o stats_isize.o stats_isize.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_split.o bam_split.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bamshuf.o bamshuf.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_tview.o bam_tview.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_tview_curses.o bam_tview_curses.c
bam_tview_curses.c: In function ‘tv_win_help’:
bam_tview_curses.c:333:14: warning: ‘base’ is used uninitialized [-Wuninitialized]
333 | tview_t* base=(tview_t*)base;
| ^~~~
bam_tview_curses.c:333:14: note: ‘base’ was declared here
333 | tview_t* base=(tview_t*)base;
| ^~~~
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_lpileup.o bam_lpileup.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_quickcheck.o bam_quickcheck.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_tview_html.o bam_tview_html.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o tmp_file.o tmp_file.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_addrprg.o bam_addrprg.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_sort.o bam_sort.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_import.o bam_import.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_ampliconclip.o bam_ampliconclip.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_samples.o bam_samples.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o stats.o stats.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_markdup.o bam_markdup.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o consensus_pileup.o consensus_pileup.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o sam_opts.o sam_opts.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o sam_utils.o sam_utils.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o amplicon_stats.o amplicon_stats.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -DMAQ_LONGREADS -I. -I./lz4 -c -o misc/maq2sam-long.o misc/maq2sam.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_consensus.o bam_consensus.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o misc/maq2sam-short.o misc/maq2sam.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o misc/md5sum-lite.o misc/md5sum-lite.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o misc/ace2sam.o misc/ace2sam.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o misc/md5fa.o misc/md5fa.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bedidx.o bedidx.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o test/test.o test/test.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o misc/wgsim.o misc/wgsim.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o test/split/test_count_rg.o test/split/test_count_rg.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o test/split/test_parse_args.o test/split/test_parse_args.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o test/vcf-miniview.o test/vcf-miniview.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bamtk.o bamtk.c
ar -rcs libst.a sam_opts.o sam_utils.o bedidx.o
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o lz4/lz4.o lz4/lz4.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 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o misc/maq2sam-long misc/maq2sam-long.o -lz
gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o misc/maq2sam-short misc/maq2sam-short.o -lz
gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o misc/md5fa misc/md5fa.o -lhts -lz
gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c
gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o misc/ace2sam misc/ace2sam.o -lhts -lz
gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o test/split/test_count_rg test/split/test_count_rg.o test/test.o libst.a -lhts -lz -lpthread
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c
gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o libst.a -lhts -lz -lpthread
gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o libst.a -lhts -lz -lpthread
gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o misc/wgsim misc/wgsim.o -lm -lhts -lz
gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -lpthread
gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o test/split/test_parse_args test/split/test_parse_args.o test/test.o libst.a -lhts -lz -lpthread
gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o test/test.o libst.a -lhts -lz -lpthread
gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o libst.a -lhts -lz -lpthread
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c
gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o test/test.o libst.a -lhts -lz -lpthread
gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o samtools bam.o bam_aux.o bam_index.o bam_plcmd.o sam_view.o bam_fastq.o bam_cat.o bam_md.o bam_plbuf.o bam_reheader.o bam_sort.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o sample.o cut_target.o phase.o bam2depth.o coverage.o padding.o bedcov.o bamshuf.o faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o bam_quickcheck.o bam_addrprg.o bam_markdup.o tmp_file.o bam_ampliconclip.o amplicon_stats.o bam_import.o bam_samples.o bam_consensus.o consensus_pileup.o ./lz4/lz4.o libst.a -lhts -lncursesw -lm -lz -lpthread
In function ‘bcf_call_glfgen’,
inlined from ‘tv_pl_func’ at bam_tview.c:196:9:
bam2bcf.c:81:33: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
81 | bca->bases = (uint16_t*)realloc(bca->bases, 2 * bca->max_bases);
| ^
/usr/include/stdlib.h: In function ‘tv_pl_func’:
/usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here
683 | extern void *realloc (void *__ptr, size_t __size)
| ^
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.W12jt7
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le
++ dirname /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ 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 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd samtools-1.15.1
+ /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le 'INSTALL=/usr/bin/install -p'
mkdir -p -m 755 /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/bin /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/bin /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/share/man/man1
/usr/bin/install -p samtools /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/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.fc40.ppc64le/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.fc40.ppc64le/usr/bin
/usr/bin/install -p -m 644 doc/samtools*.1 misc/wgsim.1 /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/share/man/man1
++ grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/bin/ace2sam /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/bin/blast2sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/bin/bowtie2sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/bin/export2sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/bin/fasta-sanitize.pl /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/bin/interpolate_sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/bin/maq2sam-long /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/bin/maq2sam-short /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/bin/md5fa /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/bin/md5sum-lite /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/bin/novo2sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/bin/plot-ampliconstats /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/bin/plot-bamstats /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/bin/psl2sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/bin/sam2vcf.pl /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/bin/samtools /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/bin/samtools.pl /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/bin/seq_cache_populate.pl /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/bin/soap2sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/bin/wgsim /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/bin/wgsim_eval.pl /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/bin/zoom2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/bin/blast2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/bin/bowtie2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/bin/export2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/bin/fasta-sanitize.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/bin/interpolate_sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/bin/novo2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/bin/plot-ampliconstats
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/bin/plot-bamstats
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/bin/psl2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/bin/sam2vcf.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/bin/samtools.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/bin/seq_cache_populate.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/bin/soap2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/bin/wgsim_eval.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/bin/zoom2sam.pl
+ /usr/bin/find-debuginfo -j5 --strict-build-id -m -i --build-id-seed 1.15.1-3.fc40 --unique-debug-suffix -1.15.1-3.fc40.ppc64le --unique-debug-src-base samtools-1.15.1-3.fc40.ppc64le --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/samtools-1.15.1
find-debuginfo: starting
Extracting debug info from 7 files
DWARF-compressing 7 files
sepdebugcrcfix: Updated 7 CRC32s, 0 CRC32s did match.
Creating .debug symlinks for symlinks to ELF files
Copying sources found by 'debugedit -l' to /usr/src/debug/samtools-1.15.1-3.fc40.ppc64le
2442 blocks
find-debuginfo: done
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-ldconfig
+ /usr/lib/rpm/brp-compress
+ /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip
+ /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip
+ /usr/lib/rpm/check-rpaths
+ /usr/lib/rpm/redhat/brp-mangle-shebangs
+ /usr/lib/rpm/brp-remove-la-files
+ env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j5
+ /usr/lib/rpm/redhat/brp-python-hardlink
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.KkJugV
+ umask 022
+ cd /builddir/build/BUILD
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ 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 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd samtools-1.15.1
+ ldd samtools
+ grep -E '/lib(64)?/libhts\.so\.'
libhts.so.3 => /lib64/libhts.so.3 (0x00007fff89a80000)
+ 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/oCV2h3_G_a/bgzip.dat.gz
.. ok
bgzip -c -b 979200 -s 6 /tmp/oCV2h3_G_a/bgzip.dat.gz
.. ok
bgzip -c -b 652804 -s 6 /tmp/oCV2h3_G_a/bgzip.dat.gz
.. ok
/builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/oCV2h3_G_a/faidx.fa 3:11-13 | grep -v '^>'
.. ok
/builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/oCV2h3_G_a/faidx.fa.gz 3:11-13 | grep -v '^>'
.. ok
/builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/oCV2h3_G_a/faidx.fa 2:998-1003 | grep -v '^>'
.. ok
/builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/oCV2h3_G_a/faidx.fa.gz 2:998-1003 | grep -v '^>'
.. ok
/builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/oCV2h3_G_a/faidx.fa 1:100-104 | grep -v '^>'
.. ok
/builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/oCV2h3_G_a/faidx.fa.gz 1:100-104 | grep -v '^>'
.. ok
/builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/oCV2h3_G_a/faidx.fa 1:99998-100007 | grep -v '^>'
.. ok
/builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/oCV2h3_G_a/faidx.fa.gz 1:99998-100007 | grep -v '^>'
.. ok
/builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/oCV2h3_G_a/fqidx.fq 3:11-13
.. ok
.. ok
/builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/oCV2h3_G_a/fqidx.fq.gz 3:11-13
.. ok
.. ok
/builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/oCV2h3_G_a/fqidx.fq 2:998-1003
.. ok
.. ok
/builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/oCV2h3_G_a/fqidx.fq.gz 2:998-1003
.. ok
.. ok
/builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/oCV2h3_G_a/fqidx.fq 1:100-104
.. ok
.. ok
/builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/oCV2h3_G_a/fqidx.fq.gz 1:100-104
.. ok
.. ok
/builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/oCV2h3_G_a/fqidx.fq 1:99998-100007
.. ok
.. ok
/builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/oCV2h3_G_a/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/oCV2h3_G_a/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/oCV2h3_G_a/large_chrom.bam ref2
.. ok
test_index:
/builddir/build/BUILD/samtools-1.15.1/samtools view /tmp/oCV2h3_G_a/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/oCV2h3_G_a/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/oCV2h3_G_a/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/oCV2h3_G_a/auto_indexed.csi && cat /tmp/oCV2h3_G_a/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/oCV2h3_G_a/auto_indexed.crai && cat /tmp/oCV2h3_G_a/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/oCV2h3_G_a/auto_indexed.csi && cat /tmp/oCV2h3_G_a/auto_indexed.csi
.. ok
test_index:
/builddir/build/BUILD/samtools-1.15.1/samtools view -@ 2 /tmp/oCV2h3_G_a/large_chrom.bam ref2
.. ok
test_index:
/builddir/build/BUILD/samtools-1.15.1/samtools view -@ 2 /tmp/oCV2h3_G_a/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/oCV2h3_G_a/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/oCV2h3_G_a/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/oCV2h3_G_a/auto_indexed.csi && cat /tmp/oCV2h3_G_a/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/oCV2h3_G_a/auto_indexed.crai && cat /tmp/oCV2h3_G_a/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/oCV2h3_G_a/auto_indexed.csi && cat /tmp/oCV2h3_G_a/auto_indexed.csi
.. ok
test_mpileup:
/builddir/build/BUILD/samtools-1.15.1/samtools mpileup -b /tmp/oCV2h3_G_a/mpileup.bam.list -f /tmp/oCV2h3_G_a/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
/builddir/build/BUILD/samtools-1.15.1/samtools mpileup -b /tmp/oCV2h3_G_a/mpileup.cram.list -f /tmp/oCV2h3_G_a/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
/builddir/build/BUILD/samtools-1.15.1/samtools mpileup -b /tmp/oCV2h3_G_a/mpileup.bam.urllist -f /tmp/oCV2h3_G_a/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
/builddir/build/BUILD/samtools-1.15.1/samtools mpileup -b /tmp/oCV2h3_G_a/mpileup.cram.urllist -f /tmp/oCV2h3_G_a/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
/builddir/build/BUILD/samtools-1.15.1/samtools mpileup -B --ff 0x14 -f /tmp/oCV2h3_G_a/mpileup.ref.fa.gz -r17:1050-1060 /tmp/oCV2h3_G_a/mpileup.1.bam | grep -v mpileup
.. ok
test_mpileup:
/builddir/build/BUILD/samtools-1.15.1/samtools mpileup -B --ff 0x14 -f /tmp/oCV2h3_G_a/mpileup.ref.fa.gz -r17:1050-1060 /tmp/oCV2h3_G_a/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/oCV2h3_G_a/view.001.fogn (SAM input) .. ok
50: Count -R /tmp/oCV2h3_G_a/view.001.fogn (SAM input) .. ok
51: Filter -R /tmp/oCV2h3_G_a/view.001.fogn (BAM input) .. ok
52: Count -R /tmp/oCV2h3_G_a/view.001.fogn (BAM input) .. ok
53: Filter -R /tmp/oCV2h3_G_a/view.001.fogn (CRAM input) .. ok
54: Count -R /tmp/oCV2h3_G_a/view.001.fogn (CRAM input) .. ok
55: Filter -R /tmp/oCV2h3_G_a/view.001.fogn -r grp2 (SAM input).. ok
56: Count -R /tmp/oCV2h3_G_a/view.001.fogn -r grp2 (SAM input).. ok
57: Filter -R /tmp/oCV2h3_G_a/view.001.fogn -r grp2 (BAM input).. ok
58: Count -R /tmp/oCV2h3_G_a/view.001.fogn -r grp2 (BAM input).. ok
59: Filter -R /tmp/oCV2h3_G_a/view.001.fogn -r grp2 (CRAM input).. ok
60: Count -R /tmp/oCV2h3_G_a/view.001.fogn -r grp2 (CRAM input).. ok
61: Filter -r grp2 -R /tmp/oCV2h3_G_a/view.001.fogn (SAM input).. ok
62: Count -r grp2 -R /tmp/oCV2h3_G_a/view.001.fogn (SAM input).. ok
63: Filter -r grp2 -R /tmp/oCV2h3_G_a/view.001.fogn (BAM input).. ok
64: Count -r grp2 -R /tmp/oCV2h3_G_a/view.001.fogn (BAM input).. ok
65: Filter -r grp2 -R /tmp/oCV2h3_G_a/view.001.fogn (CRAM input).. ok
66: Count -r grp2 -R /tmp/oCV2h3_G_a/view.001.fogn (CRAM input).. ok
67: Filter -N /tmp/oCV2h3_G_a/view.001.forn (SAM input) .. ok
68: Count -N /tmp/oCV2h3_G_a/view.001.forn (SAM input) .. ok
69: Filter -N /tmp/oCV2h3_G_a/view.001.forn (BAM input) .. ok
70: Count -N /tmp/oCV2h3_G_a/view.001.forn (BAM input) .. ok
71: Filter -N /tmp/oCV2h3_G_a/view.001.forn (CRAM input) .. ok
72: Count -N /tmp/oCV2h3_G_a/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/oCV2h3_G_a/view.001.fobc (SAM input) .. ok
86: Count -D BC:/tmp/oCV2h3_G_a/view.001.fobc (SAM input) .. ok
87: Filter -D BC:/tmp/oCV2h3_G_a/view.001.fobc (BAM input) .. ok
88: Count -D BC:/tmp/oCV2h3_G_a/view.001.fobc (BAM input) .. ok
89: Filter -D BC:/tmp/oCV2h3_G_a/view.001.fobc (CRAM input) .. ok
90: Count -D BC:/tmp/oCV2h3_G_a/view.001.fobc (CRAM input) .. ok
91: Filter -D BC:/tmp/oCV2h3_G_a/view.001.fobc -d BC:TGCA (SAM input).. ok
92: Count -D BC:/tmp/oCV2h3_G_a/view.001.fobc -d BC:TGCA (SAM input).. ok
93: Filter -D BC:/tmp/oCV2h3_G_a/view.001.fobc -d BC:TGCA (BAM input).. ok
94: Count -D BC:/tmp/oCV2h3_G_a/view.001.fobc -d BC:TGCA (BAM input).. ok
95: Filter -D BC:/tmp/oCV2h3_G_a/view.001.fobc -d BC:TGCA (CRAM input).. ok
96: Count -D BC:/tmp/oCV2h3_G_a/view.001.fobc -d BC:TGCA (CRAM input).. ok
97: Filter -d BC:TGCA -D BC:/tmp/oCV2h3_G_a/view.001.fobc (SAM input).. ok
98: Count -d BC:TGCA -D BC:/tmp/oCV2h3_G_a/view.001.fobc (SAM input).. ok
99: Filter -d BC:TGCA -D BC:/tmp/oCV2h3_G_a/view.001.fobc (BAM input).. ok
100: Count -d BC:TGCA -D BC:/tmp/oCV2h3_G_a/view.001.fobc (BAM input).. ok
101: Filter -d BC:TGCA -D BC:/tmp/oCV2h3_G_a/view.001.fobc (CRAM input).. ok
102: Count -d BC:TGCA -D BC:/tmp/oCV2h3_G_a/view.001.fobc (CRAM input).. ok
103: Filter -D RG:/tmp/oCV2h3_G_a/view.001.fogn (SAM input) .. ok
104: Count -D RG:/tmp/oCV2h3_G_a/view.001.fogn (SAM input) .. ok
105: Filter -D RG:/tmp/oCV2h3_G_a/view.001.fogn (BAM input) .. ok
106: Count -D RG:/tmp/oCV2h3_G_a/view.001.fogn (BAM input) .. ok
107: Filter -D RG:/tmp/oCV2h3_G_a/view.001.fogn (CRAM input).. ok
108: Count -D RG:/tmp/oCV2h3_G_a/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/oCV2h3_G_a/view.test115.sam -h -d TGCA /tmp/oCV2h3_G_a/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/oCV2h3_G_a/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/oCV2h3_G_a/view.test117.sam -h -d TGCA /tmp/oCV2h3_G_a/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/oCV2h3_G_a/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/oCV2h3_G_a/view.test119.sam -h -d TGCA /tmp/oCV2h3_G_a/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/oCV2h3_G_a/view.test006.cram --no-PG
.. expected failure
121: Filter -D BClong:/tmp/oCV2h3_G_a/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/oCV2h3_G_a/view.001.fobc"
Failed command:
/builddir/build/BUILD/samtools-1.15.1/samtools view -o /tmp/oCV2h3_G_a/view.test121.sam -h -D BClong:/tmp/oCV2h3_G_a/view.001.fobc /tmp/oCV2h3_G_a/view.001.sam --no-PG
.. expected failure
122: Count -D BClong:/tmp/oCV2h3_G_a/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/oCV2h3_G_a/view.001.fobc"
Failed command:
/builddir/build/BUILD/samtools-1.15.1/samtools view -c -D BClong:/tmp/oCV2h3_G_a/view.001.fobc /tmp/oCV2h3_G_a/view.001.sam --no-PG
.. expected failure
123: Filter -D BClong:/tmp/oCV2h3_G_a/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/oCV2h3_G_a/view.001.fobc"
Failed command:
/builddir/build/BUILD/samtools-1.15.1/samtools view -o /tmp/oCV2h3_G_a/view.test123.sam -h -D BClong:/tmp/oCV2h3_G_a/view.001.fobc /tmp/oCV2h3_G_a/view.test001.bam --no-PG
.. expected failure
124: Count -D BClong:/tmp/oCV2h3_G_a/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/oCV2h3_G_a/view.001.fobc"
Failed command:
/builddir/build/BUILD/samtools-1.15.1/samtools view -c -D BClong:/tmp/oCV2h3_G_a/view.001.fobc /tmp/oCV2h3_G_a/view.test001.bam --no-PG
.. expected failure
125: Filter -D BClong:/tmp/oCV2h3_G_a/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/oCV2h3_G_a/view.001.fobc"
Failed command:
/builddir/build/BUILD/samtools-1.15.1/samtools view -o /tmp/oCV2h3_G_a/view.test125.sam -h -D BClong:/tmp/oCV2h3_G_a/view.001.fobc /tmp/oCV2h3_G_a/view.test006.cram --no-PG
.. expected failure
126: Count -D BClong:/tmp/oCV2h3_G_a/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/oCV2h3_G_a/view.001.fobc"
Failed command:
/builddir/build/BUILD/samtools-1.15.1/samtools view -c -D BClong:/tmp/oCV2h3_G_a/view.001.fobc /tmp/oCV2h3_G_a/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/oCV2h3_G_a/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/oCV2h3_G_a/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/oCV2h3_G_a/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/oCV2h3_G_a/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/oCV2h3_G_a/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/oCV2h3_G_a/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/oCV2h3_G_a/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/oCV2h3_G_a/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/oCV2h3_G_a/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/oCV2h3_G_a/bam2fq.discard.s.fq -0 /tmp/oCV2h3_G_a/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/oCV2h3_G_a/bam2fq.discard.s.fq -0 /tmp/oCV2h3_G_a/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/HGqYHviuJL - /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/oCV2h3_G_a/merge.tag.1.bam /tmp/oCV2h3_G_a/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/oCV2h3_G_a/merge.tag.3.bam /tmp/oCV2h3_G_a/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/oCV2h3_G_a/merge.bed.1.bam /tmp/oCV2h3_G_a/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/4CYLXi_YdP - /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/oCV2h3_G_a/merge.tag.1.bam /tmp/oCV2h3_G_a/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/oCV2h3_G_a/merge.tag.3.bam /tmp/oCV2h3_G_a/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/oCV2h3_G_a/merge.bed.1.bam /tmp/oCV2h3_G_a/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/oCV2h3_G_a/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/oCV2h3_G_a/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/oCV2h3_G_a/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/oCV2h3_G_a/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/oCV2h3_G_a/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/oCV2h3_G_a/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/oCV2h3_G_a/longref.sam.gz
.. ok
test_large_positions:
/builddir/build/BUILD/samtools-1.15.1/samtools view -h --no-PG /tmp/oCV2h3_G_a/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/oCV2h3_G_a/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/oCV2h3_G_a/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.fc40.ppc64le
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.2EFyfe
+ umask 022
+ cd /builddir/build/BUILD
+ cd samtools-1.15.1
+ DOCDIR=/builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/share/doc/samtools
+ export LC_ALL=
+ LC_ALL=
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/share/doc/samtools
+ cp -pr /builddir/build/BUILD/samtools-1.15.1/AUTHORS /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/share/doc/samtools
+ cp -pr /builddir/build/BUILD/samtools-1.15.1/ChangeLog.old /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/share/doc/samtools
+ cp -pr /builddir/build/BUILD/samtools-1.15.1/NEWS /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/share/doc/samtools
+ cp -pr /builddir/build/BUILD/samtools-1.15.1/examples /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/share/doc/samtools
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.fALj4A
+ umask 022
+ cd /builddir/build/BUILD
+ cd samtools-1.15.1
+ LICENSEDIR=/builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/share/licenses/samtools
+ export LC_ALL=
+ LC_ALL=
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/share/licenses/samtools
+ cp -pr /builddir/build/BUILD/samtools-1.15.1/LICENSE /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le/usr/share/licenses/samtools
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: samtools = 1.15.1-3.fc40 samtools(ppc-64) = 1.15.1-3.fc40
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: /usr/bin/perl ld64.so.2()(64bit) ld64.so.2(GLIBC_2.23)(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.17)(64bit) libc.so.6(GLIBC_2.32)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libhts.so.3()(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.17)(64bit) libm.so.6(GLIBC_2.29)(64bit) libncursesw.so.6()(64bit) libtinfo.so.6()(64bit) libz.so.1()(64bit) rtld(GNU_HASH)
Processing files: samtools-debugsource-1.15.1-3.fc40.ppc64le
Provides: samtools-debugsource = 1.15.1-3.fc40 samtools-debugsource(ppc-64) = 1.15.1-3.fc40
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.fc40.ppc64le
Provides: debuginfo(build-id) = 38b975386f27206483200f281a4c504215f61e8c debuginfo(build-id) = 521b788fb56ea8c9f7506c834de2daf42d18e764 debuginfo(build-id) = 61b022e308d166d14f6a004af0c35090d4385dde debuginfo(build-id) = 74ffa0e9fa9811cef2617dad5bc20e9cb45dea74 debuginfo(build-id) = 87ab00d55f71a9101ba5d953588815aee4daffec debuginfo(build-id) = c28ef59bcbefc16777780eeec6aada2f1521b65c debuginfo(build-id) = c9147302d96d44a9a96ff70349b8b8a546b4cead samtools-debuginfo = 1.15.1-3.fc40 samtools-debuginfo(ppc-64) = 1.15.1-3.fc40
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: samtools-debugsource(ppc-64) = 1.15.1-3.fc40
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le
Wrote: /builddir/build/RPMS/samtools-1.15.1-3.fc40.ppc64le.rpm
Wrote: /builddir/build/RPMS/samtools-debugsource-1.15.1-3.fc40.ppc64le.rpm
Wrote: /builddir/build/RPMS/samtools-debuginfo-1.15.1-3.fc40.ppc64le.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.Ymug80
+ umask 022
+ cd /builddir/build/BUILD
+ cd samtools-1.15.1
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/samtools-1.15.1-3.fc40.ppc64le
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.cMuKjc
+ umask 022
+ cd /builddir/build/BUILD
+ rm -rf /builddir/build/BUILD/samtools-1.15.1-SPECPARTS
+ rm -rf samtools-1.15.1 samtools-1.15.1.gemspec
+ RPM_EC=0
++ jobs -p
+ exit 0
Finish: rpmbuild samtools-1.15.1-3.fc40.src.rpm
Finish: build phase for samtools-1.15.1-3.fc40.src.rpm
INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/fedora-rawhide-ppc64le-1695069238.164412/root/var/log/dnf.rpm.log
/var/lib/mock/fedora-rawhide-ppc64le-1695069238.164412/root/var/log/dnf.librepo.log
/var/lib/mock/fedora-rawhide-ppc64le-1695069238.164412/root/var/log/dnf.log
INFO: Done(/var/lib/copr-rpmbuild/results/samtools-1.15.1-3.fc40.src.rpm) Config(child) 1 minutes 53 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-debugsource",
"epoch": null,
"version": "1.15.1",
"release": "3.fc40",
"arch": "ppc64le"
},
{
"name": "samtools",
"epoch": null,
"version": "1.15.1",
"release": "3.fc40",
"arch": "src"
},
{
"name": "samtools",
"epoch": null,
"version": "1.15.1",
"release": "3.fc40",
"arch": "ppc64le"
},
{
"name": "samtools-debuginfo",
"epoch": null,
"version": "1.15.1",
"release": "3.fc40",
"arch": "ppc64le"
}
]
}
RPMResults finished