Warning: Permanently added '3.233.237.166' (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/8422031-fedora-rawhide-x86_64 --chroot fedora-rawhide-x86_64
Version: 1.2
PID: 55735
Logging PID: 55736
Task:
{'allow_user_ssh': False,
'appstream': False,
'background': True,
'build_id': 8422031,
'buildroot_pkgs': [],
'chroot': 'fedora-rawhide-x86_64',
'enable_net': False,
'fedora_review': False,
'git_hash': 'b5ea879f7292bc99237e893383d5313ad68d9b55',
'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/dmalcolm/gcc-15-smoketest-3/htslib',
'isolation': 'default',
'memory_reqs': 2048,
'package_name': 'htslib',
'package_version': '1.15.1-6',
'project_dirname': 'gcc-15-smoketest-3',
'project_name': 'gcc-15-smoketest-3',
'project_owner': 'dmalcolm',
'repo_priority': None,
'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/dmalcolm/gcc-15-smoketest-3/fedora-rawhide-x86_64/',
'id': 'copr_base',
'name': 'Copr repository',
'priority': None},
{'baseurl': 'https://fedorapeople.org/~dmalcolm/gcc/gcc-15-mass-prebuild/$basearch',
'id': 'https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch',
'name': 'Additional repo https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch'}],
'sandbox': 'dmalcolm/gcc-15-smoketest-3--dmalcolm',
'source_json': {},
'source_type': None,
'ssh_public_keys': None,
'storage': 0,
'submitter': 'dmalcolm',
'tags': [],
'task_id': '8422031-fedora-rawhide-x86_64',
'timeout': 115200,
'uses_devel_repo': False,
'with_opts': [],
'without_opts': []}
Running: git clone https://copr-dist-git.fedorainfracloud.org/git/dmalcolm/gcc-15-smoketest-3/htslib /var/lib/copr-rpmbuild/workspace/workdir-uzl_7l2j/htslib --depth 500 --no-single-branch --recursive
cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/dmalcolm/gcc-15-smoketest-3/htslib', '/var/lib/copr-rpmbuild/workspace/workdir-uzl_7l2j/htslib', '--depth', '500', '--no-single-branch', '--recursive']
cwd: .
rc: 0
stdout:
stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-uzl_7l2j/htslib'...
Running: git checkout b5ea879f7292bc99237e893383d5313ad68d9b55 --
cmd: ['git', 'checkout', 'b5ea879f7292bc99237e893383d5313ad68d9b55', '--']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-uzl_7l2j/htslib
rc: 0
stdout:
stderr: Note: switching to 'b5ea879f7292bc99237e893383d5313ad68d9b55'.
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 b5ea879 automatic import of htslib
Running: dist-git-client sources
cmd: ['dist-git-client', 'sources']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-uzl_7l2j/htslib
rc: 0
stdout:
stderr: INFO: Reading stdout from command: git rev-parse --abbrev-ref HEAD
INFO: Reading stdout from command: git rev-parse HEAD
INFO: Reading sources specification file: sources
INFO: Downloading htslib-1.15.1.tar.bz2
INFO: Reading stdout from command: curl --help all
INFO: Calling: curl -H Pragma: -o htslib-1.15.1.tar.bz2 --location --connect-timeout 60 --retry 3 --retry-delay 10 --remote-time --show-error --fail --retry-all-errors https://copr-dist-git.fedorainfracloud.org/repo/pkgs/dmalcolm/gcc-15-smoketest-3/htslib/htslib-1.15.1.tar.bz2/md5/9ea5cff8edcebb01f31dd02bd4d2a082/htslib-1.15.1.tar.bz2
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 4044k 100 4044k 0 0 23.4M 0 --:--:-- --:--:-- --:--:-- 23.5M
INFO: Reading stdout from command: md5sum htslib-1.15.1.tar.bz2
/usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated
Running (timeout=115200): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-uzl_7l2j/htslib/htslib.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-uzl_7l2j/htslib --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1734677548.851901 -r /var/lib/copr-rpmbuild/results/configs/child.cfg
INFO: mock.py version 5.9 starting (python version = 3.13.0, NVR = mock-5.9-1.fc41), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-uzl_7l2j/htslib/htslib.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-uzl_7l2j/htslib --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1734677548.851901 -r /var/lib/copr-rpmbuild/results/configs/child.cfg
Start(bootstrap): init plugins
INFO: tmpfs initialized
INFO: selinux enabled
INFO: chroot_scan: initialized
INFO: compress_logs: initialized
Finish(bootstrap): init plugins
Start: init plugins
INFO: tmpfs initialized
INFO: selinux enabled
INFO: chroot_scan: initialized
INFO: compress_logs: initialized
Finish: init plugins
INFO: Signal handler active
Start: run
INFO: Start(/var/lib/copr-rpmbuild/workspace/workdir-uzl_7l2j/htslib/htslib.spec) Config(fedora-rawhide-x86_64)
Start: clean chroot
Finish: clean chroot
Mock Version: 5.9
INFO: Mock Version: 5.9
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1734677548.851901/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-x86_64-bootstrap-1734677548.851901/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/9bb63223b0edd5117748d1887a39e0598d413c3632292df88c0e2c213cc02217/merged
INFO: umounting image registry.fedoraproject.org/fedora:rawhide (/var/lib/containers/storage/overlay/9bb63223b0edd5117748d1887a39e0598d413c3632292df88c0e2c213cc02217/merged) with podman image umount
INFO: Package manager dnf5 detected and used (fallback)
INFO: Not updating bootstrap chroot, bootstrap_image_ready=True
Start(bootstrap): creating root cache
Finish(bootstrap): creating root cache
Finish(bootstrap): chroot init
Start: chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-1734677548.851901/root.
INFO: calling preinit hooks
INFO: enabled root cache
INFO: enabled package manager cache
Start: cleaning package manager metadata
Finish: cleaning package manager metadata
INFO: enabled HW Info plugin
INFO: Package manager dnf5 detected and used (direct choice)
INFO: Buildroot is handled by package management downloaded with a bootstrap image:
rpm-4.20.0-1.fc42.x86_64
rpm-sequoia-1.7.0-3.fc42.x86_64
dnf5-5.2.8.1-2.fc42.x86_64
dnf5-plugins-5.2.8.1-2.fc42.x86_64
Start: installing minimal buildroot with dnf5
Updating and loading repositories:
fedora 100% | 106.3 KiB/s | 28.1 KiB | 00m00s
Copr repository 100% | 102.4 KiB/s | 1.5 KiB | 00m00s
Additional repo https_fedorapeople_org 100% | 52.6 KiB/s | 1.5 KiB | 00m00s
Copr repository 100% | 50.3 MiB/s | 3.2 MiB | 00m00s
Repositories loaded.
Package Arch Version Repository Size
Installing group/module packages:
bash x86_64 5.2.37-1.fc42 fedora 8.2 MiB
bzip2 x86_64 1.0.8-19.fc42 copr_base 96.9 KiB
coreutils x86_64 9.5-11.fc42 copr_base 5.5 MiB
cpio x86_64 2.15-2.fc41 fedora 1.1 MiB
diffutils x86_64 3.10-8.fc42 copr_base 1.6 MiB
fedora-release-common noarch 42-0.11 fedora 19.8 KiB
findutils x86_64 1:4.10.0-4.fc42 copr_base 1.9 MiB
gawk x86_64 5.3.0-4.fc41 fedora 1.7 MiB
glibc-minimal-langpack x86_64 2.40.9000-24.fc42 copr_base 0.0 B
grep x86_64 3.11-9.fc42 copr_base 1.0 MiB
gzip x86_64 1.13-2.fc42 copr_base 391.0 KiB
info x86_64 7.1.1-2.fc42 fedora 361.8 KiB
patch x86_64 2.7.6-25.fc41 fedora 266.7 KiB
redhat-rpm-config noarch 300-1.no_annobin.0.fc42 copr_base 186.6 KiB
rpm-build x86_64 4.20.0-1.fc42 fedora 194.3 KiB
sed x86_64 4.9-3.fc41 fedora 861.5 KiB
shadow-utils x86_64 2:4.17.0~rc1-1.fc42 fedora 4.1 MiB
tar x86_64 2:1.35-4.fc41 fedora 2.9 MiB
unzip x86_64 6.0-65.fc42 fedora 398.2 KiB
util-linux x86_64 2.40.2-8.fc42 fedora 3.7 MiB
which x86_64 2.21-42.fc41 fedora 80.2 KiB
xz x86_64 1:5.6.3-2.fc42 fedora 1.2 MiB
Installing dependencies:
add-determinism x86_64 0.4.3-1.fc42 fedora 2.4 MiB
alternatives x86_64 1.31-1.fc42 fedora 64.8 KiB
ansible-srpm-macros noarch 1-16.fc41 fedora 35.7 KiB
audit-libs x86_64 4.0.2-1.fc42 copr_base 331.3 KiB
authselect x86_64 1.5.0-8.fc42 copr_base 156.0 KiB
authselect-libs x86_64 1.5.0-8.fc42 copr_base 820.0 KiB
basesystem noarch 11-21.fc41 fedora 0.0 B
binutils x86_64 2.43.50-9.fc42 copr_base 25.6 MiB
build-reproducibility-srpm-macros noarch 0.4.3-1.fc42 fedora 735.0 B
bzip2-libs x86_64 1.0.8-19.fc42 copr_base 83.2 KiB
ca-certificates noarch 2024.2.69_v8.0.401-3.fc42 fedora 2.6 MiB
coreutils-common x86_64 9.5-11.fc42 copr_base 11.2 MiB
cracklib x86_64 2.9.11-6.fc42 copr_base 238.1 KiB
crypto-policies noarch 20241128-1.gitbb7b0b0.fc42 fedora 137.3 KiB
curl x86_64 8.11.1-2.fc42 copr_base 452.0 KiB
cyrus-sasl-lib x86_64 2.1.28-27.fc41 fedora 2.3 MiB
debugedit x86_64 5.1-2.fc42 copr_base 197.7 KiB
dwz x86_64 0.15-8.fc42 copr_base 295.7 KiB
ed x86_64 1.20.2-2.fc41 fedora 146.9 KiB
efi-srpm-macros noarch 5-13.fc42 fedora 40.2 KiB
elfutils x86_64 0.192-7.fc42 copr_base 2.6 MiB
elfutils-debuginfod-client x86_64 0.192-7.fc42 copr_base 81.4 KiB
elfutils-default-yama-scope noarch 0.192-7.fc42 copr_base 1.8 KiB
elfutils-libelf x86_64 0.192-7.fc42 copr_base 1.2 MiB
elfutils-libs x86_64 0.192-7.fc42 copr_base 662.9 KiB
fedora-gpg-keys noarch 42-0.3 fedora 126.4 KiB
fedora-release noarch 42-0.11 fedora 0.0 B
fedora-release-identity-basic noarch 42-0.11 fedora 719.0 B
fedora-repos noarch 42-0.3 fedora 4.9 KiB
fedora-repos-rawhide noarch 42-0.3 fedora 2.2 KiB
file x86_64 5.45-8.fc42 fedora 103.7 KiB
file-libs x86_64 5.45-8.fc42 fedora 9.9 MiB
filesystem x86_64 3.18-29.fc42 fedora 106.0 B
filesystem-srpm-macros noarch 3.18-29.fc42 fedora 36.1 KiB
fonts-srpm-macros noarch 1:2.0.5-17.fc41 fedora 55.8 KiB
forge-srpm-macros noarch 0.4.0-1.fc42 fedora 38.9 KiB
fpc-srpm-macros noarch 1.3-13.fc41 fedora 144.0 B
gdb-minimal x86_64 15.2-4.fc42 copr_base 12.8 MiB
gdbm x86_64 1:1.23-7.fc41 fedora 460.9 KiB
gdbm-libs x86_64 1:1.23-7.fc41 fedora 121.9 KiB
ghc-srpm-macros noarch 1.9.2-1.fc42 fedora 779.0 B
glibc x86_64 2.40.9000-24.fc42 copr_base 6.5 MiB
glibc-common x86_64 2.40.9000-24.fc42 copr_base 1.0 MiB
glibc-gconv-extra x86_64 2.40.9000-24.fc42 copr_base 8.0 MiB
gmp x86_64 1:6.3.0-2.fc41 fedora 811.4 KiB
gnat-srpm-macros noarch 6-6.fc41 fedora 1.0 KiB
go-srpm-macros noarch 3.6.0-5.fc42 fedora 60.8 KiB
jansson x86_64 2.14-1.fc42 fedora 93.1 KiB
json-c x86_64 0.18-1.fc42 fedora 83.3 KiB
kernel-srpm-macros noarch 1.0-24.fc41 fedora 1.9 KiB
keyutils-libs x86_64 1.6.3-4.fc41 fedora 54.4 KiB
krb5-libs x86_64 1.21.3-3.fc42 fedora 2.3 MiB
libacl x86_64 2.3.2-2.fc42 copr_base 38.3 KiB
libarchive x86_64 3.7.7-1.fc42 fedora 932.3 KiB
libattr x86_64 2.5.2-4.fc41 fedora 28.5 KiB
libblkid x86_64 2.40.2-8.fc42 fedora 262.5 KiB
libbrotli x86_64 1.1.0-5.fc42 copr_base 836.4 KiB
libcap x86_64 2.71-1.fc42 fedora 210.8 KiB
libcap-ng x86_64 0.8.5-3.fc41 fedora 69.2 KiB
libcom_err x86_64 1.47.1-6.fc42 fedora 67.2 KiB
libcurl x86_64 8.11.1-2.fc42 copr_base 829.3 KiB
libeconf x86_64 0.7.5-1.fc42 fedora 66.7 KiB
libevent x86_64 2.1.12-14.fc41 fedora 895.7 KiB
libfdisk x86_64 2.40.2-8.fc42 fedora 362.9 KiB
libffi x86_64 3.4.6-3.fc42 fedora 86.4 KiB
libgcc x86_64 15.0.0-0.2.fc42 https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch 266.9 KiB
libgomp x86_64 15.0.0-0.2.fc42 https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch 529.3 KiB
libidn2 x86_64 2.3.7-2.fc41 fedora 329.1 KiB
libmount x86_64 2.40.2-8.fc42 fedora 355.8 KiB
libnghttp2 x86_64 1.64.0-1.fc42 fedora 174.5 KiB
libnsl2 x86_64 2.0.1-2.fc41 fedora 57.9 KiB
libpkgconf x86_64 2.3.0-1.fc42 fedora 78.2 KiB
libpsl x86_64 0.21.5-4.fc41 fedora 80.5 KiB
libpwquality x86_64 1.4.5-11.fc41 fedora 417.8 KiB
libselinux x86_64 3.8-0.rc1.2.fc42 fedora 191.6 KiB
libsemanage x86_64 3.8-0.rc1.1.fc42 fedora 305.3 KiB
libsepol x86_64 3.8-0.rc1.1.fc42 fedora 822.0 KiB
libsmartcols x86_64 2.40.2-8.fc42 fedora 180.4 KiB
libssh x86_64 0.11.1-1.fc42 fedora 569.6 KiB
libssh-config noarch 0.11.1-1.fc42 fedora 277.0 B
libstdc++ x86_64 15.0.0-0.2.fc42 https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch 2.7 MiB
libtasn1 x86_64 4.19.0-9.fc41 fedora 175.7 KiB
libtirpc x86_64 1.3.6-1.fc42 fedora 205.5 KiB
libtool-ltdl x86_64 2.5.4-1.fc42 copr_base 68.1 KiB
libunistring x86_64 1.1-8.fc41 fedora 1.7 MiB
libuuid x86_64 2.40.2-8.fc42 fedora 41.4 KiB
libverto x86_64 0.3.2-9.fc41 fedora 29.5 KiB
libxcrypt x86_64 4.4.36-11.fc42 fedora 271.4 KiB
libxml2 x86_64 2.12.8-2.fc41 fedora 1.7 MiB
libzstd x86_64 1.5.6-2.fc41 fedora 795.9 KiB
lua-libs x86_64 5.4.7-1.fc42 fedora 285.0 KiB
lua-srpm-macros noarch 1-14.fc41 fedora 1.3 KiB
lz4-libs x86_64 1.10.0-1.fc41 fedora 145.5 KiB
mpfr x86_64 4.2.1-5.fc41 fedora 832.1 KiB
ncurses-base noarch 6.5-2.20240629.fc41 fedora 326.3 KiB
ncurses-libs x86_64 6.5-2.20240629.fc41 fedora 975.2 KiB
ocaml-srpm-macros noarch 10-3.fc41 fedora 1.9 KiB
openblas-srpm-macros noarch 2-18.fc41 fedora 112.0 B
openldap x86_64 2.6.8-6.fc42 fedora 647.4 KiB
openssl-libs x86_64 1:3.2.2-8.fc42 fedora 7.8 MiB
p11-kit x86_64 0.25.5-4.fc42 fedora 2.2 MiB
p11-kit-trust x86_64 0.25.5-4.fc42 fedora 403.8 KiB
package-notes-srpm-macros noarch 0.5-12.fc41 fedora 1.6 KiB
pam x86_64 1.7.0-3.fc42 fedora 1.8 MiB
pam-libs x86_64 1.7.0-3.fc42 fedora 139.4 KiB
pcre2 x86_64 10.44-1.fc41.1 fedora 653.5 KiB
pcre2-syntax noarch 10.44-1.fc41.1 fedora 251.6 KiB
perl-srpm-macros noarch 1-56.fc41 fedora 861.0 B
pkgconf x86_64 2.3.0-1.fc42 fedora 88.6 KiB
pkgconf-m4 noarch 2.3.0-1.fc42 fedora 14.4 KiB
pkgconf-pkg-config x86_64 2.3.0-1.fc42 fedora 989.0 B
popt x86_64 1.19-7.fc41 fedora 136.9 KiB
publicsuffix-list-dafsa noarch 20240107-4.fc41 fedora 67.5 KiB
pyproject-srpm-macros noarch 1.16.3-1.fc42 fedora 1.9 KiB
python-srpm-macros noarch 3.13-3.fc41 fedora 51.0 KiB
qt5-srpm-macros noarch 5.15.15-1.fc42 fedora 500.0 B
qt6-srpm-macros noarch 6.8.1-4.fc42 fedora 456.0 B
readline x86_64 8.2-11.fc42 fedora 493.1 KiB
rpm x86_64 4.20.0-1.fc42 fedora 3.1 MiB
rpm-build-libs x86_64 4.20.0-1.fc42 fedora 206.7 KiB
rpm-libs x86_64 4.20.0-1.fc42 fedora 726.1 KiB
rpm-sequoia x86_64 1.7.0-3.fc42 fedora 2.3 MiB
rust-srpm-macros noarch 26.3-3.fc42 fedora 4.8 KiB
setup noarch 2.15.0-5.fc41 fedora 720.7 KiB
sqlite-libs x86_64 3.47.2-1.fc42 fedora 1.4 MiB
systemd-libs x86_64 257-1.fc42 fedora 2.2 MiB
util-linux-core x86_64 2.40.2-8.fc42 fedora 1.5 MiB
xxhash-libs x86_64 0.8.2-4.fc42 fedora 88.4 KiB
xz-libs x86_64 1:5.6.3-2.fc42 fedora 218.4 KiB
zig-srpm-macros noarch 1-3.fc41 fedora 1.1 KiB
zip x86_64 3.0-42.fc42 fedora 695.9 KiB
zlib-ng-compat x86_64 2.2.2-1.fc42 fedora 134.0 KiB
zstd x86_64 1.5.6-2.fc41 fedora 1.7 MiB
Installing groups:
Buildsystem building group
Transaction Summary:
Installing: 155 packages
Total size of inbound packages is 51 MiB. Need to download 0 B.
After this operation, 178 MiB extra will be used (install 178 MiB, remove 0 B).
[1/1] tar-2:1.35-4.fc41.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[1/1] Total 100% | 0.0 B/s | 0.0 B | 00m00s
[1/2] rpm-build-0:4.20.0-1.fc42.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[2/2] Total 100% | 0.0 B/s | 0.0 B | 00m00s
[1/3] unzip-0:6.0-65.fc42.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[3/3] Total 100% | 0.0 B/s | 0.0 B | 00m00s
[1/4] cpio-0:2.15-2.fc41.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[4/4] Total 100% | 0.0 B/s | 0.0 B | 00m00s
[1/5] which-0:2.21-42.fc41.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[5/5] Total 100% | 0.0 B/s | 0.0 B | 00m00s
[1/6] bash-0:5.2.37-1.fc42.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[6/6] Total 100% | 0.0 B/s | 0.0 B | 00m00s
[1/7] patch-0:2.7.6-25.fc41.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[7/7] Total 100% | 0.0 B/s | 0.0 B | 00m00s
[1/8] sed-0:4.9-3.fc41.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[8/8] Total 100% | 0.0 B/s | 0.0 B | 00m00s
[1/9] shadow-utils-2:4.17.0~rc1-1.fc42. 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[9/9] Total 100% | 0.0 B/s | 0.0 B | 00m00s
[ 1/10] fedora-release-common-0:42-0.11 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[10/10] Total 100% | 0.0 B/s | 0.0 B | 00m00s
[ 1/11] info-0:7.1.1-2.fc42.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[11/11] Total 100% | 0.0 B/s | 0.0 B | 00m00s
[ 1/12] xz-1:5.6.3-2.fc42.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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>>> Already downloaded
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[ 1/14] redhat-rpm-config-0:300-1.no_an 100% | 0.0 B/s | 0.0 B | 00m00s
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[ 1/15] coreutils-0:9.5-11.fc42.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[15/15] Total 100% | 0.0 B/s | 0.0 B | 00m00s
[ 1/16] grep-0:3.11-9.fc42.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/17] util-linux-0:2.40.2-8.fc42.x86_ 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/18] diffutils-0:3.10-8.fc42.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/19] findutils-1:4.10.0-4.fc42.x86_6 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[19/19] Total 100% | 0.0 B/s | 0.0 B | 00m00s
[ 1/20] gawk-0:5.3.0-4.fc41.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/21] glibc-minimal-langpack-0:2.40.9 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[21/21] Total 100% | 0.0 B/s | 0.0 B | 00m00s
[ 1/22] gzip-0:1.13-2.fc42.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s
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[ 1/23] libselinux-0:3.8-0.rc1.2.fc42.x 100% | 0.0 B/s | 0.0 B | 00m00s
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[ 1/24] file-0:5.45-8.fc42.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/25] libarchive-0:3.7.7-1.fc42.x86_6 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/26] popt-0:1.19-7.fc41.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s
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[ 1/27] readline-0:8.2-11.fc42.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s
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[27/27] Total 100% | 0.0 B/s | 0.0 B | 00m00s
[ 1/28] rpm-0:4.20.0-1.fc42.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/29] rpm-build-libs-0:4.20.0-1.fc42. 100% | 0.0 B/s | 0.0 B | 00m00s
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[ 1/30] rpm-libs-0:4.20.0-1.fc42.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/31] zstd-0:1.5.6-2.fc41.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/32] filesystem-0:3.18-29.fc42.x86_6 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/33] ncurses-libs-0:6.5-2.20240629.f 100% | 0.0 B/s | 0.0 B | 00m00s
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[ 1/34] ed-0:1.20.2-2.fc41.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/35] libattr-0:2.5.2-4.fc41.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/36] libeconf-0:0.7.5-1.fc42.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/37] libsemanage-0:3.8-0.rc1.1.fc42. 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/38] libxcrypt-0:4.4.36-11.fc42.x86_ 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/39] pam-libs-0:1.7.0-3.fc42.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[39/39] Total 100% | 0.0 B/s | 0.0 B | 00m00s
[ 1/40] setup-0:2.15.0-5.fc41.noarch 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/41] fedora-repos-0:42-0.3.noarch 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/42] xz-libs-1:5.6.3-2.fc42.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[42/42] Total 100% | 0.0 B/s | 0.0 B | 00m00s
[ 1/43] ansible-srpm-macros-0:1-16.fc41 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/44] build-reproducibility-srpm-macr 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/45] efi-srpm-macros-0:5-13.fc42.noa 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[45/45] Total 100% | 0.0 B/s | 0.0 B | 00m00s
[ 1/46] filesystem-srpm-macros-0:3.18-2 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/47] fonts-srpm-macros-1:2.0.5-17.fc 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/48] forge-srpm-macros-0:0.4.0-1.fc4 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/49] fpc-srpm-macros-0:1.3-13.fc41.n 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[49/49] Total 100% | 0.0 B/s | 0.0 B | 00m00s
[ 1/50] ghc-srpm-macros-0:1.9.2-1.fc42. 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/51] gnat-srpm-macros-0:6-6.fc41.noa 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/52] go-srpm-macros-0:3.6.0-5.fc42.n 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/53] kernel-srpm-macros-0:1.0-24.fc4 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/54] lua-srpm-macros-0:1-14.fc41.noa 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/55] ocaml-srpm-macros-0:10-3.fc41.n 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[55/55] Total 100% | 0.0 B/s | 0.0 B | 00m00s
[ 1/56] openblas-srpm-macros-0:2-18.fc4 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/57] package-notes-srpm-macros-0:0.5 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/58] perl-srpm-macros-0:1-56.fc41.no 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/59] pyproject-srpm-macros-0:1.16.3- 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/60] python-srpm-macros-0:3.13-3.fc4 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/61] qt5-srpm-macros-0:5.15.15-1.fc4 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/62] qt6-srpm-macros-0:6.8.1-4.fc42. 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/63] rust-srpm-macros-0:26.3-3.fc42. 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/64] zig-srpm-macros-0:1-3.fc41.noar 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/65] zip-0:3.0-42.fc42.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/66] gmp-1:6.3.0-2.fc41.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/67] libcap-0:2.71-1.fc42.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/68] openssl-libs-1:3.2.2-8.fc42.x86 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/69] systemd-libs-0:257-1.fc42.x86_6 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/70] pcre2-0:10.44-1.fc41.1.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/71] libblkid-0:2.40.2-8.fc42.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/72] libcap-ng-0:0.8.5-3.fc41.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/73] libfdisk-0:2.40.2-8.fc42.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/74] libmount-0:2.40.2-8.fc42.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/75] libsmartcols-0:2.40.2-8.fc42.x8 100% | 0.0 B/s | 0.0 B | 00m00s
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[ 1/76] libuuid-0:2.40.2-8.fc42.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/77] util-linux-core-0:2.40.2-8.fc42 100% | 0.0 B/s | 0.0 B | 00m00s
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[ 1/78] zlib-ng-compat-0:2.2.2-1.fc42.x 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/79] mpfr-0:4.2.1-5.fc41.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/80] libsepol-0:3.8-0.rc1.1.fc42.x86 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/81] file-libs-0:5.45-8.fc42.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/82] libxml2-0:2.12.8-2.fc41.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/83] libzstd-0:1.5.6-2.fc41.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/84] lz4-libs-0:1.10.0-1.fc41.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/85] lua-libs-0:5.4.7-1.fc42.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/86] rpm-sequoia-0:1.7.0-3.fc42.x86_ 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/87] sqlite-libs-0:3.47.2-1.fc42.x86 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/88] ncurses-base-0:6.5-2.20240629.f 100% | 0.0 B/s | 0.0 B | 00m00s
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[ 1/89] fedora-gpg-keys-0:42-0.3.noarch 100% | 0.0 B/s | 0.0 B | 00m00s
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[ 1/90] fedora-repos-rawhide-0:42-0.3.n 100% | 0.0 B/s | 0.0 B | 00m00s
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[ 1/91] add-determinism-0:0.4.3-1.fc42. 100% | 0.0 B/s | 0.0 B | 00m00s
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[ 1/92] ca-certificates-0:2024.2.69_v8. 100% | 0.0 B/s | 0.0 B | 00m00s
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[ 1/93] crypto-policies-0:20241128-1.gi 100% | 0.0 B/s | 0.0 B | 00m00s
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[ 1/94] pcre2-syntax-0:10.44-1.fc41.1.n 100% | 0.0 B/s | 0.0 B | 00m00s
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[ 1/95] dwz-0:0.15-8.fc42.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s
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[ 1/96] glibc-0:2.40.9000-24.fc42.x86_6 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/97] basesystem-0:11-21.fc41.noarch 100% | 0.0 B/s | 0.0 B | 00m00s
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[ 1/98] glibc-common-0:2.40.9000-24.fc4 100% | 0.0 B/s | 0.0 B | 00m00s
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[ 1/99] libgcc-0:15.0.0-0.2.fc42.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/100] pam-0:1.7.0-3.fc42.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/101] p11-kit-trust-0:0.25.5-4.fc42 100% | 0.0 B/s | 0.0 B | 00m00s
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>>> Already downloaded
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[ 1/103] libffi-0:3.4.6-3.fc42.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/104] pkgconf-pkg-config-0:2.3.0-1. 100% | 0.0 B/s | 0.0 B | 00m00s
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[ 1/105] gdbm-1:1.23-7.fc41.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s
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[ 1/107] libnsl2-0:2.0.1-2.fc41.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s
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[ 1/108] libpwquality-0:1.4.5-11.fc41. 100% | 0.0 B/s | 0.0 B | 00m00s
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[ 1/109] libtirpc-0:1.3.6-1.fc42.x86_6 100% | 0.0 B/s | 0.0 B | 00m00s
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[ 1/110] libtasn1-0:4.19.0-9.fc41.x86_ 100% | 0.0 B/s | 0.0 B | 00m00s
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[ 1/112] pkgconf-m4-0:2.3.0-1.fc42.noa 100% | 0.0 B/s | 0.0 B | 00m00s
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[ 1/113] krb5-libs-0:1.21.3-3.fc42.x86 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[113/113] Total 100% | 0.0 B/s | 0.0 B | 00m00s
[ 1/114] libcom_err-0:1.47.1-6.fc42.x8 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[114/114] Total 100% | 0.0 B/s | 0.0 B | 00m00s
[ 1/115] libpkgconf-0:2.3.0-1.fc42.x86 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[115/115] Total 100% | 0.0 B/s | 0.0 B | 00m00s
[ 1/116] keyutils-libs-0:1.6.3-4.fc41. 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[116/116] Total 100% | 0.0 B/s | 0.0 B | 00m00s
[ 1/117] libverto-0:0.3.2-9.fc41.x86_6 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[117/117] Total 100% | 0.0 B/s | 0.0 B | 00m00s
[ 1/118] elfutils-libelf-0:0.192-7.fc4 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[118/118] Total 100% | 0.0 B/s | 0.0 B | 00m00s
[ 1/119] coreutils-common-0:9.5-11.fc4 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[119/119] Total 100% | 0.0 B/s | 0.0 B | 00m00s
[ 1/120] libacl-0:2.3.2-2.fc42.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[120/120] Total 100% | 0.0 B/s | 0.0 B | 00m00s
[ 1/121] bzip2-libs-0:1.0.8-19.fc42.x8 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[121/121] Total 100% | 0.0 B/s | 0.0 B | 00m00s
[ 1/122] libstdc++-0:15.0.0-0.2.fc42.x 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[122/122] Total 100% | 0.0 B/s | 0.0 B | 00m00s
[ 1/123] audit-libs-0:4.0.2-1.fc42.x86 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[123/123] Total 100% | 0.0 B/s | 0.0 B | 00m00s
[ 1/124] authselect-libs-0:1.5.0-8.fc4 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[124/124] Total 100% | 0.0 B/s | 0.0 B | 00m00s
[ 1/125] elfutils-libs-0:0.192-7.fc42. 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[125/125] Total 100% | 0.0 B/s | 0.0 B | 00m00s
[ 1/126] libgomp-0:15.0.0-0.2.fc42.x86 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[126/126] Total 100% | 0.0 B/s | 0.0 B | 00m00s
[ 1/127] binutils-0:2.43.50-9.fc42.x86 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/128] jansson-0:2.14-1.fc42.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[128/128] Total 100% | 0.0 B/s | 0.0 B | 00m00s
[ 1/129] debugedit-0:5.1-2.fc42.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[129/129] Total 100% | 0.0 B/s | 0.0 B | 00m00s
[ 1/130] elfutils-0:0.192-7.fc42.x86_6 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[130/130] Total 100% | 0.0 B/s | 0.0 B | 00m00s
[ 1/131] curl-0:8.11.1-2.fc42.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[131/131] Total 100% | 0.0 B/s | 0.0 B | 00m00s
[ 1/132] authselect-0:1.5.0-8.fc42.x86 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[132/132] Total 100% | 0.0 B/s | 0.0 B | 00m00s
[ 1/133] alternatives-0:1.31-1.fc42.x8 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[133/133] Total 100% | 0.0 B/s | 0.0 B | 00m00s
[ 1/134] cracklib-0:2.9.11-6.fc42.x86_ 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[134/134] Total 100% | 0.0 B/s | 0.0 B | 00m00s
[ 1/135] glibc-gconv-extra-0:2.40.9000 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[135/135] Total 100% | 0.0 B/s | 0.0 B | 00m00s
[ 1/136] elfutils-default-yama-scope-0 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/137] elfutils-debuginfod-client-0: 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/138] json-c-0:0.18-1.fc42.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/139] fedora-release-0:42-0.11.noar 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[139/139] Total 100% | 0.0 B/s | 0.0 B | 00m00s
[ 1/140] gdb-minimal-0:15.2-4.fc42.x86 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/141] xxhash-libs-0:0.8.2-4.fc42.x8 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[141/141] Total 100% | 0.0 B/s | 0.0 B | 00m00s
[ 1/142] fedora-release-identity-basic 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/143] libcurl-0:8.11.1-2.fc42.x86_6 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/144] libidn2-0:2.3.7-2.fc41.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/145] libnghttp2-0:1.64.0-1.fc42.x8 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/146] libpsl-0:0.21.5-4.fc41.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/147] libssh-0:0.11.1-1.fc42.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/148] openldap-0:2.6.8-6.fc42.x86_6 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/149] libunistring-0:1.1-8.fc41.x86 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/150] publicsuffix-list-dafsa-0:202 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/151] libssh-config-0:0.11.1-1.fc42 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/152] cyrus-sasl-lib-0:2.1.28-27.fc 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/153] libevent-0:2.1.12-14.fc41.x86 100% | 0.0 B/s | 0.0 B | 00m00s
>>> Already downloaded
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[ 1/154] libtool-ltdl-0:2.5.4-1.fc42.x 100% | 0.0 B/s | 0.0 B | 00m00s
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[ 1/155] libbrotli-0:1.1.0-5.fc42.x86_ 100% | 0.0 B/s | 0.0 B | 00m00s
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Running transaction
Importing OpenPGP key 0x105EF944:
UserID : "Fedora (42) <fedora-42-primary@fedoraproject.org>"
Fingerprint: B0F4950458F69E1150C6C5EDC8AC4916105EF944
From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-42-primary
The key was successfully imported.
Importing OpenPGP key 0x105EF944:
UserID : "Fedora (42) <fedora-42-primary@fedoraproject.org>"
Fingerprint: B0F4950458F69E1150C6C5EDC8AC4916105EF944
From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-42-primary
The key was successfully imported.
Importing OpenPGP key 0xE99D6AD1:
UserID : "Fedora (41) <fedora-41-primary@fedoraproject.org>"
Fingerprint: 466CF2D8B60BC3057AA9453ED0622462E99D6AD1
From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-41-primary
The key was successfully imported.
Importing OpenPGP key 0x31645531:
UserID : "Fedora (43) <fedora-43-primary@fedoraproject.org>"
Fingerprint: C6E7F081CF80E13146676E88829B606631645531
From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-43-primary
The key was successfully imported.
[ 1/157] Verify package files 100% | 790.0 B/s | 155.0 B | 00m00s
>>> Running pre-transaction scriptlet: filesystem-0:3.18-29.fc42.x86_64
>>> Finished pre-transaction scriptlet: filesystem-0:3.18-29.fc42.x86_64
>>> [RPM] /var/lib/mock/fedora-rawhide-x86_64-1734677548.851901/root/var/cache/d
[ 2/157] Prepare transaction 100% | 3.6 KiB/s | 155.0 B | 00m00s
[ 3/157] Installing libgcc-0:15.0.0-0. 100% | 262.3 MiB/s | 268.6 KiB | 00m00s
[ 4/157] Installing libssh-config-0:0. 100% | 0.0 B/s | 816.0 B | 00m00s
[ 5/157] Installing publicsuffix-list- 100% | 0.0 B/s | 68.3 KiB | 00m00s
[ 6/157] Installing fedora-release-ide 100% | 0.0 B/s | 976.0 B | 00m00s
[ 7/157] Installing fedora-gpg-keys-0: 100% | 42.0 MiB/s | 172.2 KiB | 00m00s
[ 8/157] Installing fedora-repos-rawhi 100% | 0.0 B/s | 2.4 KiB | 00m00s
[ 9/157] Installing fedora-repos-0:42- 100% | 0.0 B/s | 5.7 KiB | 00m00s
[ 10/157] Installing fedora-release-com 100% | 23.6 MiB/s | 24.1 KiB | 00m00s
[ 11/157] Installing fedora-release-0:4 100% | 0.0 B/s | 124.0 B | 00m00s
[ 12/157] Installing setup-0:2.15.0-5.f 100% | 54.5 MiB/s | 726.1 KiB | 00m00s
>>> [RPM] /etc/hosts created as /etc/hosts.rpmnew
[ 13/157] Installing filesystem-0:3.18- 100% | 3.3 MiB/s | 212.6 KiB | 00m00s
[ 14/157] Installing basesystem-0:11-21 100% | 0.0 B/s | 124.0 B | 00m00s
[ 15/157] Installing coreutils-common-0 100% | 361.0 MiB/s | 11.2 MiB | 00m00s
[ 16/157] Installing pkgconf-m4-0:2.3.0 100% | 0.0 B/s | 14.8 KiB | 00m00s
[ 17/157] Installing pcre2-syntax-0:10. 100% | 248.1 MiB/s | 254.1 KiB | 00m00s
[ 18/157] Installing ncurses-base-0:6.5 100% | 85.9 MiB/s | 351.7 KiB | 00m00s
[ 19/157] Installing glibc-minimal-lang 100% | 0.0 B/s | 124.0 B | 00m00s
[ 20/157] Installing ncurses-libs-0:6.5 100% | 239.7 MiB/s | 981.8 KiB | 00m00s
[ 21/157] Installing glibc-0:2.40.9000- 100% | 311.5 MiB/s | 6.5 MiB | 00m00s
[ 22/157] Installing bash-0:5.2.37-1.fc 100% | 408.5 MiB/s | 8.2 MiB | 00m00s
[ 23/157] Installing glibc-common-0:2.4 100% | 172.9 MiB/s | 1.0 MiB | 00m00s
[ 24/157] Installing glibc-gconv-extra- 100% | 269.4 MiB/s | 8.1 MiB | 00m00s
[ 25/157] Installing zlib-ng-compat-0:2 100% | 131.7 MiB/s | 134.9 KiB | 00m00s
[ 26/157] Installing xz-libs-1:5.6.3-2. 100% | 214.3 MiB/s | 219.5 KiB | 00m00s
[ 27/157] Installing bzip2-libs-0:1.0.8 100% | 82.3 MiB/s | 84.3 KiB | 00m00s
[ 28/157] Installing popt-0:1.19-7.fc41 100% | 70.1 MiB/s | 143.5 KiB | 00m00s
[ 29/157] Installing readline-0:8.2-11. 100% | 241.8 MiB/s | 495.3 KiB | 00m00s
[ 30/157] Installing libuuid-0:2.40.2-8 100% | 0.0 B/s | 42.5 KiB | 00m00s
[ 31/157] Installing libblkid-0:2.40.2- 100% | 257.5 MiB/s | 263.6 KiB | 00m00s
[ 32/157] Installing libattr-0:2.5.2-4. 100% | 0.0 B/s | 29.5 KiB | 00m00s
[ 33/157] Installing libacl-0:2.3.2-2.f 100% | 0.0 B/s | 39.2 KiB | 00m00s
[ 34/157] Installing libxcrypt-0:4.4.36 100% | 267.7 MiB/s | 274.1 KiB | 00m00s
[ 35/157] Installing gmp-1:6.3.0-2.fc41 100% | 397.3 MiB/s | 813.7 KiB | 00m00s
[ 36/157] Installing libzstd-0:1.5.6-2. 100% | 389.3 MiB/s | 797.2 KiB | 00m00s
[ 37/157] Installing elfutils-libelf-0: 100% | 389.0 MiB/s | 1.2 MiB | 00m00s
[ 38/157] Installing libstdc++-0:15.0.0 100% | 343.8 MiB/s | 2.8 MiB | 00m00s
[ 39/157] Installing libeconf-0:0.7.5-1 100% | 66.8 MiB/s | 68.4 KiB | 00m00s
[ 40/157] Installing gdbm-libs-1:1.23-7 100% | 120.7 MiB/s | 123.6 KiB | 00m00s
[ 41/157] Installing dwz-0:0.15-8.fc42. 100% | 290.1 MiB/s | 297.1 KiB | 00m00s
[ 42/157] Installing mpfr-0:4.2.1-5.fc4 100% | 271.4 MiB/s | 833.7 KiB | 00m00s
[ 43/157] Installing gawk-0:5.3.0-4.fc4 100% | 288.7 MiB/s | 1.7 MiB | 00m00s
[ 44/157] Installing unzip-0:6.0-65.fc4 100% | 196.2 MiB/s | 401.7 KiB | 00m00s
[ 45/157] Installing file-libs-0:5.45-8 100% | 662.6 MiB/s | 9.9 MiB | 00m00s
[ 46/157] Installing file-0:5.45-8.fc42 100% | 14.7 MiB/s | 105.2 KiB | 00m00s
[ 47/157] Installing crypto-policies-0: 100% | 32.0 MiB/s | 163.7 KiB | 00m00s
[ 48/157] Installing pcre2-0:10.44-1.fc 100% | 319.8 MiB/s | 654.9 KiB | 00m00s
[ 49/157] Installing grep-0:3.11-9.fc42 100% | 200.0 MiB/s | 1.0 MiB | 00m00s
[ 50/157] Installing xz-1:5.6.3-2.fc42. 100% | 247.4 MiB/s | 1.2 MiB | 00m00s
[ 51/157] Installing libcap-ng-0:0.8.5- 100% | 69.4 MiB/s | 71.0 KiB | 00m00s
[ 52/157] Installing audit-libs-0:4.0.2 100% | 162.8 MiB/s | 333.4 KiB | 00m00s
[ 53/157] Installing pam-libs-0:1.7.0-3 100% | 138.5 MiB/s | 141.8 KiB | 00m00s
[ 54/157] Installing libcap-0:2.71-1.fc 100% | 105.4 MiB/s | 215.8 KiB | 00m00s
[ 55/157] Installing systemd-libs-0:257 100% | 317.2 MiB/s | 2.2 MiB | 00m00s
[ 56/157] Installing libsmartcols-0:2.4 100% | 177.1 MiB/s | 181.4 KiB | 00m00s
[ 57/157] Installing libsepol-0:3.8-0.r 100% | 401.9 MiB/s | 823.0 KiB | 00m00s
[ 58/157] Installing libselinux-0:3.8-0 100% | 188.4 MiB/s | 192.9 KiB | 00m00s
[ 59/157] Installing sed-0:4.9-3.fc41.x 100% | 212.3 MiB/s | 869.7 KiB | 00m00s
[ 60/157] Installing findutils-1:4.10.0 100% | 311.2 MiB/s | 1.9 MiB | 00m00s
[ 61/157] Installing libmount-0:2.40.2- 100% | 348.6 MiB/s | 356.9 KiB | 00m00s
[ 62/157] Installing lz4-libs-0:1.10.0- 100% | 143.1 MiB/s | 146.6 KiB | 00m00s
[ 63/157] Installing lua-libs-0:5.4.7-1 100% | 279.5 MiB/s | 286.2 KiB | 00m00s
[ 64/157] Installing libffi-0:3.4.6-3.f 100% | 85.7 MiB/s | 87.8 KiB | 00m00s
[ 65/157] Installing libtasn1-0:4.19.0- 100% | 173.3 MiB/s | 177.5 KiB | 00m00s
[ 66/157] Installing p11-kit-0:0.25.5-4 100% | 277.0 MiB/s | 2.2 MiB | 00m00s
[ 67/157] Installing libcom_err-0:1.47. 100% | 0.0 B/s | 68.3 KiB | 00m00s
[ 68/157] Installing alternatives-0:1.3 100% | 64.8 MiB/s | 66.4 KiB | 00m00s
[ 69/157] Installing libunistring-0:1.1 100% | 346.1 MiB/s | 1.7 MiB | 00m00s
[ 70/157] Installing libidn2-0:2.3.7-2. 100% | 163.6 MiB/s | 335.1 KiB | 00m00s
[ 71/157] Installing libpsl-0:0.21.5-4. 100% | 79.7 MiB/s | 81.7 KiB | 00m00s
[ 72/157] Installing p11-kit-trust-0:0. 100% | 49.5 MiB/s | 405.5 KiB | 00m00s
[ 73/157] Installing openssl-libs-1:3.2 100% | 372.8 MiB/s | 7.8 MiB | 00m00s
[ 74/157] Installing coreutils-0:9.5-11 100% | 252.7 MiB/s | 5.6 MiB | 00m00s
[ 75/157] Installing ca-certificates-0: 100% | 2.0 MiB/s | 2.4 MiB | 00m01s
[ 76/157] Installing gzip-0:1.13-2.fc42 100% | 129.1 MiB/s | 396.5 KiB | 00m00s
[ 77/157] Installing authselect-libs-0: 100% | 163.1 MiB/s | 835.0 KiB | 00m00s
[ 78/157] Installing cracklib-0:2.9.11- 100% | 81.2 MiB/s | 249.4 KiB | 00m00s
[ 79/157] Installing libpwquality-0:1.4 100% | 105.0 MiB/s | 430.1 KiB | 00m00s
[ 80/157] Installing rpm-sequoia-0:1.7. 100% | 332.0 MiB/s | 2.3 MiB | 00m00s
[ 81/157] Installing libevent-0:2.1.12- 100% | 292.8 MiB/s | 899.5 KiB | 00m00s
[ 82/157] Installing zstd-0:1.5.6-2.fc4 100% | 338.3 MiB/s | 1.7 MiB | 00m00s
[ 83/157] Installing util-linux-core-0: 100% | 218.3 MiB/s | 1.5 MiB | 00m00s
[ 84/157] Installing tar-2:1.35-4.fc41. 100% | 369.8 MiB/s | 3.0 MiB | 00m00s
[ 85/157] Installing libsemanage-0:3.8- 100% | 149.9 MiB/s | 307.1 KiB | 00m00s
[ 86/157] Installing shadow-utils-2:4.1 100% | 228.9 MiB/s | 4.1 MiB | 00m00s
[ 87/157] Installing zip-0:3.0-42.fc42. 100% | 227.8 MiB/s | 699.8 KiB | 00m00s
[ 88/157] Installing gdbm-1:1.23-7.fc41 100% | 227.4 MiB/s | 465.8 KiB | 00m00s
[ 89/157] Installing cyrus-sasl-lib-0:2 100% | 384.3 MiB/s | 2.3 MiB | 00m00s
[ 90/157] Installing libfdisk-0:2.40.2- 100% | 177.7 MiB/s | 364.0 KiB | 00m00s
[ 91/157] Installing bzip2-0:1.0.8-19.f 100% | 99.0 MiB/s | 101.4 KiB | 00m00s
[ 92/157] Installing libxml2-0:2.12.8-2 100% | 342.4 MiB/s | 1.7 MiB | 00m00s
[ 93/157] Installing libarchive-0:3.7.7 100% | 304.1 MiB/s | 934.2 KiB | 00m00s
[ 94/157] Installing sqlite-libs-0:3.47 100% | 358.5 MiB/s | 1.4 MiB | 00m00s
[ 95/157] Installing rpm-libs-0:4.20.0- 100% | 236.9 MiB/s | 727.7 KiB | 00m00s
[ 96/157] Installing add-determinism-0: 100% | 347.3 MiB/s | 2.4 MiB | 00m00s
[ 97/157] Installing build-reproducibil 100% | 0.0 B/s | 1.0 KiB | 00m00s
[ 98/157] Installing ed-0:1.20.2-2.fc41 100% | 145.7 MiB/s | 149.2 KiB | 00m00s
[ 99/157] Installing patch-0:2.7.6-25.f 100% | 261.9 MiB/s | 268.2 KiB | 00m00s
[100/157] Installing filesystem-srpm-ma 100% | 0.0 B/s | 36.8 KiB | 00m00s
[101/157] Installing elfutils-default-y 100% | 340.5 KiB/s | 2.0 KiB | 00m00s
[102/157] Installing elfutils-libs-0:0. 100% | 216.4 MiB/s | 664.7 KiB | 00m00s
[103/157] Installing cpio-0:2.15-2.fc41 100% | 274.9 MiB/s | 1.1 MiB | 00m00s
[104/157] Installing diffutils-0:3.10-8 100% | 263.8 MiB/s | 1.6 MiB | 00m00s
[105/157] Installing libpkgconf-0:2.3.0 100% | 77.5 MiB/s | 79.3 KiB | 00m00s
[106/157] Installing pkgconf-0:2.3.0-1. 100% | 89.0 MiB/s | 91.1 KiB | 00m00s
[107/157] Installing pkgconf-pkg-config 100% | 0.0 B/s | 1.8 KiB | 00m00s
[108/157] Installing keyutils-libs-0:1. 100% | 54.5 MiB/s | 55.8 KiB | 00m00s
[109/157] Installing libverto-0:0.3.2-9 100% | 30.5 MiB/s | 31.3 KiB | 00m00s
[110/157] Installing krb5-libs-0:1.21.3 100% | 288.1 MiB/s | 2.3 MiB | 00m00s
[111/157] Installing libtirpc-0:1.3.6-1 100% | 202.5 MiB/s | 207.3 KiB | 00m00s
[112/157] Installing libnsl2-0:2.0.1-2. 100% | 57.7 MiB/s | 59.1 KiB | 00m00s
[113/157] Installing pam-0:1.7.0-3.fc42 100% | 157.8 MiB/s | 1.9 MiB | 00m00s
[114/157] Installing libssh-0:0.11.1-1. 100% | 279.2 MiB/s | 571.7 KiB | 00m00s
[115/157] Installing libgomp-0:15.0.0-0 100% | 259.1 MiB/s | 530.7 KiB | 00m00s
[116/157] Installing rpm-build-libs-0:4 100% | 202.6 MiB/s | 207.5 KiB | 00m00s
[117/157] Installing jansson-0:2.14-1.f 100% | 92.3 MiB/s | 94.5 KiB | 00m00s
[118/157] Installing json-c-0:0.18-1.fc 100% | 82.6 MiB/s | 84.6 KiB | 00m00s
[119/157] Installing xxhash-libs-0:0.8. 100% | 87.7 MiB/s | 89.8 KiB | 00m00s
[120/157] Installing libnghttp2-0:1.64. 100% | 171.5 MiB/s | 175.6 KiB | 00m00s
[121/157] Installing libtool-ltdl-0:2.5 100% | 67.6 MiB/s | 69.2 KiB | 00m00s
[122/157] Installing openldap-0:2.6.8-6 100% | 212.0 MiB/s | 651.2 KiB | 00m00s
[123/157] Installing libbrotli-0:1.1.0- 100% | 273.0 MiB/s | 838.7 KiB | 00m00s
[124/157] Installing libcurl-0:8.11.1-2 100% | 270.3 MiB/s | 830.4 KiB | 00m00s
[125/157] Installing elfutils-debuginfo 100% | 81.8 MiB/s | 83.8 KiB | 00m00s
[126/157] Installing binutils-0:2.43.50 100% | 371.4 MiB/s | 25.6 MiB | 00m00s
[127/157] Installing elfutils-0:0.192-7 100% | 330.1 MiB/s | 2.6 MiB | 00m00s
[128/157] Installing gdb-minimal-0:15.2 100% | 375.5 MiB/s | 12.8 MiB | 00m00s
[129/157] Installing debugedit-0:5.1-2. 100% | 195.7 MiB/s | 200.4 KiB | 00m00s
[130/157] Installing curl-0:8.11.1-2.fc 100% | 44.4 MiB/s | 454.5 KiB | 00m00s
[131/157] Installing rpm-0:4.20.0-1.fc4 100% | 179.0 MiB/s | 2.5 MiB | 00m00s
[132/157] Installing efi-srpm-macros-0: 100% | 0.0 B/s | 41.2 KiB | 00m00s
[133/157] Installing lua-srpm-macros-0: 100% | 0.0 B/s | 1.9 KiB | 00m00s
[134/157] Installing zig-srpm-macros-0: 100% | 0.0 B/s | 1.7 KiB | 00m00s
[135/157] Installing rust-srpm-macros-0 100% | 0.0 B/s | 5.6 KiB | 00m00s
[136/157] Installing qt6-srpm-macros-0: 100% | 0.0 B/s | 732.0 B | 00m00s
[137/157] Installing qt5-srpm-macros-0: 100% | 0.0 B/s | 776.0 B | 00m00s
[138/157] Installing perl-srpm-macros-0 100% | 0.0 B/s | 1.1 KiB | 00m00s
[139/157] Installing package-notes-srpm 100% | 0.0 B/s | 2.0 KiB | 00m00s
[140/157] Installing openblas-srpm-macr 100% | 0.0 B/s | 392.0 B | 00m00s
[141/157] Installing ocaml-srpm-macros- 100% | 0.0 B/s | 2.2 KiB | 00m00s
[142/157] Installing kernel-srpm-macros 100% | 0.0 B/s | 2.3 KiB | 00m00s
[143/157] Installing gnat-srpm-macros-0 100% | 0.0 B/s | 1.3 KiB | 00m00s
[144/157] Installing ghc-srpm-macros-0: 100% | 0.0 B/s | 1.0 KiB | 00m00s
[145/157] Installing fpc-srpm-macros-0: 100% | 0.0 B/s | 420.0 B | 00m00s
[146/157] Installing ansible-srpm-macro 100% | 0.0 B/s | 36.2 KiB | 00m00s
[147/157] Installing fonts-srpm-macros- 100% | 55.7 MiB/s | 57.0 KiB | 00m00s
[148/157] Installing forge-srpm-macros- 100% | 0.0 B/s | 40.3 KiB | 00m00s
[149/157] Installing go-srpm-macros-0:3 100% | 60.5 MiB/s | 62.0 KiB | 00m00s
[150/157] Installing python-srpm-macros 100% | 50.9 MiB/s | 52.2 KiB | 00m00s
[151/157] Installing redhat-rpm-config- 100% | 94.3 MiB/s | 193.2 KiB | 00m00s
[152/157] Installing rpm-build-0:4.20.0 100% | 99.1 MiB/s | 202.9 KiB | 00m00s
[153/157] Installing pyproject-srpm-mac 100% | 1.2 MiB/s | 2.5 KiB | 00m00s
[154/157] Installing util-linux-0:2.40. 100% | 168.9 MiB/s | 3.7 MiB | 00m00s
[155/157] Installing authselect-0:1.5.0 100% | 78.3 MiB/s | 160.4 KiB | 00m00s
[156/157] Installing which-0:2.21-42.fc 100% | 80.5 MiB/s | 82.4 KiB | 00m00s
[157/157] Installing info-0:7.1.1-2.fc4 100% | 222.9 KiB/s | 362.2 KiB | 00m02s
Warning: skipped OpenPGP checks for 34 packages from repositories: copr_base, https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch
Complete!
Finish: installing minimal buildroot with dnf5
Start: creating root cache
Finish: creating root cache
Finish: chroot init
INFO: Installed packages:
INFO: add-determinism-0.4.3-1.fc42.x86_64
alternatives-1.31-1.fc42.x86_64
ansible-srpm-macros-1-16.fc41.noarch
audit-libs-4.0.2-1.fc42.x86_64
authselect-1.5.0-8.fc42.x86_64
authselect-libs-1.5.0-8.fc42.x86_64
basesystem-11-21.fc41.noarch
bash-5.2.37-1.fc42.x86_64
binutils-2.43.50-9.fc42.x86_64
build-reproducibility-srpm-macros-0.4.3-1.fc42.noarch
bzip2-1.0.8-19.fc42.x86_64
bzip2-libs-1.0.8-19.fc42.x86_64
ca-certificates-2024.2.69_v8.0.401-3.fc42.noarch
coreutils-9.5-11.fc42.x86_64
coreutils-common-9.5-11.fc42.x86_64
cpio-2.15-2.fc41.x86_64
cracklib-2.9.11-6.fc42.x86_64
crypto-policies-20241128-1.gitbb7b0b0.fc42.noarch
curl-8.11.1-2.fc42.x86_64
cyrus-sasl-lib-2.1.28-27.fc41.x86_64
debugedit-5.1-2.fc42.x86_64
diffutils-3.10-8.fc42.x86_64
dwz-0.15-8.fc42.x86_64
ed-1.20.2-2.fc41.x86_64
efi-srpm-macros-5-13.fc42.noarch
elfutils-0.192-7.fc42.x86_64
elfutils-debuginfod-client-0.192-7.fc42.x86_64
elfutils-default-yama-scope-0.192-7.fc42.noarch
elfutils-libelf-0.192-7.fc42.x86_64
elfutils-libs-0.192-7.fc42.x86_64
fedora-gpg-keys-42-0.3.noarch
fedora-release-42-0.11.noarch
fedora-release-common-42-0.11.noarch
fedora-release-identity-basic-42-0.11.noarch
fedora-repos-42-0.3.noarch
fedora-repos-rawhide-42-0.3.noarch
file-5.45-8.fc42.x86_64
file-libs-5.45-8.fc42.x86_64
filesystem-3.18-29.fc42.x86_64
filesystem-srpm-macros-3.18-29.fc42.noarch
findutils-4.10.0-4.fc42.x86_64
fonts-srpm-macros-2.0.5-17.fc41.noarch
forge-srpm-macros-0.4.0-1.fc42.noarch
fpc-srpm-macros-1.3-13.fc41.noarch
gawk-5.3.0-4.fc41.x86_64
gdb-minimal-15.2-4.fc42.x86_64
gdbm-1.23-7.fc41.x86_64
gdbm-libs-1.23-7.fc41.x86_64
ghc-srpm-macros-1.9.2-1.fc42.noarch
glibc-2.40.9000-24.fc42.x86_64
glibc-common-2.40.9000-24.fc42.x86_64
glibc-gconv-extra-2.40.9000-24.fc42.x86_64
glibc-minimal-langpack-2.40.9000-24.fc42.x86_64
gmp-6.3.0-2.fc41.x86_64
gnat-srpm-macros-6-6.fc41.noarch
go-srpm-macros-3.6.0-5.fc42.noarch
gpg-pubkey-105ef944-65ca83d1
gpg-pubkey-31645531-66b6dccf
gpg-pubkey-e99d6ad1-64d2612c
grep-3.11-9.fc42.x86_64
gzip-1.13-2.fc42.x86_64
info-7.1.1-2.fc42.x86_64
jansson-2.14-1.fc42.x86_64
json-c-0.18-1.fc42.x86_64
kernel-srpm-macros-1.0-24.fc41.noarch
keyutils-libs-1.6.3-4.fc41.x86_64
krb5-libs-1.21.3-3.fc42.x86_64
libacl-2.3.2-2.fc42.x86_64
libarchive-3.7.7-1.fc42.x86_64
libattr-2.5.2-4.fc41.x86_64
libblkid-2.40.2-8.fc42.x86_64
libbrotli-1.1.0-5.fc42.x86_64
libcap-2.71-1.fc42.x86_64
libcap-ng-0.8.5-3.fc41.x86_64
libcom_err-1.47.1-6.fc42.x86_64
libcurl-8.11.1-2.fc42.x86_64
libeconf-0.7.5-1.fc42.x86_64
libevent-2.1.12-14.fc41.x86_64
libfdisk-2.40.2-8.fc42.x86_64
libffi-3.4.6-3.fc42.x86_64
libgcc-15.0.0-0.2.fc42.x86_64
libgomp-15.0.0-0.2.fc42.x86_64
libidn2-2.3.7-2.fc41.x86_64
libmount-2.40.2-8.fc42.x86_64
libnghttp2-1.64.0-1.fc42.x86_64
libnsl2-2.0.1-2.fc41.x86_64
libpkgconf-2.3.0-1.fc42.x86_64
libpsl-0.21.5-4.fc41.x86_64
libpwquality-1.4.5-11.fc41.x86_64
libselinux-3.8-0.rc1.2.fc42.x86_64
libsemanage-3.8-0.rc1.1.fc42.x86_64
libsepol-3.8-0.rc1.1.fc42.x86_64
libsmartcols-2.40.2-8.fc42.x86_64
libssh-0.11.1-1.fc42.x86_64
libssh-config-0.11.1-1.fc42.noarch
libstdc++-15.0.0-0.2.fc42.x86_64
libtasn1-4.19.0-9.fc41.x86_64
libtirpc-1.3.6-1.fc42.x86_64
libtool-ltdl-2.5.4-1.fc42.x86_64
libunistring-1.1-8.fc41.x86_64
libuuid-2.40.2-8.fc42.x86_64
libverto-0.3.2-9.fc41.x86_64
libxcrypt-4.4.36-11.fc42.x86_64
libxml2-2.12.8-2.fc41.x86_64
libzstd-1.5.6-2.fc41.x86_64
lua-libs-5.4.7-1.fc42.x86_64
lua-srpm-macros-1-14.fc41.noarch
lz4-libs-1.10.0-1.fc41.x86_64
mpfr-4.2.1-5.fc41.x86_64
ncurses-base-6.5-2.20240629.fc41.noarch
ncurses-libs-6.5-2.20240629.fc41.x86_64
ocaml-srpm-macros-10-3.fc41.noarch
openblas-srpm-macros-2-18.fc41.noarch
openldap-2.6.8-6.fc42.x86_64
openssl-libs-3.2.2-8.fc42.x86_64
p11-kit-0.25.5-4.fc42.x86_64
p11-kit-trust-0.25.5-4.fc42.x86_64
package-notes-srpm-macros-0.5-12.fc41.noarch
pam-1.7.0-3.fc42.x86_64
pam-libs-1.7.0-3.fc42.x86_64
patch-2.7.6-25.fc41.x86_64
pcre2-10.44-1.fc41.1.x86_64
pcre2-syntax-10.44-1.fc41.1.noarch
perl-srpm-macros-1-56.fc41.noarch
pkgconf-2.3.0-1.fc42.x86_64
pkgconf-m4-2.3.0-1.fc42.noarch
pkgconf-pkg-config-2.3.0-1.fc42.x86_64
popt-1.19-7.fc41.x86_64
publicsuffix-list-dafsa-20240107-4.fc41.noarch
pyproject-srpm-macros-1.16.3-1.fc42.noarch
python-srpm-macros-3.13-3.fc41.noarch
qt5-srpm-macros-5.15.15-1.fc42.noarch
qt6-srpm-macros-6.8.1-4.fc42.noarch
readline-8.2-11.fc42.x86_64
redhat-rpm-config-300-1.no_annobin.0.fc42.noarch
rpm-4.20.0-1.fc42.x86_64
rpm-build-4.20.0-1.fc42.x86_64
rpm-build-libs-4.20.0-1.fc42.x86_64
rpm-libs-4.20.0-1.fc42.x86_64
rpm-sequoia-1.7.0-3.fc42.x86_64
rust-srpm-macros-26.3-3.fc42.noarch
sed-4.9-3.fc41.x86_64
setup-2.15.0-5.fc41.noarch
shadow-utils-4.17.0~rc1-1.fc42.x86_64
sqlite-libs-3.47.2-1.fc42.x86_64
systemd-libs-257-1.fc42.x86_64
tar-1.35-4.fc41.x86_64
unzip-6.0-65.fc42.x86_64
util-linux-2.40.2-8.fc42.x86_64
util-linux-core-2.40.2-8.fc42.x86_64
which-2.21-42.fc41.x86_64
xxhash-libs-0.8.2-4.fc42.x86_64
xz-5.6.3-2.fc42.x86_64
xz-libs-5.6.3-2.fc42.x86_64
zig-srpm-macros-1-3.fc41.noarch
zip-3.0-42.fc42.x86_64
zlib-ng-compat-2.2.2-1.fc42.x86_64
zstd-1.5.6-2.fc41.x86_64
Start: buildsrpm
Start: rpmbuild -bs
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1721260800
Wrote: /builddir/build/SRPMS/htslib-1.15.1-6.fc42.src.rpm
Finish: rpmbuild -bs
INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/fedora-rawhide-x86_64-1734677548.851901/root/var/log/dnf5.log
INFO: chroot_scan: creating tarball /var/lib/copr-rpmbuild/results/chroot_scan.tar.gz
/bin/tar: Removing leading `/' from member names
Finish: buildsrpm
INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-uzl_7l2j/htslib/htslib.spec) Config(child) 0 minutes 10 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/htslib-1.15.1-6.fc42.src.rpm) Config(fedora-rawhide-x86_64)
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1734677548.851901/root.
INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1734677548.851901/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-x86_64-1734677548.851901/root.
INFO: calling preinit hooks
INFO: enabled root cache
Start: unpacking root cache
Finish: unpacking root cache
INFO: enabled package manager cache
Start: cleaning package manager metadata
Finish: cleaning package manager metadata
INFO: enabled HW Info plugin
INFO: Buildroot is handled by package management downloaded with a bootstrap image:
rpm-4.20.0-1.fc42.x86_64
rpm-sequoia-1.7.0-3.fc42.x86_64
dnf5-5.2.8.1-2.fc42.x86_64
dnf5-plugins-5.2.8.1-2.fc42.x86_64
Finish: chroot init
Start: build phase for htslib-1.15.1-6.fc42.src.rpm
Start: build setup for htslib-1.15.1-6.fc42.src.rpm
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1721260800
Wrote: /builddir/build/SRPMS/htslib-1.15.1-6.fc42.src.rpm
Updating and loading repositories:
fedora 100% | 98.8 KiB/s | 28.1 KiB | 00m00s
Additional repo https_fedorapeople_org 100% | 37.2 KiB/s | 1.5 KiB | 00m00s
Copr repository 100% | 73.1 KiB/s | 1.5 KiB | 00m00s
Repositories loaded.
Package Arch Version Repository Size
Installing:
bzip2-devel x86_64 1.0.8-19.fc42 copr_base 309.8 KiB
gcc x86_64 15.0.0-0.2.fc42 https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch 109.9 MiB
libcurl-devel x86_64 8.11.1-2.fc42 copr_base 1.3 MiB
make x86_64 1:4.4.1-9.fc42 fedora 1.8 MiB
openssl-devel x86_64 1:3.2.2-8.fc42 fedora 4.3 MiB
perl-Data-Dumper x86_64 2.189-512.fc41 fedora 111.7 KiB
perl-FindBin noarch 1.54-512.fc42 fedora 6.7 KiB
perl-Getopt-Long noarch 1:2.58-2.fc41 fedora 144.5 KiB
perl-interpreter x86_64 4:5.40.0-512.fc42 fedora 122.3 KiB
perl-lib x86_64 0.65-512.fc42 fedora 8.5 KiB
xz-devel x86_64 1:5.6.3-2.fc42 fedora 255.6 KiB
zlib-ng-compat-devel x86_64 2.2.2-1.fc42 fedora 106.8 KiB
Installing dependencies:
annobin-docs noarch 12.79-1.fc42 copr_base 98.6 KiB
annobin-plugin-gcc x86_64 12.79-1.fc42 copr_base 989.3 KiB
brotli x86_64 1.1.0-5.fc42 copr_base 30.5 KiB
brotli-devel x86_64 1.1.0-5.fc42 copr_base 65.6 KiB
cmake-filesystem x86_64 3.31.2-1.fc42 copr_base 0.0 B
cpp x86_64 15.0.0-0.2.fc42 https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch 37.5 MiB
gcc-plugin-annobin x86_64 15.0.0-0.2.fc42 https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch 59.6 KiB
glibc-devel x86_64 2.40.9000-24.fc42 copr_base 2.3 MiB
groff-base x86_64 1.23.0-7.fc42 copr_base 3.8 MiB
kernel-headers x86_64 6.13.0-0.rc3.29.fc42 fedora 6.5 MiB
keyutils-libs-devel x86_64 1.6.3-4.fc41 fedora 48.2 KiB
krb5-devel x86_64 1.21.3-3.fc42 fedora 705.9 KiB
libcom_err-devel x86_64 1.47.1-6.fc42 fedora 16.7 KiB
libidn2-devel x86_64 2.3.7-2.fc41 fedora 252.1 KiB
libkadm5 x86_64 1.21.3-3.fc42 fedora 211.6 KiB
libmpc x86_64 1.3.1-6.fc41 fedora 164.7 KiB
libnghttp2-devel x86_64 1.64.0-1.fc42 fedora 295.4 KiB
libpsl-devel x86_64 0.21.5-4.fc41 fedora 110.3 KiB
libselinux-devel x86_64 3.8-0.rc1.2.fc42 fedora 126.6 KiB
libsepol-devel x86_64 3.8-0.rc1.1.fc42 fedora 120.8 KiB
libssh-devel x86_64 0.11.1-1.fc42 fedora 177.8 KiB
libverto-devel x86_64 0.3.2-9.fc41 fedora 25.7 KiB
libxcrypt-devel x86_64 4.4.36-11.fc42 fedora 30.5 KiB
ncurses x86_64 6.5-2.20240629.fc41 fedora 627.3 KiB
pcre2-devel x86_64 10.44-1.fc41.1 fedora 2.0 MiB
pcre2-utf16 x86_64 10.44-1.fc41.1 fedora 590.1 KiB
pcre2-utf32 x86_64 10.44-1.fc41.1 fedora 562.0 KiB
perl-AutoLoader noarch 5.74-512.fc42 fedora 20.5 KiB
perl-B x86_64 1.89-512.fc42 fedora 498.0 KiB
perl-Carp noarch 1.54-511.fc41 fedora 46.6 KiB
perl-Class-Struct noarch 0.68-512.fc42 fedora 25.4 KiB
perl-Digest noarch 1.20-511.fc41 fedora 35.3 KiB
perl-Digest-MD5 x86_64 2.59-5.fc41 fedora 59.8 KiB
perl-DynaLoader x86_64 1.56-512.fc42 fedora 32.1 KiB
perl-Encode x86_64 4:3.21-511.fc41 fedora 4.7 MiB
perl-Errno x86_64 1.38-512.fc42 fedora 8.4 KiB
perl-Exporter noarch 5.78-511.fc41 fedora 54.3 KiB
perl-Fcntl x86_64 1.18-512.fc42 fedora 49.0 KiB
perl-File-Basename noarch 2.86-512.fc42 fedora 14.0 KiB
perl-File-Path noarch 2.18-511.fc41 fedora 63.5 KiB
perl-File-Temp noarch 1:0.231.100-511.fc41 fedora 162.3 KiB
perl-File-stat noarch 1.14-512.fc42 fedora 12.5 KiB
perl-FileHandle noarch 2.05-512.fc42 fedora 9.3 KiB
perl-Getopt-Std noarch 1.14-512.fc42 fedora 11.2 KiB
perl-HTTP-Tiny noarch 0.090-1.fc42 fedora 154.4 KiB
perl-IO x86_64 1.55-512.fc42 fedora 151.1 KiB
perl-IO-Socket-IP noarch 0.43-1.fc42 fedora 100.3 KiB
perl-IO-Socket-SSL noarch 2.089-1.fc42 fedora 703.3 KiB
perl-IPC-Open3 noarch 1.22-512.fc42 fedora 22.5 KiB
perl-MIME-Base32 noarch 1.303-21.fc41 fedora 30.7 KiB
perl-MIME-Base64 x86_64 3.16-511.fc41 fedora 46.1 KiB
perl-Net-SSLeay x86_64 1.94-7.fc41 fedora 1.3 MiB
perl-POSIX x86_64 2.20-512.fc42 fedora 235.1 KiB
perl-PathTools x86_64 3.91-511.fc41 fedora 180.0 KiB
perl-Pod-Escapes noarch 1:1.07-511.fc41 fedora 24.9 KiB
perl-Pod-Perldoc noarch 3.28.01-512.fc41 fedora 163.7 KiB
perl-Pod-Simple noarch 1:3.45-511.fc41 fedora 560.9 KiB
perl-Pod-Usage noarch 4:2.03-511.fc41 fedora 84.8 KiB
perl-Scalar-List-Utils x86_64 5:1.68-1.fc42 fedora 148.9 KiB
perl-SelectSaver noarch 1.02-512.fc42 fedora 2.2 KiB
perl-Socket x86_64 4:2.038-511.fc41 fedora 124.0 KiB
perl-Storable x86_64 1:3.32-511.fc41 fedora 232.4 KiB
perl-Symbol noarch 1.09-512.fc42 fedora 6.8 KiB
perl-Term-ANSIColor noarch 5.01-512.fc41 fedora 97.5 KiB
perl-Term-Cap noarch 1.18-511.fc41 fedora 29.3 KiB
perl-Text-ParseWords noarch 3.31-511.fc41 fedora 13.6 KiB
perl-Text-Tabs+Wrap noarch 2024.001-511.fc41 fedora 22.6 KiB
perl-Time-Local noarch 2:1.350-511.fc41 fedora 69.0 KiB
perl-URI noarch 5.31-1.fc42 fedora 257.0 KiB
perl-base noarch 2.27-512.fc42 fedora 12.5 KiB
perl-constant noarch 1.33-512.fc41 fedora 26.2 KiB
perl-if noarch 0.61.000-512.fc42 fedora 5.8 KiB
perl-libnet noarch 3.15-512.fc41 fedora 289.4 KiB
perl-libs x86_64 4:5.40.0-512.fc42 fedora 9.9 MiB
perl-locale noarch 1.12-512.fc42 fedora 6.5 KiB
perl-mro x86_64 1.29-512.fc42 fedora 45.6 KiB
perl-overload noarch 1.37-512.fc42 fedora 71.5 KiB
perl-overloading noarch 0.02-512.fc42 fedora 4.8 KiB
perl-parent noarch 1:0.244-1.fc42 fedora 10.3 KiB
perl-podlators noarch 1:6.0.2-2.fc41 fedora 317.5 KiB
perl-vars noarch 1.05-512.fc42 fedora 3.9 KiB
publicsuffix-list noarch 20240107-4.fc41 fedora 318.0 KiB
Transaction Summary:
Installing: 94 packages
Total size of inbound packages is 68 MiB. Need to download 1 MiB.
After this operation, 197 MiB extra will be used (install 197 MiB, remove 0 B).
[1/1] make-1:4.4.1-9.fc42.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s
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[1/2] perl-Data-Dumper-0:2.189-512.fc41 100% | 0.0 B/s | 0.0 B | 00m00s
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[1/4] perl-Getopt-Long-1:2.58-2.fc41.no 100% | 0.0 B/s | 0.0 B | 00m00s
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[36/41] perl-Symbol-0:1.09-512.fc42.noa 100% | 0.0 B/s | 0.0 B | 00m00s
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[37/42] perl-parent-1:0.244-1.fc42.noar 100% | 0.0 B/s | 0.0 B | 00m00s
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[38/43] perl-POSIX-0:2.20-512.fc42.x86_ 100% | 0.0 B/s | 0.0 B | 00m00s
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[39/44] perl-Term-ANSIColor-0:5.01-512. 100% | 0.0 B/s | 0.0 B | 00m00s
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[40/45] perl-Term-Cap-0:1.18-511.fc41.n 100% | 0.0 B/s | 0.0 B | 00m00s
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[41/46] perl-File-Path-0:2.18-511.fc41. 100% | 0.0 B/s | 0.0 B | 00m00s
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[42/47] perl-IO-Socket-SSL-0:2.089-1.fc 100% | 0.0 B/s | 0.0 B | 00m00s
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[43/48] perl-MIME-Base64-0:3.16-511.fc4 100% | 0.0 B/s | 0.0 B | 00m00s
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[44/49] perl-Net-SSLeay-0:1.94-7.fc41.x 100% | 0.0 B/s | 0.0 B | 00m00s
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[45/50] perl-Socket-4:2.038-511.fc41.x8 100% | 0.0 B/s | 0.0 B | 00m00s
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[46/51] perl-Time-Local-2:1.350-511.fc4 100% | 0.0 B/s | 0.0 B | 00m00s
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[47/52] perl-File-stat-0:1.14-512.fc42. 100% | 0.0 B/s | 0.0 B | 00m00s
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[48/53] perl-SelectSaver-0:1.02-512.fc4 100% | 0.0 B/s | 0.0 B | 00m00s
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[49/54] perl-Pod-Escapes-1:1.07-511.fc4 100% | 0.0 B/s | 0.0 B | 00m00s
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[50/55] perl-Text-Tabs+Wrap-0:2024.001- 100% | 0.0 B/s | 0.0 B | 00m00s
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[51/56] perl-locale-0:1.12-512.fc42.noa 100% | 0.0 B/s | 0.0 B | 00m00s
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[53/58] perl-IO-Socket-IP-0:0.43-1.fc42 100% | 0.0 B/s | 0.0 B | 00m00s
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[54/59] perl-URI-0:5.31-1.fc42.noarch 100% | 0.0 B/s | 0.0 B | 00m00s
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[55/60] perl-AutoLoader-0:5.74-512.fc42 100% | 0.0 B/s | 0.0 B | 00m00s
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[56/61] perl-Class-Struct-0:0.68-512.fc 100% | 0.0 B/s | 0.0 B | 00m00s
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[84/94] bzip2-devel-0:1.0.8-19.fc42.x86 100% | 19.0 MiB/s | 214.2 KiB | 00m00s
[85/94] perl-FindBin-0:1.54-512.fc42.no 100% | 1.2 MiB/s | 14.2 KiB | 00m00s
[86/94] brotli-devel-0:1.1.0-5.fc42.x86 100% | 33.7 MiB/s | 34.5 KiB | 00m00s
[87/94] brotli-0:1.1.0-5.fc42.x86_64 100% | 18.9 MiB/s | 19.4 KiB | 00m00s
[88/94] libcurl-devel-0:8.11.1-2.fc42.x 100% | 47.7 MiB/s | 781.7 KiB | 00m00s
[89/94] libnghttp2-devel-0:1.64.0-1.fc4 100% | 18.1 MiB/s | 55.7 KiB | 00m00s
[90/94] libpsl-devel-0:0.21.5-4.fc41.x8 100% | 10.8 MiB/s | 33.3 KiB | 00m00s
[91/94] libssh-devel-0:0.11.1-1.fc42.x8 100% | 20.6 MiB/s | 42.2 KiB | 00m00s
[92/94] publicsuffix-list-0:20240107-4. 100% | 42.7 MiB/s | 87.5 KiB | 00m00s
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[94/94] Total 100% | 0.0 B/s | 0.0 B | 00m00s
Running transaction
[ 1/96] Verify package files 100% | 429.0 B/s | 94.0 B | 00m00s
[ 2/96] Prepare transaction 100% | 1.6 KiB/s | 94.0 B | 00m00s
[ 3/96] Installing cmake-filesystem-0:3 100% | 7.4 MiB/s | 7.6 KiB | 00m00s
[ 4/96] Installing libmpc-0:1.3.1-6.fc4 100% | 162.3 MiB/s | 166.2 KiB | 00m00s
[ 5/96] Installing cpp-0:15.0.0-0.2.fc4 100% | 371.2 MiB/s | 37.5 MiB | 00m00s
[ 6/96] Installing zlib-ng-compat-devel 100% | 105.8 MiB/s | 108.3 KiB | 00m00s
[ 7/96] Installing libssh-devel-0:0.11. 100% | 176.1 MiB/s | 180.3 KiB | 00m00s
[ 8/96] Installing annobin-docs-0:12.79 100% | 0.0 B/s | 99.7 KiB | 00m00s
[ 9/96] Installing pcre2-utf32-0:10.44- 100% | 274.8 MiB/s | 562.8 KiB | 00m00s
[10/96] Installing pcre2-utf16-0:10.44- 100% | 288.5 MiB/s | 590.9 KiB | 00m00s
[11/96] Installing pcre2-devel-0:10.44- 100% | 221.7 MiB/s | 2.0 MiB | 00m00s
[12/96] Installing kernel-headers-0:6.1 100% | 214.3 MiB/s | 6.6 MiB | 00m00s
[13/96] Installing libxcrypt-devel-0:4. 100% | 16.0 MiB/s | 32.9 KiB | 00m00s
[14/96] Installing glibc-devel-0:2.40.9 100% | 179.0 MiB/s | 2.3 MiB | 00m00s
[15/96] Installing libverto-devel-0:0.3 100% | 0.0 B/s | 26.4 KiB | 00m00s
[16/96] Installing libsepol-devel-0:3.8 100% | 62.6 MiB/s | 128.3 KiB | 00m00s
[17/96] Installing libselinux-devel-0:3 100% | 39.4 MiB/s | 161.4 KiB | 00m00s
[18/96] Installing libcom_err-devel-0:1 100% | 17.8 MiB/s | 18.3 KiB | 00m00s
[19/96] Installing keyutils-libs-devel- 100% | 6.7 MiB/s | 55.2 KiB | 00m00s
[20/96] Installing groff-base-0:1.23.0- 100% | 192.3 MiB/s | 3.8 MiB | 00m00s
[21/96] Installing publicsuffix-list-0: 100% | 311.6 MiB/s | 319.1 KiB | 00m00s
[22/96] Installing libpsl-devel-0:0.21. 100% | 110.9 MiB/s | 113.6 KiB | 00m00s
[23/96] Installing libnghttp2-devel-0:1 100% | 289.5 MiB/s | 296.5 KiB | 00m00s
[24/96] Installing libidn2-devel-0:2.3. 100% | 127.0 MiB/s | 260.1 KiB | 00m00s
[25/96] Installing libkadm5-0:1.21.3-3. 100% | 208.6 MiB/s | 213.6 KiB | 00m00s
[26/96] Installing krb5-devel-0:1.21.3- 100% | 232.8 MiB/s | 715.2 KiB | 00m00s
[27/96] Installing brotli-0:1.1.0-5.fc4 100% | 0.0 B/s | 31.1 KiB | 00m00s
[28/96] Installing brotli-devel-0:1.1.0 100% | 66.4 MiB/s | 68.0 KiB | 00m00s
[29/96] Installing ncurses-0:6.5-2.2024 100% | 206.3 MiB/s | 633.9 KiB | 00m00s
[30/96] Installing perl-Digest-0:1.20-5 100% | 36.2 MiB/s | 37.1 KiB | 00m00s
[31/96] Installing perl-B-0:1.89-512.fc 100% | 244.8 MiB/s | 501.3 KiB | 00m00s
[32/96] Installing perl-FileHandle-0:2. 100% | 0.0 B/s | 9.8 KiB | 00m00s
[33/96] Installing perl-Digest-MD5-0:2. 100% | 60.2 MiB/s | 61.7 KiB | 00m00s
[34/96] Installing perl-MIME-Base32-0:1 100% | 31.4 MiB/s | 32.2 KiB | 00m00s
[35/96] Installing perl-libnet-0:3.15-5 100% | 143.9 MiB/s | 294.7 KiB | 00m00s
[36/96] Installing perl-Data-Dumper-0:2 100% | 110.9 MiB/s | 113.6 KiB | 00m00s
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[39/96] Installing perl-URI-0:5.31-1.fc 100% | 87.8 MiB/s | 269.6 KiB | 00m00s
[40/96] Installing perl-if-0:0.61.000-5 100% | 0.0 B/s | 6.2 KiB | 00m00s
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[42/96] Installing perl-Time-Local-2:1. 100% | 68.9 MiB/s | 70.6 KiB | 00m00s
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[45/96] Installing perl-locale-0:1.12-5 100% | 0.0 B/s | 6.9 KiB | 00m00s
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[47/96] Installing perl-IO-Socket-SSL-0 100% | 230.3 MiB/s | 707.4 KiB | 00m00s
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[50/96] Installing perl-POSIX-0:2.20-51 100% | 230.8 MiB/s | 236.4 KiB | 00m00s
[51/96] Installing perl-File-Temp-1:0.2 100% | 160.2 MiB/s | 164.1 KiB | 00m00s
[52/96] Installing perl-IPC-Open3-0:1.2 100% | 0.0 B/s | 23.3 KiB | 00m00s
[53/96] Installing perl-Class-Struct-0: 100% | 0.0 B/s | 25.9 KiB | 00m00s
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Warning: skipped OpenPGP checks for 12 packages from repositories: copr_base, https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch
Complete!
Finish: build setup for htslib-1.15.1-6.fc42.src.rpm
Start: rpmbuild htslib-1.15.1-6.fc42.src.rpm
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1721260800
Executing(%mkbuilddir): /bin/sh -e /var/tmp/rpm-tmp.BzX2G7
+ umask 022
+ cd /builddir/build/BUILD/htslib-1.15.1-build
+ test -d /builddir/build/BUILD/htslib-1.15.1-build
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w /builddir/build/BUILD/htslib-1.15.1-build
+ /usr/bin/rm -rf /builddir/build/BUILD/htslib-1.15.1-build
+ /usr/bin/mkdir -p /builddir/build/BUILD/htslib-1.15.1-build
+ /usr/bin/mkdir -p /builddir/build/BUILD/htslib-1.15.1-build/SPECPARTS
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.TNd1cb
+ umask 022
+ cd /builddir/build/BUILD/htslib-1.15.1-build
+ cd /builddir/build/BUILD/htslib-1.15.1-build
+ rm -rf htslib-1.15.1
+ /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/htslib-1.15.1.tar.bz2
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd htslib-1.15.1
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ echo 'Patch #0 (htslib-1.15.1-gcc12.patch):'
Patch #0 (htslib-1.15.1-gcc12.patch):
+ /usr/bin/patch --no-backup-if-mismatch -f -p1 --fuzz=0
patching file htscodecs/htscodecs/rANS_word.h
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.dXJ4D1
+ umask 022
+ cd /builddir/build/BUILD/htslib-1.15.1-build
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd htslib-1.15.1
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ '[' '-flto=auto -ffat-lto-objectsx' '!=' x ']'
++ find . -type f -name configure -print
+ for file in $(find . -type f -name configure -print)
+ /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\) = /__attribute__ ((used)) char (*f) () = /g' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\);/__attribute__ ((used)) char (*f) ();/g' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ /usr/bin/sed -r --in-place=.backup 's/^char \$2 \(\);/__attribute__ ((used)) char \$2 ();/g' ./configure
+ diff -u ./configure.backup ./configure
--- ./configure.backup 2022-04-07 15:42:52.000000000 +0000
+++ ./configure 2024-12-20 06:52:46.360627466 +0000
@@ -1697,7 +1697,7 @@
#ifdef __cplusplus
extern "C"
#endif
-char $2 ();
+__attribute__ ((used)) char $2 ();
/* The GNU C library defines this for functions which it implements
to always fail with ENOSYS. Some functions are actually named
something starting with __ and the normal name is an alias. */
+ /usr/bin/sed --in-place=.backup '1{$!N;$!N};$!N;s/int x = 1;\nint y = 0;\nint z;\nint nan;/volatile int x = 1; volatile int y = 0; volatile int z, nan;/;P;D' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ /usr/bin/sed --in-place=.backup 's#^lt_cv_sys_global_symbol_to_cdecl=.*#lt_cv_sys_global_symbol_to_cdecl="sed -n -e '\''s/^T .* \\(.*\\)$/extern int \\1();/p'\'' -e '\''s/^$symcode* .* \\(.*\\)$/extern char \\1;/p'\''"#' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ '[' 1 = 1 ']'
+++ dirname ./configure
++ find . -name config.guess -o -name config.sub
+ '[' 1 = 1 ']'
+ '[' x '!=' 'x-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' ']'
++ find . -name ltmain.sh
++ grep -q runstatedir=DIR ./configure
++ echo --runstatedir=/run
+ ./configure --build=x86_64-redhat-linux --host=x86_64-redhat-linux --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/libexec --localstatedir=/var --runstatedir=/run --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info 'CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer' 'LDFLAGS=-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' --prefix=/usr --libdir=/usr/lib64 --enable-plugins '--with-plugin-path=/usr/local/libexec/htslib:$(plugindir)' --enable-gcs --enable-libcurl --enable-s3
configure: WARNING: unrecognized options: --disable-dependency-tracking
checking for x86_64-redhat-linux-gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for x86_64-redhat-linux-ranlib... no
checking for ranlib... ranlib
checking for grep that handles long lines and -e... /usr/bin/grep
checking for C compiler warning flags... -Wall
checking for x86_64-redhat-linux-pkg-config... 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 x86_64-redhat-linux... plain .so
checking whether the compiler accepts -fvisibility=hidden... yes
checking how to run the C preprocessor... gcc -E
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking for gmtime_r... yes
checking for fsync... yes
checking for drand48... yes
checking for srand48_deterministic... no
checking whether fdatasync is declared... yes
checking for fdatasync... yes
checking for library containing dlsym... none required
checking whether the compiler accepts -rdynamic... yes
checking for library containing log... -lm
checking for zlib.h... yes
checking for inflate in -lz... yes
checking for library containing recv... none required
checking for bzlib.h... yes
checking for BZ2_bzBuffToBuffCompress in -lbz2... yes
checking for lzma.h... yes
checking for lzma_easy_buffer_encode in -llzma... yes
checking whether htscodecs files are present... yes
checking for libdeflate.h... no
checking for libdeflate_deflate_compress in -ldeflate... no
checking for curl/curl.h... yes
checking for curl_easy_pause in -lcurl... yes
checking for CCHmac... no
checking for library containing HMAC... -lcrypto
checking for library containing regcomp... none required
checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes
configure: creating ./config.status
config.status: creating config.mk
config.status: creating htslib.pc.tmp
config.status: creating config.h
config.status: linking htscodecs_bundled.mk to htscodecs.mk
configure: WARNING: unrecognized options: --disable-dependency-tracking
+ /usr/bin/make -O -j4 V=1 VERBOSE=1
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o kfunc.o kfunc.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o kstring.o kstring.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o errmod.o errmod.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o bcf_sr_sort.o bcf_sr_sort.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o faidx.o faidx.c
echo '#define HTS_VERSION_TEXT "1.15.1"' > version.h
echo '#define HTS_CC "gcc"' > config_vars.h
echo '#define HTS_CPPFLAGS ""' >> config_vars.h
echo '#define HTS_CFLAGS "-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden"' >> config_vars.h
echo '#define HTS_LDFLAGS "-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic"' >> config_vars.h
echo '#define HTS_LIBS "-llzma -lbz2 -lz -lm "' >> config_vars.h
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o bgzf.o bgzf.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o hts_os.o hts_os.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o md5.o md5.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o hts_expr.o hts_expr.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o hfile.o hfile.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o multipart.o multipart.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o probaln.o probaln.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o realn.o realn.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o region.o region.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o regidx.o regidx.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o header.o header.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o vcf_sweep.o vcf_sweep.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o tbx.o tbx.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o textutils.o textutils.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o thread_pool.o thread_pool.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o synced_bcf_reader.o synced_bcf_reader.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o vcfutils.o vcfutils.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o cram/cram_codecs.o cram/cram_codecs.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o cram/cram_decode.o cram/cram_decode.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o cram/cram_external.o cram/cram_external.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o sam.o sam.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o cram/cram_index.o cram/cram_index.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o cram/cram_stats.o cram/cram_stats.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o cram/mFILE.o cram/mFILE.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o cram/cram_encode.o cram/cram_encode.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o cram/open_trace_file.o cram/open_trace_file.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o cram/string_alloc.o cram/string_alloc.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o vcf.o vcf.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o cram/cram_io.o cram/cram_io.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -DPLUGINPATH=\"/usr/local/libexec/htslib:/usr/libexec/htslib\" -c -o plugin.o plugin.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o kfunc.pico kfunc.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o kstring.pico kstring.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o errmod.pico errmod.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o bcf_sr_sort.pico bcf_sr_sort.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o faidx.pico faidx.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o bgzf.pico bgzf.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o hfile.pico hfile.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o hts_os.pico hts_os.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o hts_expr.pico hts_expr.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o md5.pico md5.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o multipart.pico multipart.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o probaln.pico probaln.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o realn.pico realn.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o header.pico header.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o region.pico region.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o regidx.pico regidx.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o vcf_sweep.pico vcf_sweep.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o tbx.pico tbx.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o textutils.pico textutils.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o synced_bcf_reader.pico synced_bcf_reader.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o thread_pool.pico thread_pool.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o hts.pico hts.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o vcfutils.pico vcfutils.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o cram/cram_codecs.pico cram/cram_codecs.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o sam.pico sam.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o cram/cram_decode.pico cram/cram_decode.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o cram/cram_external.pico cram/cram_external.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o cram/cram_index.pico cram/cram_index.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o cram/cram_stats.pico cram/cram_stats.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o cram/mFILE.pico cram/mFILE.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o cram/open_trace_file.pico cram/open_trace_file.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o cram/pooled_alloc.pico cram/pooled_alloc.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o cram/string_alloc.pico cram/string_alloc.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o vcf.pico vcf.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o cram/cram_encode.pico cram/cram_encode.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/htscodecs.pico htscodecs/htscodecs/htscodecs.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/pack.pico htscodecs/htscodecs/pack.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/arith_dynamic.pico htscodecs/htscodecs/arith_dynamic.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/fqzcomp_qual.pico htscodecs/htscodecs/fqzcomp_qual.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rle.pico htscodecs/htscodecs/rle.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o cram/cram_io.pico cram/cram_io.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -DPLUGINPATH=\"/usr/local/libexec/htslib:/usr/libexec/htslib\" -fpic -c -o plugin.pico plugin.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rANS_static.pico htscodecs/htscodecs/rANS_static.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o bgzip.o bgzip.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rANS_static4x16pr.pico htscodecs/htscodecs/rANS_static4x16pr.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o htsfile.o htsfile.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o hfile_gcs.pico hfile_gcs.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o tabix.o tabix.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/tokenise_name3.pico htscodecs/htscodecs/tokenise_name3.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/hts_endian.o test/hts_endian.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/fieldarith.o test/fieldarith.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o hfile_s3_write.pico hfile_s3_write.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o hfile_libcurl.pico hfile_libcurl.c
hfile_libcurl.c: In function ‘libcurl_open’:
hfile_libcurl.c:1335:9: warning: ‘CURLINFO_CONTENT_LENGTH_DOWNLOAD’ is deprecated: since 7.55.0. Use CURLINFO_CONTENT_LENGTH_DOWNLOAD_T [-Wdeprecated-declarations]
1335 | if (curl_easy_getinfo(fp->easy, CURLINFO_CONTENT_LENGTH_DOWNLOAD,
| ^~
In file included from hfile_libcurl.c:47:
/usr/include/curl/curl.h:2897:3: note: declared here
2897 | CURLINFO_CONTENT_LENGTH_DOWNLOAD
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/pileup.o test/pileup.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/plugins-dlhts.o test/plugins-dlhts.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/hfile.o test/hfile.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/pileup_mod.o test/pileup_mod.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o hfile_s3.pico hfile_s3.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test_expr.o test/test_expr.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test_kfunc.o test/test_kfunc.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test_mod.o test/test_mod.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test_realn.o test/test_realn.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test_kstring.o test/test_kstring.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test_bgzf.o test/test_bgzf.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test_str2int.o test/test_str2int.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test-regidx.o test/test-regidx.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test_index.o test/test_index.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test_view.o test/test_view.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/fuzz/hts_open_fuzzer.o test/fuzz/hts_open_fuzzer.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test-bcf-sr.o test/test-bcf-sr.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test-bcf-translate.o test/test-bcf-translate.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/sam.o test/sam.c
sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' htslib.pc.tmp > htslib_static.mk
sed -e 's#@-includedir@#'`pwd`'#g;s#@-libdir@#'`pwd`'#g' htslib.pc.tmp > htslib-uninstalled.pc
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test_introspection.o test/test_introspection.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test-vcf-api.o test/test-vcf-api.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test-parse-reg.o test/test-parse-reg.c
gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/plugins-dlhts test/plugins-dlhts.o -llzma -lbz2 -lz -lm
gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/hts_endian test/hts_endian.o -llzma -lbz2 -lz -lm
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o hts.o hts.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_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o plugin.o
ranlib libhts.a
gcc -shared -Wl,-soname,libhts.so.3 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o libhts.so kfunc.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico header.pico hfile.pico hts.pico hts_expr.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico region.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_stats.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/string_alloc.pico htscodecs/htscodecs/arith_dynamic.pico htscodecs/htscodecs/fqzcomp_qual.pico htscodecs/htscodecs/htscodecs.pico htscodecs/htscodecs/pack.pico htscodecs/htscodecs/rANS_static4x16pr.pico htscodecs/htscodecs/rANS_static.pico htscodecs/htscodecs/rle.pico htscodecs/htscodecs/tokenise_name3.pico plugin.pico -llzma -lbz2 -lz -lm -lpthread
ln -sf libhts.so libhts.so.3
gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o bgzip bgzip.o libhts.a -llzma -lbz2 -lz -lm -lpthread
gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o tabix tabix.o libhts.a -llzma -lbz2 -lz -lm -lpthread
gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o htsfile htsfile.o libhts.a -llzma -lbz2 -lz -lm -lpthread
gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/fieldarith test/fieldarith.o libhts.a -llzma -lbz2 -lz -lm -lpthread
gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/hfile test/hfile.o libhts.a -llzma -lbz2 -lz -lm -lpthread
gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/pileup test/pileup.o libhts.a -llzma -lbz2 -lz -lm -lpthread
gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/pileup_mod test/pileup_mod.o libhts.a -llzma -lbz2 -lz -lm -lpthread
gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test_expr test/test_expr.o libhts.a -lz -llzma -lbz2 -lz -lm -lpthread
gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test_kfunc test/test_kfunc.o libhts.a -lz -llzma -lbz2 -lz -lm -lpthread
gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test_kstring test/test_kstring.o libhts.a -lz -llzma -lbz2 -lz -lm -lpthread
gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/sam test/sam.o libhts.a -llzma -lbz2 -lz -lm -lpthread
gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test_bgzf test/test_bgzf.o libhts.a -lz -llzma -lbz2 -lz -lm -lpthread
gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test_mod test/test_mod.o libhts.a -llzma -lbz2 -lz -lm -lpthread
gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test_realn test/test_realn.o libhts.a -llzma -lbz2 -lz -lm -lpthread
gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test-regidx test/test-regidx.o libhts.a -llzma -lbz2 -lz -lm -lpthread
gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test_str2int test/test_str2int.o libhts.a -llzma -lbz2 -lz -lm -lpthread
gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test_view test/test_view.o libhts.a -llzma -lbz2 -lz -lm -lpthread
gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test-vcf-api test/test-vcf-api.o libhts.a -llzma -lbz2 -lz -lm -lpthread
gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test_index test/test_index.o libhts.a -llzma -lbz2 -lz -lm -lpthread
gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -llzma -lbz2 -lz -lm -lpthread
gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -llzma -lbz2 -lz -lm -lpthread
gcc -shared -Wl,-E -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o hfile_libcurl.so hfile_libcurl.pico libhts.so -llzma -lbz2 -lz -lm -lcurl -lpthread
gcc -shared -Wl,-E -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o hfile_gcs.so hfile_gcs.pico libhts.so -llzma -lbz2 -lz -lm -lpthread
gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test-parse-reg test/test-parse-reg.o libhts.a -llzma -lbz2 -lz -lm -lpthread
gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -lz -llzma -lbz2 -lz -lm -lpthread
gcc -shared -Wl,-E -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o hfile_s3_write.so hfile_s3_write.pico libhts.so -llzma -lbz2 -lz -lm -lcrypto -lcurl -lpthread
gcc -shared -Wl,-E -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o hfile_s3.so hfile_s3.pico libhts.so -llzma -lbz2 -lz -lm -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o test/test_introspection test/test_introspection.o libhts.a -llzma -lbz2 -lz -lm -lpthread
+ sed -i -E '/^(Libs|Requires)\.private:/d' htslib.pc.tmp
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.sYVYP7
+ umask 022
+ cd /builddir/build/BUILD/htslib-1.15.1-build
+ '[' /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT '!=' / ']'
+ rm -rf /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT
++ dirname /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT
+ mkdir -p /builddir/build/BUILD/htslib-1.15.1-build
+ mkdir /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd htslib-1.15.1
+ /usr/bin/make install DESTDIR=/builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT 'INSTALL=/usr/bin/install -p'
mkdir -p -m 755 /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT/usr/bin /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT/usr/include /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT/usr/include/htslib /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT/usr/lib64 /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT/usr/share/man/man1 /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT/usr/share/man/man5 /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT/usr/share/man/man7 /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT/usr/lib64/pkgconfig
if test -n "/usr/libexec/htslib"; then mkdir -p -m 755 /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT/usr/libexec/htslib; fi
/usr/bin/install -p -m 644 libhts.so /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT/usr/lib64/libhts.so.1.15.1
ln -sf libhts.so.1.15.1 /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT/usr/lib64/libhts.so
ln -sf libhts.so.1.15.1 /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT/usr/lib64/libhts.so.3
sed -e 's#@-includedir@#/usr/include#g;s#@-libdir@#/usr/lib64#g;s#@-PACKAGE_VERSION@#1.15.1#g' htslib.pc.tmp > /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT/usr/lib64/pkgconfig/htslib.pc
chmod 644 /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT/usr/lib64/pkgconfig/htslib.pc
/usr/bin/install -p bgzip htsfile tabix /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT/usr/bin
if test -n "hfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so"; then /usr/bin/install -p hfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT/usr/libexec/htslib; fi
/usr/bin/install -p -m 644 htslib/*.h /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT/usr/include/htslib
/usr/bin/install -p -m 644 libhts.a /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT/usr/lib64/libhts.a
/usr/bin/install -p -m 644 bgzip.1 htsfile.1 tabix.1 /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT/usr/share/man/man1
/usr/bin/install -p -m 644 faidx.5 sam.5 vcf.5 /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT/usr/share/man/man5
/usr/bin/install -p -m 644 htslib-s3-plugin.7 /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT/usr/share/man/man7
+ pushd /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT//usr/lib64
~/build/BUILD/htslib-1.15.1-build/BUILDROOT/usr/lib64 ~/build/BUILD/htslib-1.15.1-build/htslib-1.15.1
+ chmod 755 libhts.so.1.15.1
+ popd
~/build/BUILD/htslib-1.15.1-build/htslib-1.15.1
+ find /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT -name '*.la' -delete
+ rm -f /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT//usr/lib64/libhts.a
+ /usr/bin/find-debuginfo -j4 --strict-build-id -m -i --build-id-seed 1.15.1-6.fc42 --unique-debug-suffix -1.15.1-6.fc42.x86_64 --unique-debug-src-base htslib-1.15.1-6.fc42.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1
find-debuginfo: starting
Extracting debug info from 8 files
DWARF-compressing 8 files
sepdebugcrcfix: Updated 8 CRC32s, 0 CRC32s did match.
Creating .debug symlinks for symlinks to ELF files
Copying sources found by 'debugedit -l' to /usr/src/debug/htslib-1.15.1-6.fc42.x86_64
find-debuginfo: done
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-ldconfig
+ /usr/lib/rpm/brp-compress
+ /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip
+ /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip
+ /usr/lib/rpm/check-rpaths
+ /usr/lib/rpm/redhat/brp-mangle-shebangs
+ /usr/lib/rpm/brp-remove-la-files
+ env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j4
+ /usr/lib/rpm/redhat/brp-python-hardlink
+ /usr/bin/add-determinism --brp -j4 /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT
Scanned 29 directories and 162 files,
processed 0 inodes,
0 modified (0 replaced + 0 rewritten),
0 unsupported format, 0 errors
Reading /builddir/build/BUILD/htslib-1.15.1-build/SPECPARTS/rpm-debuginfo.specpart
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.dbVnDh
+ umask 022
+ cd /builddir/build/BUILD/htslib-1.15.1-build
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd htslib-1.15.1
+ make test
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -Ihtscodecs -D_POSIX_C_SOURCE=200112L -c -o htscodecs/tests/rANS_static_test.o htscodecs/tests/rANS_static_test.c
gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o htscodecs/tests/rans4x8 htscodecs/tests/rANS_static_test.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o -llzma -lbz2 -lz -lm -lm -lpthread
cd htscodecs/tests && srcdir=. && export srcdir && ./rans4x8.test
Testing rans4x8 -r -o0 on ./dat/q4 11674
Testing rans4x8 -r -o1 on ./dat/q4 10870
Testing rans4x8 -r -o0 on ./dat/q40+dir 50258
Testing rans4x8 -r -o1 on ./dat/q40+dir 50537
Testing rans4x8 -r -o0 on ./dat/q8 33099
Testing rans4x8 -r -o1 on ./dat/q8 31428
Testing rans4x8 -r -o0 on ./dat/qvar 32997
Testing rans4x8 -r -o1 on ./dat/qvar 32832
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -Ihtscodecs -D_POSIX_C_SOURCE=200112L -c -o htscodecs/tests/rANS_static4x16pr_test.o htscodecs/tests/rANS_static4x16pr_test.c
gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o htscodecs/tests/rans4x16pr htscodecs/tests/rANS_static4x16pr_test.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o -llzma -lbz2 -lz -lm -lm -lpthread
cd htscodecs/tests && srcdir=. && export srcdir && ./rans4x16.test
Testing rans4x16 -r -o0 on ./dat/q4 11660
Testing rans4x16 -r -o1 on ./dat/q4 10848
Testing rans4x16 -r -o64 on ./dat/q4 12878
Testing rans4x16 -r -o65 on ./dat/q4 10672
Testing rans4x16 -r -o128 on ./dat/q4 10902
Testing rans4x16 -r -o129 on ./dat/q4 10890
Testing rans4x16 -r -o192 on ./dat/q4 11225
Testing rans4x16 -r -o193 on ./dat/q4 10825
Testing rans4x16 -r -o8 on ./dat/q4 11731
Testing rans4x16 -r -o9 on ./dat/q4 11111
Testing rans4x16 -r -o0 on ./dat/q40+dir 50247
Testing rans4x16 -r -o1 on ./dat/q40+dir 49449
Testing rans4x16 -r -o8 on ./dat/q40+dir 50072
Testing rans4x16 -r -o9 on ./dat/q40+dir 50072
Testing rans4x16 -r -o0 on ./dat/q8 33088
Testing rans4x16 -r -o1 on ./dat/q8 31372
Testing rans4x16 -r -o64 on ./dat/q8 33458
Testing rans4x16 -r -o65 on ./dat/q8 31025
Testing rans4x16 -r -o128 on ./dat/q8 32237
Testing rans4x16 -r -o129 on ./dat/q8 31258
Testing rans4x16 -r -o192 on ./dat/q8 32024
Testing rans4x16 -r -o193 on ./dat/q8 31146
Testing rans4x16 -r -o0 on ./dat/qvar 32987
Testing rans4x16 -r -o1 on ./dat/qvar 32261
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -Ihtscodecs -D_POSIX_C_SOURCE=200112L -c -o htscodecs/tests/arith_dynamic_test.o htscodecs/tests/arith_dynamic_test.c
gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o htscodecs/tests/arith_dynamic htscodecs/tests/arith_dynamic_test.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o -llzma -lbz2 -lz -lm -lm -lpthread
cd htscodecs/tests && srcdir=. && export srcdir && ./arith.test
Testing arith_dynamic -r -o0 on ./dat/q4 11615
Testing arith_dynamic -r -o1 on ./dat/q4 10831
Testing arith_dynamic -r -o64 on ./dat/q4 13360
Testing arith_dynamic -r -o65 on ./dat/q4 10484
Testing arith_dynamic -r -o128 on ./dat/q4 10774
Testing arith_dynamic -r -o129 on ./dat/q4 10329
Testing arith_dynamic -r -o192 on ./dat/q4 11095
Testing arith_dynamic -r -o193 on ./dat/q4 10283
Testing arith_dynamic -r -o8 on ./dat/q4 11448
Testing arith_dynamic -r -o9 on ./dat/q4 11083
Testing arith_dynamic -r -o0 on ./dat/q40+dir 49949
Testing arith_dynamic -r -o1 on ./dat/q40+dir 49034
Testing arith_dynamic -r -o64 on ./dat/q40+dir 51242
Testing arith_dynamic -r -o65 on ./dat/q40+dir 49061
Testing arith_dynamic -r -o8 on ./dat/q40+dir 49820
Testing arith_dynamic -r -o9 on ./dat/q40+dir 49448
Testing arith_dynamic -r -o0 on ./dat/q8 32752
Testing arith_dynamic -r -o1 on ./dat/q8 31331
Testing arith_dynamic -r -o64 on ./dat/q8 35211
Testing arith_dynamic -r -o65 on ./dat/q8 30907
Testing arith_dynamic -r -o128 on ./dat/q8 32063
Testing arith_dynamic -r -o129 on ./dat/q8 31084
Testing arith_dynamic -r -o192 on ./dat/q8 32267
Testing arith_dynamic -r -o193 on ./dat/q8 30931
Testing arith_dynamic -r -o0 on ./dat/qvar 32597
Testing arith_dynamic -r -o1 on ./dat/qvar 31982
Testing arith_dynamic -r -o64 on ./dat/qvar 33237
Testing arith_dynamic -r -o65 on ./dat/qvar 31993
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -Ihtscodecs -D_POSIX_C_SOURCE=200112L -c -o htscodecs/tests/tokenise_name3_test.o htscodecs/tests/tokenise_name3_test.c
gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o htscodecs/tests/tokenise_name3 htscodecs/tests/tokenise_name3_test.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o -llzma -lbz2 -lz -lm -lm -lpthread
cd htscodecs/tests && srcdir=. && export srcdir && ./tok3.test
Testing tokenise_name3 -r -1 on ./names/01.names 3392
Testing tokenise_name3 -r -3 on ./names/01.names 2471
Testing tokenise_name3 -r -5 on ./names/01.names 2283
Testing tokenise_name3 -r -7 on ./names/01.names 2234
Testing tokenise_name3 -r -9 on ./names/01.names 2234
Testing tokenise_name3 -r -11 on ./names/01.names 3151
Testing tokenise_name3 -r -13 on ./names/01.names 2424
Testing tokenise_name3 -r -15 on ./names/01.names 2061
Testing tokenise_name3 -r -17 on ./names/01.names 2051
Testing tokenise_name3 -r -19 on ./names/01.names 2049
Testing tokenise_name3 -r -1 on ./names/02.names 6633
Testing tokenise_name3 -r -3 on ./names/02.names 4983
Testing tokenise_name3 -r -5 on ./names/02.names 4942
Testing tokenise_name3 -r -7 on ./names/02.names 4922
Testing tokenise_name3 -r -9 on ./names/02.names 4918
Testing tokenise_name3 -r -11 on ./names/02.names 6087
Testing tokenise_name3 -r -13 on ./names/02.names 4797
Testing tokenise_name3 -r -15 on ./names/02.names 4714
Testing tokenise_name3 -r -17 on ./names/02.names 4695
Testing tokenise_name3 -r -19 on ./names/02.names 4695
Testing tokenise_name3 -r -1 on ./names/03.names 10557
Testing tokenise_name3 -r -3 on ./names/03.names 7822
Testing tokenise_name3 -r -5 on ./names/03.names 7557
Testing tokenise_name3 -r -7 on ./names/03.names 7521
Testing tokenise_name3 -r -9 on ./names/03.names 7521
Testing tokenise_name3 -r -11 on ./names/03.names 9294
Testing tokenise_name3 -r -13 on ./names/03.names 7291
Testing tokenise_name3 -r -15 on ./names/03.names 7125
Testing tokenise_name3 -r -17 on ./names/03.names 7069
Testing tokenise_name3 -r -19 on ./names/03.names 7068
Testing tokenise_name3 -r -1 on ./names/05.names 5098
Testing tokenise_name3 -r -3 on ./names/05.names 3600
Testing tokenise_name3 -r -5 on ./names/05.names 3551
Testing tokenise_name3 -r -7 on ./names/05.names 3534
Testing tokenise_name3 -r -9 on ./names/05.names 3534
Testing tokenise_name3 -r -11 on ./names/05.names 4648
Testing tokenise_name3 -r -13 on ./names/05.names 3405
Testing tokenise_name3 -r -15 on ./names/05.names 3381
Testing tokenise_name3 -r -17 on ./names/05.names 3377
Testing tokenise_name3 -r -19 on ./names/05.names 3377
Testing tokenise_name3 -r -1 on ./names/08.names 6841
Testing tokenise_name3 -r -3 on ./names/08.names 5291
Testing tokenise_name3 -r -5 on ./names/08.names 5206
Testing tokenise_name3 -r -7 on ./names/08.names 5160
Testing tokenise_name3 -r -9 on ./names/08.names 5160
Testing tokenise_name3 -r -11 on ./names/08.names 6374
Testing tokenise_name3 -r -13 on ./names/08.names 4895
Testing tokenise_name3 -r -15 on ./names/08.names 4851
Testing tokenise_name3 -r -17 on ./names/08.names 4805
Testing tokenise_name3 -r -19 on ./names/08.names 4805
Testing tokenise_name3 -r -1 on ./names/09.names 5339
Testing tokenise_name3 -r -3 on ./names/09.names 3598
Testing tokenise_name3 -r -5 on ./names/09.names 3527
Testing tokenise_name3 -r -7 on ./names/09.names 3493
Testing tokenise_name3 -r -9 on ./names/09.names 3493
Testing tokenise_name3 -r -11 on ./names/09.names 4861
Testing tokenise_name3 -r -13 on ./names/09.names 3427
Testing tokenise_name3 -r -15 on ./names/09.names 3391
Testing tokenise_name3 -r -17 on ./names/09.names 3366
Testing tokenise_name3 -r -19 on ./names/09.names 3366
Testing tokenise_name3 -r -1 on ./names/10.names 6458
Testing tokenise_name3 -r -3 on ./names/10.names 4843
Testing tokenise_name3 -r -5 on ./names/10.names 4799
Testing tokenise_name3 -r -7 on ./names/10.names 4746
Testing tokenise_name3 -r -9 on ./names/10.names 4744
Testing tokenise_name3 -r -11 on ./names/10.names 5785
Testing tokenise_name3 -r -13 on ./names/10.names 4567
Testing tokenise_name3 -r -15 on ./names/10.names 4492
Testing tokenise_name3 -r -17 on ./names/10.names 4472
Testing tokenise_name3 -r -19 on ./names/10.names 4472
Testing tokenise_name3 -r -1 on ./names/20.names 2511
Testing tokenise_name3 -r -3 on ./names/20.names 1701
Testing tokenise_name3 -r -5 on ./names/20.names 1659
Testing tokenise_name3 -r -7 on ./names/20.names 1632
Testing tokenise_name3 -r -9 on ./names/20.names 1632
Testing tokenise_name3 -r -11 on ./names/20.names 2319
Testing tokenise_name3 -r -13 on ./names/20.names 1629
Testing tokenise_name3 -r -15 on ./names/20.names 1605
Testing tokenise_name3 -r -17 on ./names/20.names 1600
Testing tokenise_name3 -r -19 on ./names/20.names 1600
Testing tokenise_name3 -r -1 on ./names/nv.names 6816
Testing tokenise_name3 -r -3 on ./names/nv.names 4989
Testing tokenise_name3 -r -5 on ./names/nv.names 4972
Testing tokenise_name3 -r -7 on ./names/nv.names 4937
Testing tokenise_name3 -r -9 on ./names/nv.names 4937
Testing tokenise_name3 -r -11 on ./names/nv.names 6084
Testing tokenise_name3 -r -13 on ./names/nv.names 4825
Testing tokenise_name3 -r -15 on ./names/nv.names 4771
Testing tokenise_name3 -r -17 on ./names/nv.names 4767
Testing tokenise_name3 -r -19 on ./names/nv.names 4767
Testing tokenise_name3 -r -1 on ./names/nv2.names 1181
Testing tokenise_name3 -r -3 on ./names/nv2.names 903
Testing tokenise_name3 -r -5 on ./names/nv2.names 879
Testing tokenise_name3 -r -7 on ./names/nv2.names 846
Testing tokenise_name3 -r -9 on ./names/nv2.names 846
Testing tokenise_name3 -r -11 on ./names/nv2.names 891
Testing tokenise_name3 -r -13 on ./names/nv2.names 836
Testing tokenise_name3 -r -15 on ./names/nv2.names 764
Testing tokenise_name3 -r -17 on ./names/nv2.names 747
Testing tokenise_name3 -r -19 on ./names/nv2.names 747
Testing tokenise_name3 -r -1 on ./names/rr.names 8788
Testing tokenise_name3 -r -3 on ./names/rr.names 6290
Testing tokenise_name3 -r -5 on ./names/rr.names 6252
Testing tokenise_name3 -r -7 on ./names/rr.names 6230
Testing tokenise_name3 -r -9 on ./names/rr.names 6230
Testing tokenise_name3 -r -11 on ./names/rr.names 8319
Testing tokenise_name3 -r -13 on ./names/rr.names 6066
Testing tokenise_name3 -r -15 on ./names/rr.names 5972
Testing tokenise_name3 -r -17 on ./names/rr.names 5963
Testing tokenise_name3 -r -19 on ./names/rr.names 5963
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -Ihtscodecs -D_POSIX_C_SOURCE=200112L -c -o htscodecs/tests/fqzcomp_qual_test.o htscodecs/tests/fqzcomp_qual_test.c
gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o htscodecs/tests/fqzcomp_qual htscodecs/tests/fqzcomp_qual_test.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o -llzma -lbz2 -lz -lm -lm -lpthread
cd htscodecs/tests && srcdir=. && export srcdir && ./fqzcomp.test
Testing fqzcomp_qual -r -s 0 on ./dat/q4 9307
Testing fqzcomp_qual -r -s 1 on ./dat/q4 9618
Testing fqzcomp_qual -r -s 2 on ./dat/q4 9453
Testing fqzcomp_qual -r -s 3 on ./dat/q4 10481
Testing fqzcomp_qual -r -s 0 on ./dat/q40+dir 47674
Testing fqzcomp_qual -r -s 1 on ./dat/q40+dir 45016
Testing fqzcomp_qual -r -s 2 on ./dat/q40+dir 47760
Testing fqzcomp_qual -r -s 3 on ./dat/q40+dir 48583
Testing fqzcomp_qual -r -s 0 on ./dat/q8 30012
Testing fqzcomp_qual -r -s 1 on ./dat/q8 33742
Testing fqzcomp_qual -r -s 2 on ./dat/q8 30982
Testing fqzcomp_qual -r -s 3 on ./dat/q8 31709
Testing fqzcomp_qual -r -s 0 on ./dat/qvar 32868
Testing fqzcomp_qual -r -s 1 on ./dat/qvar 35007
Testing fqzcomp_qual -r -s 2 on ./dat/qvar 32400
Testing fqzcomp_qual -r -s 3 on ./dat/qvar 32073
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -Ihtscodecs -D_POSIX_C_SOURCE=200112L -c -o htscodecs/tests/varint_test.o htscodecs/tests/varint_test.c
gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o htscodecs/tests/varint htscodecs/tests/varint_test.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o -llzma -lbz2 -lz -lm -lm -lpthread
cd htscodecs/tests && ./varint
test/hts_endian
test/test_expr
test/test_kfunc
test/test_kstring
test/test_str2int
test/fieldarith test/fieldarith.sam
test/hfile
HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -g ./libhts.so
HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -l ./libhts.so
test/test_bgzf test/bgziptest.txt
test/test-parse-reg -t test/colons.bam
Expected error: [E::hts_parse_region] Range is ambiguous. Use {chr1:100-200} or {chr1}:100-200 instead
Expected error: [E::hts_parse_region] Range is ambiguous. Use {chr1:100-200,chr3} or {chr1}:100-200,chr3 instead
Expected error: [E::hts_parse_region] Mismatching braces in "{chr1"
Expected error: [E::hts_parse_region] Unexpected string "x" after region
Expected error: [E::hts_parse_region] Unexpected string "y" after region
Expected error: [E::hts_parse_region] Unexpected string "chr3" after region
cd test/sam_filter && ./filter.sh filter.tst
Testing sam_filter...
PASS : $tv -i 'filter=qname =~ "\.1" && cigar =~ "D"' ../ce#1000.sam
PASS : $tv -i 'filter=rname=="CHROMOSOME_II"' ../ce#5b.sam
PASS : $tv -i 'filter=rname=~"CHROMOSOME_II"' ../ce#5b.sam
PASS : $tv -i 'filter=cigar=~"D"' ../ce#1000.sam
PASS : $tv -i 'filter=seq =~ "(AT){2}"' ../ce#1000.sam
PASS : $tv -i 'filter=library=="x"' ../xx#rg.sam
PASS : $tv -i 'filter=library!="x"' ../xx#rg.sam
PASS : $tv -i 'filter=pos % 23 == 11' ../ce#1000.sam |egrep -cv '^@'
PASS : $tv -i 'filter=qlen/(flag*mapq+pos)>5' ../ce#1000.sam |egrep -cv '^@'
PASS : $tv -i 'filter=[NM]>=10 || [MD]=~"A.*A.*A"' -t4 ../ce#1000.sam |egrep -cv '^@'
PASS : $tv -i 'filter=length(seq) != qlen' ../ce#5b.sam | egrep -cv '^@'
PASS : $tv -i 'filter=min(qual) >= 20' ../ce#1000.sam | egrep -cv '^@'
PASS : $tv -i 'filter=max(qual) <= 20' ../ce#1000.sam | egrep -cv '^@'
PASS : $tv -i 'filter=avg(qual) >= 20 && avg(qual) <= 30' ../ce#1000.sam | egrep -cv '^@'
Expected passes: 14
Unexpected passes: 0
Expected failures: 0
Unexpected failures: 0
cd test/tabix && ./test-tabix.sh tabix.tst
Testing tabix...
PASS : $tabix -f -p vcf vcf_file.tbi.tmp.vcf.gz
PASS : $tabix vcf_file.tbi.tmp.vcf.gz 1:3000151-3000151
PASS : $tabix vcf_file.tbi.tmp.vcf.gz 2:3199812-3199812
PASS : $tabix -f -C -p vcf vcf_file.csi.tmp.vcf.gz
PASS : $tabix vcf_file.csi.tmp.vcf.gz 1:3000151-3000151
PASS : $tabix vcf_file.csi.tmp.vcf.gz 2:3199812-3199812
PASS : $tabix -f -p vcf large_chr.tmp.vcf.gz (must exit non-zero)
PASS : $tabix -f -C -p vcf large_chr.tmp.vcf.gz
PASS : $tabix large_chr.tmp.vcf.gz chr20:1-2147483647
PASS : $tabix -f -p bed bed_file.tbi.tmp.bed.gz
PASS : $tabix bed_file.tbi.tmp.bed.gz Y:100200-100200
PASS : $tabix -f -p gff gff_file.tbi.tmp.gff.gz
PASS : $tabix gff_file.tbi.tmp.gff.gz X:2934832-2935190
PASS : $tabix --separate-regions bed_file.tbi.tmp.bed.gz X:1100-1400 Y:100000-100550 Z:100000-100005
Expected passes: 14
Unexpected passes: 0
Expected failures: 0
Unexpected failures: 0
cd test/mpileup && ./test-pileup.sh mpileup.tst
Testing (m)pileup...
PASS : $pileup mp_D.sam
PASS : $pileup -m mp_D.sam
PASS : $pileup mp_DI.sam
PASS : $pileup -m mp_DI.sam
PASS : $pileup mp_I.sam
PASS : $pileup -m mp_I.sam
PASS : $pileup mp_P.sam
PASS : $pileup -m mp_P.sam
PASS : $pileup mp_ID.sam
PASS : $pileup -m mp_ID.sam
PASS : $pileup mp_N.sam
PASS : $pileup -m mp_N.sam
PASS : $pileup mp_N2.sam
PASS : $pileup -m mp_N2.sam
PASS : $pileup c1#pad1.sam
PASS : $pileup -m c1#pad1.sam
PASS : $pileup c1#pad2.sam
PASS : $pileup -m c1#pad2.sam
PASS : $pileup c1#pad3.sam
PASS : $pileup -m c1#pad3.sam
PASS : $pileup -m small.bam
Expected passes: 21
Unexpected passes: 0
Expected failures: 0
Unexpected failures: 0
cd test/fastq && ./test-fastq.sh
Testing fastq support
PASS : $tview minimal.fq
PASS : $tview minimal.fa
PASS : $tview multiline.fq
PASS : $tview multiline.fa
PASS : $tview single.fq
PASS : $tview single.fa
PASS : $tview -i fastq_aux single.fq
PASS : $tview -i fastq_aux single.fa
PASS : $tview interleaved.fq
PASS : $tview interleaved.fa
PASS : $tview -i fastq_aux interleaved.fq
PASS : $tview -i fastq_aux interleaved.fa
PASS : $tview -i fastq_casava interleaved_casava.fq
PASS : $tview -i fastq_barcode=OX -i fastq_casava interleaved_casava.fq
PASS : $tview -i fastq_casava interleaved_casava.fa
PASS : $tview -i fastq_barcode=OX -i fastq_casava interleaved_casava.fa
PASS : $tview -i fastq_casava filter_casava.fq
PASS : $tview -i fastq_casava filter_casava.fa
PASS : $tview -i fastq_aux r1.fq
PASS : $tview -i fastq_aux r2.fq
PASS : $tview -i fastq_aux r1.fa
PASS : $tview -i fastq_aux r2.fa
PASS : $tview -i fastq_name2 name2.fq
PASS : $tview -i fastq_name2 name2.fa
PASS : $tview -f minimal.sam
PASS : $tview -F minimal.sam
PASS : $tview -f -o fastq_aux single_aux.sam
PASS : $tview -F -o fastq_aux single_aux.sam
PASS : $tview -f -o fastq_aux -o fastq_rnum inter_aux.sam
PASS : $tview -F -o fastq_aux -o fastq_rnum inter_aux.sam
PASS : $tview -f -o fastq_casava inter_casava.sam
PASS : $tview -f -o fastq_barcode=OX -o fastq_casava inter_casavaOX.sam
PASS : $tview -F -o fastq_casava inter_casava.sam
PASS : $tview -F -o fastq_barcode=OX -o fastq_casava inter_casavaOX.sam
PASS : $tview -f -o fastq_casava filter_casava.sam
PASS : $tview -F -o fastq_casava filter_casava.sam
PASS : $tview -f -o fastq_aux -o fastq_rnum r1.sam
PASS : $tview -f -o fastq_aux -o fastq_rnum r2.sam
PASS : $tview -F -o fastq_aux -o fastq_rnum r1.sam
PASS : $tview -F -o fastq_aux -o fastq_rnum r2.sam
Expected passes: 40
Unexpected passes: 0
Expected failures: 0
Unexpected failures: 0
cd test/base_mods && ./base-mods.sh base-mods.tst
Testing base-modifications...
PASS : $test_mod MM-chebi.sam
PASS : $test_mod MM-double.sam
PASS : $test_mod MM-multi.sam
PASS : $pileup_mod < MM-pileup.sam
PASS : $pileup_mod < MM-pileup2.sam
Expected passes: 5
Unexpected passes: 0
Expected failures: 0
Unexpected failures: 0
REF_PATH=: test/sam test/ce.fa test/faidx.fa test/fastqs.fq
(Expect trailing 'x' message for " -1,001x")
[W::hts_parse_decimal] Ignoring unknown characters after -1,001[x]
(Expect trailing 'k' message for "1.5e+3k")
[W::hts_parse_decimal] Ignoring unknown characters after 1.5e+3[k]
(Expect dropped fraction message for "12.3456k")
[W::hts_parse_decimal] Discarding fractional part of 12.3456k
[W::hts_parse_decimal] Discarding fractional part of 12.3456k
(Expect invalid numeric message for "A")
[W::hts_parse_decimal] Invalid numeric value A[truncated]
(Expect invalid numeric message for "G")
[W::hts_parse_decimal] Invalid numeric value G[truncated]
(Expect invalid numeric message for " +/-")
[W::hts_parse_decimal] Invalid numeric value +/-[truncated]
(Expect invalid numeric message for " -.e+9999")
[W::hts_parse_decimal] Invalid numeric value -.e+9999[truncated]
test/test-regidx
cd test && REF_PATH=: ./test.pl ${TEST_OPTS:-}
"my" variable @p masks earlier declaration in same scope at ./test.pl line 617.
bgzip round-trip no threads: .. ok
bgzip -b no threads: .. ok
bgzip -b -I no threads: .. ok
bgzip round-trip 4 threads: .. ok
bgzip -b 4 threads: .. ok
bgzip -b -I 4 threads: .. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view -l 0 -b -m 14 -x /tmp/OP8kXQo1Nb/index.bam.csi /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/index.sam > /tmp/OP8kXQo1Nb/index.bam
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_index -c /tmp/OP8kXQo1Nb/index.bam
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view -l 0 -b -m 0 -x /tmp/OP8kXQo1Nb/index.bam.bai /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/index.sam > /tmp/OP8kXQo1Nb/index.bam
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_index -b /tmp/OP8kXQo1Nb/index.bam
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view -l 0 -z -m 14 -x /tmp/OP8kXQo1Nb/index.sam.gz.csi /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/index.sam > /tmp/OP8kXQo1Nb/index.sam.gz
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_index -c /tmp/OP8kXQo1Nb/index.sam.gz
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view -l 0 -z -m 0 -x /tmp/OP8kXQo1Nb/index.sam.gz.bai /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/index.sam > /tmp/OP8kXQo1Nb/index.sam.gz
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_index -b /tmp/OP8kXQo1Nb/index.sam.gz
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view -l 0 -z -m 14 -x /tmp/OP8kXQo1Nb/index.sam.gz.csi /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/index_dos.sam > /tmp/OP8kXQo1Nb/index.sam.gz
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_index -c /tmp/OP8kXQo1Nb/index.sam.gz
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view -l 0 -z -m 0 -x /tmp/OP8kXQo1Nb/index.sam.gz.bai /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/index_dos.sam > /tmp/OP8kXQo1Nb/index.sam.gz
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_index -b /tmp/OP8kXQo1Nb/index.sam.gz
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view -l 0 -C -x /tmp/OP8kXQo1Nb/index.cram.crai /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/index.sam > /tmp/OP8kXQo1Nb/index.cram
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_index /tmp/OP8kXQo1Nb/index.cram
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view -l 0 -b -m 14 -x /tmp/OP8kXQo1Nb/index.bcf.csi /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/index.vcf > /tmp/OP8kXQo1Nb/index.bcf
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_index -c /tmp/OP8kXQo1Nb/index.bcf
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view -l 0 -z -m 14 -x /tmp/OP8kXQo1Nb/index.vcf.gz.csi /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/index.vcf > /tmp/OP8kXQo1Nb/index.vcf.gz
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_index -c /tmp/OP8kXQo1Nb/index.vcf.gz
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view -l 0 -z -m 0 -x /tmp/OP8kXQo1Nb/index.vcf.gz.tbi /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/index.vcf > /tmp/OP8kXQo1Nb/index.vcf.gz
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_index -t /tmp/OP8kXQo1Nb/index.vcf.gz
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/tabix /tmp/OP8kXQo1Nb/index.vcf.gz##idx##/tmp/OP8kXQo1Nb/index.vcf.gz.tbi 1:10000060-10000060
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view /tmp/OP8kXQo1Nb/index2.bam 1:1000000-1000000
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view /tmp/OP8kXQo1Nb/index2.bam 1:2000000-2000000
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view /tmp/OP8kXQo1Nb/index2.bam 2:1000000-1000000
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view /tmp/OP8kXQo1Nb/index2.bam 2:2000000-2000000
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view -@4 -l 0 -b -m 14 -x /tmp/OP8kXQo1Nb/index.bam.csi /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/index.sam > /tmp/OP8kXQo1Nb/index.bam
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_index -c /tmp/OP8kXQo1Nb/index.bam
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view -@4 -l 0 -b -m 0 -x /tmp/OP8kXQo1Nb/index.bam.bai /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/index.sam > /tmp/OP8kXQo1Nb/index.bam
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_index -b /tmp/OP8kXQo1Nb/index.bam
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view -@4 -l 0 -z -m 14 -x /tmp/OP8kXQo1Nb/index.sam.gz.csi /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/index.sam > /tmp/OP8kXQo1Nb/index.sam.gz
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_index -c /tmp/OP8kXQo1Nb/index.sam.gz
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view -@4 -l 0 -z -m 0 -x /tmp/OP8kXQo1Nb/index.sam.gz.bai /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/index.sam > /tmp/OP8kXQo1Nb/index.sam.gz
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_index -b /tmp/OP8kXQo1Nb/index.sam.gz
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view -@4 -l 0 -z -m 14 -x /tmp/OP8kXQo1Nb/index.sam.gz.csi /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/index_dos.sam > /tmp/OP8kXQo1Nb/index.sam.gz
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_index -c /tmp/OP8kXQo1Nb/index.sam.gz
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view -@4 -l 0 -z -m 0 -x /tmp/OP8kXQo1Nb/index.sam.gz.bai /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/index_dos.sam > /tmp/OP8kXQo1Nb/index.sam.gz
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_index -b /tmp/OP8kXQo1Nb/index.sam.gz
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view -@4 -l 0 -C -x /tmp/OP8kXQo1Nb/index.cram.crai /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/index.sam > /tmp/OP8kXQo1Nb/index.cram
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_index /tmp/OP8kXQo1Nb/index.cram
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view -@4 -l 0 -b -m 14 -x /tmp/OP8kXQo1Nb/index.bcf.csi /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/index.vcf > /tmp/OP8kXQo1Nb/index.bcf
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_index -c /tmp/OP8kXQo1Nb/index.bcf
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view -@4 -l 0 -z -m 14 -x /tmp/OP8kXQo1Nb/index.vcf.gz.csi /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/index.vcf > /tmp/OP8kXQo1Nb/index.vcf.gz
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_index -c /tmp/OP8kXQo1Nb/index.vcf.gz
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view -@4 -l 0 -z -m 0 -x /tmp/OP8kXQo1Nb/index.vcf.gz.tbi /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/index.vcf > /tmp/OP8kXQo1Nb/index.vcf.gz
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_index -t /tmp/OP8kXQo1Nb/index.vcf.gz
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/tabix /tmp/OP8kXQo1Nb/index.vcf.gz##idx##/tmp/OP8kXQo1Nb/index.vcf.gz.tbi 1:10000060-10000060
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view /tmp/OP8kXQo1Nb/index2.bam 1:1000000-1000000
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view /tmp/OP8kXQo1Nb/index2.bam 1:2000000-2000000
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view /tmp/OP8kXQo1Nb/index2.bam 2:1000000-1000000
.. ok
test_index:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view /tmp/OP8kXQo1Nb/index2.bam 2:2000000-2000000
.. ok
test_view testing multi-ref CRAM modes:
./test_view -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=-1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram
./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_
./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_
./test_view -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=0 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram
./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_
./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_
./test_view -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram
./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_
./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_
.. ok
test_view testing multi-ref CRAM modes:
./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=-1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram
./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_
./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_
./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=0 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram
./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_
./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_
./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram
./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_
./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_
.. ok
test_view testing auxf#values.sam, ref auxf.fa:
./test_view -S -l0 -b auxf#values.sam > auxf#values.tmp.bam
./test_view auxf#values.tmp.bam > auxf#values.tmp.bam.sam_
./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_
./test_view -t auxf.fa -S -C -o VERSION=2.1 auxf#values.sam > auxf#values.tmp.cram
./test_view -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_
./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_
./test_view -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram
./test_view auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_
./test_view -i reference=auxf.fa auxf#values_java.cram > auxf#values_java.tmp.sam_
./compare_sam.pl -Baux -nomd auxf#values.sam auxf#values_java.tmp.sam_
.. ok
test_view testing c1#bounds.sam, ref c1.fa:
./test_view -S -l0 -b c1#bounds.sam > c1#bounds.tmp.bam
./test_view c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_
./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_
./test_view -t c1.fa -S -C -o VERSION=2.1 c1#bounds.sam > c1#bounds.tmp.cram
./test_view -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_
./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_
./test_view -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram
./test_view c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_
.. ok
test_view testing c1#clip.sam, ref c1.fa:
./test_view -S -l0 -b c1#clip.sam > c1#clip.tmp.bam
./test_view c1#clip.tmp.bam > c1#clip.tmp.bam.sam_
./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_
./test_view -t c1.fa -S -C -o VERSION=2.1 c1#clip.sam > c1#clip.tmp.cram
./test_view -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_
./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_
./test_view -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.bam > c1#clip.tmp.bam.cram
./test_view c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_
.. ok
test_view testing c1#noseq.sam, ref c1.fa:
./test_view -S -l0 -b c1#noseq.sam > c1#noseq.tmp.bam
./test_view c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_
./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_
./test_view -t c1.fa -S -C -o VERSION=2.1 c1#noseq.sam > c1#noseq.tmp.cram
./test_view -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_
./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_
./test_view -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram
./test_view c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_
.. ok
test_view testing c1#pad1.sam, ref c1.fa:
./test_view -S -l0 -b c1#pad1.sam > c1#pad1.tmp.bam
./test_view c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_
./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_
./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad1.sam > c1#pad1.tmp.cram
./test_view -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_
./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_
./test_view -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram
./test_view c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_
.. ok
test_view testing c1#pad2.sam, ref c1.fa:
./test_view -S -l0 -b c1#pad2.sam > c1#pad2.tmp.bam
./test_view c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_
./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_
./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad2.sam > c1#pad2.tmp.cram
./test_view -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_
./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_
./test_view -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram
./test_view c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_
.. ok
test_view testing c1#pad3.sam, ref c1.fa:
./test_view -S -l0 -b c1#pad3.sam > c1#pad3.tmp.bam
./test_view c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_
./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_
./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad3.sam > c1#pad3.tmp.cram
./test_view -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_
./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_
./test_view -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram
./test_view c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_
.. ok
test_view testing c1#unknown.sam, ref c1.fa:
./test_view -S -l0 -b c1#unknown.sam > c1#unknown.tmp.bam
./test_view c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_
./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_
./test_view -t c1.fa -S -C -o VERSION=2.1 c1#unknown.sam > c1#unknown.tmp.cram
./test_view -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_
./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_
./test_view -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram
./test_view c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_
.. ok
test_view testing c2#pad.sam, ref c2.fa:
./test_view -S -l0 -b c2#pad.sam > c2#pad.tmp.bam
./test_view c2#pad.tmp.bam > c2#pad.tmp.bam.sam_
./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_
./test_view -t c2.fa -S -C -o VERSION=2.1 c2#pad.sam > c2#pad.tmp.cram
./test_view -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_
./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_
./test_view -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.bam > c2#pad.tmp.bam.cram
./test_view c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_
.. ok
test_view testing ce#1.sam, ref ce.fa:
./test_view -S -l0 -b ce#1.sam > ce#1.tmp.bam
./test_view ce#1.tmp.bam > ce#1.tmp.bam.sam_
./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_
./test_view -t ce.fa -S -C -o VERSION=2.1 ce#1.sam > ce#1.tmp.cram
./test_view -D ce#1.tmp.cram > ce#1.tmp.cram.sam_
./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_
./test_view -t ce.fa -C -o VERSION=3.0 ce#1.tmp.bam > ce#1.tmp.bam.cram
./test_view ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_
.. ok
test_view testing ce#1000.sam, ref ce.fa:
./test_view -S -b ce#1000.sam > ce#1000.tmp.bam
./test_view ce#1000.tmp.bam > ce#1000.tmp.bam.sam_
./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_
./test_view -S -l0 -b ce#1000.sam > ce#1000.tmp.bam
./test_view ce#1000.tmp.bam > ce#1000.tmp.bam.sam_
./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_
./test_view -t ce.fa -S -C -o VERSION=2.1 ce#1000.sam > ce#1000.tmp.cram
./test_view -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_
./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_
./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1000.sam > ce#1000.tmp.cram
./test_view -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_
./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_
./test_view -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.bam > ce#1000.tmp.bam.cram
./test_view ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_
.. ok
test_view testing ce#2.sam, ref ce.fa:
./test_view -S -l0 -b ce#2.sam > ce#2.tmp.bam
./test_view ce#2.tmp.bam > ce#2.tmp.bam.sam_
./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_
./test_view -t ce.fa -S -C -o VERSION=2.1 ce#2.sam > ce#2.tmp.cram
./test_view -D ce#2.tmp.cram > ce#2.tmp.cram.sam_
./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_
./test_view -t ce.fa -C -o VERSION=3.0 ce#2.tmp.bam > ce#2.tmp.bam.cram
./test_view ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_
.. ok
test_view testing ce#5.sam, ref ce.fa:
./test_view -S -l0 -b ce#5.sam > ce#5.tmp.bam
./test_view ce#5.tmp.bam > ce#5.tmp.bam.sam_
./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_
./test_view -t ce.fa -S -C -o VERSION=2.1 ce#5.sam > ce#5.tmp.cram
./test_view -D ce#5.tmp.cram > ce#5.tmp.cram.sam_
./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_
./test_view -t ce.fa -C -o VERSION=3.0 ce#5.tmp.bam > ce#5.tmp.bam.cram
./test_view ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_
.. ok
test_view testing ce#5b.sam, ref ce.fa:
./test_view -S -l0 -b ce#5b.sam > ce#5b.tmp.bam
./test_view ce#5b.tmp.bam > ce#5b.tmp.bam.sam_
./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_
./test_view -t ce.fa -S -C -o VERSION=2.1 ce#5b.sam > ce#5b.tmp.cram
./test_view -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_
./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_
./test_view -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.bam > ce#5b.tmp.bam.cram
./test_view ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_
./test_view -i reference=ce.fa ce#5b_java.cram > ce#5b_java.tmp.sam_
./compare_sam.pl -Baux -nomd ce#5b.sam ce#5b_java.tmp.sam_
.. ok
test_view testing ce#large_seq.sam, ref ce.fa:
./test_view -S -l0 -b ce#large_seq.sam > ce#large_seq.tmp.bam
./test_view ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_
./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_
./test_view -t ce.fa -S -C -o VERSION=2.1 ce#large_seq.sam > ce#large_seq.tmp.cram
./test_view -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_
./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_
./test_view -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram
./test_view ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_
.. ok
test_view testing ce#supp.sam, ref ce.fa:
./test_view -S -l0 -b ce#supp.sam > ce#supp.tmp.bam
./test_view ce#supp.tmp.bam > ce#supp.tmp.bam.sam_
./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_
./test_view -t ce.fa -S -C -o VERSION=2.1 ce#supp.sam > ce#supp.tmp.cram
./test_view -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_
./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_
./test_view -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.bam > ce#supp.tmp.bam.cram
./test_view ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_
.. ok
test_view testing ce#tag_depadded.sam, ref ce.fa:
./test_view -S -l0 -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam
./test_view ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_
./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_
./test_view -t ce.fa -S -C -o VERSION=2.1 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram
./test_view -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_
./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_
./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram
./test_view ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_
.. ok
test_view testing ce#tag_padded.sam, ref ce.fa:
./test_view -S -l0 -b ce#tag_padded.sam > ce#tag_padded.tmp.bam
./test_view ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_
./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_
./test_view -t ce.fa -S -C -o VERSION=2.1 ce#tag_padded.sam > ce#tag_padded.tmp.cram
./test_view -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_
./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_
./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram
./test_view ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_
.. ok
test_view testing ce#unmap.sam, ref ce.fa:
./test_view -S -l0 -b ce#unmap.sam > ce#unmap.tmp.bam
./test_view ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_
./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_
./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap.sam > ce#unmap.tmp.cram
./test_view -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_
./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_
./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram
./test_view ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_
.. ok
test_view testing ce#unmap1.sam, ref ce.fa:
./test_view -S -l0 -b ce#unmap1.sam > ce#unmap1.tmp.bam
./test_view ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_
./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_
./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap1.sam > ce#unmap1.tmp.cram
./test_view -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_
./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_
./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram
./test_view ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_
.. ok
test_view testing ce#unmap2.sam, ref ce.fa:
./test_view -S -l0 -b ce#unmap2.sam > ce#unmap2.tmp.bam
./test_view ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_
./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_
./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap2.sam > ce#unmap2.tmp.cram
./test_view -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_
./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_
./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram
./test_view ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_
.. ok
test_view testing md#1.sam, ref md.fa:
./test_view -S -l0 -b md#1.sam > md#1.tmp.bam
./test_view md#1.tmp.bam > md#1.tmp.bam.sam_
./compare_sam.pl md#1.sam md#1.tmp.bam.sam_
./test_view -t md.fa -S -C -o VERSION=2.1 md#1.sam > md#1.tmp.cram
./test_view -D md#1.tmp.cram > md#1.tmp.cram.sam_
./compare_sam.pl md#1.sam md#1.tmp.cram.sam_
./test_view -t md.fa -C -o VERSION=3.0 md#1.tmp.bam > md#1.tmp.bam.cram
./test_view md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam.sam_
./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_
.. ok
test_view testing xx#blank.sam, ref xx.fa:
./test_view -S -l0 -b xx#blank.sam > xx#blank.tmp.bam
./test_view xx#blank.tmp.bam > xx#blank.tmp.bam.sam_
./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_
./test_view -t xx.fa -S -C -o VERSION=2.1 xx#blank.sam > xx#blank.tmp.cram
./test_view -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_
./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_
./test_view -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.bam > xx#blank.tmp.bam.cram
./test_view xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_
.. ok
test_view testing xx#large_aux.sam, ref xx.fa:
./test_view -S -l0 -b xx#large_aux.sam > xx#large_aux.tmp.bam
./test_view xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_
./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_
./test_view -t xx.fa -S -C -o VERSION=2.1 xx#large_aux.sam > xx#large_aux.tmp.cram
./test_view -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_
./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_
./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram
./test_view xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_
./test_view -i reference=xx.fa xx#large_aux_java.cram > xx#large_aux_java.tmp.sam_
[W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 30 vs 20
./compare_sam.pl -Baux -nomd xx#large_aux.sam xx#large_aux_java.tmp.sam_
.. ok
test_view testing xx#large_aux2.sam, ref xx.fa:
./test_view -S -l0 -b xx#large_aux2.sam > xx#large_aux2.tmp.bam
./test_view xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_
./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_
./test_view -t xx.fa -S -C -o VERSION=2.1 xx#large_aux2.sam > xx#large_aux2.tmp.cram
./test_view -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_
./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_
./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram
./test_view xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_
.. ok
test_view testing xx#MD.sam, ref xx.fa:
./test_view -S -l0 -b xx#MD.sam > xx#MD.tmp.bam
./test_view xx#MD.tmp.bam > xx#MD.tmp.bam.sam_
./compare_sam.pl xx#MD.sam xx#MD.tmp.bam.sam_
./test_view -t xx.fa -S -C -o VERSION=2.1 xx#MD.sam > xx#MD.tmp.cram
./test_view -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
./test_view -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.bam > xx#MD.tmp.bam.cram
./test_view xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_
.. ok
test_view testing xx#MD2.sam, ref xx.fa:
./test_view -S -l0 -b xx#MD2.sam > xx#MD2.tmp.bam
./test_view xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_
./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_
./test_view -t xx.fa -S -C -o VERSION=2.1 xx#MD2.sam > xx#MD2.tmp.cram
./test_view -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram
./test_view xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_
.. ok
test_view testing xx#minimal.sam, ref xx.fa:
./test_view -S -l0 -b xx#minimal.sam > xx#minimal.tmp.bam
./test_view xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_
./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_
./test_view -t xx.fa -S -C -o VERSION=2.1 xx#minimal.sam > xx#minimal.tmp.cram
./test_view -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_
./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_
./test_view -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram
./test_view xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_
.. ok
test_view testing xx#pair.sam, ref xx.fa:
./test_view -S -l0 -b xx#pair.sam > xx#pair.tmp.bam
./test_view xx#pair.tmp.bam > xx#pair.tmp.bam.sam_
./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_
./test_view -t xx.fa -S -C -o VERSION=2.1 xx#pair.sam > xx#pair.tmp.cram
./test_view -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_
./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_
./test_view -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.bam > xx#pair.tmp.bam.cram
./test_view xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_
.. ok
test_view testing xx#repeated.sam, ref xx.fa:
./test_view -S -l0 -b xx#repeated.sam > xx#repeated.tmp.bam
./test_view xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_
./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_
./test_view -t xx.fa -S -C -o VERSION=2.1 xx#repeated.sam > xx#repeated.tmp.cram
./test_view -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_
./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_
./test_view -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram
./test_view xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_
.. ok
test_view testing xx#rg.sam, ref xx.fa:
./test_view -S -l0 -b xx#rg.sam > xx#rg.tmp.bam
./test_view xx#rg.tmp.bam > xx#rg.tmp.bam.sam_
./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_
./test_view -t xx.fa -S -C -o VERSION=2.1 xx#rg.sam > xx#rg.tmp.cram
./test_view -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_
./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_
./test_view -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.bam > xx#rg.tmp.bam.cram
./test_view xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_
.. ok
test_view testing xx#tlen.sam, ref xx.fa:
./test_view -S -l0 -b xx#tlen.sam > xx#tlen.tmp.bam
./test_view xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_
./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_
./test_view -t xx.fa -S -C -o VERSION=2.1 xx#tlen.sam > xx#tlen.tmp.cram
./test_view -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_
./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_
./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram
./test_view xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_
.. ok
test_view testing xx#tlen2.sam, ref xx.fa:
./test_view -S -l0 -b xx#tlen2.sam > xx#tlen2.tmp.bam
./test_view xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_
./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_
./test_view -t xx.fa -S -C -o VERSION=2.1 xx#tlen2.sam > xx#tlen2.tmp.cram
./test_view -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_
./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_
./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram
./test_view xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_
.. ok
test_view testing xx#triplet.sam, ref xx.fa:
./test_view -S -l0 -b xx#triplet.sam > xx#triplet.tmp.bam
./test_view xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_
./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_
./test_view -t xx.fa -S -C -o VERSION=2.1 xx#triplet.sam > xx#triplet.tmp.cram
./test_view -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_
./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_
./test_view -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram
./test_view xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_
.. ok
test_view testing xx#unsorted.sam, ref xx.fa:
./test_view -S -l0 -b xx#unsorted.sam > xx#unsorted.tmp.bam
./test_view xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_
./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_
./test_view -t xx.fa -S -C -o VERSION=2.1 xx#unsorted.sam > xx#unsorted.tmp.cram
./test_view -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_
./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_
./test_view -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram
./test_view xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_
.. ok
test_view testing region queries:
./test_view -i reference=ce.fa range.cram CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp
./compare_sam.pl range.tmp range.out
./test_view range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp
./compare_sam.pl range.tmp range.out
.. ok
test_view testing BAM files with absent @SQ lines:
./test_view -p no_hdr_sq_1.tmp.sam no_hdr_sq_1.bam
./compare_sam.pl no_hdr_sq_1.tmp.sam no_hdr_sq_1.expected.sam
./test_view -p no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.bam CHROMOSOME_I
./compare_sam.pl no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.expected.sam
.. ok
test_view testing large (> 2Gbases) positions:
./test_view -z -p longrefs/longref.tmp.sam.gz -x longrefs/longref.tmp.sam.gz.csi.otf -m 14 longrefs/longref.sam
./test_view -p longrefs/longref.tmp.sam_ longrefs/longref.tmp.sam.gz
./compare_sam.pl longrefs/longref.sam longrefs/longref.tmp.sam_
test_view:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_index -c longrefs/longref.tmp.sam.gz
.. ok
./test_view -p longrefs/longref_itr.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003
./compare_sam.pl longrefs/longref_itr.expected.sam longrefs/longref_itr.tmp.sam
./test_view -M -p longrefs/longref_multi.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 CHROMOSOME_I:10000000100-10000000110
./compare_sam.pl longrefs/longref_multi.expected.sam longrefs/longref_multi.tmp.sam
.. ok
test_view testing auxf#values.sam, ref auxf.fa:
./test_view -@4 -S -l0 -b auxf#values.sam > auxf#values.tmp.bam
./test_view -@4 auxf#values.tmp.bam > auxf#values.tmp.bam.sam_
./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_
./test_view -@4 -t auxf.fa -S -C -o VERSION=2.1 auxf#values.sam > auxf#values.tmp.cram
./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_
./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_
./test_view -@4 -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram
./test_view -@4 auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_
./test_view -@4 -t auxf.fa -S -l7 -C -o VERSION=3.1 -o archive auxf#values.sam > auxf#values.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_
./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_
./test_view -@4 -t auxf.fa -S -l7 -C -o VERSION=4.0 -o archive auxf#values.sam > auxf#values.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_
./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_
./test_view -@4 -i reference=auxf.fa auxf#values_java.cram > auxf#values_java.tmp.sam_
./compare_sam.pl -Baux -nomd auxf#values.sam auxf#values_java.tmp.sam_
.. ok
test_view testing c1#bounds.sam, ref c1.fa:
./test_view -@4 -S -l0 -b c1#bounds.sam > c1#bounds.tmp.bam
./test_view -@4 c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_
./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_
./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#bounds.sam > c1#bounds.tmp.cram
./test_view -@4 -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_
./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_
./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram
./test_view -@4 c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_
.. ok
test_view testing c1#clip.sam, ref c1.fa:
./test_view -@4 -S -l0 -b c1#clip.sam > c1#clip.tmp.bam
./test_view -@4 c1#clip.tmp.bam > c1#clip.tmp.bam.sam_
./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_
./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#clip.sam > c1#clip.tmp.cram
./test_view -@4 -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_
./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_
./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.bam > c1#clip.tmp.bam.cram
./test_view -@4 c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_
.. ok
test_view testing c1#noseq.sam, ref c1.fa:
./test_view -@4 -S -l0 -b c1#noseq.sam > c1#noseq.tmp.bam
./test_view -@4 c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_
./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_
./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#noseq.sam > c1#noseq.tmp.cram
./test_view -@4 -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_
./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_
./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram
./test_view -@4 c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_
.. ok
test_view testing c1#pad1.sam, ref c1.fa:
./test_view -@4 -S -l0 -b c1#pad1.sam > c1#pad1.tmp.bam
./test_view -@4 c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_
./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_
./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad1.sam > c1#pad1.tmp.cram
./test_view -@4 -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_
./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_
./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram
./test_view -@4 c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_
.. ok
test_view testing c1#pad2.sam, ref c1.fa:
./test_view -@4 -S -l0 -b c1#pad2.sam > c1#pad2.tmp.bam
./test_view -@4 c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_
./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_
./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad2.sam > c1#pad2.tmp.cram
./test_view -@4 -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_
./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_
./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram
./test_view -@4 c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_
.. ok
test_view testing c1#pad3.sam, ref c1.fa:
./test_view -@4 -S -l0 -b c1#pad3.sam > c1#pad3.tmp.bam
./test_view -@4 c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_
./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_
./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad3.sam > c1#pad3.tmp.cram
./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_
./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_
./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram
./test_view -@4 c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_
./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=3.1 -o archive c1#pad3.sam > c1#pad3.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_
./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_
./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=4.0 -o archive c1#pad3.sam > c1#pad3.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_
./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_
.. ok
test_view testing c1#unknown.sam, ref c1.fa:
./test_view -@4 -S -l0 -b c1#unknown.sam > c1#unknown.tmp.bam
./test_view -@4 c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_
./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_
./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#unknown.sam > c1#unknown.tmp.cram
./test_view -@4 -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_
./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_
./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram
./test_view -@4 c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_
.. ok
test_view testing c2#pad.sam, ref c2.fa:
./test_view -@4 -S -l0 -b c2#pad.sam > c2#pad.tmp.bam
./test_view -@4 c2#pad.tmp.bam > c2#pad.tmp.bam.sam_
./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_
./test_view -@4 -t c2.fa -S -C -o VERSION=2.1 c2#pad.sam > c2#pad.tmp.cram
./test_view -@4 -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_
./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_
./test_view -@4 -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.bam > c2#pad.tmp.bam.cram
./test_view -@4 c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_
.. ok
test_view testing ce#1.sam, ref ce.fa:
./test_view -@4 -S -l0 -b ce#1.sam > ce#1.tmp.bam
./test_view -@4 ce#1.tmp.bam > ce#1.tmp.bam.sam_
./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_
./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1.sam > ce#1.tmp.cram
./test_view -@4 -D ce#1.tmp.cram > ce#1.tmp.cram.sam_
./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1.tmp.bam > ce#1.tmp.bam.cram
./test_view -@4 ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_
.. ok
test_view testing ce#1000.sam, ref ce.fa:
./test_view -@4 -S -b ce#1000.sam > ce#1000.tmp.bam
./test_view -@4 ce#1000.tmp.bam > ce#1000.tmp.bam.sam_
./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_
./test_view -@4 -S -l0 -b ce#1000.sam > ce#1000.tmp.bam
./test_view -@4 ce#1000.tmp.bam > ce#1000.tmp.bam.sam_
./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_
./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1000.sam > ce#1000.tmp.cram
./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_
./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_
./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1000.sam > ce#1000.tmp.cram
./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_
./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.bam > ce#1000.tmp.bam.cram
./test_view -@4 ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_
./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.ms
./test_view -@4 ce#1000.tmp.bam.cram.ms > ce#1000.tmp.bam.cram.sam_
./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.sam_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#1000.sam > ce#1000.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_
./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o normal ce#1000.sam > ce#1000.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_
./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o small ce#1000.sam > ce#1000.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_
./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#1000.sam > ce#1000.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_
./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#1000.sam > ce#1000.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_
./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_
.. ok
test_view testing ce#2.sam, ref ce.fa:
./test_view -@4 -S -l0 -b ce#2.sam > ce#2.tmp.bam
./test_view -@4 ce#2.tmp.bam > ce#2.tmp.bam.sam_
./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_
./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#2.sam > ce#2.tmp.cram
./test_view -@4 -D ce#2.tmp.cram > ce#2.tmp.cram.sam_
./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#2.tmp.bam > ce#2.tmp.bam.cram
./test_view -@4 ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_
.. ok
test_view testing ce#5.sam, ref ce.fa:
./test_view -@4 -S -l0 -b ce#5.sam > ce#5.tmp.bam
./test_view -@4 ce#5.tmp.bam > ce#5.tmp.bam.sam_
./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_
./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#5.sam > ce#5.tmp.cram
./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_
./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5.tmp.bam > ce#5.tmp.bam.cram
./test_view -@4 ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_
./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.ms
./test_view -@4 ce#5.tmp.bam.cram.ms > ce#5.tmp.bam.cram.sam_
./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.sam_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#5.sam > ce#5.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_
./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#5.sam > ce#5.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_
./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_
.. ok
test_view testing ce#5b.sam, ref ce.fa:
./test_view -@4 -S -l0 -b ce#5b.sam > ce#5b.tmp.bam
./test_view -@4 ce#5b.tmp.bam > ce#5b.tmp.bam.sam_
./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_
./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#5b.sam > ce#5b.tmp.cram
./test_view -@4 -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_
./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.bam > ce#5b.tmp.bam.cram
./test_view -@4 ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_
./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.ms
./test_view -@4 ce#5b.tmp.bam.cram.ms > ce#5b.tmp.bam.cram.sam_
./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.sam_
./test_view -@4 -i reference=ce.fa ce#5b_java.cram > ce#5b_java.tmp.sam_
./compare_sam.pl -Baux -nomd ce#5b.sam ce#5b_java.tmp.sam_
.. ok
test_view testing ce#large_seq.sam, ref ce.fa:
./test_view -@4 -S -l0 -b ce#large_seq.sam > ce#large_seq.tmp.bam
./test_view -@4 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_
./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_
./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#large_seq.sam > ce#large_seq.tmp.cram
./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_
./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram
./test_view -@4 ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#large_seq.sam > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_
./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o fast ce#large_seq.sam > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_
./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o normal ce#large_seq.sam > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_
./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o small ce#large_seq.sam > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_
./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#large_seq.sam > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_
./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_
.. ok
test_view testing ce#supp.sam, ref ce.fa:
./test_view -@4 -S -l0 -b ce#supp.sam > ce#supp.tmp.bam
./test_view -@4 ce#supp.tmp.bam > ce#supp.tmp.bam.sam_
./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_
./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#supp.sam > ce#supp.tmp.cram
./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_
./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.bam > ce#supp.tmp.bam.cram
./test_view -@4 ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#supp.sam > ce#supp.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_
./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#supp.sam > ce#supp.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_
./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_
.. ok
test_view testing ce#tag_depadded.sam, ref ce.fa:
./test_view -@4 -S -l0 -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam
./test_view -@4 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_
./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_
./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram
./test_view -@4 -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_
./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram
./test_view -@4 ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_
.. ok
test_view testing ce#tag_padded.sam, ref ce.fa:
./test_view -@4 -S -l0 -b ce#tag_padded.sam > ce#tag_padded.tmp.bam
./test_view -@4 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_
./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_
./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#tag_padded.sam > ce#tag_padded.tmp.cram
./test_view -@4 -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_
./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram
./test_view -@4 ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_
.. ok
test_view testing ce#unmap.sam, ref ce.fa:
./test_view -@4 -S -l0 -b ce#unmap.sam > ce#unmap.tmp.bam
./test_view -@4 ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_
./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_
./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap.sam > ce#unmap.tmp.cram
./test_view -@4 -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_
./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram
./test_view -@4 ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_
./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.ms
./test_view -@4 ce#unmap.tmp.bam.cram.ms > ce#unmap.tmp.bam.cram.sam_
./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.sam_
.. ok
test_view testing ce#unmap1.sam, ref ce.fa:
./test_view -@4 -S -l0 -b ce#unmap1.sam > ce#unmap1.tmp.bam
./test_view -@4 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_
./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_
./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap1.sam > ce#unmap1.tmp.cram
./test_view -@4 -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_
./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram
./test_view -@4 ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_
./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.ms
./test_view -@4 ce#unmap1.tmp.bam.cram.ms > ce#unmap1.tmp.bam.cram.sam_
./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.sam_
.. ok
test_view testing ce#unmap2.sam, ref ce.fa:
./test_view -@4 -S -l0 -b ce#unmap2.sam > ce#unmap2.tmp.bam
./test_view -@4 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_
./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_
./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap2.sam > ce#unmap2.tmp.cram
./test_view -@4 -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_
./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram
./test_view -@4 ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_
./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.ms
./test_view -@4 ce#unmap2.tmp.bam.cram.ms > ce#unmap2.tmp.bam.cram.sam_
./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.sam_
.. ok
test_view testing md#1.sam, ref md.fa:
./test_view -@4 -S -l0 -b md#1.sam > md#1.tmp.bam
./test_view -@4 md#1.tmp.bam > md#1.tmp.bam.sam_
./compare_sam.pl md#1.sam md#1.tmp.bam.sam_
./test_view -@4 -t md.fa -S -C -o VERSION=2.1 md#1.sam > md#1.tmp.cram
./test_view -@4 -D md#1.tmp.cram > md#1.tmp.cram.sam_
./compare_sam.pl md#1.sam md#1.tmp.cram.sam_
./test_view -@4 -t md.fa -C -o VERSION=3.0 md#1.tmp.bam > md#1.tmp.bam.cram
./test_view -@4 md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam.sam_
./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_
.. ok
test_view testing xx#blank.sam, ref xx.fa:
./test_view -@4 -S -l0 -b xx#blank.sam > xx#blank.tmp.bam
./test_view -@4 xx#blank.tmp.bam > xx#blank.tmp.bam.sam_
./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_
./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#blank.sam > xx#blank.tmp.cram
./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_
./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.bam > xx#blank.tmp.bam.cram
./test_view -@4 xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.ms
./test_view -@4 xx#blank.tmp.bam.cram.ms > xx#blank.tmp.bam.cram.sam_
./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#blank.sam > xx#blank.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_
./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#blank.sam > xx#blank.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_
./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_
.. ok
test_view testing xx#large_aux.sam, ref xx.fa:
./test_view -@4 -S -l0 -b xx#large_aux.sam > xx#large_aux.tmp.bam
./test_view -@4 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_
./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_
./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#large_aux.sam > xx#large_aux.tmp.cram
./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_
./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram
./test_view -@4 xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#large_aux.sam > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_
./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o fast xx#large_aux.sam > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_
./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o normal xx#large_aux.sam > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_
./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o small xx#large_aux.sam > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_
./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#large_aux.sam > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_
./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_
./test_view -@4 -i reference=xx.fa xx#large_aux_java.cram > xx#large_aux_java.tmp.sam_
[W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 30 vs 20
./compare_sam.pl -Baux -nomd xx#large_aux.sam xx#large_aux_java.tmp.sam_
.. ok
test_view testing xx#large_aux2.sam, ref xx.fa:
./test_view -@4 -S -l0 -b xx#large_aux2.sam > xx#large_aux2.tmp.bam
./test_view -@4 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_
./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_
./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#large_aux2.sam > xx#large_aux2.tmp.cram
./test_view -@4 -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_
./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram
./test_view -@4 xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_
.. ok
test_view testing xx#MD.sam, ref xx.fa:
./test_view -@4 -S -l0 -b xx#MD.sam > xx#MD.tmp.bam
./test_view -@4 xx#MD.tmp.bam > xx#MD.tmp.bam.sam_
./compare_sam.pl xx#MD.sam xx#MD.tmp.bam.sam_
./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#MD.sam > xx#MD.tmp.cram
./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.bam > xx#MD.tmp.bam.cram
./test_view -@4 xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#MD.sam > xx#MD.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#MD.sam > xx#MD.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
.. ok
test_view testing xx#MD2.sam, ref xx.fa:
./test_view -@4 -S -l0 -b xx#MD2.sam > xx#MD2.tmp.bam
./test_view -@4 xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_
./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_
./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#MD2.sam > xx#MD2.tmp.cram
./test_view -@4 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram
./test_view -@4 xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_
.. ok
test_view testing xx#minimal.sam, ref xx.fa:
./test_view -@4 -S -l0 -b xx#minimal.sam > xx#minimal.tmp.bam
./test_view -@4 xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_
./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_
./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#minimal.sam > xx#minimal.tmp.cram
./test_view -@4 -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_
./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram
./test_view -@4 xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.ms
./test_view -@4 xx#minimal.tmp.bam.cram.ms > xx#minimal.tmp.bam.cram.sam_
./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.sam_
.. ok
test_view testing xx#pair.sam, ref xx.fa:
./test_view -@4 -S -l0 -b xx#pair.sam > xx#pair.tmp.bam
./test_view -@4 xx#pair.tmp.bam > xx#pair.tmp.bam.sam_
./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_
./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#pair.sam > xx#pair.tmp.cram
./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_
./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.bam > xx#pair.tmp.bam.cram
./test_view -@4 xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#pair.sam > xx#pair.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_
./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#pair.sam > xx#pair.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_
./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_
.. ok
test_view testing xx#repeated.sam, ref xx.fa:
./test_view -@4 -S -l0 -b xx#repeated.sam > xx#repeated.tmp.bam
./test_view -@4 xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_
./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_
./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#repeated.sam > xx#repeated.tmp.cram
./test_view -@4 -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_
./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram
./test_view -@4 xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_
.. ok
test_view testing xx#rg.sam, ref xx.fa:
./test_view -@4 -S -l0 -b xx#rg.sam > xx#rg.tmp.bam
./test_view -@4 xx#rg.tmp.bam > xx#rg.tmp.bam.sam_
./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_
./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#rg.sam > xx#rg.tmp.cram
./test_view -@4 -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_
./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.bam > xx#rg.tmp.bam.cram
./test_view -@4 xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_
.. ok
test_view testing xx#tlen.sam, ref xx.fa:
./test_view -@4 -S -l0 -b xx#tlen.sam > xx#tlen.tmp.bam
./test_view -@4 xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_
./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_
./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#tlen.sam > xx#tlen.tmp.cram
./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_
./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram
./test_view -@4 xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.ms
./test_view -@4 xx#tlen.tmp.bam.cram.ms > xx#tlen.tmp.bam.cram.sam_
./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#tlen.sam > xx#tlen.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_
./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#tlen.sam > xx#tlen.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_
./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_
.. ok
test_view testing xx#tlen2.sam, ref xx.fa:
./test_view -@4 -S -l0 -b xx#tlen2.sam > xx#tlen2.tmp.bam
./test_view -@4 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_
./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_
./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#tlen2.sam > xx#tlen2.tmp.cram
./test_view -@4 -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_
./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram
./test_view -@4 xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.ms
./test_view -@4 xx#tlen2.tmp.bam.cram.ms > xx#tlen2.tmp.bam.cram.sam_
./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.sam_
.. ok
test_view testing xx#triplet.sam, ref xx.fa:
./test_view -@4 -S -l0 -b xx#triplet.sam > xx#triplet.tmp.bam
./test_view -@4 xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_
./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_
./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#triplet.sam > xx#triplet.tmp.cram
./test_view -@4 -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_
./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram
./test_view -@4 xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.ms
./test_view -@4 xx#triplet.tmp.bam.cram.ms > xx#triplet.tmp.bam.cram.sam_
./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.sam_
.. ok
test_view testing xx#unsorted.sam, ref xx.fa:
./test_view -@4 -S -l0 -b xx#unsorted.sam > xx#unsorted.tmp.bam
./test_view -@4 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_
./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_
./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#unsorted.sam > xx#unsorted.tmp.cram
./test_view -@4 -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_
./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram
./test_view -@4 xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_
.. ok
test_view testing region queries:
./test_view -@4 -i reference=ce.fa range.cram CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp
./compare_sam.pl range.tmp range.out
./test_view -@4 range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp
./compare_sam.pl range.tmp range.out
.. ok
test_view testing BAM files with absent @SQ lines:
./test_view -@4 -p no_hdr_sq_1.tmp.sam no_hdr_sq_1.bam
./compare_sam.pl no_hdr_sq_1.tmp.sam no_hdr_sq_1.expected.sam
./test_view -@4 -p no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.bam CHROMOSOME_I
./compare_sam.pl no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.expected.sam
.. ok
test_view testing large (> 2Gbases) positions:
./test_view -@4 -z -p longrefs/longref.tmp.sam.gz -x longrefs/longref.tmp.sam.gz.csi.otf -m 14 longrefs/longref.sam
./test_view -@4 -p longrefs/longref.tmp.sam_ longrefs/longref.tmp.sam.gz
./compare_sam.pl longrefs/longref.sam longrefs/longref.tmp.sam_
test_view:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_index -c longrefs/longref.tmp.sam.gz
.. ok
./test_view -@4 -p longrefs/longref_itr.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003
./compare_sam.pl longrefs/longref_itr.expected.sam longrefs/longref_itr.tmp.sam
./test_view -@4 -M -p longrefs/longref_multi.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 CHROMOSOME_I:10000000100-10000000110
./compare_sam.pl longrefs/longref_multi.expected.sam longrefs/longref_multi.tmp.sam
.. ok
test_MD testing xx#MD.sam, ref xx.fa:
./test_view -o store_nm=1 -o store_md=1 -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram
./test_view -i decode_md=0 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl xx#MD.sam xx#MD.tmp.cram.sam_
./test_view -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram
./test_view -i decode_md=0 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -partialmd=2 xx#MD.sam xx#MD.tmp.cram.sam_
Checking for MD/NM in xx#MD.sam
./test_view -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram
./test_view -i decode_md=1 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -partialmd=1 xx#MD.sam xx#MD.tmp.cram.sam_
.. ok
test_MD testing xx#MD2.sam, ref xx.fa:
./test_view -o store_nm=1 -o store_md=1 -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram
./test_view -i decode_md=0 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram
./test_view -i decode_md=0 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -partialmd=2 xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram
./test_view -i decode_md=1 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -partialmd=1 xx#MD2.sam xx#MD2.tmp.cram.sam_
.. ok
test_vcf_api:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test-vcf-api /tmp/OP8kXQo1Nb/test-vcf-api.bcf
[W::bcf_record_check] Bad BCF record at 1:1: No REF allele
[E::bcf_index_build3] TBI indices for BCF files are not supported
[E::idx_find_and_load] Could not retrieve index file for '/tmp/OP8kXQo1Nb/test-vcf-api.bcf'
.. ok
test_bcf2vcf:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/tabix/vcf_file.bcf
.. ok
test_vcf_sweep:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test-vcf-sweep /tmp/OP8kXQo1Nb/test-vcf-api.bcf
.. ok
test_vcf_various:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/htsfile -ch /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test-vcf-hdr-in.vcf
.. ok
test_vcf_various:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/htsfile -c /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/formatcols.vcf
.. ok
test_vcf_various:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/htsfile -c /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/noroundtrip.vcf
.. ok
test_vcf_various:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/htsfile -c /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/formatmissing.vcf
.. ok
test_vcf_various:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/htsfile -c /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/vcf_meta_meta.vcf
.. ok
test-bcf-sr:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/OP8kXQo1Nb -s 121062482
.. ok
test-bcf-sr:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/OP8kXQo1Nb -s 877225996
.. ok
test-bcf-sr:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/OP8kXQo1Nb -s 465357825
.. ok
test-bcf-sr:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/OP8kXQo1Nb -s 1686484059
.. ok
test-bcf-sr:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/OP8kXQo1Nb -s 1449241910
.. ok
test-bcf-sr:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/OP8kXQo1Nb -s 148435922
.. ok
test-bcf-sr:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/OP8kXQo1Nb -s 1186569007
.. ok
test-bcf-sr:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/OP8kXQo1Nb -s 451107903
.. ok
test-bcf-sr:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/OP8kXQo1Nb -s 1424659383
.. ok
test-bcf-sr:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/OP8kXQo1Nb -s 1200825566
.. ok
test_command:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test-bcf-translate -
.. ok
test_convert_padded_header:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view -t ce.fa -C /tmp/OP8kXQo1Nb/headernul0.bam
.. ok
test_convert_padded_header:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view -t ce.fa -C /tmp/OP8kXQo1Nb/headernul1.bam
.. ok
test_convert_padded_header:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view -t ce.fa -C /tmp/OP8kXQo1Nb/headernul678.bam
.. ok
test_rebgzip: Alternate zlib/deflate library detected
test_rebgzip:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/bgzip -I /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/bgziptest.txt.tmp.gz.gzi -c -g /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/bgziptest.txt
.. ok
test-logging:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test-logging.pl
.. ok
test_plugin_loading:
HTS_PATH=/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1 /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/with-shlib.sh /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/htsfile https://localhost:99999/invalid_port
.. ok
test_realn:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_realn -f /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/realn01.fa -i /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/realn01.sam -o -
.. ok
test_realn:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_realn -f /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/realn02.fa -i /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/realn02.sam -o -
.. ok
test_realn:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_realn -a -f /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/realn01.fa -i /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/realn01.sam -o -
.. ok
test_realn:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_realn -a -f /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/realn02.fa -i /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/realn02.sam -o -
.. ok
test_realn:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_realn -e -f /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/realn01.fa -i /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/realn01.sam -o -
.. ok
test_realn:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_realn -e -f /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/realn02.fa -i /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/realn02.sam -o -
.. ok
test_realn:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_realn -r -f /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/realn02.fa -i /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/realn02-r.sam -o -
.. ok
test_realn:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_realn -a -f /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/realn02.fa -i /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/realn02_exp.sam -o -
.. ok
test_realn:
/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_realn -f /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/realn02.fa -i /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/realn02_exp-a.sam -o -
.. ok
Number of tests:
total .. 172
passed .. 172
failed .. 0
+ RPM_EC=0
++ jobs -p
+ exit 0
Processing files: htslib-1.15.1-6.fc42.x86_64
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.5ZIfAI
+ umask 022
+ cd /builddir/build/BUILD/htslib-1.15.1-build
+ cd htslib-1.15.1
+ DOCDIR=/builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT/usr/share/doc/htslib
+ export LC_ALL=C.UTF-8
+ LC_ALL=C.UTF-8
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT/usr/share/doc/htslib
+ cp -pr /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/NEWS /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT/usr/share/doc/htslib
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.bhaVme
+ umask 022
+ cd /builddir/build/BUILD/htslib-1.15.1-build
+ cd htslib-1.15.1
+ LICENSEDIR=/builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT/usr/share/licenses/htslib
+ export LC_ALL=C.UTF-8
+ LC_ALL=C.UTF-8
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT/usr/share/licenses/htslib
+ cp -pr /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/LICENSE /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT/usr/share/licenses/htslib
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: htslib = 1.15.1-6.fc42 htslib(x86-64) = 1.15.1-6.fc42 libhts.so.3()(64bit)
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: libbz2.so.1()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(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_ABI_DT_RELR)(64bit) libcrypto.so.3()(64bit) libcrypto.so.3(OPENSSL_3.0.0)(64bit) libcurl.so.4()(64bit) libhts.so.3()(64bit) liblzma.so.5()(64bit) liblzma.so.5(XZ_5.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.23)(64bit) libm.so.6(GLIBC_2.29)(64bit) libz.so.1()(64bit) rtld(GNU_HASH)
Processing files: htslib-devel-1.15.1-6.fc42.x86_64
Provides: htslib-devel = 1.15.1-6.fc42 htslib-devel(x86-64) = 1.15.1-6.fc42 pkgconfig(htslib) = 1.15.1
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: /usr/bin/pkg-config libhts.so.3()(64bit)
Processing files: htslib-tools-1.15.1-6.fc42.x86_64
Provides: htslib-tools = 1.15.1-6.fc42 htslib-tools(x86-64) = 1.15.1-6.fc42
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: libbz2.so.1()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(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_ABI_DT_RELR)(64bit) liblzma.so.5()(64bit) liblzma.so.5(XZ_5.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.29)(64bit) libz.so.1()(64bit) rtld(GNU_HASH)
Processing files: htslib-debugsource-1.15.1-6.fc42.x86_64
Provides: htslib-debugsource = 1.15.1-6.fc42 htslib-debugsource(x86-64) = 1.15.1-6.fc42
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: htslib-debuginfo-1.15.1-6.fc42.x86_64
Provides: debuginfo(build-id) = 345e55f0284f95d30cbd53c3fc8ed94db8f8dbe6 debuginfo(build-id) = 441aac141b0dfbb063a322c479e9f67873bb83c7 debuginfo(build-id) = 596e93da9da9a6cf3457c1ae00c3cd8fcb92eabf debuginfo(build-id) = b6f9f759585ca289ea50613dedc1e2623d6f817f debuginfo(build-id) = d34b23b41a936a57912350d3fbba568863bf79f1 htslib-debuginfo = 1.15.1-6.fc42 htslib-debuginfo(x86-64) = 1.15.1-6.fc42 libhts.so.1.15.1-1.15.1-6.fc42.x86_64.debug()(64bit)
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: htslib-debugsource(x86-64) = 1.15.1-6.fc42
Processing files: htslib-tools-debuginfo-1.15.1-6.fc42.x86_64
Provides: debuginfo(build-id) = 531144fc4e261df424a702c74b66cb3c78f5bc1f debuginfo(build-id) = 728a93d04d97efa08fba2df394db14e832089cd8 debuginfo(build-id) = 84c0e074714b919770d5730b5721dde852042280 htslib-tools-debuginfo = 1.15.1-6.fc42 htslib-tools-debuginfo(x86-64) = 1.15.1-6.fc42
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: htslib-debugsource(x86-64) = 1.15.1-6.fc42
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT
Wrote: /builddir/build/RPMS/htslib-tools-1.15.1-6.fc42.x86_64.rpm
Wrote: /builddir/build/RPMS/htslib-debuginfo-1.15.1-6.fc42.x86_64.rpm
Wrote: /builddir/build/RPMS/htslib-debugsource-1.15.1-6.fc42.x86_64.rpm
Wrote: /builddir/build/RPMS/htslib-1.15.1-6.fc42.x86_64.rpm
Wrote: /builddir/build/RPMS/htslib-devel-1.15.1-6.fc42.x86_64.rpm
Wrote: /builddir/build/RPMS/htslib-tools-debuginfo-1.15.1-6.fc42.x86_64.rpm
Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.e5Rs7H
+ umask 022
+ cd /builddir/build/BUILD/htslib-1.15.1-build
+ test -d /builddir/build/BUILD/htslib-1.15.1-build
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w /builddir/build/BUILD/htslib-1.15.1-build
+ rm -rf /builddir/build/BUILD/htslib-1.15.1-build
+ RPM_EC=0
++ jobs -p
+ exit 0
Finish: rpmbuild htslib-1.15.1-6.fc42.src.rpm
Finish: build phase for htslib-1.15.1-6.fc42.src.rpm
INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/fedora-rawhide-x86_64-1734677548.851901/root/var/log/dnf5.log
INFO: chroot_scan: creating tarball /var/lib/copr-rpmbuild/results/chroot_scan.tar.gz
/bin/tar: Removing leading `/' from member names
INFO: Done(/var/lib/copr-rpmbuild/results/htslib-1.15.1-6.fc42.src.rpm) Config(child) 3 minutes 39 seconds
INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results
INFO: Cleaning up build root ('cleanup_on_success=True')
Start: clean chroot
INFO: unmounting tmpfs.
Finish: clean chroot
Finish: run
Running RPMResults tool
Package info:
{
"packages": [
{
"name": "htslib-devel",
"epoch": null,
"version": "1.15.1",
"release": "6.fc42",
"arch": "x86_64"
},
{
"name": "htslib",
"epoch": null,
"version": "1.15.1",
"release": "6.fc42",
"arch": "x86_64"
},
{
"name": "htslib",
"epoch": null,
"version": "1.15.1",
"release": "6.fc42",
"arch": "src"
},
{
"name": "htslib-debuginfo",
"epoch": null,
"version": "1.15.1",
"release": "6.fc42",
"arch": "x86_64"
},
{
"name": "htslib-tools-debuginfo",
"epoch": null,
"version": "1.15.1",
"release": "6.fc42",
"arch": "x86_64"
},
{
"name": "htslib-debugsource",
"epoch": null,
"version": "1.15.1",
"release": "6.fc42",
"arch": "x86_64"
},
{
"name": "htslib-tools",
"epoch": null,
"version": "1.15.1",
"release": "6.fc42",
"arch": "x86_64"
}
]
}
RPMResults finished