Warning: Permanently added '162.133.138.184' (ED25519) to the list of known hosts.
Running: /usr/bin/copr-rpmbuild --verbose --drop-resultdir --build-id 5171082 --chroot fedora-rawhide-s390x --detached
Version: 0.62
PID: 19839
Logging PID: 19840
Task:
{'appstream': False,
'background': True,
'build_id': 5171082,
'buildroot_pkgs': [],
'chroot': 'fedora-rawhide-s390x',
'enable_net': False,
'fedora_review': False,
'git_hash': '2e8067a3d2106d0f694fdea14d7f475152026227',
'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/jakub/gcc-13-test/htslib',
'isolation': 'default',
'memory_reqs': 2048,
'package_name': 'htslib',
'package_version': '1.15.1-1',
'project_dirname': 'gcc-13-test',
'project_name': 'gcc-13-test',
'project_owner': 'jakub',
'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/jakub/gcc-13-test/fedora-rawhide-s390x/',
'id': 'copr_base',
'name': 'Copr repository'},
{'baseurl': 'https://jakub.fedorapeople.org/fedora-gcc13-$arch/',
'id': 'https_jakub_fedorapeople_org_fedora_gcc13_arch',
'name': 'Additional repo https_jakub_fedorapeople_org_fedora_gcc13_arch'}],
'sandbox': 'jakub/gcc-13-test--jakub',
'source_json': {},
'source_type': None,
'submitter': 'jakub',
'tags': [],
'task_id': '5171082-fedora-rawhide-s390x',
'timeout': 115200,
'uses_devel_repo': False,
'with_opts': [],
'without_opts': []}
Running: git clone https://copr-dist-git.fedorainfracloud.org/git/jakub/gcc-13-test/htslib /var/lib/copr-rpmbuild/workspace/workdir-xbkpkar1/htslib --depth 500 --no-single-branch --recursive
cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/jakub/gcc-13-test/htslib', '/var/lib/copr-rpmbuild/workspace/workdir-xbkpkar1/htslib', '--depth', '500', '--no-single-branch', '--recursive']
cwd: .
rc: 0
stdout:
stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-xbkpkar1/htslib'...
Running: git checkout 2e8067a3d2106d0f694fdea14d7f475152026227
cmd: ['git', 'checkout', '2e8067a3d2106d0f694fdea14d7f475152026227']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-xbkpkar1/htslib
rc: 0
stdout:
stderr: Note: switching to '2e8067a3d2106d0f694fdea14d7f475152026227'.
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 2e8067a automatic import of htslib
Running: copr-distgit-client sources
cmd: ['copr-distgit-client', 'sources']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-xbkpkar1/htslib
rc: 0
stdout:
stderr: INFO: Reading stdout from command: git rev-parse --abbrev-ref HEAD
INFO: Reading stdout from command: git rev-parse HEAD
INFO: Reading sources specification file: sources
INFO: Downloading htslib-1.15.1.tar.bz2
INFO: Calling: curl -H Pragma: -o htslib-1.15.1.tar.bz2 --location --remote-time --show-error --fail https://copr-dist-git.fedorainfracloud.org/repo/pkgs/jakub/gcc-13-test/htslib/htslib-1.15.1.tar.bz2/md5/9ea5cff8edcebb01f31dd02bd4d2a082/htslib-1.15.1.tar.bz2
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 4044k 100 4044k 0 0 2417k 0 0:00:01 0:00:01 --:--:-- 2418k
INFO: Reading stdout from command: md5sum htslib-1.15.1.tar.bz2
/usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated
Running (timeout=115200): unbuffer mock --buildsrpm --spec /var/lib/copr-rpmbuild/workspace/workdir-xbkpkar1/htslib/htslib.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-xbkpkar1/htslib --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1671942858.428762 -r /var/lib/copr-rpmbuild/results/configs/child.cfg
INFO: mock.py version 3.5 starting (python version = 3.11.0, NVR = mock-3.5-1.fc37)...
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-xbkpkar1/htslib/htslib.spec) Config(fedora-rawhide-s390x)
Start: clean chroot
Finish: clean chroot
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-s390x-bootstrap-1671942858.428762/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: enabled HW Info plugin
Mock Version: 3.5
INFO: Mock Version: 3.5
Start(bootstrap): dnf install
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Updating Subscription Management repositories.
Unable to read consumer identity
This system is not registered with an entitlement server. You can use subscription-manager to register.
Copr repository 1.9 MB/s | 16 MB 00:08
Additional repo https_jakub_fedorapeople_org_fe 52 kB/s | 86 kB 00:01
fedora 5.5 MB/s | 59 MB 00:10
Dependencies resolved.
=========================================================================================================================
Package Arch Version Repository Size
=========================================================================================================================
Installing:
dnf noarch 4.14.0-1.fc38 fedora 480 k
dnf-plugins-core noarch 4.3.1-1.fc38 fedora 34 k
Installing dependencies:
alternatives s390x 1.21-1.fc38 copr_base 39 k
audit-libs s390x 3.0.9-2.fc38 fedora 114 k
basesystem noarch 11-14.fc37 fedora 7.0 k
bash s390x 5.2.9-3.fc38 copr_base 1.8 M
bzip2-libs s390x 1.0.8-12.fc38 copr_base 47 k
ca-certificates noarch 2022.2.54-5.fc37 fedora 829 k
coreutils s390x 9.1-8.fc38 copr_base 1.1 M
coreutils-common s390x 9.1-8.fc38 copr_base 2.0 M
crypto-policies noarch 20221215-1.gita4c31a3.fc38 fedora 90 k
curl s390x 7.87.0-1.fc38 copr_base 345 k
cyrus-sasl-lib s390x 2.1.28-8.fc38 copr_base 773 k
dbus-libs s390x 1:1.14.4-1.fc38 copr_base 159 k
dnf-data noarch 4.14.0-1.fc38 fedora 43 k
elfutils-default-yama-scope noarch 0.188-3.fc38 copr_base 16 k
elfutils-libelf s390x 0.188-3.fc38 copr_base 202 k
elfutils-libs s390x 0.188-3.fc38 copr_base 275 k
expat s390x 2.5.0-1.fc38 copr_base 114 k
fedora-gpg-keys noarch 38-0.3 fedora 125 k
fedora-release noarch 38-0.6 fedora 11 k
fedora-release-common noarch 38-0.6 fedora 21 k
fedora-release-identity-basic noarch 38-0.6 fedora 11 k
fedora-repos noarch 38-0.3 fedora 10 k
fedora-repos-rawhide noarch 38-0.3 fedora 9.7 k
file-libs s390x 5.42-4.fc38 copr_base 683 k
filesystem s390x 3.18-2.fc37 fedora 1.1 M
findutils s390x 1:4.9.0-2.fc38 copr_base 489 k
gawk s390x 5.1.1-4.fc38 copr_base 1.0 M
gdbm-libs s390x 1:1.23-2.fc38 copr_base 59 k
glib2 s390x 2.74.1-2.fc38 copr_base 2.7 M
glibc s390x 2.36.9000-19.fc38 fedora 1.6 M
glibc-common s390x 2.36.9000-19.fc38 fedora 306 k
glibc-minimal-langpack s390x 2.36.9000-19.fc38 fedora 30 k
gmp s390x 1:6.2.1-3.fc38 copr_base 326 k
gnupg2 s390x 2.3.8-1.fc38 copr_base 2.6 M
gnutls s390x 3.7.8-9.fc38 copr_base 1.0 M
gpgme s390x 1.17.1-3.fc38 copr_base 219 k
grep s390x 3.8-1.fc38 copr_base 290 k
ima-evm-utils s390x 1.4-6.fc37 fedora 62 k
json-c s390x 0.16-3.fc38 fedora 41 k
keyutils-libs s390x 1.6.1-5.fc37 fedora 31 k
krb5-libs s390x 1.20.1-3.fc38 fedora 706 k
libacl s390x 2.3.1-4.fc38 copr_base 25 k
libarchive s390x 3.6.1-3.fc38 fedora 394 k
libassuan s390x 2.5.5-5.fc37 fedora 64 k
libattr s390x 2.5.1-5.fc38 copr_base 19 k
libb2 s390x 0.98.1-7.fc37 fedora 26 k
libblkid s390x 2.38.1-3.fc38 fedora 103 k
libbrotli s390x 1.0.9-9.fc38 copr_base 344 k
libcap s390x 2.48-5.fc37 fedora 66 k
libcap-ng s390x 0.8.3-4.fc38 fedora 32 k
libcom_err s390x 1.46.5-3.fc38 copr_base 26 k
libcomps s390x 0.1.18-4.fc37 fedora 74 k
libcurl s390x 7.87.0-1.fc38 copr_base 320 k
libdnf s390x 0.68.0-1.fc38 fedora 627 k
libevent s390x 2.1.12-7.fc37 fedora 252 k
libffi s390x 3.4.4-1.fc38 fedora 34 k
libfsverity s390x 1.4-8.fc38 copr_base 20 k
libgcc s390x 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 66 k
libgcrypt s390x 1.10.1-6.fc38 fedora 457 k
libgomp s390x 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 305 k
libgpg-error s390x 1.46-1.fc38 fedora 226 k
libidn2 s390x 2.3.4-1.fc38 fedora 161 k
libksba s390x 1.6.3-1.fc38 fedora 152 k
libmodulemd s390x 2.14.0-4.fc37 fedora 210 k
libmount s390x 2.38.1-3.fc38 fedora 132 k
libnghttp2 s390x 1.51.0-1.fc38 fedora 73 k
libnsl2 s390x 2.0.0-4.fc37 fedora 30 k
libpsl s390x 0.21.1-6.fc37 fedora 63 k
librepo s390x 1.15.1-1.fc38 fedora 92 k
libreport-filesystem noarch 2.17.6-1.fc38 fedora 14 k
libselinux s390x 3.4-6.fc38 fedora 85 k
libsemanage s390x 3.4-6.fc38 fedora 115 k
libsepol s390x 3.4-4.fc38 fedora 302 k
libsigsegv s390x 2.14-3.fc37 fedora 27 k
libsmartcols s390x 2.38.1-3.fc38 fedora 63 k
libsolv s390x 0.7.22-3.fc37 fedora 387 k
libssh s390x 0.10.4-2.fc38 fedora 199 k
libssh-config noarch 0.10.4-2.fc38 fedora 8.8 k
libstdc++ s390x 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 889 k
libtasn1 s390x 4.19.0-1.fc38 fedora 74 k
libtirpc s390x 1.3.3-0.fc37 fedora 90 k
libunistring s390x 1.0-2.fc37 fedora 547 k
libuuid s390x 2.38.1-3.fc38 fedora 27 k
libverto s390x 0.3.2-4.fc37 fedora 20 k
libxcrypt s390x 4.4.33-5.fc38 fedora 121 k
libxml2 s390x 2.10.3-2.fc38 fedora 670 k
libyaml s390x 0.2.5-8.fc37 fedora 55 k
libzstd s390x 1.5.2-3.fc37 fedora 274 k
lua-libs s390x 5.4.4-6.fc38 fedora 129 k
lz4-libs s390x 1.9.3-5.fc37 fedora 68 k
mpdecimal s390x 2.5.1-4.fc37 fedora 104 k
mpfr s390x 4.1.1-2.fc38 fedora 522 k
ncurses-base noarch 6.3-5.20221126.fc38 fedora 86 k
ncurses-libs s390x 6.3-5.20221126.fc38 fedora 324 k
nettle s390x 3.8-2.fc37 fedora 430 k
npth s390x 1.6-10.fc38 fedora 24 k
openldap s390x 2.6.3-1.fc38 fedora 248 k
openssl-libs s390x 1:3.0.5-6.fc38 fedora 1.8 M
p11-kit s390x 0.24.1-5.fc38 fedora 378 k
p11-kit-trust s390x 0.24.1-5.fc38 fedora 131 k
pcre2 s390x 10.40-1.fc37.1 fedora 219 k
pcre2-syntax noarch 10.40-1.fc37.1 fedora 142 k
popt s390x 1.19-1.fc38 fedora 67 k
publicsuffix-list-dafsa noarch 20221208-1.fc38 fedora 59 k
python-pip-wheel noarch 22.3.1-1.fc38 fedora 1.4 M
python-setuptools-wheel noarch 65.5.1-1.fc38 fedora 715 k
python3 s390x 3.11.1-1.fc38 fedora 27 k
python3-dateutil noarch 1:2.8.2-4.fc37 fedora 361 k
python3-dbus s390x 1.3.2-1.fc38 copr_base 147 k
python3-distro noarch 1.8.0-1.fc38 fedora 49 k
python3-dnf noarch 4.14.0-1.fc38 fedora 607 k
python3-dnf-plugins-core noarch 4.3.1-1.fc38 fedora 277 k
python3-gpg s390x 1.17.1-3.fc38 copr_base 281 k
python3-hawkey s390x 0.68.0-1.fc38 fedora 99 k
python3-libcomps s390x 0.1.18-4.fc37 fedora 47 k
python3-libdnf s390x 0.68.0-1.fc38 fedora 738 k
python3-libs s390x 3.11.1-1.fc38 fedora 9.5 M
python3-rpm s390x 4.18.0-8.fc38 fedora 95 k
python3-six noarch 1.16.0-8.fc37 fedora 42 k
readline s390x 8.2-2.fc38 fedora 213 k
rpm s390x 4.18.0-8.fc38 fedora 569 k
rpm-build-libs s390x 4.18.0-8.fc38 fedora 92 k
rpm-libs s390x 4.18.0-8.fc38 fedora 307 k
rpm-sequoia s390x 1.2.0-1.fc38 fedora 960 k
rpm-sign-libs s390x 4.18.0-8.fc38 fedora 26 k
sed s390x 4.8-11.fc37 fedora 304 k
setup noarch 2.14.3-1.fc38 fedora 152 k
shadow-utils s390x 2:4.13-3.fc38 fedora 1.2 M
sqlite-libs s390x 3.40.0-1.fc38 fedora 651 k
systemd-libs s390x 252.4-598.fc38 fedora 591 k
tpm2-tss s390x 4.0.0-0.1.rc2.fc38 fedora 630 k
tzdata noarch 2022g-1.fc38 fedora 716 k
xz-libs s390x 5.2.9-1.fc38 fedora 93 k
zchunk-libs s390x 1.2.3-1.fc38 fedora 49 k
zlib s390x 1.2.13-1.fc38 fedora 96 k
Transaction Summary
=========================================================================================================================
Install 137 Packages
Total download size: 56 M
Installed size: 200 M
Downloading Packages:
(1/137): bzip2-libs-1.0.8-12.fc38.s390x.rpm 517 kB/s | 47 kB 00:00
(2/137): alternatives-1.21-1.fc38.s390x.rpm 416 kB/s | 39 kB 00:00
(3/137): bash-5.2.9-3.fc38.s390x.rpm 12 MB/s | 1.8 MB 00:00
(4/137): coreutils-9.1-8.fc38.s390x.rpm 15 MB/s | 1.1 MB 00:00
(5/137): curl-7.87.0-1.fc38.s390x.rpm 13 MB/s | 345 kB 00:00
(6/137): cyrus-sasl-lib-2.1.28-8.fc38.s390x.rpm 35 MB/s | 773 kB 00:00
(7/137): dbus-libs-1.14.4-1.fc38.s390x.rpm 15 MB/s | 159 kB 00:00
(8/137): elfutils-default-yama-scope-0.188-3.fc 1.6 MB/s | 16 kB 00:00
(9/137): coreutils-common-9.1-8.fc38.s390x.rpm 17 MB/s | 2.0 MB 00:00
(10/137): elfutils-libelf-0.188-3.fc38.s390x.rp 8.8 MB/s | 202 kB 00:00
(11/137): expat-2.5.0-1.fc38.s390x.rpm 9.4 MB/s | 114 kB 00:00
(12/137): elfutils-libs-0.188-3.fc38.s390x.rpm 9.8 MB/s | 275 kB 00:00
(13/137): findutils-4.9.0-2.fc38.s390x.rpm 37 MB/s | 489 kB 00:00
(14/137): gdbm-libs-1.23-2.fc38.s390x.rpm 12 MB/s | 59 kB 00:00
(15/137): file-libs-5.42-4.fc38.s390x.rpm 8.9 MB/s | 683 kB 00:00
(16/137): gmp-6.2.1-3.fc38.s390x.rpm 24 MB/s | 326 kB 00:00
(17/137): gawk-5.1.1-4.fc38.s390x.rpm 10 MB/s | 1.0 MB 00:00
(18/137): gnutls-3.7.8-9.fc38.s390x.rpm 17 MB/s | 1.0 MB 00:00
(19/137): gpgme-1.17.1-3.fc38.s390x.rpm 14 MB/s | 219 kB 00:00
(20/137): glib2-2.74.1-2.fc38.s390x.rpm 16 MB/s | 2.7 MB 00:00
(21/137): libacl-2.3.1-4.fc38.s390x.rpm 1.6 MB/s | 25 kB 00:00
(22/137): grep-3.8-1.fc38.s390x.rpm 12 MB/s | 290 kB 00:00
(23/137): libattr-2.5.1-5.fc38.s390x.rpm 3.7 MB/s | 19 kB 00:00
(24/137): libcom_err-1.46.5-3.fc38.s390x.rpm 6.2 MB/s | 26 kB 00:00
(25/137): gnupg2-2.3.8-1.fc38.s390x.rpm 18 MB/s | 2.6 MB 00:00
(26/137): libbrotli-1.0.9-9.fc38.s390x.rpm 15 MB/s | 344 kB 00:00
(27/137): libcurl-7.87.0-1.fc38.s390x.rpm 19 MB/s | 320 kB 00:00
(28/137): libfsverity-1.4-8.fc38.s390x.rpm 4.3 MB/s | 20 kB 00:00
(29/137): python3-dbus-1.3.2-1.fc38.s390x.rpm 15 MB/s | 147 kB 00:00
(30/137): python3-gpg-1.17.1-3.fc38.s390x.rpm 20 MB/s | 281 kB 00:00
(31/137): libgcc-13.0.0-0.4.fc38.s390x.rpm 68 kB/s | 66 kB 00:00
(32/137): libgomp-13.0.0-0.4.fc38.s390x.rpm 236 kB/s | 305 kB 00:01
(33/137): basesystem-11-14.fc37.noarch.rpm 23 kB/s | 7.0 kB 00:00
(34/137): libstdc++-13.0.0-0.4.fc38.s390x.rpm 536 kB/s | 889 kB 00:01
(35/137): audit-libs-3.0.9-2.fc38.s390x.rpm 123 kB/s | 114 kB 00:00
(36/137): dnf-4.14.0-1.fc38.noarch.rpm 908 kB/s | 480 kB 00:00
(37/137): crypto-policies-20221215-1.gita4c31a3 117 kB/s | 90 kB 00:00
(38/137): dnf-data-4.14.0-1.fc38.noarch.rpm 266 kB/s | 43 kB 00:00
(39/137): ca-certificates-2022.2.54-5.fc37.noar 830 kB/s | 829 kB 00:00
(40/137): dnf-plugins-core-4.3.1-1.fc38.noarch. 165 kB/s | 34 kB 00:00
(41/137): fedora-release-38-0.6.noarch.rpm 70 kB/s | 11 kB 00:00
(42/137): fedora-gpg-keys-38-0.3.noarch.rpm 712 kB/s | 125 kB 00:00
(43/137): fedora-release-common-38-0.6.noarch.r 114 kB/s | 21 kB 00:00
(44/137): fedora-release-identity-basic-38-0.6. 75 kB/s | 11 kB 00:00
(45/137): fedora-repos-38-0.3.noarch.rpm 67 kB/s | 10 kB 00:00
(46/137): fedora-repos-rawhide-38-0.3.noarch.rp 58 kB/s | 9.7 kB 00:00
(47/137): filesystem-3.18-2.fc37.s390x.rpm 3.3 MB/s | 1.1 MB 00:00
(48/137): glibc-2.36.9000-19.fc38.s390x.rpm 3.6 MB/s | 1.6 MB 00:00
(49/137): glibc-minimal-langpack-2.36.9000-19.f 197 kB/s | 30 kB 00:00
(50/137): ima-evm-utils-1.4-6.fc37.s390x.rpm 402 kB/s | 62 kB 00:00
(51/137): glibc-common-2.36.9000-19.fc38.s390x. 584 kB/s | 306 kB 00:00
(52/137): json-c-0.16-3.fc38.s390x.rpm 264 kB/s | 41 kB 00:00
(53/137): keyutils-libs-1.6.1-5.fc37.s390x.rpm 202 kB/s | 31 kB 00:00
(54/137): libarchive-3.6.1-3.fc38.s390x.rpm 2.2 MB/s | 394 kB 00:00
(55/137): libassuan-2.5.5-5.fc37.s390x.rpm 415 kB/s | 64 kB 00:00
(56/137): libb2-0.98.1-7.fc37.s390x.rpm 169 kB/s | 26 kB 00:00
(57/137): krb5-libs-1.20.1-3.fc38.s390x.rpm 1.6 MB/s | 706 kB 00:00
(58/137): libblkid-2.38.1-3.fc38.s390x.rpm 658 kB/s | 103 kB 00:00
(59/137): libcap-2.48-5.fc37.s390x.rpm 427 kB/s | 66 kB 00:00
(60/137): libcap-ng-0.8.3-4.fc38.s390x.rpm 199 kB/s | 32 kB 00:00
(61/137): libcomps-0.1.18-4.fc37.s390x.rpm 478 kB/s | 74 kB 00:00
(62/137): libdnf-0.68.0-1.fc38.s390x.rpm 3.2 MB/s | 627 kB 00:00
(63/137): libffi-3.4.4-1.fc38.s390x.rpm 226 kB/s | 34 kB 00:00
(64/137): libevent-2.1.12-7.fc37.s390x.rpm 1.3 MB/s | 252 kB 00:00
(65/137): libgcrypt-1.10.1-6.fc38.s390x.rpm 2.5 MB/s | 457 kB 00:00
(66/137): libgpg-error-1.46-1.fc38.s390x.rpm 1.3 MB/s | 226 kB 00:00
(67/137): libidn2-2.3.4-1.fc38.s390x.rpm 900 kB/s | 161 kB 00:00
(68/137): libksba-1.6.3-1.fc38.s390x.rpm 950 kB/s | 152 kB 00:00
(69/137): libmodulemd-2.14.0-4.fc37.s390x.rpm 1.3 MB/s | 210 kB 00:00
(70/137): libmount-2.38.1-3.fc38.s390x.rpm 752 kB/s | 132 kB 00:00
(71/137): libnghttp2-1.51.0-1.fc38.s390x.rpm 474 kB/s | 73 kB 00:00
(72/137): libnsl2-2.0.0-4.fc37.s390x.rpm 194 kB/s | 30 kB 00:00
(73/137): libpsl-0.21.1-6.fc37.s390x.rpm 383 kB/s | 63 kB 00:00
(74/137): librepo-1.15.1-1.fc38.s390x.rpm 591 kB/s | 92 kB 00:00
(75/137): libreport-filesystem-2.17.6-1.fc38.no 91 kB/s | 14 kB 00:00
(76/137): libselinux-3.4-6.fc38.s390x.rpm 509 kB/s | 85 kB 00:00
(77/137): libsemanage-3.4-6.fc38.s390x.rpm 729 kB/s | 115 kB 00:00
(78/137): libsepol-3.4-4.fc38.s390x.rpm 1.7 MB/s | 302 kB 00:00
(79/137): libsigsegv-2.14-3.fc37.s390x.rpm 168 kB/s | 27 kB 00:00
(80/137): libsmartcols-2.38.1-3.fc38.s390x.rpm 409 kB/s | 63 kB 00:00
(81/137): libsolv-0.7.22-3.fc37.s390x.rpm 2.2 MB/s | 387 kB 00:00
(82/137): libssh-config-0.10.4-2.fc38.noarch.rp 58 kB/s | 8.8 kB 00:00
(83/137): libssh-0.10.4-2.fc38.s390x.rpm 1.1 MB/s | 199 kB 00:00
(84/137): libtasn1-4.19.0-1.fc38.s390x.rpm 477 kB/s | 74 kB 00:00
(85/137): libtirpc-1.3.3-0.fc37.s390x.rpm 578 kB/s | 90 kB 00:00
(86/137): libunistring-1.0-2.fc37.s390x.rpm 2.3 MB/s | 547 kB 00:00
(87/137): libuuid-2.38.1-3.fc38.s390x.rpm 177 kB/s | 27 kB 00:00
(88/137): libverto-0.3.2-4.fc37.s390x.rpm 133 kB/s | 20 kB 00:00
(89/137): libxcrypt-4.4.33-5.fc38.s390x.rpm 699 kB/s | 121 kB 00:00
(90/137): libxml2-2.10.3-2.fc38.s390x.rpm 3.4 MB/s | 670 kB 00:00
(91/137): libyaml-0.2.5-8.fc37.s390x.rpm 354 kB/s | 55 kB 00:00
(92/137): lua-libs-5.4.4-6.fc38.s390x.rpm 813 kB/s | 129 kB 00:00
(93/137): libzstd-1.5.2-3.fc37.s390x.rpm 1.4 MB/s | 274 kB 00:00
(94/137): lz4-libs-1.9.3-5.fc37.s390x.rpm 436 kB/s | 68 kB 00:00
(95/137): mpdecimal-2.5.1-4.fc37.s390x.rpm 668 kB/s | 104 kB 00:00
(96/137): ncurses-base-6.3-5.20221126.fc38.noar 551 kB/s | 86 kB 00:00
(97/137): mpfr-4.1.1-2.fc38.s390x.rpm 2.2 MB/s | 522 kB 00:00
(98/137): ncurses-libs-6.3-5.20221126.fc38.s390 1.9 MB/s | 324 kB 00:00
(99/137): nettle-3.8-2.fc37.s390x.rpm 2.4 MB/s | 430 kB 00:00
(100/137): npth-1.6-10.fc38.s390x.rpm 150 kB/s | 24 kB 00:00
(101/137): openldap-2.6.3-1.fc38.s390x.rpm 1.5 MB/s | 248 kB 00:00
(102/137): openssl-libs-3.0.5-6.fc38.s390x.rpm 6.7 MB/s | 1.8 MB 00:00
(103/137): p11-kit-0.24.1-5.fc38.s390x.rpm 1.7 MB/s | 378 kB 00:00
(104/137): p11-kit-trust-0.24.1-5.fc38.s390x.rp 825 kB/s | 131 kB 00:00
(105/137): pcre2-10.40-1.fc37.1.s390x.rpm 1.3 MB/s | 219 kB 00:00
(106/137): pcre2-syntax-10.40-1.fc37.1.noarch.r 809 kB/s | 142 kB 00:00
(107/137): popt-1.19-1.fc38.s390x.rpm 434 kB/s | 67 kB 00:00
(108/137): publicsuffix-list-dafsa-20221208-1.f 385 kB/s | 59 kB 00:00
(109/137): python-setuptools-wheel-65.5.1-1.fc3 3.6 MB/s | 715 kB 00:00
(110/137): python3-3.11.1-1.fc38.s390x.rpm 178 kB/s | 27 kB 00:00
(111/137): python-pip-wheel-22.3.1-1.fc38.noarc 3.8 MB/s | 1.4 MB 00:00
(112/137): python3-dateutil-2.8.2-4.fc37.noarch 2.1 MB/s | 361 kB 00:00
(113/137): python3-distro-1.8.0-1.fc38.noarch.r 321 kB/s | 49 kB 00:00
(114/137): python3-dnf-plugins-core-4.3.1-1.fc3 1.6 MB/s | 277 kB 00:00
(115/137): python3-dnf-4.14.0-1.fc38.noarch.rpm 3.2 MB/s | 607 kB 00:00
(116/137): python3-hawkey-0.68.0-1.fc38.s390x.r 637 kB/s | 99 kB 00:00
(117/137): python3-libcomps-0.1.18-4.fc37.s390x 306 kB/s | 47 kB 00:00
(118/137): python3-libdnf-0.68.0-1.fc38.s390x.r 3.7 MB/s | 738 kB 00:00
(119/137): python3-rpm-4.18.0-8.fc38.s390x.rpm 609 kB/s | 95 kB 00:00
(120/137): python3-six-1.16.0-8.fc37.noarch.rpm 267 kB/s | 42 kB 00:00
(121/137): readline-8.2-2.fc38.s390x.rpm 1.3 MB/s | 213 kB 00:00
(122/137): rpm-4.18.0-8.fc38.s390x.rpm 3.0 MB/s | 569 kB 00:00
(123/137): rpm-build-libs-4.18.0-8.fc38.s390x.r 592 kB/s | 92 kB 00:00
(124/137): python3-libs-3.11.1-1.fc38.s390x.rpm 15 MB/s | 9.5 MB 00:00
(125/137): rpm-libs-4.18.0-8.fc38.s390x.rpm 1.8 MB/s | 307 kB 00:00
(126/137): rpm-sequoia-1.2.0-1.fc38.s390x.rpm 4.5 MB/s | 960 kB 00:00
(127/137): rpm-sign-libs-4.18.0-8.fc38.s390x.rp 173 kB/s | 26 kB 00:00
(128/137): sed-4.8-11.fc37.s390x.rpm 1.7 MB/s | 304 kB 00:00
(129/137): setup-2.14.3-1.fc38.noarch.rpm 954 kB/s | 152 kB 00:00
(130/137): shadow-utils-4.13-3.fc38.s390x.rpm 7.2 MB/s | 1.2 MB 00:00
(131/137): sqlite-libs-3.40.0-1.fc38.s390x.rpm 3.4 MB/s | 651 kB 00:00
(132/137): tpm2-tss-4.0.0-0.1.rc2.fc38.s390x.rp 3.8 MB/s | 630 kB 00:00
(133/137): systemd-libs-252.4-598.fc38.s390x.rp 3.1 MB/s | 591 kB 00:00
(134/137): tzdata-2022g-1.fc38.noarch.rpm 3.6 MB/s | 716 kB 00:00
(135/137): xz-libs-5.2.9-1.fc38.s390x.rpm 607 kB/s | 93 kB 00:00
(136/137): zchunk-libs-1.2.3-1.fc38.s390x.rpm 318 kB/s | 49 kB 00:00
(137/137): zlib-1.2.13-1.fc38.s390x.rpm 596 kB/s | 96 kB 00:00
--------------------------------------------------------------------------------
Total 5.7 MB/s | 56 MB 00:09
fedora 1.6 MB/s | 1.6 kB 00:00
Importing GPG key 0xEB10B464:
Userid : "Fedora (38) <fedora-38-primary@fedoraproject.org>"
Fingerprint: 6A51 BBAB BA3D 5467 B617 1221 809A 8D7C EB10 B464
From : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-38-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-38-primary (0xEB10B464) is already installed
fedora 1.6 MB/s | 1.6 kB 00:00
Importing GPG key 0x5323552A:
Userid : "Fedora (37) <fedora-37-primary@fedoraproject.org>"
Fingerprint: ACB5 EE4E 831C 74BB 7C16 8D27 F55A D3FB 5323 552A
From : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-37-primary
Key imported successfully
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
Running scriptlet: filesystem-3.18-2.fc37.s390x 1/1
Preparing : 1/1
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Running scriptlet: libgcc-13.0.0-0.4.fc38.s390x 1/137
Installing : crypto-policies-20221215-1.gita4c31a3.fc38.noarc 2/137
Running scriptlet: crypto-policies-20221215-1.gita4c31a3.fc38.noarc 2/137
Installing : tzdata-2022g-1.fc38.noarch 3/137
Installing : fedora-release-identity-basic-38-0.6.noarch 4/137
Installing : python-setuptools-wheel-65.5.1-1.fc38.noarch 5/137
Installing : publicsuffix-list-dafsa-20221208-1.fc38.noarch 6/137
Installing : pcre2-syntax-10.40-1.fc37.1.noarch 7/137
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Installing : libssh-config-0.10.4-2.fc38.noarch 9/137
Installing : libreport-filesystem-2.17.6-1.fc38.noarch 10/137
Installing : dnf-data-4.14.0-1.fc38.noarch 11/137
warning: /etc/dnf/dnf.conf created as /etc/dnf/dnf.conf.rpmnew
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Installing : fedora-repos-rawhide-38-0.3.noarch 15/137
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useradd: Warning: missing or non-executable shell '/usr/sbin/nologin'
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Verifying : dnf-plugins-core-4.3.1-1.fc38.noarch 40/137
Verifying : fedora-gpg-keys-38-0.3.noarch 41/137
Verifying : fedora-release-38-0.6.noarch 42/137
Verifying : fedora-release-common-38-0.6.noarch 43/137
Verifying : fedora-release-identity-basic-38-0.6.noarch 44/137
Verifying : fedora-repos-38-0.3.noarch 45/137
Verifying : fedora-repos-rawhide-38-0.3.noarch 46/137
Verifying : filesystem-3.18-2.fc37.s390x 47/137
Verifying : glibc-2.36.9000-19.fc38.s390x 48/137
Verifying : glibc-common-2.36.9000-19.fc38.s390x 49/137
Verifying : glibc-minimal-langpack-2.36.9000-19.fc38.s390x 50/137
Verifying : ima-evm-utils-1.4-6.fc37.s390x 51/137
Verifying : json-c-0.16-3.fc38.s390x 52/137
Verifying : keyutils-libs-1.6.1-5.fc37.s390x 53/137
Verifying : krb5-libs-1.20.1-3.fc38.s390x 54/137
Verifying : libarchive-3.6.1-3.fc38.s390x 55/137
Verifying : libassuan-2.5.5-5.fc37.s390x 56/137
Verifying : libb2-0.98.1-7.fc37.s390x 57/137
Verifying : libblkid-2.38.1-3.fc38.s390x 58/137
Verifying : libcap-2.48-5.fc37.s390x 59/137
Verifying : libcap-ng-0.8.3-4.fc38.s390x 60/137
Verifying : libcomps-0.1.18-4.fc37.s390x 61/137
Verifying : libdnf-0.68.0-1.fc38.s390x 62/137
Verifying : libevent-2.1.12-7.fc37.s390x 63/137
Verifying : libffi-3.4.4-1.fc38.s390x 64/137
Verifying : libgcrypt-1.10.1-6.fc38.s390x 65/137
Verifying : libgpg-error-1.46-1.fc38.s390x 66/137
Verifying : libidn2-2.3.4-1.fc38.s390x 67/137
Verifying : libksba-1.6.3-1.fc38.s390x 68/137
Verifying : libmodulemd-2.14.0-4.fc37.s390x 69/137
Verifying : libmount-2.38.1-3.fc38.s390x 70/137
Verifying : libnghttp2-1.51.0-1.fc38.s390x 71/137
Verifying : libnsl2-2.0.0-4.fc37.s390x 72/137
Verifying : libpsl-0.21.1-6.fc37.s390x 73/137
Verifying : librepo-1.15.1-1.fc38.s390x 74/137
Verifying : libreport-filesystem-2.17.6-1.fc38.noarch 75/137
Verifying : libselinux-3.4-6.fc38.s390x 76/137
Verifying : libsemanage-3.4-6.fc38.s390x 77/137
Verifying : libsepol-3.4-4.fc38.s390x 78/137
Verifying : libsigsegv-2.14-3.fc37.s390x 79/137
Verifying : libsmartcols-2.38.1-3.fc38.s390x 80/137
Verifying : libsolv-0.7.22-3.fc37.s390x 81/137
Verifying : libssh-0.10.4-2.fc38.s390x 82/137
Verifying : libssh-config-0.10.4-2.fc38.noarch 83/137
Verifying : libtasn1-4.19.0-1.fc38.s390x 84/137
Verifying : libtirpc-1.3.3-0.fc37.s390x 85/137
Verifying : libunistring-1.0-2.fc37.s390x 86/137
Verifying : libuuid-2.38.1-3.fc38.s390x 87/137
Verifying : libverto-0.3.2-4.fc37.s390x 88/137
Verifying : libxcrypt-4.4.33-5.fc38.s390x 89/137
Verifying : libxml2-2.10.3-2.fc38.s390x 90/137
Verifying : libyaml-0.2.5-8.fc37.s390x 91/137
Verifying : libzstd-1.5.2-3.fc37.s390x 92/137
Verifying : lua-libs-5.4.4-6.fc38.s390x 93/137
Verifying : lz4-libs-1.9.3-5.fc37.s390x 94/137
Verifying : mpdecimal-2.5.1-4.fc37.s390x 95/137
Verifying : mpfr-4.1.1-2.fc38.s390x 96/137
Verifying : ncurses-base-6.3-5.20221126.fc38.noarch 97/137
Verifying : ncurses-libs-6.3-5.20221126.fc38.s390x 98/137
Verifying : nettle-3.8-2.fc37.s390x 99/137
Verifying : npth-1.6-10.fc38.s390x 100/137
Verifying : openldap-2.6.3-1.fc38.s390x 101/137
Verifying : openssl-libs-1:3.0.5-6.fc38.s390x 102/137
Verifying : p11-kit-0.24.1-5.fc38.s390x 103/137
Verifying : p11-kit-trust-0.24.1-5.fc38.s390x 104/137
Verifying : pcre2-10.40-1.fc37.1.s390x 105/137
Verifying : pcre2-syntax-10.40-1.fc37.1.noarch 106/137
Verifying : popt-1.19-1.fc38.s390x 107/137
Verifying : publicsuffix-list-dafsa-20221208-1.fc38.noarch 108/137
Verifying : python-pip-wheel-22.3.1-1.fc38.noarch 109/137
Verifying : python-setuptools-wheel-65.5.1-1.fc38.noarch 110/137
Verifying : python3-3.11.1-1.fc38.s390x 111/137
Verifying : python3-dateutil-1:2.8.2-4.fc37.noarch 112/137
Verifying : python3-distro-1.8.0-1.fc38.noarch 113/137
Verifying : python3-dnf-4.14.0-1.fc38.noarch 114/137
Verifying : python3-dnf-plugins-core-4.3.1-1.fc38.noarch 115/137
Verifying : python3-hawkey-0.68.0-1.fc38.s390x 116/137
Verifying : python3-libcomps-0.1.18-4.fc37.s390x 117/137
Verifying : python3-libdnf-0.68.0-1.fc38.s390x 118/137
Verifying : python3-libs-3.11.1-1.fc38.s390x 119/137
Verifying : python3-rpm-4.18.0-8.fc38.s390x 120/137
Verifying : python3-six-1.16.0-8.fc37.noarch 121/137
Verifying : readline-8.2-2.fc38.s390x 122/137
Verifying : rpm-4.18.0-8.fc38.s390x 123/137
Verifying : rpm-build-libs-4.18.0-8.fc38.s390x 124/137
Verifying : rpm-libs-4.18.0-8.fc38.s390x 125/137
Verifying : rpm-sequoia-1.2.0-1.fc38.s390x 126/137
Verifying : rpm-sign-libs-4.18.0-8.fc38.s390x 127/137
Verifying : sed-4.8-11.fc37.s390x 128/137
Verifying : setup-2.14.3-1.fc38.noarch 129/137
Verifying : shadow-utils-2:4.13-3.fc38.s390x 130/137
Verifying : sqlite-libs-3.40.0-1.fc38.s390x 131/137
Verifying : systemd-libs-252.4-598.fc38.s390x 132/137
Verifying : tpm2-tss-4.0.0-0.1.rc2.fc38.s390x 133/137
Verifying : tzdata-2022g-1.fc38.noarch 134/137
Verifying : xz-libs-5.2.9-1.fc38.s390x 135/137
Verifying : zchunk-libs-1.2.3-1.fc38.s390x 136/137
Verifying : zlib-1.2.13-1.fc38.s390x 137/137
Installed products updated.
Installed:
alternatives-1.21-1.fc38.s390x
audit-libs-3.0.9-2.fc38.s390x
basesystem-11-14.fc37.noarch
bash-5.2.9-3.fc38.s390x
bzip2-libs-1.0.8-12.fc38.s390x
ca-certificates-2022.2.54-5.fc37.noarch
coreutils-9.1-8.fc38.s390x
coreutils-common-9.1-8.fc38.s390x
crypto-policies-20221215-1.gita4c31a3.fc38.noarch
curl-7.87.0-1.fc38.s390x
cyrus-sasl-lib-2.1.28-8.fc38.s390x
dbus-libs-1:1.14.4-1.fc38.s390x
dnf-4.14.0-1.fc38.noarch
dnf-data-4.14.0-1.fc38.noarch
dnf-plugins-core-4.3.1-1.fc38.noarch
elfutils-default-yama-scope-0.188-3.fc38.noarch
elfutils-libelf-0.188-3.fc38.s390x
elfutils-libs-0.188-3.fc38.s390x
expat-2.5.0-1.fc38.s390x
fedora-gpg-keys-38-0.3.noarch
fedora-release-38-0.6.noarch
fedora-release-common-38-0.6.noarch
fedora-release-identity-basic-38-0.6.noarch
fedora-repos-38-0.3.noarch
fedora-repos-rawhide-38-0.3.noarch
file-libs-5.42-4.fc38.s390x
filesystem-3.18-2.fc37.s390x
findutils-1:4.9.0-2.fc38.s390x
gawk-5.1.1-4.fc38.s390x
gdbm-libs-1:1.23-2.fc38.s390x
glib2-2.74.1-2.fc38.s390x
glibc-2.36.9000-19.fc38.s390x
glibc-common-2.36.9000-19.fc38.s390x
glibc-minimal-langpack-2.36.9000-19.fc38.s390x
gmp-1:6.2.1-3.fc38.s390x
gnupg2-2.3.8-1.fc38.s390x
gnutls-3.7.8-9.fc38.s390x
gpgme-1.17.1-3.fc38.s390x
grep-3.8-1.fc38.s390x
ima-evm-utils-1.4-6.fc37.s390x
json-c-0.16-3.fc38.s390x
keyutils-libs-1.6.1-5.fc37.s390x
krb5-libs-1.20.1-3.fc38.s390x
libacl-2.3.1-4.fc38.s390x
libarchive-3.6.1-3.fc38.s390x
libassuan-2.5.5-5.fc37.s390x
libattr-2.5.1-5.fc38.s390x
libb2-0.98.1-7.fc37.s390x
libblkid-2.38.1-3.fc38.s390x
libbrotli-1.0.9-9.fc38.s390x
libcap-2.48-5.fc37.s390x
libcap-ng-0.8.3-4.fc38.s390x
libcom_err-1.46.5-3.fc38.s390x
libcomps-0.1.18-4.fc37.s390x
libcurl-7.87.0-1.fc38.s390x
libdnf-0.68.0-1.fc38.s390x
libevent-2.1.12-7.fc37.s390x
libffi-3.4.4-1.fc38.s390x
libfsverity-1.4-8.fc38.s390x
libgcc-13.0.0-0.4.fc38.s390x
libgcrypt-1.10.1-6.fc38.s390x
libgomp-13.0.0-0.4.fc38.s390x
libgpg-error-1.46-1.fc38.s390x
libidn2-2.3.4-1.fc38.s390x
libksba-1.6.3-1.fc38.s390x
libmodulemd-2.14.0-4.fc37.s390x
libmount-2.38.1-3.fc38.s390x
libnghttp2-1.51.0-1.fc38.s390x
libnsl2-2.0.0-4.fc37.s390x
libpsl-0.21.1-6.fc37.s390x
librepo-1.15.1-1.fc38.s390x
libreport-filesystem-2.17.6-1.fc38.noarch
libselinux-3.4-6.fc38.s390x
libsemanage-3.4-6.fc38.s390x
libsepol-3.4-4.fc38.s390x
libsigsegv-2.14-3.fc37.s390x
libsmartcols-2.38.1-3.fc38.s390x
libsolv-0.7.22-3.fc37.s390x
libssh-0.10.4-2.fc38.s390x
libssh-config-0.10.4-2.fc38.noarch
libstdc++-13.0.0-0.4.fc38.s390x
libtasn1-4.19.0-1.fc38.s390x
libtirpc-1.3.3-0.fc37.s390x
libunistring-1.0-2.fc37.s390x
libuuid-2.38.1-3.fc38.s390x
libverto-0.3.2-4.fc37.s390x
libxcrypt-4.4.33-5.fc38.s390x
libxml2-2.10.3-2.fc38.s390x
libyaml-0.2.5-8.fc37.s390x
libzstd-1.5.2-3.fc37.s390x
lua-libs-5.4.4-6.fc38.s390x
lz4-libs-1.9.3-5.fc37.s390x
mpdecimal-2.5.1-4.fc37.s390x
mpfr-4.1.1-2.fc38.s390x
ncurses-base-6.3-5.20221126.fc38.noarch
ncurses-libs-6.3-5.20221126.fc38.s390x
nettle-3.8-2.fc37.s390x
npth-1.6-10.fc38.s390x
openldap-2.6.3-1.fc38.s390x
openssl-libs-1:3.0.5-6.fc38.s390x
p11-kit-0.24.1-5.fc38.s390x
p11-kit-trust-0.24.1-5.fc38.s390x
pcre2-10.40-1.fc37.1.s390x
pcre2-syntax-10.40-1.fc37.1.noarch
popt-1.19-1.fc38.s390x
publicsuffix-list-dafsa-20221208-1.fc38.noarch
python-pip-wheel-22.3.1-1.fc38.noarch
python-setuptools-wheel-65.5.1-1.fc38.noarch
python3-3.11.1-1.fc38.s390x
python3-dateutil-1:2.8.2-4.fc37.noarch
python3-dbus-1.3.2-1.fc38.s390x
python3-distro-1.8.0-1.fc38.noarch
python3-dnf-4.14.0-1.fc38.noarch
python3-dnf-plugins-core-4.3.1-1.fc38.noarch
python3-gpg-1.17.1-3.fc38.s390x
python3-hawkey-0.68.0-1.fc38.s390x
python3-libcomps-0.1.18-4.fc37.s390x
python3-libdnf-0.68.0-1.fc38.s390x
python3-libs-3.11.1-1.fc38.s390x
python3-rpm-4.18.0-8.fc38.s390x
python3-six-1.16.0-8.fc37.noarch
readline-8.2-2.fc38.s390x
rpm-4.18.0-8.fc38.s390x
rpm-build-libs-4.18.0-8.fc38.s390x
rpm-libs-4.18.0-8.fc38.s390x
rpm-sequoia-1.2.0-1.fc38.s390x
rpm-sign-libs-4.18.0-8.fc38.s390x
sed-4.8-11.fc37.s390x
setup-2.14.3-1.fc38.noarch
shadow-utils-2:4.13-3.fc38.s390x
sqlite-libs-3.40.0-1.fc38.s390x
systemd-libs-252.4-598.fc38.s390x
tpm2-tss-4.0.0-0.1.rc2.fc38.s390x
tzdata-2022g-1.fc38.noarch
xz-libs-5.2.9-1.fc38.s390x
zchunk-libs-1.2.3-1.fc38.s390x
zlib-1.2.13-1.fc38.s390x
Complete!
Finish(bootstrap): dnf install
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-s390x-1671942858.428762/root.
INFO: calling preinit hooks
INFO: enabled root cache
INFO: enabled package manager cache
Start: cleaning package manager metadata
Finish: cleaning package manager metadata
INFO: enabled HW Info plugin
Mock Version: 3.5
INFO: Mock Version: 3.5
Start: dnf install
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Copr repository 4.4 kB/s | 3.0 kB 00:00
Copr repository 3.0 MB/s | 16 MB 00:05
Additional repo https_jakub_fedorapeople_org_fe 4.2 kB/s | 3.0 kB 00:00
fedora 1.0 kB/s | 6.3 kB 00:05
Dependencies resolved.
=========================================================================================================================
Package Arch Version Repository Size
=========================================================================================================================
Installing group/module packages:
bash s390x 5.2.9-3.fc38 copr_base 1.8 M
bzip2 s390x 1.0.8-12.fc38 copr_base 54 k
coreutils s390x 9.1-8.fc38 copr_base 1.1 M
cpio s390x 2.13-13.fc38 copr_base 275 k
diffutils s390x 3.8-3.fc38 copr_base 381 k
fedora-release-common noarch 38-0.6 fedora 21 k
findutils s390x 1:4.9.0-2.fc38 copr_base 489 k
gawk s390x 5.1.1-4.fc38 copr_base 1.0 M
glibc-minimal-langpack s390x 2.36.9000-19.fc38 fedora 30 k
grep s390x 3.8-1.fc38 copr_base 290 k
gzip s390x 1.12-2.fc38 copr_base 165 k
info s390x 7.0.1-1.fc38 fedora 180 k
patch s390x 2.7.6-17.fc37 fedora 122 k
redhat-rpm-config noarch 235-1.fc38 fedora 80 k
rpm-build s390x 4.18.0-8.fc38 fedora 76 k
sed s390x 4.8-11.fc37 fedora 304 k
shadow-utils s390x 2:4.13-3.fc38 fedora 1.2 M
tar s390x 2:1.34-5.fc38 fedora 876 k
unzip s390x 6.0-58.fc38 fedora 177 k
util-linux s390x 2.38.1-3.fc38 fedora 2.3 M
which s390x 2.21-36.fc38 fedora 42 k
xz s390x 5.2.9-1.fc38 fedora 306 k
Installing dependencies:
alternatives s390x 1.21-1.fc38 copr_base 39 k
ansible-srpm-macros noarch 1-8.1.fc38 fedora 8.6 k
audit-libs s390x 3.0.9-2.fc38 fedora 114 k
authselect s390x 1.4.2-1.fc38 copr_base 139 k
authselect-libs s390x 1.4.2-1.fc38 copr_base 235 k
basesystem noarch 11-14.fc37 fedora 7.0 k
binutils s390x 2.39-6.fc38 copr_base 5.7 M
binutils-gold s390x 2.39-6.fc38 copr_base 994 k
bzip2-libs s390x 1.0.8-12.fc38 copr_base 47 k
ca-certificates noarch 2022.2.54-5.fc37 fedora 829 k
coreutils-common s390x 9.1-8.fc38 copr_base 2.0 M
cracklib s390x 2.9.7-30.fc38 copr_base 82 k
crypto-policies noarch 20221215-1.gita4c31a3.fc38 fedora 90 k
curl s390x 7.87.0-1.fc38 copr_base 345 k
cyrus-sasl-lib s390x 2.1.28-8.fc38 copr_base 773 k
debugedit s390x 5.0-5.fc37 fedora 76 k
dwz s390x 0.15-1.fc38 copr_base 144 k
ed s390x 1.18-2.fc38 copr_base 80 k
efi-srpm-macros noarch 5-6.fc37 fedora 22 k
elfutils s390x 0.188-3.fc38 copr_base 547 k
elfutils-debuginfod-client s390x 0.188-3.fc38 copr_base 41 k
elfutils-default-yama-scope noarch 0.188-3.fc38 copr_base 16 k
elfutils-libelf s390x 0.188-3.fc38 copr_base 202 k
elfutils-libs s390x 0.188-3.fc38 copr_base 275 k
fedora-gpg-keys noarch 38-0.3 fedora 125 k
fedora-release noarch 38-0.6 fedora 11 k
fedora-release-identity-basic noarch 38-0.6 fedora 11 k
fedora-repos noarch 38-0.3 fedora 10 k
fedora-repos-rawhide noarch 38-0.3 fedora 9.7 k
file s390x 5.42-4.fc38 copr_base 49 k
file-libs s390x 5.42-4.fc38 copr_base 683 k
filesystem s390x 3.18-2.fc37 fedora 1.1 M
fonts-srpm-macros noarch 1:2.0.5-10.fc38 fedora 26 k
fpc-srpm-macros noarch 1.3-6.fc37 fedora 7.7 k
gdb-minimal s390x 12.1-10.fc38 fedora 3.3 M
gdbm-libs s390x 1:1.23-2.fc38 copr_base 59 k
ghc-srpm-macros noarch 1.5.0-7.fc37 fedora 7.8 k
glibc s390x 2.36.9000-19.fc38 fedora 1.6 M
glibc-common s390x 2.36.9000-19.fc38 fedora 306 k
glibc-gconv-extra s390x 2.36.9000-19.fc38 fedora 1.6 M
gmp s390x 1:6.2.1-3.fc38 copr_base 326 k
gnat-srpm-macros noarch 4-16.fc37 fedora 8.3 k
go-srpm-macros noarch 3.2.0-1.fc38 fedora 27 k
jansson s390x 2.13.1-5.fc37 fedora 42 k
kernel-srpm-macros noarch 1.0-15.fc37 fedora 9.4 k
keyutils-libs s390x 1.6.1-5.fc37 fedora 31 k
krb5-libs s390x 1.20.1-3.fc38 fedora 706 k
libacl s390x 2.3.1-4.fc38 copr_base 25 k
libarchive s390x 3.6.1-3.fc38 fedora 394 k
libattr s390x 2.5.1-5.fc38 copr_base 19 k
libblkid s390x 2.38.1-3.fc38 fedora 103 k
libbrotli s390x 1.0.9-9.fc38 copr_base 344 k
libcap s390x 2.48-5.fc37 fedora 66 k
libcap-ng s390x 0.8.3-4.fc38 fedora 32 k
libcom_err s390x 1.46.5-3.fc38 copr_base 26 k
libcurl s390x 7.87.0-1.fc38 copr_base 320 k
libdb s390x 5.3.28-54.fc38 fedora 727 k
libeconf s390x 0.4.0-4.fc37 fedora 26 k
libevent s390x 2.1.12-7.fc37 fedora 252 k
libfdisk s390x 2.38.1-3.fc38 fedora 156 k
libffi s390x 3.4.4-1.fc38 fedora 34 k
libgcc s390x 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 66 k
libgomp s390x 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 305 k
libidn2 s390x 2.3.4-1.fc38 fedora 161 k
libmount s390x 2.38.1-3.fc38 fedora 132 k
libnghttp2 s390x 1.51.0-1.fc38 fedora 73 k
libnsl2 s390x 2.0.0-4.fc37 fedora 30 k
libpkgconf s390x 1.8.0-3.fc37 fedora 34 k
libpsl s390x 0.21.1-6.fc37 fedora 63 k
libpwquality s390x 1.4.5-1.fc38 fedora 119 k
libselinux s390x 3.4-6.fc38 fedora 85 k
libsemanage s390x 3.4-6.fc38 fedora 115 k
libsepol s390x 3.4-4.fc38 fedora 302 k
libsigsegv s390x 2.14-3.fc37 fedora 27 k
libsmartcols s390x 2.38.1-3.fc38 fedora 63 k
libssh s390x 0.10.4-2.fc38 fedora 199 k
libssh-config noarch 0.10.4-2.fc38 fedora 8.8 k
libstdc++ s390x 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 889 k
libtasn1 s390x 4.19.0-1.fc38 fedora 74 k
libtirpc s390x 1.3.3-0.fc37 fedora 90 k
libunistring s390x 1.0-2.fc37 fedora 547 k
libutempter s390x 1.2.1-7.fc37 fedora 26 k
libuuid s390x 2.38.1-3.fc38 fedora 27 k
libverto s390x 0.3.2-4.fc37 fedora 20 k
libxcrypt s390x 4.4.33-5.fc38 fedora 121 k
libxml2 s390x 2.10.3-2.fc38 fedora 670 k
libzstd s390x 1.5.2-3.fc37 fedora 274 k
lua-libs s390x 5.4.4-6.fc38 fedora 129 k
lua-srpm-macros noarch 1-7.fc37 fedora 8.8 k
lz4-libs s390x 1.9.3-5.fc37 fedora 68 k
mpfr s390x 4.1.1-2.fc38 fedora 522 k
ncurses-base noarch 6.3-5.20221126.fc38 fedora 86 k
ncurses-libs s390x 6.3-5.20221126.fc38 fedora 324 k
nettle s390x 3.8-2.fc37 fedora 430 k
nim-srpm-macros noarch 3-7.fc37 fedora 8.4 k
ocaml-srpm-macros noarch 7-2.fc37 fedora 13 k
openblas-srpm-macros noarch 2-12.fc37 fedora 7.5 k
openldap s390x 2.6.3-1.fc38 fedora 248 k
openssl-libs s390x 1:3.0.5-6.fc38 fedora 1.8 M
p11-kit s390x 0.24.1-5.fc38 fedora 378 k
p11-kit-trust s390x 0.24.1-5.fc38 fedora 131 k
package-notes-srpm-macros noarch 0.5-6.fc38 fedora 11 k
pam s390x 1.5.2-15.fc38 fedora 554 k
pam-libs s390x 1.5.2-15.fc38 fedora 56 k
pcre2 s390x 10.40-1.fc37.1 fedora 219 k
pcre2-syntax noarch 10.40-1.fc37.1 fedora 142 k
perl-srpm-macros noarch 1-47.fc38 fedora 8.2 k
pkgconf s390x 1.8.0-3.fc37 fedora 41 k
pkgconf-m4 noarch 1.8.0-3.fc37 fedora 14 k
pkgconf-pkg-config s390x 1.8.0-3.fc37 fedora 10 k
popt s390x 1.19-1.fc38 fedora 67 k
publicsuffix-list-dafsa noarch 20221208-1.fc38 fedora 59 k
python-srpm-macros noarch 3.11-6.fc38 fedora 25 k
qt5-srpm-macros noarch 5.15.7-1.fc38 fedora 7.9 k
readline s390x 8.2-2.fc38 fedora 213 k
rpm s390x 4.18.0-8.fc38 fedora 569 k
rpm-build-libs s390x 4.18.0-8.fc38 fedora 92 k
rpm-libs s390x 4.18.0-8.fc38 fedora 307 k
rpm-sequoia s390x 1.2.0-1.fc38 fedora 960 k
rpmautospec-rpm-macros noarch 0.3.1-1.fc38 fedora 8.8 k
rust-srpm-macros noarch 23-1.fc38 fedora 9.4 k
setup noarch 2.14.3-1.fc38 fedora 152 k
sqlite-libs s390x 3.40.0-1.fc38 fedora 651 k
systemd-libs s390x 252.4-598.fc38 fedora 591 k
tzdata noarch 2022g-1.fc38 fedora 716 k
util-linux-core s390x 2.38.1-3.fc38 fedora 462 k
xxhash-libs s390x 0.8.1-3.fc37 fedora 36 k
xz-libs s390x 5.2.9-1.fc38 fedora 93 k
zip s390x 3.0-35.fc38 fedora 261 k
zlib s390x 1.2.13-1.fc38 fedora 96 k
zstd s390x 1.5.2-3.fc37 fedora 410 k
Installing Groups:
Buildsystem building group
Transaction Summary
=========================================================================================================================
Install 153 Packages
Total size: 52 M
Installed size: 182 M
Downloading Packages:
[SKIPPED] alternatives-1.21-1.fc38.s390x.rpm: Already downloaded
[SKIPPED] authselect-1.4.2-1.fc38.s390x.rpm: Already downloaded
[SKIPPED] authselect-libs-1.4.2-1.fc38.s390x.rpm: Already downloaded
[SKIPPED] bash-5.2.9-3.fc38.s390x.rpm: Already downloaded
[SKIPPED] binutils-2.39-6.fc38.s390x.rpm: Already downloaded
[SKIPPED] binutils-gold-2.39-6.fc38.s390x.rpm: Already downloaded
[SKIPPED] bzip2-1.0.8-12.fc38.s390x.rpm: Already downloaded
[SKIPPED] bzip2-libs-1.0.8-12.fc38.s390x.rpm: Already downloaded
[SKIPPED] coreutils-9.1-8.fc38.s390x.rpm: Already downloaded
[SKIPPED] coreutils-common-9.1-8.fc38.s390x.rpm: Already downloaded
[SKIPPED] cpio-2.13-13.fc38.s390x.rpm: Already downloaded
[SKIPPED] cracklib-2.9.7-30.fc38.s390x.rpm: Already downloaded
[SKIPPED] curl-7.87.0-1.fc38.s390x.rpm: Already downloaded
[SKIPPED] cyrus-sasl-lib-2.1.28-8.fc38.s390x.rpm: Already downloaded
[SKIPPED] diffutils-3.8-3.fc38.s390x.rpm: Already downloaded
[SKIPPED] dwz-0.15-1.fc38.s390x.rpm: Already downloaded
[SKIPPED] ed-1.18-2.fc38.s390x.rpm: Already downloaded
[SKIPPED] elfutils-0.188-3.fc38.s390x.rpm: Already downloaded
[SKIPPED] elfutils-debuginfod-client-0.188-3.fc38.s390x.rpm: Already downloaded
[SKIPPED] elfutils-default-yama-scope-0.188-3.fc38.noarch.rpm: Already downloaded
[SKIPPED] elfutils-libelf-0.188-3.fc38.s390x.rpm: Already downloaded
[SKIPPED] elfutils-libs-0.188-3.fc38.s390x.rpm: Already downloaded
[SKIPPED] file-5.42-4.fc38.s390x.rpm: Already downloaded
[SKIPPED] file-libs-5.42-4.fc38.s390x.rpm: Already downloaded
[SKIPPED] findutils-4.9.0-2.fc38.s390x.rpm: Already downloaded
[SKIPPED] gawk-5.1.1-4.fc38.s390x.rpm: Already downloaded
[SKIPPED] gdbm-libs-1.23-2.fc38.s390x.rpm: Already downloaded
[SKIPPED] gmp-6.2.1-3.fc38.s390x.rpm: Already downloaded
[SKIPPED] grep-3.8-1.fc38.s390x.rpm: Already downloaded
[SKIPPED] gzip-1.12-2.fc38.s390x.rpm: Already downloaded
[SKIPPED] libacl-2.3.1-4.fc38.s390x.rpm: Already downloaded
[SKIPPED] libattr-2.5.1-5.fc38.s390x.rpm: Already downloaded
[SKIPPED] libbrotli-1.0.9-9.fc38.s390x.rpm: Already downloaded
[SKIPPED] libcom_err-1.46.5-3.fc38.s390x.rpm: Already downloaded
[SKIPPED] libcurl-7.87.0-1.fc38.s390x.rpm: Already downloaded
[SKIPPED] libgcc-13.0.0-0.4.fc38.s390x.rpm: Already downloaded
[SKIPPED] libgomp-13.0.0-0.4.fc38.s390x.rpm: Already downloaded
[SKIPPED] libstdc++-13.0.0-0.4.fc38.s390x.rpm: Already downloaded
[SKIPPED] ansible-srpm-macros-1-8.1.fc38.noarch.rpm: Already downloaded
[SKIPPED] audit-libs-3.0.9-2.fc38.s390x.rpm: Already downloaded
[SKIPPED] basesystem-11-14.fc37.noarch.rpm: Already downloaded
[SKIPPED] ca-certificates-2022.2.54-5.fc37.noarch.rpm: Already downloaded
[SKIPPED] crypto-policies-20221215-1.gita4c31a3.fc38.noarch.rpm: Already downloaded
[SKIPPED] debugedit-5.0-5.fc37.s390x.rpm: Already downloaded
[SKIPPED] efi-srpm-macros-5-6.fc37.noarch.rpm: Already downloaded
[SKIPPED] fedora-gpg-keys-38-0.3.noarch.rpm: Already downloaded
[SKIPPED] fedora-release-38-0.6.noarch.rpm: Already downloaded
[SKIPPED] fedora-release-common-38-0.6.noarch.rpm: Already downloaded
[SKIPPED] fedora-release-identity-basic-38-0.6.noarch.rpm: Already downloaded
[SKIPPED] fedora-repos-38-0.3.noarch.rpm: Already downloaded
[SKIPPED] fedora-repos-rawhide-38-0.3.noarch.rpm: Already downloaded
[SKIPPED] filesystem-3.18-2.fc37.s390x.rpm: Already downloaded
[SKIPPED] fonts-srpm-macros-2.0.5-10.fc38.noarch.rpm: Already downloaded
[SKIPPED] fpc-srpm-macros-1.3-6.fc37.noarch.rpm: Already downloaded
[SKIPPED] gdb-minimal-12.1-10.fc38.s390x.rpm: Already downloaded
[SKIPPED] ghc-srpm-macros-1.5.0-7.fc37.noarch.rpm: Already downloaded
[SKIPPED] glibc-2.36.9000-19.fc38.s390x.rpm: Already downloaded
[SKIPPED] glibc-common-2.36.9000-19.fc38.s390x.rpm: Already downloaded
[SKIPPED] glibc-gconv-extra-2.36.9000-19.fc38.s390x.rpm: Already downloaded
[SKIPPED] glibc-minimal-langpack-2.36.9000-19.fc38.s390x.rpm: Already downloaded
[SKIPPED] gnat-srpm-macros-4-16.fc37.noarch.rpm: Already downloaded
[SKIPPED] go-srpm-macros-3.2.0-1.fc38.noarch.rpm: Already downloaded
[SKIPPED] info-7.0.1-1.fc38.s390x.rpm: Already downloaded
[SKIPPED] jansson-2.13.1-5.fc37.s390x.rpm: Already downloaded
[SKIPPED] kernel-srpm-macros-1.0-15.fc37.noarch.rpm: Already downloaded
[SKIPPED] keyutils-libs-1.6.1-5.fc37.s390x.rpm: Already downloaded
[SKIPPED] krb5-libs-1.20.1-3.fc38.s390x.rpm: Already downloaded
[SKIPPED] libarchive-3.6.1-3.fc38.s390x.rpm: Already downloaded
[SKIPPED] libblkid-2.38.1-3.fc38.s390x.rpm: Already downloaded
[SKIPPED] libcap-2.48-5.fc37.s390x.rpm: Already downloaded
[SKIPPED] libcap-ng-0.8.3-4.fc38.s390x.rpm: Already downloaded
[SKIPPED] libdb-5.3.28-54.fc38.s390x.rpm: Already downloaded
[SKIPPED] libeconf-0.4.0-4.fc37.s390x.rpm: Already downloaded
[SKIPPED] libevent-2.1.12-7.fc37.s390x.rpm: Already downloaded
[SKIPPED] libfdisk-2.38.1-3.fc38.s390x.rpm: Already downloaded
[SKIPPED] libffi-3.4.4-1.fc38.s390x.rpm: Already downloaded
[SKIPPED] libidn2-2.3.4-1.fc38.s390x.rpm: Already downloaded
[SKIPPED] libmount-2.38.1-3.fc38.s390x.rpm: Already downloaded
[SKIPPED] libnghttp2-1.51.0-1.fc38.s390x.rpm: Already downloaded
[SKIPPED] libnsl2-2.0.0-4.fc37.s390x.rpm: Already downloaded
[SKIPPED] libpkgconf-1.8.0-3.fc37.s390x.rpm: Already downloaded
[SKIPPED] libpsl-0.21.1-6.fc37.s390x.rpm: Already downloaded
[SKIPPED] libpwquality-1.4.5-1.fc38.s390x.rpm: Already downloaded
[SKIPPED] libselinux-3.4-6.fc38.s390x.rpm: Already downloaded
[SKIPPED] libsemanage-3.4-6.fc38.s390x.rpm: Already downloaded
[SKIPPED] libsepol-3.4-4.fc38.s390x.rpm: Already downloaded
[SKIPPED] libsigsegv-2.14-3.fc37.s390x.rpm: Already downloaded
[SKIPPED] libsmartcols-2.38.1-3.fc38.s390x.rpm: Already downloaded
[SKIPPED] libssh-0.10.4-2.fc38.s390x.rpm: Already downloaded
[SKIPPED] libssh-config-0.10.4-2.fc38.noarch.rpm: Already downloaded
[SKIPPED] libtasn1-4.19.0-1.fc38.s390x.rpm: Already downloaded
[SKIPPED] libtirpc-1.3.3-0.fc37.s390x.rpm: Already downloaded
[SKIPPED] libunistring-1.0-2.fc37.s390x.rpm: Already downloaded
[SKIPPED] libutempter-1.2.1-7.fc37.s390x.rpm: Already downloaded
[SKIPPED] libuuid-2.38.1-3.fc38.s390x.rpm: Already downloaded
[SKIPPED] libverto-0.3.2-4.fc37.s390x.rpm: Already downloaded
[SKIPPED] libxcrypt-4.4.33-5.fc38.s390x.rpm: Already downloaded
[SKIPPED] libxml2-2.10.3-2.fc38.s390x.rpm: Already downloaded
[SKIPPED] libzstd-1.5.2-3.fc37.s390x.rpm: Already downloaded
[SKIPPED] lua-libs-5.4.4-6.fc38.s390x.rpm: Already downloaded
[SKIPPED] lua-srpm-macros-1-7.fc37.noarch.rpm: Already downloaded
[SKIPPED] lz4-libs-1.9.3-5.fc37.s390x.rpm: Already downloaded
[SKIPPED] mpfr-4.1.1-2.fc38.s390x.rpm: Already downloaded
[SKIPPED] ncurses-base-6.3-5.20221126.fc38.noarch.rpm: Already downloaded
[SKIPPED] ncurses-libs-6.3-5.20221126.fc38.s390x.rpm: Already downloaded
[SKIPPED] nettle-3.8-2.fc37.s390x.rpm: Already downloaded
[SKIPPED] nim-srpm-macros-3-7.fc37.noarch.rpm: Already downloaded
[SKIPPED] ocaml-srpm-macros-7-2.fc37.noarch.rpm: Already downloaded
[SKIPPED] openblas-srpm-macros-2-12.fc37.noarch.rpm: Already downloaded
[SKIPPED] openldap-2.6.3-1.fc38.s390x.rpm: Already downloaded
[SKIPPED] openssl-libs-3.0.5-6.fc38.s390x.rpm: Already downloaded
[SKIPPED] p11-kit-0.24.1-5.fc38.s390x.rpm: Already downloaded
[SKIPPED] p11-kit-trust-0.24.1-5.fc38.s390x.rpm: Already downloaded
[SKIPPED] package-notes-srpm-macros-0.5-6.fc38.noarch.rpm: Already downloaded
[SKIPPED] pam-1.5.2-15.fc38.s390x.rpm: Already downloaded
[SKIPPED] pam-libs-1.5.2-15.fc38.s390x.rpm: Already downloaded
[SKIPPED] patch-2.7.6-17.fc37.s390x.rpm: Already downloaded
[SKIPPED] pcre2-10.40-1.fc37.1.s390x.rpm: Already downloaded
[SKIPPED] pcre2-syntax-10.40-1.fc37.1.noarch.rpm: Already downloaded
[SKIPPED] perl-srpm-macros-1-47.fc38.noarch.rpm: Already downloaded
[SKIPPED] pkgconf-1.8.0-3.fc37.s390x.rpm: Already downloaded
[SKIPPED] pkgconf-m4-1.8.0-3.fc37.noarch.rpm: Already downloaded
[SKIPPED] pkgconf-pkg-config-1.8.0-3.fc37.s390x.rpm: Already downloaded
[SKIPPED] popt-1.19-1.fc38.s390x.rpm: Already downloaded
[SKIPPED] publicsuffix-list-dafsa-20221208-1.fc38.noarch.rpm: Already downloaded
[SKIPPED] python-srpm-macros-3.11-6.fc38.noarch.rpm: Already downloaded
[SKIPPED] qt5-srpm-macros-5.15.7-1.fc38.noarch.rpm: Already downloaded
[SKIPPED] readline-8.2-2.fc38.s390x.rpm: Already downloaded
[SKIPPED] redhat-rpm-config-235-1.fc38.noarch.rpm: Already downloaded
[SKIPPED] rpm-4.18.0-8.fc38.s390x.rpm: Already downloaded
[SKIPPED] rpm-build-4.18.0-8.fc38.s390x.rpm: Already downloaded
[SKIPPED] rpm-build-libs-4.18.0-8.fc38.s390x.rpm: Already downloaded
[SKIPPED] rpm-libs-4.18.0-8.fc38.s390x.rpm: Already downloaded
[SKIPPED] rpm-sequoia-1.2.0-1.fc38.s390x.rpm: Already downloaded
[SKIPPED] rpmautospec-rpm-macros-0.3.1-1.fc38.noarch.rpm: Already downloaded
[SKIPPED] rust-srpm-macros-23-1.fc38.noarch.rpm: Already downloaded
[SKIPPED] sed-4.8-11.fc37.s390x.rpm: Already downloaded
[SKIPPED] setup-2.14.3-1.fc38.noarch.rpm: Already downloaded
[SKIPPED] shadow-utils-4.13-3.fc38.s390x.rpm: Already downloaded
[SKIPPED] sqlite-libs-3.40.0-1.fc38.s390x.rpm: Already downloaded
[SKIPPED] systemd-libs-252.4-598.fc38.s390x.rpm: Already downloaded
[SKIPPED] tar-1.34-5.fc38.s390x.rpm: Already downloaded
[SKIPPED] tzdata-2022g-1.fc38.noarch.rpm: Already downloaded
[SKIPPED] unzip-6.0-58.fc38.s390x.rpm: Already downloaded
[SKIPPED] util-linux-2.38.1-3.fc38.s390x.rpm: Already downloaded
[SKIPPED] util-linux-core-2.38.1-3.fc38.s390x.rpm: Already downloaded
[SKIPPED] which-2.21-36.fc38.s390x.rpm: Already downloaded
[SKIPPED] xxhash-libs-0.8.1-3.fc37.s390x.rpm: Already downloaded
[SKIPPED] xz-5.2.9-1.fc38.s390x.rpm: Already downloaded
[SKIPPED] xz-libs-5.2.9-1.fc38.s390x.rpm: Already downloaded
[SKIPPED] zip-3.0-35.fc38.s390x.rpm: Already downloaded
[SKIPPED] zlib-1.2.13-1.fc38.s390x.rpm: Already downloaded
[SKIPPED] zstd-1.5.2-3.fc37.s390x.rpm: Already downloaded
fedora 1.6 MB/s | 1.6 kB 00:00
Importing GPG key 0xEB10B464:
Userid : "Fedora (38) <fedora-38-primary@fedoraproject.org>"
Fingerprint: 6A51 BBAB BA3D 5467 B617 1221 809A 8D7C EB10 B464
From : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-38-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-38-primary (0xEB10B464) is already installed
fedora 1.6 MB/s | 1.6 kB 00:00
Importing GPG key 0x5323552A:
Userid : "Fedora (37) <fedora-37-primary@fedoraproject.org>"
Fingerprint: ACB5 EE4E 831C 74BB 7C16 8D27 F55A D3FB 5323 552A
From : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-37-primary
Key imported successfully
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
Running scriptlet: filesystem-3.18-2.fc37.s390x 1/1
Preparing : 1/1
Installing : libgcc-13.0.0-0.4.fc38.s390x 1/153
Running scriptlet: libgcc-13.0.0-0.4.fc38.s390x 1/153
Installing : crypto-policies-20221215-1.gita4c31a3.fc38.noarc 2/153
Running scriptlet: crypto-policies-20221215-1.gita4c31a3.fc38.noarc 2/153
Installing : fedora-release-identity-basic-38-0.6.noarch 3/153
Installing : tzdata-2022g-1.fc38.noarch 4/153
Installing : rust-srpm-macros-23-1.fc38.noarch 5/153
Installing : qt5-srpm-macros-5.15.7-1.fc38.noarch 6/153
Installing : publicsuffix-list-dafsa-20221208-1.fc38.noarch 7/153
Installing : pkgconf-m4-1.8.0-3.fc37.noarch 8/153
Installing : perl-srpm-macros-1-47.fc38.noarch 9/153
Installing : pcre2-syntax-10.40-1.fc37.1.noarch 10/153
Installing : package-notes-srpm-macros-0.5-6.fc38.noarch 11/153
Installing : openblas-srpm-macros-2-12.fc37.noarch 12/153
Installing : ocaml-srpm-macros-7-2.fc37.noarch 13/153
Installing : nim-srpm-macros-3-7.fc37.noarch 14/153
Installing : ncurses-base-6.3-5.20221126.fc38.noarch 15/153
Installing : libssh-config-0.10.4-2.fc38.noarch 16/153
Installing : kernel-srpm-macros-1.0-15.fc37.noarch 17/153
Installing : gnat-srpm-macros-4-16.fc37.noarch 18/153
Installing : ghc-srpm-macros-1.5.0-7.fc37.noarch 19/153
Installing : fpc-srpm-macros-1.3-6.fc37.noarch 20/153
Installing : fedora-gpg-keys-38-0.3.noarch 21/153
Installing : fedora-release-38-0.6.noarch 22/153
Installing : fedora-release-common-38-0.6.noarch 23/153
Installing : fedora-repos-rawhide-38-0.3.noarch 24/153
Installing : fedora-repos-38-0.3.noarch 25/153
Installing : setup-2.14.3-1.fc38.noarch 26/153
warning: /etc/hosts created as /etc/hosts.rpmnew
Running scriptlet: setup-2.14.3-1.fc38.noarch 26/153
Installing : filesystem-3.18-2.fc37.s390x 27/153
Installing : basesystem-11-14.fc37.noarch 28/153
Installing : glibc-gconv-extra-2.36.9000-19.fc38.s390x 29/153
Running scriptlet: glibc-gconv-extra-2.36.9000-19.fc38.s390x 29/153
Installing : ncurses-libs-6.3-5.20221126.fc38.s390x 30/153
Running scriptlet: glibc-2.36.9000-19.fc38.s390x 31/153
Installing : glibc-2.36.9000-19.fc38.s390x 31/153
Running scriptlet: glibc-2.36.9000-19.fc38.s390x 31/153
Installing : bash-5.2.9-3.fc38.s390x 32/153
Running scriptlet: bash-5.2.9-3.fc38.s390x 32/153
Installing : glibc-common-2.36.9000-19.fc38.s390x 33/153
Installing : glibc-minimal-langpack-2.36.9000-19.fc38.s390x 34/153
Installing : zlib-1.2.13-1.fc38.s390x 35/153
Installing : xz-libs-5.2.9-1.fc38.s390x 36/153
Installing : bzip2-libs-1.0.8-12.fc38.s390x 37/153
Installing : elfutils-libelf-0.188-3.fc38.s390x 38/153
Installing : gmp-1:6.2.1-3.fc38.s390x 39/153
Installing : libstdc++-13.0.0-0.4.fc38.s390x 40/153
Installing : libuuid-2.38.1-3.fc38.s390x 41/153
Installing : libzstd-1.5.2-3.fc37.s390x 42/153
Installing : popt-1.19-1.fc38.s390x 43/153
Installing : libblkid-2.38.1-3.fc38.s390x 44/153
Installing : libattr-2.5.1-5.fc38.s390x 45/153
Installing : libacl-2.3.1-4.fc38.s390x 46/153
Installing : libcap-2.48-5.fc37.s390x 47/153
Installing : libxcrypt-4.4.33-5.fc38.s390x 48/153
Installing : readline-8.2-2.fc38.s390x 49/153
Installing : lz4-libs-1.9.3-5.fc37.s390x 50/153
Installing : systemd-libs-252.4-598.fc38.s390x 51/153
Installing : mpfr-4.1.1-2.fc38.s390x 52/153
Installing : dwz-0.15-1.fc38.s390x 53/153
Installing : unzip-6.0-58.fc38.s390x 54/153
Installing : file-libs-5.42-4.fc38.s390x 55/153
Installing : file-5.42-4.fc38.s390x 56/153
Installing : sqlite-libs-3.40.0-1.fc38.s390x 57/153
Installing : alternatives-1.21-1.fc38.s390x 58/153
Installing : libcom_err-1.46.5-3.fc38.s390x 59/153
Installing : libcap-ng-0.8.3-4.fc38.s390x 60/153
Installing : audit-libs-3.0.9-2.fc38.s390x 61/153
Installing : libeconf-0.4.0-4.fc37.s390x 62/153
Installing : pam-libs-1.5.2-15.fc38.s390x 63/153
Installing : libsepol-3.4-4.fc38.s390x 64/153
Installing : libsmartcols-2.38.1-3.fc38.s390x 65/153
Installing : libunistring-1.0-2.fc37.s390x 66/153
Installing : libidn2-2.3.4-1.fc38.s390x 67/153
Installing : lua-libs-5.4.4-6.fc38.s390x 68/153
Installing : pcre2-10.40-1.fc37.1.s390x 69/153
Installing : libselinux-3.4-6.fc38.s390x 70/153
Installing : sed-4.8-11.fc37.s390x 71/153
Installing : grep-3.8-1.fc38.s390x 72/153
Installing : findutils-1:4.9.0-2.fc38.s390x 73/153
Installing : xz-5.2.9-1.fc38.s390x 74/153
Installing : libmount-2.38.1-3.fc38.s390x 75/153
Installing : util-linux-core-2.38.1-3.fc38.s390x 76/153
Installing : libsemanage-3.4-6.fc38.s390x 77/153
Installing : shadow-utils-2:4.13-3.fc38.s390x 78/153
Running scriptlet: libutempter-1.2.1-7.fc37.s390x 79/153
Installing : libutempter-1.2.1-7.fc37.s390x 79/153
Installing : tar-2:1.34-5.fc38.s390x 80/153
Installing : libpsl-0.21.1-6.fc37.s390x 81/153
Installing : zip-3.0-35.fc38.s390x 82/153
Installing : zstd-1.5.2-3.fc37.s390x 83/153
Installing : libfdisk-2.38.1-3.fc38.s390x 84/153
Installing : nettle-3.8-2.fc37.s390x 85/153
Installing : rpm-sequoia-1.2.0-1.fc38.s390x 86/153
Installing : rpm-libs-4.18.0-8.fc38.s390x 87/153
Installing : bzip2-1.0.8-12.fc38.s390x 88/153
Installing : libxml2-2.10.3-2.fc38.s390x 89/153
Installing : ed-1.18-2.fc38.s390x 90/153
Installing : patch-2.7.6-17.fc37.s390x 91/153
Installing : elfutils-default-yama-scope-0.188-3.fc38.noarch 92/153
Running scriptlet: elfutils-default-yama-scope-0.188-3.fc38.noarch 92/153
Installing : cpio-2.13-13.fc38.s390x 93/153
Installing : diffutils-3.8-3.fc38.s390x 94/153
Installing : gdbm-libs-1:1.23-2.fc38.s390x 95/153
Installing : cyrus-sasl-lib-2.1.28-8.fc38.s390x 96/153
Installing : libbrotli-1.0.9-9.fc38.s390x 97/153
Installing : libgomp-13.0.0-0.4.fc38.s390x 98/153
Installing : jansson-2.13.1-5.fc37.s390x 99/153
Installing : keyutils-libs-1.6.1-5.fc37.s390x 100/153
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Installing : libffi-3.4.4-1.fc38.s390x 102/153
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Installing : libnghttp2-1.51.0-1.fc38.s390x 104/153
Installing : libpkgconf-1.8.0-3.fc37.s390x 105/153
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Installing : libsigsegv-2.14-3.fc37.s390x 108/153
Installing : gawk-5.1.1-4.fc38.s390x 109/153
Installing : libtasn1-4.19.0-1.fc38.s390x 110/153
Installing : p11-kit-trust-0.24.1-5.fc38.s390x 111/153
Running scriptlet: p11-kit-trust-0.24.1-5.fc38.s390x 111/153
Installing : libverto-0.3.2-4.fc37.s390x 112/153
Installing : xxhash-libs-0.8.1-3.fc37.s390x 113/153
Installing : ansible-srpm-macros-1-8.1.fc38.noarch 114/153
Installing : coreutils-common-9.1-8.fc38.s390x 115/153
Installing : openssl-libs-1:3.0.5-6.fc38.s390x 116/153
Installing : coreutils-9.1-8.fc38.s390x 117/153
Running scriptlet: ca-certificates-2022.2.54-5.fc37.noarch 118/153
Installing : ca-certificates-2022.2.54-5.fc37.noarch 118/153
Running scriptlet: ca-certificates-2022.2.54-5.fc37.noarch 118/153
Installing : krb5-libs-1.20.1-3.fc38.s390x 119/153
Installing : libtirpc-1.3.3-0.fc37.s390x 120/153
Running scriptlet: authselect-libs-1.4.2-1.fc38.s390x 121/153
Installing : authselect-libs-1.4.2-1.fc38.s390x 121/153
Installing : gzip-1.12-2.fc38.s390x 122/153
Installing : cracklib-2.9.7-30.fc38.s390x 123/153
Installing : libpwquality-1.4.5-1.fc38.s390x 124/153
Installing : authselect-1.4.2-1.fc38.s390x 125/153
Installing : libnsl2-2.0.0-4.fc37.s390x 126/153
Installing : pam-1.5.2-15.fc38.s390x 127/153
Installing : libssh-0.10.4-2.fc38.s390x 128/153
Installing : libarchive-3.6.1-3.fc38.s390x 129/153
Installing : libevent-2.1.12-7.fc37.s390x 130/153
Installing : openldap-2.6.3-1.fc38.s390x 131/153
Installing : libcurl-7.87.0-1.fc38.s390x 132/153
Installing : elfutils-libs-0.188-3.fc38.s390x 133/153
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Installing : binutils-gold-2.39-6.fc38.s390x 135/153
Installing : binutils-2.39-6.fc38.s390x 136/153
Running scriptlet: binutils-2.39-6.fc38.s390x 136/153
Installing : elfutils-0.188-3.fc38.s390x 137/153
Installing : gdb-minimal-12.1-10.fc38.s390x 138/153
Installing : debugedit-5.0-5.fc37.s390x 139/153
Installing : rpm-build-libs-4.18.0-8.fc38.s390x 140/153
Installing : curl-7.87.0-1.fc38.s390x 141/153
Running scriptlet: rpm-4.18.0-8.fc38.s390x 142/153
Installing : rpm-4.18.0-8.fc38.s390x 142/153
Installing : efi-srpm-macros-5-6.fc37.noarch 143/153
Installing : lua-srpm-macros-1-7.fc37.noarch 144/153
Installing : rpmautospec-rpm-macros-0.3.1-1.fc38.noarch 145/153
Installing : fonts-srpm-macros-1:2.0.5-10.fc38.noarch 146/153
Installing : go-srpm-macros-3.2.0-1.fc38.noarch 147/153
Installing : python-srpm-macros-3.11-6.fc38.noarch 148/153
Installing : redhat-rpm-config-235-1.fc38.noarch 149/153
Installing : rpm-build-4.18.0-8.fc38.s390x 150/153
Installing : util-linux-2.38.1-3.fc38.s390x 151/153
Installing : which-2.21-36.fc38.s390x 152/153
Installing : info-7.0.1-1.fc38.s390x 153/153
Running scriptlet: filesystem-3.18-2.fc37.s390x 153/153
Running scriptlet: ca-certificates-2022.2.54-5.fc37.noarch 153/153
Running scriptlet: authselect-libs-1.4.2-1.fc38.s390x 153/153
Running scriptlet: rpm-4.18.0-8.fc38.s390x 153/153
Running scriptlet: info-7.0.1-1.fc38.s390x 153/153
Verifying : alternatives-1.21-1.fc38.s390x 1/153
Verifying : authselect-1.4.2-1.fc38.s390x 2/153
Verifying : authselect-libs-1.4.2-1.fc38.s390x 3/153
Verifying : bash-5.2.9-3.fc38.s390x 4/153
Verifying : binutils-2.39-6.fc38.s390x 5/153
Verifying : binutils-gold-2.39-6.fc38.s390x 6/153
Verifying : bzip2-1.0.8-12.fc38.s390x 7/153
Verifying : bzip2-libs-1.0.8-12.fc38.s390x 8/153
Verifying : coreutils-9.1-8.fc38.s390x 9/153
Verifying : coreutils-common-9.1-8.fc38.s390x 10/153
Verifying : cpio-2.13-13.fc38.s390x 11/153
Verifying : cracklib-2.9.7-30.fc38.s390x 12/153
Verifying : curl-7.87.0-1.fc38.s390x 13/153
Verifying : cyrus-sasl-lib-2.1.28-8.fc38.s390x 14/153
Verifying : diffutils-3.8-3.fc38.s390x 15/153
Verifying : dwz-0.15-1.fc38.s390x 16/153
Verifying : ed-1.18-2.fc38.s390x 17/153
Verifying : elfutils-0.188-3.fc38.s390x 18/153
Verifying : elfutils-debuginfod-client-0.188-3.fc38.s390x 19/153
Verifying : elfutils-default-yama-scope-0.188-3.fc38.noarch 20/153
Verifying : elfutils-libelf-0.188-3.fc38.s390x 21/153
Verifying : elfutils-libs-0.188-3.fc38.s390x 22/153
Verifying : file-5.42-4.fc38.s390x 23/153
Verifying : file-libs-5.42-4.fc38.s390x 24/153
Verifying : findutils-1:4.9.0-2.fc38.s390x 25/153
Verifying : gawk-5.1.1-4.fc38.s390x 26/153
Verifying : gdbm-libs-1:1.23-2.fc38.s390x 27/153
Verifying : gmp-1:6.2.1-3.fc38.s390x 28/153
Verifying : grep-3.8-1.fc38.s390x 29/153
Verifying : gzip-1.12-2.fc38.s390x 30/153
Verifying : libacl-2.3.1-4.fc38.s390x 31/153
Verifying : libattr-2.5.1-5.fc38.s390x 32/153
Verifying : libbrotli-1.0.9-9.fc38.s390x 33/153
Verifying : libcom_err-1.46.5-3.fc38.s390x 34/153
Verifying : libcurl-7.87.0-1.fc38.s390x 35/153
Verifying : libgcc-13.0.0-0.4.fc38.s390x 36/153
Verifying : libgomp-13.0.0-0.4.fc38.s390x 37/153
Verifying : libstdc++-13.0.0-0.4.fc38.s390x 38/153
Verifying : ansible-srpm-macros-1-8.1.fc38.noarch 39/153
Verifying : audit-libs-3.0.9-2.fc38.s390x 40/153
Verifying : basesystem-11-14.fc37.noarch 41/153
Verifying : ca-certificates-2022.2.54-5.fc37.noarch 42/153
Verifying : crypto-policies-20221215-1.gita4c31a3.fc38.noarc 43/153
Verifying : debugedit-5.0-5.fc37.s390x 44/153
Verifying : efi-srpm-macros-5-6.fc37.noarch 45/153
Verifying : fedora-gpg-keys-38-0.3.noarch 46/153
Verifying : fedora-release-38-0.6.noarch 47/153
Verifying : fedora-release-common-38-0.6.noarch 48/153
Verifying : fedora-release-identity-basic-38-0.6.noarch 49/153
Verifying : fedora-repos-38-0.3.noarch 50/153
Verifying : fedora-repos-rawhide-38-0.3.noarch 51/153
Verifying : filesystem-3.18-2.fc37.s390x 52/153
Verifying : fonts-srpm-macros-1:2.0.5-10.fc38.noarch 53/153
Verifying : fpc-srpm-macros-1.3-6.fc37.noarch 54/153
Verifying : gdb-minimal-12.1-10.fc38.s390x 55/153
Verifying : ghc-srpm-macros-1.5.0-7.fc37.noarch 56/153
Verifying : glibc-2.36.9000-19.fc38.s390x 57/153
Verifying : glibc-common-2.36.9000-19.fc38.s390x 58/153
Verifying : glibc-gconv-extra-2.36.9000-19.fc38.s390x 59/153
Verifying : glibc-minimal-langpack-2.36.9000-19.fc38.s390x 60/153
Verifying : gnat-srpm-macros-4-16.fc37.noarch 61/153
Verifying : go-srpm-macros-3.2.0-1.fc38.noarch 62/153
Verifying : info-7.0.1-1.fc38.s390x 63/153
Verifying : jansson-2.13.1-5.fc37.s390x 64/153
Verifying : kernel-srpm-macros-1.0-15.fc37.noarch 65/153
Verifying : keyutils-libs-1.6.1-5.fc37.s390x 66/153
Verifying : krb5-libs-1.20.1-3.fc38.s390x 67/153
Verifying : libarchive-3.6.1-3.fc38.s390x 68/153
Verifying : libblkid-2.38.1-3.fc38.s390x 69/153
Verifying : libcap-2.48-5.fc37.s390x 70/153
Verifying : libcap-ng-0.8.3-4.fc38.s390x 71/153
Verifying : libdb-5.3.28-54.fc38.s390x 72/153
Verifying : libeconf-0.4.0-4.fc37.s390x 73/153
Verifying : libevent-2.1.12-7.fc37.s390x 74/153
Verifying : libfdisk-2.38.1-3.fc38.s390x 75/153
Verifying : libffi-3.4.4-1.fc38.s390x 76/153
Verifying : libidn2-2.3.4-1.fc38.s390x 77/153
Verifying : libmount-2.38.1-3.fc38.s390x 78/153
Verifying : libnghttp2-1.51.0-1.fc38.s390x 79/153
Verifying : libnsl2-2.0.0-4.fc37.s390x 80/153
Verifying : libpkgconf-1.8.0-3.fc37.s390x 81/153
Verifying : libpsl-0.21.1-6.fc37.s390x 82/153
Verifying : libpwquality-1.4.5-1.fc38.s390x 83/153
Verifying : libselinux-3.4-6.fc38.s390x 84/153
Verifying : libsemanage-3.4-6.fc38.s390x 85/153
Verifying : libsepol-3.4-4.fc38.s390x 86/153
Verifying : libsigsegv-2.14-3.fc37.s390x 87/153
Verifying : libsmartcols-2.38.1-3.fc38.s390x 88/153
Verifying : libssh-0.10.4-2.fc38.s390x 89/153
Verifying : libssh-config-0.10.4-2.fc38.noarch 90/153
Verifying : libtasn1-4.19.0-1.fc38.s390x 91/153
Verifying : libtirpc-1.3.3-0.fc37.s390x 92/153
Verifying : libunistring-1.0-2.fc37.s390x 93/153
Verifying : libutempter-1.2.1-7.fc37.s390x 94/153
Verifying : libuuid-2.38.1-3.fc38.s390x 95/153
Verifying : libverto-0.3.2-4.fc37.s390x 96/153
Verifying : libxcrypt-4.4.33-5.fc38.s390x 97/153
Verifying : libxml2-2.10.3-2.fc38.s390x 98/153
Verifying : libzstd-1.5.2-3.fc37.s390x 99/153
Verifying : lua-libs-5.4.4-6.fc38.s390x 100/153
Verifying : lua-srpm-macros-1-7.fc37.noarch 101/153
Verifying : lz4-libs-1.9.3-5.fc37.s390x 102/153
Verifying : mpfr-4.1.1-2.fc38.s390x 103/153
Verifying : ncurses-base-6.3-5.20221126.fc38.noarch 104/153
Verifying : ncurses-libs-6.3-5.20221126.fc38.s390x 105/153
Verifying : nettle-3.8-2.fc37.s390x 106/153
Verifying : nim-srpm-macros-3-7.fc37.noarch 107/153
Verifying : ocaml-srpm-macros-7-2.fc37.noarch 108/153
Verifying : openblas-srpm-macros-2-12.fc37.noarch 109/153
Verifying : openldap-2.6.3-1.fc38.s390x 110/153
Verifying : openssl-libs-1:3.0.5-6.fc38.s390x 111/153
Verifying : p11-kit-0.24.1-5.fc38.s390x 112/153
Verifying : p11-kit-trust-0.24.1-5.fc38.s390x 113/153
Verifying : package-notes-srpm-macros-0.5-6.fc38.noarch 114/153
Verifying : pam-1.5.2-15.fc38.s390x 115/153
Verifying : pam-libs-1.5.2-15.fc38.s390x 116/153
Verifying : patch-2.7.6-17.fc37.s390x 117/153
Verifying : pcre2-10.40-1.fc37.1.s390x 118/153
Verifying : pcre2-syntax-10.40-1.fc37.1.noarch 119/153
Verifying : perl-srpm-macros-1-47.fc38.noarch 120/153
Verifying : pkgconf-1.8.0-3.fc37.s390x 121/153
Verifying : pkgconf-m4-1.8.0-3.fc37.noarch 122/153
Verifying : pkgconf-pkg-config-1.8.0-3.fc37.s390x 123/153
Verifying : popt-1.19-1.fc38.s390x 124/153
Verifying : publicsuffix-list-dafsa-20221208-1.fc38.noarch 125/153
Verifying : python-srpm-macros-3.11-6.fc38.noarch 126/153
Verifying : qt5-srpm-macros-5.15.7-1.fc38.noarch 127/153
Verifying : readline-8.2-2.fc38.s390x 128/153
Verifying : redhat-rpm-config-235-1.fc38.noarch 129/153
Verifying : rpm-4.18.0-8.fc38.s390x 130/153
Verifying : rpm-build-4.18.0-8.fc38.s390x 131/153
Verifying : rpm-build-libs-4.18.0-8.fc38.s390x 132/153
Verifying : rpm-libs-4.18.0-8.fc38.s390x 133/153
Verifying : rpm-sequoia-1.2.0-1.fc38.s390x 134/153
Verifying : rpmautospec-rpm-macros-0.3.1-1.fc38.noarch 135/153
Verifying : rust-srpm-macros-23-1.fc38.noarch 136/153
Verifying : sed-4.8-11.fc37.s390x 137/153
Verifying : setup-2.14.3-1.fc38.noarch 138/153
Verifying : shadow-utils-2:4.13-3.fc38.s390x 139/153
Verifying : sqlite-libs-3.40.0-1.fc38.s390x 140/153
Verifying : systemd-libs-252.4-598.fc38.s390x 141/153
Verifying : tar-2:1.34-5.fc38.s390x 142/153
Verifying : tzdata-2022g-1.fc38.noarch 143/153
Verifying : unzip-6.0-58.fc38.s390x 144/153
Verifying : util-linux-2.38.1-3.fc38.s390x 145/153
Verifying : util-linux-core-2.38.1-3.fc38.s390x 146/153
Verifying : which-2.21-36.fc38.s390x 147/153
Verifying : xxhash-libs-0.8.1-3.fc37.s390x 148/153
Verifying : xz-5.2.9-1.fc38.s390x 149/153
Verifying : xz-libs-5.2.9-1.fc38.s390x 150/153
Verifying : zip-3.0-35.fc38.s390x 151/153
Verifying : zlib-1.2.13-1.fc38.s390x 152/153
Verifying : zstd-1.5.2-3.fc37.s390x 153/153
Installed:
alternatives-1.21-1.fc38.s390x
ansible-srpm-macros-1-8.1.fc38.noarch
audit-libs-3.0.9-2.fc38.s390x
authselect-1.4.2-1.fc38.s390x
authselect-libs-1.4.2-1.fc38.s390x
basesystem-11-14.fc37.noarch
bash-5.2.9-3.fc38.s390x
binutils-2.39-6.fc38.s390x
binutils-gold-2.39-6.fc38.s390x
bzip2-1.0.8-12.fc38.s390x
bzip2-libs-1.0.8-12.fc38.s390x
ca-certificates-2022.2.54-5.fc37.noarch
coreutils-9.1-8.fc38.s390x
coreutils-common-9.1-8.fc38.s390x
cpio-2.13-13.fc38.s390x
cracklib-2.9.7-30.fc38.s390x
crypto-policies-20221215-1.gita4c31a3.fc38.noarch
curl-7.87.0-1.fc38.s390x
cyrus-sasl-lib-2.1.28-8.fc38.s390x
debugedit-5.0-5.fc37.s390x
diffutils-3.8-3.fc38.s390x
dwz-0.15-1.fc38.s390x
ed-1.18-2.fc38.s390x
efi-srpm-macros-5-6.fc37.noarch
elfutils-0.188-3.fc38.s390x
elfutils-debuginfod-client-0.188-3.fc38.s390x
elfutils-default-yama-scope-0.188-3.fc38.noarch
elfutils-libelf-0.188-3.fc38.s390x
elfutils-libs-0.188-3.fc38.s390x
fedora-gpg-keys-38-0.3.noarch
fedora-release-38-0.6.noarch
fedora-release-common-38-0.6.noarch
fedora-release-identity-basic-38-0.6.noarch
fedora-repos-38-0.3.noarch
fedora-repos-rawhide-38-0.3.noarch
file-5.42-4.fc38.s390x
file-libs-5.42-4.fc38.s390x
filesystem-3.18-2.fc37.s390x
findutils-1:4.9.0-2.fc38.s390x
fonts-srpm-macros-1:2.0.5-10.fc38.noarch
fpc-srpm-macros-1.3-6.fc37.noarch
gawk-5.1.1-4.fc38.s390x
gdb-minimal-12.1-10.fc38.s390x
gdbm-libs-1:1.23-2.fc38.s390x
ghc-srpm-macros-1.5.0-7.fc37.noarch
glibc-2.36.9000-19.fc38.s390x
glibc-common-2.36.9000-19.fc38.s390x
glibc-gconv-extra-2.36.9000-19.fc38.s390x
glibc-minimal-langpack-2.36.9000-19.fc38.s390x
gmp-1:6.2.1-3.fc38.s390x
gnat-srpm-macros-4-16.fc37.noarch
go-srpm-macros-3.2.0-1.fc38.noarch
grep-3.8-1.fc38.s390x
gzip-1.12-2.fc38.s390x
info-7.0.1-1.fc38.s390x
jansson-2.13.1-5.fc37.s390x
kernel-srpm-macros-1.0-15.fc37.noarch
keyutils-libs-1.6.1-5.fc37.s390x
krb5-libs-1.20.1-3.fc38.s390x
libacl-2.3.1-4.fc38.s390x
libarchive-3.6.1-3.fc38.s390x
libattr-2.5.1-5.fc38.s390x
libblkid-2.38.1-3.fc38.s390x
libbrotli-1.0.9-9.fc38.s390x
libcap-2.48-5.fc37.s390x
libcap-ng-0.8.3-4.fc38.s390x
libcom_err-1.46.5-3.fc38.s390x
libcurl-7.87.0-1.fc38.s390x
libdb-5.3.28-54.fc38.s390x
libeconf-0.4.0-4.fc37.s390x
libevent-2.1.12-7.fc37.s390x
libfdisk-2.38.1-3.fc38.s390x
libffi-3.4.4-1.fc38.s390x
libgcc-13.0.0-0.4.fc38.s390x
libgomp-13.0.0-0.4.fc38.s390x
libidn2-2.3.4-1.fc38.s390x
libmount-2.38.1-3.fc38.s390x
libnghttp2-1.51.0-1.fc38.s390x
libnsl2-2.0.0-4.fc37.s390x
libpkgconf-1.8.0-3.fc37.s390x
libpsl-0.21.1-6.fc37.s390x
libpwquality-1.4.5-1.fc38.s390x
libselinux-3.4-6.fc38.s390x
libsemanage-3.4-6.fc38.s390x
libsepol-3.4-4.fc38.s390x
libsigsegv-2.14-3.fc37.s390x
libsmartcols-2.38.1-3.fc38.s390x
libssh-0.10.4-2.fc38.s390x
libssh-config-0.10.4-2.fc38.noarch
libstdc++-13.0.0-0.4.fc38.s390x
libtasn1-4.19.0-1.fc38.s390x
libtirpc-1.3.3-0.fc37.s390x
libunistring-1.0-2.fc37.s390x
libutempter-1.2.1-7.fc37.s390x
libuuid-2.38.1-3.fc38.s390x
libverto-0.3.2-4.fc37.s390x
libxcrypt-4.4.33-5.fc38.s390x
libxml2-2.10.3-2.fc38.s390x
libzstd-1.5.2-3.fc37.s390x
lua-libs-5.4.4-6.fc38.s390x
lua-srpm-macros-1-7.fc37.noarch
lz4-libs-1.9.3-5.fc37.s390x
mpfr-4.1.1-2.fc38.s390x
ncurses-base-6.3-5.20221126.fc38.noarch
ncurses-libs-6.3-5.20221126.fc38.s390x
nettle-3.8-2.fc37.s390x
nim-srpm-macros-3-7.fc37.noarch
ocaml-srpm-macros-7-2.fc37.noarch
openblas-srpm-macros-2-12.fc37.noarch
openldap-2.6.3-1.fc38.s390x
openssl-libs-1:3.0.5-6.fc38.s390x
p11-kit-0.24.1-5.fc38.s390x
p11-kit-trust-0.24.1-5.fc38.s390x
package-notes-srpm-macros-0.5-6.fc38.noarch
pam-1.5.2-15.fc38.s390x
pam-libs-1.5.2-15.fc38.s390x
patch-2.7.6-17.fc37.s390x
pcre2-10.40-1.fc37.1.s390x
pcre2-syntax-10.40-1.fc37.1.noarch
perl-srpm-macros-1-47.fc38.noarch
pkgconf-1.8.0-3.fc37.s390x
pkgconf-m4-1.8.0-3.fc37.noarch
pkgconf-pkg-config-1.8.0-3.fc37.s390x
popt-1.19-1.fc38.s390x
publicsuffix-list-dafsa-20221208-1.fc38.noarch
python-srpm-macros-3.11-6.fc38.noarch
qt5-srpm-macros-5.15.7-1.fc38.noarch
readline-8.2-2.fc38.s390x
redhat-rpm-config-235-1.fc38.noarch
rpm-4.18.0-8.fc38.s390x
rpm-build-4.18.0-8.fc38.s390x
rpm-build-libs-4.18.0-8.fc38.s390x
rpm-libs-4.18.0-8.fc38.s390x
rpm-sequoia-1.2.0-1.fc38.s390x
rpmautospec-rpm-macros-0.3.1-1.fc38.noarch
rust-srpm-macros-23-1.fc38.noarch
sed-4.8-11.fc37.s390x
setup-2.14.3-1.fc38.noarch
shadow-utils-2:4.13-3.fc38.s390x
sqlite-libs-3.40.0-1.fc38.s390x
systemd-libs-252.4-598.fc38.s390x
tar-2:1.34-5.fc38.s390x
tzdata-2022g-1.fc38.noarch
unzip-6.0-58.fc38.s390x
util-linux-2.38.1-3.fc38.s390x
util-linux-core-2.38.1-3.fc38.s390x
which-2.21-36.fc38.s390x
xxhash-libs-0.8.1-3.fc37.s390x
xz-5.2.9-1.fc38.s390x
xz-libs-5.2.9-1.fc38.s390x
zip-3.0-35.fc38.s390x
zlib-1.2.13-1.fc38.s390x
zstd-1.5.2-3.fc37.s390x
Complete!
Finish: dnf install
Start: creating root cache
Finish: creating root cache
Finish: chroot init
INFO: Installed packages:
INFO: libcap-ng-0.8.3-4.fc38.s390x
lua-libs-5.4.4-6.fc38.s390x
coreutils-common-9.1-8.fc38.s390x
libffi-3.4.4-1.fc38.s390x
libbrotli-1.0.9-9.fc38.s390x
rpm-libs-4.18.0-8.fc38.s390x
lz4-libs-1.9.3-5.fc37.s390x
cpio-2.13-13.fc38.s390x
crypto-policies-20221215-1.gita4c31a3.fc38.noarch
grep-3.8-1.fc38.s390x
lua-srpm-macros-1-7.fc37.noarch
libgomp-13.0.0-0.4.fc38.s390x
openssl-libs-3.0.5-6.fc38.s390x
libblkid-2.38.1-3.fc38.s390x
jansson-2.13.1-5.fc37.s390x
patch-2.7.6-17.fc37.s390x
glibc-minimal-langpack-2.36.9000-19.fc38.s390x
libpsl-0.21.1-6.fc37.s390x
p11-kit-trust-0.24.1-5.fc38.s390x
binutils-2.39-6.fc38.s390x
libcom_err-1.46.5-3.fc38.s390x
glibc-2.36.9000-19.fc38.s390x
cyrus-sasl-lib-2.1.28-8.fc38.s390x
libattr-2.5.1-5.fc38.s390x
p11-kit-0.24.1-5.fc38.s390x
rpm-sequoia-1.2.0-1.fc38.s390x
ed-1.18-2.fc38.s390x
elfutils-debuginfod-client-0.188-3.fc38.s390x
gmp-6.2.1-3.fc38.s390x
libsigsegv-2.14-3.fc37.s390x
gdb-minimal-12.1-10.fc38.s390x
ansible-srpm-macros-1-8.1.fc38.noarch
filesystem-3.18-2.fc37.s390x
util-linux-2.38.1-3.fc38.s390x
rpmautospec-rpm-macros-0.3.1-1.fc38.noarch
libtasn1-4.19.0-1.fc38.s390x
popt-1.19-1.fc38.s390x
package-notes-srpm-macros-0.5-6.fc38.noarch
elfutils-libelf-0.188-3.fc38.s390x
shadow-utils-4.13-3.fc38.s390x
basesystem-11-14.fc37.noarch
efi-srpm-macros-5-6.fc37.noarch
libacl-2.3.1-4.fc38.s390x
glibc-common-2.36.9000-19.fc38.s390x
kernel-srpm-macros-1.0-15.fc37.noarch
gpg-pubkey-5323552a-6112bcdc
xxhash-libs-0.8.1-3.fc37.s390x
openldap-2.6.3-1.fc38.s390x
libarchive-3.6.1-3.fc38.s390x
gpg-pubkey-eb10b464-6202d9c6
dwz-0.15-1.fc38.s390x
pkgconf-pkg-config-1.8.0-3.fc37.s390x
info-7.0.1-1.fc38.s390x
pam-1.5.2-15.fc38.s390x
libssh-0.10.4-2.fc38.s390x
sqlite-libs-3.40.0-1.fc38.s390x
pkgconf-m4-1.8.0-3.fc37.noarch
libevent-2.1.12-7.fc37.s390x
elfutils-libs-0.188-3.fc38.s390x
libpwquality-1.4.5-1.fc38.s390x
audit-libs-3.0.9-2.fc38.s390x
libeconf-0.4.0-4.fc37.s390x
keyutils-libs-1.6.1-5.fc37.s390x
unzip-6.0-58.fc38.s390x
qt5-srpm-macros-5.15.7-1.fc38.noarch
libselinux-3.4-6.fc38.s390x
libsmartcols-2.38.1-3.fc38.s390x
authselect-libs-1.4.2-1.fc38.s390x
openblas-srpm-macros-2-12.fc37.noarch
elfutils-0.188-3.fc38.s390x
libdb-5.3.28-54.fc38.s390x
libssh-config-0.10.4-2.fc38.noarch
elfutils-default-yama-scope-0.188-3.fc38.noarch
systemd-libs-252.4-598.fc38.s390x
fedora-repos-38-0.3.noarch
authselect-1.4.2-1.fc38.s390x
libcurl-7.87.0-1.fc38.s390x
zstd-1.5.2-3.fc37.s390x
readline-8.2-2.fc38.s390x
mpfr-4.1.1-2.fc38.s390x
glibc-gconv-extra-2.36.9000-19.fc38.s390x
nim-srpm-macros-3-7.fc37.noarch
publicsuffix-list-dafsa-20221208-1.fc38.noarch
ocaml-srpm-macros-7-2.fc37.noarch
rpm-build-4.18.0-8.fc38.s390x
perl-srpm-macros-1-47.fc38.noarch
libxml2-2.10.3-2.fc38.s390x
libmount-2.38.1-3.fc38.s390x
alternatives-1.21-1.fc38.s390x
libutempter-1.2.1-7.fc37.s390x
file-libs-5.42-4.fc38.s390x
ghc-srpm-macros-1.5.0-7.fc37.noarch
curl-7.87.0-1.fc38.s390x
which-2.21-36.fc38.s390x
setup-2.14.3-1.fc38.noarch
libtirpc-1.3.3-0.fc37.s390x
coreutils-9.1-8.fc38.s390x
pkgconf-1.8.0-3.fc37.s390x
diffutils-3.8-3.fc38.s390x
tzdata-2022g-1.fc38.noarch
gdbm-libs-1.23-2.fc38.s390x
gnat-srpm-macros-4-16.fc37.noarch
fedora-release-38-0.6.noarch
pam-libs-1.5.2-15.fc38.s390x
libxcrypt-4.4.33-5.fc38.s390x
bzip2-1.0.8-12.fc38.s390x
redhat-rpm-config-235-1.fc38.noarch
fedora-release-common-38-0.6.noarch
rust-srpm-macros-23-1.fc38.noarch
xz-5.2.9-1.fc38.s390x
nettle-3.8-2.fc37.s390x
fpc-srpm-macros-1.3-6.fc37.noarch
pcre2-10.40-1.fc37.1.s390x
pcre2-syntax-10.40-1.fc37.1.noarch
python-srpm-macros-3.11-6.fc38.noarch
libunistring-1.0-2.fc37.s390x
xz-libs-5.2.9-1.fc38.s390x
rpm-build-libs-4.18.0-8.fc38.s390x
fonts-srpm-macros-2.0.5-10.fc38.noarch
tar-1.34-5.fc38.s390x
util-linux-core-2.38.1-3.fc38.s390x
go-srpm-macros-3.2.0-1.fc38.noarch
zlib-1.2.13-1.fc38.s390x
krb5-libs-1.20.1-3.fc38.s390x
rpm-4.18.0-8.fc38.s390x
libsemanage-3.4-6.fc38.s390x
file-5.42-4.fc38.s390x
ncurses-base-6.3-5.20221126.fc38.noarch
fedora-release-identity-basic-38-0.6.noarch
bzip2-libs-1.0.8-12.fc38.s390x
libidn2-2.3.4-1.fc38.s390x
gawk-5.1.1-4.fc38.s390x
libpkgconf-1.8.0-3.fc37.s390x
libnsl2-2.0.0-4.fc37.s390x
libstdc++-13.0.0-0.4.fc38.s390x
findutils-4.9.0-2.fc38.s390x
cracklib-2.9.7-30.fc38.s390x
fedora-repos-rawhide-38-0.3.noarch
libzstd-1.5.2-3.fc37.s390x
debugedit-5.0-5.fc37.s390x
bash-5.2.9-3.fc38.s390x
zip-3.0-35.fc38.s390x
libfdisk-2.38.1-3.fc38.s390x
ncurses-libs-6.3-5.20221126.fc38.s390x
libsepol-3.4-4.fc38.s390x
libverto-0.3.2-4.fc37.s390x
binutils-gold-2.39-6.fc38.s390x
libnghttp2-1.51.0-1.fc38.s390x
fedora-gpg-keys-38-0.3.noarch
libuuid-2.38.1-3.fc38.s390x
sed-4.8-11.fc37.s390x
ca-certificates-2022.2.54-5.fc37.noarch
gzip-1.12-2.fc38.s390x
libgcc-13.0.0-0.4.fc38.s390x
libcap-2.48-5.fc37.s390x
Start: buildsrpm
Start: rpmbuild -bs
Building target platforms: s390x
Building for target s390x
setting SOURCE_DATE_EPOCH=1660521600
Wrote: /builddir/build/SRPMS/htslib-1.15.1-1.fc38.src.rpm
Finish: rpmbuild -bs
cp: ‘var/lib/mock/fedora-rawhide-s390x-1671942858.428762/root/var/log’: No such file or directory
INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/fedora-rawhide-s390x-1671942858.428762/root/var/log/dnf.rpm.log
/var/lib/mock/fedora-rawhide-s390x-1671942858.428762/root/var/log/dnf.librepo.log
/var/lib/mock/fedora-rawhide-s390x-1671942858.428762/root/var/log/dnf.log
Finish: buildsrpm
INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-xbkpkar1/htslib/htslib.spec) Config(child) 1 minutes 42 seconds
INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results
INFO: Cleaning up build root ('cleanup_on_success=True')
Start: clean chroot
INFO: unmounting tmpfs.
Finish: clean chroot
Finish: run
Running (timeout=115200): unbuffer mock --rebuild /var/lib/copr-rpmbuild/results/htslib-1.15.1-1.fc38.src.rpm --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1671942858.428762 -r /var/lib/copr-rpmbuild/results/configs/child.cfg
INFO: mock.py version 3.5 starting (python version = 3.11.0, NVR = mock-3.5-1.fc37)...
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/results/htslib-1.15.1-1.fc38.src.rpm) Config(fedora-rawhide-s390x)
Start: clean chroot
Finish: clean chroot
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-s390x-bootstrap-1671942858.428762/root.
INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-s390x-bootstrap-1671942858.428762/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: enabled HW Info plugin
Mock Version: 3.5
INFO: Mock Version: 3.5
Finish(bootstrap): chroot init
Start: chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-s390x-1671942858.428762/root.
INFO: calling preinit hooks
INFO: enabled root cache
Start: unpacking root cache
Finish: unpacking root cache
INFO: enabled package manager cache
Start: cleaning package manager metadata
Finish: cleaning package manager metadata
INFO: enabled HW Info plugin
Mock Version: 3.5
INFO: Mock Version: 3.5
Start: dnf update
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Copr repository 599 B/s | 3.0 kB 00:05
Copr repository 2.8 MB/s | 16 MB 00:05
Additional repo https_jakub_fedorapeople_org_fe 4.2 kB/s | 3.0 kB 00:00
fedora 8.3 kB/s | 6.3 kB 00:00
Dependencies resolved.
Nothing to do.
Complete!
Finish: dnf update
Finish: chroot init
Start: build phase for htslib-1.15.1-1.fc38.src.rpm
Start: build setup for htslib-1.15.1-1.fc38.src.rpm
Building target platforms: s390x
Building for target s390x
setting SOURCE_DATE_EPOCH=1660521600
Wrote: /builddir/build/SRPMS/htslib-1.15.1-1.fc38.src.rpm
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Copr repository 3.8 kB/s | 3.0 kB 00:00
Copr repository 21 MB/s | 16 MB 00:00
Additional repo https_jakub_fedorapeople_org_fe 4.2 kB/s | 3.0 kB 00:00
fedora 8.4 kB/s | 6.3 kB 00:00
Dependencies resolved.
============================================================================================================
Package Arch Version Repository Size
============================================================================================================
Installing:
bzip2-devel s390x 1.0.8-12.fc38 copr_base 214 k
gcc s390x 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 28 M
libcurl-devel s390x 7.87.0-1.fc38 copr_base 895 k
make s390x 1:4.3-11.fc37 fedora 536 k
openssl-devel s390x 1:3.0.5-6.fc38 fedora 3.1 M
perl-Data-Dumper s390x 2.184-490.fc37 fedora 56 k
perl-FindBin noarch 1.53-492.fc38 fedora 17 k
perl-Getopt-Long noarch 1:2.54-1.fc38 fedora 60 k
perl-interpreter s390x 4:5.36.0-492.fc38 fedora 75 k
perl-lib s390x 0.65-492.fc38 fedora 18 k
xz-devel s390x 5.2.9-1.fc38 fedora 58 k
zlib-devel s390x 1.2.13-1.fc38 fedora 45 k
Installing dependencies:
annobin-docs noarch 10.99-1.0.1.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 93 k
annobin-plugin-gcc s390x 10.99-1.0.1.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 888 k
cpp s390x 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 8.9 M
gc s390x 8.2.2-1.fc38 copr_base 114 k
gcc-plugin-annobin s390x 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 28 k
glibc-devel s390x 2.36.9000-19.fc38 fedora 55 k
glibc-headers-s390 noarch 2.36.9000-19.fc38 fedora 516 k
groff-base s390x 1.22.4-10.fc38 copr_base 1.1 M
guile22 s390x 2.2.7-6.fc38 copr_base 6.4 M
kernel-headers s390x 6.1.0-1.fc38 fedora 1.5 M
libasan s390x 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 492 k
libatomic s390x 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 18 k
libmpc s390x 1.2.1-5.fc37 fedora 61 k
libtool-ltdl s390x 2.4.7-3.0.1.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 38 k
libubsan s390x 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 203 k
libxcrypt-devel s390x 4.4.33-5.fc38 fedora 30 k
ncurses s390x 6.3-5.20221126.fc38 fedora 413 k
perl-B s390x 1.83-492.fc38 fedora 184 k
perl-Carp noarch 1.52-489.fc37 fedora 29 k
perl-Class-Struct noarch 0.66-492.fc38 fedora 25 k
perl-DynaLoader s390x 1.52-492.fc38 fedora 29 k
perl-Encode s390x 4:3.19-492.fc38 fedora 1.7 M
perl-Errno s390x 1.36-492.fc38 fedora 18 k
perl-Exporter noarch 5.77-489.fc37 fedora 31 k
perl-Fcntl s390x 1.15-492.fc38 fedora 23 k
perl-File-Basename noarch 2.85-492.fc38 fedora 20 k
perl-File-Path noarch 2.18-489.fc37 fedora 35 k
perl-File-Temp noarch 1:0.231.100-489.fc37 fedora 59 k
perl-File-stat noarch 1.12-492.fc38 fedora 20 k
perl-Getopt-Std noarch 1.13-492.fc38 fedora 19 k
perl-HTTP-Tiny noarch 0.082-1.fc37 fedora 55 k
perl-IO s390x 1.50-492.fc38 fedora 95 k
perl-IPC-Open3 noarch 1.22-492.fc38 fedora 26 k
perl-MIME-Base64 s390x 3.16-489.fc37 fedora 30 k
perl-POSIX s390x 2.03-492.fc38 fedora 99 k
perl-PathTools s390x 3.84-489.fc37 fedora 89 k
perl-Pod-Escapes noarch 1:1.07-489.fc37 fedora 20 k
perl-Pod-Perldoc noarch 3.28.01-490.fc37 fedora 90 k
perl-Pod-Simple noarch 1:3.43-490.fc37 fedora 225 k
perl-Pod-Usage noarch 4:2.03-3.fc37 fedora 40 k
perl-Scalar-List-Utils s390x 5:1.63-489.fc38 fedora 71 k
perl-SelectSaver noarch 1.02-492.fc38 fedora 15 k
perl-Socket s390x 4:2.036-1.fc38 fedora 55 k
perl-Storable s390x 1:3.26-489.fc37 fedora 93 k
perl-Symbol noarch 1.09-492.fc38 fedora 17 k
perl-Term-ANSIColor noarch 5.01-490.fc37 fedora 48 k
perl-Term-Cap noarch 1.17-489.fc37 fedora 22 k
perl-Text-ParseWords noarch 3.31-489.fc37 fedora 16 k
perl-Text-Tabs+Wrap noarch 2021.0814-489.fc37 fedora 22 k
perl-Time-Local noarch 2:1.300-489.fc37 fedora 33 k
perl-constant noarch 1.33-490.fc37 fedora 23 k
perl-if noarch 0.61.000-492.fc38 fedora 17 k
perl-libs s390x 4:5.36.0-492.fc38 fedora 2.2 M
perl-mro s390x 1.26-492.fc38 fedora 31 k
perl-overload noarch 1.35-492.fc38 fedora 49 k
perl-overloading noarch 0.02-492.fc38 fedora 16 k
perl-parent noarch 1:0.239-1.fc38 fedora 14 k
perl-podlators noarch 1:5.00-1.fc38 fedora 127 k
perl-vars noarch 1.05-492.fc38 fedora 16 k
Transaction Summary
============================================================================================================
Install 71 Packages
Total size: 60 M
Total download size: 1.2 M
Installed size: 183 M
Downloading Packages:
[SKIPPED] gc-8.2.2-1.fc38.s390x.rpm: Already downloaded
[SKIPPED] groff-base-1.22.4-10.fc38.s390x.rpm: Already downloaded
[SKIPPED] guile22-2.2.7-6.fc38.s390x.rpm: Already downloaded
[SKIPPED] annobin-docs-10.99-1.0.1.fc38.noarch.rpm: Already downloaded
[SKIPPED] annobin-plugin-gcc-10.99-1.0.1.fc38.s390x.rpm: Already downloaded
[SKIPPED] cpp-13.0.0-0.4.fc38.s390x.rpm: Already downloaded
[SKIPPED] gcc-13.0.0-0.4.fc38.s390x.rpm: Already downloaded
[SKIPPED] gcc-plugin-annobin-13.0.0-0.4.fc38.s390x.rpm: Already downloaded
[SKIPPED] libasan-13.0.0-0.4.fc38.s390x.rpm: Already downloaded
[SKIPPED] libatomic-13.0.0-0.4.fc38.s390x.rpm: Already downloaded
[SKIPPED] libtool-ltdl-2.4.7-3.0.1.fc38.s390x.rpm: Already downloaded
[SKIPPED] libubsan-13.0.0-0.4.fc38.s390x.rpm: Already downloaded
[SKIPPED] glibc-devel-2.36.9000-19.fc38.s390x.rpm: Already downloaded
[SKIPPED] glibc-headers-s390-2.36.9000-19.fc38.noarch.rpm: Already downloaded
[SKIPPED] kernel-headers-6.1.0-1.fc38.s390x.rpm: Already downloaded
[SKIPPED] libmpc-1.2.1-5.fc37.s390x.rpm: Already downloaded
[SKIPPED] libxcrypt-devel-4.4.33-5.fc38.s390x.rpm: Already downloaded
[SKIPPED] make-4.3-11.fc37.s390x.rpm: Already downloaded
[SKIPPED] ncurses-6.3-5.20221126.fc38.s390x.rpm: Already downloaded
[SKIPPED] openssl-devel-3.0.5-6.fc38.s390x.rpm: Already downloaded
[SKIPPED] perl-B-1.83-492.fc38.s390x.rpm: Already downloaded
[SKIPPED] perl-Carp-1.52-489.fc37.noarch.rpm: Already downloaded
[SKIPPED] perl-Class-Struct-0.66-492.fc38.noarch.rpm: Already downloaded
[SKIPPED] perl-Data-Dumper-2.184-490.fc37.s390x.rpm: Already downloaded
[SKIPPED] perl-DynaLoader-1.52-492.fc38.s390x.rpm: Already downloaded
[SKIPPED] perl-Encode-3.19-492.fc38.s390x.rpm: Already downloaded
[SKIPPED] perl-Errno-1.36-492.fc38.s390x.rpm: Already downloaded
[SKIPPED] perl-Exporter-5.77-489.fc37.noarch.rpm: Already downloaded
[SKIPPED] perl-Fcntl-1.15-492.fc38.s390x.rpm: Already downloaded
[SKIPPED] perl-File-Basename-2.85-492.fc38.noarch.rpm: Already downloaded
[SKIPPED] perl-File-Path-2.18-489.fc37.noarch.rpm: Already downloaded
[SKIPPED] perl-File-Temp-0.231.100-489.fc37.noarch.rpm: Already downloaded
[SKIPPED] perl-File-stat-1.12-492.fc38.noarch.rpm: Already downloaded
[SKIPPED] perl-Getopt-Long-2.54-1.fc38.noarch.rpm: Already downloaded
[SKIPPED] perl-Getopt-Std-1.13-492.fc38.noarch.rpm: Already downloaded
[SKIPPED] perl-HTTP-Tiny-0.082-1.fc37.noarch.rpm: Already downloaded
[SKIPPED] perl-IO-1.50-492.fc38.s390x.rpm: Already downloaded
[SKIPPED] perl-IPC-Open3-1.22-492.fc38.noarch.rpm: Already downloaded
[SKIPPED] perl-MIME-Base64-3.16-489.fc37.s390x.rpm: Already downloaded
[SKIPPED] perl-POSIX-2.03-492.fc38.s390x.rpm: Already downloaded
[SKIPPED] perl-PathTools-3.84-489.fc37.s390x.rpm: Already downloaded
[SKIPPED] perl-Pod-Escapes-1.07-489.fc37.noarch.rpm: Already downloaded
[SKIPPED] perl-Pod-Perldoc-3.28.01-490.fc37.noarch.rpm: Already downloaded
[SKIPPED] perl-Pod-Simple-3.43-490.fc37.noarch.rpm: Already downloaded
[SKIPPED] perl-Pod-Usage-2.03-3.fc37.noarch.rpm: Already downloaded
[SKIPPED] perl-Scalar-List-Utils-1.63-489.fc38.s390x.rpm: Already downloaded
[SKIPPED] perl-SelectSaver-1.02-492.fc38.noarch.rpm: Already downloaded
[SKIPPED] perl-Socket-2.036-1.fc38.s390x.rpm: Already downloaded
[SKIPPED] perl-Storable-3.26-489.fc37.s390x.rpm: Already downloaded
[SKIPPED] perl-Symbol-1.09-492.fc38.noarch.rpm: Already downloaded
[SKIPPED] perl-Term-ANSIColor-5.01-490.fc37.noarch.rpm: Already downloaded
[SKIPPED] perl-Term-Cap-1.17-489.fc37.noarch.rpm: Already downloaded
[SKIPPED] perl-Text-ParseWords-3.31-489.fc37.noarch.rpm: Already downloaded
[SKIPPED] perl-Text-Tabs+Wrap-2021.0814-489.fc37.noarch.rpm: Already downloaded
[SKIPPED] perl-Time-Local-1.300-489.fc37.noarch.rpm: Already downloaded
[SKIPPED] perl-constant-1.33-490.fc37.noarch.rpm: Already downloaded
[SKIPPED] perl-if-0.61.000-492.fc38.noarch.rpm: Already downloaded
[SKIPPED] perl-interpreter-5.36.0-492.fc38.s390x.rpm: Already downloaded
[SKIPPED] perl-libs-5.36.0-492.fc38.s390x.rpm: Already downloaded
[SKIPPED] perl-mro-1.26-492.fc38.s390x.rpm: Already downloaded
[SKIPPED] perl-overload-1.35-492.fc38.noarch.rpm: Already downloaded
[SKIPPED] perl-overloading-0.02-492.fc38.noarch.rpm: Already downloaded
[SKIPPED] perl-parent-0.239-1.fc38.noarch.rpm: Already downloaded
[SKIPPED] perl-podlators-5.00-1.fc38.noarch.rpm: Already downloaded
[SKIPPED] perl-vars-1.05-492.fc38.noarch.rpm: Already downloaded
[SKIPPED] zlib-devel-1.2.13-1.fc38.s390x.rpm: Already downloaded
(67/71): bzip2-devel-1.0.8-12.fc38.s390x.rpm 3.8 MB/s | 214 kB 00:00
(68/71): libcurl-devel-7.87.0-1.fc38.s390x.rpm 177 kB/s | 895 kB 00:05
(69/71): perl-lib-0.65-492.fc38.s390x.rpm 3.4 kB/s | 18 kB 00:05
(70/71): perl-FindBin-1.53-492.fc38.noarch.rpm 3.2 kB/s | 17 kB 00:05
(71/71): xz-devel-5.2.9-1.fc38.s390x.rpm 102 kB/s | 58 kB 00:00
--------------------------------------------------------------------------------
Total 186 kB/s | 1.2 MB 00:06
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
Preparing : 1/1
Installing : libmpc-1.2.1-5.fc37.s390x 1/71
Installing : cpp-13.0.0-0.4.fc38.s390x 2/71
Installing : ncurses-6.3-5.20221126.fc38.s390x 3/71
Installing : kernel-headers-6.1.0-1.fc38.s390x 4/71
Installing : glibc-headers-s390-2.36.9000-19.fc38.noarch 5/71
Installing : libxcrypt-devel-4.4.33-5.fc38.s390x 6/71
Installing : glibc-devel-2.36.9000-19.fc38.s390x 7/71
Installing : libubsan-13.0.0-0.4.fc38.s390x 8/71
Installing : libtool-ltdl-2.4.7-3.0.1.fc38.s390x 9/71
Installing : libatomic-13.0.0-0.4.fc38.s390x 10/71
Installing : libasan-13.0.0-0.4.fc38.s390x 11/71
Installing : annobin-docs-10.99-1.0.1.fc38.noarch 12/71
Running scriptlet: groff-base-1.22.4-10.fc38.s390x 13/71
Installing : groff-base-1.22.4-10.fc38.s390x 13/71
Running scriptlet: groff-base-1.22.4-10.fc38.s390x 13/71
Installing : perl-Text-Tabs+Wrap-2021.0814-489.fc37.noarch 14/71
Installing : perl-if-0.61.000-492.fc38.noarch 15/71
Installing : perl-Time-Local-2:1.300-489.fc37.noarch 16/71
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Installing : perl-POSIX-2.03-492.fc38.s390x 20/71
Installing : perl-Term-ANSIColor-5.01-490.fc37.noarch 21/71
Installing : perl-IPC-Open3-1.22-492.fc38.noarch 22/71
Installing : perl-HTTP-Tiny-0.082-1.fc37.noarch 23/71
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Installing : perl-File-stat-1.12-492.fc38.noarch 30/71
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Installing : perl-Getopt-Long-1:2.54-1.fc38.noarch 49/71
Installing : perl-Carp-1.52-489.fc37.noarch 50/71
Installing : perl-Exporter-5.77-489.fc37.noarch 51/71
Installing : perl-PathTools-3.84-489.fc37.s390x 52/71
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Installing : guile22-2.2.7-6.fc38.s390x 60/71
Installing : make-1:4.3-11.fc37.s390x 61/71
Installing : gcc-13.0.0-0.4.fc38.s390x 62/71
Running scriptlet: gcc-13.0.0-0.4.fc38.s390x 62/71
Installing : annobin-plugin-gcc-10.99-1.0.1.fc38.s390x 63/71
Running scriptlet: annobin-plugin-gcc-10.99-1.0.1.fc38.s390x 63/71
Installing : gcc-plugin-annobin-13.0.0-0.4.fc38.s390x 64/71
Installing : perl-FindBin-1.53-492.fc38.noarch 65/71
Installing : perl-lib-0.65-492.fc38.s390x 66/71
Installing : zlib-devel-1.2.13-1.fc38.s390x 67/71
Installing : xz-devel-5.2.9-1.fc38.s390x 68/71
Installing : openssl-devel-1:3.0.5-6.fc38.s390x 69/71
Installing : libcurl-devel-7.87.0-1.fc38.s390x 70/71
Installing : bzip2-devel-1.0.8-12.fc38.s390x 71/71
Running scriptlet: bzip2-devel-1.0.8-12.fc38.s390x 71/71
Verifying : bzip2-devel-1.0.8-12.fc38.s390x 1/71
Verifying : gc-8.2.2-1.fc38.s390x 2/71
Verifying : groff-base-1.22.4-10.fc38.s390x 3/71
Verifying : guile22-2.2.7-6.fc38.s390x 4/71
Verifying : libcurl-devel-7.87.0-1.fc38.s390x 5/71
Verifying : annobin-docs-10.99-1.0.1.fc38.noarch 6/71
Verifying : annobin-plugin-gcc-10.99-1.0.1.fc38.s390x 7/71
Verifying : cpp-13.0.0-0.4.fc38.s390x 8/71
Verifying : gcc-13.0.0-0.4.fc38.s390x 9/71
Verifying : gcc-plugin-annobin-13.0.0-0.4.fc38.s390x 10/71
Verifying : libasan-13.0.0-0.4.fc38.s390x 11/71
Verifying : libatomic-13.0.0-0.4.fc38.s390x 12/71
Verifying : libtool-ltdl-2.4.7-3.0.1.fc38.s390x 13/71
Verifying : libubsan-13.0.0-0.4.fc38.s390x 14/71
Verifying : glibc-devel-2.36.9000-19.fc38.s390x 15/71
Verifying : glibc-headers-s390-2.36.9000-19.fc38.noarch 16/71
Verifying : kernel-headers-6.1.0-1.fc38.s390x 17/71
Verifying : libmpc-1.2.1-5.fc37.s390x 18/71
Verifying : libxcrypt-devel-4.4.33-5.fc38.s390x 19/71
Verifying : make-1:4.3-11.fc37.s390x 20/71
Verifying : ncurses-6.3-5.20221126.fc38.s390x 21/71
Verifying : openssl-devel-1:3.0.5-6.fc38.s390x 22/71
Verifying : perl-B-1.83-492.fc38.s390x 23/71
Verifying : perl-Carp-1.52-489.fc37.noarch 24/71
Verifying : perl-Class-Struct-0.66-492.fc38.noarch 25/71
Verifying : perl-Data-Dumper-2.184-490.fc37.s390x 26/71
Verifying : perl-DynaLoader-1.52-492.fc38.s390x 27/71
Verifying : perl-Encode-4:3.19-492.fc38.s390x 28/71
Verifying : perl-Errno-1.36-492.fc38.s390x 29/71
Verifying : perl-Exporter-5.77-489.fc37.noarch 30/71
Verifying : perl-Fcntl-1.15-492.fc38.s390x 31/71
Verifying : perl-File-Basename-2.85-492.fc38.noarch 32/71
Verifying : perl-File-Path-2.18-489.fc37.noarch 33/71
Verifying : perl-File-Temp-1:0.231.100-489.fc37.noarch 34/71
Verifying : perl-File-stat-1.12-492.fc38.noarch 35/71
Verifying : perl-FindBin-1.53-492.fc38.noarch 36/71
Verifying : perl-Getopt-Long-1:2.54-1.fc38.noarch 37/71
Verifying : perl-Getopt-Std-1.13-492.fc38.noarch 38/71
Verifying : perl-HTTP-Tiny-0.082-1.fc37.noarch 39/71
Verifying : perl-IO-1.50-492.fc38.s390x 40/71
Verifying : perl-IPC-Open3-1.22-492.fc38.noarch 41/71
Verifying : perl-MIME-Base64-3.16-489.fc37.s390x 42/71
Verifying : perl-POSIX-2.03-492.fc38.s390x 43/71
Verifying : perl-PathTools-3.84-489.fc37.s390x 44/71
Verifying : perl-Pod-Escapes-1:1.07-489.fc37.noarch 45/71
Verifying : perl-Pod-Perldoc-3.28.01-490.fc37.noarch 46/71
Verifying : perl-Pod-Simple-1:3.43-490.fc37.noarch 47/71
Verifying : perl-Pod-Usage-4:2.03-3.fc37.noarch 48/71
Verifying : perl-Scalar-List-Utils-5:1.63-489.fc38.s390x 49/71
Verifying : perl-SelectSaver-1.02-492.fc38.noarch 50/71
Verifying : perl-Socket-4:2.036-1.fc38.s390x 51/71
Verifying : perl-Storable-1:3.26-489.fc37.s390x 52/71
Verifying : perl-Symbol-1.09-492.fc38.noarch 53/71
Verifying : perl-Term-ANSIColor-5.01-490.fc37.noarch 54/71
Verifying : perl-Term-Cap-1.17-489.fc37.noarch 55/71
Verifying : perl-Text-ParseWords-3.31-489.fc37.noarch 56/71
Verifying : perl-Text-Tabs+Wrap-2021.0814-489.fc37.noarch 57/71
Verifying : perl-Time-Local-2:1.300-489.fc37.noarch 58/71
Verifying : perl-constant-1.33-490.fc37.noarch 59/71
Verifying : perl-if-0.61.000-492.fc38.noarch 60/71
Verifying : perl-interpreter-4:5.36.0-492.fc38.s390x 61/71
Verifying : perl-lib-0.65-492.fc38.s390x 62/71
Verifying : perl-libs-4:5.36.0-492.fc38.s390x 63/71
Verifying : perl-mro-1.26-492.fc38.s390x 64/71
Verifying : perl-overload-1.35-492.fc38.noarch 65/71
Verifying : perl-overloading-0.02-492.fc38.noarch 66/71
Verifying : perl-parent-1:0.239-1.fc38.noarch 67/71
Verifying : perl-podlators-1:5.00-1.fc38.noarch 68/71
Verifying : perl-vars-1.05-492.fc38.noarch 69/71
Verifying : xz-devel-5.2.9-1.fc38.s390x 70/71
Verifying : zlib-devel-1.2.13-1.fc38.s390x 71/71
Installed:
annobin-docs-10.99-1.0.1.fc38.noarch
annobin-plugin-gcc-10.99-1.0.1.fc38.s390x
bzip2-devel-1.0.8-12.fc38.s390x
cpp-13.0.0-0.4.fc38.s390x
gc-8.2.2-1.fc38.s390x
gcc-13.0.0-0.4.fc38.s390x
gcc-plugin-annobin-13.0.0-0.4.fc38.s390x
glibc-devel-2.36.9000-19.fc38.s390x
glibc-headers-s390-2.36.9000-19.fc38.noarch
groff-base-1.22.4-10.fc38.s390x
guile22-2.2.7-6.fc38.s390x
kernel-headers-6.1.0-1.fc38.s390x
libasan-13.0.0-0.4.fc38.s390x
libatomic-13.0.0-0.4.fc38.s390x
libcurl-devel-7.87.0-1.fc38.s390x
libmpc-1.2.1-5.fc37.s390x
libtool-ltdl-2.4.7-3.0.1.fc38.s390x
libubsan-13.0.0-0.4.fc38.s390x
libxcrypt-devel-4.4.33-5.fc38.s390x
make-1:4.3-11.fc37.s390x
ncurses-6.3-5.20221126.fc38.s390x
openssl-devel-1:3.0.5-6.fc38.s390x
perl-B-1.83-492.fc38.s390x
perl-Carp-1.52-489.fc37.noarch
perl-Class-Struct-0.66-492.fc38.noarch
perl-Data-Dumper-2.184-490.fc37.s390x
perl-DynaLoader-1.52-492.fc38.s390x
perl-Encode-4:3.19-492.fc38.s390x
perl-Errno-1.36-492.fc38.s390x
perl-Exporter-5.77-489.fc37.noarch
perl-Fcntl-1.15-492.fc38.s390x
perl-File-Basename-2.85-492.fc38.noarch
perl-File-Path-2.18-489.fc37.noarch
perl-File-Temp-1:0.231.100-489.fc37.noarch
perl-File-stat-1.12-492.fc38.noarch
perl-FindBin-1.53-492.fc38.noarch
perl-Getopt-Long-1:2.54-1.fc38.noarch
perl-Getopt-Std-1.13-492.fc38.noarch
perl-HTTP-Tiny-0.082-1.fc37.noarch
perl-IO-1.50-492.fc38.s390x
perl-IPC-Open3-1.22-492.fc38.noarch
perl-MIME-Base64-3.16-489.fc37.s390x
perl-POSIX-2.03-492.fc38.s390x
perl-PathTools-3.84-489.fc37.s390x
perl-Pod-Escapes-1:1.07-489.fc37.noarch
perl-Pod-Perldoc-3.28.01-490.fc37.noarch
perl-Pod-Simple-1:3.43-490.fc37.noarch
perl-Pod-Usage-4:2.03-3.fc37.noarch
perl-Scalar-List-Utils-5:1.63-489.fc38.s390x
perl-SelectSaver-1.02-492.fc38.noarch
perl-Socket-4:2.036-1.fc38.s390x
perl-Storable-1:3.26-489.fc37.s390x
perl-Symbol-1.09-492.fc38.noarch
perl-Term-ANSIColor-5.01-490.fc37.noarch
perl-Term-Cap-1.17-489.fc37.noarch
perl-Text-ParseWords-3.31-489.fc37.noarch
perl-Text-Tabs+Wrap-2021.0814-489.fc37.noarch
perl-Time-Local-2:1.300-489.fc37.noarch
perl-constant-1.33-490.fc37.noarch
perl-if-0.61.000-492.fc38.noarch
perl-interpreter-4:5.36.0-492.fc38.s390x
perl-lib-0.65-492.fc38.s390x
perl-libs-4:5.36.0-492.fc38.s390x
perl-mro-1.26-492.fc38.s390x
perl-overload-1.35-492.fc38.noarch
perl-overloading-0.02-492.fc38.noarch
perl-parent-1:0.239-1.fc38.noarch
perl-podlators-1:5.00-1.fc38.noarch
perl-vars-1.05-492.fc38.noarch
xz-devel-5.2.9-1.fc38.s390x
zlib-devel-1.2.13-1.fc38.s390x
Complete!
Finish: build setup for htslib-1.15.1-1.fc38.src.rpm
Start: rpmbuild htslib-1.15.1-1.fc38.src.rpm
Building target platforms: s390x
Building for target s390x
setting SOURCE_DATE_EPOCH=1660521600
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.3u2vl3
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf htslib-1.15.1
+ /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/htslib-1.15.1.tar.bz2
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd htslib-1.15.1
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
Patch #0 (htslib-1.15.1-gcc12.patch):
+ echo 'Patch #0 (htslib-1.15.1-gcc12.patch):'
+ /usr/bin/patch --no-backup-if-mismatch -f -p1 --fuzz=0
patching file htscodecs/htscodecs/rANS_word.h
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.sLVtyf
+ umask 022
+ cd /builddir/build/BUILD
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules'
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ 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 htslib-1.15.1
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules'
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ 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' ./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
--- ./configure.backup 2022-04-07 15:42:52.000000000 +0000
+++ ./configure 2022-12-25 04:36:46.345505494 +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' ./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* .* \\(.*\\)$/extern char \\1;/p'\''"#' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ '[' 1 = 1 ']'
+++ dirname ./configure
++ find . -name config.guess -o -name config.sub
+ '[' 1 = 1 ']'
+ '[' x '!=' 'x-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' ']'
++ find . -name ltmain.sh
++ grep -q runstatedir=DIR ./configure
++ echo --runstatedir=/run
+ ./configure --build=s390x-redhat-linux-gnu --host=s390x-redhat-linux-gnu --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/libexec --localstatedir=/var --runstatedir=/run --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info 'CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection' 'LDFLAGS=-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes' --prefix=/usr --libdir=/usr/lib64 --enable-plugins '--with-plugin-path=/usr/local/libexec/htslib:$(plugindir)' --enable-gcs --enable-libcurl --enable-s3
configure: WARNING: unrecognized options: --disable-dependency-tracking
checking for s390x-redhat-linux-gnu-gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for s390x-redhat-linux-gnu-ranlib... no
checking for ranlib... ranlib
checking for grep that handles long lines and -e... /usr/bin/grep
checking for C compiler warning flags... -Wall
checking for s390x-redhat-linux-gnu-pkg-config... /usr/bin/s390x-redhat-linux-gnu-pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking shared library type for s390x-redhat-linux-gnu... plain .so
checking whether the compiler accepts -fvisibility=hidden... yes
checking how to run the C preprocessor... gcc -E
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking for gmtime_r... yes
checking for fsync... yes
checking for drand48... yes
checking for srand48_deterministic... no
checking whether fdatasync is declared... yes
checking for fdatasync... yes
checking for library containing dlsym... none required
checking whether the compiler accepts -rdynamic... yes
checking for library containing log... -lm
checking for zlib.h... yes
checking for inflate in -lz... yes
checking for library containing recv... none required
checking for bzlib.h... yes
checking for BZ2_bzBuffToBuffCompress in -lbz2... yes
checking for lzma.h... yes
checking for lzma_easy_buffer_encode in -llzma... yes
checking whether htscodecs files are present... yes
checking for libdeflate.h... no
checking for libdeflate_deflate_compress in -ldeflate... no
checking for curl/curl.h... yes
checking for curl_easy_pause in -lcurl... yes
checking for CCHmac... no
checking for library containing HMAC... -lcrypto
checking for library containing regcomp... none required
checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes
configure: creating ./config.status
config.status: creating config.mk
config.status: creating htslib.pc.tmp
config.status: creating config.h
config.status: linking htscodecs_bundled.mk to htscodecs.mk
configure: WARNING: unrecognized options: --disable-dependency-tracking
+ /usr/bin/make -O -j2 V=1 VERBOSE=1
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o kfunc.o kfunc.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o kstring.o kstring.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o bcf_sr_sort.o bcf_sr_sort.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o errmod.o errmod.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o bgzf.o bgzf.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o faidx.o faidx.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o hfile.o hfile.c
echo '#define HTS_VERSION_TEXT "1.15.1"' > version.h
echo '#define HTS_CC "gcc"' > config_vars.h
echo '#define HTS_CPPFLAGS ""' >> config_vars.h
echo '#define HTS_CFLAGS "-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden"' >> config_vars.h
echo '#define HTS_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 -fvisibility=hidden -rdynamic"' >> config_vars.h
echo '#define HTS_LIBS "-llzma -lbz2 -lz -lm "' >> config_vars.h
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o hts_expr.o hts_expr.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o hts_os.o hts_os.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o header.o header.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o multipart.o multipart.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o md5.o md5.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o probaln.o probaln.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o realn.o realn.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o region.o region.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o regidx.o regidx.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o synced_bcf_reader.o synced_bcf_reader.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o vcf_sweep.o vcf_sweep.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o tbx.o tbx.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o textutils.o textutils.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o thread_pool.o thread_pool.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o sam.o sam.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o vcfutils.o vcfutils.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o vcf.o vcf.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/cram_codecs.o cram/cram_codecs.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/cram_decode.o cram/cram_decode.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/cram_external.o cram/cram_external.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/cram_encode.o cram/cram_encode.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/cram_index.o cram/cram_index.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/cram_stats.o cram/cram_stats.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/mFILE.o cram/mFILE.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/open_trace_file.o cram/open_trace_file.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/string_alloc.o cram/string_alloc.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/cram_io.o cram/cram_io.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -DPLUGINPATH=\"/usr/local/libexec/htslib:/usr/libexec/htslib\" -c -o plugin.o plugin.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o kfunc.pico kfunc.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o kstring.pico kstring.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o bcf_sr_sort.pico bcf_sr_sort.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o errmod.pico errmod.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o faidx.pico faidx.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o bgzf.pico bgzf.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o hfile.pico hfile.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o header.pico header.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o hts_expr.pico hts_expr.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o hts_os.pico hts_os.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o md5.pico md5.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o multipart.pico multipart.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o probaln.pico probaln.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o realn.pico realn.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o hts.pico hts.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o regidx.pico regidx.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o region.pico region.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o synced_bcf_reader.pico synced_bcf_reader.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o vcf_sweep.pico vcf_sweep.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o tbx.pico tbx.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o textutils.pico textutils.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o thread_pool.pico thread_pool.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o sam.pico sam.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o vcfutils.pico vcfutils.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o vcf.pico vcf.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o cram/cram_codecs.pico cram/cram_codecs.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o cram/cram_decode.pico cram/cram_decode.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o cram/cram_external.pico cram/cram_external.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o cram/cram_index.pico cram/cram_index.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o cram/cram_encode.pico cram/cram_encode.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o cram/cram_stats.pico cram/cram_stats.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o cram/mFILE.pico cram/mFILE.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o cram/open_trace_file.pico cram/open_trace_file.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o cram/pooled_alloc.pico cram/pooled_alloc.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o cram/string_alloc.pico cram/string_alloc.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o cram/cram_io.pico cram/cram_io.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/arith_dynamic.pico htscodecs/htscodecs/arith_dynamic.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/htscodecs.pico htscodecs/htscodecs/htscodecs.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/pack.pico htscodecs/htscodecs/pack.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/fqzcomp_qual.pico htscodecs/htscodecs/fqzcomp_qual.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rANS_static.pico htscodecs/htscodecs/rANS_static.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rle.pico htscodecs/htscodecs/rle.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rANS_static4x16pr.pico htscodecs/htscodecs/rANS_static4x16pr.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -DPLUGINPATH=\"/usr/local/libexec/htslib:/usr/libexec/htslib\" -fpic -c -o plugin.pico plugin.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o bgzip.o bgzip.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/tokenise_name3.pico htscodecs/htscodecs/tokenise_name3.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o htsfile.o htsfile.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o tabix.o tabix.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o hfile_gcs.pico hfile_gcs.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o hfile_libcurl.pico hfile_libcurl.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o hfile_s3_write.pico hfile_s3_write.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o hfile_s3.pico hfile_s3.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/fieldarith.o test/fieldarith.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/hts_endian.o test/hts_endian.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/pileup.o test/pileup.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/hfile.o test/hfile.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/pileup_mod.o test/pileup_mod.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/plugins-dlhts.o test/plugins-dlhts.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_bgzf.o test/test_bgzf.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_expr.o test/test_expr.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_kfunc.o test/test_kfunc.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/sam.o test/sam.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_mod.o test/test_mod.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_realn.o test/test_realn.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_kstring.o test/test_kstring.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test-regidx.o test/test-regidx.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_str2int.o test/test_str2int.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_index.o test/test_index.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_view.o test/test_view.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test-bcf-sr.o test/test-bcf-sr.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/fuzz/hts_open_fuzzer.o test/fuzz/hts_open_fuzzer.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test-bcf-translate.o test/test-bcf-translate.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test-vcf-api.o test/test-vcf-api.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test-parse-reg.o test/test-parse-reg.c
sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' htslib.pc.tmp > htslib_static.mk
sed -e 's#@-includedir@#'`pwd`'#g;s#@-libdir@#'`pwd`'#g' htslib.pc.tmp > htslib-uninstalled.pc
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_introspection.o test/test_introspection.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o hts.o hts.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 -fvisibility=hidden -rdynamic -o test/hts_endian test/hts_endian.o -llzma -lbz2 -lz -lm
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 -fvisibility=hidden -rdynamic -o test/plugins-dlhts test/plugins-dlhts.o -llzma -lbz2 -lz -lm
ar -rc libhts.a kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o plugin.o
ranlib libhts.a
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 -fvisibility=hidden -rdynamic -o bgzip bgzip.o libhts.a -llzma -lbz2 -lz -lm -lpthread
gcc -shared -Wl,-soname,libhts.so.3 -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 -fvisibility=hidden -rdynamic -o libhts.so kfunc.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico header.pico hfile.pico hts.pico hts_expr.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico region.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_stats.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/string_alloc.pico htscodecs/htscodecs/arith_dynamic.pico htscodecs/htscodecs/fqzcomp_qual.pico htscodecs/htscodecs/htscodecs.pico htscodecs/htscodecs/pack.pico htscodecs/htscodecs/rANS_static4x16pr.pico htscodecs/htscodecs/rANS_static.pico htscodecs/htscodecs/rle.pico htscodecs/htscodecs/tokenise_name3.pico plugin.pico -llzma -lbz2 -lz -lm -lpthread
ln -sf libhts.so libhts.so.3
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 -fvisibility=hidden -rdynamic -o htsfile htsfile.o libhts.a -llzma -lbz2 -lz -lm -lpthread
gcc -shared -Wl,-E -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 -fvisibility=hidden -rdynamic -o hfile_libcurl.so hfile_libcurl.pico libhts.so -llzma -lbz2 -lz -lm -lcurl -lpthread
gcc -shared -Wl,-E -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 -fvisibility=hidden -rdynamic -o hfile_gcs.so hfile_gcs.pico libhts.so -llzma -lbz2 -lz -lm -lpthread
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 -fvisibility=hidden -rdynamic -o tabix tabix.o libhts.a -llzma -lbz2 -lz -lm -lpthread
gcc -shared -Wl,-E -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 -fvisibility=hidden -rdynamic -o hfile_s3.so hfile_s3.pico libhts.so -llzma -lbz2 -lz -lm -lcrypto -lpthread
gcc -shared -Wl,-E -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 -fvisibility=hidden -rdynamic -o hfile_s3_write.so hfile_s3_write.pico libhts.so -llzma -lbz2 -lz -lm -lcrypto -lcurl -lpthread
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 -fvisibility=hidden -rdynamic -o test/fieldarith test/fieldarith.o libhts.a -llzma -lbz2 -lz -lm -lpthread
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 -fvisibility=hidden -rdynamic -o test/hfile test/hfile.o libhts.a -llzma -lbz2 -lz -lm -lpthread
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 -fvisibility=hidden -rdynamic -o test/pileup test/pileup.o libhts.a -llzma -lbz2 -lz -lm -lpthread
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 -fvisibility=hidden -rdynamic -o test/pileup_mod test/pileup_mod.o libhts.a -llzma -lbz2 -lz -lm -lpthread
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 -fvisibility=hidden -rdynamic -o test/sam test/sam.o libhts.a -llzma -lbz2 -lz -lm -lpthread
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 -fvisibility=hidden -rdynamic -o test/test_expr test/test_expr.o libhts.a -lz -llzma -lbz2 -lz -lm -lpthread
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 -fvisibility=hidden -rdynamic -o test/test_kfunc test/test_kfunc.o libhts.a -lz -llzma -lbz2 -lz -lm -lpthread
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 -fvisibility=hidden -rdynamic -o test/test_bgzf test/test_bgzf.o libhts.a -lz -llzma -lbz2 -lz -lm -lpthread
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 -fvisibility=hidden -rdynamic -o test/test_kstring test/test_kstring.o libhts.a -lz -llzma -lbz2 -lz -lm -lpthread
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 -fvisibility=hidden -rdynamic -o test/test_mod test/test_mod.o libhts.a -llzma -lbz2 -lz -lm -lpthread
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 -fvisibility=hidden -rdynamic -o test/test_realn test/test_realn.o libhts.a -llzma -lbz2 -lz -lm -lpthread
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 -fvisibility=hidden -rdynamic -o test/test-regidx test/test-regidx.o libhts.a -llzma -lbz2 -lz -lm -lpthread
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 -fvisibility=hidden -rdynamic -o test/test_str2int test/test_str2int.o libhts.a -llzma -lbz2 -lz -lm -lpthread
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 -fvisibility=hidden -rdynamic -o test/test_view test/test_view.o libhts.a -llzma -lbz2 -lz -lm -lpthread
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 -fvisibility=hidden -rdynamic -o test/test_index test/test_index.o libhts.a -llzma -lbz2 -lz -lm -lpthread
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 -fvisibility=hidden -rdynamic -o test/test-vcf-api test/test-vcf-api.o libhts.a -llzma -lbz2 -lz -lm -lpthread
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 -fvisibility=hidden -rdynamic -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -llzma -lbz2 -lz -lm -lpthread
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 -fvisibility=hidden -rdynamic -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -llzma -lbz2 -lz -lm -lpthread
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 -fvisibility=hidden -rdynamic -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -lz -llzma -lbz2 -lz -lm -lpthread
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 -fvisibility=hidden -rdynamic -o test/test-parse-reg test/test-parse-reg.o libhts.a -llzma -lbz2 -lz -lm -lpthread
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 -fvisibility=hidden -rdynamic -o test/test_introspection test/test_introspection.o libhts.a -llzma -lbz2 -lz -lm -lpthread
+ sed -i -E '/^(Libs|Requires)\.private:/d' htslib.pc.tmp
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.hsVnsK
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x
++ dirname /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules'
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ 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 htslib-1.15.1
+ /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x 'INSTALL=/usr/bin/install -p'
mkdir -p -m 755 /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/bin /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/include /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/include/htslib /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/lib64 /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/share/man/man1 /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/share/man/man5 /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/share/man/man7 /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/lib64/pkgconfig
if test -n "/usr/libexec/htslib"; then mkdir -p -m 755 /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/libexec/htslib; fi
/usr/bin/install -p -m 644 libhts.so /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/lib64/libhts.so.1.15.1
ln -sf libhts.so.1.15.1 /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/lib64/libhts.so
ln -sf libhts.so.1.15.1 /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/lib64/libhts.so.3
sed -e 's#@-includedir@#/usr/include#g;s#@-libdir@#/usr/lib64#g;s#@-PACKAGE_VERSION@#1.15.1#g' htslib.pc.tmp > /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/lib64/pkgconfig/htslib.pc
chmod 644 /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/lib64/pkgconfig/htslib.pc
/usr/bin/install -p bgzip htsfile tabix /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/bin
if test -n "hfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so"; then /usr/bin/install -p hfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/libexec/htslib; fi
/usr/bin/install -p -m 644 htslib/*.h /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/include/htslib
/usr/bin/install -p -m 644 libhts.a /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/lib64/libhts.a
/usr/bin/install -p -m 644 bgzip.1 htsfile.1 tabix.1 /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/share/man/man1
/usr/bin/install -p -m 644 faidx.5 sam.5 vcf.5 /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/share/man/man5
/usr/bin/install -p -m 644 htslib-s3-plugin.7 /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/share/man/man7
+ pushd /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x//usr/lib64
~/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/lib64 ~/build/BUILD/htslib-1.15.1
+ chmod 755 libhts.so.1.15.1
+ popd
~/build/BUILD/htslib-1.15.1
+ find /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x -name '*.la' -delete
+ rm -f /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x//usr/lib64/libhts.a
+ /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 1.15.1-1.fc38 --unique-debug-suffix -1.15.1-1.fc38.s390x --unique-debug-src-base htslib-1.15.1-1.fc38.s390x --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/htslib-1.15.1
extracting debug info from /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/bin/bgzip
extracting debug info from /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/bin/htsfile
extracting debug info from /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/bin/tabix
extracting debug info from /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/lib64/libhts.so.1.15.1
extracting debug info from /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/libexec/htslib/hfile_gcs.so
extracting debug info from /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/libexec/htslib/hfile_libcurl.so
extracting debug info from /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/libexec/htslib/hfile_s3.so
extracting debug info from /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/libexec/htslib/hfile_s3_write.so
original debug info size: 12552kB, size after compression: 10988kB
/usr/bin/sepdebugcrcfix: Updated 8 CRC32s, 0 CRC32s did match.
5259 blocks
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-ldconfig
+ /usr/lib/rpm/brp-compress
+ /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip
+ /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip
+ /usr/lib/rpm/check-rpaths
+ /usr/lib/rpm/redhat/brp-mangle-shebangs
+ /usr/lib/rpm/brp-remove-la-files
+ /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0
+ /usr/lib/rpm/redhat/brp-python-hardlink
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.PQ43uw
+ umask 022
+ cd /builddir/build/BUILD
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules'
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ 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 htslib-1.15.1
+ make test
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -Ihtscodecs -D_POSIX_C_SOURCE=200112L -c -o htscodecs/tests/rANS_static_test.o htscodecs/tests/rANS_static_test.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 -fvisibility=hidden -rdynamic -o htscodecs/tests/rans4x8 htscodecs/tests/rANS_static_test.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o -llzma -lbz2 -lz -lm -lm -lpthread
cd htscodecs/tests && srcdir=. && export srcdir && ./rans4x8.test
Testing rans4x8 -r -o0 on ./dat/q4 11674
Testing rans4x8 -r -o1 on ./dat/q4 10870
Testing rans4x8 -r -o0 on ./dat/q40+dir 50258
Testing rans4x8 -r -o1 on ./dat/q40+dir 50537
Testing rans4x8 -r -o0 on ./dat/q8 33099
Testing rans4x8 -r -o1 on ./dat/q8 31428
Testing rans4x8 -r -o0 on ./dat/qvar 32997
Testing rans4x8 -r -o1 on ./dat/qvar 32832
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -Ihtscodecs -D_POSIX_C_SOURCE=200112L -c -o htscodecs/tests/rANS_static4x16pr_test.o htscodecs/tests/rANS_static4x16pr_test.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 -fvisibility=hidden -rdynamic -o htscodecs/tests/rans4x16pr htscodecs/tests/rANS_static4x16pr_test.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o -llzma -lbz2 -lz -lm -lm -lpthread
cd htscodecs/tests && srcdir=. && export srcdir && ./rans4x16.test
Testing rans4x16 -r -o0 on ./dat/q4 11660
Testing rans4x16 -r -o1 on ./dat/q4 10848
Testing rans4x16 -r -o64 on ./dat/q4 12878
Testing rans4x16 -r -o65 on ./dat/q4 10672
Testing rans4x16 -r -o128 on ./dat/q4 10902
Testing rans4x16 -r -o129 on ./dat/q4 10890
Testing rans4x16 -r -o192 on ./dat/q4 11225
Testing rans4x16 -r -o193 on ./dat/q4 10825
Testing rans4x16 -r -o8 on ./dat/q4 11731
Testing rans4x16 -r -o9 on ./dat/q4 11111
Testing rans4x16 -r -o0 on ./dat/q40+dir 50247
Testing rans4x16 -r -o1 on ./dat/q40+dir 49449
Testing rans4x16 -r -o8 on ./dat/q40+dir 50072
Testing rans4x16 -r -o9 on ./dat/q40+dir 50072
Testing rans4x16 -r -o0 on ./dat/q8 33088
Testing rans4x16 -r -o1 on ./dat/q8 31372
Testing rans4x16 -r -o64 on ./dat/q8 33458
Testing rans4x16 -r -o65 on ./dat/q8 31025
Testing rans4x16 -r -o128 on ./dat/q8 32237
Testing rans4x16 -r -o129 on ./dat/q8 31258
Testing rans4x16 -r -o192 on ./dat/q8 32024
Testing rans4x16 -r -o193 on ./dat/q8 31146
Testing rans4x16 -r -o0 on ./dat/qvar 32987
Testing rans4x16 -r -o1 on ./dat/qvar 32261
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -Ihtscodecs -D_POSIX_C_SOURCE=200112L -c -o htscodecs/tests/arith_dynamic_test.o htscodecs/tests/arith_dynamic_test.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 -fvisibility=hidden -rdynamic -o htscodecs/tests/arith_dynamic htscodecs/tests/arith_dynamic_test.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o -llzma -lbz2 -lz -lm -lm -lpthread
cd htscodecs/tests && srcdir=. && export srcdir && ./arith.test
Testing arith_dynamic -r -o0 on ./dat/q4 11615
Testing arith_dynamic -r -o1 on ./dat/q4 10831
Testing arith_dynamic -r -o64 on ./dat/q4 13360
Testing arith_dynamic -r -o65 on ./dat/q4 10484
Testing arith_dynamic -r -o128 on ./dat/q4 10774
Testing arith_dynamic -r -o129 on ./dat/q4 10329
Testing arith_dynamic -r -o192 on ./dat/q4 11095
Testing arith_dynamic -r -o193 on ./dat/q4 10283
Testing arith_dynamic -r -o8 on ./dat/q4 11448
Testing arith_dynamic -r -o9 on ./dat/q4 11083
Testing arith_dynamic -r -o0 on ./dat/q40+dir 49949
Testing arith_dynamic -r -o1 on ./dat/q40+dir 49034
Testing arith_dynamic -r -o64 on ./dat/q40+dir 51242
Testing arith_dynamic -r -o65 on ./dat/q40+dir 49061
Testing arith_dynamic -r -o8 on ./dat/q40+dir 49820
Testing arith_dynamic -r -o9 on ./dat/q40+dir 49448
Testing arith_dynamic -r -o0 on ./dat/q8 32752
Testing arith_dynamic -r -o1 on ./dat/q8 31331
Testing arith_dynamic -r -o64 on ./dat/q8 35211
Testing arith_dynamic -r -o65 on ./dat/q8 30907
Testing arith_dynamic -r -o128 on ./dat/q8 32063
Testing arith_dynamic -r -o129 on ./dat/q8 31084
Testing arith_dynamic -r -o192 on ./dat/q8 32267
Testing arith_dynamic -r -o193 on ./dat/q8 30931
Testing arith_dynamic -r -o0 on ./dat/qvar 32597
Testing arith_dynamic -r -o1 on ./dat/qvar 31982
Testing arith_dynamic -r -o64 on ./dat/qvar 33237
Testing arith_dynamic -r -o65 on ./dat/qvar 31993
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -Ihtscodecs -D_POSIX_C_SOURCE=200112L -c -o htscodecs/tests/tokenise_name3_test.o htscodecs/tests/tokenise_name3_test.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 -fvisibility=hidden -rdynamic -o htscodecs/tests/tokenise_name3 htscodecs/tests/tokenise_name3_test.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o -llzma -lbz2 -lz -lm -lm -lpthread
cd htscodecs/tests && srcdir=. && export srcdir && ./tok3.test
Testing tokenise_name3 -r -1 on ./names/01.names 3392
Testing tokenise_name3 -r -3 on ./names/01.names 2471
Testing tokenise_name3 -r -5 on ./names/01.names 2283
Testing tokenise_name3 -r -7 on ./names/01.names 2234
Testing tokenise_name3 -r -9 on ./names/01.names 2234
Testing tokenise_name3 -r -11 on ./names/01.names 3151
Testing tokenise_name3 -r -13 on ./names/01.names 2424
Testing tokenise_name3 -r -15 on ./names/01.names 2061
Testing tokenise_name3 -r -17 on ./names/01.names 2051
Testing tokenise_name3 -r -19 on ./names/01.names 2049
Testing tokenise_name3 -r -1 on ./names/02.names 6633
Testing tokenise_name3 -r -3 on ./names/02.names 4983
Testing tokenise_name3 -r -5 on ./names/02.names 4942
Testing tokenise_name3 -r -7 on ./names/02.names 4922
Testing tokenise_name3 -r -9 on ./names/02.names 4918
Testing tokenise_name3 -r -11 on ./names/02.names 6087
Testing tokenise_name3 -r -13 on ./names/02.names 4797
Testing tokenise_name3 -r -15 on ./names/02.names 4714
Testing tokenise_name3 -r -17 on ./names/02.names 4695
Testing tokenise_name3 -r -19 on ./names/02.names 4695
Testing tokenise_name3 -r -1 on ./names/03.names 10557
Testing tokenise_name3 -r -3 on ./names/03.names 7822
Testing tokenise_name3 -r -5 on ./names/03.names 7557
Testing tokenise_name3 -r -7 on ./names/03.names 7521
Testing tokenise_name3 -r -9 on ./names/03.names 7521
Testing tokenise_name3 -r -11 on ./names/03.names 9294
Testing tokenise_name3 -r -13 on ./names/03.names 7291
Testing tokenise_name3 -r -15 on ./names/03.names 7125
Testing tokenise_name3 -r -17 on ./names/03.names 7069
Testing tokenise_name3 -r -19 on ./names/03.names 7068
Testing tokenise_name3 -r -1 on ./names/05.names 5098
Testing tokenise_name3 -r -3 on ./names/05.names 3600
Testing tokenise_name3 -r -5 on ./names/05.names 3551
Testing tokenise_name3 -r -7 on ./names/05.names 3534
Testing tokenise_name3 -r -9 on ./names/05.names 3534
Testing tokenise_name3 -r -11 on ./names/05.names 4648
Testing tokenise_name3 -r -13 on ./names/05.names 3405
Testing tokenise_name3 -r -15 on ./names/05.names 3381
Testing tokenise_name3 -r -17 on ./names/05.names 3377
Testing tokenise_name3 -r -19 on ./names/05.names 3377
Testing tokenise_name3 -r -1 on ./names/08.names 6841
Testing tokenise_name3 -r -3 on ./names/08.names 5291
Testing tokenise_name3 -r -5 on ./names/08.names 5206
Testing tokenise_name3 -r -7 on ./names/08.names 5160
Testing tokenise_name3 -r -9 on ./names/08.names 5160
Testing tokenise_name3 -r -11 on ./names/08.names 6374
Testing tokenise_name3 -r -13 on ./names/08.names 4895
Testing tokenise_name3 -r -15 on ./names/08.names 4851
Testing tokenise_name3 -r -17 on ./names/08.names 4805
Testing tokenise_name3 -r -19 on ./names/08.names 4805
Testing tokenise_name3 -r -1 on ./names/09.names 5339
Testing tokenise_name3 -r -3 on ./names/09.names 3598
Testing tokenise_name3 -r -5 on ./names/09.names 3527
Testing tokenise_name3 -r -7 on ./names/09.names 3493
Testing tokenise_name3 -r -9 on ./names/09.names 3493
Testing tokenise_name3 -r -11 on ./names/09.names 4861
Testing tokenise_name3 -r -13 on ./names/09.names 3427
Testing tokenise_name3 -r -15 on ./names/09.names 3391
Testing tokenise_name3 -r -17 on ./names/09.names 3366
Testing tokenise_name3 -r -19 on ./names/09.names 3366
Testing tokenise_name3 -r -1 on ./names/10.names 6458
Testing tokenise_name3 -r -3 on ./names/10.names 4843
Testing tokenise_name3 -r -5 on ./names/10.names 4799
Testing tokenise_name3 -r -7 on ./names/10.names 4746
Testing tokenise_name3 -r -9 on ./names/10.names 4744
Testing tokenise_name3 -r -11 on ./names/10.names 5785
Testing tokenise_name3 -r -13 on ./names/10.names 4567
Testing tokenise_name3 -r -15 on ./names/10.names 4492
Testing tokenise_name3 -r -17 on ./names/10.names 4472
Testing tokenise_name3 -r -19 on ./names/10.names 4472
Testing tokenise_name3 -r -1 on ./names/20.names 2511
Testing tokenise_name3 -r -3 on ./names/20.names 1701
Testing tokenise_name3 -r -5 on ./names/20.names 1659
Testing tokenise_name3 -r -7 on ./names/20.names 1632
Testing tokenise_name3 -r -9 on ./names/20.names 1632
Testing tokenise_name3 -r -11 on ./names/20.names 2319
Testing tokenise_name3 -r -13 on ./names/20.names 1629
Testing tokenise_name3 -r -15 on ./names/20.names 1605
Testing tokenise_name3 -r -17 on ./names/20.names 1600
Testing tokenise_name3 -r -19 on ./names/20.names 1600
Testing tokenise_name3 -r -1 on ./names/nv.names 6816
Testing tokenise_name3 -r -3 on ./names/nv.names 4989
Testing tokenise_name3 -r -5 on ./names/nv.names 4972
Testing tokenise_name3 -r -7 on ./names/nv.names 4937
Testing tokenise_name3 -r -9 on ./names/nv.names 4937
Testing tokenise_name3 -r -11 on ./names/nv.names 6084
Testing tokenise_name3 -r -13 on ./names/nv.names 4825
Testing tokenise_name3 -r -15 on ./names/nv.names 4771
Testing tokenise_name3 -r -17 on ./names/nv.names 4767
Testing tokenise_name3 -r -19 on ./names/nv.names 4767
Testing tokenise_name3 -r -1 on ./names/nv2.names 1181
Testing tokenise_name3 -r -3 on ./names/nv2.names 903
Testing tokenise_name3 -r -5 on ./names/nv2.names 879
Testing tokenise_name3 -r -7 on ./names/nv2.names 846
Testing tokenise_name3 -r -9 on ./names/nv2.names 846
Testing tokenise_name3 -r -11 on ./names/nv2.names 891
Testing tokenise_name3 -r -13 on ./names/nv2.names 836
Testing tokenise_name3 -r -15 on ./names/nv2.names 764
Testing tokenise_name3 -r -17 on ./names/nv2.names 747
Testing tokenise_name3 -r -19 on ./names/nv2.names 747
Testing tokenise_name3 -r -1 on ./names/rr.names 8788
Testing tokenise_name3 -r -3 on ./names/rr.names 6290
Testing tokenise_name3 -r -5 on ./names/rr.names 6252
Testing tokenise_name3 -r -7 on ./names/rr.names 6230
Testing tokenise_name3 -r -9 on ./names/rr.names 6230
Testing tokenise_name3 -r -11 on ./names/rr.names 8319
Testing tokenise_name3 -r -13 on ./names/rr.names 6066
Testing tokenise_name3 -r -15 on ./names/rr.names 5972
Testing tokenise_name3 -r -17 on ./names/rr.names 5963
Testing tokenise_name3 -r -19 on ./names/rr.names 5963
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -Ihtscodecs -D_POSIX_C_SOURCE=200112L -c -o htscodecs/tests/fqzcomp_qual_test.o htscodecs/tests/fqzcomp_qual_test.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 -fvisibility=hidden -rdynamic -o htscodecs/tests/fqzcomp_qual htscodecs/tests/fqzcomp_qual_test.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o -llzma -lbz2 -lz -lm -lm -lpthread
cd htscodecs/tests && srcdir=. && export srcdir && ./fqzcomp.test
Testing fqzcomp_qual -r -s 0 on ./dat/q4 9307
Testing fqzcomp_qual -r -s 1 on ./dat/q4 9618
Testing fqzcomp_qual -r -s 2 on ./dat/q4 9453
Testing fqzcomp_qual -r -s 3 on ./dat/q4 10481
Testing fqzcomp_qual -r -s 0 on ./dat/q40+dir 47674
Testing fqzcomp_qual -r -s 1 on ./dat/q40+dir 45016
Testing fqzcomp_qual -r -s 2 on ./dat/q40+dir 47760
Testing fqzcomp_qual -r -s 3 on ./dat/q40+dir 48583
Testing fqzcomp_qual -r -s 0 on ./dat/q8 30012
Testing fqzcomp_qual -r -s 1 on ./dat/q8 33742
Testing fqzcomp_qual -r -s 2 on ./dat/q8 30982
Testing fqzcomp_qual -r -s 3 on ./dat/q8 31709
Testing fqzcomp_qual -r -s 0 on ./dat/qvar 32868
Testing fqzcomp_qual -r -s 1 on ./dat/qvar 35007
Testing fqzcomp_qual -r -s 2 on ./dat/qvar 32400
Testing fqzcomp_qual -r -s 3 on ./dat/qvar 32073
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -Ihtscodecs -D_POSIX_C_SOURCE=200112L -c -o htscodecs/tests/varint_test.o htscodecs/tests/varint_test.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 -fvisibility=hidden -rdynamic -o htscodecs/tests/varint htscodecs/tests/varint_test.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o -llzma -lbz2 -lz -lm -lm -lpthread
cd htscodecs/tests && ./varint
test/hts_endian
test/test_expr
test/test_kfunc
test/test_kstring
test/test_str2int
test/fieldarith test/fieldarith.sam
test/hfile
HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -g ./libhts.so
HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -l ./libhts.so
test/test_bgzf test/bgziptest.txt
test/test-parse-reg -t test/colons.bam
Expected error: [E::hts_parse_region] Range is ambiguous. Use {chr1:100-200} or {chr1}:100-200 instead
Expected error: [E::hts_parse_region] Range is ambiguous. Use {chr1:100-200,chr3} or {chr1}:100-200,chr3 instead
Expected error: [E::hts_parse_region] Mismatching braces in "{chr1"
Expected error: [E::hts_parse_region] Unexpected string "x" after region
Expected error: [E::hts_parse_region] Unexpected string "y" after region
Expected error: [E::hts_parse_region] Unexpected string "chr3" after region
cd test/sam_filter && ./filter.sh filter.tst
Testing sam_filter...
PASS : $tv -i 'filter=qname =~ "\.1" && cigar =~ "D"' ../ce#1000.sam
PASS : $tv -i 'filter=rname=="CHROMOSOME_II"' ../ce#5b.sam
PASS : $tv -i 'filter=rname=~"CHROMOSOME_II"' ../ce#5b.sam
PASS : $tv -i 'filter=cigar=~"D"' ../ce#1000.sam
PASS : $tv -i 'filter=seq =~ "(AT){2}"' ../ce#1000.sam
PASS : $tv -i 'filter=library=="x"' ../xx#rg.sam
PASS : $tv -i 'filter=library!="x"' ../xx#rg.sam
PASS : $tv -i 'filter=pos % 23 == 11' ../ce#1000.sam |egrep -cv '^@'
PASS : $tv -i 'filter=qlen/(flag*mapq+pos)>5' ../ce#1000.sam |egrep -cv '^@'
PASS : $tv -i 'filter=[NM]>=10 || [MD]=~"A.*A.*A"' -t4 ../ce#1000.sam |egrep -cv '^@'
PASS : $tv -i 'filter=length(seq) != qlen' ../ce#5b.sam | egrep -cv '^@'
PASS : $tv -i 'filter=min(qual) >= 20' ../ce#1000.sam | egrep -cv '^@'
PASS : $tv -i 'filter=max(qual) <= 20' ../ce#1000.sam | egrep -cv '^@'
PASS : $tv -i 'filter=avg(qual) >= 20 && avg(qual) <= 30' ../ce#1000.sam | egrep -cv '^@'
Expected passes: 14
Unexpected passes: 0
Expected failures: 0
Unexpected failures: 0
cd test/tabix && ./test-tabix.sh tabix.tst
Testing tabix...
PASS : $tabix -f -p vcf vcf_file.tbi.tmp.vcf.gz
PASS : $tabix vcf_file.tbi.tmp.vcf.gz 1:3000151-3000151
PASS : $tabix vcf_file.tbi.tmp.vcf.gz 2:3199812-3199812
PASS : $tabix -f -C -p vcf vcf_file.csi.tmp.vcf.gz
PASS : $tabix vcf_file.csi.tmp.vcf.gz 1:3000151-3000151
PASS : $tabix vcf_file.csi.tmp.vcf.gz 2:3199812-3199812
PASS : $tabix -f -p vcf large_chr.tmp.vcf.gz (must exit non-zero)
PASS : $tabix -f -C -p vcf large_chr.tmp.vcf.gz
PASS : $tabix large_chr.tmp.vcf.gz chr20:1-2147483647
PASS : $tabix -f -p bed bed_file.tbi.tmp.bed.gz
PASS : $tabix bed_file.tbi.tmp.bed.gz Y:100200-100200
PASS : $tabix -f -p gff gff_file.tbi.tmp.gff.gz
PASS : $tabix gff_file.tbi.tmp.gff.gz X:2934832-2935190
PASS : $tabix --separate-regions bed_file.tbi.tmp.bed.gz X:1100-1400 Y:100000-100550 Z:100000-100005
Expected passes: 14
Unexpected passes: 0
Expected failures: 0
Unexpected failures: 0
cd test/mpileup && ./test-pileup.sh mpileup.tst
Testing (m)pileup...
PASS : $pileup mp_D.sam
PASS : $pileup -m mp_D.sam
PASS : $pileup mp_DI.sam
PASS : $pileup -m mp_DI.sam
PASS : $pileup mp_I.sam
PASS : $pileup -m mp_I.sam
PASS : $pileup mp_P.sam
PASS : $pileup -m mp_P.sam
PASS : $pileup mp_ID.sam
PASS : $pileup -m mp_ID.sam
PASS : $pileup mp_N.sam
PASS : $pileup -m mp_N.sam
PASS : $pileup mp_N2.sam
PASS : $pileup -m mp_N2.sam
PASS : $pileup c1#pad1.sam
PASS : $pileup -m c1#pad1.sam
PASS : $pileup c1#pad2.sam
PASS : $pileup -m c1#pad2.sam
PASS : $pileup c1#pad3.sam
PASS : $pileup -m c1#pad3.sam
PASS : $pileup -m small.bam
Expected passes: 21
Unexpected passes: 0
Expected failures: 0
Unexpected failures: 0
cd test/fastq && ./test-fastq.sh
Testing fastq support
PASS : $tview minimal.fq
PASS : $tview minimal.fa
PASS : $tview multiline.fq
PASS : $tview multiline.fa
PASS : $tview single.fq
PASS : $tview single.fa
PASS : $tview -i fastq_aux single.fq
PASS : $tview -i fastq_aux single.fa
PASS : $tview interleaved.fq
PASS : $tview interleaved.fa
PASS : $tview -i fastq_aux interleaved.fq
PASS : $tview -i fastq_aux interleaved.fa
PASS : $tview -i fastq_casava interleaved_casava.fq
PASS : $tview -i fastq_barcode=OX -i fastq_casava interleaved_casava.fq
PASS : $tview -i fastq_casava interleaved_casava.fa
PASS : $tview -i fastq_barcode=OX -i fastq_casava interleaved_casava.fa
PASS : $tview -i fastq_casava filter_casava.fq
PASS : $tview -i fastq_casava filter_casava.fa
PASS : $tview -i fastq_aux r1.fq
PASS : $tview -i fastq_aux r2.fq
PASS : $tview -i fastq_aux r1.fa
PASS : $tview -i fastq_aux r2.fa
PASS : $tview -i fastq_name2 name2.fq
PASS : $tview -i fastq_name2 name2.fa
PASS : $tview -f minimal.sam
PASS : $tview -F minimal.sam
PASS : $tview -f -o fastq_aux single_aux.sam
PASS : $tview -F -o fastq_aux single_aux.sam
PASS : $tview -f -o fastq_aux -o fastq_rnum inter_aux.sam
PASS : $tview -F -o fastq_aux -o fastq_rnum inter_aux.sam
PASS : $tview -f -o fastq_casava inter_casava.sam
PASS : $tview -f -o fastq_barcode=OX -o fastq_casava inter_casavaOX.sam
PASS : $tview -F -o fastq_casava inter_casava.sam
PASS : $tview -F -o fastq_barcode=OX -o fastq_casava inter_casavaOX.sam
PASS : $tview -f -o fastq_casava filter_casava.sam
PASS : $tview -F -o fastq_casava filter_casava.sam
PASS : $tview -f -o fastq_aux -o fastq_rnum r1.sam
PASS : $tview -f -o fastq_aux -o fastq_rnum r2.sam
PASS : $tview -F -o fastq_aux -o fastq_rnum r1.sam
PASS : $tview -F -o fastq_aux -o fastq_rnum r2.sam
Expected passes: 40
Unexpected passes: 0
Expected failures: 0
Unexpected failures: 0
cd test/base_mods && ./base-mods.sh base-mods.tst
Testing base-modifications...
PASS : $test_mod MM-chebi.sam
PASS : $test_mod MM-double.sam
PASS : $test_mod MM-multi.sam
PASS : $pileup_mod < MM-pileup.sam
PASS : $pileup_mod < MM-pileup2.sam
Expected passes: 5
Unexpected passes: 0
Expected failures: 0
Unexpected failures: 0
REF_PATH=: test/sam test/ce.fa test/faidx.fa test/fastqs.fq
(Expect trailing 'x' message for " -1,001x")
[W::hts_parse_decimal] Ignoring unknown characters after -1,001[x]
(Expect trailing 'k' message for "1.5e+3k")
[W::hts_parse_decimal] Ignoring unknown characters after 1.5e+3[k]
(Expect dropped fraction message for "12.3456k")
[W::hts_parse_decimal] Discarding fractional part of 12.3456k
[W::hts_parse_decimal] Discarding fractional part of 12.3456k
(Expect invalid numeric message for "A")
[W::hts_parse_decimal] Invalid numeric value A[truncated]
(Expect invalid numeric message for "G")
[W::hts_parse_decimal] Invalid numeric value G[truncated]
(Expect invalid numeric message for " +/-")
[W::hts_parse_decimal] Invalid numeric value +/-[truncated]
(Expect invalid numeric message for " -.e+9999")
[W::hts_parse_decimal] Invalid numeric value -.e+9999[truncated]
test/test-regidx
cd test && REF_PATH=: ./test.pl ${TEST_OPTS:-}
"my" variable @p masks earlier declaration in same scope at ./test.pl line 617.
bgzip round-trip no threads: .. ok
bgzip -b no threads: .. ok
bgzip -b -I no threads: .. ok
bgzip round-trip 4 threads: .. ok
bgzip -b 4 threads: .. ok
bgzip -b -I 4 threads: .. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -b -m 14 -x /tmp/2QdanlUByc/index.bam.csi /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/2QdanlUByc/index.bam
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/2QdanlUByc/index.bam
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -b -m 0 -x /tmp/2QdanlUByc/index.bam.bai /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/2QdanlUByc/index.bam
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1/test/test_index -b /tmp/2QdanlUByc/index.bam
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -z -m 14 -x /tmp/2QdanlUByc/index.sam.gz.csi /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/2QdanlUByc/index.sam.gz
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/2QdanlUByc/index.sam.gz
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -z -m 0 -x /tmp/2QdanlUByc/index.sam.gz.bai /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/2QdanlUByc/index.sam.gz
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1/test/test_index -b /tmp/2QdanlUByc/index.sam.gz
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -z -m 14 -x /tmp/2QdanlUByc/index.sam.gz.csi /builddir/build/BUILD/htslib-1.15.1/test/index_dos.sam > /tmp/2QdanlUByc/index.sam.gz
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/2QdanlUByc/index.sam.gz
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -z -m 0 -x /tmp/2QdanlUByc/index.sam.gz.bai /builddir/build/BUILD/htslib-1.15.1/test/index_dos.sam > /tmp/2QdanlUByc/index.sam.gz
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1/test/test_index -b /tmp/2QdanlUByc/index.sam.gz
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -C -x /tmp/2QdanlUByc/index.cram.crai /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/2QdanlUByc/index.cram
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1/test/test_index /tmp/2QdanlUByc/index.cram
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -b -m 14 -x /tmp/2QdanlUByc/index.bcf.csi /builddir/build/BUILD/htslib-1.15.1/test/index.vcf > /tmp/2QdanlUByc/index.bcf
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/2QdanlUByc/index.bcf
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -z -m 14 -x /tmp/2QdanlUByc/index.vcf.gz.csi /builddir/build/BUILD/htslib-1.15.1/test/index.vcf > /tmp/2QdanlUByc/index.vcf.gz
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/2QdanlUByc/index.vcf.gz
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -z -m 0 -x /tmp/2QdanlUByc/index.vcf.gz.tbi /builddir/build/BUILD/htslib-1.15.1/test/index.vcf > /tmp/2QdanlUByc/index.vcf.gz
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1/test/test_index -t /tmp/2QdanlUByc/index.vcf.gz
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1/tabix /tmp/2QdanlUByc/index.vcf.gz##idx##/tmp/2QdanlUByc/index.vcf.gz.tbi 1:10000060-10000060
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1/test/test_view /tmp/2QdanlUByc/index2.bam 1:1000000-1000000
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1/test/test_view /tmp/2QdanlUByc/index2.bam 1:2000000-2000000
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1/test/test_view /tmp/2QdanlUByc/index2.bam 2:1000000-1000000
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1/test/test_view /tmp/2QdanlUByc/index2.bam 2:2000000-2000000
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -b -m 14 -x /tmp/2QdanlUByc/index.bam.csi /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/2QdanlUByc/index.bam
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/2QdanlUByc/index.bam
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -b -m 0 -x /tmp/2QdanlUByc/index.bam.bai /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/2QdanlUByc/index.bam
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1/test/test_index -b /tmp/2QdanlUByc/index.bam
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -z -m 14 -x /tmp/2QdanlUByc/index.sam.gz.csi /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/2QdanlUByc/index.sam.gz
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/2QdanlUByc/index.sam.gz
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -z -m 0 -x /tmp/2QdanlUByc/index.sam.gz.bai /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/2QdanlUByc/index.sam.gz
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1/test/test_index -b /tmp/2QdanlUByc/index.sam.gz
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -z -m 14 -x /tmp/2QdanlUByc/index.sam.gz.csi /builddir/build/BUILD/htslib-1.15.1/test/index_dos.sam > /tmp/2QdanlUByc/index.sam.gz
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/2QdanlUByc/index.sam.gz
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -z -m 0 -x /tmp/2QdanlUByc/index.sam.gz.bai /builddir/build/BUILD/htslib-1.15.1/test/index_dos.sam > /tmp/2QdanlUByc/index.sam.gz
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1/test/test_index -b /tmp/2QdanlUByc/index.sam.gz
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -C -x /tmp/2QdanlUByc/index.cram.crai /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/2QdanlUByc/index.cram
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1/test/test_index /tmp/2QdanlUByc/index.cram
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -b -m 14 -x /tmp/2QdanlUByc/index.bcf.csi /builddir/build/BUILD/htslib-1.15.1/test/index.vcf > /tmp/2QdanlUByc/index.bcf
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/2QdanlUByc/index.bcf
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -z -m 14 -x /tmp/2QdanlUByc/index.vcf.gz.csi /builddir/build/BUILD/htslib-1.15.1/test/index.vcf > /tmp/2QdanlUByc/index.vcf.gz
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/2QdanlUByc/index.vcf.gz
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -z -m 0 -x /tmp/2QdanlUByc/index.vcf.gz.tbi /builddir/build/BUILD/htslib-1.15.1/test/index.vcf > /tmp/2QdanlUByc/index.vcf.gz
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1/test/test_index -t /tmp/2QdanlUByc/index.vcf.gz
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1/tabix /tmp/2QdanlUByc/index.vcf.gz##idx##/tmp/2QdanlUByc/index.vcf.gz.tbi 1:10000060-10000060
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1/test/test_view /tmp/2QdanlUByc/index2.bam 1:1000000-1000000
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1/test/test_view /tmp/2QdanlUByc/index2.bam 1:2000000-2000000
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1/test/test_view /tmp/2QdanlUByc/index2.bam 2:1000000-1000000
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1/test/test_view /tmp/2QdanlUByc/index2.bam 2:2000000-2000000
.. ok
test_view testing multi-ref CRAM modes:
./test_view -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=-1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram
./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_
./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_
./test_view -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=0 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram
./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_
./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_
./test_view -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram
./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_
./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_
.. ok
test_view testing multi-ref CRAM modes:
./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=-1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram
./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_
./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_
./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=0 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram
./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_
./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_
./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram
./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_
./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_
.. ok
test_view testing auxf#values.sam, ref auxf.fa:
./test_view -S -l0 -b auxf#values.sam > auxf#values.tmp.bam
./test_view auxf#values.tmp.bam > auxf#values.tmp.bam.sam_
./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_
./test_view -t auxf.fa -S -C -o VERSION=2.1 auxf#values.sam > auxf#values.tmp.cram
./test_view -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_
./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_
./test_view -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram
./test_view auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_
./test_view -i reference=auxf.fa auxf#values_java.cram > auxf#values_java.tmp.sam_
./compare_sam.pl -Baux -nomd auxf#values.sam auxf#values_java.tmp.sam_
.. ok
test_view testing c1#bounds.sam, ref c1.fa:
./test_view -S -l0 -b c1#bounds.sam > c1#bounds.tmp.bam
./test_view c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_
./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_
./test_view -t c1.fa -S -C -o VERSION=2.1 c1#bounds.sam > c1#bounds.tmp.cram
./test_view -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_
./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_
./test_view -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram
./test_view c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_
.. ok
test_view testing c1#clip.sam, ref c1.fa:
./test_view -S -l0 -b c1#clip.sam > c1#clip.tmp.bam
./test_view c1#clip.tmp.bam > c1#clip.tmp.bam.sam_
./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_
./test_view -t c1.fa -S -C -o VERSION=2.1 c1#clip.sam > c1#clip.tmp.cram
./test_view -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_
./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_
./test_view -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.bam > c1#clip.tmp.bam.cram
./test_view c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_
.. ok
test_view testing c1#noseq.sam, ref c1.fa:
./test_view -S -l0 -b c1#noseq.sam > c1#noseq.tmp.bam
./test_view c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_
./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_
./test_view -t c1.fa -S -C -o VERSION=2.1 c1#noseq.sam > c1#noseq.tmp.cram
./test_view -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_
./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_
./test_view -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram
./test_view c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_
.. ok
test_view testing c1#pad1.sam, ref c1.fa:
./test_view -S -l0 -b c1#pad1.sam > c1#pad1.tmp.bam
./test_view c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_
./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_
./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad1.sam > c1#pad1.tmp.cram
./test_view -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_
./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_
./test_view -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram
./test_view c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_
.. ok
test_view testing c1#pad2.sam, ref c1.fa:
./test_view -S -l0 -b c1#pad2.sam > c1#pad2.tmp.bam
./test_view c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_
./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_
./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad2.sam > c1#pad2.tmp.cram
./test_view -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_
./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_
./test_view -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram
./test_view c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_
.. ok
test_view testing c1#pad3.sam, ref c1.fa:
./test_view -S -l0 -b c1#pad3.sam > c1#pad3.tmp.bam
./test_view c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_
./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_
./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad3.sam > c1#pad3.tmp.cram
./test_view -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_
./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_
./test_view -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram
./test_view c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_
.. ok
test_view testing c1#unknown.sam, ref c1.fa:
./test_view -S -l0 -b c1#unknown.sam > c1#unknown.tmp.bam
./test_view c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_
./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_
./test_view -t c1.fa -S -C -o VERSION=2.1 c1#unknown.sam > c1#unknown.tmp.cram
./test_view -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_
./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_
./test_view -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram
./test_view c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_
.. ok
test_view testing c2#pad.sam, ref c2.fa:
./test_view -S -l0 -b c2#pad.sam > c2#pad.tmp.bam
./test_view c2#pad.tmp.bam > c2#pad.tmp.bam.sam_
./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_
./test_view -t c2.fa -S -C -o VERSION=2.1 c2#pad.sam > c2#pad.tmp.cram
./test_view -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_
./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_
./test_view -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.bam > c2#pad.tmp.bam.cram
./test_view c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_
.. ok
test_view testing ce#1.sam, ref ce.fa:
./test_view -S -l0 -b ce#1.sam > ce#1.tmp.bam
./test_view ce#1.tmp.bam > ce#1.tmp.bam.sam_
./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_
./test_view -t ce.fa -S -C -o VERSION=2.1 ce#1.sam > ce#1.tmp.cram
./test_view -D ce#1.tmp.cram > ce#1.tmp.cram.sam_
./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_
./test_view -t ce.fa -C -o VERSION=3.0 ce#1.tmp.bam > ce#1.tmp.bam.cram
./test_view ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_
.. ok
test_view testing ce#1000.sam, ref ce.fa:
./test_view -S -b ce#1000.sam > ce#1000.tmp.bam
./test_view ce#1000.tmp.bam > ce#1000.tmp.bam.sam_
./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_
./test_view -S -l0 -b ce#1000.sam > ce#1000.tmp.bam
./test_view ce#1000.tmp.bam > ce#1000.tmp.bam.sam_
./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_
./test_view -t ce.fa -S -C -o VERSION=2.1 ce#1000.sam > ce#1000.tmp.cram
./test_view -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_
./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_
./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1000.sam > ce#1000.tmp.cram
./test_view -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_
./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_
./test_view -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.bam > ce#1000.tmp.bam.cram
./test_view ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_
.. ok
test_view testing ce#2.sam, ref ce.fa:
./test_view -S -l0 -b ce#2.sam > ce#2.tmp.bam
./test_view ce#2.tmp.bam > ce#2.tmp.bam.sam_
./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_
./test_view -t ce.fa -S -C -o VERSION=2.1 ce#2.sam > ce#2.tmp.cram
./test_view -D ce#2.tmp.cram > ce#2.tmp.cram.sam_
./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_
./test_view -t ce.fa -C -o VERSION=3.0 ce#2.tmp.bam > ce#2.tmp.bam.cram
./test_view ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_
.. ok
test_view testing ce#5.sam, ref ce.fa:
./test_view -S -l0 -b ce#5.sam > ce#5.tmp.bam
./test_view ce#5.tmp.bam > ce#5.tmp.bam.sam_
./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_
./test_view -t ce.fa -S -C -o VERSION=2.1 ce#5.sam > ce#5.tmp.cram
./test_view -D ce#5.tmp.cram > ce#5.tmp.cram.sam_
./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_
./test_view -t ce.fa -C -o VERSION=3.0 ce#5.tmp.bam > ce#5.tmp.bam.cram
./test_view ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_
.. ok
test_view testing ce#5b.sam, ref ce.fa:
./test_view -S -l0 -b ce#5b.sam > ce#5b.tmp.bam
./test_view ce#5b.tmp.bam > ce#5b.tmp.bam.sam_
./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_
./test_view -t ce.fa -S -C -o VERSION=2.1 ce#5b.sam > ce#5b.tmp.cram
./test_view -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_
./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_
./test_view -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.bam > ce#5b.tmp.bam.cram
./test_view ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_
./test_view -i reference=ce.fa ce#5b_java.cram > ce#5b_java.tmp.sam_
./compare_sam.pl -Baux -nomd ce#5b.sam ce#5b_java.tmp.sam_
.. ok
test_view testing ce#large_seq.sam, ref ce.fa:
./test_view -S -l0 -b ce#large_seq.sam > ce#large_seq.tmp.bam
./test_view ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_
./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_
./test_view -t ce.fa -S -C -o VERSION=2.1 ce#large_seq.sam > ce#large_seq.tmp.cram
./test_view -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_
./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_
./test_view -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram
./test_view ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_
.. ok
test_view testing ce#supp.sam, ref ce.fa:
./test_view -S -l0 -b ce#supp.sam > ce#supp.tmp.bam
./test_view ce#supp.tmp.bam > ce#supp.tmp.bam.sam_
./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_
./test_view -t ce.fa -S -C -o VERSION=2.1 ce#supp.sam > ce#supp.tmp.cram
./test_view -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_
./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_
./test_view -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.bam > ce#supp.tmp.bam.cram
./test_view ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_
.. ok
test_view testing ce#tag_depadded.sam, ref ce.fa:
./test_view -S -l0 -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam
./test_view ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_
./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_
./test_view -t ce.fa -S -C -o VERSION=2.1 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram
./test_view -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_
./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_
./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram
./test_view ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_
.. ok
test_view testing ce#tag_padded.sam, ref ce.fa:
./test_view -S -l0 -b ce#tag_padded.sam > ce#tag_padded.tmp.bam
./test_view ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_
./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_
./test_view -t ce.fa -S -C -o VERSION=2.1 ce#tag_padded.sam > ce#tag_padded.tmp.cram
./test_view -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_
./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_
./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram
./test_view ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_
.. ok
test_view testing ce#unmap.sam, ref ce.fa:
./test_view -S -l0 -b ce#unmap.sam > ce#unmap.tmp.bam
./test_view ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_
./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_
./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap.sam > ce#unmap.tmp.cram
./test_view -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_
./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_
./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram
./test_view ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_
.. ok
test_view testing ce#unmap1.sam, ref ce.fa:
./test_view -S -l0 -b ce#unmap1.sam > ce#unmap1.tmp.bam
./test_view ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_
./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_
./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap1.sam > ce#unmap1.tmp.cram
./test_view -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_
./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_
./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram
./test_view ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_
.. ok
test_view testing ce#unmap2.sam, ref ce.fa:
./test_view -S -l0 -b ce#unmap2.sam > ce#unmap2.tmp.bam
./test_view ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_
./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_
./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap2.sam > ce#unmap2.tmp.cram
./test_view -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_
./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_
./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram
./test_view ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_
.. ok
test_view testing md#1.sam, ref md.fa:
./test_view -S -l0 -b md#1.sam > md#1.tmp.bam
./test_view md#1.tmp.bam > md#1.tmp.bam.sam_
./compare_sam.pl md#1.sam md#1.tmp.bam.sam_
./test_view -t md.fa -S -C -o VERSION=2.1 md#1.sam > md#1.tmp.cram
./test_view -D md#1.tmp.cram > md#1.tmp.cram.sam_
./compare_sam.pl md#1.sam md#1.tmp.cram.sam_
./test_view -t md.fa -C -o VERSION=3.0 md#1.tmp.bam > md#1.tmp.bam.cram
./test_view md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam.sam_
./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_
.. ok
test_view testing xx#blank.sam, ref xx.fa:
./test_view -S -l0 -b xx#blank.sam > xx#blank.tmp.bam
./test_view xx#blank.tmp.bam > xx#blank.tmp.bam.sam_
./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_
./test_view -t xx.fa -S -C -o VERSION=2.1 xx#blank.sam > xx#blank.tmp.cram
./test_view -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_
./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_
./test_view -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.bam > xx#blank.tmp.bam.cram
./test_view xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_
.. ok
test_view testing xx#large_aux.sam, ref xx.fa:
./test_view -S -l0 -b xx#large_aux.sam > xx#large_aux.tmp.bam
./test_view xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_
./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_
./test_view -t xx.fa -S -C -o VERSION=2.1 xx#large_aux.sam > xx#large_aux.tmp.cram
./test_view -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_
./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_
./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram
./test_view xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_
./test_view -i reference=xx.fa xx#large_aux_java.cram > xx#large_aux_java.tmp.sam_
[W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 30 vs 20
./compare_sam.pl -Baux -nomd xx#large_aux.sam xx#large_aux_java.tmp.sam_
.. ok
test_view testing xx#large_aux2.sam, ref xx.fa:
./test_view -S -l0 -b xx#large_aux2.sam > xx#large_aux2.tmp.bam
./test_view xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_
./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_
./test_view -t xx.fa -S -C -o VERSION=2.1 xx#large_aux2.sam > xx#large_aux2.tmp.cram
./test_view -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_
./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_
./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram
./test_view xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_
.. ok
test_view testing xx#MD.sam, ref xx.fa:
./test_view -S -l0 -b xx#MD.sam > xx#MD.tmp.bam
./test_view xx#MD.tmp.bam > xx#MD.tmp.bam.sam_
./compare_sam.pl xx#MD.sam xx#MD.tmp.bam.sam_
./test_view -t xx.fa -S -C -o VERSION=2.1 xx#MD.sam > xx#MD.tmp.cram
./test_view -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
./test_view -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.bam > xx#MD.tmp.bam.cram
./test_view xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_
.. ok
test_view testing xx#MD2.sam, ref xx.fa:
./test_view -S -l0 -b xx#MD2.sam > xx#MD2.tmp.bam
./test_view xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_
./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_
./test_view -t xx.fa -S -C -o VERSION=2.1 xx#MD2.sam > xx#MD2.tmp.cram
./test_view -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram
./test_view xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_
.. ok
test_view testing xx#minimal.sam, ref xx.fa:
./test_view -S -l0 -b xx#minimal.sam > xx#minimal.tmp.bam
./test_view xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_
./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_
./test_view -t xx.fa -S -C -o VERSION=2.1 xx#minimal.sam > xx#minimal.tmp.cram
./test_view -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_
./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_
./test_view -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram
./test_view xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_
.. ok
test_view testing xx#pair.sam, ref xx.fa:
./test_view -S -l0 -b xx#pair.sam > xx#pair.tmp.bam
./test_view xx#pair.tmp.bam > xx#pair.tmp.bam.sam_
./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_
./test_view -t xx.fa -S -C -o VERSION=2.1 xx#pair.sam > xx#pair.tmp.cram
./test_view -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_
./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_
./test_view -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.bam > xx#pair.tmp.bam.cram
./test_view xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_
.. ok
test_view testing xx#repeated.sam, ref xx.fa:
./test_view -S -l0 -b xx#repeated.sam > xx#repeated.tmp.bam
./test_view xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_
./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_
./test_view -t xx.fa -S -C -o VERSION=2.1 xx#repeated.sam > xx#repeated.tmp.cram
./test_view -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_
./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_
./test_view -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram
./test_view xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_
.. ok
test_view testing xx#rg.sam, ref xx.fa:
./test_view -S -l0 -b xx#rg.sam > xx#rg.tmp.bam
./test_view xx#rg.tmp.bam > xx#rg.tmp.bam.sam_
./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_
./test_view -t xx.fa -S -C -o VERSION=2.1 xx#rg.sam > xx#rg.tmp.cram
./test_view -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_
./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_
./test_view -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.bam > xx#rg.tmp.bam.cram
./test_view xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_
.. ok
test_view testing xx#tlen.sam, ref xx.fa:
./test_view -S -l0 -b xx#tlen.sam > xx#tlen.tmp.bam
./test_view xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_
./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_
./test_view -t xx.fa -S -C -o VERSION=2.1 xx#tlen.sam > xx#tlen.tmp.cram
./test_view -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_
./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_
./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram
./test_view xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_
.. ok
test_view testing xx#tlen2.sam, ref xx.fa:
./test_view -S -l0 -b xx#tlen2.sam > xx#tlen2.tmp.bam
./test_view xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_
./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_
./test_view -t xx.fa -S -C -o VERSION=2.1 xx#tlen2.sam > xx#tlen2.tmp.cram
./test_view -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_
./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_
./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram
./test_view xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_
.. ok
test_view testing xx#triplet.sam, ref xx.fa:
./test_view -S -l0 -b xx#triplet.sam > xx#triplet.tmp.bam
./test_view xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_
./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_
./test_view -t xx.fa -S -C -o VERSION=2.1 xx#triplet.sam > xx#triplet.tmp.cram
./test_view -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_
./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_
./test_view -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram
./test_view xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_
.. ok
test_view testing xx#unsorted.sam, ref xx.fa:
./test_view -S -l0 -b xx#unsorted.sam > xx#unsorted.tmp.bam
./test_view xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_
./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_
./test_view -t xx.fa -S -C -o VERSION=2.1 xx#unsorted.sam > xx#unsorted.tmp.cram
./test_view -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_
./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_
./test_view -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram
./test_view xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_
.. ok
test_view testing region queries:
./test_view -i reference=ce.fa range.cram CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp
./compare_sam.pl range.tmp range.out
./test_view range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp
./compare_sam.pl range.tmp range.out
.. ok
test_view testing BAM files with absent @SQ lines:
./test_view -p no_hdr_sq_1.tmp.sam no_hdr_sq_1.bam
./compare_sam.pl no_hdr_sq_1.tmp.sam no_hdr_sq_1.expected.sam
./test_view -p no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.bam CHROMOSOME_I
./compare_sam.pl no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.expected.sam
.. ok
test_view testing large (> 2Gbases) positions:
./test_view -z -p longrefs/longref.tmp.sam.gz -x longrefs/longref.tmp.sam.gz.csi.otf -m 14 longrefs/longref.sam
./test_view -p longrefs/longref.tmp.sam_ longrefs/longref.tmp.sam.gz
./compare_sam.pl longrefs/longref.sam longrefs/longref.tmp.sam_
test_view:
/builddir/build/BUILD/htslib-1.15.1/test/test_index -c longrefs/longref.tmp.sam.gz
.. ok
./test_view -p longrefs/longref_itr.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003
./compare_sam.pl longrefs/longref_itr.expected.sam longrefs/longref_itr.tmp.sam
./test_view -M -p longrefs/longref_multi.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 CHROMOSOME_I:10000000100-10000000110
./compare_sam.pl longrefs/longref_multi.expected.sam longrefs/longref_multi.tmp.sam
.. ok
test_view testing auxf#values.sam, ref auxf.fa:
./test_view -@4 -S -l0 -b auxf#values.sam > auxf#values.tmp.bam
./test_view -@4 auxf#values.tmp.bam > auxf#values.tmp.bam.sam_
./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_
./test_view -@4 -t auxf.fa -S -C -o VERSION=2.1 auxf#values.sam > auxf#values.tmp.cram
./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_
./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_
./test_view -@4 -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram
./test_view -@4 auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_
./test_view -@4 -t auxf.fa -S -l7 -C -o VERSION=3.1 -o archive auxf#values.sam > auxf#values.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_
./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_
./test_view -@4 -t auxf.fa -S -l7 -C -o VERSION=4.0 -o archive auxf#values.sam > auxf#values.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_
./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_
./test_view -@4 -i reference=auxf.fa auxf#values_java.cram > auxf#values_java.tmp.sam_
./compare_sam.pl -Baux -nomd auxf#values.sam auxf#values_java.tmp.sam_
.. ok
test_view testing c1#bounds.sam, ref c1.fa:
./test_view -@4 -S -l0 -b c1#bounds.sam > c1#bounds.tmp.bam
./test_view -@4 c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_
./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_
./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#bounds.sam > c1#bounds.tmp.cram
./test_view -@4 -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_
./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_
./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram
./test_view -@4 c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_
.. ok
test_view testing c1#clip.sam, ref c1.fa:
./test_view -@4 -S -l0 -b c1#clip.sam > c1#clip.tmp.bam
./test_view -@4 c1#clip.tmp.bam > c1#clip.tmp.bam.sam_
./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_
./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#clip.sam > c1#clip.tmp.cram
./test_view -@4 -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_
./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_
./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.bam > c1#clip.tmp.bam.cram
./test_view -@4 c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_
.. ok
test_view testing c1#noseq.sam, ref c1.fa:
./test_view -@4 -S -l0 -b c1#noseq.sam > c1#noseq.tmp.bam
./test_view -@4 c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_
./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_
./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#noseq.sam > c1#noseq.tmp.cram
./test_view -@4 -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_
./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_
./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram
./test_view -@4 c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_
.. ok
test_view testing c1#pad1.sam, ref c1.fa:
./test_view -@4 -S -l0 -b c1#pad1.sam > c1#pad1.tmp.bam
./test_view -@4 c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_
./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_
./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad1.sam > c1#pad1.tmp.cram
./test_view -@4 -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_
./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_
./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram
./test_view -@4 c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_
.. ok
test_view testing c1#pad2.sam, ref c1.fa:
./test_view -@4 -S -l0 -b c1#pad2.sam > c1#pad2.tmp.bam
./test_view -@4 c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_
./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_
./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad2.sam > c1#pad2.tmp.cram
./test_view -@4 -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_
./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_
./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram
./test_view -@4 c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_
.. ok
test_view testing c1#pad3.sam, ref c1.fa:
./test_view -@4 -S -l0 -b c1#pad3.sam > c1#pad3.tmp.bam
./test_view -@4 c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_
./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_
./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad3.sam > c1#pad3.tmp.cram
./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_
./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_
./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram
./test_view -@4 c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_
./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=3.1 -o archive c1#pad3.sam > c1#pad3.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_
./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_
./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=4.0 -o archive c1#pad3.sam > c1#pad3.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_
./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_
.. ok
test_view testing c1#unknown.sam, ref c1.fa:
./test_view -@4 -S -l0 -b c1#unknown.sam > c1#unknown.tmp.bam
./test_view -@4 c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_
./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_
./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#unknown.sam > c1#unknown.tmp.cram
./test_view -@4 -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_
./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_
./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram
./test_view -@4 c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_
.. ok
test_view testing c2#pad.sam, ref c2.fa:
./test_view -@4 -S -l0 -b c2#pad.sam > c2#pad.tmp.bam
./test_view -@4 c2#pad.tmp.bam > c2#pad.tmp.bam.sam_
./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_
./test_view -@4 -t c2.fa -S -C -o VERSION=2.1 c2#pad.sam > c2#pad.tmp.cram
./test_view -@4 -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_
./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_
./test_view -@4 -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.bam > c2#pad.tmp.bam.cram
./test_view -@4 c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_
.. ok
test_view testing ce#1.sam, ref ce.fa:
./test_view -@4 -S -l0 -b ce#1.sam > ce#1.tmp.bam
./test_view -@4 ce#1.tmp.bam > ce#1.tmp.bam.sam_
./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_
./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1.sam > ce#1.tmp.cram
./test_view -@4 -D ce#1.tmp.cram > ce#1.tmp.cram.sam_
./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1.tmp.bam > ce#1.tmp.bam.cram
./test_view -@4 ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_
.. ok
test_view testing ce#1000.sam, ref ce.fa:
./test_view -@4 -S -b ce#1000.sam > ce#1000.tmp.bam
./test_view -@4 ce#1000.tmp.bam > ce#1000.tmp.bam.sam_
./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_
./test_view -@4 -S -l0 -b ce#1000.sam > ce#1000.tmp.bam
./test_view -@4 ce#1000.tmp.bam > ce#1000.tmp.bam.sam_
./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_
./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1000.sam > ce#1000.tmp.cram
./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_
./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_
./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1000.sam > ce#1000.tmp.cram
./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_
./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.bam > ce#1000.tmp.bam.cram
./test_view -@4 ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_
./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.ms
./test_view -@4 ce#1000.tmp.bam.cram.ms > ce#1000.tmp.bam.cram.sam_
./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.sam_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#1000.sam > ce#1000.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_
./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o normal ce#1000.sam > ce#1000.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_
./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o small ce#1000.sam > ce#1000.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_
./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#1000.sam > ce#1000.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_
./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#1000.sam > ce#1000.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_
./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_
.. ok
test_view testing ce#2.sam, ref ce.fa:
./test_view -@4 -S -l0 -b ce#2.sam > ce#2.tmp.bam
./test_view -@4 ce#2.tmp.bam > ce#2.tmp.bam.sam_
./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_
./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#2.sam > ce#2.tmp.cram
./test_view -@4 -D ce#2.tmp.cram > ce#2.tmp.cram.sam_
./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#2.tmp.bam > ce#2.tmp.bam.cram
./test_view -@4 ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_
.. ok
test_view testing ce#5.sam, ref ce.fa:
./test_view -@4 -S -l0 -b ce#5.sam > ce#5.tmp.bam
./test_view -@4 ce#5.tmp.bam > ce#5.tmp.bam.sam_
./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_
./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#5.sam > ce#5.tmp.cram
./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_
./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5.tmp.bam > ce#5.tmp.bam.cram
./test_view -@4 ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_
./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.ms
./test_view -@4 ce#5.tmp.bam.cram.ms > ce#5.tmp.bam.cram.sam_
./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.sam_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#5.sam > ce#5.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_
./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#5.sam > ce#5.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_
./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_
.. ok
test_view testing ce#5b.sam, ref ce.fa:
./test_view -@4 -S -l0 -b ce#5b.sam > ce#5b.tmp.bam
./test_view -@4 ce#5b.tmp.bam > ce#5b.tmp.bam.sam_
./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_
./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#5b.sam > ce#5b.tmp.cram
./test_view -@4 -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_
./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.bam > ce#5b.tmp.bam.cram
./test_view -@4 ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_
./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.ms
./test_view -@4 ce#5b.tmp.bam.cram.ms > ce#5b.tmp.bam.cram.sam_
./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.sam_
./test_view -@4 -i reference=ce.fa ce#5b_java.cram > ce#5b_java.tmp.sam_
./compare_sam.pl -Baux -nomd ce#5b.sam ce#5b_java.tmp.sam_
.. ok
test_view testing ce#large_seq.sam, ref ce.fa:
./test_view -@4 -S -l0 -b ce#large_seq.sam > ce#large_seq.tmp.bam
./test_view -@4 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_
./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_
./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#large_seq.sam > ce#large_seq.tmp.cram
./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_
./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram
./test_view -@4 ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#large_seq.sam > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_
./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o fast ce#large_seq.sam > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_
./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o normal ce#large_seq.sam > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_
./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o small ce#large_seq.sam > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_
./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#large_seq.sam > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_
./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_
.. ok
test_view testing ce#supp.sam, ref ce.fa:
./test_view -@4 -S -l0 -b ce#supp.sam > ce#supp.tmp.bam
./test_view -@4 ce#supp.tmp.bam > ce#supp.tmp.bam.sam_
./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_
./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#supp.sam > ce#supp.tmp.cram
./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_
./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.bam > ce#supp.tmp.bam.cram
./test_view -@4 ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#supp.sam > ce#supp.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_
./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#supp.sam > ce#supp.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_
./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_
.. ok
test_view testing ce#tag_depadded.sam, ref ce.fa:
./test_view -@4 -S -l0 -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam
./test_view -@4 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_
./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_
./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram
./test_view -@4 -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_
./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram
./test_view -@4 ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_
.. ok
test_view testing ce#tag_padded.sam, ref ce.fa:
./test_view -@4 -S -l0 -b ce#tag_padded.sam > ce#tag_padded.tmp.bam
./test_view -@4 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_
./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_
./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#tag_padded.sam > ce#tag_padded.tmp.cram
./test_view -@4 -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_
./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram
./test_view -@4 ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_
.. ok
test_view testing ce#unmap.sam, ref ce.fa:
./test_view -@4 -S -l0 -b ce#unmap.sam > ce#unmap.tmp.bam
./test_view -@4 ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_
./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_
./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap.sam > ce#unmap.tmp.cram
./test_view -@4 -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_
./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram
./test_view -@4 ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_
./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.ms
./test_view -@4 ce#unmap.tmp.bam.cram.ms > ce#unmap.tmp.bam.cram.sam_
./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.sam_
.. ok
test_view testing ce#unmap1.sam, ref ce.fa:
./test_view -@4 -S -l0 -b ce#unmap1.sam > ce#unmap1.tmp.bam
./test_view -@4 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_
./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_
./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap1.sam > ce#unmap1.tmp.cram
./test_view -@4 -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_
./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram
./test_view -@4 ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_
./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.ms
./test_view -@4 ce#unmap1.tmp.bam.cram.ms > ce#unmap1.tmp.bam.cram.sam_
./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.sam_
.. ok
test_view testing ce#unmap2.sam, ref ce.fa:
./test_view -@4 -S -l0 -b ce#unmap2.sam > ce#unmap2.tmp.bam
./test_view -@4 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_
./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_
./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap2.sam > ce#unmap2.tmp.cram
./test_view -@4 -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_
./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram
./test_view -@4 ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_
./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.ms
./test_view -@4 ce#unmap2.tmp.bam.cram.ms > ce#unmap2.tmp.bam.cram.sam_
./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.sam_
.. ok
test_view testing md#1.sam, ref md.fa:
./test_view -@4 -S -l0 -b md#1.sam > md#1.tmp.bam
./test_view -@4 md#1.tmp.bam > md#1.tmp.bam.sam_
./compare_sam.pl md#1.sam md#1.tmp.bam.sam_
./test_view -@4 -t md.fa -S -C -o VERSION=2.1 md#1.sam > md#1.tmp.cram
./test_view -@4 -D md#1.tmp.cram > md#1.tmp.cram.sam_
./compare_sam.pl md#1.sam md#1.tmp.cram.sam_
./test_view -@4 -t md.fa -C -o VERSION=3.0 md#1.tmp.bam > md#1.tmp.bam.cram
./test_view -@4 md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam.sam_
./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_
.. ok
test_view testing xx#blank.sam, ref xx.fa:
./test_view -@4 -S -l0 -b xx#blank.sam > xx#blank.tmp.bam
./test_view -@4 xx#blank.tmp.bam > xx#blank.tmp.bam.sam_
./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_
./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#blank.sam > xx#blank.tmp.cram
./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_
./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.bam > xx#blank.tmp.bam.cram
./test_view -@4 xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.ms
./test_view -@4 xx#blank.tmp.bam.cram.ms > xx#blank.tmp.bam.cram.sam_
./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#blank.sam > xx#blank.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_
./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#blank.sam > xx#blank.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_
./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_
.. ok
test_view testing xx#large_aux.sam, ref xx.fa:
./test_view -@4 -S -l0 -b xx#large_aux.sam > xx#large_aux.tmp.bam
./test_view -@4 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_
./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_
./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#large_aux.sam > xx#large_aux.tmp.cram
./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_
./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram
./test_view -@4 xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#large_aux.sam > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_
./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o fast xx#large_aux.sam > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_
./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o normal xx#large_aux.sam > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_
./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o small xx#large_aux.sam > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_
./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#large_aux.sam > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_
./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_
./test_view -@4 -i reference=xx.fa xx#large_aux_java.cram > xx#large_aux_java.tmp.sam_
[W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 30 vs 20
./compare_sam.pl -Baux -nomd xx#large_aux.sam xx#large_aux_java.tmp.sam_
.. ok
test_view testing xx#large_aux2.sam, ref xx.fa:
./test_view -@4 -S -l0 -b xx#large_aux2.sam > xx#large_aux2.tmp.bam
./test_view -@4 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_
./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_
./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#large_aux2.sam > xx#large_aux2.tmp.cram
./test_view -@4 -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_
./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram
./test_view -@4 xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_
.. ok
test_view testing xx#MD.sam, ref xx.fa:
./test_view -@4 -S -l0 -b xx#MD.sam > xx#MD.tmp.bam
./test_view -@4 xx#MD.tmp.bam > xx#MD.tmp.bam.sam_
./compare_sam.pl xx#MD.sam xx#MD.tmp.bam.sam_
./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#MD.sam > xx#MD.tmp.cram
./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.bam > xx#MD.tmp.bam.cram
./test_view -@4 xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#MD.sam > xx#MD.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#MD.sam > xx#MD.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
.. ok
test_view testing xx#MD2.sam, ref xx.fa:
./test_view -@4 -S -l0 -b xx#MD2.sam > xx#MD2.tmp.bam
./test_view -@4 xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_
./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_
./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#MD2.sam > xx#MD2.tmp.cram
./test_view -@4 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram
./test_view -@4 xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_
.. ok
test_view testing xx#minimal.sam, ref xx.fa:
./test_view -@4 -S -l0 -b xx#minimal.sam > xx#minimal.tmp.bam
./test_view -@4 xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_
./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_
./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#minimal.sam > xx#minimal.tmp.cram
./test_view -@4 -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_
./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram
./test_view -@4 xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.ms
./test_view -@4 xx#minimal.tmp.bam.cram.ms > xx#minimal.tmp.bam.cram.sam_
./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.sam_
.. ok
test_view testing xx#pair.sam, ref xx.fa:
./test_view -@4 -S -l0 -b xx#pair.sam > xx#pair.tmp.bam
./test_view -@4 xx#pair.tmp.bam > xx#pair.tmp.bam.sam_
./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_
./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#pair.sam > xx#pair.tmp.cram
./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_
./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.bam > xx#pair.tmp.bam.cram
./test_view -@4 xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#pair.sam > xx#pair.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_
./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#pair.sam > xx#pair.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_
./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_
.. ok
test_view testing xx#repeated.sam, ref xx.fa:
./test_view -@4 -S -l0 -b xx#repeated.sam > xx#repeated.tmp.bam
./test_view -@4 xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_
./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_
./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#repeated.sam > xx#repeated.tmp.cram
./test_view -@4 -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_
./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram
./test_view -@4 xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_
.. ok
test_view testing xx#rg.sam, ref xx.fa:
./test_view -@4 -S -l0 -b xx#rg.sam > xx#rg.tmp.bam
./test_view -@4 xx#rg.tmp.bam > xx#rg.tmp.bam.sam_
./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_
./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#rg.sam > xx#rg.tmp.cram
./test_view -@4 -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_
./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.bam > xx#rg.tmp.bam.cram
./test_view -@4 xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_
.. ok
test_view testing xx#tlen.sam, ref xx.fa:
./test_view -@4 -S -l0 -b xx#tlen.sam > xx#tlen.tmp.bam
./test_view -@4 xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_
./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_
./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#tlen.sam > xx#tlen.tmp.cram
./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_
./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram
./test_view -@4 xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.ms
./test_view -@4 xx#tlen.tmp.bam.cram.ms > xx#tlen.tmp.bam.cram.sam_
./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#tlen.sam > xx#tlen.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_
./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#tlen.sam > xx#tlen.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_
./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_
.. ok
test_view testing xx#tlen2.sam, ref xx.fa:
./test_view -@4 -S -l0 -b xx#tlen2.sam > xx#tlen2.tmp.bam
./test_view -@4 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_
./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_
./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#tlen2.sam > xx#tlen2.tmp.cram
./test_view -@4 -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_
./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram
./test_view -@4 xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.ms
./test_view -@4 xx#tlen2.tmp.bam.cram.ms > xx#tlen2.tmp.bam.cram.sam_
./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.sam_
.. ok
test_view testing xx#triplet.sam, ref xx.fa:
./test_view -@4 -S -l0 -b xx#triplet.sam > xx#triplet.tmp.bam
./test_view -@4 xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_
./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_
./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#triplet.sam > xx#triplet.tmp.cram
./test_view -@4 -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_
./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram
./test_view -@4 xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.ms
./test_view -@4 xx#triplet.tmp.bam.cram.ms > xx#triplet.tmp.bam.cram.sam_
./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.sam_
.. ok
test_view testing xx#unsorted.sam, ref xx.fa:
./test_view -@4 -S -l0 -b xx#unsorted.sam > xx#unsorted.tmp.bam
./test_view -@4 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_
./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_
./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#unsorted.sam > xx#unsorted.tmp.cram
./test_view -@4 -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_
./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram
./test_view -@4 xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_
.. ok
test_view testing region queries:
./test_view -@4 -i reference=ce.fa range.cram CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp
./compare_sam.pl range.tmp range.out
./test_view -@4 range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp
./compare_sam.pl range.tmp range.out
.. ok
test_view testing BAM files with absent @SQ lines:
./test_view -@4 -p no_hdr_sq_1.tmp.sam no_hdr_sq_1.bam
./compare_sam.pl no_hdr_sq_1.tmp.sam no_hdr_sq_1.expected.sam
./test_view -@4 -p no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.bam CHROMOSOME_I
./compare_sam.pl no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.expected.sam
.. ok
test_view testing large (> 2Gbases) positions:
./test_view -@4 -z -p longrefs/longref.tmp.sam.gz -x longrefs/longref.tmp.sam.gz.csi.otf -m 14 longrefs/longref.sam
./test_view -@4 -p longrefs/longref.tmp.sam_ longrefs/longref.tmp.sam.gz
./compare_sam.pl longrefs/longref.sam longrefs/longref.tmp.sam_
test_view:
/builddir/build/BUILD/htslib-1.15.1/test/test_index -c longrefs/longref.tmp.sam.gz
.. ok
./test_view -@4 -p longrefs/longref_itr.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003
./compare_sam.pl longrefs/longref_itr.expected.sam longrefs/longref_itr.tmp.sam
./test_view -@4 -M -p longrefs/longref_multi.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 CHROMOSOME_I:10000000100-10000000110
./compare_sam.pl longrefs/longref_multi.expected.sam longrefs/longref_multi.tmp.sam
.. ok
test_MD testing xx#MD.sam, ref xx.fa:
./test_view -o store_nm=1 -o store_md=1 -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram
./test_view -i decode_md=0 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl xx#MD.sam xx#MD.tmp.cram.sam_
./test_view -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram
./test_view -i decode_md=0 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -partialmd=2 xx#MD.sam xx#MD.tmp.cram.sam_
Checking for MD/NM in xx#MD.sam
./test_view -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram
./test_view -i decode_md=1 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -partialmd=1 xx#MD.sam xx#MD.tmp.cram.sam_
.. ok
test_MD testing xx#MD2.sam, ref xx.fa:
./test_view -o store_nm=1 -o store_md=1 -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram
./test_view -i decode_md=0 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram
./test_view -i decode_md=0 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -partialmd=2 xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram
./test_view -i decode_md=1 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -partialmd=1 xx#MD2.sam xx#MD2.tmp.cram.sam_
.. ok
test_vcf_api:
/builddir/build/BUILD/htslib-1.15.1/test/test-vcf-api /tmp/2QdanlUByc/test-vcf-api.bcf
[W::bcf_record_check] Bad BCF record at 1:1: No REF allele
[E::bcf_index_build3] TBI indices for BCF files are not supported
[E::idx_find_and_load] Could not retrieve index file for '/tmp/2QdanlUByc/test-vcf-api.bcf'
.. ok
test_bcf2vcf:
/builddir/build/BUILD/htslib-1.15.1/test/test_view /builddir/build/BUILD/htslib-1.15.1/test/tabix/vcf_file.bcf
.. ok
test_vcf_sweep:
/builddir/build/BUILD/htslib-1.15.1/test/test-vcf-sweep /tmp/2QdanlUByc/test-vcf-api.bcf
.. ok
test_vcf_various:
/builddir/build/BUILD/htslib-1.15.1/htsfile -ch /builddir/build/BUILD/htslib-1.15.1/test/test-vcf-hdr-in.vcf
.. ok
test_vcf_various:
/builddir/build/BUILD/htslib-1.15.1/htsfile -c /builddir/build/BUILD/htslib-1.15.1/test/formatcols.vcf
.. ok
test_vcf_various:
/builddir/build/BUILD/htslib-1.15.1/htsfile -c /builddir/build/BUILD/htslib-1.15.1/test/noroundtrip.vcf
.. ok
test_vcf_various:
/builddir/build/BUILD/htslib-1.15.1/htsfile -c /builddir/build/BUILD/htslib-1.15.1/test/formatmissing.vcf
.. ok
test_vcf_various:
/builddir/build/BUILD/htslib-1.15.1/htsfile -c /builddir/build/BUILD/htslib-1.15.1/test/vcf_meta_meta.vcf
.. ok
test-bcf-sr:
/builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/2QdanlUByc -s 1420980187
.. ok
test-bcf-sr:
/builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/2QdanlUByc -s 320815204
.. ok
test-bcf-sr:
/builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/2QdanlUByc -s 458742908
.. ok
test-bcf-sr:
/builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/2QdanlUByc -s 1626428260
.. ok
test-bcf-sr:
/builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/2QdanlUByc -s 1449092975
.. ok
test-bcf-sr:
/builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/2QdanlUByc -s 875773942
.. ok
test-bcf-sr:
/builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/2QdanlUByc -s 730838607
.. ok
test-bcf-sr:
/builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/2QdanlUByc -s 537161593
.. ok
test-bcf-sr:
/builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/2QdanlUByc -s 1128300927
.. ok
test-bcf-sr:
/builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/2QdanlUByc -s 973442679
.. ok
test_command:
/builddir/build/BUILD/htslib-1.15.1/test/test-bcf-translate -
.. ok
test_convert_padded_header:
/builddir/build/BUILD/htslib-1.15.1/test/test_view -t ce.fa -C /tmp/2QdanlUByc/headernul0.bam
.. ok
test_convert_padded_header:
/builddir/build/BUILD/htslib-1.15.1/test/test_view -t ce.fa -C /tmp/2QdanlUByc/headernul1.bam
.. ok
test_convert_padded_header:
/builddir/build/BUILD/htslib-1.15.1/test/test_view -t ce.fa -C /tmp/2QdanlUByc/headernul678.bam
.. ok
test_rebgzip:
/builddir/build/BUILD/htslib-1.15.1/bgzip -I /builddir/build/BUILD/htslib-1.15.1/test/bgziptest.txt.gz.gzi -c -g /builddir/build/BUILD/htslib-1.15.1/test/bgziptest.txt
.. ok
test-logging:
/builddir/build/BUILD/htslib-1.15.1/test/test-logging.pl
.. ok
test_plugin_loading:
HTS_PATH=/builddir/build/BUILD/htslib-1.15.1 /builddir/build/BUILD/htslib-1.15.1/test/with-shlib.sh /builddir/build/BUILD/htslib-1.15.1/htsfile https://localhost:99999/invalid_port
.. ok
test_realn:
/builddir/build/BUILD/htslib-1.15.1/test/test_realn -f /builddir/build/BUILD/htslib-1.15.1/test/realn01.fa -i /builddir/build/BUILD/htslib-1.15.1/test/realn01.sam -o -
.. ok
test_realn:
/builddir/build/BUILD/htslib-1.15.1/test/test_realn -f /builddir/build/BUILD/htslib-1.15.1/test/realn02.fa -i /builddir/build/BUILD/htslib-1.15.1/test/realn02.sam -o -
.. ok
test_realn:
/builddir/build/BUILD/htslib-1.15.1/test/test_realn -a -f /builddir/build/BUILD/htslib-1.15.1/test/realn01.fa -i /builddir/build/BUILD/htslib-1.15.1/test/realn01.sam -o -
.. ok
test_realn:
/builddir/build/BUILD/htslib-1.15.1/test/test_realn -a -f /builddir/build/BUILD/htslib-1.15.1/test/realn02.fa -i /builddir/build/BUILD/htslib-1.15.1/test/realn02.sam -o -
.. ok
test_realn:
/builddir/build/BUILD/htslib-1.15.1/test/test_realn -e -f /builddir/build/BUILD/htslib-1.15.1/test/realn01.fa -i /builddir/build/BUILD/htslib-1.15.1/test/realn01.sam -o -
.. ok
test_realn:
/builddir/build/BUILD/htslib-1.15.1/test/test_realn -e -f /builddir/build/BUILD/htslib-1.15.1/test/realn02.fa -i /builddir/build/BUILD/htslib-1.15.1/test/realn02.sam -o -
.. ok
test_realn:
/builddir/build/BUILD/htslib-1.15.1/test/test_realn -r -f /builddir/build/BUILD/htslib-1.15.1/test/realn02.fa -i /builddir/build/BUILD/htslib-1.15.1/test/realn02-r.sam -o -
.. ok
test_realn:
/builddir/build/BUILD/htslib-1.15.1/test/test_realn -a -f /builddir/build/BUILD/htslib-1.15.1/test/realn02.fa -i /builddir/build/BUILD/htslib-1.15.1/test/realn02_exp.sam -o -
.. ok
test_realn:
/builddir/build/BUILD/htslib-1.15.1/test/test_realn -f /builddir/build/BUILD/htslib-1.15.1/test/realn02.fa -i /builddir/build/BUILD/htslib-1.15.1/test/realn02_exp-a.sam -o -
.. ok
Number of tests:
total .. 172
passed .. 172
failed .. 0
+ RPM_EC=0
++ jobs -p
+ exit 0
Processing files: htslib-1.15.1-1.fc38.s390x
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.rzw0LP
+ umask 022
+ cd /builddir/build/BUILD
+ cd htslib-1.15.1
+ DOCDIR=/builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/share/doc/htslib
+ export LC_ALL=C
+ LC_ALL=C
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/share/doc/htslib
+ cp -pr NEWS /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/share/doc/htslib
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.16Mb0i
+ umask 022
+ cd /builddir/build/BUILD
+ cd htslib-1.15.1
+ LICENSEDIR=/builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/share/licenses/htslib
+ export LC_ALL=C
+ LC_ALL=C
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/share/licenses/htslib
+ cp -pr LICENSE /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x/usr/share/licenses/htslib
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: htslib = 1.15.1-1.fc38 htslib(s390-64) = 1.15.1-1.fc38 libhts.so.3()(64bit)
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: libbz2.so.1()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.2)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.2)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.7)(64bit) libcrypto.so.3()(64bit) libcrypto.so.3(OPENSSL_3.0.0)(64bit) libcurl.so.4()(64bit) libhts.so.3()(64bit) liblzma.so.5()(64bit) liblzma.so.5(XZ_5.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2)(64bit) libm.so.6(GLIBC_2.23)(64bit) libm.so.6(GLIBC_2.29)(64bit) libz.so.1()(64bit) rtld(GNU_HASH)
Processing files: htslib-devel-1.15.1-1.fc38.s390x
Provides: htslib-devel = 1.15.1-1.fc38 htslib-devel(s390-64) = 1.15.1-1.fc38 pkgconfig(htslib) = 1.15.1
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: /usr/bin/pkg-config libhts.so.3()(64bit)
Processing files: htslib-tools-1.15.1-1.fc38.s390x
Provides: htslib-tools = 1.15.1-1.fc38 htslib-tools(s390-64) = 1.15.1-1.fc38
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: libbz2.so.1()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.2)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.2)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.7)(64bit) liblzma.so.5()(64bit) liblzma.so.5(XZ_5.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.29)(64bit) libz.so.1()(64bit) rtld(GNU_HASH)
Processing files: htslib-debugsource-1.15.1-1.fc38.s390x
Provides: htslib-debugsource = 1.15.1-1.fc38 htslib-debugsource(s390-64) = 1.15.1-1.fc38
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: htslib-debuginfo-1.15.1-1.fc38.s390x
Provides: debuginfo(build-id) = 86e1cad18638eabbaf6147f3130c4b919d8a2658 debuginfo(build-id) = 8f9e64718f387d5f290b91fa61abda861ae9741f debuginfo(build-id) = 962a4d6e90b26743c8845984b9c5f0c6371976d3 debuginfo(build-id) = c3ed2da1748f8c7532be8066306a26e5bf530df8 debuginfo(build-id) = f679b7efa696b33d6f3386e387f66b75ae3321ee htslib-debuginfo = 1.15.1-1.fc38 htslib-debuginfo(s390-64) = 1.15.1-1.fc38 libhts.so.1.15.1-1.15.1-1.fc38.s390x.debug()(64bit)
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: htslib-debugsource(s390-64) = 1.15.1-1.fc38
Processing files: htslib-tools-debuginfo-1.15.1-1.fc38.s390x
Provides: debuginfo(build-id) = b72b5dba3f9adfe70fd998bba77b9a04d1ffb99d debuginfo(build-id) = ca569f4491501f64040812f05b187d6f2d4d7486 debuginfo(build-id) = d06e7812f25ee0aabfb7003278c67f7e6c1557df htslib-tools-debuginfo = 1.15.1-1.fc38 htslib-tools-debuginfo(s390-64) = 1.15.1-1.fc38
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: htslib-debugsource(s390-64) = 1.15.1-1.fc38
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x
Wrote: /builddir/build/RPMS/htslib-debuginfo-1.15.1-1.fc38.s390x.rpm
Wrote: /builddir/build/RPMS/htslib-tools-1.15.1-1.fc38.s390x.rpm
Wrote: /builddir/build/RPMS/htslib-tools-debuginfo-1.15.1-1.fc38.s390x.rpm
Wrote: /builddir/build/RPMS/htslib-1.15.1-1.fc38.s390x.rpm
Wrote: /builddir/build/RPMS/htslib-devel-1.15.1-1.fc38.s390x.rpm
Wrote: /builddir/build/RPMS/htslib-debugsource-1.15.1-1.fc38.s390x.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.mbTYmE
+ umask 022
+ cd /builddir/build/BUILD
+ cd htslib-1.15.1
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.s390x
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.WwF8yq
+ umask 022
+ cd /builddir/build/BUILD
+ rm -rf htslib-1.15.1 htslib-1.15.1.gemspec
+ RPM_EC=0
++ jobs -p
+ exit 0
Finish: rpmbuild htslib-1.15.1-1.fc38.src.rpm
Finish: build phase for htslib-1.15.1-1.fc38.src.rpm
INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/fedora-rawhide-s390x-1671942858.428762/root/var/log/dnf.rpm.log
/var/lib/mock/fedora-rawhide-s390x-1671942858.428762/root/var/log/dnf.librepo.log
/var/lib/mock/fedora-rawhide-s390x-1671942858.428762/root/var/log/dnf.log
INFO: Done(/var/lib/copr-rpmbuild/results/htslib-1.15.1-1.fc38.src.rpm) Config(child) 6 minutes 39 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