Warning: Permanently added '162.133.129.242' (ED25519) to the list of known hosts.
You can reproduce this build on your computer by running:
sudo dnf install copr-rpmbuild
/usr/bin/copr-rpmbuild --verbose --drop-resultdir --task-url https://copr.fedorainfracloud.org/backend/get-build-task/6407839-fedora-rawhide-s390x --chroot fedora-rawhide-s390x
Version: 0.69
PID: 32826
Logging PID: 32827
Task:
{'appstream': False,
'background': True,
'build_id': 6407839,
'buildroot_pkgs': [],
'chroot': 'fedora-rawhide-s390x',
'enable_net': False,
'fedora_review': False,
'git_hash': 'df6b1de2eecf9ffcb551247d0ec58aa16cf5b345',
'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/tuliom/zlib-ng-compat-mpb/python-pysam',
'isolation': 'default',
'memory_reqs': 2048,
'package_name': 'python-pysam',
'package_version': '0.21.0-2',
'project_dirname': 'zlib-ng-compat-mpb',
'project_name': 'zlib-ng-compat-mpb',
'project_owner': 'tuliom',
'repo_priority': None,
'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/tuliom/zlib-ng-compat-mpb/fedora-rawhide-s390x/',
'id': 'copr_base',
'name': 'Copr repository',
'priority': None}],
'sandbox': 'tuliom/zlib-ng-compat-mpb--tuliom',
'source_json': {},
'source_type': None,
'submitter': 'tuliom',
'tags': [],
'task_id': '6407839-fedora-rawhide-s390x',
'timeout': 115200,
'uses_devel_repo': False,
'with_opts': [],
'without_opts': []}
Running: git clone https://copr-dist-git.fedorainfracloud.org/git/tuliom/zlib-ng-compat-mpb/python-pysam /var/lib/copr-rpmbuild/workspace/workdir-8x23x416/python-pysam --depth 500 --no-single-branch --recursive
cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/tuliom/zlib-ng-compat-mpb/python-pysam', '/var/lib/copr-rpmbuild/workspace/workdir-8x23x416/python-pysam', '--depth', '500', '--no-single-branch', '--recursive']
cwd: .
rc: 0
stdout:
stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-8x23x416/python-pysam'...
Running: git checkout df6b1de2eecf9ffcb551247d0ec58aa16cf5b345 --
cmd: ['git', 'checkout', 'df6b1de2eecf9ffcb551247d0ec58aa16cf5b345', '--']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-8x23x416/python-pysam
rc: 0
stdout:
stderr: Note: switching to 'df6b1de2eecf9ffcb551247d0ec58aa16cf5b345'.
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 df6b1de automatic import of python-pysam
Running: copr-distgit-client sources
/usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated
cmd: ['copr-distgit-client', 'sources']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-8x23x416/python-pysam
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 pysam-0.21.0.tar.gz
INFO: Reading stdout from command: curl --help all
INFO: Calling: curl -H Pragma: -o pysam-0.21.0.tar.gz --location --connect-timeout 60 --retry 3 --retry-delay 10 --remote-time --show-error --fail --retry-all-errors https://copr-dist-git.fedorainfracloud.org/repo/pkgs/tuliom/zlib-ng-compat-mpb/python-pysam/pysam-0.21.0.tar.gz/md5/dca7fb36d2cf69ef887fe05ddd726998/pysam-0.21.0.tar.gz
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 3957k 100 3957k 0 0 2084k 0 0:00:01 0:00:01 --:--:-- 2084k
INFO: Reading stdout from command: md5sum pysam-0.21.0.tar.gz
Running (timeout=115200): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-8x23x416/python-pysam/python-pysam.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-8x23x416/python-pysam --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1694975550.734558 -r /var/lib/copr-rpmbuild/results/configs/child.cfg
INFO: mock.py version 5.1 starting (python version = 3.11.3, NVR = mock-5.1-1.fc38)...
Start(bootstrap): init plugins
INFO: tmpfs initialized
INFO: selinux enabled
INFO: chroot_scan: initialized
INFO: compress_logs: initialized
Finish(bootstrap): init plugins
Start: init plugins
INFO: tmpfs initialized
INFO: selinux enabled
INFO: chroot_scan: initialized
INFO: compress_logs: initialized
Finish: init plugins
INFO: Signal handler active
Start: run
INFO: Start(/var/lib/copr-rpmbuild/workspace/workdir-8x23x416/python-pysam/python-pysam.spec) Config(fedora-rawhide-s390x)
Start: clean chroot
Finish: clean chroot
Mock Version: 5.1
INFO: Mock Version: 5.1
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-s390x-bootstrap-1694975550.734558/root.
INFO: calling preinit hooks
INFO: enabled root cache
INFO: enabled package manager cache
Start(bootstrap): cleaning package manager metadata
Finish(bootstrap): cleaning package manager metadata
INFO: Guessed host environment type: unknown
INFO: Using bootstrap image: registry.fedoraproject.org/fedora:rawhide
INFO: Pulling image: registry.fedoraproject.org/fedora:rawhide
INFO: Copy content of container registry.fedoraproject.org/fedora:rawhide to /var/lib/mock/fedora-rawhide-s390x-bootstrap-1694975550.734558/root
INFO: Checking that registry.fedoraproject.org/fedora:rawhide image matches host's architecture
INFO: mounting registry.fedoraproject.org/fedora:rawhide with podman image mount
INFO: image registry.fedoraproject.org/fedora:rawhide as /var/lib/containers/storage/overlay/048a30d242435471510b8c750dbc9cf86e41860183b8bd626e06a27f1e4c6a85/merged
INFO: umounting image registry.fedoraproject.org/fedora:rawhide (/var/lib/containers/storage/overlay/048a30d242435471510b8c750dbc9cf86e41860183b8bd626e06a27f1e4c6a85/merged) with podman image umount
INFO: Package manager dnf detected and used (fallback)
INFO: Bootstrap image not marked ready
Start(bootstrap): installing dnf tooling
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Copr repository 330 kB/s | 1.8 MB 00:05
fedora 6.1 MB/s | 63 MB 00:10
Last metadata expiration check: 0:00:01 ago on Sun Sep 17 18:32:51 2023.
Package python3-dnf-4.16.2-4.fc40.noarch is already installed.
Dependencies resolved.
================================================================================
Package Arch Version Repository Size
================================================================================
Installing:
python3-dnf-plugins-core noarch 4.4.2-1.fc39 fedora 293 k
Installing dependencies:
dbus-libs s390x 1:1.14.10-1.fc40 fedora 159 k
python3-dateutil noarch 1:2.8.2-10.fc39 fedora 355 k
python3-dbus s390x 1.3.2-4.fc39 fedora 157 k
python3-distro noarch 1.8.0-6.fc39 fedora 49 k
python3-six noarch 1.16.0-12.fc39 fedora 41 k
python3-systemd s390x 235-5.fc39 fedora 106 k
Transaction Summary
================================================================================
Install 7 Packages
Total download size: 1.1 M
Installed size: 3.5 M
Downloading Packages:
(1/7): dbus-libs-1.14.10-1.fc40.s390x.rpm 152 kB/s | 159 kB 00:01
(2/7): python3-dbus-1.3.2-4.fc39.s390x.rpm 145 kB/s | 157 kB 00:01
(3/7): python3-distro-1.8.0-6.fc39.noarch.rpm 222 kB/s | 49 kB 00:00
(4/7): python3-dateutil-2.8.2-10.fc39.noarch.rp 270 kB/s | 355 kB 00:01
(5/7): python3-six-1.16.0-12.fc39.noarch.rpm 193 kB/s | 41 kB 00:00
(6/7): python3-systemd-235-5.fc39.s390x.rpm 469 kB/s | 106 kB 00:00
(7/7): python3-dnf-plugins-core-4.4.2-1.fc39.no 610 kB/s | 293 kB 00:00
--------------------------------------------------------------------------------
Total 556 kB/s | 1.1 MB 00:02
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
Preparing : 1/1
Installing : python3-systemd-235-5.fc39.s390x 1/7
Installing : python3-six-1.16.0-12.fc39.noarch 2/7
Installing : python3-dateutil-1:2.8.2-10.fc39.noarch 3/7
Installing : python3-distro-1.8.0-6.fc39.noarch 4/7
Installing : dbus-libs-1:1.14.10-1.fc40.s390x 5/7
Installing : python3-dbus-1.3.2-4.fc39.s390x 6/7
Installing : python3-dnf-plugins-core-4.4.2-1.fc39.noarch 7/7
Running scriptlet: python3-dnf-plugins-core-4.4.2-1.fc39.noarch 7/7
Verifying : dbus-libs-1:1.14.10-1.fc40.s390x 1/7
Verifying : python3-dateutil-1:2.8.2-10.fc39.noarch 2/7
Verifying : python3-dbus-1.3.2-4.fc39.s390x 3/7
Verifying : python3-distro-1.8.0-6.fc39.noarch 4/7
Verifying : python3-dnf-plugins-core-4.4.2-1.fc39.noarch 5/7
Verifying : python3-six-1.16.0-12.fc39.noarch 6/7
Verifying : python3-systemd-235-5.fc39.s390x 7/7
Installed:
dbus-libs-1:1.14.10-1.fc40.s390x
python3-dateutil-1:2.8.2-10.fc39.noarch
python3-dbus-1.3.2-4.fc39.s390x
python3-distro-1.8.0-6.fc39.noarch
python3-dnf-plugins-core-4.4.2-1.fc39.noarch
python3-six-1.16.0-12.fc39.noarch
python3-systemd-235-5.fc39.s390x
Complete!
Finish(bootstrap): installing dnf tooling
Start(bootstrap): creating root cache
Finish(bootstrap): creating root cache
Finish(bootstrap): chroot init
Start: chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-s390x-1694975550.734558/root.
INFO: calling preinit hooks
INFO: enabled root cache
INFO: enabled package manager cache
Start: cleaning package manager metadata
Finish: cleaning package manager metadata
INFO: enabled HW Info plugin
INFO: Package manager dnf detected and used (direct choice)
Start: installing minimal buildroot with dnf
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Copr repository 8.2 kB/s | 1.5 kB 00:00
Copr repository 173 kB/s | 1.8 MB 00:10
fedora 10 kB/s | 5.5 kB 00:00
Dependencies resolved.
================================================================================
Package Arch Version Repo Size
================================================================================
Installing group/module packages:
bash s390x 5.2.15-5.fc39 fedora 1.8 M
bzip2 s390x 1.0.8-16.fc39 fedora 53 k
coreutils s390x 9.4-1.fc40 fedora 1.2 M
cpio s390x 2.14-4.fc39 fedora 283 k
diffutils s390x 3.10-3.fc39 fedora 407 k
fedora-release-common noarch 40-0.7 fedora 18 k
findutils s390x 1:4.9.0-6.fc40 fedora 497 k
gawk s390x 5.2.2-2.fc39 fedora 1.1 M
glibc-minimal-langpack s390x 2.38.9000-8.fc40 copr_base 73 k
grep s390x 3.11-5.fc40 fedora 305 k
gzip s390x 1.12-6.fc39 fedora 173 k
info s390x 7.0.3-3.fc39 fedora 192 k
patch s390x 2.7.6-22.fc39 fedora 134 k
redhat-rpm-config noarch 270-1.fc40 copr_base 74 k
rpm-build s390x 4.18.99-1.fc40 fedora 78 k
sed s390x 4.8-14.fc39 fedora 309 k
shadow-utils s390x 2:4.14.0-1.fc40 fedora 1.3 M
tar s390x 2:1.35-2.fc40 fedora 874 k
unzip s390x 6.0-62.fc39 fedora 194 k
util-linux s390x 2.39.2-1.fc40 fedora 1.1 M
which s390x 2.21-40.fc39 fedora 43 k
xz s390x 5.4.4-1.fc39 fedora 557 k
Installing dependencies:
alternatives s390x 1.25-1.fc39 fedora 39 k
ansible-srpm-macros noarch 1-11.fc39 fedora 21 k
audit-libs s390x 3.1.2-4.fc40 fedora 121 k
authselect s390x 1.4.2-3.fc39 fedora 144 k
authselect-libs s390x 1.4.2-3.fc39 fedora 247 k
basesystem noarch 11-18.fc39 fedora 7.2 k
binutils s390x 2.41-5.fc40 fedora 5.9 M
binutils-gold s390x 2.41-5.fc40 fedora 993 k
bzip2-libs s390x 1.0.8-16.fc39 fedora 46 k
ca-certificates noarch 2023.2.60_v7.0.306-3.fc40 fedora 837 k
coreutils-common s390x 9.4-1.fc40 fedora 2.1 M
cracklib s390x 2.9.11-2.fc40 copr_base 84 k
crypto-policies noarch 20230731-1.git5ed06e0.fc39 fedora 99 k
curl s390x 8.3.0-1.fc40 copr_base 354 k
cyrus-sasl-lib s390x 2.1.28-11.fc39 fedora 819 k
debugedit s390x 5.0-10.fc39 fedora 81 k
dwz s390x 0.15-3.fc39 fedora 144 k
ed s390x 1.19-4.fc39 fedora 80 k
efi-srpm-macros noarch 5-9.fc39 fedora 22 k
elfutils s390x 0.189-6.fc40 fedora 560 k
elfutils-debuginfod-client s390x 0.189-6.fc40 fedora 38 k
elfutils-default-yama-scope noarch 0.189-6.fc40 fedora 13 k
elfutils-libelf s390x 0.189-6.fc40 fedora 200 k
elfutils-libs s390x 0.189-6.fc40 fedora 275 k
fedora-gpg-keys noarch 40-0.1 fedora 130 k
fedora-release noarch 40-0.7 fedora 8.0 k
fedora-release-identity-basic
noarch 40-0.7 fedora 8.8 k
fedora-repos noarch 40-0.1 fedora 9.4 k
fedora-repos-rawhide noarch 40-0.1 fedora 9.0 k
file s390x 5.45-1.fc40 copr_base 50 k
file-libs s390x 5.45-1.fc40 copr_base 770 k
filesystem s390x 3.18-6.fc39 fedora 1.1 M
fonts-srpm-macros noarch 1:2.0.5-12.fc39 fedora 26 k
forge-srpm-macros noarch 0.1.0-1.fc40 fedora 18 k
fpc-srpm-macros noarch 1.3-8.fc39 fedora 7.4 k
gdb-minimal s390x 13.2-8.fc40 fedora 4.0 M
gdbm-libs s390x 1:1.23-4.fc39 fedora 58 k
ghc-srpm-macros noarch 1.6.1-2.fc39 fedora 7.8 k
glibc s390x 2.38.9000-8.fc40 copr_base 1.8 M
glibc-common s390x 2.38.9000-8.fc40 copr_base 368 k
glibc-gconv-extra s390x 2.38.9000-8.fc40 copr_base 1.6 M
gmp s390x 1:6.2.1-5.fc39 fedora 325 k
gnat-srpm-macros noarch 6-3.fc39 fedora 8.8 k
go-srpm-macros noarch 3.2.0-7.fc40 fedora 27 k
jansson s390x 2.13.1-7.fc39 fedora 44 k
kernel-srpm-macros noarch 1.0-20.fc39 fedora 10 k
keyutils-libs s390x 1.6.1-7.fc39 fedora 31 k
krb5-libs s390x 1.21.2-1.fc40 fedora 780 k
libacl s390x 2.3.1-9.fc40 fedora 24 k
libarchive s390x 3.7.2-1.fc40 fedora 440 k
libattr s390x 2.5.1-9.fc40 fedora 18 k
libblkid s390x 2.39.2-1.fc40 fedora 120 k
libbrotli s390x 1.1.0-1.fc40 fedora 379 k
libcap s390x 2.48-7.fc39 fedora 69 k
libcap-ng s390x 0.8.3-8.fc40 fedora 32 k
libcom_err s390x 1.47.0-2.fc39 fedora 26 k
libcurl s390x 8.3.0-1.fc40 copr_base 362 k
libdb s390x 5.3.28-58.fc40 copr_base 775 k
libeconf s390x 0.5.2-1.fc40 fedora 32 k
libevent s390x 2.1.12-9.fc39 fedora 260 k
libfdisk s390x 2.39.2-1.fc40 fedora 165 k
libffi s390x 3.4.4-4.fc39 fedora 36 k
libgcc s390x 13.2.1-1.fc40 copr_base 82 k
libgomp s390x 13.2.1-1.fc40 copr_base 323 k
libidn2 s390x 2.3.4-3.fc39 fedora 118 k
libmount s390x 2.39.2-1.fc40 fedora 158 k
libnghttp2 s390x 1.56.0-1.fc40 fedora 78 k
libnsl2 s390x 2.0.0-6.fc39 fedora 30 k
libpkgconf s390x 1.9.5-2.fc39 fedora 38 k
libpsl s390x 0.21.2-4.fc39 fedora 63 k
libpwquality s390x 1.4.5-6.fc39 fedora 121 k
libselinux s390x 3.5-5.fc39 fedora 91 k
libsemanage s390x 3.5-4.fc39 fedora 122 k
libsepol s390x 3.5-2.fc39 fedora 330 k
libsigsegv s390x 2.14-5.fc39 fedora 27 k
libsmartcols s390x 2.39.2-1.fc40 fedora 70 k
libssh s390x 0.10.5-2.fc39 fedora 209 k
libssh-config noarch 0.10.5-2.fc39 fedora 9.2 k
libstdc++ s390x 13.2.1-1.fc40 copr_base 949 k
libtasn1 s390x 4.19.0-3.fc39 fedora 77 k
libtirpc s390x 1.3.3-1.rc2.fc39 fedora 95 k
libunistring s390x 1.1-5.fc40 fedora 556 k
libutempter s390x 1.2.1-10.fc39 fedora 26 k
libuuid s390x 2.39.2-1.fc40 fedora 28 k
libverto s390x 0.3.2-6.fc39 fedora 21 k
libxcrypt s390x 4.4.36-2.fc39 fedora 124 k
libxml2 s390x 2.11.5-1.fc40 copr_base 711 k
libzstd s390x 1.5.5-4.fc40 copr_base 343 k
lua-libs s390x 5.4.6-3.fc39 fedora 142 k
lua-srpm-macros noarch 1-9.fc39 fedora 8.6 k
lz4-libs s390x 1.9.4-4.fc39 fedora 81 k
mpfr s390x 4.2.0-3.fc39 fedora 298 k
ncurses-base noarch 6.4-7.20230520.fc40 fedora 88 k
ncurses-libs s390x 6.4-7.20230520.fc40 fedora 361 k
ocaml-srpm-macros noarch 8-2.fc39 fedora 14 k
openblas-srpm-macros noarch 2-14.fc39 fedora 7.5 k
openldap s390x 2.6.6-1.fc39 fedora 262 k
openssl-libs s390x 1:3.1.1-4.fc40 copr_base 1.9 M
p11-kit s390x 0.25.0-2.fc39 fedora 507 k
p11-kit-trust s390x 0.25.0-2.fc39 fedora 141 k
package-notes-srpm-macros noarch 0.5-9.fc39 fedora 11 k
pam s390x 1.5.3-2.fc39 fedora 558 k
pam-libs s390x 1.5.3-2.fc39 fedora 59 k
pcre2 s390x 10.42-1.fc39.2 fedora 250 k
pcre2-syntax noarch 10.42-1.fc39.2 fedora 143 k
perl-srpm-macros noarch 1-51.fc39 fedora 8.0 k
pkgconf s390x 1.9.5-2.fc39 fedora 43 k
pkgconf-m4 noarch 1.9.5-2.fc39 fedora 14 k
pkgconf-pkg-config s390x 1.9.5-2.fc39 fedora 9.6 k
popt s390x 1.19-3.fc39 fedora 69 k
publicsuffix-list-dafsa noarch 20230812-1.fc40 fedora 57 k
pyproject-srpm-macros noarch 1.9.0-2.fc39 fedora 14 k
python-srpm-macros noarch 3.12-4.fc40 fedora 25 k
qt5-srpm-macros noarch 5.15.10-2.fc39 fedora 8.3 k
qt6-srpm-macros noarch 6.5.2-2.fc39 fedora 9.2 k
readline s390x 8.2-4.fc39 fedora 229 k
rpm s390x 4.18.99-1.fc40 fedora 538 k
rpm-build-libs s390x 4.18.99-1.fc40 fedora 97 k
rpm-libs s390x 4.18.99-1.fc40 fedora 323 k
rpm-sequoia s390x 1.5.0-1.fc40 fedora 1.0 M
rust-srpm-macros noarch 24-5.fc40 fedora 12 k
setup noarch 2.14.4-1.fc39 fedora 154 k
sqlite-libs s390x 3.43.1-1.fc40 fedora 737 k
systemd-libs s390x 254.1-2.fc40 fedora 696 k
tzdata noarch 2023c-3.fc40 fedora 718 k
util-linux-core s390x 2.39.2-1.fc40 fedora 496 k
xxhash-libs s390x 0.8.2-1.fc39 fedora 37 k
xz-libs s390x 5.4.4-1.fc39 fedora 114 k
zip s390x 3.0-38.fc39 fedora 283 k
zlib-ng-compat s390x 2.1.3-3.fc40 copr_base 71 k
zstd s390x 1.5.5-4.fc40 copr_base 506 k
Installing Groups:
Buildsystem building group
Transaction Summary
================================================================================
Install 153 Packages
Total size: 53 M
Installed size: 181 M
Downloading Packages:
[SKIPPED] cracklib-2.9.11-2.fc40.s390x.rpm: Already downloaded
[SKIPPED] curl-8.3.0-1.fc40.s390x.rpm: Already downloaded
[SKIPPED] file-5.45-1.fc40.s390x.rpm: Already downloaded
[SKIPPED] file-libs-5.45-1.fc40.s390x.rpm: Already downloaded
[SKIPPED] glibc-2.38.9000-8.fc40.s390x.rpm: Already downloaded
[SKIPPED] glibc-common-2.38.9000-8.fc40.s390x.rpm: Already downloaded
[SKIPPED] glibc-gconv-extra-2.38.9000-8.fc40.s390x.rpm: Already downloaded
[SKIPPED] glibc-minimal-langpack-2.38.9000-8.fc40.s390x.rpm: Already downloaded
[SKIPPED] libcurl-8.3.0-1.fc40.s390x.rpm: Already downloaded
[SKIPPED] libdb-5.3.28-58.fc40.s390x.rpm: Already downloaded
[SKIPPED] libgcc-13.2.1-1.fc40.s390x.rpm: Already downloaded
[SKIPPED] libgomp-13.2.1-1.fc40.s390x.rpm: Already downloaded
[SKIPPED] libstdc++-13.2.1-1.fc40.s390x.rpm: Already downloaded
[SKIPPED] libxml2-2.11.5-1.fc40.s390x.rpm: Already downloaded
[SKIPPED] libzstd-1.5.5-4.fc40.s390x.rpm: Already downloaded
[SKIPPED] openssl-libs-3.1.1-4.fc40.s390x.rpm: Already downloaded
[SKIPPED] redhat-rpm-config-270-1.fc40.noarch.rpm: Already downloaded
[SKIPPED] zlib-ng-compat-2.1.3-3.fc40.s390x.rpm: Already downloaded
[SKIPPED] zstd-1.5.5-4.fc40.s390x.rpm: Already downloaded
[SKIPPED] alternatives-1.25-1.fc39.s390x.rpm: Already downloaded
[SKIPPED] ansible-srpm-macros-1-11.fc39.noarch.rpm: Already downloaded
[SKIPPED] audit-libs-3.1.2-4.fc40.s390x.rpm: Already downloaded
[SKIPPED] authselect-1.4.2-3.fc39.s390x.rpm: Already downloaded
[SKIPPED] authselect-libs-1.4.2-3.fc39.s390x.rpm: Already downloaded
[SKIPPED] basesystem-11-18.fc39.noarch.rpm: Already downloaded
[SKIPPED] bash-5.2.15-5.fc39.s390x.rpm: Already downloaded
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fedora 1.6 MB/s | 1.6 kB 00:00
Importing GPG key 0xA15B79CC:
Userid : "Fedora (40) <fedora-40-primary@fedoraproject.org>"
Fingerprint: 115D F9AE F857 853E E844 5D0A 0727 707E A15B 79CC
From : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-40-primary
Key imported successfully
fedora 1.6 MB/s | 1.6 kB 00:00
GPG key at file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-40-primary (0xA15B79CC) is already installed
fedora 1.6 MB/s | 1.6 kB 00:00
Importing GPG key 0x18B8E74C:
Userid : "Fedora (39) <fedora-39-primary@fedoraproject.org>"
Fingerprint: E8F2 3996 F232 1864 0CB4 4CBE 75CF 5AC4 18B8 E74C
From : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-39-primary
Key imported successfully
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
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Installing : gdb-minimal-13.2-8.fc40.s390x 135/153
Installing : debugedit-5.0-10.fc39.s390x 136/153
Installing : curl-8.3.0-1.fc40.s390x 137/153
Installing : rpm-sequoia-1.5.0-1.fc40.s390x 138/153
Installing : rpm-libs-4.18.99-1.fc40.s390x 139/153
Running scriptlet: rpm-4.18.99-1.fc40.s390x 140/153
Installing : rpm-4.18.99-1.fc40.s390x 140/153
Installing : efi-srpm-macros-5-9.fc39.noarch 141/153
Installing : lua-srpm-macros-1-9.fc39.noarch 142/153
Installing : rpm-build-libs-4.18.99-1.fc40.s390x 143/153
Installing : ansible-srpm-macros-1-11.fc39.noarch 144/153
Installing : fonts-srpm-macros-1:2.0.5-12.fc39.noarch 145/153
Installing : forge-srpm-macros-0.1.0-1.fc40.noarch 146/153
Installing : go-srpm-macros-3.2.0-7.fc40.noarch 147/153
Installing : python-srpm-macros-3.12-4.fc40.noarch 148/153
Installing : redhat-rpm-config-270-1.fc40.noarch 149/153
Installing : rpm-build-4.18.99-1.fc40.s390x 150/153
Installing : util-linux-2.39.2-1.fc40.s390x 151/153
Installing : which-2.21-40.fc39.s390x 152/153
Installing : info-7.0.3-3.fc39.s390x 153/153
Running scriptlet: filesystem-3.18-6.fc39.s390x 153/153
Running scriptlet: ca-certificates-2023.2.60_v7.0.306-3.fc40.noarch 153/153
Running scriptlet: authselect-libs-1.4.2-3.fc39.s390x 153/153
Running scriptlet: rpm-4.18.99-1.fc40.s390x 153/153
Running scriptlet: info-7.0.3-3.fc39.s390x 153/153
Verifying : cracklib-2.9.11-2.fc40.s390x 1/153
Verifying : curl-8.3.0-1.fc40.s390x 2/153
Verifying : file-5.45-1.fc40.s390x 3/153
Verifying : file-libs-5.45-1.fc40.s390x 4/153
Verifying : glibc-2.38.9000-8.fc40.s390x 5/153
Verifying : glibc-common-2.38.9000-8.fc40.s390x 6/153
Verifying : glibc-gconv-extra-2.38.9000-8.fc40.s390x 7/153
Verifying : glibc-minimal-langpack-2.38.9000-8.fc40.s390x 8/153
Verifying : libcurl-8.3.0-1.fc40.s390x 9/153
Verifying : libdb-5.3.28-58.fc40.s390x 10/153
Verifying : libgcc-13.2.1-1.fc40.s390x 11/153
Verifying : libgomp-13.2.1-1.fc40.s390x 12/153
Verifying : libstdc++-13.2.1-1.fc40.s390x 13/153
Verifying : libxml2-2.11.5-1.fc40.s390x 14/153
Verifying : libzstd-1.5.5-4.fc40.s390x 15/153
Verifying : openssl-libs-1:3.1.1-4.fc40.s390x 16/153
Verifying : redhat-rpm-config-270-1.fc40.noarch 17/153
Verifying : zlib-ng-compat-2.1.3-3.fc40.s390x 18/153
Verifying : zstd-1.5.5-4.fc40.s390x 19/153
Verifying : alternatives-1.25-1.fc39.s390x 20/153
Verifying : ansible-srpm-macros-1-11.fc39.noarch 21/153
Verifying : audit-libs-3.1.2-4.fc40.s390x 22/153
Verifying : authselect-1.4.2-3.fc39.s390x 23/153
Verifying : authselect-libs-1.4.2-3.fc39.s390x 24/153
Verifying : basesystem-11-18.fc39.noarch 25/153
Verifying : bash-5.2.15-5.fc39.s390x 26/153
Verifying : binutils-2.41-5.fc40.s390x 27/153
Verifying : binutils-gold-2.41-5.fc40.s390x 28/153
Verifying : bzip2-1.0.8-16.fc39.s390x 29/153
Verifying : bzip2-libs-1.0.8-16.fc39.s390x 30/153
Verifying : ca-certificates-2023.2.60_v7.0.306-3.fc40.noarch 31/153
Verifying : coreutils-9.4-1.fc40.s390x 32/153
Verifying : coreutils-common-9.4-1.fc40.s390x 33/153
Verifying : cpio-2.14-4.fc39.s390x 34/153
Verifying : crypto-policies-20230731-1.git5ed06e0.fc39.noarc 35/153
Verifying : cyrus-sasl-lib-2.1.28-11.fc39.s390x 36/153
Verifying : debugedit-5.0-10.fc39.s390x 37/153
Verifying : diffutils-3.10-3.fc39.s390x 38/153
Verifying : dwz-0.15-3.fc39.s390x 39/153
Verifying : ed-1.19-4.fc39.s390x 40/153
Verifying : efi-srpm-macros-5-9.fc39.noarch 41/153
Verifying : elfutils-0.189-6.fc40.s390x 42/153
Verifying : elfutils-debuginfod-client-0.189-6.fc40.s390x 43/153
Verifying : elfutils-default-yama-scope-0.189-6.fc40.noarch 44/153
Verifying : elfutils-libelf-0.189-6.fc40.s390x 45/153
Verifying : elfutils-libs-0.189-6.fc40.s390x 46/153
Verifying : fedora-gpg-keys-40-0.1.noarch 47/153
Verifying : fedora-release-40-0.7.noarch 48/153
Verifying : fedora-release-common-40-0.7.noarch 49/153
Verifying : fedora-release-identity-basic-40-0.7.noarch 50/153
Verifying : fedora-repos-40-0.1.noarch 51/153
Verifying : fedora-repos-rawhide-40-0.1.noarch 52/153
Verifying : filesystem-3.18-6.fc39.s390x 53/153
Verifying : findutils-1:4.9.0-6.fc40.s390x 54/153
Verifying : fonts-srpm-macros-1:2.0.5-12.fc39.noarch 55/153
Verifying : forge-srpm-macros-0.1.0-1.fc40.noarch 56/153
Verifying : fpc-srpm-macros-1.3-8.fc39.noarch 57/153
Verifying : gawk-5.2.2-2.fc39.s390x 58/153
Verifying : gdb-minimal-13.2-8.fc40.s390x 59/153
Verifying : gdbm-libs-1:1.23-4.fc39.s390x 60/153
Verifying : ghc-srpm-macros-1.6.1-2.fc39.noarch 61/153
Verifying : gmp-1:6.2.1-5.fc39.s390x 62/153
Verifying : gnat-srpm-macros-6-3.fc39.noarch 63/153
Verifying : go-srpm-macros-3.2.0-7.fc40.noarch 64/153
Verifying : grep-3.11-5.fc40.s390x 65/153
Verifying : gzip-1.12-6.fc39.s390x 66/153
Verifying : info-7.0.3-3.fc39.s390x 67/153
Verifying : jansson-2.13.1-7.fc39.s390x 68/153
Verifying : kernel-srpm-macros-1.0-20.fc39.noarch 69/153
Verifying : keyutils-libs-1.6.1-7.fc39.s390x 70/153
Verifying : krb5-libs-1.21.2-1.fc40.s390x 71/153
Verifying : libacl-2.3.1-9.fc40.s390x 72/153
Verifying : libarchive-3.7.2-1.fc40.s390x 73/153
Verifying : libattr-2.5.1-9.fc40.s390x 74/153
Verifying : libblkid-2.39.2-1.fc40.s390x 75/153
Verifying : libbrotli-1.1.0-1.fc40.s390x 76/153
Verifying : libcap-2.48-7.fc39.s390x 77/153
Verifying : libcap-ng-0.8.3-8.fc40.s390x 78/153
Verifying : libcom_err-1.47.0-2.fc39.s390x 79/153
Verifying : libeconf-0.5.2-1.fc40.s390x 80/153
Verifying : libevent-2.1.12-9.fc39.s390x 81/153
Verifying : libfdisk-2.39.2-1.fc40.s390x 82/153
Verifying : libffi-3.4.4-4.fc39.s390x 83/153
Verifying : libidn2-2.3.4-3.fc39.s390x 84/153
Verifying : libmount-2.39.2-1.fc40.s390x 85/153
Verifying : libnghttp2-1.56.0-1.fc40.s390x 86/153
Verifying : libnsl2-2.0.0-6.fc39.s390x 87/153
Verifying : libpkgconf-1.9.5-2.fc39.s390x 88/153
Verifying : libpsl-0.21.2-4.fc39.s390x 89/153
Verifying : libpwquality-1.4.5-6.fc39.s390x 90/153
Verifying : libselinux-3.5-5.fc39.s390x 91/153
Verifying : libsemanage-3.5-4.fc39.s390x 92/153
Verifying : libsepol-3.5-2.fc39.s390x 93/153
Verifying : libsigsegv-2.14-5.fc39.s390x 94/153
Verifying : libsmartcols-2.39.2-1.fc40.s390x 95/153
Verifying : libssh-0.10.5-2.fc39.s390x 96/153
Verifying : libssh-config-0.10.5-2.fc39.noarch 97/153
Verifying : libtasn1-4.19.0-3.fc39.s390x 98/153
Verifying : libtirpc-1.3.3-1.rc2.fc39.s390x 99/153
Verifying : libunistring-1.1-5.fc40.s390x 100/153
Verifying : libutempter-1.2.1-10.fc39.s390x 101/153
Verifying : libuuid-2.39.2-1.fc40.s390x 102/153
Verifying : libverto-0.3.2-6.fc39.s390x 103/153
Verifying : libxcrypt-4.4.36-2.fc39.s390x 104/153
Verifying : lua-libs-5.4.6-3.fc39.s390x 105/153
Verifying : lua-srpm-macros-1-9.fc39.noarch 106/153
Verifying : lz4-libs-1.9.4-4.fc39.s390x 107/153
Verifying : mpfr-4.2.0-3.fc39.s390x 108/153
Verifying : ncurses-base-6.4-7.20230520.fc40.noarch 109/153
Verifying : ncurses-libs-6.4-7.20230520.fc40.s390x 110/153
Verifying : ocaml-srpm-macros-8-2.fc39.noarch 111/153
Verifying : openblas-srpm-macros-2-14.fc39.noarch 112/153
Verifying : openldap-2.6.6-1.fc39.s390x 113/153
Verifying : p11-kit-0.25.0-2.fc39.s390x 114/153
Verifying : p11-kit-trust-0.25.0-2.fc39.s390x 115/153
Verifying : package-notes-srpm-macros-0.5-9.fc39.noarch 116/153
Verifying : pam-1.5.3-2.fc39.s390x 117/153
Verifying : pam-libs-1.5.3-2.fc39.s390x 118/153
Verifying : patch-2.7.6-22.fc39.s390x 119/153
Verifying : pcre2-10.42-1.fc39.2.s390x 120/153
Verifying : pcre2-syntax-10.42-1.fc39.2.noarch 121/153
Verifying : perl-srpm-macros-1-51.fc39.noarch 122/153
Verifying : pkgconf-1.9.5-2.fc39.s390x 123/153
Verifying : pkgconf-m4-1.9.5-2.fc39.noarch 124/153
Verifying : pkgconf-pkg-config-1.9.5-2.fc39.s390x 125/153
Verifying : popt-1.19-3.fc39.s390x 126/153
Verifying : publicsuffix-list-dafsa-20230812-1.fc40.noarch 127/153
Verifying : pyproject-srpm-macros-1.9.0-2.fc39.noarch 128/153
Verifying : python-srpm-macros-3.12-4.fc40.noarch 129/153
Verifying : qt5-srpm-macros-5.15.10-2.fc39.noarch 130/153
Verifying : qt6-srpm-macros-6.5.2-2.fc39.noarch 131/153
Verifying : readline-8.2-4.fc39.s390x 132/153
Verifying : rpm-4.18.99-1.fc40.s390x 133/153
Verifying : rpm-build-4.18.99-1.fc40.s390x 134/153
Verifying : rpm-build-libs-4.18.99-1.fc40.s390x 135/153
Verifying : rpm-libs-4.18.99-1.fc40.s390x 136/153
Verifying : rpm-sequoia-1.5.0-1.fc40.s390x 137/153
Verifying : rust-srpm-macros-24-5.fc40.noarch 138/153
Verifying : sed-4.8-14.fc39.s390x 139/153
Verifying : setup-2.14.4-1.fc39.noarch 140/153
Verifying : shadow-utils-2:4.14.0-1.fc40.s390x 141/153
Verifying : sqlite-libs-3.43.1-1.fc40.s390x 142/153
Verifying : systemd-libs-254.1-2.fc40.s390x 143/153
Verifying : tar-2:1.35-2.fc40.s390x 144/153
Verifying : tzdata-2023c-3.fc40.noarch 145/153
Verifying : unzip-6.0-62.fc39.s390x 146/153
Verifying : util-linux-2.39.2-1.fc40.s390x 147/153
Verifying : util-linux-core-2.39.2-1.fc40.s390x 148/153
Verifying : which-2.21-40.fc39.s390x 149/153
Verifying : xxhash-libs-0.8.2-1.fc39.s390x 150/153
Verifying : xz-5.4.4-1.fc39.s390x 151/153
Verifying : xz-libs-5.4.4-1.fc39.s390x 152/153
Verifying : zip-3.0-38.fc39.s390x 153/153
Installed:
alternatives-1.25-1.fc39.s390x
ansible-srpm-macros-1-11.fc39.noarch
audit-libs-3.1.2-4.fc40.s390x
authselect-1.4.2-3.fc39.s390x
authselect-libs-1.4.2-3.fc39.s390x
basesystem-11-18.fc39.noarch
bash-5.2.15-5.fc39.s390x
binutils-2.41-5.fc40.s390x
binutils-gold-2.41-5.fc40.s390x
bzip2-1.0.8-16.fc39.s390x
bzip2-libs-1.0.8-16.fc39.s390x
ca-certificates-2023.2.60_v7.0.306-3.fc40.noarch
coreutils-9.4-1.fc40.s390x
coreutils-common-9.4-1.fc40.s390x
cpio-2.14-4.fc39.s390x
cracklib-2.9.11-2.fc40.s390x
crypto-policies-20230731-1.git5ed06e0.fc39.noarch
curl-8.3.0-1.fc40.s390x
cyrus-sasl-lib-2.1.28-11.fc39.s390x
debugedit-5.0-10.fc39.s390x
diffutils-3.10-3.fc39.s390x
dwz-0.15-3.fc39.s390x
ed-1.19-4.fc39.s390x
efi-srpm-macros-5-9.fc39.noarch
elfutils-0.189-6.fc40.s390x
elfutils-debuginfod-client-0.189-6.fc40.s390x
elfutils-default-yama-scope-0.189-6.fc40.noarch
elfutils-libelf-0.189-6.fc40.s390x
elfutils-libs-0.189-6.fc40.s390x
fedora-gpg-keys-40-0.1.noarch
fedora-release-40-0.7.noarch
fedora-release-common-40-0.7.noarch
fedora-release-identity-basic-40-0.7.noarch
fedora-repos-40-0.1.noarch
fedora-repos-rawhide-40-0.1.noarch
file-5.45-1.fc40.s390x
file-libs-5.45-1.fc40.s390x
filesystem-3.18-6.fc39.s390x
findutils-1:4.9.0-6.fc40.s390x
fonts-srpm-macros-1:2.0.5-12.fc39.noarch
forge-srpm-macros-0.1.0-1.fc40.noarch
fpc-srpm-macros-1.3-8.fc39.noarch
gawk-5.2.2-2.fc39.s390x
gdb-minimal-13.2-8.fc40.s390x
gdbm-libs-1:1.23-4.fc39.s390x
ghc-srpm-macros-1.6.1-2.fc39.noarch
glibc-2.38.9000-8.fc40.s390x
glibc-common-2.38.9000-8.fc40.s390x
glibc-gconv-extra-2.38.9000-8.fc40.s390x
glibc-minimal-langpack-2.38.9000-8.fc40.s390x
gmp-1:6.2.1-5.fc39.s390x
gnat-srpm-macros-6-3.fc39.noarch
go-srpm-macros-3.2.0-7.fc40.noarch
grep-3.11-5.fc40.s390x
gzip-1.12-6.fc39.s390x
info-7.0.3-3.fc39.s390x
jansson-2.13.1-7.fc39.s390x
kernel-srpm-macros-1.0-20.fc39.noarch
keyutils-libs-1.6.1-7.fc39.s390x
krb5-libs-1.21.2-1.fc40.s390x
libacl-2.3.1-9.fc40.s390x
libarchive-3.7.2-1.fc40.s390x
libattr-2.5.1-9.fc40.s390x
libblkid-2.39.2-1.fc40.s390x
libbrotli-1.1.0-1.fc40.s390x
libcap-2.48-7.fc39.s390x
libcap-ng-0.8.3-8.fc40.s390x
libcom_err-1.47.0-2.fc39.s390x
libcurl-8.3.0-1.fc40.s390x
libdb-5.3.28-58.fc40.s390x
libeconf-0.5.2-1.fc40.s390x
libevent-2.1.12-9.fc39.s390x
libfdisk-2.39.2-1.fc40.s390x
libffi-3.4.4-4.fc39.s390x
libgcc-13.2.1-1.fc40.s390x
libgomp-13.2.1-1.fc40.s390x
libidn2-2.3.4-3.fc39.s390x
libmount-2.39.2-1.fc40.s390x
libnghttp2-1.56.0-1.fc40.s390x
libnsl2-2.0.0-6.fc39.s390x
libpkgconf-1.9.5-2.fc39.s390x
libpsl-0.21.2-4.fc39.s390x
libpwquality-1.4.5-6.fc39.s390x
libselinux-3.5-5.fc39.s390x
libsemanage-3.5-4.fc39.s390x
libsepol-3.5-2.fc39.s390x
libsigsegv-2.14-5.fc39.s390x
libsmartcols-2.39.2-1.fc40.s390x
libssh-0.10.5-2.fc39.s390x
libssh-config-0.10.5-2.fc39.noarch
libstdc++-13.2.1-1.fc40.s390x
libtasn1-4.19.0-3.fc39.s390x
libtirpc-1.3.3-1.rc2.fc39.s390x
libunistring-1.1-5.fc40.s390x
libutempter-1.2.1-10.fc39.s390x
libuuid-2.39.2-1.fc40.s390x
libverto-0.3.2-6.fc39.s390x
libxcrypt-4.4.36-2.fc39.s390x
libxml2-2.11.5-1.fc40.s390x
libzstd-1.5.5-4.fc40.s390x
lua-libs-5.4.6-3.fc39.s390x
lua-srpm-macros-1-9.fc39.noarch
lz4-libs-1.9.4-4.fc39.s390x
mpfr-4.2.0-3.fc39.s390x
ncurses-base-6.4-7.20230520.fc40.noarch
ncurses-libs-6.4-7.20230520.fc40.s390x
ocaml-srpm-macros-8-2.fc39.noarch
openblas-srpm-macros-2-14.fc39.noarch
openldap-2.6.6-1.fc39.s390x
openssl-libs-1:3.1.1-4.fc40.s390x
p11-kit-0.25.0-2.fc39.s390x
p11-kit-trust-0.25.0-2.fc39.s390x
package-notes-srpm-macros-0.5-9.fc39.noarch
pam-1.5.3-2.fc39.s390x
pam-libs-1.5.3-2.fc39.s390x
patch-2.7.6-22.fc39.s390x
pcre2-10.42-1.fc39.2.s390x
pcre2-syntax-10.42-1.fc39.2.noarch
perl-srpm-macros-1-51.fc39.noarch
pkgconf-1.9.5-2.fc39.s390x
pkgconf-m4-1.9.5-2.fc39.noarch
pkgconf-pkg-config-1.9.5-2.fc39.s390x
popt-1.19-3.fc39.s390x
publicsuffix-list-dafsa-20230812-1.fc40.noarch
pyproject-srpm-macros-1.9.0-2.fc39.noarch
python-srpm-macros-3.12-4.fc40.noarch
qt5-srpm-macros-5.15.10-2.fc39.noarch
qt6-srpm-macros-6.5.2-2.fc39.noarch
readline-8.2-4.fc39.s390x
redhat-rpm-config-270-1.fc40.noarch
rpm-4.18.99-1.fc40.s390x
rpm-build-4.18.99-1.fc40.s390x
rpm-build-libs-4.18.99-1.fc40.s390x
rpm-libs-4.18.99-1.fc40.s390x
rpm-sequoia-1.5.0-1.fc40.s390x
rust-srpm-macros-24-5.fc40.noarch
sed-4.8-14.fc39.s390x
setup-2.14.4-1.fc39.noarch
shadow-utils-2:4.14.0-1.fc40.s390x
sqlite-libs-3.43.1-1.fc40.s390x
systemd-libs-254.1-2.fc40.s390x
tar-2:1.35-2.fc40.s390x
tzdata-2023c-3.fc40.noarch
unzip-6.0-62.fc39.s390x
util-linux-2.39.2-1.fc40.s390x
util-linux-core-2.39.2-1.fc40.s390x
which-2.21-40.fc39.s390x
xxhash-libs-0.8.2-1.fc39.s390x
xz-5.4.4-1.fc39.s390x
xz-libs-5.4.4-1.fc39.s390x
zip-3.0-38.fc39.s390x
zlib-ng-compat-2.1.3-3.fc40.s390x
zstd-1.5.5-4.fc40.s390x
Complete!
Finish: installing minimal buildroot with dnf
Start: creating root cache
Finish: creating root cache
Finish: chroot init
INFO: Installed packages:
INFO: alternatives-1.25-1.fc39.s390x
ansible-srpm-macros-1-11.fc39.noarch
audit-libs-3.1.2-4.fc40.s390x
authselect-1.4.2-3.fc39.s390x
authselect-libs-1.4.2-3.fc39.s390x
basesystem-11-18.fc39.noarch
bash-5.2.15-5.fc39.s390x
binutils-2.41-5.fc40.s390x
binutils-gold-2.41-5.fc40.s390x
bzip2-1.0.8-16.fc39.s390x
bzip2-libs-1.0.8-16.fc39.s390x
ca-certificates-2023.2.60_v7.0.306-3.fc40.noarch
coreutils-9.4-1.fc40.s390x
coreutils-common-9.4-1.fc40.s390x
cpio-2.14-4.fc39.s390x
cracklib-2.9.11-2.fc40.s390x
crypto-policies-20230731-1.git5ed06e0.fc39.noarch
curl-8.3.0-1.fc40.s390x
cyrus-sasl-lib-2.1.28-11.fc39.s390x
debugedit-5.0-10.fc39.s390x
diffutils-3.10-3.fc39.s390x
dwz-0.15-3.fc39.s390x
ed-1.19-4.fc39.s390x
efi-srpm-macros-5-9.fc39.noarch
elfutils-0.189-6.fc40.s390x
elfutils-debuginfod-client-0.189-6.fc40.s390x
elfutils-default-yama-scope-0.189-6.fc40.noarch
elfutils-libelf-0.189-6.fc40.s390x
elfutils-libs-0.189-6.fc40.s390x
fedora-gpg-keys-40-0.1.noarch
fedora-release-40-0.7.noarch
fedora-release-common-40-0.7.noarch
fedora-release-identity-basic-40-0.7.noarch
fedora-repos-40-0.1.noarch
fedora-repos-rawhide-40-0.1.noarch
file-5.45-1.fc40.s390x
file-libs-5.45-1.fc40.s390x
filesystem-3.18-6.fc39.s390x
findutils-4.9.0-6.fc40.s390x
fonts-srpm-macros-2.0.5-12.fc39.noarch
forge-srpm-macros-0.1.0-1.fc40.noarch
fpc-srpm-macros-1.3-8.fc39.noarch
gawk-5.2.2-2.fc39.s390x
gdb-minimal-13.2-8.fc40.s390x
gdbm-libs-1.23-4.fc39.s390x
ghc-srpm-macros-1.6.1-2.fc39.noarch
glibc-2.38.9000-8.fc40.s390x
glibc-common-2.38.9000-8.fc40.s390x
glibc-gconv-extra-2.38.9000-8.fc40.s390x
glibc-minimal-langpack-2.38.9000-8.fc40.s390x
gmp-6.2.1-5.fc39.s390x
gnat-srpm-macros-6-3.fc39.noarch
go-srpm-macros-3.2.0-7.fc40.noarch
gpg-pubkey-18b8e74c-62f2920f
gpg-pubkey-a15b79cc-63d04c2c
grep-3.11-5.fc40.s390x
gzip-1.12-6.fc39.s390x
info-7.0.3-3.fc39.s390x
jansson-2.13.1-7.fc39.s390x
kernel-srpm-macros-1.0-20.fc39.noarch
keyutils-libs-1.6.1-7.fc39.s390x
krb5-libs-1.21.2-1.fc40.s390x
libacl-2.3.1-9.fc40.s390x
libarchive-3.7.2-1.fc40.s390x
libattr-2.5.1-9.fc40.s390x
libblkid-2.39.2-1.fc40.s390x
libbrotli-1.1.0-1.fc40.s390x
libcap-2.48-7.fc39.s390x
libcap-ng-0.8.3-8.fc40.s390x
libcom_err-1.47.0-2.fc39.s390x
libcurl-8.3.0-1.fc40.s390x
libdb-5.3.28-58.fc40.s390x
libeconf-0.5.2-1.fc40.s390x
libevent-2.1.12-9.fc39.s390x
libfdisk-2.39.2-1.fc40.s390x
libffi-3.4.4-4.fc39.s390x
libgcc-13.2.1-1.fc40.s390x
libgomp-13.2.1-1.fc40.s390x
libidn2-2.3.4-3.fc39.s390x
libmount-2.39.2-1.fc40.s390x
libnghttp2-1.56.0-1.fc40.s390x
libnsl2-2.0.0-6.fc39.s390x
libpkgconf-1.9.5-2.fc39.s390x
libpsl-0.21.2-4.fc39.s390x
libpwquality-1.4.5-6.fc39.s390x
libselinux-3.5-5.fc39.s390x
libsemanage-3.5-4.fc39.s390x
libsepol-3.5-2.fc39.s390x
libsigsegv-2.14-5.fc39.s390x
libsmartcols-2.39.2-1.fc40.s390x
libssh-0.10.5-2.fc39.s390x
libssh-config-0.10.5-2.fc39.noarch
libstdc++-13.2.1-1.fc40.s390x
libtasn1-4.19.0-3.fc39.s390x
libtirpc-1.3.3-1.rc2.fc39.s390x
libunistring-1.1-5.fc40.s390x
libutempter-1.2.1-10.fc39.s390x
libuuid-2.39.2-1.fc40.s390x
libverto-0.3.2-6.fc39.s390x
libxcrypt-4.4.36-2.fc39.s390x
libxml2-2.11.5-1.fc40.s390x
libzstd-1.5.5-4.fc40.s390x
lua-libs-5.4.6-3.fc39.s390x
lua-srpm-macros-1-9.fc39.noarch
lz4-libs-1.9.4-4.fc39.s390x
mpfr-4.2.0-3.fc39.s390x
ncurses-base-6.4-7.20230520.fc40.noarch
ncurses-libs-6.4-7.20230520.fc40.s390x
ocaml-srpm-macros-8-2.fc39.noarch
openblas-srpm-macros-2-14.fc39.noarch
openldap-2.6.6-1.fc39.s390x
openssl-libs-3.1.1-4.fc40.s390x
p11-kit-0.25.0-2.fc39.s390x
p11-kit-trust-0.25.0-2.fc39.s390x
package-notes-srpm-macros-0.5-9.fc39.noarch
pam-1.5.3-2.fc39.s390x
pam-libs-1.5.3-2.fc39.s390x
patch-2.7.6-22.fc39.s390x
pcre2-10.42-1.fc39.2.s390x
pcre2-syntax-10.42-1.fc39.2.noarch
perl-srpm-macros-1-51.fc39.noarch
pkgconf-1.9.5-2.fc39.s390x
pkgconf-m4-1.9.5-2.fc39.noarch
pkgconf-pkg-config-1.9.5-2.fc39.s390x
popt-1.19-3.fc39.s390x
publicsuffix-list-dafsa-20230812-1.fc40.noarch
pyproject-srpm-macros-1.9.0-2.fc39.noarch
python-srpm-macros-3.12-4.fc40.noarch
qt5-srpm-macros-5.15.10-2.fc39.noarch
qt6-srpm-macros-6.5.2-2.fc39.noarch
readline-8.2-4.fc39.s390x
redhat-rpm-config-270-1.fc40.noarch
rpm-4.18.99-1.fc40.s390x
rpm-build-4.18.99-1.fc40.s390x
rpm-build-libs-4.18.99-1.fc40.s390x
rpm-libs-4.18.99-1.fc40.s390x
rpm-sequoia-1.5.0-1.fc40.s390x
rust-srpm-macros-24-5.fc40.noarch
sed-4.8-14.fc39.s390x
setup-2.14.4-1.fc39.noarch
shadow-utils-4.14.0-1.fc40.s390x
sqlite-libs-3.43.1-1.fc40.s390x
systemd-libs-254.1-2.fc40.s390x
tar-1.35-2.fc40.s390x
tzdata-2023c-3.fc40.noarch
unzip-6.0-62.fc39.s390x
util-linux-2.39.2-1.fc40.s390x
util-linux-core-2.39.2-1.fc40.s390x
which-2.21-40.fc39.s390x
xxhash-libs-0.8.2-1.fc39.s390x
xz-5.4.4-1.fc39.s390x
xz-libs-5.4.4-1.fc39.s390x
zip-3.0-38.fc39.s390x
zlib-ng-compat-2.1.3-3.fc40.s390x
zstd-1.5.5-4.fc40.s390x
Start: buildsrpm
Start: rpmbuild -bs
Building target platforms: s390x
Building for target s390x
setting SOURCE_DATE_EPOCH=1693872000
Wrote: /builddir/build/SRPMS/python-pysam-0.21.0-2.fc40.src.rpm
Finish: rpmbuild -bs
INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/fedora-rawhide-s390x-1694975550.734558/root/var/log/dnf.rpm.log
/var/lib/mock/fedora-rawhide-s390x-1694975550.734558/root/var/log/dnf.librepo.log
/var/lib/mock/fedora-rawhide-s390x-1694975550.734558/root/var/log/dnf.log
Finish: buildsrpm
INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-8x23x416/python-pysam/python-pysam.spec) Config(child) 1 minutes 23 seconds
INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results
INFO: Cleaning up build root ('cleanup_on_success=True')
Start: clean chroot
INFO: unmounting tmpfs.
Finish: clean chroot
INFO: Start(/var/lib/copr-rpmbuild/results/python-pysam-0.21.0-2.fc40.src.rpm) Config(fedora-rawhide-s390x)
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-s390x-bootstrap-1694975550.734558/root.
INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-s390x-bootstrap-1694975550.734558/root.
INFO: calling preinit hooks
INFO: enabled root cache
INFO: enabled package manager cache
Start(bootstrap): cleaning package manager metadata
Finish(bootstrap): cleaning package manager metadata
Finish(bootstrap): chroot init
Start: chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-s390x-1694975550.734558/root.
INFO: calling preinit hooks
INFO: enabled root cache
Start: unpacking root cache
Finish: unpacking root cache
INFO: enabled package manager cache
Start: cleaning package manager metadata
Finish: cleaning package manager metadata
INFO: enabled HW Info plugin
Finish: chroot init
INFO: Buildroot is handled by package management downloaded with a bootstrap image:
rpm-4.18.99-1.fc40.s390x
rpm-sequoia-1.5.0-1.fc40.s390x
python3-dnf-4.16.2-4.fc40.noarch
python3-dnf-plugins-core-4.4.2-1.fc39.noarch
yum-4.16.2-4.fc40.noarch
Start: build phase for python-pysam-0.21.0-2.fc40.src.rpm
Start: build setup for python-pysam-0.21.0-2.fc40.src.rpm
Building target platforms: s390x
Building for target s390x
setting SOURCE_DATE_EPOCH=1693872000
Wrote: /builddir/build/SRPMS/python-pysam-0.21.0-2.fc40.src.rpm
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Copr repository 276 B/s | 1.5 kB 00:05
Copr repository 356 kB/s | 1.8 MB 00:05
fedora 7.1 kB/s | 5.5 kB 00:00
Dependencies resolved.
=========================================================================================
Package Arch Version Repo Size
=========================================================================================
Installing:
bzip2-devel s390x 1.0.8-16.fc39 fedora 214 k
gcc s390x 13.2.1-1.fc40 copr_base 28 M
python3-cython s390x 3.0.2-1.fc40 fedora 3.9 M
python3-devel s390x 3.12.0~rc2-1.fc40 fedora 311 k
python3-setuptools noarch 67.7.2-7.fc40 fedora 1.5 M
python3-sphinx noarch 1:7.1.2-1.fc40 fedora 2.6 M
xz-devel s390x 5.4.4-1.fc39 fedora 66 k
zlib-ng-compat-devel s390x 2.1.3-3.fc40 copr_base 34 k
Installing dependencies:
annobin-docs noarch 12.26-1.fc40 fedora 94 k
annobin-plugin-gcc s390x 12.26-1.fc40 fedora 958 k
cpp s390x 13.2.1-1.fc40 copr_base 8.8 M
expat s390x 2.5.0-3.fc39 fedora 114 k
gc s390x 8.2.2-4.fc39 fedora 114 k
gcc-plugin-annobin s390x 13.2.1-1.fc40 copr_base 46 k
glibc-devel s390x 2.38.9000-8.fc40 copr_base 96 k
glibc-headers-s390 noarch 2.38.9000-8.fc40 copr_base 489 k
guile22 s390x 2.2.7-9.fc39 fedora 6.5 M
kernel-headers s390x 6.6.0-0.rc1.git0.1.fc40 fedora 1.5 M
libasan s390x 13.2.1-1.fc40 copr_base 507 k
libatomic s390x 13.2.1-1.fc40 copr_base 34 k
libb2 s390x 0.98.1-9.fc39 fedora 27 k
libmpc s390x 1.3.1-3.fc39 fedora 73 k
libtool-ltdl s390x 2.4.7-8.fc40 fedora 37 k
libubsan s390x 13.2.1-1.fc40 copr_base 219 k
libxcrypt-devel s390x 4.4.36-2.fc39 fedora 30 k
make s390x 1:4.4.1-2.fc39 fedora 605 k
mpdecimal s390x 2.5.1-7.fc39 fedora 100 k
pyproject-rpm-macros noarch 1.9.0-2.fc39 fedora 41 k
python-pip-wheel noarch 23.2.1-1.fc39 fedora 1.5 M
python-rpm-macros noarch 3.12-4.fc40 fedora 19 k
python3 s390x 3.12.0~rc2-1.fc40 fedora 26 k
python3-babel noarch 2.12.1-4.fc39~bootstrap fedora 6.9 M
python3-charset-normalizer noarch 3.2.0-2.fc39 fedora 105 k
python3-docutils noarch 0.20.1-1.fc40 fedora 1.0 M
python3-idna noarch 3.4-5.fc40 fedora 109 k
python3-imagesize noarch 1.4.1-5.fc40 fedora 22 k
python3-jinja2 noarch 3.1.2-6.fc40 fedora 505 k
python3-libs s390x 3.12.0~rc2-1.fc40 fedora 9.2 M
python3-markupsafe s390x 2.1.3-2.fc39 fedora 30 k
python3-packaging noarch 23.1-5.fc40 fedora 115 k
python3-pygments noarch 2.16.1-1.fc40 fedora 2.4 M
python3-pysocks noarch 1.7.1-20.fc39 fedora 39 k
python3-requests noarch 2.28.2-6.fc40 fedora 151 k
python3-rpm-generators noarch 14-7.fc39 fedora 30 k
python3-rpm-macros noarch 3.12-4.fc40 fedora 14 k
python3-snowballstemmer noarch 2.2.0-7.fc39 fedora 257 k
python3-sphinx-theme-alabaster noarch 0.7.12-19.fc39 fedora 29 k
python3-sphinxcontrib-applehelp noarch 1.0.6-1.fc40 fedora 45 k
python3-sphinxcontrib-devhelp noarch 1.0.2-14.fc39 fedora 41 k
python3-sphinxcontrib-htmlhelp noarch 2.0.3-1.fc40 fedora 54 k
python3-sphinxcontrib-jsmath noarch 1.0.1-22.fc39 fedora 17 k
python3-sphinxcontrib-qthelp noarch 1.0.3-15.fc39 fedora 47 k
python3-sphinxcontrib-serializinghtml noarch 1.1.5-10.fc39 fedora 47 k
python3-urllib3 noarch 1.26.16-3.fc40 fedora 273 k
python3-urllib3+socks noarch 1.26.16-3.fc40 fedora 9.9 k
Transaction Summary
=========================================================================================
Install 55 Packages
Total size: 80 M
Total download size: 19 M
Installed size: 287 M
Downloading Packages:
[SKIPPED] cpp-13.2.1-1.fc40.s390x.rpm: Already downloaded
[SKIPPED] gcc-13.2.1-1.fc40.s390x.rpm: Already downloaded
[SKIPPED] gcc-plugin-annobin-13.2.1-1.fc40.s390x.rpm: Already downloaded
[SKIPPED] glibc-devel-2.38.9000-8.fc40.s390x.rpm: Already downloaded
[SKIPPED] glibc-headers-s390-2.38.9000-8.fc40.noarch.rpm: Already downloaded
[SKIPPED] libasan-13.2.1-1.fc40.s390x.rpm: Already downloaded
[SKIPPED] libatomic-13.2.1-1.fc40.s390x.rpm: Already downloaded
[SKIPPED] libubsan-13.2.1-1.fc40.s390x.rpm: Already downloaded
[SKIPPED] zlib-ng-compat-devel-2.1.3-3.fc40.s390x.rpm: Already downloaded
[SKIPPED] annobin-docs-12.26-1.fc40.noarch.rpm: Already downloaded
[SKIPPED] annobin-plugin-gcc-12.26-1.fc40.s390x.rpm: Already downloaded
[SKIPPED] expat-2.5.0-3.fc39.s390x.rpm: Already downloaded
[SKIPPED] gc-8.2.2-4.fc39.s390x.rpm: Already downloaded
[SKIPPED] guile22-2.2.7-9.fc39.s390x.rpm: Already downloaded
[SKIPPED] kernel-headers-6.6.0-0.rc1.git0.1.fc40.s390x.rpm: Already downloaded
[SKIPPED] libb2-0.98.1-9.fc39.s390x.rpm: Already downloaded
[SKIPPED] libmpc-1.3.1-3.fc39.s390x.rpm: Already downloaded
[SKIPPED] libtool-ltdl-2.4.7-8.fc40.s390x.rpm: Already downloaded
[SKIPPED] libxcrypt-devel-4.4.36-2.fc39.s390x.rpm: Already downloaded
[SKIPPED] make-4.4.1-2.fc39.s390x.rpm: Already downloaded
[SKIPPED] mpdecimal-2.5.1-7.fc39.s390x.rpm: Already downloaded
[SKIPPED] pyproject-rpm-macros-1.9.0-2.fc39.noarch.rpm: Already downloaded
[SKIPPED] python-pip-wheel-23.2.1-1.fc39.noarch.rpm: Already downloaded
[SKIPPED] python-rpm-macros-3.12-4.fc40.noarch.rpm: Already downloaded
[SKIPPED] python3-3.12.0~rc2-1.fc40.s390x.rpm: Already downloaded
[SKIPPED] python3-devel-3.12.0~rc2-1.fc40.s390x.rpm: Already downloaded
[SKIPPED] python3-libs-3.12.0~rc2-1.fc40.s390x.rpm: Already downloaded
[SKIPPED] python3-packaging-23.1-5.fc40.noarch.rpm: Already downloaded
[SKIPPED] python3-rpm-generators-14-7.fc39.noarch.rpm: Already downloaded
[SKIPPED] python3-rpm-macros-3.12-4.fc40.noarch.rpm: Already downloaded
[SKIPPED] python3-setuptools-67.7.2-7.fc40.noarch.rpm: Already downloaded
(32/55): python3-charset-normalizer-3.2.0-2.fc3 106 kB/s | 105 kB 00:00
(33/55): bzip2-devel-1.0.8-16.fc39.s390x.rpm 190 kB/s | 214 kB 00:01
(34/55): python3-docutils-0.20.1-1.fc40.noarch. 1.5 MB/s | 1.0 MB 00:00
(35/55): python3-idna-3.4-5.fc40.noarch.rpm 532 kB/s | 109 kB 00:00
(36/55): python3-babel-2.12.1-4.fc39~bootstrap. 3.1 MB/s | 6.9 MB 00:02
(37/55): python3-imagesize-1.4.1-5.fc40.noarch. 100 kB/s | 22 kB 00:00
(38/55): python3-cython-3.0.2-1.fc40.s390x.rpm 3.0 MB/s | 3.9 MB 00:01
(39/55): python3-markupsafe-2.1.3-2.fc39.s390x. 147 kB/s | 30 kB 00:00
(40/55): python3-jinja2-3.1.2-6.fc40.noarch.rpm 1.9 MB/s | 505 kB 00:00
(41/55): python3-pygments-2.16.1-1.fc40.noarch. 8.4 MB/s | 2.4 MB 00:00
(42/55): python3-pysocks-1.7.1-20.fc39.noarch.r 192 kB/s | 39 kB 00:00
(43/55): python3-requests-2.28.2-6.fc40.noarch. 715 kB/s | 151 kB 00:00
(44/55): python3-snowballstemmer-2.2.0-7.fc39.n 1.2 MB/s | 257 kB 00:00
(45/55): python3-sphinx-theme-alabaster-0.7.12- 149 kB/s | 29 kB 00:00
(46/55): python3-sphinx-7.1.2-1.fc40.noarch.rpm 9.5 MB/s | 2.6 MB 00:00
(47/55): python3-sphinxcontrib-applehelp-1.0.6- 220 kB/s | 45 kB 00:00
(48/55): python3-sphinxcontrib-devhelp-1.0.2-14 211 kB/s | 41 kB 00:00
(49/55): python3-sphinxcontrib-htmlhelp-2.0.3-1 275 kB/s | 54 kB 00:00
(50/55): python3-sphinxcontrib-jsmath-1.0.1-22. 85 kB/s | 17 kB 00:00
(51/55): python3-sphinxcontrib-qthelp-1.0.3-15. 243 kB/s | 47 kB 00:00
(52/55): python3-sphinxcontrib-serializinghtml- 230 kB/s | 47 kB 00:00
(53/55): python3-urllib3+socks-1.26.16-3.fc40.n 49 kB/s | 9.9 kB 00:00
(54/55): python3-urllib3-1.26.16-3.fc40.noarch. 1.2 MB/s | 273 kB 00:00
(55/55): xz-devel-5.4.4-1.fc39.s390x.rpm 321 kB/s | 66 kB 00:00
--------------------------------------------------------------------------------
Total 4.3 MB/s | 19 MB 00:04
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
Preparing : 1/1
Installing : python-rpm-macros-3.12-4.fc40.noarch 1/55
Installing : python3-rpm-macros-3.12-4.fc40.noarch 2/55
Installing : libmpc-1.3.1-3.fc39.s390x 3/55
Installing : cpp-13.2.1-1.fc40.s390x 4/55
Installing : pyproject-rpm-macros-1.9.0-2.fc39.noarch 5/55
Installing : python-pip-wheel-23.2.1-1.fc39.noarch 6/55
Installing : mpdecimal-2.5.1-7.fc39.s390x 7/55
Installing : libtool-ltdl-2.4.7-8.fc40.s390x 8/55
Installing : libb2-0.98.1-9.fc39.s390x 9/55
Installing : kernel-headers-6.6.0-0.rc1.git0.1.fc40.s390x 10/55
Installing : gc-8.2.2-4.fc39.s390x 11/55
Installing : guile22-2.2.7-9.fc39.s390x 12/55
Installing : make-1:4.4.1-2.fc39.s390x 13/55
Installing : expat-2.5.0-3.fc39.s390x 14/55
Installing : python3-3.12.0~rc2-1.fc40.s390x 15/55
Installing : python3-libs-3.12.0~rc2-1.fc40.s390x 16/55
Installing : python3-idna-3.4-5.fc40.noarch 17/55
Installing : python3-packaging-23.1-5.fc40.noarch 18/55
Installing : python3-rpm-generators-14-7.fc39.noarch 19/55
Installing : python3-babel-2.12.1-4.fc39~bootstrap.noarch 20/55
Installing : python3-charset-normalizer-3.2.0-2.fc39.noarch 21/55
Installing : python3-docutils-0.20.1-1.fc40.noarch 22/55
Installing : python3-imagesize-1.4.1-5.fc40.noarch 23/55
Installing : python3-markupsafe-2.1.3-2.fc39.s390x 24/55
Installing : python3-jinja2-3.1.2-6.fc40.noarch 25/55
Installing : python3-pygments-2.16.1-1.fc40.noarch 26/55
Installing : python3-pysocks-1.7.1-20.fc39.noarch 27/55
Installing : python3-urllib3+socks-1.26.16-3.fc40.noarch 28/55
Installing : python3-urllib3-1.26.16-3.fc40.noarch 29/55
Installing : python3-requests-2.28.2-6.fc40.noarch 30/55
Installing : python3-snowballstemmer-2.2.0-7.fc39.noarch 31/55
Installing : python3-sphinx-theme-alabaster-0.7.12-19.fc39.noar 32/55
Installing : python3-sphinxcontrib-devhelp-1.0.2-14.fc39.noarch 33/55
Installing : python3-sphinxcontrib-jsmath-1.0.1-22.fc39.noarch 34/55
Installing : python3-sphinxcontrib-qthelp-1.0.3-15.fc39.noarch 35/55
Installing : python3-sphinxcontrib-serializinghtml-1.1.5-10.fc3 36/55
Installing : python3-sphinxcontrib-applehelp-1.0.6-1.fc40.noarc 37/55
Installing : python3-sphinxcontrib-htmlhelp-2.0.3-1.fc40.noarch 38/55
Installing : python3-sphinx-1:7.1.2-1.fc40.noarch 39/55
Installing : annobin-docs-12.26-1.fc40.noarch 40/55
Installing : libubsan-13.2.1-1.fc40.s390x 41/55
Installing : libatomic-13.2.1-1.fc40.s390x 42/55
Installing : libasan-13.2.1-1.fc40.s390x 43/55
Installing : glibc-headers-s390-2.38.9000-8.fc40.noarch 44/55
Installing : libxcrypt-devel-4.4.36-2.fc39.s390x 45/55
Installing : glibc-devel-2.38.9000-8.fc40.s390x 46/55
Installing : gcc-13.2.1-1.fc40.s390x 47/55
Running scriptlet: gcc-13.2.1-1.fc40.s390x 47/55
Installing : gcc-plugin-annobin-13.2.1-1.fc40.s390x 48/55
Running scriptlet: gcc-plugin-annobin-13.2.1-1.fc40.s390x 48/55
Installing : annobin-plugin-gcc-12.26-1.fc40.s390x 49/55
Running scriptlet: annobin-plugin-gcc-12.26-1.fc40.s390x 49/55
Installing : python3-devel-3.12.0~rc2-1.fc40.s390x 50/55
Installing : python3-cython-3.0.2-1.fc40.s390x 51/55
Installing : python3-setuptools-67.7.2-7.fc40.noarch 52/55
Installing : xz-devel-5.4.4-1.fc39.s390x 53/55
Installing : bzip2-devel-1.0.8-16.fc39.s390x 54/55
Installing : zlib-ng-compat-devel-2.1.3-3.fc40.s390x 55/55
Running scriptlet: zlib-ng-compat-devel-2.1.3-3.fc40.s390x 55/55
Verifying : cpp-13.2.1-1.fc40.s390x 1/55
Verifying : gcc-13.2.1-1.fc40.s390x 2/55
Verifying : gcc-plugin-annobin-13.2.1-1.fc40.s390x 3/55
Verifying : glibc-devel-2.38.9000-8.fc40.s390x 4/55
Verifying : glibc-headers-s390-2.38.9000-8.fc40.noarch 5/55
Verifying : libasan-13.2.1-1.fc40.s390x 6/55
Verifying : libatomic-13.2.1-1.fc40.s390x 7/55
Verifying : libubsan-13.2.1-1.fc40.s390x 8/55
Verifying : zlib-ng-compat-devel-2.1.3-3.fc40.s390x 9/55
Verifying : annobin-docs-12.26-1.fc40.noarch 10/55
Verifying : annobin-plugin-gcc-12.26-1.fc40.s390x 11/55
Verifying : bzip2-devel-1.0.8-16.fc39.s390x 12/55
Verifying : expat-2.5.0-3.fc39.s390x 13/55
Verifying : gc-8.2.2-4.fc39.s390x 14/55
Verifying : guile22-2.2.7-9.fc39.s390x 15/55
Verifying : kernel-headers-6.6.0-0.rc1.git0.1.fc40.s390x 16/55
Verifying : libb2-0.98.1-9.fc39.s390x 17/55
Verifying : libmpc-1.3.1-3.fc39.s390x 18/55
Verifying : libtool-ltdl-2.4.7-8.fc40.s390x 19/55
Verifying : libxcrypt-devel-4.4.36-2.fc39.s390x 20/55
Verifying : make-1:4.4.1-2.fc39.s390x 21/55
Verifying : mpdecimal-2.5.1-7.fc39.s390x 22/55
Verifying : pyproject-rpm-macros-1.9.0-2.fc39.noarch 23/55
Verifying : python-pip-wheel-23.2.1-1.fc39.noarch 24/55
Verifying : python-rpm-macros-3.12-4.fc40.noarch 25/55
Verifying : python3-3.12.0~rc2-1.fc40.s390x 26/55
Verifying : python3-babel-2.12.1-4.fc39~bootstrap.noarch 27/55
Verifying : python3-charset-normalizer-3.2.0-2.fc39.noarch 28/55
Verifying : python3-cython-3.0.2-1.fc40.s390x 29/55
Verifying : python3-devel-3.12.0~rc2-1.fc40.s390x 30/55
Verifying : python3-docutils-0.20.1-1.fc40.noarch 31/55
Verifying : python3-idna-3.4-5.fc40.noarch 32/55
Verifying : python3-imagesize-1.4.1-5.fc40.noarch 33/55
Verifying : python3-jinja2-3.1.2-6.fc40.noarch 34/55
Verifying : python3-libs-3.12.0~rc2-1.fc40.s390x 35/55
Verifying : python3-markupsafe-2.1.3-2.fc39.s390x 36/55
Verifying : python3-packaging-23.1-5.fc40.noarch 37/55
Verifying : python3-pygments-2.16.1-1.fc40.noarch 38/55
Verifying : python3-pysocks-1.7.1-20.fc39.noarch 39/55
Verifying : python3-requests-2.28.2-6.fc40.noarch 40/55
Verifying : python3-rpm-generators-14-7.fc39.noarch 41/55
Verifying : python3-rpm-macros-3.12-4.fc40.noarch 42/55
Verifying : python3-setuptools-67.7.2-7.fc40.noarch 43/55
Verifying : python3-snowballstemmer-2.2.0-7.fc39.noarch 44/55
Verifying : python3-sphinx-1:7.1.2-1.fc40.noarch 45/55
Verifying : python3-sphinx-theme-alabaster-0.7.12-19.fc39.noar 46/55
Verifying : python3-sphinxcontrib-applehelp-1.0.6-1.fc40.noarc 47/55
Verifying : python3-sphinxcontrib-devhelp-1.0.2-14.fc39.noarch 48/55
Verifying : python3-sphinxcontrib-htmlhelp-2.0.3-1.fc40.noarch 49/55
Verifying : python3-sphinxcontrib-jsmath-1.0.1-22.fc39.noarch 50/55
Verifying : python3-sphinxcontrib-qthelp-1.0.3-15.fc39.noarch 51/55
Verifying : python3-sphinxcontrib-serializinghtml-1.1.5-10.fc3 52/55
Verifying : python3-urllib3+socks-1.26.16-3.fc40.noarch 53/55
Verifying : python3-urllib3-1.26.16-3.fc40.noarch 54/55
Verifying : xz-devel-5.4.4-1.fc39.s390x 55/55
Installed:
annobin-docs-12.26-1.fc40.noarch
annobin-plugin-gcc-12.26-1.fc40.s390x
bzip2-devel-1.0.8-16.fc39.s390x
cpp-13.2.1-1.fc40.s390x
expat-2.5.0-3.fc39.s390x
gc-8.2.2-4.fc39.s390x
gcc-13.2.1-1.fc40.s390x
gcc-plugin-annobin-13.2.1-1.fc40.s390x
glibc-devel-2.38.9000-8.fc40.s390x
glibc-headers-s390-2.38.9000-8.fc40.noarch
guile22-2.2.7-9.fc39.s390x
kernel-headers-6.6.0-0.rc1.git0.1.fc40.s390x
libasan-13.2.1-1.fc40.s390x
libatomic-13.2.1-1.fc40.s390x
libb2-0.98.1-9.fc39.s390x
libmpc-1.3.1-3.fc39.s390x
libtool-ltdl-2.4.7-8.fc40.s390x
libubsan-13.2.1-1.fc40.s390x
libxcrypt-devel-4.4.36-2.fc39.s390x
make-1:4.4.1-2.fc39.s390x
mpdecimal-2.5.1-7.fc39.s390x
pyproject-rpm-macros-1.9.0-2.fc39.noarch
python-pip-wheel-23.2.1-1.fc39.noarch
python-rpm-macros-3.12-4.fc40.noarch
python3-3.12.0~rc2-1.fc40.s390x
python3-babel-2.12.1-4.fc39~bootstrap.noarch
python3-charset-normalizer-3.2.0-2.fc39.noarch
python3-cython-3.0.2-1.fc40.s390x
python3-devel-3.12.0~rc2-1.fc40.s390x
python3-docutils-0.20.1-1.fc40.noarch
python3-idna-3.4-5.fc40.noarch
python3-imagesize-1.4.1-5.fc40.noarch
python3-jinja2-3.1.2-6.fc40.noarch
python3-libs-3.12.0~rc2-1.fc40.s390x
python3-markupsafe-2.1.3-2.fc39.s390x
python3-packaging-23.1-5.fc40.noarch
python3-pygments-2.16.1-1.fc40.noarch
python3-pysocks-1.7.1-20.fc39.noarch
python3-requests-2.28.2-6.fc40.noarch
python3-rpm-generators-14-7.fc39.noarch
python3-rpm-macros-3.12-4.fc40.noarch
python3-setuptools-67.7.2-7.fc40.noarch
python3-snowballstemmer-2.2.0-7.fc39.noarch
python3-sphinx-1:7.1.2-1.fc40.noarch
python3-sphinx-theme-alabaster-0.7.12-19.fc39.noarch
python3-sphinxcontrib-applehelp-1.0.6-1.fc40.noarch
python3-sphinxcontrib-devhelp-1.0.2-14.fc39.noarch
python3-sphinxcontrib-htmlhelp-2.0.3-1.fc40.noarch
python3-sphinxcontrib-jsmath-1.0.1-22.fc39.noarch
python3-sphinxcontrib-qthelp-1.0.3-15.fc39.noarch
python3-sphinxcontrib-serializinghtml-1.1.5-10.fc39.noarch
python3-urllib3-1.26.16-3.fc40.noarch
python3-urllib3+socks-1.26.16-3.fc40.noarch
xz-devel-5.4.4-1.fc39.s390x
zlib-ng-compat-devel-2.1.3-3.fc40.s390x
Complete!
Finish: build setup for python-pysam-0.21.0-2.fc40.src.rpm
Start: rpmbuild python-pysam-0.21.0-2.fc40.src.rpm
Building target platforms: s390x
Building for target s390x
setting SOURCE_DATE_EPOCH=1693872000
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.heeDh4
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf pysam-0.21.0
+ /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/pysam-0.21.0.tar.gz
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd pysam-0.21.0
+ rm -rf /builddir/build/BUILD/pysam-0.21.0-SPECPARTS
+ /usr/bin/mkdir -p /builddir/build/BUILD/pysam-0.21.0-SPECPARTS
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ rm -rf pysam.egg-info
++ grep -rl '/\* Generated by Cython'
+ rm pysam/libcvcf.c pysam/libcutils.c pysam/libctabixproxies.c pysam/libctabix.c pysam/libcsamtools.c pysam/libcsamfile.c pysam/libchtslib.c pysam/libcfaidx.c pysam/libcbgzf.c pysam/libcbcftools.c pysam/libcbcf.c pysam/libcalignmentfile.c pysam/libcalignedsegment.c
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.61I3oD
+ umask 022
+ cd /builddir/build/BUILD
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd pysam-0.21.0
+ FORCE_CYTHON=1
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=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 '
+ /usr/bin/python3 setup.py build '--executable=/usr/bin/python3 -sP'
/builddir/build/BUILD/pysam-0.21.0/setup.py:435: SyntaxWarning: invalid escape sequence '\S'
"#define (\S+)\s+(\S+)", line).groups()
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is shared
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
# pysam: (env) CC=gcc
# pysam: (env) CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC
# pysam: (env) 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
checking for 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 ranlib... ranlib
checking for grep that handles long lines and -e... /usr/bin/grep
checking for C compiler warning flags... -Wall
configure: Default CFLAGS_ARM/X86: -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC
checking whether C compiler accepts -mssse3 -mpopcnt -msse4.1... no
checking whether C compiler accepts -mavx2... no
checking whether C compiler accepts -mavx512f... no
checking whether C compiler supports ARM Neon... no
checking for pkg-config... /usr/bin/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 unknown-Linux... plain .so
checking whether the linker supports versioned symbols... no
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 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... no
checking for curl_easy_pause in -lcurl... no
checking for curl_easy_init in -lcurl... no
configure: error: libcurl library not found
Support for HTTPS and other SSL-based URLs requires routines from the libcurl
library <http://curl.se/libcurl/>. Building HTSlib with libcurl enabled
requires libcurl development files to be installed on the build machine; you
may need to ensure a package such as libcurl4-{gnutls,nss,openssl}-dev (on
Debian or Ubuntu Linux) or libcurl-devel (on RPM-based Linux distributions
or Cygwin) is installed.
Either configure with --disable-libcurl or resolve this error to build HTSlib.
checking for 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 ranlib... ranlib
checking for grep that handles long lines and -e... /usr/bin/grep
checking for C compiler warning flags... -Wall
configure: Default CFLAGS_ARM/X86: -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC
checking whether C compiler accepts -mssse3 -mpopcnt -msse4.1... no
checking whether C compiler accepts -mavx2... no
checking whether C compiler accepts -mavx512f... no
checking whether C compiler supports ARM Neon... no
checking for pkg-config... /usr/bin/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 unknown-Linux... plain .so
checking whether the linker supports versioned symbols... no
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 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
configure: WARNING: GCS support not enabled: requires libcurl support
configure: WARNING: S3 support not enabled: requires libcurl support
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
# pysam: htslib configure options: --disable-libcurl
# pysam: htslib_config HTS_CFLAGS_AVX2=
# pysam: htslib_config HTS_CFLAGS_AVX512=
# pysam: htslib_config HTS_CFLAGS_SSE4=
# pysam: htslib_config HTS_HAVE_NEON=
# pysam: htslib_config LIBHTS_OBJS=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_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o
# pysam: htslib_config LIBS=-llzma -lbz2 -lz -lm
# pysam: htslib_config PLATFORM=default
# pysam: config_option: ENABLE_GCS=0
# pysam: config_option: ENABLE_PLUGINS=0
# pysam: config_option: ENABLE_S3=0
# pysam: config_option: HAVE_COMMONCRYPTO=0
# pysam: config_option: HAVE_HMAC=0
# pysam: config_option: HAVE_LIBBZ2=1
# pysam: config_option: HAVE_LIBCURL=0
# pysam: config_option: HAVE_LIBDEFLATE=0
# pysam: config_option: HAVE_LIBLZMA=1
# pysam: config_option: HAVE_MMAP=1
running build
running build_py
creating build
creating build/lib.linux-s390x-cpython-312
creating build/lib.linux-s390x-cpython-312/pysam
copying pysam/config.py -> build/lib.linux-s390x-cpython-312/pysam
copying pysam/version.py -> build/lib.linux-s390x-cpython-312/pysam
copying pysam/utils.py -> build/lib.linux-s390x-cpython-312/pysam
copying pysam/samtools.py -> build/lib.linux-s390x-cpython-312/pysam
copying pysam/bcftools.py -> build/lib.linux-s390x-cpython-312/pysam
copying pysam/__init__.py -> build/lib.linux-s390x-cpython-312/pysam
copying pysam/Pileup.py -> build/lib.linux-s390x-cpython-312/pysam
creating build/lib.linux-s390x-cpython-312/pysam/include
copying pysam/include/__init__.py -> build/lib.linux-s390x-cpython-312/pysam/include
running egg_info
creating pysam.egg-info
writing pysam.egg-info/PKG-INFO
writing dependency_links to pysam.egg-info/dependency_links.txt
writing requirements to pysam.egg-info/requires.txt
writing top-level names to pysam.egg-info/top_level.txt
writing manifest file 'pysam.egg-info/SOURCES.txt'
reading manifest file 'pysam.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'KNOWN_BUGS'
warning: no files found matching 'THANKS'
warning: no files found matching 'pysam/libc*.c'
no previously-included directories found matching 'tests/'
adding license file 'COPYING'
adding license file 'AUTHORS'
writing manifest file 'pysam.egg-info/SOURCES.txt'
/usr/lib/python3.12/site-packages/setuptools/command/build_py.py:201: _Warning: Package 'pysam.include.htslib.cram' is absent from the `packages` configuration.
!!
********************************************************************************
############################
# Package would be ignored #
############################
Python recognizes 'pysam.include.htslib.cram' as an importable package[^1],
but it is absent from setuptools' `packages` configuration.
This leads to an ambiguous overall configuration. If you want to distribute this
package, please make sure that 'pysam.include.htslib.cram' is explicitly added
to the `packages` configuration field.
Alternatively, you can also rely on setuptools' discovery methods
(for example by using `find_namespace_packages(...)`/`find_namespace:`
instead of `find_packages(...)`/`find:`).
You can read more about "package discovery" on setuptools documentation page:
- https://setuptools.pypa.io/en/latest/userguide/package_discovery.html
If you don't want 'pysam.include.htslib.cram' to be distributed and are
already explicitly excluding 'pysam.include.htslib.cram' via
`find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
you can try to use `exclude_package_data`, or `include-package-data=False` in
combination with a more fine grained `package-data` configuration.
You can read more about "package data files" on setuptools documentation page:
- https://setuptools.pypa.io/en/latest/userguide/datafiles.html
[^1]: For Python, any directory (with suitable naming) can be imported,
even if it does not contain any `.py` files.
On the other hand, currently there is no concept of package data
directory, all directories are treated like packages.
********************************************************************************
!!
check.warn(importable)
/usr/lib/python3.12/site-packages/setuptools/command/build_py.py:201: _Warning: Package 'pysam.include.htslib.htscodecs.htscodecs' is absent from the `packages` configuration.
!!
********************************************************************************
############################
# Package would be ignored #
############################
Python recognizes 'pysam.include.htslib.htscodecs.htscodecs' as an importable package[^1],
but it is absent from setuptools' `packages` configuration.
This leads to an ambiguous overall configuration. If you want to distribute this
package, please make sure that 'pysam.include.htslib.htscodecs.htscodecs' is explicitly added
to the `packages` configuration field.
Alternatively, you can also rely on setuptools' discovery methods
(for example by using `find_namespace_packages(...)`/`find_namespace:`
instead of `find_packages(...)`/`find:`).
You can read more about "package discovery" on setuptools documentation page:
- https://setuptools.pypa.io/en/latest/userguide/package_discovery.html
If you don't want 'pysam.include.htslib.htscodecs.htscodecs' to be distributed and are
already explicitly excluding 'pysam.include.htslib.htscodecs.htscodecs' via
`find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
you can try to use `exclude_package_data`, or `include-package-data=False` in
combination with a more fine grained `package-data` configuration.
You can read more about "package data files" on setuptools documentation page:
- https://setuptools.pypa.io/en/latest/userguide/datafiles.html
[^1]: For Python, any directory (with suitable naming) can be imported,
even if it does not contain any `.py` files.
On the other hand, currently there is no concept of package data
directory, all directories are treated like packages.
********************************************************************************
!!
check.warn(importable)
/usr/lib/python3.12/site-packages/setuptools/command/build_py.py:201: _Warning: Package 'pysam.include.htslib.m4' is absent from the `packages` configuration.
!!
********************************************************************************
############################
# Package would be ignored #
############################
Python recognizes 'pysam.include.htslib.m4' as an importable package[^1],
but it is absent from setuptools' `packages` configuration.
This leads to an ambiguous overall configuration. If you want to distribute this
package, please make sure that 'pysam.include.htslib.m4' is explicitly added
to the `packages` configuration field.
Alternatively, you can also rely on setuptools' discovery methods
(for example by using `find_namespace_packages(...)`/`find_namespace:`
instead of `find_packages(...)`/`find:`).
You can read more about "package discovery" on setuptools documentation page:
- https://setuptools.pypa.io/en/latest/userguide/package_discovery.html
If you don't want 'pysam.include.htslib.m4' to be distributed and are
already explicitly excluding 'pysam.include.htslib.m4' via
`find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
you can try to use `exclude_package_data`, or `include-package-data=False` in
combination with a more fine grained `package-data` configuration.
You can read more about "package data files" on setuptools documentation page:
- https://setuptools.pypa.io/en/latest/userguide/datafiles.html
[^1]: For Python, any directory (with suitable naming) can be imported,
even if it does not contain any `.py` files.
On the other hand, currently there is no concept of package data
directory, all directories are treated like packages.
********************************************************************************
!!
check.warn(importable)
/usr/lib/python3.12/site-packages/setuptools/command/build_py.py:201: _Warning: Package 'pysam.include.htslib.os' is absent from the `packages` configuration.
!!
********************************************************************************
############################
# Package would be ignored #
############################
Python recognizes 'pysam.include.htslib.os' as an importable package[^1],
but it is absent from setuptools' `packages` configuration.
This leads to an ambiguous overall configuration. If you want to distribute this
package, please make sure that 'pysam.include.htslib.os' is explicitly added
to the `packages` configuration field.
Alternatively, you can also rely on setuptools' discovery methods
(for example by using `find_namespace_packages(...)`/`find_namespace:`
instead of `find_packages(...)`/`find:`).
You can read more about "package discovery" on setuptools documentation page:
- https://setuptools.pypa.io/en/latest/userguide/package_discovery.html
If you don't want 'pysam.include.htslib.os' to be distributed and are
already explicitly excluding 'pysam.include.htslib.os' via
`find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
you can try to use `exclude_package_data`, or `include-package-data=False` in
combination with a more fine grained `package-data` configuration.
You can read more about "package data files" on setuptools documentation page:
- https://setuptools.pypa.io/en/latest/userguide/datafiles.html
[^1]: For Python, any directory (with suitable naming) can be imported,
even if it does not contain any `.py` files.
On the other hand, currently there is no concept of package data
directory, all directories are treated like packages.
********************************************************************************
!!
check.warn(importable)
/usr/lib/python3.12/site-packages/setuptools/command/build_py.py:201: _Warning: Package 'pysam.include.samtools.lz4' is absent from the `packages` configuration.
!!
********************************************************************************
############################
# Package would be ignored #
############################
Python recognizes 'pysam.include.samtools.lz4' as an importable package[^1],
but it is absent from setuptools' `packages` configuration.
This leads to an ambiguous overall configuration. If you want to distribute this
package, please make sure that 'pysam.include.samtools.lz4' is explicitly added
to the `packages` configuration field.
Alternatively, you can also rely on setuptools' discovery methods
(for example by using `find_namespace_packages(...)`/`find_namespace:`
instead of `find_packages(...)`/`find:`).
You can read more about "package discovery" on setuptools documentation page:
- https://setuptools.pypa.io/en/latest/userguide/package_discovery.html
If you don't want 'pysam.include.samtools.lz4' to be distributed and are
already explicitly excluding 'pysam.include.samtools.lz4' via
`find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
you can try to use `exclude_package_data`, or `include-package-data=False` in
combination with a more fine grained `package-data` configuration.
You can read more about "package data files" on setuptools documentation page:
- https://setuptools.pypa.io/en/latest/userguide/datafiles.html
[^1]: For Python, any directory (with suitable naming) can be imported,
even if it does not contain any `.py` files.
On the other hand, currently there is no concept of package data
directory, all directories are treated like packages.
********************************************************************************
!!
check.warn(importable)
copying pysam/cbcftools_util.h -> build/lib.linux-s390x-cpython-312/pysam
copying pysam/csamtools_util.h -> build/lib.linux-s390x-cpython-312/pysam
copying pysam/htslib_util.c -> build/lib.linux-s390x-cpython-312/pysam
copying pysam/htslib_util.h -> build/lib.linux-s390x-cpython-312/pysam
copying pysam/libcalignedsegment.pxd -> build/lib.linux-s390x-cpython-312/pysam
copying pysam/libcalignedsegment.pyi -> build/lib.linux-s390x-cpython-312/pysam
copying pysam/libcalignedsegment.pyx -> build/lib.linux-s390x-cpython-312/pysam
copying pysam/libcalignmentfile.pxd -> build/lib.linux-s390x-cpython-312/pysam
copying pysam/libcalignmentfile.pyi -> build/lib.linux-s390x-cpython-312/pysam
copying pysam/libcalignmentfile.pyx -> build/lib.linux-s390x-cpython-312/pysam
copying pysam/libcbcf.pxd -> build/lib.linux-s390x-cpython-312/pysam
copying pysam/libcbcf.pyi -> build/lib.linux-s390x-cpython-312/pysam
copying pysam/libcbcf.pyx -> build/lib.linux-s390x-cpython-312/pysam
copying pysam/libcbcftools.pxd -> build/lib.linux-s390x-cpython-312/pysam
copying pysam/libcbcftools.pyi -> build/lib.linux-s390x-cpython-312/pysam
copying pysam/libcbcftools.pyx -> build/lib.linux-s390x-cpython-312/pysam
copying pysam/libcbgzf.pyi -> build/lib.linux-s390x-cpython-312/pysam
copying pysam/libcbgzf.pyx -> build/lib.linux-s390x-cpython-312/pysam
copying pysam/libcfaidx.pxd -> build/lib.linux-s390x-cpython-312/pysam
copying pysam/libcfaidx.pyi -> build/lib.linux-s390x-cpython-312/pysam
copying pysam/libcfaidx.pyx -> build/lib.linux-s390x-cpython-312/pysam
copying pysam/libchtslib.pxd -> build/lib.linux-s390x-cpython-312/pysam
copying pysam/libchtslib.pyi -> build/lib.linux-s390x-cpython-312/pysam
copying pysam/libchtslib.pyx -> build/lib.linux-s390x-cpython-312/pysam
copying pysam/libcsamfile.pxd -> build/lib.linux-s390x-cpython-312/pysam
copying pysam/libcsamfile.pyi -> build/lib.linux-s390x-cpython-312/pysam
copying pysam/libcsamfile.pyx -> build/lib.linux-s390x-cpython-312/pysam
copying pysam/libcsamtools.pxd -> build/lib.linux-s390x-cpython-312/pysam
copying pysam/libcsamtools.pyi -> build/lib.linux-s390x-cpython-312/pysam
copying pysam/libcsamtools.pyx -> build/lib.linux-s390x-cpython-312/pysam
copying pysam/libctabix.pxd -> build/lib.linux-s390x-cpython-312/pysam
copying pysam/libctabix.pyi -> build/lib.linux-s390x-cpython-312/pysam
copying pysam/libctabix.pyx -> build/lib.linux-s390x-cpython-312/pysam
copying pysam/libctabixproxies.pxd -> build/lib.linux-s390x-cpython-312/pysam
copying pysam/libctabixproxies.pyi -> build/lib.linux-s390x-cpython-312/pysam
copying pysam/libctabixproxies.pyx -> build/lib.linux-s390x-cpython-312/pysam
copying pysam/libcutils.pxd -> build/lib.linux-s390x-cpython-312/pysam
copying pysam/libcutils.pyi -> build/lib.linux-s390x-cpython-312/pysam
copying pysam/libcutils.pyx -> build/lib.linux-s390x-cpython-312/pysam
copying pysam/libcvcf.pxd -> build/lib.linux-s390x-cpython-312/pysam
copying pysam/libcvcf.pyi -> build/lib.linux-s390x-cpython-312/pysam
copying pysam/libcvcf.pyx -> build/lib.linux-s390x-cpython-312/pysam
copying pysam/py.typed -> build/lib.linux-s390x-cpython-312/pysam
copying pysam/pysam_stream.h -> build/lib.linux-s390x-cpython-312/pysam
copying pysam/pysam_util.c -> build/lib.linux-s390x-cpython-312/pysam
copying pysam/pysam_util.h -> build/lib.linux-s390x-cpython-312/pysam
copying pysam/version.h -> build/lib.linux-s390x-cpython-312/pysam
copying pysam/version.pyi -> build/lib.linux-s390x-cpython-312/pysam
creating build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/LICENSE -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/README -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/amplicon_stats.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/amplicon_stats.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bam.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bam.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bam.h -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bam2depth.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bam2depth.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bam_addrprg.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bam_addrprg.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bam_ampliconclip.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bam_ampliconclip.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bam_ampliconclip.h -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bam_aux.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bam_aux.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bam_cat.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bam_cat.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bam_color.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bam_color.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bam_consensus.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bam_consensus.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bam_fastq.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bam_fastq.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bam_flags.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bam_flags.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bam_import.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bam_import.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bam_index.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bam_index.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bam_lpileup.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bam_lpileup.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bam_lpileup.h -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bam_markdup.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bam_markdup.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bam_mate.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bam_mate.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bam_md.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bam_md.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bam_plbuf.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bam_plbuf.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bam_plbuf.h -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bam_plcmd.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bam_plcmd.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bam_quickcheck.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bam_quickcheck.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bam_reheader.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bam_reheader.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bam_rmdup.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bam_rmdup.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bam_rmdupse.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bam_rmdupse.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bam_samples.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bam_samples.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bam_sort.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bam_sort.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bam_split.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bam_split.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bam_stat.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bam_stat.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bamshuf.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bamshuf.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bamtk.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bamtk.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bedcov.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bedcov.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bedidx.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bedidx.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/bedidx.h -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/consensus_pileup.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/consensus_pileup.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/consensus_pileup.h -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/coverage.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/coverage.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/cram_size.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/cram_size.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/cut_target.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/cut_target.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/dict.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/dict.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/faidx.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/faidx.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/padding.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/padding.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/phase.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/phase.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/reference.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/reference.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/reset.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/reset.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/sam_opts.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/sam_opts.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/sam_opts.h -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/sam_utils.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/sam_utils.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/sam_utils.h -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/sam_view.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/sam_view.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/sample.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/sample.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/sample.h -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/samtools.h -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/samtools.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/samtools.pysam.h -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/splaysort.h -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/stats.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/stats.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/stats_isize.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/stats_isize.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/stats_isize.h -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/tmp_file.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/tmp_file.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/tmp_file.h -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
copying samtools/version.sh -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
creating build/lib.linux-s390x-cpython-312/pysam/include/samtools/lz4
copying samtools/lz4/LICENSE -> build/lib.linux-s390x-cpython-312/pysam/include/samtools/lz4
copying samtools/lz4/lz4.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools/lz4
copying samtools/lz4/lz4.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/samtools/lz4
copying samtools/lz4/lz4.h -> build/lib.linux-s390x-cpython-312/pysam/include/samtools/lz4
copying samtools/config.h -> build/lib.linux-s390x-cpython-312/pysam/include/samtools
creating build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/HMM.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/HMM.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/HMM.h -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/LICENSE -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/README -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/abuf.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/abuf.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/abuf.h -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/bam2bcf.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/bam2bcf.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/bam2bcf.h -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/bam2bcf_iaux.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/bam2bcf_iaux.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/bam2bcf_indel.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/bam2bcf_indel.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/bam_sample.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/bam_sample.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/bam_sample.h -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/bcftools.h -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/bcftools.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/bcftools.pysam.h -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/bin.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/bin.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/bin.h -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/call.h -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/ccall.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/ccall.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/cigar_state.h -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/cols.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/cols.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/cols.h -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/consensus.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/consensus.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/convert.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/convert.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/convert.h -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/csq.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/csq.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/dbuf.h -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/dist.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/dist.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/dist.h -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/em.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/em.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/extsort.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/extsort.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/extsort.h -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/filter.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/filter.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/filter.h -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/gvcf.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/gvcf.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/gvcf.h -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/hclust.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/hclust.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/hclust.h -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/hex.h -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/khash_str2str.h -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/kheap.h -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/kmin.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/kmin.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/kmin.h -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/main.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/main.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/mcall.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/mcall.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/mpileup.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/mpileup.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/mw.h -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/ploidy.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/ploidy.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/ploidy.h -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/prob1.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/prob1.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/prob1.h -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/rbuf.h -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/read_consensus.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/read_consensus.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/read_consensus.h -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/regidx.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/regidx.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/regidx.h -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/reheader.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/reheader.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/smpl_ilist.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/smpl_ilist.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/smpl_ilist.h -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/str_finder.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/str_finder.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/str_finder.h -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/tabix.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/tabix.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/tsv2vcf.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/tsv2vcf.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/tsv2vcf.h -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/utlist.h -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/variantkey.h -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/vcfannotate.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/vcfannotate.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/vcfbuf.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/vcfbuf.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/vcfbuf.h -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/vcfcall.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/vcfcall.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/vcfcnv.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/vcfcnv.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/vcfconcat.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/vcfconcat.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/vcfconvert.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/vcfconvert.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/vcffilter.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/vcffilter.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/vcfgtcheck.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/vcfgtcheck.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/vcfhead.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/vcfhead.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/vcfindex.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/vcfindex.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/vcfisec.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/vcfisec.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/vcfmerge.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/vcfmerge.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/vcfnorm.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/vcfnorm.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/vcfplugin.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/vcfplugin.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/vcfquery.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/vcfquery.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/vcfroh.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/vcfroh.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/vcfsom.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/vcfsom.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/vcfsort.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/vcfsort.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/vcfstats.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/vcfstats.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/vcfview.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/vcfview.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/vcmp.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/vcmp.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/vcmp.h -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/version.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/version.c.pysam.c -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/version.sh -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
copying bcftools/config.h -> build/lib.linux-s390x-cpython-312/pysam/include/bcftools
creating build/lib.linux-s390x-cpython-312/pysam/include/htslib
copying htslib/LICENSE -> build/lib.linux-s390x-cpython-312/pysam/include/htslib
copying htslib/Makefile -> build/lib.linux-s390x-cpython-312/pysam/include/htslib
copying htslib/README -> build/lib.linux-s390x-cpython-312/pysam/include/htslib
copying htslib/bcf_sr_sort.c -> build/lib.linux-s390x-cpython-312/pysam/include/htslib
copying htslib/bcf_sr_sort.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib
copying htslib/bgzf.c -> build/lib.linux-s390x-cpython-312/pysam/include/htslib
copying htslib/bgzip.c -> build/lib.linux-s390x-cpython-312/pysam/include/htslib
copying htslib/builddir_vars.mk.in -> build/lib.linux-s390x-cpython-312/pysam/include/htslib
copying htslib/config.h.in -> build/lib.linux-s390x-cpython-312/pysam/include/htslib
copying htslib/config.mk.in -> build/lib.linux-s390x-cpython-312/pysam/include/htslib
copying htslib/configure -> build/lib.linux-s390x-cpython-312/pysam/include/htslib
copying htslib/configure.ac -> build/lib.linux-s390x-cpython-312/pysam/include/htslib
copying htslib/errmod.c -> build/lib.linux-s390x-cpython-312/pysam/include/htslib
copying htslib/faidx.c -> build/lib.linux-s390x-cpython-312/pysam/include/htslib
copying htslib/header.c -> build/lib.linux-s390x-cpython-312/pysam/include/htslib
copying htslib/header.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib
copying htslib/hfile.c -> build/lib.linux-s390x-cpython-312/pysam/include/htslib
copying htslib/hfile_gcs.c -> build/lib.linux-s390x-cpython-312/pysam/include/htslib
copying htslib/hfile_internal.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib
copying htslib/hfile_libcurl.c -> build/lib.linux-s390x-cpython-312/pysam/include/htslib
copying htslib/hfile_s3.c -> build/lib.linux-s390x-cpython-312/pysam/include/htslib
copying htslib/hfile_s3_write.c -> build/lib.linux-s390x-cpython-312/pysam/include/htslib
copying htslib/hts.c -> build/lib.linux-s390x-cpython-312/pysam/include/htslib
copying htslib/hts_expr.c -> build/lib.linux-s390x-cpython-312/pysam/include/htslib
copying htslib/hts_internal.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib
copying htslib/hts_os.c -> build/lib.linux-s390x-cpython-312/pysam/include/htslib
copying htslib/hts_time_funcs.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib
copying htslib/htscodecs_bundled.mk -> build/lib.linux-s390x-cpython-312/pysam/include/htslib
copying htslib/htscodecs_external.mk -> build/lib.linux-s390x-cpython-312/pysam/include/htslib
copying htslib/htsfile.c -> build/lib.linux-s390x-cpython-312/pysam/include/htslib
copying htslib/htslib.mk -> build/lib.linux-s390x-cpython-312/pysam/include/htslib
copying htslib/htslib.pc.in -> build/lib.linux-s390x-cpython-312/pysam/include/htslib
copying htslib/htslib_vars.mk -> build/lib.linux-s390x-cpython-312/pysam/include/htslib
copying htslib/kfunc.c -> build/lib.linux-s390x-cpython-312/pysam/include/htslib
copying htslib/kstring.c -> build/lib.linux-s390x-cpython-312/pysam/include/htslib
copying htslib/md5.c -> build/lib.linux-s390x-cpython-312/pysam/include/htslib
copying htslib/multipart.c -> build/lib.linux-s390x-cpython-312/pysam/include/htslib
copying htslib/plugin.c -> build/lib.linux-s390x-cpython-312/pysam/include/htslib
copying htslib/probaln.c -> build/lib.linux-s390x-cpython-312/pysam/include/htslib
copying htslib/realn.c -> build/lib.linux-s390x-cpython-312/pysam/include/htslib
copying htslib/regidx.c -> build/lib.linux-s390x-cpython-312/pysam/include/htslib
copying htslib/region.c -> build/lib.linux-s390x-cpython-312/pysam/include/htslib
copying htslib/sam.c -> build/lib.linux-s390x-cpython-312/pysam/include/htslib
copying htslib/sam_internal.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib
copying htslib/synced_bcf_reader.c -> build/lib.linux-s390x-cpython-312/pysam/include/htslib
copying htslib/tabix.c -> build/lib.linux-s390x-cpython-312/pysam/include/htslib
copying htslib/tbx.c -> build/lib.linux-s390x-cpython-312/pysam/include/htslib
copying htslib/textutils.c -> build/lib.linux-s390x-cpython-312/pysam/include/htslib
copying htslib/textutils_internal.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib
copying htslib/thread_pool.c -> build/lib.linux-s390x-cpython-312/pysam/include/htslib
copying htslib/thread_pool_internal.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib
copying htslib/vcf.c -> build/lib.linux-s390x-cpython-312/pysam/include/htslib
copying htslib/vcf_sweep.c -> build/lib.linux-s390x-cpython-312/pysam/include/htslib
copying htslib/vcfutils.c -> build/lib.linux-s390x-cpython-312/pysam/include/htslib
copying htslib/version.sh -> build/lib.linux-s390x-cpython-312/pysam/include/htslib
creating build/lib.linux-s390x-cpython-312/pysam/include/htslib/cram
copying htslib/cram/cram.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/cram
copying htslib/cram/cram_codecs.c -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/cram
copying htslib/cram/cram_codecs.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/cram
copying htslib/cram/cram_decode.c -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/cram
copying htslib/cram/cram_decode.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/cram
copying htslib/cram/cram_encode.c -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/cram
copying htslib/cram/cram_encode.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/cram
copying htslib/cram/cram_external.c -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/cram
copying htslib/cram/cram_index.c -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/cram
copying htslib/cram/cram_index.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/cram
copying htslib/cram/cram_io.c -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/cram
copying htslib/cram/cram_io.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/cram
copying htslib/cram/cram_samtools.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/cram
copying htslib/cram/cram_stats.c -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/cram
copying htslib/cram/cram_stats.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/cram
copying htslib/cram/cram_structs.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/cram
copying htslib/cram/mFILE.c -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/cram
copying htslib/cram/mFILE.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/cram
copying htslib/cram/misc.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/cram
copying htslib/cram/open_trace_file.c -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/cram
copying htslib/cram/open_trace_file.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/cram
copying htslib/cram/os.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/cram
copying htslib/cram/pooled_alloc.c -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/cram
copying htslib/cram/pooled_alloc.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/cram
copying htslib/cram/string_alloc.c -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/cram
copying htslib/cram/string_alloc.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/cram
creating build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs
creating build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/arith_dynamic.c -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/arith_dynamic.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/c_range_coder.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/c_simple_model.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/fqzcomp_qual.c -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/fqzcomp_qual.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/htscodecs.c -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/htscodecs.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/htscodecs_endian.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/pack.c -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/pack.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/permute.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/pooled_alloc.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/rANS_byte.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/rANS_static.c -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/rANS_static.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/rANS_static16_int.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/rANS_static32x16pr.c -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/rANS_static32x16pr.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/rANS_static32x16pr_avx2.c -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/rANS_static32x16pr_avx512.c -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/rANS_static32x16pr_neon.c -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/rANS_static32x16pr_sse4.c -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/rANS_static4x16.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/rANS_static4x16pr.c -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/rANS_word.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/rle.c -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/rle.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/tokenise_name3.c -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/tokenise_name3.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/utils.c -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/utils.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/varint.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/varint2.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/version.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs
creating build/lib.linux-s390x-cpython-312/pysam/include/htslib/m4
copying htslib/m4/ax_check_compile_flag.m4 -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/m4
copying htslib/m4/hts_hide_dynamic_syms.m4 -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/m4
copying htslib/m4/hts_prog_cc_warnings.m4 -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/m4
copying htslib/m4/pkg.m4 -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/m4
creating build/lib.linux-s390x-cpython-312/pysam/include/htslib/os
copying htslib/os/lzma_stub.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/os
copying htslib/os/rand.c -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/os
copying htslib/config.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib
creating build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib
copying htslib/htslib/bgzf.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib
copying htslib/htslib/cram.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib
copying htslib/htslib/faidx.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib
copying htslib/htslib/hfile.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib
copying htslib/htslib/hts.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib
copying htslib/htslib/hts_defs.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib
copying htslib/htslib/hts_endian.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib
copying htslib/htslib/hts_expr.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib
copying htslib/htslib/hts_log.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib
copying htslib/htslib/hts_os.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib
copying htslib/htslib/kbitset.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib
copying htslib/htslib/kfunc.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib
copying htslib/htslib/khash.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib
copying htslib/htslib/khash_str2int.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib
copying htslib/htslib/klist.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib
copying htslib/htslib/knetfile.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib
copying htslib/htslib/kroundup.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib
copying htslib/htslib/kseq.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib
copying htslib/htslib/ksort.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib
copying htslib/htslib/kstring.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib
copying htslib/htslib/regidx.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib
copying htslib/htslib/sam.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib
copying htslib/htslib/synced_bcf_reader.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib
copying htslib/htslib/tbx.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib
copying htslib/htslib/thread_pool.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib
copying htslib/htslib/vcf.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib
copying htslib/htslib/vcf_sweep.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib
copying htslib/htslib/vcfutils.h -> build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib
running build_ext
creating htslib/config_vars.h for 'pysam.libchtslib' extension
building 'libhts.a'
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o kfunc.o kfunc.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o kstring.o kstring.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o bgzf.o bgzf.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o errmod.o errmod.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o faidx.o faidx.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o header.o header.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o hfile.o hfile.c
echo '#define HTS_VERSION_TEXT "1.17"' > version.h
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o hts.o hts.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o md5.o md5.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o multipart.o multipart.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o probaln.o probaln.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o realn.o realn.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o regidx.o regidx.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o region.o region.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o sam.o sam.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o tbx.o tbx.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o textutils.o textutils.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o vcf.o vcf.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o vcfutils.o vcfutils.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static32x16pr.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/utils.o htscodecs/htscodecs/utils.c
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_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o
ranlib libhts.a
warning: pysam/libchtslib.pyx:39:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
warning: pysam/libchtslib.pyx:40:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
warning: pysam/libchtslib.pyx:41:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
Compiling pysam/libchtslib.pyx because it changed.
[1/1] Cythonizing pysam/libchtslib.pyx
building 'pysam.libchtslib' extension
creating build/temp.linux-s390x-cpython-312
creating build/temp.linux-s390x-cpython-312/pysam
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c pysam/htslib_util.c -o build/temp.linux-s390x-cpython-312/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c pysam/libchtslib.c -o build/temp.linux-s390x-cpython-312/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -shared -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 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC build/temp.linux-s390x-cpython-312/pysam/htslib_util.o build/temp.linux-s390x-cpython-312/pysam/libchtslib.o htslib/kfunc.o htslib/kstring.o htslib/bcf_sr_sort.o htslib/bgzf.o htslib/errmod.o htslib/faidx.o htslib/header.o htslib/hfile.o htslib/hts.o htslib/hts_expr.o htslib/hts_os.o htslib/md5.o htslib/multipart.o htslib/probaln.o htslib/realn.o htslib/regidx.o htslib/region.o htslib/sam.o htslib/synced_bcf_reader.o htslib/vcf_sweep.o htslib/tbx.o htslib/textutils.o htslib/thread_pool.o htslib/vcf.o htslib/vcfutils.o htslib/cram/cram_codecs.o htslib/cram/cram_decode.o htslib/cram/cram_encode.o htslib/cram/cram_external.o htslib/cram/cram_index.o htslib/cram/cram_io.o htslib/cram/cram_stats.o htslib/cram/mFILE.o htslib/cram/open_trace_file.o htslib/cram/pooled_alloc.o htslib/cram/string_alloc.o htslib/htscodecs/htscodecs/arith_dynamic.o htslib/htscodecs/htscodecs/fqzcomp_qual.o htslib/htscodecs/htscodecs/htscodecs.o htslib/htscodecs/htscodecs/pack.o htslib/htscodecs/htscodecs/rANS_static4x16pr.o htslib/htscodecs/htscodecs/rANS_static32x16pr.o htslib/htscodecs/htscodecs/rANS_static.o htslib/htscodecs/htscodecs/rle.o htslib/htscodecs/htscodecs/tokenise_name3.o htslib/htscodecs/htscodecs/utils.o -L/builddir/build/BUILD/pysam-0.21.0/pysam -L/builddir/build/BUILD/pysam-0.21.0 -Lbuild/lib.linux-s390x-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -o build/lib.linux-s390x-cpython-312/pysam/libchtslib.cpython-312-s390x-linux-gnu.so -Wl,-rpath,$ORIGIN
creating samtools/samtools_config_vars.h for 'pysam.libcsamtools' extension
Compiling pysam/libcsamtools.pyx because it changed.
[1/1] Cythonizing pysam/libcsamtools.pyx
building 'pysam.libcsamtools' extension
creating build/temp.linux-s390x-cpython-312/samtools
creating build/temp.linux-s390x-cpython-312/samtools/lz4
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c pysam/libcsamtools.c -o build/temp.linux-s390x-cpython-312/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/amplicon_stats.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/amplicon_stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bam.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bam2depth.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bam_ampliconclip.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bam_ampliconclip.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bam_aux.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bam_cat.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bam_color.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bam_consensus.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bam_consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bam_fastq.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bam_fastq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bam_flags.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bam_import.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bam_index.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bam_markdup.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bam_mate.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bam_md.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bam_samples.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bam_samples.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bam_sort.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
samtools/bam_sort.c.pysam.c: In function ‘reverse_complement.isra.0’:
samtools/bam_sort.c.pysam.c:2533:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
2533 | seq[j] = comp[tmp];
| ~~~~~~~^~~~~~~~~~~
samtools/bam_sort.c.pysam.c:2520:10: note: at offset 2147483647 into destination object ‘seq_’ of size 10000
2520 | char seq_[10000], *seq = seq_;
| ^~~~
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bam_split.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bam_stat.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bamshuf.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bamtk.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bedcov.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/bedidx.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/consensus_pileup.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/consensus_pileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/coverage.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/coverage.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/cram_size.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/cram_size.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/cut_target.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/dict.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/faidx.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/lz4/lz4.c -o build/temp.linux-s390x-cpython-312/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/padding.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/phase.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/reference.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/reference.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/reset.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/reset.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/sam_opts.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/sam_utils.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/sam_view.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/sample.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/samtools.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/stats.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/stats_isize.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c samtools/tmp_file.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -shared -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 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC build/temp.linux-s390x-cpython-312/pysam/libcsamtools.o build/temp.linux-s390x-cpython-312/samtools/amplicon_stats.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bam.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bam2depth.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bam_addrprg.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bam_ampliconclip.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bam_aux.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bam_cat.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bam_color.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bam_consensus.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bam_fastq.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bam_flags.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bam_import.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bam_index.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bam_lpileup.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bam_markdup.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bam_mate.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bam_md.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bam_plbuf.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bam_plcmd.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bam_quickcheck.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bam_reheader.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bam_rmdup.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bam_rmdupse.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bam_samples.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bam_sort.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bam_split.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bam_stat.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bamshuf.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bamtk.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bedcov.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bedidx.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/consensus_pileup.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/coverage.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/cram_size.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/cut_target.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/dict.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/faidx.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/lz4/lz4.o build/temp.linux-s390x-cpython-312/samtools/padding.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/phase.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/reference.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/reset.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/sam_opts.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/sam_utils.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/sam_view.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/sample.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/samtools.pysam.o build/temp.linux-s390x-cpython-312/samtools/stats.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/stats_isize.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/tmp_file.c.pysam.o -L/builddir/build/BUILD/pysam-0.21.0/pysam -L/builddir/build/BUILD/pysam-0.21.0 -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-s390x-linux-gnu -o build/lib.linux-s390x-cpython-312/pysam/libcsamtools.cpython-312-s390x-linux-gnu.so -Wl,-rpath,$ORIGIN
samtools/bam_sort.c.pysam.c: In function ‘reverse_complement.isra’:
samtools/bam_sort.c.pysam.c:2533:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
2533 | seq[j] = comp[tmp];
| ^
samtools/bam_sort.c.pysam.c:2520:10: note: at offset 2147483647 into destination object ‘seq_’ of size 10000
2520 | char seq_[10000], *seq = seq_;
| ^
Compiling pysam/libcbcftools.pyx because it changed.
[1/1] Cythonizing pysam/libcbcftools.pyx
building 'pysam.libcbcftools' extension
creating build/temp.linux-s390x-cpython-312/bcftools
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/HMM.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/abuf.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/abuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/bam2bcf.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/bam2bcf_iaux.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/bam2bcf_iaux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/bam_sample.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/bcftools.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/bin.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/ccall.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/cols.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/cols.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/consensus.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/convert.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/csq.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/dist.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/dist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/em.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/extsort.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/extsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/filter.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/gvcf.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/hclust.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/kmin.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/main.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/mcall.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/mpileup.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/ploidy.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/prob1.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/read_consensus.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/read_consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/regidx.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/reheader.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/smpl_ilist.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/str_finder.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/str_finder.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/tabix.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/vcfbuf.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/vcfhead.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/vcfhead.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
bcftools/vcfmerge.c.pysam.c: In function ‘maux_init’:
bcftools/vcfmerge.c.pysam.c:751:34: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
751 | ma->gvcf = (gvcf_aux_t*) calloc(ma->n,sizeof(gvcf_aux_t)); // -Walloc-size-larger-than gives a harmless warning caused by signed integer ma->n
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /builddir/build/BUILD/pysam-0.21.0/htslib/htslib/kstring.h:30,
from /builddir/build/BUILD/pysam-0.21.0/htslib/htslib/hts.h:37,
from /builddir/build/BUILD/pysam-0.21.0/htslib/htslib/vcf.h:39,
from bcftools/vcfmerge.c.pysam.c:35:
/usr/include/stdlib.h:675:14: note: in a call to allocation function ‘calloc’ declared here
675 | extern void *calloc (size_t __nmemb, size_t __size)
| ^~~~~~
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/vcfsort.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/vcfview.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/vcmp.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c bcftools/version.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c pysam/libcbcftools.c -o build/temp.linux-s390x-cpython-312/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -shared -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 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC build/temp.linux-s390x-cpython-312/bcftools/HMM.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/abuf.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/bam2bcf.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/bam2bcf_iaux.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/bam_sample.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/bcftools.pysam.o build/temp.linux-s390x-cpython-312/bcftools/bin.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/ccall.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/cols.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/consensus.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/convert.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/csq.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/dist.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/em.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/extsort.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/filter.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/gvcf.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/hclust.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/kmin.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/main.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/mcall.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/mpileup.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/ploidy.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/prob1.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/read_consensus.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/regidx.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/reheader.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/smpl_ilist.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/str_finder.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/tabix.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/tsv2vcf.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/vcfannotate.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/vcfbuf.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/vcfcall.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/vcfcnv.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/vcfconcat.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/vcfconvert.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/vcffilter.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/vcfhead.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/vcfindex.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/vcfisec.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/vcfmerge.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/vcfnorm.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/vcfplugin.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/vcfquery.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/vcfroh.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/vcfsom.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/vcfsort.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/vcfstats.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/vcfview.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/vcmp.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/version.c.pysam.o build/temp.linux-s390x-cpython-312/pysam/libcbcftools.o -L/builddir/build/BUILD/pysam-0.21.0/pysam -L/builddir/build/BUILD/pysam-0.21.0 -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-s390x-linux-gnu -o build/lib.linux-s390x-cpython-312/pysam/libcbcftools.cpython-312-s390x-linux-gnu.so -Wl,-rpath,$ORIGIN
bcftools/vcfmerge.c.pysam.c: In function ‘maux_init’:
bcftools/vcfmerge.c.pysam.c:751:34: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
751 | ma->gvcf = (gvcf_aux_t*) calloc(ma->n,sizeof(gvcf_aux_t)); // -Walloc-size-larger-than gives a harmless warning caused by signed integer ma->n
| ^
/usr/include/stdlib.h:675:14: note: in a call to allocation function ‘calloc’ declared here
675 | extern void *calloc (size_t __nmemb, size_t __size)
| ^
Compiling pysam/libcutils.pyx because it changed.
[1/1] Cythonizing pysam/libcutils.pyx
building 'pysam.libcutils' extension
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c pysam/libcutils.c -o build/temp.linux-s390x-cpython-312/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c pysam/pysam_util.c -o build/temp.linux-s390x-cpython-312/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -shared -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 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC build/temp.linux-s390x-cpython-312/pysam/libcutils.o build/temp.linux-s390x-cpython-312/pysam/pysam_util.o -L/builddir/build/BUILD/pysam-0.21.0/pysam -L/builddir/build/BUILD/pysam-0.21.0 -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-s390x-linux-gnu -lcsamtools.cpython-312-s390x-linux-gnu -lcbcftools.cpython-312-s390x-linux-gnu -o build/lib.linux-s390x-cpython-312/pysam/libcutils.cpython-312-s390x-linux-gnu.so -Wl,-rpath,$ORIGIN
warning: pysam/libcalignmentfile.pyx:2572:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
warning: pysam/libcalignmentfile.pyx:2577:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
warning: pysam/libcalignmentfile.pyx:2582:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
warning: pysam/libcalignmentfile.pyx:2621:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
warning: pysam/libcalignmentfile.pyx:2626:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
warning: pysam/libcalignmentfile.pyx:2631:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
Compiling pysam/libcalignmentfile.pyx because it changed.
[1/1] Cythonizing pysam/libcalignmentfile.pyx
building 'pysam.libcalignmentfile' extension
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c pysam/libcalignmentfile.c -o build/temp.linux-s390x-cpython-312/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcalignmentfile.c: In function ‘__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_6_open’:
pysam/libcalignmentfile.c:20430:20: warning: ignoring return value of ‘sam_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
20430 | (void)(sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_hdr));
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext’:
pysam/libcalignmentfile.c:37151:16: warning: ignoring return value of ‘bgzf_seek’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
37151 | (void)(bgzf_seek(hts_get_bgzfp(__pyx_v_self->__pyx_base.htsfile), __pyx_v_pos, 0));
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -shared -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 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC build/temp.linux-s390x-cpython-312/pysam/libcalignmentfile.o -L/builddir/build/BUILD/pysam-0.21.0/pysam -L/builddir/build/BUILD/pysam-0.21.0 -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-s390x-linux-gnu -lcutils.cpython-312-s390x-linux-gnu -o build/lib.linux-s390x-cpython-312/pysam/libcalignmentfile.cpython-312-s390x-linux-gnu.so -Wl,-rpath,$ORIGIN
Compiling pysam/libcsamfile.pyx because it changed.
[1/1] Cythonizing pysam/libcsamfile.pyx
building 'pysam.libcsamfile' extension
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c pysam/libcsamfile.c -o build/temp.linux-s390x-cpython-312/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -shared -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 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC build/temp.linux-s390x-cpython-312/pysam/libcsamfile.o -L/builddir/build/BUILD/pysam-0.21.0/pysam -L/builddir/build/BUILD/pysam-0.21.0 -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-s390x-linux-gnu -lcutils.cpython-312-s390x-linux-gnu -o build/lib.linux-s390x-cpython-312/pysam/libcsamfile.cpython-312-s390x-linux-gnu.so -Wl,-rpath,$ORIGIN
Compiling pysam/libcalignedsegment.pyx because it changed.
[1/1] Cythonizing pysam/libcalignedsegment.pyx
building 'pysam.libcalignedsegment' extension
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c pysam/libcalignedsegment.c -o build/temp.linux-s390x-cpython-312/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcalignedsegment.c: In function ‘__pyx_pf_5pysam_18libcalignedsegment_14AlignedSegment_18fromstring’:
pysam/libcalignedsegment.c:35814:10: warning: ignoring return value of ‘sam_parse1’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
35814 | (void)(sam_parse1((&__pyx_v_line), __pyx_v_dest->header->ptr, __pyx_v_dest->_delegate));
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -shared -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 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC build/temp.linux-s390x-cpython-312/pysam/libcalignedsegment.o -L/builddir/build/BUILD/pysam-0.21.0/pysam -L/builddir/build/BUILD/pysam-0.21.0 -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-s390x-linux-gnu -lcutils.cpython-312-s390x-linux-gnu -o build/lib.linux-s390x-cpython-312/pysam/libcalignedsegment.cpython-312-s390x-linux-gnu.so -Wl,-rpath,$ORIGIN
Compiling pysam/libctabix.pyx because it changed.
[1/1] Cythonizing pysam/libctabix.pyx
building 'pysam.libctabix' extension
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c pysam/libctabix.c -o build/temp.linux-s390x-cpython-312/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -shared -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 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC build/temp.linux-s390x-cpython-312/pysam/libctabix.o -L/builddir/build/BUILD/pysam-0.21.0/pysam -L/builddir/build/BUILD/pysam-0.21.0 -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-s390x-linux-gnu -lcutils.cpython-312-s390x-linux-gnu -o build/lib.linux-s390x-cpython-312/pysam/libctabix.cpython-312-s390x-linux-gnu.so -Wl,-rpath,$ORIGIN
Compiling pysam/libcfaidx.pyx because it changed.
[1/1] Cythonizing pysam/libcfaidx.pyx
building 'pysam.libcfaidx' extension
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c pysam/libcfaidx.c -o build/temp.linux-s390x-cpython-312/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -shared -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 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC build/temp.linux-s390x-cpython-312/pysam/libcfaidx.o -L/builddir/build/BUILD/pysam-0.21.0/pysam -L/builddir/build/BUILD/pysam-0.21.0 -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-s390x-linux-gnu -lcutils.cpython-312-s390x-linux-gnu -o build/lib.linux-s390x-cpython-312/pysam/libcfaidx.cpython-312-s390x-linux-gnu.so -Wl,-rpath,$ORIGIN
Compiling pysam/libcbcf.pyx because it changed.
[1/1] Cythonizing pysam/libcbcf.pyx
building 'pysam.libcbcf' extension
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c pysam/libcbcf.c -o build/temp.linux-s390x-cpython-312/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcbcf.c: In function ‘__pyx_f_5pysam_7libcbcf_11VariantFile_write’:
pysam/libcbcf.c:86755:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
86755 | (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr));
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_11VariantFile_6close’:
pysam/libcbcf.c:81419:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
81419 | (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr));
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_13VariantHeader_20add_meta’:
pysam/libcbcf.c:44519:11: warning: ignoring return value of ‘bcf_hrec_add_key’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
44519 | bcf_hrec_add_key(__pyx_v_hrec, __pyx_t_17, ((int)__pyx_t_18));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c:44545:11: warning: ignoring return value of ‘bcf_hrec_set_val’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
44545 | bcf_hrec_set_val(__pyx_v_hrec, (__pyx_v_hrec->nkeys - 1), __pyx_t_19, ((int)__pyx_t_18), __pyx_v_quoted);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_11VariantFile_4__dealloc__’:
pysam/libcbcf.c:81103:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
81103 | (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr));
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -shared -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 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC build/temp.linux-s390x-cpython-312/pysam/libcbcf.o -L/builddir/build/BUILD/pysam-0.21.0/pysam -L/builddir/build/BUILD/pysam-0.21.0 -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-s390x-linux-gnu -lcutils.cpython-312-s390x-linux-gnu -o build/lib.linux-s390x-cpython-312/pysam/libcbcf.cpython-312-s390x-linux-gnu.so -Wl,-rpath,$ORIGIN
Compiling pysam/libcbgzf.pyx because it changed.
[1/1] Cythonizing pysam/libcbgzf.pyx
building 'pysam.libcbgzf' extension
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c pysam/libcbgzf.c -o build/temp.linux-s390x-cpython-312/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -shared -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 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC build/temp.linux-s390x-cpython-312/pysam/libcbgzf.o -L/builddir/build/BUILD/pysam-0.21.0/pysam -L/builddir/build/BUILD/pysam-0.21.0 -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-s390x-linux-gnu -lcutils.cpython-312-s390x-linux-gnu -o build/lib.linux-s390x-cpython-312/pysam/libcbgzf.cpython-312-s390x-linux-gnu.so -Wl,-rpath,$ORIGIN
Compiling pysam/libctabixproxies.pyx because it changed.
[1/1] Cythonizing pysam/libctabixproxies.pyx
building 'pysam.libctabixproxies' extension
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c pysam/libctabixproxies.c -o build/temp.linux-s390x-cpython-312/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -shared -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 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC build/temp.linux-s390x-cpython-312/pysam/libctabixproxies.o -L/builddir/build/BUILD/pysam-0.21.0/pysam -L/builddir/build/BUILD/pysam-0.21.0 -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-s390x-linux-gnu -lcutils.cpython-312-s390x-linux-gnu -o build/lib.linux-s390x-cpython-312/pysam/libctabixproxies.cpython-312-s390x-linux-gnu.so -Wl,-rpath,$ORIGIN
warning: pysam/libcvcf.pyx:1083:27: Unreachable code
Compiling pysam/libcvcf.pyx because it changed.
[1/1] Cythonizing pysam/libcvcf.pyx
building 'pysam.libcvcf' extension
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.21.0/pysam -I/builddir/build/BUILD/pysam-0.21.0/htslib -I/builddir/build/BUILD/pysam-0.21.0/samtools -I/builddir/build/BUILD/pysam-0.21.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.21.0/bcftools -I/builddir/build/BUILD/pysam-0.21.0 -I/usr/include/python3.12 -c pysam/libcvcf.c -o build/temp.linux-s390x-cpython-312/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcvcf.c: In function ‘__pyx_pf_5pysam_7libcvcf_3VCF_32parse_data.isra.0’:
pysam/libcvcf.c:29574:16: warning: ‘__pyx_v_qual’ may be used uninitialized [-Wmaybe-uninitialized]
29574 | __pyx_t_11 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 873, __pyx_L1_error)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcvcf.c:24723:10: note: ‘__pyx_v_qual’ was declared here
24723 | double __pyx_v_qual;
| ^~~~~~~~~~~~
gcc -shared -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 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC build/temp.linux-s390x-cpython-312/pysam/libcvcf.o -L/builddir/build/BUILD/pysam-0.21.0/pysam -L/builddir/build/BUILD/pysam-0.21.0 -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -Lbuild/lib.linux-s390x-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-s390x-linux-gnu -lcutils.cpython-312-s390x-linux-gnu -o build/lib.linux-s390x-cpython-312/pysam/libcvcf.cpython-312-s390x-linux-gnu.so -Wl,-rpath,$ORIGIN
++ echo /builddir/build/BUILD/pysam-0.21.0/build/lib.linux-s390x-cpython-312
+ PYTHONPATH=/builddir/build/BUILD/pysam-0.21.0/build/lib.linux-s390x-cpython-312
+ sphinx-build-3 doc html
Running Sphinx v7.1.2
making output directory... done
[autosummary] generating autosummary for: api.rst, benchmarking.rst, developer.rst, faq.rst, glossary.rst, index.rst, installation.rst, release.rst, usage.rst
loading intersphinx inventory from https://docs.python.org/3.12/objects.inv...
WARNING: failed to reach any of the inventories with the following issues:
intersphinx inventory 'https://docs.python.org/3.12/objects.inv' not fetchable due to <class 'requests.exceptions.ConnectionError'>: HTTPSConnectionPool(host='docs.python.org', port=443): Max retries exceeded with url: /3.12/objects.inv (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x3ff9bb9ac30>: Failed to establish a new connection: [Errno -3] Temporary failure in name resolution'))
building [mo]: targets for 0 po files that are out of date
writing output...
building [html]: targets for 9 source files that are out of date
updating environment: [new config] 9 added, 0 changed, 0 removed
reading sources... [100%] usage
looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
copying assets... copying static files... done
copying extra files... done
done
writing output... [100%] usage
generating indices... genindex done
writing additional pages... search done
dumping search index in English (code: en)... done
dumping object inventory... done
build succeeded, 1 warning.
The HTML pages are in html.
+ rm -rf html/.doctrees html/.buildinfo
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.eOgOtc
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x
++ dirname /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd pysam-0.21.0
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=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 '
+ /usr/bin/python3 setup.py install -O1 --skip-build --root /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x --prefix /usr
/builddir/build/BUILD/pysam-0.21.0/setup.py:435: SyntaxWarning: invalid escape sequence '\S'
"#define (\S+)\s+(\S+)", line).groups()
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is shared
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
# pysam: (env) CC=gcc
# pysam: (env) CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC
# pysam: (env) 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
checking for 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 ranlib... ranlib
checking for grep that handles long lines and -e... /usr/bin/grep
checking for C compiler warning flags... -Wall
configure: Default CFLAGS_ARM/X86: -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC
checking whether C compiler accepts -mssse3 -mpopcnt -msse4.1... no
checking whether C compiler accepts -mavx2... no
checking whether C compiler accepts -mavx512f... no
checking whether C compiler supports ARM Neon... no
checking for pkg-config... /usr/bin/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 unknown-Linux... plain .so
checking whether the linker supports versioned symbols... no
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 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... no
checking for curl_easy_pause in -lcurl... no
checking for curl_easy_init in -lcurl... no
configure: error: libcurl library not found
Support for HTTPS and other SSL-based URLs requires routines from the libcurl
library <http://curl.se/libcurl/>. Building HTSlib with libcurl enabled
requires libcurl development files to be installed on the build machine; you
may need to ensure a package such as libcurl4-{gnutls,nss,openssl}-dev (on
Debian or Ubuntu Linux) or libcurl-devel (on RPM-based Linux distributions
or Cygwin) is installed.
Either configure with --disable-libcurl or resolve this error to build HTSlib.
checking for 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 ranlib... ranlib
checking for grep that handles long lines and -e... /usr/bin/grep
checking for C compiler warning flags... -Wall
configure: Default CFLAGS_ARM/X86: -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC
checking whether C compiler accepts -mssse3 -mpopcnt -msse4.1... no
checking whether C compiler accepts -mavx2... no
checking whether C compiler accepts -mavx512f... no
checking whether C compiler supports ARM Neon... no
checking for pkg-config... /usr/bin/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 unknown-Linux... plain .so
checking whether the linker supports versioned symbols... no
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 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
configure: WARNING: GCS support not enabled: requires libcurl support
configure: WARNING: S3 support not enabled: requires libcurl support
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: config.h is unchanged
config.status: linking htscodecs_bundled.mk to htscodecs.mk
# pysam: htslib configure options: --disable-libcurl
# pysam: htslib_config HTS_CFLAGS_AVX2=
# pysam: htslib_config HTS_CFLAGS_AVX512=
# pysam: htslib_config HTS_CFLAGS_SSE4=
# pysam: htslib_config HTS_HAVE_NEON=
# pysam: htslib_config LIBHTS_OBJS=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_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o
# pysam: htslib_config LIBS=-llzma -lbz2 -lz -lm
# pysam: htslib_config PLATFORM=default
# pysam: config_option: ENABLE_GCS=0
# pysam: config_option: ENABLE_PLUGINS=0
# pysam: config_option: ENABLE_S3=0
# pysam: config_option: HAVE_COMMONCRYPTO=0
# pysam: config_option: HAVE_HMAC=0
# pysam: config_option: HAVE_LIBBZ2=1
# pysam: config_option: HAVE_LIBCURL=0
# pysam: config_option: HAVE_LIBDEFLATE=0
# pysam: config_option: HAVE_LIBLZMA=1
# pysam: config_option: HAVE_MMAP=1
running install
/usr/lib/python3.12/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
!!
********************************************************************************
Please avoid running ``setup.py`` directly.
Instead, use pypa/build, pypa/installer, pypa/build or
other standards-based tools.
Follow the current Python packaging guidelines when building
Python RPM packages.
See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html
and https://docs.fedoraproject.org/en-US/packaging-guidelines/Python/ for details.
********************************************************************************
!!
self.initialize_options()
running install_lib
creating /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr
creating /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64
creating /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12
creating /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages
creating /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
creating /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/__pycache__
copying build/lib.linux-s390x-cpython-312/pysam/__pycache__/version.cpython-312.pyc -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/__pycache__
copying build/lib.linux-s390x-cpython-312/pysam/__pycache__/config.cpython-312.pyc -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/__pycache__
copying build/lib.linux-s390x-cpython-312/pysam/__pycache__/samtools.cpython-312.pyc -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/__pycache__
copying build/lib.linux-s390x-cpython-312/pysam/__pycache__/Pileup.cpython-312.pyc -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/__pycache__
copying build/lib.linux-s390x-cpython-312/pysam/__pycache__/utils.cpython-312.pyc -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/__pycache__
copying build/lib.linux-s390x-cpython-312/pysam/__pycache__/__init__.cpython-312.pyc -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/__pycache__
copying build/lib.linux-s390x-cpython-312/pysam/libcvcf.cpython-312-s390x-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/libctabixproxies.cpython-312-s390x-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/libcbgzf.cpython-312-s390x-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/libcbcf.cpython-312-s390x-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/libcfaidx.cpython-312-s390x-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/libctabix.cpython-312-s390x-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/libcalignedsegment.cpython-312-s390x-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/libcsamfile.cpython-312-s390x-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/libcalignmentfile.cpython-312-s390x-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/libcutils.cpython-312-s390x-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/libcbcftools.cpython-312-s390x-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/libcsamtools.cpython-312-s390x-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/libchtslib.cpython-312-s390x-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/version.pyi -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/version.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/pysam_util.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/pysam_util.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/pysam_stream.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/py.typed -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/libcvcf.pyx -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/libcvcf.pyi -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/libcvcf.pxd -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/libcutils.pyx -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/libcutils.pyi -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/libcutils.pxd -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/libctabixproxies.pyx -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/libctabixproxies.pyi -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/libctabixproxies.pxd -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/libctabix.pyx -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/libctabix.pyi -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/libctabix.pxd -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/libcsamtools.pyx -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/libcsamtools.pyi -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/libcsamtools.pxd -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/libcsamfile.pyx -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/libcsamfile.pyi -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/libcsamfile.pxd -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/libchtslib.pyx -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/libchtslib.pyi -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/libchtslib.pxd -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/libcfaidx.pyx -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/libcfaidx.pyi -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/libcfaidx.pxd -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/libcbgzf.pyx -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/libcbgzf.pyi -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/libcbcftools.pyx -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/libcbcftools.pyi -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/libcbcftools.pxd -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/libcbcf.pyx -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/libcbcf.pyi -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/libcbcf.pxd -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/libcalignmentfile.pyx -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/libcalignmentfile.pyi -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/libcalignmentfile.pxd -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/libcalignedsegment.pyx -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/libcalignedsegment.pyi -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/libcalignedsegment.pxd -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/htslib_util.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/htslib_util.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/csamtools_util.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/cbcftools_util.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
creating /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include
creating /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib
creating /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib/vcfutils.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib/vcf_sweep.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib/vcf.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib/thread_pool.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib/tbx.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib/synced_bcf_reader.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib/sam.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib/regidx.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib/kstring.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib/ksort.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib/kseq.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib/kroundup.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib/knetfile.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib/klist.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib/khash_str2int.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib/khash.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib/kfunc.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib/kbitset.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib/hts_os.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib/hts_log.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib/hts_expr.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib/hts_endian.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib/hts_defs.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib/hts.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib/hfile.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib/faidx.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib/cram.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib/bgzf.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/config.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib
creating /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/os
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/os/rand.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/os
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/os/lzma_stub.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/os
creating /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/m4
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/m4/pkg.m4 -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/m4
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/m4/hts_prog_cc_warnings.m4 -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/m4
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/m4/hts_hide_dynamic_syms.m4 -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/m4
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/m4/ax_check_compile_flag.m4 -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/m4
creating /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs
creating /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs/version.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs/varint2.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs/varint.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs/utils.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs/utils.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs/tokenise_name3.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs/tokenise_name3.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rle.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rle.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_word.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static4x16pr.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static4x16.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_sse4.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_neon.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_avx512.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_avx2.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static16_int.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_byte.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs/pooled_alloc.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs/permute.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs/pack.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs/pack.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs/htscodecs_endian.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs/htscodecs.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs/htscodecs.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs/fqzcomp_qual.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs/fqzcomp_qual.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs/c_simple_model.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs/c_range_coder.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs/arith_dynamic.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs/htscodecs/arith_dynamic.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs
creating /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/cram/string_alloc.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/cram/string_alloc.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/cram/pooled_alloc.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/cram/pooled_alloc.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/cram/os.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/cram/open_trace_file.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/cram/open_trace_file.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/cram/misc.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/cram/mFILE.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/cram/mFILE.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/cram/cram_structs.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/cram/cram_stats.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/cram/cram_stats.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/cram/cram_samtools.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/cram/cram_io.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/cram/cram_io.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/cram/cram_index.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/cram/cram_index.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/cram/cram_external.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/cram/cram_encode.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/cram/cram_encode.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/cram/cram_decode.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/cram/cram_decode.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/cram/cram_codecs.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/cram/cram_codecs.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/cram/cram.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/version.sh -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/vcfutils.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/vcf_sweep.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/vcf.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/thread_pool_internal.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/thread_pool.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/textutils_internal.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/textutils.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/tbx.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/tabix.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/synced_bcf_reader.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/sam_internal.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/sam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/region.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/regidx.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/realn.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/probaln.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/plugin.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/multipart.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/md5.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/kstring.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/kfunc.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib_vars.mk -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib.pc.in -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htslib.mk -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htsfile.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs_external.mk -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/htscodecs_bundled.mk -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/hts_time_funcs.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/hts_os.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/hts_internal.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/hts_expr.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/hts.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/hfile_s3_write.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/hfile_s3.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/hfile_libcurl.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/hfile_internal.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/hfile_gcs.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/hfile.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/header.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/header.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/faidx.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/errmod.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/configure.ac -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/configure -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/config.mk.in -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/config.h.in -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/builddir_vars.mk.in -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/bgzip.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/bgzf.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/bcf_sr_sort.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/bcf_sr_sort.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/README -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/Makefile -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib
copying build/lib.linux-s390x-cpython-312/pysam/include/htslib/LICENSE -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/htslib
creating /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/config.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/version.sh -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/version.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/version.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/vcmp.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/vcmp.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/vcmp.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/vcfview.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/vcfview.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/vcfstats.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/vcfstats.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/vcfsort.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/vcfsort.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/vcfsom.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/vcfsom.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/vcfroh.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/vcfroh.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/vcfquery.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/vcfquery.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/vcfplugin.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/vcfplugin.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/vcfnorm.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/vcfnorm.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/vcfmerge.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/vcfmerge.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/vcfisec.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/vcfisec.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/vcfindex.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/vcfindex.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/vcfhead.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/vcfhead.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/vcfgtcheck.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/vcfgtcheck.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/vcffilter.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/vcffilter.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/vcfconvert.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/vcfconvert.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/vcfconcat.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/vcfconcat.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/vcfcnv.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/vcfcnv.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/vcfcall.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/vcfcall.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/vcfbuf.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/vcfbuf.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/vcfbuf.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/vcfannotate.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/vcfannotate.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/variantkey.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/utlist.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/tsv2vcf.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/tsv2vcf.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/tsv2vcf.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/tabix.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/tabix.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/str_finder.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/str_finder.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/str_finder.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/smpl_ilist.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/smpl_ilist.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/smpl_ilist.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/reheader.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/reheader.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/regidx.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/regidx.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/regidx.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/read_consensus.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/read_consensus.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/read_consensus.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/rbuf.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/prob1.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/prob1.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/prob1.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/ploidy.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/ploidy.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/ploidy.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/mw.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/mpileup.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/mpileup.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/mcall.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/mcall.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/main.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/main.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/kmin.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/kmin.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/kmin.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/kheap.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/khash_str2str.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/hex.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/hclust.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/hclust.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/hclust.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/gvcf.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/gvcf.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/gvcf.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/filter.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/filter.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/filter.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/extsort.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/extsort.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/extsort.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/em.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/em.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/dist.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/dist.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/dist.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/dbuf.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/csq.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/csq.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/convert.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/convert.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/convert.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/consensus.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/consensus.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/cols.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/cols.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/cols.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/cigar_state.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/ccall.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/ccall.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/call.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/bin.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/bin.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/bin.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/bcftools.pysam.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/bcftools.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/bcftools.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/bam_sample.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/bam_sample.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/bam_sample.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/bam2bcf_indel.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/bam2bcf_indel.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/bam2bcf_iaux.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/bam2bcf_iaux.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/bam2bcf.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/bam2bcf.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/bam2bcf.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/abuf.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/abuf.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/abuf.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/README -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/LICENSE -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/HMM.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/HMM.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
copying build/lib.linux-s390x-cpython-312/pysam/include/bcftools/HMM.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/bcftools
creating /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/config.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
creating /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools/lz4
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/lz4/lz4.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools/lz4
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/lz4/lz4.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools/lz4
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/lz4/lz4.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools/lz4
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/lz4/LICENSE -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools/lz4
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/version.sh -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/tmp_file.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/tmp_file.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/tmp_file.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/stats_isize.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/stats_isize.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/stats_isize.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/stats.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/stats.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/splaysort.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/samtools.pysam.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/samtools.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/samtools.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/sample.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/sample.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/sample.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/sam_view.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/sam_view.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/sam_utils.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/sam_utils.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/sam_utils.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/sam_opts.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/sam_opts.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/sam_opts.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/reset.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/reset.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/reference.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/reference.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/phase.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/phase.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/padding.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/padding.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/faidx.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/faidx.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/dict.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/dict.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/cut_target.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/cut_target.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/cram_size.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/cram_size.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/coverage.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/coverage.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/consensus_pileup.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/consensus_pileup.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/consensus_pileup.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bedidx.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bedidx.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bedidx.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bedcov.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bedcov.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bamtk.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bamtk.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bamshuf.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bamshuf.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bam_stat.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bam_stat.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bam_split.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bam_split.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bam_sort.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bam_sort.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bam_samples.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bam_samples.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bam_rmdupse.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bam_rmdupse.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bam_rmdup.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bam_rmdup.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bam_reheader.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bam_reheader.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bam_quickcheck.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bam_quickcheck.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bam_plcmd.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bam_plcmd.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bam_plbuf.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bam_plbuf.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bam_plbuf.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bam_md.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bam_md.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bam_mate.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bam_mate.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bam_markdup.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bam_markdup.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bam_lpileup.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bam_lpileup.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bam_lpileup.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bam_index.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bam_index.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bam_import.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bam_import.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bam_flags.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bam_flags.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bam_fastq.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bam_fastq.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bam_consensus.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bam_consensus.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bam_color.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bam_color.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bam_cat.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bam_cat.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bam_aux.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bam_aux.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bam_ampliconclip.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bam_ampliconclip.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bam_ampliconclip.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bam_addrprg.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bam_addrprg.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bam2depth.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bam2depth.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bam.h -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bam.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/bam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/amplicon_stats.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/amplicon_stats.c -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/README -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/samtools/LICENSE -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/samtools
copying build/lib.linux-s390x-cpython-312/pysam/include/__init__.py -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include
copying build/lib.linux-s390x-cpython-312/pysam/Pileup.py -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/__init__.py -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/bcftools.py -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/samtools.py -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/utils.py -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/version.py -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
copying build/lib.linux-s390x-cpython-312/pysam/config.py -> /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam
byte-compiling /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/include/__init__.py to __init__.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/bcftools.py to bcftools.cpython-312.pyc
writing byte-compilation script '/tmp/tmpfh0zilkw.py'
/usr/bin/python3 /tmp/tmpfh0zilkw.py
removing /tmp/tmpfh0zilkw.py
running install_egg_info
running egg_info
writing pysam.egg-info/PKG-INFO
writing dependency_links to pysam.egg-info/dependency_links.txt
writing requirements to pysam.egg-info/requires.txt
writing top-level names to pysam.egg-info/top_level.txt
reading manifest file 'pysam.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'KNOWN_BUGS'
warning: no files found matching 'THANKS'
no previously-included directories found matching 'tests/'
adding license file 'COPYING'
adding license file 'AUTHORS'
writing manifest file 'pysam.egg-info/SOURCES.txt'
Copying pysam.egg-info to /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam-0.21.0-py3.12.egg-info
running install_scripts
+ rm -rfv /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/bin/__pycache__
+ rm /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/libcalignedsegment.pyx /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/libcalignmentfile.pyx /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/libcbcf.pyx /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/libcbcftools.pyx /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/libcbgzf.pyx /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/libcfaidx.pyx /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/libchtslib.pyx /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/libcsamfile.pyx /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/libcsamtools.pyx /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/libctabix.pyx /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/libctabixproxies.pyx /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/libcutils.pyx /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/libcvcf.pyx
+ rm /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/htslib_util.c /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12/site-packages/pysam/pysam_util.c
+ /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 0.21.0-2.fc40 --unique-debug-suffix -0.21.0-2.fc40.s390x --unique-debug-src-base python-pysam-0.21.0-2.fc40.s390x --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/pysam-0.21.0
find-debuginfo: starting
Extracting debug info from 13 files
DWARF-compressing 13 files
sepdebugcrcfix: Updated 13 CRC32s, 0 CRC32s did match.
Creating .debug symlinks for symlinks to ELF files
Copying sources found by 'debugedit -l' to /usr/src/debug/python-pysam-0.21.0-2.fc40.s390x
52963 blocks
find-debuginfo: done
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-ldconfig
+ /usr/lib/rpm/brp-compress
+ /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip
+ /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip
+ /usr/lib/rpm/check-rpaths
+ /usr/lib/rpm/redhat/brp-mangle-shebangs
mangling shebang in /usr/lib64/python3.12/site-packages/pysam/include/samtools/version.sh from /bin/sh to #!/usr/bin/sh
mangling shebang in /usr/lib64/python3.12/site-packages/pysam/include/bcftools/version.sh from /bin/sh to #!/usr/bin/sh
mangling shebang in /usr/lib64/python3.12/site-packages/pysam/include/htslib/configure from /bin/sh to #!/usr/bin/sh
mangling shebang in /usr/lib64/python3.12/site-packages/pysam/include/htslib/version.sh from /bin/sh to #!/usr/bin/sh
+ /usr/lib/rpm/brp-remove-la-files
+ env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j2
Bytecompiling .py files below /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib/debug/usr/lib64/python3.12 using python3.12
Bytecompiling .py files below /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/lib64/python3.12 using python3.12
+ /usr/lib/rpm/redhat/brp-python-hardlink
Processing files: python3-pysam-0.21.0-2.fc40.s390x
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.T9Y7hW
+ umask 022
+ cd /builddir/build/BUILD
+ cd pysam-0.21.0
+ DOCDIR=/builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/share/doc/python3-pysam
+ export LC_ALL=
+ LC_ALL=
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/share/doc/python3-pysam
+ cp -pr /builddir/build/BUILD/pysam-0.21.0/README.rst /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/share/doc/python3-pysam
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.4g73OL
+ umask 022
+ cd /builddir/build/BUILD
+ cd pysam-0.21.0
+ LICENSEDIR=/builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/share/licenses/python3-pysam
+ export LC_ALL=
+ LC_ALL=
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/share/licenses/python3-pysam
+ cp -pr /builddir/build/BUILD/pysam-0.21.0/COPYING /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/share/licenses/python3-pysam
+ cp -pr /builddir/build/BUILD/pysam-0.21.0/bcftools/LICENSE /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/share/licenses/python3-pysam
+ cp -pr /builddir/build/BUILD/pysam-0.21.0/htslib/LICENSE /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/share/licenses/python3-pysam
+ cp -pr /builddir/build/BUILD/pysam-0.21.0/samtools/LICENSE /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/share/licenses/python3-pysam
+ RPM_EC=0
++ jobs -p
+ exit 0
warning: File listed twice: /usr/share/licenses/python3-pysam/LICENSE
warning: File listed twice: /usr/share/licenses/python3-pysam/LICENSE
Provides: bundled(bcftools) = 1.18 bundled(htslib) = 1.18 bundled(samtools) = 1.18 libcalignedsegment.cpython-312-s390x-linux-gnu.so()(64bit) libcalignmentfile.cpython-312-s390x-linux-gnu.so()(64bit) libcbcf.cpython-312-s390x-linux-gnu.so()(64bit) libcbcftools.cpython-312-s390x-linux-gnu.so()(64bit) libcbgzf.cpython-312-s390x-linux-gnu.so()(64bit) libcfaidx.cpython-312-s390x-linux-gnu.so()(64bit) libchtslib.cpython-312-s390x-linux-gnu.so()(64bit) libcsamfile.cpython-312-s390x-linux-gnu.so()(64bit) libcsamtools.cpython-312-s390x-linux-gnu.so()(64bit) libctabix.cpython-312-s390x-linux-gnu.so()(64bit) libctabixproxies.cpython-312-s390x-linux-gnu.so()(64bit) libcutils.cpython-312-s390x-linux-gnu.so()(64bit) libcvcf.cpython-312-s390x-linux-gnu.so()(64bit) python-pysam = 0.21.0-2.fc40 python3-pysam = 0.21.0-2.fc40 python3-pysam(s390-64) = 0.21.0-2.fc40 python3.12-pysam = 0.21.0-2.fc40 python3.12dist(pysam) = 0.21 python3dist(pysam) = 0.21
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PartialHardlinkSets) <= 4.0.4-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: libbz2.so.1()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.11)(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_2.38)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.7)(64bit) libcbcftools.cpython-312-s390x-linux-gnu.so()(64bit) libchtslib.cpython-312-s390x-linux-gnu.so()(64bit) libcsamtools.cpython-312-s390x-linux-gnu.so()(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) libm.so.6(GLIBC_2.4)(64bit) libz.so.1()(64bit) python(abi) = 3.12 python3.12dist(cython) rtld(GNU_HASH)
Obsoletes: python-pysam < 0.21.0-2.fc40
Processing files: python3-pysam-devel-0.21.0-2.fc40.s390x
Provides: python-pysam-devel = 0.21.0-2.fc40 python3-pysam-devel = 0.21.0-2.fc40 python3-pysam-devel(s390-64) = 0.21.0-2.fc40 python3.12-pysam-devel = 0.21.0-2.fc40
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PartialHardlinkSets) <= 4.0.4-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: /usr/bin/sh python(abi) = 3.12
Processing files: python-pysam-doc-0.21.0-2.fc40.noarch
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.QOUC59
+ umask 022
+ cd /builddir/build/BUILD
+ cd pysam-0.21.0
+ DOCDIR=/builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/share/doc/python-pysam-doc
+ export LC_ALL=
+ LC_ALL=
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/share/doc/python-pysam-doc
+ cp -pr /builddir/build/BUILD/pysam-0.21.0/html /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x/usr/share/doc/python-pysam-doc
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: python-pysam-doc = 0.21.0-2.fc40
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: python-pysam-debugsource-0.21.0-2.fc40.s390x
Provides: python-pysam-debugsource = 0.21.0-2.fc40 python-pysam-debugsource(s390-64) = 0.21.0-2.fc40
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: python3-pysam-debuginfo-0.21.0-2.fc40.s390x
Provides: debuginfo(build-id) = 03c9f971459bf204a23d2f49327e974bde853e6f debuginfo(build-id) = 0578e0281ee1875b2128ee4a690a8dff55c16db3 debuginfo(build-id) = 2d61f6ce32510012ac4c8edb132e2d7c2b84c8d7 debuginfo(build-id) = 38645d08635723c6ae3f4a2620f633ee69b082c4 debuginfo(build-id) = 5005a4b5f690b900ad3a6379f511d3b2ebd56eb7 debuginfo(build-id) = 50c7ae32090e5f5761baf9dbf845ce73bde7833c debuginfo(build-id) = 549587f08ea58fdf80ddf0739536bc4dab08b9e8 debuginfo(build-id) = 58d73d8ba20fb8e66347500ab02716dfacd64ad0 debuginfo(build-id) = 69db5fd6389ef0d7bb450694351f084787e4c1e1 debuginfo(build-id) = 8fea07f6f84e188598296fdaf04cc6a2e2f90e89 debuginfo(build-id) = 918153547ecba172430a42785492cd0f80c59ff5 debuginfo(build-id) = b2a3172b79b6fc1b303187291954eed987ff48e5 debuginfo(build-id) = b3b7e94bd28b87a252c4f0411674ec56953e41b2 libcalignedsegment.cpython-312-s390x-linux-gnu.so-0.21.0-2.fc40.s390x.debug()(64bit) libcalignmentfile.cpython-312-s390x-linux-gnu.so-0.21.0-2.fc40.s390x.debug()(64bit) libcbcf.cpython-312-s390x-linux-gnu.so-0.21.0-2.fc40.s390x.debug()(64bit) libcbcftools.cpython-312-s390x-linux-gnu.so-0.21.0-2.fc40.s390x.debug()(64bit) libcbgzf.cpython-312-s390x-linux-gnu.so-0.21.0-2.fc40.s390x.debug()(64bit) libcfaidx.cpython-312-s390x-linux-gnu.so-0.21.0-2.fc40.s390x.debug()(64bit) libchtslib.cpython-312-s390x-linux-gnu.so-0.21.0-2.fc40.s390x.debug()(64bit) libcsamfile.cpython-312-s390x-linux-gnu.so-0.21.0-2.fc40.s390x.debug()(64bit) libcsamtools.cpython-312-s390x-linux-gnu.so-0.21.0-2.fc40.s390x.debug()(64bit) libctabix.cpython-312-s390x-linux-gnu.so-0.21.0-2.fc40.s390x.debug()(64bit) libctabixproxies.cpython-312-s390x-linux-gnu.so-0.21.0-2.fc40.s390x.debug()(64bit) libcutils.cpython-312-s390x-linux-gnu.so-0.21.0-2.fc40.s390x.debug()(64bit) libcvcf.cpython-312-s390x-linux-gnu.so-0.21.0-2.fc40.s390x.debug()(64bit) python-pysam-debuginfo = 0.21.0-2.fc40 python3-pysam-debuginfo = 0.21.0-2.fc40 python3-pysam-debuginfo(s390-64) = 0.21.0-2.fc40 python3.12-pysam-debuginfo = 0.21.0-2.fc40
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: python-pysam-debugsource(s390-64) = 0.21.0-2.fc40
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x
Wrote: /builddir/build/RPMS/python3-pysam-debuginfo-0.21.0-2.fc40.s390x.rpm
Wrote: /builddir/build/RPMS/python-pysam-debugsource-0.21.0-2.fc40.s390x.rpm
Wrote: /builddir/build/RPMS/python3-pysam-devel-0.21.0-2.fc40.s390x.rpm
Wrote: /builddir/build/RPMS/python-pysam-doc-0.21.0-2.fc40.noarch.rpm
Wrote: /builddir/build/RPMS/python3-pysam-0.21.0-2.fc40.s390x.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.GPZd2q
+ umask 022
+ cd /builddir/build/BUILD
+ cd pysam-0.21.0
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/python-pysam-0.21.0-2.fc40.s390x
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.65zAg8
+ umask 022
+ cd /builddir/build/BUILD
+ rm -rf /builddir/build/BUILD/pysam-0.21.0-SPECPARTS
+ rm -rf pysam-0.21.0 pysam-0.21.0.gemspec
+ RPM_EC=0
++ jobs -p
+ exit 0
RPM build warnings:
File listed twice: /usr/share/licenses/python3-pysam/LICENSE
File listed twice: /usr/share/licenses/python3-pysam/LICENSE
Finish: rpmbuild python-pysam-0.21.0-2.fc40.src.rpm
Finish: build phase for python-pysam-0.21.0-2.fc40.src.rpm
INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/fedora-rawhide-s390x-1694975550.734558/root/var/log/dnf.rpm.log
/var/lib/mock/fedora-rawhide-s390x-1694975550.734558/root/var/log/dnf.librepo.log
/var/lib/mock/fedora-rawhide-s390x-1694975550.734558/root/var/log/dnf.log
INFO: Done(/var/lib/copr-rpmbuild/results/python-pysam-0.21.0-2.fc40.src.rpm) Config(child) 8 minutes 11 seconds
INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results
INFO: Cleaning up build root ('cleanup_on_success=True')
Start: clean chroot
INFO: unmounting tmpfs.
Finish: clean chroot
Finish: run
Running RPMResults tool
Package info:
{
"packages": [
{
"name": "python3-pysam-debuginfo",
"epoch": null,
"version": "0.21.0",
"release": "2.fc40",
"arch": "s390x"
},
{
"name": "python-pysam",
"epoch": null,
"version": "0.21.0",
"release": "2.fc40",
"arch": "src"
},
{
"name": "python-pysam-doc",
"epoch": null,
"version": "0.21.0",
"release": "2.fc40",
"arch": "noarch"
},
{
"name": "python-pysam-debugsource",
"epoch": null,
"version": "0.21.0",
"release": "2.fc40",
"arch": "s390x"
},
{
"name": "python3-pysam",
"epoch": null,
"version": "0.21.0",
"release": "2.fc40",
"arch": "s390x"
},
{
"name": "python3-pysam-devel",
"epoch": null,
"version": "0.21.0",
"release": "2.fc40",
"arch": "s390x"
}
]
}
RPMResults finished