Warning: Permanently added '54.146.179.113' (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/10066099-fedora-43-aarch64 --chroot fedora-43-aarch64 Version: 1.6 PID: 9278 Logging PID: 9280 Task: {'allow_user_ssh': False, 'appstream': False, 'background': False, 'build_id': 10066099, 'buildroot_pkgs': [], 'chroot': 'fedora-43-aarch64', 'enable_net': False, 'fedora_review': False, 'git_hash': '83436232d36d75a3868c654aad8cc10b0bc7e683', 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/ron/bioinformatics/htslib', 'isolation': 'default', 'memory_reqs': 2048, 'package_name': 'htslib', 'package_version': '1.23-1', 'project_dirname': 'bioinformatics', 'project_name': 'bioinformatics', 'project_owner': 'ron', 'repo_priority': None, 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/ron/bioinformatics/fedora-43-aarch64/', 'id': 'copr_base', 'name': 'Copr repository', 'priority': None}], 'sandbox': 'ron/bioinformatics--ron', 'source_json': {}, 'source_type': None, 'ssh_public_keys': None, 'storage': 0, 'submitter': 'ron', 'tags': [], 'task_id': '10066099-fedora-43-aarch64', 'timeout': 18000, 'uses_devel_repo': False, 'with_opts': [], 'without_opts': []} Running: git clone https://copr-dist-git.fedorainfracloud.org/git/ron/bioinformatics/htslib /var/lib/copr-rpmbuild/workspace/workdir-u7a_kz2q/htslib --depth 500 --no-single-branch --recursive cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/ron/bioinformatics/htslib', '/var/lib/copr-rpmbuild/workspace/workdir-u7a_kz2q/htslib', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-u7a_kz2q/htslib'... Running: git checkout 83436232d36d75a3868c654aad8cc10b0bc7e683 -- cmd: ['git', 'checkout', '83436232d36d75a3868c654aad8cc10b0bc7e683', '--'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-u7a_kz2q/htslib rc: 0 stdout: stderr: Note: switching to '83436232d36d75a3868c654aad8cc10b0bc7e683'. 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 Or undo this operation with: git switch - Turn off this advice by setting config variable advice.detachedHead to false HEAD is now at 8343623 automatic import of htslib Running: dist-git-client sources cmd: ['dist-git-client', 'sources'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-u7a_kz2q/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-1.23.tar.bz2 INFO: Reading stdout from command: curl --help all INFO: Calling: curl -H Pragma: -o htslib-1.23.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/ron/bioinformatics/htslib/htslib-1.23.tar.bz2/md5/686ccffe2ba88ec57d85cca0e3eb2f3a/htslib-1.23.tar.bz2 % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 4786k 100 4786k 0 0 15.3M 0 --:--:-- --:--:-- --:--:-- 15.3M INFO: Reading stdout from command: md5sum htslib-1.23.tar.bz2 tail: /var/lib/copr-rpmbuild/main.log: file truncated Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-u7a_kz2q/htslib/htslib.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-u7a_kz2q/htslib --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1769500621.615308 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 6.6 starting (python version = 3.14.2, NVR = mock-6.6-1.fc43), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-u7a_kz2q/htslib/htslib.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-u7a_kz2q/htslib --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1769500621.615308 -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-u7a_kz2q/htslib/htslib.spec) Config(fedora-43-aarch64) Start: clean chroot Finish: clean chroot Mock Version: 6.6 INFO: Mock Version: 6.6 Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-43-aarch64-bootstrap-1769500621.615308/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 container image: registry.fedoraproject.org/fedora:43 INFO: Pulling image: registry.fedoraproject.org/fedora:43 INFO: Tagging container image as mock-bootstrap-e8735491-ed0f-40fe-b252-9158263b26f0 INFO: Checking that 0408e3a235e023749ec630188259e505268f3bca79fd5092e87ca814167ade54 image matches host's architecture INFO: Copy content of container 0408e3a235e023749ec630188259e505268f3bca79fd5092e87ca814167ade54 to /var/lib/mock/fedora-43-aarch64-bootstrap-1769500621.615308/root INFO: mounting 0408e3a235e023749ec630188259e505268f3bca79fd5092e87ca814167ade54 with podman image mount INFO: image 0408e3a235e023749ec630188259e505268f3bca79fd5092e87ca814167ade54 as /var/lib/containers/storage/overlay/317d1fcd34cd3938caa94d134963e97c9ec799d4cdf26c8ec19da18b75d4f032/merged INFO: umounting image 0408e3a235e023749ec630188259e505268f3bca79fd5092e87ca814167ade54 (/var/lib/containers/storage/overlay/317d1fcd34cd3938caa94d134963e97c9ec799d4cdf26c8ec19da18b75d4f032/merged) with podman image umount INFO: Removing image mock-bootstrap-e8735491-ed0f-40fe-b252-9158263b26f0 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-43-aarch64-1769500621.615308/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-6.0.1-1.fc43.aarch64 rpm-sequoia-1.10.0-1.fc43.aarch64 dnf5-5.2.17.0-2.fc43.aarch64 dnf5-plugins-5.2.17.0-2.fc43.aarch64 Start: installing minimal buildroot with dnf5 Updating and loading repositories: fedora 100% | 19.1 MiB/s | 34.2 MiB | 00m02s Copr repository 100% | 1.1 KiB/s | 1.6 KiB | 00m01s updates 100% | 12.6 MiB/s | 22.3 MiB | 00m02s Repositories loaded. Package Arch Version Repository Size Installing group/module packages: bash aarch64 5.3.0-2.fc43 fedora 8.4 MiB bzip2 aarch64 1.0.8-21.fc43 fedora 171.3 KiB coreutils aarch64 9.7-7.fc43 updates 8.2 MiB cpio aarch64 2.15-6.fc43 fedora 1.1 MiB diffutils aarch64 3.12-3.fc43 fedora 1.6 MiB fedora-release-common noarch 43-25 fedora 20.6 KiB findutils aarch64 1:4.10.0-6.fc43 fedora 1.9 MiB gawk aarch64 5.3.2-2.fc43 fedora 2.6 MiB glibc-minimal-langpack aarch64 2.42-9.fc43 updates 0.0 B grep aarch64 3.12-2.fc43 fedora 1.0 MiB gzip aarch64 1.13-4.fc43 fedora 424.7 KiB info aarch64 7.2-6.fc43 fedora 421.6 KiB patch aarch64 2.8-2.fc43 fedora 262.5 KiB redhat-rpm-config noarch 343-11.fc43 fedora 182.9 KiB rpm-build aarch64 6.0.1-1.fc43 updates 599.0 KiB sed aarch64 4.9-5.fc43 fedora 873.2 KiB shadow-utils aarch64 2:4.18.0-3.fc43 fedora 4.4 MiB tar aarch64 2:1.35-6.fc43 fedora 3.0 MiB unzip aarch64 6.0-67.fc43 fedora 470.2 KiB util-linux aarch64 2.41.3-7.fc43 updates 6.8 MiB which aarch64 2.23-3.fc43 fedora 123.4 KiB xz aarch64 1:5.8.1-4.fc43 updates 1.4 MiB Installing dependencies: add-determinism aarch64 0.6.0-2.fc43 fedora 2.1 MiB alternatives aarch64 1.33-3.fc43 updates 90.2 KiB ansible-srpm-macros noarch 1-18.1.fc43 fedora 35.7 KiB audit-libs aarch64 4.1.2-2.fc43 updates 486.9 KiB binutils aarch64 2.45.1-4.fc43 updates 31.0 MiB build-reproducibility-srpm-macros noarch 0.6.0-2.fc43 fedora 735.0 B bzip2-libs aarch64 1.0.8-21.fc43 fedora 72.6 KiB ca-certificates noarch 2025.2.80_v9.0.304-1.1.fc43 fedora 2.7 MiB coreutils-common aarch64 9.7-7.fc43 updates 11.3 MiB crypto-policies noarch 20251125-1.git63291f8.fc43 updates 147.1 KiB curl aarch64 8.15.0-5.fc43 updates 457.6 KiB cyrus-sasl-lib aarch64 2.1.28-33.fc43 fedora 2.4 MiB debugedit aarch64 5.2-3.fc43 fedora 317.9 KiB dwz aarch64 0.16-2.fc43 fedora 322.6 KiB ed aarch64 1.22.2-1.fc43 fedora 156.0 KiB efi-srpm-macros noarch 6-4.fc43 fedora 40.1 KiB elfutils aarch64 0.194-1.fc43 updates 3.2 MiB elfutils-debuginfod-client aarch64 0.194-1.fc43 updates 144.0 KiB elfutils-default-yama-scope noarch 0.194-1.fc43 updates 1.8 KiB elfutils-libelf aarch64 0.194-1.fc43 updates 1.1 MiB elfutils-libs aarch64 0.194-1.fc43 updates 746.7 KiB fedora-gpg-keys noarch 43-1 fedora 131.2 KiB fedora-release noarch 43-25 fedora 0.0 B fedora-release-identity-basic noarch 43-25 fedora 631.0 B fedora-repos noarch 43-1 fedora 4.9 KiB file aarch64 5.46-8.fc43 fedora 140.2 KiB file-libs aarch64 5.46-8.fc43 fedora 11.9 MiB filesystem aarch64 3.18-50.fc43 fedora 112.0 B filesystem-srpm-macros noarch 3.18-50.fc43 fedora 38.2 KiB fonts-srpm-macros noarch 1:2.0.5-23.fc43 fedora 55.8 KiB forge-srpm-macros noarch 0.4.0-3.fc43 fedora 38.9 KiB fpc-srpm-macros noarch 1.3-15.fc43 fedora 144.0 B gap-srpm-macros noarch 2-1.fc43 fedora 2.1 KiB gdb-minimal aarch64 17.1-1.fc43 updates 13.4 MiB gdbm-libs aarch64 1:1.23-10.fc43 fedora 233.9 KiB ghc-srpm-macros noarch 1.9.2-3.fc43 fedora 779.0 B glibc aarch64 2.42-9.fc43 updates 6.3 MiB glibc-common aarch64 2.42-9.fc43 updates 1.3 MiB glibc-gconv-extra aarch64 2.42-9.fc43 updates 18.6 MiB gmp aarch64 1:6.3.0-4.fc43 fedora 657.9 KiB gnat-srpm-macros noarch 7-1.fc43 updates 1.0 KiB gnulib-l10n noarch 20241231-1.fc43 fedora 655.0 KiB gnupg2 aarch64 2.4.9-4.fc43 updates 6.5 MiB gnupg2-dirmngr aarch64 2.4.9-4.fc43 updates 646.4 KiB gnupg2-gpg-agent aarch64 2.4.9-4.fc43 updates 847.3 KiB gnupg2-gpgconf aarch64 2.4.9-4.fc43 updates 321.9 KiB gnupg2-keyboxd aarch64 2.4.9-4.fc43 updates 233.3 KiB gnupg2-verify aarch64 2.4.9-4.fc43 updates 364.4 KiB gnutls aarch64 3.8.11-5.fc43 updates 3.6 MiB go-srpm-macros noarch 3.8.0-1.fc43 fedora 61.9 KiB gpgverify noarch 2.2-3.fc43 fedora 8.7 KiB ima-evm-utils-libs aarch64 1.6.2-6.fc43 fedora 92.7 KiB jansson aarch64 2.14-3.fc43 fedora 93.1 KiB java-srpm-macros noarch 1-7.fc43 fedora 870.0 B json-c aarch64 0.18-7.fc43 fedora 138.7 KiB kernel-srpm-macros noarch 1.0-27.fc43 fedora 1.9 KiB keyutils-libs aarch64 1.6.3-6.fc43 fedora 98.3 KiB krb5-libs aarch64 1.21.3-7.fc43 fedora 2.5 MiB libacl aarch64 2.3.2-4.fc43 fedora 68.0 KiB libarchive aarch64 3.8.4-1.fc43 updates 975.3 KiB libassuan aarch64 2.5.7-4.fc43 fedora 215.8 KiB libattr aarch64 2.5.2-6.fc43 fedora 68.5 KiB libblkid aarch64 2.41.3-7.fc43 updates 290.5 KiB libbrotli aarch64 1.2.0-1.fc43 updates 909.5 KiB libcap aarch64 2.76-3.fc43 fedora 508.8 KiB libcap-ng aarch64 0.8.5-8.fc43 fedora 160.9 KiB libcom_err aarch64 1.47.3-2.fc43 fedora 111.2 KiB libcurl aarch64 8.15.0-5.fc43 updates 915.1 KiB libeconf aarch64 0.7.9-2.fc43 fedora 81.0 KiB libevent aarch64 2.1.12-16.fc43 fedora 1.1 MiB libfdisk aarch64 2.41.3-7.fc43 updates 418.9 KiB libffi aarch64 3.5.2-1.fc43 updates 155.9 KiB libfsverity aarch64 1.6-3.fc43 fedora 68.5 KiB libgcc aarch64 15.2.1-5.fc43 updates 222.2 KiB libgcrypt aarch64 1.11.1-3.fc43 updates 1.2 MiB libgomp aarch64 15.2.1-5.fc43 updates 517.1 KiB libgpg-error aarch64 1.55-2.fc43 fedora 971.3 KiB libidn2 aarch64 2.3.8-2.fc43 fedora 560.6 KiB libksba aarch64 1.6.7-4.fc43 fedora 398.4 KiB liblastlog2 aarch64 2.41.3-7.fc43 updates 138.0 KiB libmount aarch64 2.41.3-7.fc43 updates 420.2 KiB libnghttp2 aarch64 1.66.0-2.fc43 fedora 197.9 KiB libpkgconf aarch64 2.3.0-3.fc43 fedora 134.0 KiB libpsl aarch64 0.21.5-6.fc43 fedora 132.5 KiB libselinux aarch64 3.9-5.fc43 fedora 201.1 KiB libsemanage aarch64 3.9-4.fc43 fedora 360.2 KiB libsepol aarch64 3.9-2.fc43 fedora 809.8 KiB libsmartcols aarch64 2.41.3-7.fc43 updates 224.6 KiB libssh aarch64 0.11.3-1.fc43 fedora 587.0 KiB libssh-config noarch 0.11.3-1.fc43 fedora 277.0 B libstdc++ aarch64 15.2.1-5.fc43 updates 2.8 MiB libtasn1 aarch64 4.20.0-2.fc43 fedora 220.4 KiB libtool-ltdl aarch64 2.5.4-8.fc43 updates 94.0 KiB libunistring aarch64 1.1-10.fc43 fedora 1.7 MiB libusb1 aarch64 1.0.29-4.fc43 fedora 178.9 KiB libuuid aarch64 2.41.3-7.fc43 updates 69.4 KiB libverto aarch64 0.3.2-11.fc43 fedora 69.4 KiB libxcrypt aarch64 4.5.2-1.fc43 updates 273.4 KiB libxml2 aarch64 2.12.10-5.fc43 fedora 1.9 MiB libzstd aarch64 1.5.7-2.fc43 fedora 667.7 KiB lua-libs aarch64 5.4.8-4.fc43 updates 329.9 KiB lua-srpm-macros noarch 1-16.fc43 fedora 1.3 KiB lz4-libs aarch64 1.10.0-3.fc43 fedora 197.4 KiB mpfr aarch64 4.2.2-2.fc43 fedora 755.5 KiB ncurses-base noarch 6.5-7.20250614.fc43 fedora 328.1 KiB ncurses-libs aarch64 6.5-7.20250614.fc43 fedora 1.2 MiB nettle aarch64 3.10.1-2.fc43 fedora 765.3 KiB npth aarch64 1.8-3.fc43 fedora 93.5 KiB ocaml-srpm-macros noarch 11-2.fc43 fedora 1.9 KiB openblas-srpm-macros noarch 2-20.fc43 fedora 112.0 B openldap aarch64 2.6.10-4.fc43 fedora 761.9 KiB openssl-libs aarch64 1:3.5.4-1.fc43 updates 7.4 MiB p11-kit aarch64 0.25.8-1.fc43 fedora 2.5 MiB p11-kit-trust aarch64 0.25.8-1.fc43 fedora 530.3 KiB package-notes-srpm-macros noarch 0.5-14.fc43 fedora 1.6 KiB pam-libs aarch64 1.7.1-4.fc43 updates 223.0 KiB pcre2 aarch64 10.47-1.fc43 updates 714.5 KiB pcre2-syntax noarch 10.47-1.fc43 updates 281.9 KiB perl-srpm-macros noarch 1-60.fc43 fedora 861.0 B pkgconf aarch64 2.3.0-3.fc43 fedora 112.4 KiB pkgconf-m4 noarch 2.3.0-3.fc43 fedora 14.4 KiB pkgconf-pkg-config aarch64 2.3.0-3.fc43 fedora 990.0 B popt aarch64 1.19-9.fc43 fedora 144.8 KiB publicsuffix-list-dafsa noarch 20260116-1.fc43 updates 70.4 KiB pyproject-srpm-macros noarch 1.18.6-1.fc43 updates 1.9 KiB python-srpm-macros noarch 3.14-5.fc43 fedora 51.5 KiB qt5-srpm-macros noarch 5.15.18-1.fc43 updates 500.0 B qt6-srpm-macros noarch 6.10.1-1.fc43 updates 464.0 B readline aarch64 8.3-2.fc43 fedora 563.8 KiB rpm aarch64 6.0.1-1.fc43 updates 3.4 MiB rpm-build-libs aarch64 6.0.1-1.fc43 updates 264.1 KiB rpm-libs aarch64 6.0.1-1.fc43 updates 995.5 KiB rpm-sequoia aarch64 1.10.0-1.fc43 updates 2.3 MiB rpm-sign-libs aarch64 6.0.1-1.fc43 updates 67.8 KiB rust-srpm-macros noarch 28.4-1.fc43 updates 5.5 KiB setup noarch 2.15.0-26.fc43 fedora 725.0 KiB sqlite-libs aarch64 3.50.2-2.fc43 fedora 1.5 MiB systemd-libs aarch64 258.3-2.fc43 updates 2.4 MiB systemd-standalone-sysusers aarch64 258.3-2.fc43 updates 329.6 KiB tpm2-tss aarch64 4.1.3-8.fc43 fedora 2.1 MiB tree-sitter-srpm-macros noarch 0.4.2-1.fc43 fedora 8.3 KiB util-linux-core aarch64 2.41.3-7.fc43 updates 2.4 MiB xxhash-libs aarch64 0.8.3-3.fc43 fedora 86.0 KiB xz-libs aarch64 1:5.8.1-4.fc43 updates 201.6 KiB zig-srpm-macros noarch 1-5.fc43 fedora 1.1 KiB zip aarch64 3.0-44.fc43 fedora 762.5 KiB zlib-ng-compat aarch64 2.3.2-2.fc43 updates 133.5 KiB zstd aarch64 1.5.7-2.fc43 fedora 1.5 MiB Installing groups: Buildsystem building group Transaction Summary: Installing: 170 packages Total size of inbound packages is 58 MiB. Need to download 58 MiB. After this operation, 226 MiB extra will be used (install 226 MiB, remove 0 B). [ 1/170] cpio-0:2.15-6.fc43.aarch64 100% | 16.6 MiB/s | 289.6 KiB | 00m00s [ 2/170] bzip2-0:1.0.8-21.fc43.aarch64 100% | 2.8 MiB/s | 51.6 KiB | 00m00s [ 3/170] fedora-release-common-0:43-25 100% | 4.0 MiB/s | 24.6 KiB | 00m00s [ 4/170] bash-0:5.3.0-2.fc43.aarch64 100% | 68.1 MiB/s | 1.8 MiB | 00m00s [ 5/170] diffutils-0:3.12-3.fc43.aarch 100% | 34.6 MiB/s | 389.7 KiB | 00m00s [ 6/170] findutils-1:4.10.0-6.fc43.aar 100% | 90.0 MiB/s | 552.7 KiB | 00m00s [ 7/170] grep-0:3.12-2.fc43.aarch64 100% | 57.9 MiB/s | 296.2 KiB | 00m00s [ 8/170] gawk-0:5.3.2-2.fc43.aarch64 100% | 139.2 MiB/s | 1.1 MiB | 00m00s [ 9/170] gzip-0:1.13-4.fc43.aarch64 100% | 23.4 MiB/s | 167.6 KiB | 00m00s [ 10/170] info-0:7.2-6.fc43.aarch64 100% | 43.8 MiB/s | 179.4 KiB | 00m00s [ 11/170] patch-0:2.8-2.fc43.aarch64 100% | 27.2 MiB/s | 111.6 KiB | 00m00s [ 12/170] redhat-rpm-config-0:343-11.fc 100% | 19.3 MiB/s | 79.1 KiB | 00m00s [ 13/170] sed-0:4.9-5.fc43.aarch64 100% | 76.7 MiB/s | 314.4 KiB | 00m00s [ 14/170] shadow-utils-2:4.18.0-3.fc43. 100% | 142.2 MiB/s | 1.3 MiB | 00m00s [ 15/170] unzip-0:6.0-67.fc43.aarch64 100% | 22.6 MiB/s | 185.4 KiB | 00m00s [ 16/170] tar-2:1.35-6.fc43.aarch64 100% | 75.5 MiB/s | 850.8 KiB | 00m00s [ 17/170] which-0:2.23-3.fc43.aarch64 100% | 13.5 MiB/s | 41.4 KiB | 00m00s [ 18/170] glibc-minimal-langpack-0:2.42 100% | 10.0 MiB/s | 40.9 KiB | 00m00s [ 19/170] rpm-build-0:6.0.1-1.fc43.aarc 100% | 21.6 MiB/s | 132.4 KiB | 00m00s [ 20/170] coreutils-0:9.7-7.fc43.aarch6 100% | 78.3 MiB/s | 1.1 MiB | 00m00s [ 21/170] xz-1:5.8.1-4.fc43.aarch64 100% | 62.2 MiB/s | 573.5 KiB | 00m00s [ 22/170] util-linux-0:2.41.3-7.fc43.aa 100% | 69.4 MiB/s | 1.2 MiB | 00m00s [ 23/170] filesystem-0:3.18-50.fc43.aar 100% | 121.2 MiB/s | 1.3 MiB | 00m00s [ 24/170] ncurses-libs-0:6.5-7.20250614 100% | 35.2 MiB/s | 324.6 KiB | 00m00s [ 25/170] bzip2-libs-0:1.0.8-21.fc43.aa 100% | 10.0 MiB/s | 40.9 KiB | 00m00s [ 26/170] fedora-repos-0:43-1.noarch 100% | 3.0 MiB/s | 9.1 KiB | 00m00s [ 27/170] gmp-1:6.3.0-4.fc43.aarch64 100% | 53.0 MiB/s | 271.3 KiB | 00m00s [ 28/170] libselinux-0:3.9-5.fc43.aarch 100% | 15.7 MiB/s | 96.6 KiB | 00m00s [ 29/170] mpfr-0:4.2.2-2.fc43.aarch64 100% | 44.9 MiB/s | 322.0 KiB | 00m00s [ 30/170] readline-0:8.3-2.fc43.aarch64 100% | 43.3 MiB/s | 221.8 KiB | 00m00s [ 31/170] ed-0:1.22.2-1.fc43.aarch64 100% | 16.2 MiB/s | 83.1 KiB | 00m00s [ 32/170] libattr-0:2.5.2-6.fc43.aarch6 100% | 8.7 MiB/s | 17.7 KiB | 00m00s [ 33/170] ansible-srpm-macros-0:1-18.1. 100% | 9.7 MiB/s | 19.9 KiB | 00m00s [ 34/170] build-reproducibility-srpm-ma 100% | 5.8 MiB/s | 11.8 KiB | 00m00s [ 35/170] efi-srpm-macros-0:6-4.fc43.no 100% | 10.9 MiB/s | 22.4 KiB | 00m00s [ 36/170] dwz-0:0.16-2.fc43.aarch64 100% | 43.0 MiB/s | 132.2 KiB | 00m00s [ 37/170] file-0:5.46-8.fc43.aarch64 100% | 16.0 MiB/s | 49.2 KiB | 00m00s [ 38/170] filesystem-srpm-macros-0:3.18 100% | 8.6 MiB/s | 26.4 KiB | 00m00s [ 39/170] fonts-srpm-macros-1:2.0.5-23. 100% | 13.3 MiB/s | 27.2 KiB | 00m00s [ 40/170] forge-srpm-macros-0:0.4.0-3.f 100% | 9.8 MiB/s | 20.1 KiB | 00m00s [ 41/170] fpc-srpm-macros-0:1.3-15.fc43 100% | 3.9 MiB/s | 7.9 KiB | 00m00s [ 42/170] gap-srpm-macros-0:2-1.fc43.no 100% | 4.4 MiB/s | 9.0 KiB | 00m00s [ 43/170] ghc-srpm-macros-0:1.9.2-3.fc4 100% | 4.3 MiB/s | 8.7 KiB | 00m00s [ 44/170] java-srpm-macros-0:1-7.fc43.n 100% | 3.9 MiB/s | 7.9 KiB | 00m00s [ 45/170] kernel-srpm-macros-0:1.0-27.f 100% | 4.4 MiB/s | 8.9 KiB | 00m00s [ 46/170] go-srpm-macros-0:3.8.0-1.fc43 100% | 5.5 MiB/s | 28.3 KiB | 00m00s [ 47/170] lua-srpm-macros-0:1-16.fc43.n 100% | 2.9 MiB/s | 8.8 KiB | 00m00s [ 48/170] ocaml-srpm-macros-0:11-2.fc43 100% | 4.5 MiB/s | 9.3 KiB | 00m00s [ 49/170] openblas-srpm-macros-0:2-20.f 100% | 3.7 MiB/s | 7.6 KiB | 00m00s [ 50/170] perl-srpm-macros-0:1-60.fc43. 100% | 4.0 MiB/s | 8.3 KiB | 00m00s [ 51/170] package-notes-srpm-macros-0:0 100% | 2.9 MiB/s | 9.0 KiB | 00m00s [ 52/170] python-srpm-macros-0:3.14-5.f 100% | 7.6 MiB/s | 23.4 KiB | 00m00s [ 53/170] tree-sitter-srpm-macros-0:0.4 100% | 4.3 MiB/s | 13.4 KiB | 00m00s [ 54/170] zig-srpm-macros-0:1-5.fc43.no 100% | 2.7 MiB/s | 8.4 KiB | 00m00s [ 55/170] libacl-0:2.3.2-4.fc43.aarch64 100% | 11.8 MiB/s | 24.2 KiB | 00m00s [ 56/170] libeconf-0:0.7.9-2.fc43.aarch 100% | 17.2 MiB/s | 35.2 KiB | 00m00s [ 57/170] zip-0:3.0-44.fc43.aarch64 100% | 64.1 MiB/s | 262.6 KiB | 00m00s [ 58/170] libsemanage-0:3.9-4.fc43.aarc 100% | 29.2 MiB/s | 119.5 KiB | 00m00s [ 59/170] setup-0:2.15.0-26.fc43.noarch 100% | 38.4 MiB/s | 157.3 KiB | 00m00s [ 60/170] libcap-0:2.76-3.fc43.aarch64 100% | 14.3 MiB/s | 87.9 KiB | 00m00s [ 61/170] glibc-0:2.42-9.fc43.aarch64 100% | 130.0 MiB/s | 1.8 MiB | 00m00s [ 62/170] coreutils-common-0:9.7-7.fc43 100% | 116.6 MiB/s | 2.1 MiB | 00m00s [ 63/170] glibc-common-0:2.42-9.fc43.aa 100% | 20.6 MiB/s | 315.9 KiB | 00m00s [ 64/170] debugedit-0:5.2-3.fc43.aarch6 100% | 13.8 MiB/s | 84.7 KiB | 00m00s [ 65/170] pkgconf-pkg-config-0:2.3.0-3. 100% | 3.1 MiB/s | 9.6 KiB | 00m00s [ 66/170] popt-0:1.19-9.fc43.aarch64 100% | 12.8 MiB/s | 65.3 KiB | 00m00s [ 67/170] zstd-0:1.5.7-2.fc43.aarch64 100% | 87.3 MiB/s | 446.9 KiB | 00m00s [ 68/170] libcap-ng-0:0.8.5-8.fc43.aarc 100% | 10.5 MiB/s | 32.2 KiB | 00m00s [ 69/170] rpm-0:6.0.1-1.fc43.aarch64 100% | 70.4 MiB/s | 576.3 KiB | 00m00s [ 70/170] libblkid-0:2.41.3-7.fc43.aarc 100% | 23.7 MiB/s | 121.5 KiB | 00m00s [ 71/170] liblastlog2-0:2.41.3-7.fc43.a 100% | 5.7 MiB/s | 23.5 KiB | 00m00s [ 72/170] libfdisk-0:2.41.3-7.fc43.aarc 100% | 21.5 MiB/s | 154.2 KiB | 00m00s [ 73/170] libmount-0:2.41.3-7.fc43.aarc 100% | 31.0 MiB/s | 158.6 KiB | 00m00s [ 74/170] libsmartcols-0:2.41.3-7.fc43. 100% | 16.1 MiB/s | 82.5 KiB | 00m00s [ 75/170] libuuid-0:2.41.3-7.fc43.aarch 100% | 6.3 MiB/s | 26.0 KiB | 00m00s [ 76/170] ncurses-base-0:6.5-7.20250614 100% | 17.2 MiB/s | 88.2 KiB | 00m00s [ 77/170] xz-libs-1:5.8.1-4.fc43.aarch6 100% | 18.1 MiB/s | 111.1 KiB | 00m00s [ 78/170] util-linux-core-0:2.41.3-7.fc 100% | 52.8 MiB/s | 541.1 KiB | 00m00s [ 79/170] fedora-gpg-keys-0:43-1.noarch 100% | 33.9 MiB/s | 138.9 KiB | 00m00s [ 80/170] libsepol-0:3.9-2.fc43.aarch64 100% | 63.2 MiB/s | 323.6 KiB | 00m00s [ 81/170] add-determinism-0:0.6.0-2.fc4 100% | 118.8 MiB/s | 851.5 KiB | 00m00s [ 82/170] file-libs-0:5.46-8.fc43.aarch 100% | 118.3 MiB/s | 848.0 KiB | 00m00s [ 83/170] gnulib-l10n-0:20241231-1.fc43 100% | 20.9 MiB/s | 150.2 KiB | 00m00s [ 84/170] pkgconf-0:2.3.0-3.fc43.aarch6 100% | 10.8 MiB/s | 44.4 KiB | 00m00s [ 85/170] pkgconf-m4-0:2.3.0-3.fc43.noa 100% | 3.4 MiB/s | 13.9 KiB | 00m00s [ 86/170] glibc-gconv-extra-0:2.42-9.fc 100% | 165.9 MiB/s | 1.7 MiB | 00m00s [ 87/170] lz4-libs-0:1.10.0-3.fc43.aarc 100% | 12.9 MiB/s | 79.5 KiB | 00m00s [ 88/170] sqlite-libs-0:3.50.2-2.fc43.a 100% | 90.7 MiB/s | 742.8 KiB | 00m00s [ 89/170] libpkgconf-0:2.3.0-3.fc43.aar 100% | 4.1 MiB/s | 37.9 KiB | 00m00s [ 90/170] libzstd-0:1.5.7-2.fc43.aarch6 100% | 55.4 MiB/s | 283.6 KiB | 00m00s [ 91/170] rpm-libs-0:6.0.1-1.fc43.aarch 100% | 41.2 MiB/s | 379.8 KiB | 00m00s [ 92/170] rpm-build-libs-0:6.0.1-1.fc43 100% | 23.0 MiB/s | 117.5 KiB | 00m00s [ 93/170] rpm-sign-libs-0:6.0.1-1.fc43. 100% | 8.9 MiB/s | 27.3 KiB | 00m00s [ 94/170] ima-evm-utils-libs-0:1.6.2-6. 100% | 9.5 MiB/s | 29.3 KiB | 00m00s [ 95/170] json-c-0:0.18-7.fc43.aarch64 100% | 14.7 MiB/s | 45.1 KiB | 00m00s [ 96/170] libfsverity-0:1.6-3.fc43.aarc 100% | 3.0 MiB/s | 18.6 KiB | 00m00s [ 97/170] tpm2-tss-0:4.1.3-8.fc43.aarch 100% | 48.9 MiB/s | 400.5 KiB | 00m00s [ 98/170] libgcc-0:15.2.1-5.fc43.aarch6 100% | 19.4 MiB/s | 119.1 KiB | 00m00s [ 99/170] libusb1-0:1.0.29-4.fc43.aarch 100% | 9.5 MiB/s | 77.5 KiB | 00m00s [100/170] libxcrypt-0:4.5.2-1.fc43.aarc 100% | 15.3 MiB/s | 125.2 KiB | 00m00s [101/170] audit-libs-0:4.1.2-2.fc43.aar 100% | 27.3 MiB/s | 139.9 KiB | 00m00s [102/170] pam-libs-0:1.7.1-4.fc43.aarch 100% | 18.5 MiB/s | 56.8 KiB | 00m00s [103/170] systemd-libs-0:258.3-2.fc43.a 100% | 69.9 MiB/s | 787.3 KiB | 00m00s [104/170] zlib-ng-compat-0:2.3.2-2.fc43 100% | 14.1 MiB/s | 72.2 KiB | 00m00s [105/170] gpgverify-0:2.2-3.fc43.noarch 100% | 2.7 MiB/s | 11.1 KiB | 00m00s [106/170] libassuan-0:2.5.7-4.fc43.aarc 100% | 13.0 MiB/s | 66.5 KiB | 00m00s [107/170] gnupg2-0:2.4.9-4.fc43.aarch64 100% | 161.6 MiB/s | 1.6 MiB | 00m00s [108/170] npth-0:1.8-3.fc43.aarch64 100% | 12.2 MiB/s | 25.0 KiB | 00m00s [109/170] libgpg-error-0:1.55-2.fc43.aa 100% | 47.5 MiB/s | 243.5 KiB | 00m00s [110/170] gnupg2-dirmngr-0:2.4.9-4.fc43 100% | 52.0 MiB/s | 266.2 KiB | 00m00s [111/170] gnupg2-gpg-agent-0:2.4.9-4.fc 100% | 52.0 MiB/s | 266.3 KiB | 00m00s [112/170] gnupg2-gpgconf-0:2.4.9-4.fc43 100% | 18.6 MiB/s | 114.1 KiB | 00m00s [113/170] gnupg2-keyboxd-0:2.4.9-4.fc43 100% | 22.3 MiB/s | 91.4 KiB | 00m00s [114/170] gnupg2-verify-0:2.4.9-4.fc43. 100% | 40.1 MiB/s | 164.4 KiB | 00m00s [115/170] libksba-0:1.6.7-4.fc43.aarch6 100% | 38.5 MiB/s | 157.5 KiB | 00m00s [116/170] openldap-0:2.6.10-4.fc43.aarc 100% | 49.0 MiB/s | 251.1 KiB | 00m00s [117/170] cyrus-sasl-lib-0:2.1.28-33.fc 100% | 151.2 MiB/s | 774.0 KiB | 00m00s [118/170] libevent-0:2.1.12-16.fc43.aar 100% | 35.3 MiB/s | 253.4 KiB | 00m00s [119/170] gdbm-libs-1:1.23-10.fc43.aarc 100% | 9.1 MiB/s | 56.0 KiB | 00m00s [120/170] lua-libs-0:5.4.8-4.fc43.aarch 100% | 18.0 MiB/s | 129.1 KiB | 00m00s [121/170] libstdc++-0:15.2.1-5.fc43.aar 100% | 59.5 MiB/s | 853.6 KiB | 00m00s [122/170] rpm-sequoia-0:1.10.0-1.fc43.a 100% | 62.2 MiB/s | 891.7 KiB | 00m00s [123/170] elfutils-libelf-0:0.194-1.fc4 100% | 19.8 MiB/s | 202.3 KiB | 00m00s [124/170] elfutils-libs-0:0.194-1.fc43. 100% | 43.3 MiB/s | 266.0 KiB | 00m00s [125/170] elfutils-debuginfod-client-0: 100% | 22.6 MiB/s | 46.3 KiB | 00m00s [126/170] elfutils-0:0.194-1.fc43.aarch 100% | 87.2 MiB/s | 535.6 KiB | 00m00s [127/170] libgomp-0:15.2.1-5.fc43.aarch 100% | 39.5 MiB/s | 364.2 KiB | 00m00s [128/170] jansson-0:2.14-3.fc43.aarch64 100% | 3.8 MiB/s | 46.7 KiB | 00m00s [129/170] libxml2-0:2.12.10-5.fc43.aarc 100% | 110.5 MiB/s | 678.7 KiB | 00m00s [130/170] binutils-0:2.45.1-4.fc43.aarc 100% | 149.6 MiB/s | 6.3 MiB | 00m00s [131/170] curl-0:8.15.0-5.fc43.aarch64 100% | 11.0 MiB/s | 224.9 KiB | 00m00s [132/170] libarchive-0:3.8.4-1.fc43.aar 100% | 11.5 MiB/s | 413.6 KiB | 00m00s [133/170] p11-kit-0:0.25.8-1.fc43.aarch 100% | 34.3 MiB/s | 492.3 KiB | 00m00s [134/170] ca-certificates-0:2025.2.80_v 100% | 52.9 MiB/s | 975.4 KiB | 00m00s [135/170] openssl-libs-1:3.5.4-1.fc43.a 100% | 98.0 MiB/s | 2.4 MiB | 00m00s [136/170] p11-kit-trust-0:0.25.8-1.fc43 100% | 13.5 MiB/s | 138.6 KiB | 00m00s [137/170] libtasn1-0:4.20.0-2.fc43.aarc 100% | 9.0 MiB/s | 73.8 KiB | 00m00s [138/170] libgcrypt-0:1.11.1-3.fc43.aar 100% | 72.3 MiB/s | 518.4 KiB | 00m00s [139/170] libidn2-0:2.3.8-2.fc43.aarch6 100% | 28.4 MiB/s | 174.6 KiB | 00m00s [140/170] libunistring-0:1.1-10.fc43.aa 100% | 105.3 MiB/s | 539.2 KiB | 00m00s [141/170] nettle-0:3.10.1-2.fc43.aarch6 100% | 59.4 MiB/s | 425.7 KiB | 00m00s [142/170] elfutils-default-yama-scope-0 100% | 3.0 MiB/s | 12.4 KiB | 00m00s [143/170] alternatives-0:1.33-3.fc43.aa 100% | 9.8 MiB/s | 40.3 KiB | 00m00s [144/170] gnat-srpm-macros-0:7-1.fc43.n 100% | 2.8 MiB/s | 8.7 KiB | 00m00s [145/170] qt5-srpm-macros-0:5.15.18-1.f 100% | 4.2 MiB/s | 8.6 KiB | 00m00s [146/170] pyproject-srpm-macros-0:1.18. 100% | 6.5 MiB/s | 13.4 KiB | 00m00s [147/170] qt6-srpm-macros-0:6.10.1-1.fc 100% | 4.6 MiB/s | 9.4 KiB | 00m00s [148/170] rust-srpm-macros-0:28.4-1.fc4 100% | 2.6 MiB/s | 10.8 KiB | 00m00s [149/170] libffi-0:3.5.2-1.fc43.aarch64 100% | 19.2 MiB/s | 39.4 KiB | 00m00s [150/170] libtool-ltdl-0:2.5.4-8.fc43.a 100% | 8.7 MiB/s | 35.6 KiB | 00m00s [151/170] pcre2-0:10.47-1.fc43.aarch64 100% | 40.1 MiB/s | 246.2 KiB | 00m00s [152/170] pcre2-syntax-0:10.47-1.fc43.n 100% | 17.9 MiB/s | 164.7 KiB | 00m00s [153/170] crypto-policies-0:20251125-1. 100% | 15.9 MiB/s | 97.8 KiB | 00m00s [154/170] systemd-standalone-sysusers-0 100% | 34.5 MiB/s | 141.4 KiB | 00m00s [155/170] xxhash-libs-0:0.8.3-3.fc43.aa 100% | 16.8 MiB/s | 34.5 KiB | 00m00s [156/170] gnutls-0:3.8.11-5.fc43.aarch6 100% | 23.4 MiB/s | 1.3 MiB | 00m00s [157/170] libcurl-0:8.15.0-5.fc43.aarch 100% | 47.9 MiB/s | 392.7 KiB | 00m00s [158/170] libnghttp2-0:1.66.0-2.fc43.aa 100% | 6.4 MiB/s | 72.2 KiB | 00m00s [159/170] krb5-libs-0:1.21.3-7.fc43.aar 100% | 48.9 MiB/s | 751.0 KiB | 00m00s [160/170] libpsl-0:0.21.5-6.fc43.aarch6 100% | 8.0 MiB/s | 65.1 KiB | 00m00s [161/170] libssh-0:0.11.3-1.fc43.aarch6 100% | 28.2 MiB/s | 230.6 KiB | 00m00s [162/170] gdb-minimal-0:17.1-1.fc43.aar 100% | 100.6 MiB/s | 4.2 MiB | 00m00s [163/170] keyutils-libs-0:1.6.3-6.fc43. 100% | 4.4 MiB/s | 31.5 KiB | 00m00s [164/170] libcom_err-0:1.47.3-2.fc43.aa 100% | 5.2 MiB/s | 26.7 KiB | 00m00s [165/170] libssh-config-0:0.11.3-1.fc43 100% | 4.4 MiB/s | 9.1 KiB | 00m00s [166/170] libverto-0:0.3.2-11.fc43.aarc 100% | 6.6 MiB/s | 20.4 KiB | 00m00s [167/170] fedora-release-0:43-25.noarch 100% | 3.3 MiB/s | 13.5 KiB | 00m00s [168/170] fedora-release-identity-basic 100% | 7.0 MiB/s | 14.3 KiB | 00m00s [169/170] publicsuffix-list-dafsa-0:202 100% | 19.6 MiB/s | 60.3 KiB | 00m00s [170/170] libbrotli-0:1.2.0-1.fc43.aarc 100% | 85.5 MiB/s | 350.4 KiB | 00m00s -------------------------------------------------------------------------------- [170/170] Total 100% | 128.2 MiB/s | 57.8 MiB | 00m00s Running transaction Importing OpenPGP key 0x31645531: UserID : "Fedora (43) " Fingerprint: C6E7F081CF80E13146676E88829B606631645531 From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-43-primary The key was successfully imported. [ 1/172] Verify package files 100% | 798.0 B/s | 170.0 B | 00m00s [ 2/172] Prepare transaction 100% | 2.6 KiB/s | 170.0 B | 00m00s [ 3/172] Installing libgcc-0:15.2.1-5. 100% | 109.3 MiB/s | 223.9 KiB | 00m00s [ 4/172] Installing fedora-release-ide 100% | 867.2 KiB/s | 888.0 B | 00m00s [ 5/172] Installing fedora-gpg-keys-0: 100% | 29.1 MiB/s | 179.0 KiB | 00m00s [ 6/172] Installing fedora-repos-0:43- 100% | 0.0 B/s | 5.7 KiB | 00m00s [ 7/172] Installing fedora-release-com 100% | 24.3 MiB/s | 24.9 KiB | 00m00s [ 8/172] Installing fedora-release-0:4 100% | 15.1 KiB/s | 124.0 B | 00m00s >>> Running sysusers scriptlet: setup-0:2.15.0-26.fc43.noarch >>> Finished sysusers scriptlet: setup-0:2.15.0-26.fc43.noarch >>> Scriptlet output: >>> Creating group 'adm' with GID 4. >>> Creating group 'audio' with GID 63. >>> Creating group 'cdrom' with GID 11. >>> Creating group 'clock' with GID 103. >>> Creating group 'dialout' with GID 18. >>> Creating group 'disk' with GID 6. >>> Creating group 'floppy' with GID 19. >>> Creating group 'ftp' with GID 50. >>> Creating group 'games' with GID 20. >>> Creating group 'input' with GID 104. >>> Creating group 'kmem' with GID 9. >>> Creating group 'kvm' with GID 36. >>> Creating group 'lock' with GID 54. >>> Creating group 'lp' with GID 7. >>> Creating group 'mail' with GID 12. >>> Creating group 'man' with GID 15. >>> Creating group 'mem' with GID 8. >>> Creating group 'nobody' with GID 65534. >>> Creating group 'render' with GID 105. >>> Creating group 'root' with GID 0. >>> Creating group 'sgx' with GID 106. >>> Creating group 'sys' with GID 3. >>> Creating group 'tape' with GID 33. >>> Creating group 'tty' with GID 5. >>> Creating group 'users' with GID 100. >>> Creating group 'utmp' with GID 22. >>> Creating group 'video' with GID 39. >>> Creating group 'wheel' with GID 10. >>> Creating user 'adm' (adm) with UID 3 and GID 4. >>> Creating group 'bin' with GID 1. >>> Creating user 'bin' (bin) with UID 1 and GID 1. >>> Creating group 'daemon' with GID 2. >>> Creating user 'daemon' (daemon) with UID 2 and GID 2. >>> Creating user 'ftp' (FTP User) with UID 14 and GID 50. >>> Creating user 'games' (games) with UID 12 and GID 100. >>> Creating user 'halt' (halt) with UID 7 and GID 0. >>> Creating user 'lp' (lp) with UID 4 and GID 7. >>> Creating user 'mail' (mail) with UID 8 and GID 12. >>> Creating user 'nobody' (Kernel Overflow User) with UID 65534 and GID 65534. >>> Creating user 'operator' (operator) with UID 11 and GID 0. >>> Creating user 'root' (Super User) with UID 0 and GID 0. >>> Creating user 'shutdown' (shutdown) with UID 6 and GID 0. >>> Creating user 'sync' (sync) with UID 5 and GID 0. >>> [ 9/172] Installing setup-0:2.15.0-26. 100% | 35.7 MiB/s | 730.6 KiB | 00m00s >>> [RPM] /etc/hosts created as /etc/hosts.rpmnew [ 10/172] Installing filesystem-0:3.18- 100% | 1.9 MiB/s | 212.8 KiB | 00m00s [ 11/172] Installing publicsuffix-list- 100% | 69.4 MiB/s | 71.1 KiB | 00m00s [ 12/172] Installing libssh-config-0:0. 100% | 0.0 B/s | 816.0 B | 00m00s [ 13/172] Installing pcre2-syntax-0:10. 100% | 138.8 MiB/s | 284.3 KiB | 00m00s [ 14/172] Installing rust-srpm-macros-0 100% | 0.0 B/s | 6.4 KiB | 00m00s [ 15/172] Installing qt6-srpm-macros-0: 100% | 0.0 B/s | 740.0 B | 00m00s [ 16/172] Installing qt5-srpm-macros-0: 100% | 0.0 B/s | 776.0 B | 00m00s [ 17/172] Installing gnat-srpm-macros-0 100% | 0.0 B/s | 1.3 KiB | 00m00s [ 18/172] Installing pkgconf-m4-0:2.3.0 100% | 14.5 MiB/s | 14.8 KiB | 00m00s [ 19/172] Installing gnulib-l10n-0:2024 100% | 129.3 MiB/s | 661.9 KiB | 00m00s [ 20/172] Installing coreutils-common-0 100% | 289.5 MiB/s | 11.3 MiB | 00m00s [ 21/172] Installing ncurses-base-0:6.5 100% | 49.3 MiB/s | 353.5 KiB | 00m00s [ 22/172] Installing bash-0:5.3.0-2.fc4 100% | 200.7 MiB/s | 8.4 MiB | 00m00s [ 23/172] Installing glibc-common-0:2.4 100% | 57.6 MiB/s | 1.3 MiB | 00m00s [ 24/172] Installing glibc-gconv-extra- 100% | 380.9 MiB/s | 18.7 MiB | 00m00s [ 25/172] Installing glibc-0:2.42-9.fc4 100% | 142.7 MiB/s | 6.3 MiB | 00m00s [ 26/172] Installing ncurses-libs-0:6.5 100% | 249.5 MiB/s | 1.2 MiB | 00m00s [ 27/172] Installing glibc-minimal-lang 100% | 0.0 B/s | 124.0 B | 00m00s [ 28/172] Installing zlib-ng-compat-0:2 100% | 131.1 MiB/s | 134.3 KiB | 00m00s [ 29/172] Installing bzip2-libs-0:1.0.8 100% | 72.0 MiB/s | 73.8 KiB | 00m00s [ 30/172] Installing libgpg-error-0:1.5 100% | 45.4 MiB/s | 977.1 KiB | 00m00s [ 31/172] Installing libstdc++-0:15.2.1 100% | 315.1 MiB/s | 2.8 MiB | 00m00s [ 32/172] Installing xz-libs-1:5.8.1-4. 100% | 197.9 MiB/s | 202.7 KiB | 00m00s [ 33/172] Installing libassuan-0:2.5.7- 100% | 212.6 MiB/s | 217.7 KiB | 00m00s [ 34/172] Installing libgcrypt-0:1.11.1 100% | 238.9 MiB/s | 1.2 MiB | 00m00s [ 35/172] Installing readline-0:8.3-2.f 100% | 184.2 MiB/s | 565.9 KiB | 00m00s [ 36/172] Installing gmp-1:6.3.0-4.fc43 100% | 214.9 MiB/s | 660.1 KiB | 00m00s [ 37/172] Installing libuuid-0:2.41.3-7 100% | 68.9 MiB/s | 70.6 KiB | 00m00s [ 38/172] Installing popt-0:1.19-9.fc43 100% | 37.0 MiB/s | 151.4 KiB | 00m00s [ 39/172] Installing npth-0:1.8-3.fc43. 100% | 92.4 MiB/s | 94.6 KiB | 00m00s [ 40/172] Installing libblkid-0:2.41.3- 100% | 142.4 MiB/s | 291.6 KiB | 00m00s [ 41/172] Installing sqlite-libs-0:3.50 100% | 250.2 MiB/s | 1.5 MiB | 00m00s [ 42/172] Installing libzstd-0:1.5.7-2. 100% | 217.8 MiB/s | 669.0 KiB | 00m00s [ 43/172] Installing elfutils-libelf-0: 100% | 286.1 MiB/s | 1.1 MiB | 00m00s [ 44/172] Installing libxcrypt-0:4.5.2- 100% | 134.8 MiB/s | 276.1 KiB | 00m00s [ 45/172] Installing gnupg2-gpgconf-0:2 100% | 18.6 MiB/s | 324.0 KiB | 00m00s [ 46/172] Installing libattr-0:2.5.2-6. 100% | 67.8 MiB/s | 69.4 KiB | 00m00s [ 47/172] Installing libacl-0:2.3.2-4.f 100% | 67.2 MiB/s | 68.8 KiB | 00m00s [ 48/172] Installing libtasn1-0:4.20.0- 100% | 108.5 MiB/s | 222.2 KiB | 00m00s [ 49/172] Installing libunistring-0:1.1 100% | 291.0 MiB/s | 1.7 MiB | 00m00s [ 50/172] Installing libidn2-0:2.3.8-2. 100% | 50.3 MiB/s | 566.7 KiB | 00m00s [ 51/172] Installing crypto-policies-0: 100% | 21.0 MiB/s | 172.2 KiB | 00m00s [ 52/172] Installing dwz-0:0.16-2.fc43. 100% | 16.7 MiB/s | 324.0 KiB | 00m00s [ 53/172] Installing gnupg2-verify-0:2. 100% | 19.8 MiB/s | 365.8 KiB | 00m00s [ 54/172] Installing mpfr-0:4.2.2-2.fc4 100% | 184.9 MiB/s | 757.2 KiB | 00m00s [ 55/172] Installing gawk-0:5.3.2-2.fc4 100% | 99.3 MiB/s | 2.6 MiB | 00m00s [ 56/172] Installing libksba-0:1.6.7-4. 100% | 195.8 MiB/s | 401.0 KiB | 00m00s [ 57/172] Installing unzip-0:6.0-67.fc4 100% | 25.7 MiB/s | 473.7 KiB | 00m00s [ 58/172] Installing file-libs-0:5.46-8 100% | 540.0 MiB/s | 11.9 MiB | 00m00s [ 59/172] Installing file-0:5.46-8.fc43 100% | 8.1 MiB/s | 141.7 KiB | 00m00s [ 60/172] Installing libeconf-0:0.7.9-2 100% | 80.7 MiB/s | 82.6 KiB | 00m00s [ 61/172] Installing libcap-ng-0:0.8.5- 100% | 159.0 MiB/s | 162.8 KiB | 00m00s [ 62/172] Installing audit-libs-0:4.1.2 100% | 239.1 MiB/s | 489.6 KiB | 00m00s [ 63/172] Installing pam-libs-0:1.7.1-4 100% | 110.0 MiB/s | 225.3 KiB | 00m00s [ 64/172] Installing libcap-0:2.76-3.fc 100% | 27.9 MiB/s | 513.9 KiB | 00m00s [ 65/172] Installing systemd-libs-0:258 100% | 300.0 MiB/s | 2.4 MiB | 00m00s [ 66/172] Installing libsmartcols-0:2.4 100% | 220.4 MiB/s | 225.7 KiB | 00m00s [ 67/172] Installing libsepol-0:3.9-2.f 100% | 263.9 MiB/s | 810.8 KiB | 00m00s [ 68/172] Installing lz4-libs-0:1.10.0- 100% | 193.9 MiB/s | 198.5 KiB | 00m00s [ 69/172] Installing json-c-0:0.18-7.fc 100% | 136.7 MiB/s | 139.9 KiB | 00m00s [ 70/172] Installing lua-libs-0:5.4.8-4 100% | 161.8 MiB/s | 331.4 KiB | 00m00s [ 71/172] Installing alternatives-0:1.3 100% | 5.3 MiB/s | 91.8 KiB | 00m00s [ 72/172] Installing libffi-0:3.5.2-1.f 100% | 76.8 MiB/s | 157.3 KiB | 00m00s [ 73/172] Installing p11-kit-0:0.25.8-1 100% | 89.8 MiB/s | 2.5 MiB | 00m00s [ 74/172] Installing p11-kit-trust-0:0. 100% | 20.0 MiB/s | 532.0 KiB | 00m00s [ 75/172] Installing pcre2-0:10.47-1.fc 100% | 233.0 MiB/s | 715.9 KiB | 00m00s [ 76/172] Installing libselinux-0:3.9-5 100% | 98.8 MiB/s | 202.4 KiB | 00m00s [ 77/172] Installing grep-0:3.12-2.fc43 100% | 43.2 MiB/s | 1.0 MiB | 00m00s [ 78/172] Installing findutils-1:4.10.0 100% | 76.8 MiB/s | 1.9 MiB | 00m00s [ 79/172] Installing sed-0:4.9-5.fc43.a 100% | 39.1 MiB/s | 881.4 KiB | 00m00s [ 80/172] Installing xz-1:5.8.1-4.fc43. 100% | 56.5 MiB/s | 1.4 MiB | 00m00s [ 81/172] Installing libmount-0:2.41.3- 100% | 137.1 MiB/s | 421.2 KiB | 00m00s [ 82/172] Installing util-linux-core-0: 100% | 94.9 MiB/s | 2.5 MiB | 00m00s [ 83/172] Installing openssl-libs-1:3.5 100% | 285.5 MiB/s | 7.4 MiB | 00m00s [ 84/172] Installing coreutils-0:9.7-7. 100% | 175.0 MiB/s | 8.2 MiB | 00m00s [ 85/172] Installing ca-certificates-0: 100% | 1.4 MiB/s | 2.5 MiB | 00m02s [ 86/172] Installing gzip-0:1.13-4.fc43 100% | 21.0 MiB/s | 430.2 KiB | 00m00s [ 87/172] Installing libfsverity-0:1.6- 100% | 67.8 MiB/s | 69.4 KiB | 00m00s [ 88/172] Installing libevent-0:2.1.12- 100% | 271.3 MiB/s | 1.1 MiB | 00m00s [ 89/172] Installing rpm-sequoia-0:1.10 100% | 288.4 MiB/s | 2.3 MiB | 00m00s [ 90/172] Installing tar-2:1.35-6.fc43. 100% | 107.3 MiB/s | 3.0 MiB | 00m00s [ 91/172] Installing libsemanage-0:3.9- 100% | 176.7 MiB/s | 361.9 KiB | 00m00s [ 92/172] Installing systemd-standalone 100% | 17.9 MiB/s | 330.1 KiB | 00m00s [ 93/172] Installing rpm-libs-0:6.0.1-1 100% | 243.4 MiB/s | 997.1 KiB | 00m00s [ 94/172] Installing zstd-0:1.5.7-2.fc4 100% | 68.5 MiB/s | 1.5 MiB | 00m00s [ 95/172] Installing libusb1-0:1.0.29-4 100% | 17.6 MiB/s | 180.6 KiB | 00m00s >>> Running sysusers scriptlet: tpm2-tss-0:4.1.3-8.fc43.aarch64 >>> Finished sysusers scriptlet: tpm2-tss-0:4.1.3-8.fc43.aarch64 >>> Scriptlet output: >>> Creating group 'tss' with GID 59. >>> Creating user 'tss' (Account used for TPM access) with UID 59 and GID 59. >>> [ 96/172] Installing tpm2-tss-0:4.1.3-8 100% | 239.9 MiB/s | 2.2 MiB | 00m00s [ 97/172] Installing ima-evm-utils-libs 100% | 91.8 MiB/s | 94.0 KiB | 00m00s [ 98/172] Installing gnupg2-gpg-agent-0 100% | 28.7 MiB/s | 851.2 KiB | 00m00s [ 99/172] Installing zip-0:3.0-44.fc43. 100% | 37.4 MiB/s | 766.4 KiB | 00m00s [100/172] Installing gnupg2-keyboxd-0:2 100% | 32.7 MiB/s | 234.6 KiB | 00m00s [101/172] Installing libpsl-0:0.21.5-6. 100% | 130.5 MiB/s | 133.6 KiB | 00m00s [102/172] Installing liblastlog2-0:2.41 100% | 19.5 MiB/s | 140.0 KiB | 00m00s [103/172] Installing libfdisk-0:2.41.3- 100% | 136.7 MiB/s | 419.9 KiB | 00m00s [104/172] Installing nettle-0:3.10.1-2. 100% | 187.6 MiB/s | 768.4 KiB | 00m00s [105/172] Installing gnutls-0:3.8.11-5. 100% | 279.6 MiB/s | 3.6 MiB | 00m00s [106/172] Installing libxml2-0:2.12.10- 100% | 75.7 MiB/s | 1.9 MiB | 00m00s [107/172] Installing libarchive-0:3.8.4 100% | 238.6 MiB/s | 977.2 KiB | 00m00s [108/172] Installing bzip2-0:1.0.8-21.f 100% | 9.5 MiB/s | 175.8 KiB | 00m00s [109/172] Installing add-determinism-0: 100% | 91.4 MiB/s | 2.1 MiB | 00m00s [110/172] Installing build-reproducibil 100% | 1.0 MiB/s | 1.0 KiB | 00m00s [111/172] Installing cpio-0:2.15-6.fc43 100% | 49.8 MiB/s | 1.1 MiB | 00m00s [112/172] Installing diffutils-0:3.12-3 100% | 67.6 MiB/s | 1.6 MiB | 00m00s [113/172] Installing ed-0:1.22.2-1.fc43 100% | 8.6 MiB/s | 158.3 KiB | 00m00s [114/172] Installing patch-0:2.8-2.fc43 100% | 14.3 MiB/s | 264.1 KiB | 00m00s [115/172] Installing libpkgconf-0:2.3.0 100% | 132.0 MiB/s | 135.1 KiB | 00m00s [116/172] Installing pkgconf-0:2.3.0-3. 100% | 6.2 MiB/s | 114.9 KiB | 00m00s [117/172] Installing pkgconf-pkg-config 100% | 104.3 KiB/s | 1.8 KiB | 00m00s [118/172] Installing gdbm-libs-1:1.23-1 100% | 115.1 MiB/s | 235.6 KiB | 00m00s [119/172] Installing cyrus-sasl-lib-0:2 100% | 96.7 MiB/s | 2.4 MiB | 00m00s [120/172] Installing libgomp-0:15.2.1-5 100% | 253.2 MiB/s | 518.5 KiB | 00m00s [121/172] Installing jansson-0:2.14-3.f 100% | 92.3 MiB/s | 94.5 KiB | 00m00s [122/172] Installing libtool-ltdl-0:2.5 100% | 92.9 MiB/s | 95.1 KiB | 00m00s [123/172] Installing openldap-0:2.6.10- 100% | 186.9 MiB/s | 765.6 KiB | 00m00s [124/172] Installing gnupg2-dirmngr-0:2 100% | 23.5 MiB/s | 649.1 KiB | 00m00s [125/172] Installing gnupg2-0:2.4.9-4.f 100% | 163.5 MiB/s | 6.5 MiB | 00m00s [126/172] Installing rpm-sign-libs-0:6. 100% | 67.0 MiB/s | 68.6 KiB | 00m00s [127/172] Installing gpgverify-0:2.2-3. 100% | 9.2 MiB/s | 9.4 KiB | 00m00s [128/172] Installing xxhash-libs-0:0.8. 100% | 85.3 MiB/s | 87.4 KiB | 00m00s [129/172] Installing libnghttp2-0:1.66. 100% | 194.4 MiB/s | 199.1 KiB | 00m00s [130/172] Installing keyutils-libs-0:1. 100% | 97.4 MiB/s | 99.8 KiB | 00m00s [131/172] Installing libcom_err-0:1.47. 100% | 109.5 MiB/s | 112.2 KiB | 00m00s [132/172] Installing libverto-0:0.3.2-1 100% | 69.5 MiB/s | 71.2 KiB | 00m00s [133/172] Installing krb5-libs-0:1.21.3 100% | 253.2 MiB/s | 2.5 MiB | 00m00s [134/172] Installing libssh-0:0.11.3-1. 100% | 191.7 MiB/s | 589.1 KiB | 00m00s [135/172] Installing libbrotli-0:1.2.0- 100% | 222.6 MiB/s | 911.8 KiB | 00m00s [136/172] Installing libcurl-0:8.15.0-5 100% | 223.7 MiB/s | 916.2 KiB | 00m00s [137/172] Installing curl-0:8.15.0-5.fc 100% | 16.0 MiB/s | 460.1 KiB | 00m00s [138/172] Installing rpm-0:6.0.1-1.fc43 100% | 58.7 MiB/s | 2.8 MiB | 00m00s [139/172] Installing efi-srpm-macros-0: 100% | 40.2 MiB/s | 41.1 KiB | 00m00s [140/172] Installing java-srpm-macros-0 100% | 0.0 B/s | 1.1 KiB | 00m00s [141/172] Installing lua-srpm-macros-0: 100% | 1.9 MiB/s | 1.9 KiB | 00m00s [142/172] Installing tree-sitter-srpm-m 100% | 9.1 MiB/s | 9.3 KiB | 00m00s [143/172] Installing zig-srpm-macros-0: 100% | 0.0 B/s | 1.7 KiB | 00m00s [144/172] Installing filesystem-srpm-ma 100% | 38.0 MiB/s | 38.9 KiB | 00m00s [145/172] Installing elfutils-default-y 100% | 340.5 KiB/s | 2.0 KiB | 00m00s [146/172] Installing elfutils-libs-0:0. 100% | 182.7 MiB/s | 748.5 KiB | 00m00s [147/172] Installing elfutils-debuginfo 100% | 7.1 MiB/s | 146.3 KiB | 00m00s [148/172] Installing elfutils-0:0.194-1 100% | 118.6 MiB/s | 3.2 MiB | 00m00s [149/172] Installing binutils-0:2.45.1- 100% | 276.9 MiB/s | 31.0 MiB | 00m00s [150/172] Installing gdb-minimal-0:17.1 100% | 222.5 MiB/s | 13.4 MiB | 00m00s [151/172] Installing debugedit-0:5.2-3. 100% | 16.5 MiB/s | 321.2 KiB | 00m00s [152/172] Installing rpm-build-libs-0:6 100% | 129.4 MiB/s | 265.0 KiB | 00m00s [153/172] Installing perl-srpm-macros-0 100% | 0.0 B/s | 1.1 KiB | 00m00s [154/172] Installing package-notes-srpm 100% | 0.0 B/s | 2.0 KiB | 00m00s [155/172] Installing openblas-srpm-macr 100% | 0.0 B/s | 392.0 B | 00m00s [156/172] Installing ocaml-srpm-macros- 100% | 0.0 B/s | 2.1 KiB | 00m00s [157/172] Installing kernel-srpm-macros 100% | 0.0 B/s | 2.3 KiB | 00m00s [158/172] Installing ghc-srpm-macros-0: 100% | 0.0 B/s | 1.0 KiB | 00m00s [159/172] Installing gap-srpm-macros-0: 100% | 0.0 B/s | 2.7 KiB | 00m00s [160/172] Installing fpc-srpm-macros-0: 100% | 0.0 B/s | 420.0 B | 00m00s [161/172] Installing ansible-srpm-macro 100% | 35.4 MiB/s | 36.2 KiB | 00m00s [162/172] Installing rpm-build-0:6.0.1- 100% | 29.7 MiB/s | 608.1 KiB | 00m00s [163/172] Installing pyproject-srpm-mac 100% | 2.4 MiB/s | 2.5 KiB | 00m00s [164/172] Installing redhat-rpm-config- 100% | 61.6 MiB/s | 189.1 KiB | 00m00s [165/172] Installing forge-srpm-macros- 100% | 39.3 MiB/s | 40.3 KiB | 00m00s [166/172] Installing fonts-srpm-macros- 100% | 55.7 MiB/s | 57.0 KiB | 00m00s [167/172] Installing go-srpm-macros-0:3 100% | 61.6 MiB/s | 63.0 KiB | 00m00s [168/172] Installing python-srpm-macros 100% | 25.8 MiB/s | 52.8 KiB | 00m00s [169/172] Installing util-linux-0:2.41. 100% | 127.1 MiB/s | 6.9 MiB | 00m00s [170/172] Installing shadow-utils-2:4.1 100% | 102.1 MiB/s | 4.5 MiB | 00m00s [171/172] Installing which-0:2.23-3.fc4 100% | 6.8 MiB/s | 125.6 KiB | 00m00s [172/172] Installing info-0:7.2-6.fc43. 100% | 184.1 KiB/s | 422.0 KiB | 00m02s Complete! Finish: installing minimal buildroot with dnf5 Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: add-determinism-0.6.0-2.fc43.aarch64 alternatives-1.33-3.fc43.aarch64 ansible-srpm-macros-1-18.1.fc43.noarch audit-libs-4.1.2-2.fc43.aarch64 bash-5.3.0-2.fc43.aarch64 binutils-2.45.1-4.fc43.aarch64 build-reproducibility-srpm-macros-0.6.0-2.fc43.noarch bzip2-1.0.8-21.fc43.aarch64 bzip2-libs-1.0.8-21.fc43.aarch64 ca-certificates-2025.2.80_v9.0.304-1.1.fc43.noarch coreutils-9.7-7.fc43.aarch64 coreutils-common-9.7-7.fc43.aarch64 cpio-2.15-6.fc43.aarch64 crypto-policies-20251125-1.git63291f8.fc43.noarch curl-8.15.0-5.fc43.aarch64 cyrus-sasl-lib-2.1.28-33.fc43.aarch64 debugedit-5.2-3.fc43.aarch64 diffutils-3.12-3.fc43.aarch64 dwz-0.16-2.fc43.aarch64 ed-1.22.2-1.fc43.aarch64 efi-srpm-macros-6-4.fc43.noarch elfutils-0.194-1.fc43.aarch64 elfutils-debuginfod-client-0.194-1.fc43.aarch64 elfutils-default-yama-scope-0.194-1.fc43.noarch elfutils-libelf-0.194-1.fc43.aarch64 elfutils-libs-0.194-1.fc43.aarch64 fedora-gpg-keys-43-1.noarch fedora-release-43-25.noarch fedora-release-common-43-25.noarch fedora-release-identity-basic-43-25.noarch fedora-repos-43-1.noarch file-5.46-8.fc43.aarch64 file-libs-5.46-8.fc43.aarch64 filesystem-3.18-50.fc43.aarch64 filesystem-srpm-macros-3.18-50.fc43.noarch findutils-4.10.0-6.fc43.aarch64 fonts-srpm-macros-2.0.5-23.fc43.noarch forge-srpm-macros-0.4.0-3.fc43.noarch fpc-srpm-macros-1.3-15.fc43.noarch gap-srpm-macros-2-1.fc43.noarch gawk-5.3.2-2.fc43.aarch64 gdb-minimal-17.1-1.fc43.aarch64 gdbm-libs-1.23-10.fc43.aarch64 ghc-srpm-macros-1.9.2-3.fc43.noarch glibc-2.42-9.fc43.aarch64 glibc-common-2.42-9.fc43.aarch64 glibc-gconv-extra-2.42-9.fc43.aarch64 glibc-minimal-langpack-2.42-9.fc43.aarch64 gmp-6.3.0-4.fc43.aarch64 gnat-srpm-macros-7-1.fc43.noarch gnulib-l10n-20241231-1.fc43.noarch gnupg2-2.4.9-4.fc43.aarch64 gnupg2-dirmngr-2.4.9-4.fc43.aarch64 gnupg2-gpg-agent-2.4.9-4.fc43.aarch64 gnupg2-gpgconf-2.4.9-4.fc43.aarch64 gnupg2-keyboxd-2.4.9-4.fc43.aarch64 gnupg2-verify-2.4.9-4.fc43.aarch64 gnutls-3.8.11-5.fc43.aarch64 go-srpm-macros-3.8.0-1.fc43.noarch gpg-pubkey-c6e7f081cf80e13146676e88829b606631645531-66b6dccf gpgverify-2.2-3.fc43.noarch grep-3.12-2.fc43.aarch64 gzip-1.13-4.fc43.aarch64 ima-evm-utils-libs-1.6.2-6.fc43.aarch64 info-7.2-6.fc43.aarch64 jansson-2.14-3.fc43.aarch64 java-srpm-macros-1-7.fc43.noarch json-c-0.18-7.fc43.aarch64 kernel-srpm-macros-1.0-27.fc43.noarch keyutils-libs-1.6.3-6.fc43.aarch64 krb5-libs-1.21.3-7.fc43.aarch64 libacl-2.3.2-4.fc43.aarch64 libarchive-3.8.4-1.fc43.aarch64 libassuan-2.5.7-4.fc43.aarch64 libattr-2.5.2-6.fc43.aarch64 libblkid-2.41.3-7.fc43.aarch64 libbrotli-1.2.0-1.fc43.aarch64 libcap-2.76-3.fc43.aarch64 libcap-ng-0.8.5-8.fc43.aarch64 libcom_err-1.47.3-2.fc43.aarch64 libcurl-8.15.0-5.fc43.aarch64 libeconf-0.7.9-2.fc43.aarch64 libevent-2.1.12-16.fc43.aarch64 libfdisk-2.41.3-7.fc43.aarch64 libffi-3.5.2-1.fc43.aarch64 libfsverity-1.6-3.fc43.aarch64 libgcc-15.2.1-5.fc43.aarch64 libgcrypt-1.11.1-3.fc43.aarch64 libgomp-15.2.1-5.fc43.aarch64 libgpg-error-1.55-2.fc43.aarch64 libidn2-2.3.8-2.fc43.aarch64 libksba-1.6.7-4.fc43.aarch64 liblastlog2-2.41.3-7.fc43.aarch64 libmount-2.41.3-7.fc43.aarch64 libnghttp2-1.66.0-2.fc43.aarch64 libpkgconf-2.3.0-3.fc43.aarch64 libpsl-0.21.5-6.fc43.aarch64 libselinux-3.9-5.fc43.aarch64 libsemanage-3.9-4.fc43.aarch64 libsepol-3.9-2.fc43.aarch64 libsmartcols-2.41.3-7.fc43.aarch64 libssh-0.11.3-1.fc43.aarch64 libssh-config-0.11.3-1.fc43.noarch libstdc++-15.2.1-5.fc43.aarch64 libtasn1-4.20.0-2.fc43.aarch64 libtool-ltdl-2.5.4-8.fc43.aarch64 libunistring-1.1-10.fc43.aarch64 libusb1-1.0.29-4.fc43.aarch64 libuuid-2.41.3-7.fc43.aarch64 libverto-0.3.2-11.fc43.aarch64 libxcrypt-4.5.2-1.fc43.aarch64 libxml2-2.12.10-5.fc43.aarch64 libzstd-1.5.7-2.fc43.aarch64 lua-libs-5.4.8-4.fc43.aarch64 lua-srpm-macros-1-16.fc43.noarch lz4-libs-1.10.0-3.fc43.aarch64 mpfr-4.2.2-2.fc43.aarch64 ncurses-base-6.5-7.20250614.fc43.noarch ncurses-libs-6.5-7.20250614.fc43.aarch64 nettle-3.10.1-2.fc43.aarch64 npth-1.8-3.fc43.aarch64 ocaml-srpm-macros-11-2.fc43.noarch openblas-srpm-macros-2-20.fc43.noarch openldap-2.6.10-4.fc43.aarch64 openssl-libs-3.5.4-1.fc43.aarch64 p11-kit-0.25.8-1.fc43.aarch64 p11-kit-trust-0.25.8-1.fc43.aarch64 package-notes-srpm-macros-0.5-14.fc43.noarch pam-libs-1.7.1-4.fc43.aarch64 patch-2.8-2.fc43.aarch64 pcre2-10.47-1.fc43.aarch64 pcre2-syntax-10.47-1.fc43.noarch perl-srpm-macros-1-60.fc43.noarch pkgconf-2.3.0-3.fc43.aarch64 pkgconf-m4-2.3.0-3.fc43.noarch pkgconf-pkg-config-2.3.0-3.fc43.aarch64 popt-1.19-9.fc43.aarch64 publicsuffix-list-dafsa-20260116-1.fc43.noarch pyproject-srpm-macros-1.18.6-1.fc43.noarch python-srpm-macros-3.14-5.fc43.noarch qt5-srpm-macros-5.15.18-1.fc43.noarch qt6-srpm-macros-6.10.1-1.fc43.noarch readline-8.3-2.fc43.aarch64 redhat-rpm-config-343-11.fc43.noarch rpm-6.0.1-1.fc43.aarch64 rpm-build-6.0.1-1.fc43.aarch64 rpm-build-libs-6.0.1-1.fc43.aarch64 rpm-libs-6.0.1-1.fc43.aarch64 rpm-sequoia-1.10.0-1.fc43.aarch64 rpm-sign-libs-6.0.1-1.fc43.aarch64 rust-srpm-macros-28.4-1.fc43.noarch sed-4.9-5.fc43.aarch64 setup-2.15.0-26.fc43.noarch shadow-utils-4.18.0-3.fc43.aarch64 sqlite-libs-3.50.2-2.fc43.aarch64 systemd-libs-258.3-2.fc43.aarch64 systemd-standalone-sysusers-258.3-2.fc43.aarch64 tar-1.35-6.fc43.aarch64 tpm2-tss-4.1.3-8.fc43.aarch64 tree-sitter-srpm-macros-0.4.2-1.fc43.noarch unzip-6.0-67.fc43.aarch64 util-linux-2.41.3-7.fc43.aarch64 util-linux-core-2.41.3-7.fc43.aarch64 which-2.23-3.fc43.aarch64 xxhash-libs-0.8.3-3.fc43.aarch64 xz-5.8.1-4.fc43.aarch64 xz-libs-5.8.1-4.fc43.aarch64 zig-srpm-macros-1-5.fc43.noarch zip-3.0-44.fc43.aarch64 zlib-ng-compat-2.3.2-2.fc43.aarch64 zstd-1.5.7-2.fc43.aarch64 Start: buildsrpm Start: rpmbuild -bs Building target platforms: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1769040000 Wrote: /builddir/build/SRPMS/htslib-1.23-1.fc43.src.rpm Finish: rpmbuild -bs INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-43-aarch64-1769500621.615308/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-u7a_kz2q/htslib/htslib.spec) Config(child) 0 minutes 23 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot INFO: Start(/var/lib/copr-rpmbuild/results/htslib-1.23-1.fc43.src.rpm) Config(fedora-43-aarch64) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-43-aarch64-bootstrap-1769500621.615308/root. INFO: reusing tmpfs at /var/lib/mock/fedora-43-aarch64-bootstrap-1769500621.615308/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-43-aarch64-1769500621.615308/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-6.0.1-1.fc43.aarch64 rpm-sequoia-1.10.0-1.fc43.aarch64 dnf5-5.2.17.0-2.fc43.aarch64 dnf5-plugins-5.2.17.0-2.fc43.aarch64 Finish: chroot init Start: build phase for htslib-1.23-1.fc43.src.rpm Start: build setup for htslib-1.23-1.fc43.src.rpm Building target platforms: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1769040000 Wrote: /builddir/build/SRPMS/htslib-1.23-1.fc43.src.rpm Updating and loading repositories: Copr repository 100% | 6.8 KiB/s | 1.5 KiB | 00m00s fedora 100% | 41.2 KiB/s | 13.7 KiB | 00m00s updates 100% | 49.4 KiB/s | 13.6 KiB | 00m00s Repositories loaded. Package Arch Version Repository Size Installing: bzip2-devel aarch64 1.0.8-21.fc43 fedora 309.8 KiB gcc aarch64 15.2.1-5.fc43 updates 99.6 MiB libcurl-devel aarch64 8.15.0-5.fc43 updates 1.3 MiB make aarch64 1:4.4.1-11.fc43 fedora 1.8 MiB openssl-devel aarch64 1:3.5.4-1.fc43 updates 4.6 MiB perl-Data-Dumper aarch64 2.191-521.fc43 fedora 135.7 KiB perl-FindBin noarch 1.54-520.fc43 fedora 6.8 KiB perl-Getopt-Long noarch 1:2.58-520.fc43 fedora 144.5 KiB perl-interpreter aarch64 4:5.42.0-520.fc43 fedora 174.6 KiB perl-lib aarch64 0.65-520.fc43 fedora 8.5 KiB xz-devel aarch64 1:5.8.1-4.fc43 updates 258.8 KiB zlib-ng-compat-devel aarch64 2.3.2-2.fc43 updates 107.0 KiB Installing dependencies: annobin-docs noarch 12.99-1.fc43 fedora 98.9 KiB annobin-plugin-gcc aarch64 12.99-1.fc43 fedora 1.0 MiB brotli aarch64 1.2.0-1.fc43 updates 69.6 KiB brotli-devel aarch64 1.2.0-1.fc43 updates 65.9 KiB cmake-filesystem aarch64 3.31.10-3.fc43 updates 0.0 B cpp aarch64 15.2.1-5.fc43 updates 35.5 MiB gcc-plugin-annobin aarch64 15.2.1-5.fc43 updates 69.2 KiB glibc-devel aarch64 2.42-9.fc43 updates 2.2 MiB groff-base aarch64 1.23.0-11.fc43 updates 4.2 MiB kernel-headers aarch64 6.18.3-200.fc43 updates 6.7 MiB keyutils-libs-devel aarch64 1.6.3-6.fc43 fedora 48.2 KiB krb5-devel aarch64 1.21.3-7.fc43 fedora 705.9 KiB libasan aarch64 15.2.1-5.fc43 updates 1.5 MiB libatomic aarch64 15.2.1-5.fc43 updates 68.8 KiB libcom_err-devel aarch64 1.47.3-2.fc43 fedora 16.7 KiB libidn2-devel aarch64 2.3.8-2.fc43 fedora 149.1 KiB libkadm5 aarch64 1.21.3-7.fc43 fedora 266.2 KiB libmpc aarch64 1.3.1-8.fc43 fedora 152.7 KiB libnghttp2-devel aarch64 1.66.0-2.fc43 fedora 286.3 KiB libpsl-devel aarch64 0.21.5-6.fc43 fedora 110.2 KiB libselinux-devel aarch64 3.9-5.fc43 fedora 127.3 KiB libsepol-devel aarch64 3.9-2.fc43 fedora 121.4 KiB libssh-devel aarch64 0.11.3-1.fc43 fedora 178.0 KiB libubsan aarch64 15.2.1-5.fc43 updates 475.6 KiB libverto-devel aarch64 0.3.2-11.fc43 fedora 25.7 KiB libxcrypt-devel aarch64 4.5.2-1.fc43 updates 31.1 KiB ncurses aarch64 6.5-7.20250614.fc43 fedora 893.6 KiB pcre2-devel aarch64 10.47-1.fc43 updates 2.1 MiB pcre2-utf16 aarch64 10.47-1.fc43 updates 583.0 KiB pcre2-utf32 aarch64 10.47-1.fc43 updates 582.9 KiB perl-AutoLoader noarch 5.74-520.fc43 fedora 20.6 KiB perl-B aarch64 1.89-520.fc43 fedora 545.4 KiB perl-Carp noarch 1.54-520.fc43 fedora 46.6 KiB perl-Class-Struct noarch 0.68-520.fc43 fedora 25.4 KiB perl-Digest noarch 1.20-520.fc43 fedora 35.3 KiB perl-Digest-MD5 aarch64 2.59-520.fc43 fedora 103.7 KiB perl-DynaLoader aarch64 1.57-520.fc43 fedora 32.1 KiB perl-Encode aarch64 4:3.21-520.fc43 fedora 4.8 MiB perl-Errno aarch64 1.38-520.fc43 fedora 8.4 KiB perl-Exporter noarch 5.79-520.fc43 fedora 54.3 KiB perl-Fcntl aarch64 1.20-520.fc43 fedora 92.8 KiB perl-File-Basename noarch 2.86-520.fc43 fedora 14.0 KiB perl-File-Path noarch 2.18-520.fc43 fedora 63.5 KiB perl-File-Temp noarch 1:0.231.100-520.fc43 fedora 162.3 KiB perl-File-stat noarch 1.14-520.fc43 fedora 12.5 KiB perl-FileHandle noarch 2.05-520.fc43 fedora 9.4 KiB perl-Getopt-Std noarch 1.14-520.fc43 fedora 11.2 KiB perl-HTTP-Tiny noarch 0.090-521.fc43 fedora 154.4 KiB perl-IO aarch64 1.55-520.fc43 fedora 191.4 KiB perl-IO-Socket-IP noarch 0.43-521.fc43 fedora 100.3 KiB perl-IO-Socket-SSL noarch 2.095-2.fc43 fedora 714.5 KiB perl-IPC-Open3 noarch 1.24-520.fc43 fedora 27.7 KiB perl-MIME-Base32 noarch 1.303-24.fc43 fedora 30.7 KiB perl-MIME-Base64 aarch64 3.16-520.fc43 fedora 94.1 KiB perl-Net-SSLeay aarch64 1.94-11.fc43 fedora 1.4 MiB perl-POSIX aarch64 2.23-520.fc43 fedora 263.5 KiB perl-PathTools aarch64 3.94-520.fc43 fedora 224.0 KiB perl-Pod-Escapes noarch 1:1.07-520.fc43 fedora 24.9 KiB perl-Pod-Perldoc noarch 3.28.01-521.fc43 fedora 163.7 KiB perl-Pod-Simple noarch 1:3.47-3.fc43 fedora 565.3 KiB perl-Pod-Usage noarch 4:2.05-520.fc43 fedora 86.3 KiB perl-Scalar-List-Utils aarch64 5:1.70-1.fc43 fedora 152.9 KiB perl-SelectSaver noarch 1.02-520.fc43 fedora 2.2 KiB perl-Socket aarch64 4:2.040-2.fc43 fedora 144.3 KiB perl-Storable aarch64 1:3.37-521.fc43 fedora 243.2 KiB perl-Symbol noarch 1.09-520.fc43 fedora 6.8 KiB perl-Term-ANSIColor noarch 5.01-521.fc43 fedora 97.5 KiB perl-Term-Cap noarch 1.18-520.fc43 fedora 29.3 KiB perl-Text-ParseWords noarch 3.31-520.fc43 fedora 13.6 KiB perl-Text-Tabs+Wrap noarch 2024.001-520.fc43 fedora 22.6 KiB perl-Time-Local noarch 2:1.350-520.fc43 fedora 69.0 KiB perl-URI noarch 5.34-2.fc43 updates 268.0 KiB perl-base noarch 2.27-520.fc43 fedora 12.6 KiB perl-constant noarch 1.33-521.fc43 fedora 26.2 KiB perl-if noarch 0.61.000-520.fc43 fedora 5.8 KiB perl-libnet noarch 3.15-521.fc43 fedora 289.4 KiB perl-libs aarch64 4:5.42.0-520.fc43 fedora 11.6 MiB perl-locale noarch 1.13-520.fc43 fedora 6.1 KiB perl-mro aarch64 1.29-520.fc43 fedora 81.6 KiB perl-overload noarch 1.40-520.fc43 fedora 71.6 KiB perl-overloading noarch 0.02-520.fc43 fedora 4.9 KiB perl-parent noarch 1:0.244-520.fc43 fedora 10.3 KiB perl-podlators noarch 1:6.0.2-520.fc43 fedora 317.5 KiB perl-vars noarch 1.05-520.fc43 fedora 3.9 KiB publicsuffix-list noarch 20260116-1.fc43 updates 342.2 KiB Transaction Summary: Installing: 97 packages Total size of inbound packages is 67 MiB. Need to download 67 MiB. After this operation, 190 MiB extra will be used (install 190 MiB, remove 0 B). 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Building target platforms: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1769040000 Wrote: /builddir/build/SRPMS/htslib-1.23-1.fc43.src.rpm Updating and loading repositories: Copr repository 100% | 100.6 KiB/s | 1.5 KiB | 00m00s fedora 100% | 63.3 KiB/s | 13.7 KiB | 00m00s updates 100% | 184.1 KiB/s | 13.6 KiB | 00m00s Repositories loaded. Package "bzip2-devel-1.0.8-21.fc43.aarch64" is already installed. Package "gcc-15.2.1-5.fc43.aarch64" is already installed. Package "libcurl-devel-8.15.0-5.fc43.aarch64" is already installed. Package "make-1:4.4.1-11.fc43.aarch64" is already installed. Package "openssl-devel-1:3.5.4-1.fc43.aarch64" is already installed. Package "perl-Data-Dumper-2.191-521.fc43.aarch64" is already installed. Package "perl-FindBin-1.54-520.fc43.noarch" is already installed. Package "perl-Getopt-Long-1:2.58-520.fc43.noarch" is already installed. Package "perl-lib-0.65-520.fc43.aarch64" is already installed. Package "perl-interpreter-4:5.42.0-520.fc43.aarch64" is already installed. Package "xz-devel-1:5.8.1-4.fc43.aarch64" is already installed. Package "zlib-ng-compat-devel-2.3.2-2.fc43.aarch64" is already installed. Nothing to do. Finish: build setup for htslib-1.23-1.fc43.src.rpm Start: rpmbuild htslib-1.23-1.fc43.src.rpm Building target platforms: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1769040000 Executing(%mkbuilddir): /bin/sh -e /var/tmp/rpm-tmp.3DWgrQ Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.E8vl62 + umask 022 + cd /builddir/build/BUILD/htslib-1.23-build + cd /builddir/build/BUILD/htslib-1.23-build + rm -rf htslib-1.23 + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/htslib-1.23.tar.bz2 + STATUS=0 + '[' 0 -ne 0 ']' + cd htslib-1.23 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.WQrEQg + umask 022 + cd /builddir/build/BUILD/htslib-1.23-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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-hardened-ld-errors -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-1.23 + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-hardened-ld-errors -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 + mv ./configure.backup ./configure + /usr/bin/sed --in-place=.backup '1{$!N;$!N};$!N;s/int x = 1;\nint y = 0;\nint z;\nint nan;/volatile int x = 1; volatile int y = 0; volatile int z, nan;/;P;D' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed -r --in-place=.backup '/lt_cv_sys_global_symbol_to_cdecl=/s#(".*"|'\''.*'\'')#"sed -n -e '\''s/^T .* \\(.*\\)$/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 + for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub) ++ basename ./config.guess + '[' -f /usr/lib/rpm/redhat/config.guess ']' + /usr/bin/rm -f ./config.guess ++ basename ./config.guess + /usr/bin/cp -fv /usr/lib/rpm/redhat/config.guess ./config.guess '/usr/lib/rpm/redhat/config.guess' -> './config.guess' + for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub) ++ basename ./config.sub + '[' -f /usr/lib/rpm/redhat/config.sub ']' + /usr/bin/rm -f ./config.sub ++ basename ./config.sub + /usr/bin/cp -fv /usr/lib/rpm/redhat/config.sub ./config.sub '/usr/lib/rpm/redhat/config.sub' -> './config.sub' + '[' 1 = 1 ']' + '[' x '!=' 'x-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors' ']' ++ find . -name ltmain.sh ++ grep -q runstatedir=DIR ./configure ++ echo --runstatedir=/run + ./configure --build=aarch64-redhat-linux --host=aarch64-redhat-linux --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/bin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/libexec --localstatedir=/var --runstatedir=/run --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info 'CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer' 'LDFLAGS=-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' --prefix=/usr --libdir=/usr/lib64 --enable-plugins '--with-plugin-path=/usr/local/libexec/htslib:$(plugindir)' --enable-gcs --enable-libcurl --enable-s3 configure: WARNING: unrecognized options: --disable-dependency-tracking checking for aarch64-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 the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking for aarch64-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 gcc options needed to detect all undeclared functions... none needed checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for sys/param.h... yes checking whether _XOPEN_SOURCE is declared... no checking whether __get_cpuid_max is declared... no checking whether __cpuid_count is declared... no checking for x86intrin.h... no checking for aarch64-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 gcc option to enable large file support... none needed checking shared library type for aarch64-redhat-linux... plain .so checking whether the linker supports versioned symbols... yes checking whether the compiler accepts -fvisibility=hidden... yes checking build system type... aarch64-redhat-linux-gnu checking host system type... aarch64-redhat-linux-gnu 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 for getauxval... yes checking for elf_aux_info... no checking for posix_memalign... yes checking whether fdatasync is declared... yes checking for fdatasync... yes checking for __attribute__((constructor))... yes checking for clock_gettime with CLOCK_PROCESS_CPUTIME_ID... 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 fstatat... yes checking for CMSG_LEN... yes checking for epoll... yes (edge triggered) checking for sendfile... yes, Linux-style checking whether EHOSTDOWN is declared... yes checking whether ENONET is declared... yes checking whether AI_V4MAPPED is declared... yes checking whether AI_ADDRCONFIG is declared... yes checking whether the compiler accepts -Wextra... yes checking whether the compiler accepts -Wformat... yes checking whether the compiler accepts -Wformat=2... yes checking whether the compiler accepts -Wconversion... yes checking whether the compiler accepts -Wtrampolines... yes checking whether the compiler accepts -Wstrict-aliasing... yes checking whether the compiler accepts -fstack-clash-protection... yes checking whether the compiler accepts -fstack-protector-strong... yes checking whether the compiler accepts -fcf-protection=full... no checking whether the compiler accepts -mbranch-protection=standard... yes checking whether the compiler accepts -fno-delete-null-pointer-checks... yes checking whether the compiler accepts -Wl,-z,noexecstack... yes checking whether the compiler accepts -Wl,-z,relro... yes checking whether the compiler accepts -Wl,-z,now... yes checking whether the compiler accepts -Wl,--as-needed... yes checking whether the compiler accepts -Wl,--no-copy-dt-needed-entries... yes checking whether the compiler accepts -Wl,-z,nodlopen... yes checking for library containing regcomp... none required 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o faidx.o faidx.c echo '#define HTS_VERSION_TEXT "1.23"' > version.h printf '#define HTS_CC "%s"\n#define HTS_CPPFLAGS "%s"\n#define HTS_CFLAGS "%s"\n#define HTS_LDFLAGS "%s"\n#define HTS_LIBS "%s"\n' \ '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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden' \ '-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-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic' \ '-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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o sam_mods.o sam_mods.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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o simd.o simd.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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx2.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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_avx512.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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_sse4.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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static32x16pr.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o htscodecs/htscodecs/utils.o htscodecs/htscodecs/utils.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr_neon.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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o sam_mods.pico sam_mods.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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o simd.pico simd.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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.pico htscodecs/htscodecs/rANS_static32x16pr_avx2.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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.pico htscodecs/htscodecs/rANS_static32x16pr_avx512.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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.pico htscodecs/htscodecs/rANS_static32x16pr_sse4.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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr.pico htscodecs/htscodecs/rANS_static32x16pr.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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/utils.pico htscodecs/htscodecs/utils.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr_neon.pico htscodecs/htscodecs/rANS_static32x16pr_neon.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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o annot-tsv.o annot-tsv.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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o hfile_libcurl.pico hfile_libcurl.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test_faidx.o test/test_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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test_khash.o test/test_khash.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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test_nibbles.o test/test_nibbles.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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/sam.o test/sam.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test_time_funcs.o test/test_time_funcs.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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test_introspection.o test/test_introspection.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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -mbranch-protection=standard -fno-delete-null-pointer-checks -I. -c -o ref_cache/cmsg_wrap.o ref_cache/cmsg_wrap.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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -mbranch-protection=standard -fno-delete-null-pointer-checks -I. -c -o ref_cache/listener.o ref_cache/listener.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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -mbranch-protection=standard -fno-delete-null-pointer-checks -I. -c -o ref_cache/http_parser.o ref_cache/http_parser.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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -mbranch-protection=standard -fno-delete-null-pointer-checks -I. -c -o ref_cache/log_files.o ref_cache/log_files.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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -mbranch-protection=standard -fno-delete-null-pointer-checks -I. -c -o ref_cache/misc.o ref_cache/misc.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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -mbranch-protection=standard -fno-delete-null-pointer-checks -I. -c -o ref_cache/ping.o ref_cache/ping.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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -mbranch-protection=standard -fno-delete-null-pointer-checks -I. -c -o ref_cache/poll_wrap_epoll.o ref_cache/poll_wrap_epoll.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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -mbranch-protection=standard -fno-delete-null-pointer-checks -I. -c -o ref_cache/poll_wrap_poll.o ref_cache/poll_wrap_poll.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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -mbranch-protection=standard -fno-delete-null-pointer-checks -I. -c -o ref_cache/request_handler.o ref_cache/request_handler.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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -mbranch-protection=standard -fno-delete-null-pointer-checks -I. -c -o ref_cache/ref_files.o ref_cache/ref_files.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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -mbranch-protection=standard -fno-delete-null-pointer-checks -I. -c -o ref_cache/sendfile_wrap.o ref_cache/sendfile_wrap.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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -mbranch-protection=standard -fno-delete-null-pointer-checks -I. -c -o ref_cache/main.o ref_cache/main.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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -mbranch-protection=standard -fno-delete-null-pointer-checks -I. -c -o ref_cache/transaction.o ref_cache/transaction.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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -mbranch-protection=standard -fno-delete-null-pointer-checks -I. -c -o ref_cache/server.o ref_cache/server.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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -mbranch-protection=standard -fno-delete-null-pointer-checks -I. -c -o ref_cache/upstream.o ref_cache/upstream.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-hardened-ld-errors -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o hts.o hts.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-hardened-ld-errors -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-hardened-ld-errors -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_time_funcs test/test_time_funcs.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test-bcf_set_variant_type.o test/test-bcf_set_variant_type.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 sam_mods.o simd.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o plugin.o ranlib libhts.a 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-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -Wl,-z,noexecstack -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-copy-dt-needed-entries -Wl,-z,nodlopen -o ref_cache/ref-cache ref_cache/cmsg_wrap.o ref_cache/http_parser.o ref_cache/listener.o ref_cache/log_files.o ref_cache/main.o ref_cache/misc.o ref_cache/ping.o ref_cache/poll_wrap_epoll.o ref_cache/poll_wrap_poll.o ref_cache/ref_files.o ref_cache/request_handler.o ref_cache/sendfile_wrap.o ref_cache/server.o ref_cache/transaction.o ref_cache/upstream.o cram/pooled_alloc.o md5.o -lcurl gcc -shared -Wl,-soname,libhts.so.3 -Wl,-version-script,htslib.map -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-hardened-ld-errors -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 sam_mods.pico simd.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_static32x16pr_avx2.pico htscodecs/htscodecs/rANS_static32x16pr_avx512.pico htscodecs/htscodecs/rANS_static32x16pr_sse4.pico htscodecs/htscodecs/rANS_static32x16pr_neon.pico htscodecs/htscodecs/rANS_static32x16pr.pico htscodecs/htscodecs/rANS_static.pico htscodecs/htscodecs/rle.pico htscodecs/htscodecs/tokenise_name3.pico htscodecs/htscodecs/utils.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-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o annot-tsv annot-tsv.o libhts.a -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-hardened-ld-errors -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 -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-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -fvisibility=hidden -rdynamic -o bgzip bgzip.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -shared -Wl,-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-hardened-ld-errors -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 -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-hardened-ld-errors -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 -lcurl -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-hardened-ld-errors -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-hardened-ld-errors -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-hardened-ld-errors -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-hardened-ld-errors -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-hardened-ld-errors -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-hardened-ld-errors -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-hardened-ld-errors -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-hardened-ld-errors -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 -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-hardened-ld-errors -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_khash test/test_khash.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-hardened-ld-errors -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 -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-hardened-ld-errors -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 -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-hardened-ld-errors -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 -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-hardened-ld-errors -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_faidx test/test_faidx.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-hardened-ld-errors -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-hardened-ld-errors -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_nibbles test/test_nibbles.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-hardened-ld-errors -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-hardened-ld-errors -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-hardened-ld-errors -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-hardened-ld-errors -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-hardened-ld-errors -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-hardened-ld-errors -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-hardened-ld-errors -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-hardened-ld-errors -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 -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-hardened-ld-errors -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 -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-hardened-ld-errors -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-hardened-ld-errors -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 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-hardened-ld-errors -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_set_variant_type test/test-bcf_set_variant_type.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.tzNNXH + umask 022 + cd /builddir/build/BUILD/htslib-1.23-build + '[' /builddir/build/BUILD/htslib-1.23-build/BUILDROOT '!=' / ']' + rm -rf /builddir/build/BUILD/htslib-1.23-build/BUILDROOT ++ dirname /builddir/build/BUILD/htslib-1.23-build/BUILDROOT + mkdir -p /builddir/build/BUILD/htslib-1.23-build + mkdir /builddir/build/BUILD/htslib-1.23-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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-hardened-ld-errors -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-1.23 + /usr/bin/make install DESTDIR=/builddir/build/BUILD/htslib-1.23-build/BUILDROOT 'INSTALL=/usr/bin/install -p' mkdir -p -m 755 /builddir/build/BUILD/htslib-1.23-build/BUILDROOT/usr/bin /builddir/build/BUILD/htslib-1.23-build/BUILDROOT/usr/include /builddir/build/BUILD/htslib-1.23-build/BUILDROOT/usr/include/htslib /builddir/build/BUILD/htslib-1.23-build/BUILDROOT/usr/lib64 /builddir/build/BUILD/htslib-1.23-build/BUILDROOT/usr/share/man/man1 /builddir/build/BUILD/htslib-1.23-build/BUILDROOT/usr/share/man/man5 /builddir/build/BUILD/htslib-1.23-build/BUILDROOT/usr/share/man/man7 /builddir/build/BUILD/htslib-1.23-build/BUILDROOT/usr/lib64/pkgconfig if test -n "/usr/libexec/htslib"; then mkdir -p -m 755 /builddir/build/BUILD/htslib-1.23-build/BUILDROOT/usr/libexec/htslib; fi /usr/bin/install -p -m 644 libhts.so /builddir/build/BUILD/htslib-1.23-build/BUILDROOT/usr/lib64/libhts.so.1.23 ln -sf libhts.so.1.23 /builddir/build/BUILD/htslib-1.23-build/BUILDROOT/usr/lib64/libhts.so ln -sf libhts.so.1.23 /builddir/build/BUILD/htslib-1.23-build/BUILDROOT/usr/lib64/libhts.so.3 sed -e 's#@-includedir@#/usr/include#g;s#@-libdir@#/usr/lib64#g;s#@-PACKAGE_VERSION@#1.23#g' htslib.pc.tmp > /builddir/build/BUILD/htslib-1.23-build/BUILDROOT/usr/lib64/pkgconfig/htslib.pc chmod 644 /builddir/build/BUILD/htslib-1.23-build/BUILDROOT/usr/lib64/pkgconfig/htslib.pc /usr/bin/install -p annot-tsv bgzip htsfile tabix ref_cache/ref-cache /builddir/build/BUILD/htslib-1.23-build/BUILDROOT/usr/bin if test -n "hfile_libcurl.so hfile_gcs.so hfile_s3.so"; then /usr/bin/install -p hfile_libcurl.so hfile_gcs.so hfile_s3.so /builddir/build/BUILD/htslib-1.23-build/BUILDROOT/usr/libexec/htslib; fi /usr/bin/install -p -m 644 htslib/*.h /builddir/build/BUILD/htslib-1.23-build/BUILDROOT/usr/include/htslib /usr/bin/install -p -m 644 libhts.a /builddir/build/BUILD/htslib-1.23-build/BUILDROOT/usr/lib64/libhts.a /usr/bin/install -p -m 644 annot-tsv.1 bgzip.1 htsfile.1 tabix.1 /builddir/build/BUILD/htslib-1.23-build/BUILDROOT/usr/share/man/man1 if test "xref_cache/ref-cache" != "x" ; then \ /usr/bin/install -p -m 644 ref_cache/ref-cache.1 /builddir/build/BUILD/htslib-1.23-build/BUILDROOT/usr/share/man/man1 ; \ fi /usr/bin/install -p -m 644 faidx.5 sam.5 vcf.5 /builddir/build/BUILD/htslib-1.23-build/BUILDROOT/usr/share/man/man5 /usr/bin/install -p -m 644 htslib-s3-plugin.7 /builddir/build/BUILD/htslib-1.23-build/BUILDROOT/usr/share/man/man7 + pushd /builddir/build/BUILD/htslib-1.23-build/BUILDROOT//usr/lib64 ~/build/BUILD/htslib-1.23-build/BUILDROOT/usr/lib64 ~/build/BUILD/htslib-1.23-build/htslib-1.23 + chmod 755 libhts.so.1.23 + popd ~/build/BUILD/htslib-1.23-build/htslib-1.23 + find /builddir/build/BUILD/htslib-1.23-build/BUILDROOT -name '*.la' -delete + rm -f /builddir/build/BUILD/htslib-1.23-build/BUILDROOT//usr/lib64/libhts.a + /usr/bin/find-debuginfo -j4 --strict-build-id -m -i --build-id-seed 1.23-1.fc43 --unique-debug-suffix -1.23-1.fc43.aarch64 --unique-debug-src-base htslib-1.23-1.fc43.aarch64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/htslib-1.23-build/htslib-1.23 find-debuginfo: starting Extracting debug info from 9 files DWARF-compressing 9 files sepdebugcrcfix: Updated 9 CRC32s, 0 CRC32s did match. Creating .debug symlinks for symlinks to ELF files Copying sources found by 'debugedit -l' to /usr/src/debug/htslib-1.23-1.fc43.aarch64 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/check-rpaths + /usr/lib/rpm/redhat/brp-mangle-shebangs + /usr/lib/rpm/brp-remove-la-files + /usr/lib/rpm/redhat/brp-python-rpm-in-distinfo + 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-1.23-build/BUILDROOT Scanned 30 directories and 208 files, processed 9 inodes, 0 modified (0 replaced + 0 rewritten), 0 unsupported format, 0 errors Reading /builddir/build/BUILD/htslib-1.23-build/SPECPARTS/rpm-debuginfo.specpart Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.XfRBXR + umask 022 + cd /builddir/build/BUILD/htslib-1.23-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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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-hardened-ld-errors -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-1.23 + make test 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -Ihtscodecs -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-hardened-ld-errors -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_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -Ihtscodecs -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-hardened-ld-errors -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_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.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 -o4 on ./dat/q4 11746 11746 11746 11746 Testing rans4x16 -r -o5 on ./dat/q4 10932 10932 10932 10932 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 -o4 on ./dat/q40+dir 50331 50331 50331 50331 Testing rans4x16 -r -o5 on ./dat/q40+dir 49537 49537 49537 49537 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 -o4 on ./dat/q8 33176 33176 33176 33176 Testing rans4x16 -r -o5 on ./dat/q8 31458 31458 31458 31458 Testing rans4x16 -r -o69 on ./dat/qsimd 35 Testing rans4x16 -r -o4 on ./dat/qsimd 219 219 219 219 Testing rans4x16 -r -o5 on ./dat/qsimd 151 151 151 151 Testing rans4x16 -r -o0 on ./dat/qvar 32987 Testing rans4x16 -r -o1 on ./dat/qvar 32261 Testing rans4x16 -r -o4 on ./dat/qvar 33073 33073 33073 33073 Testing rans4x16 -r -o5 on ./dat/qvar 32353 32353 32353 32353 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -Ihtscodecs -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-hardened-ld-errors -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_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.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 Testing arith_dynamic -r -o1 on ./dat/u32 27005 Testing arith_dynamic -r -o65 on ./dat/u32 23864 Testing arith_dynamic -r -o9 on ./dat/u32 24811 Testing arith_dynamic -r -o4 on ./dat/u32 20849 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -Ihtscodecs -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-hardened-ld-errors -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_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o -llzma -lbz2 -lz -lm -lm -lpthread cd htscodecs/tests && srcdir=. && export srcdir && ./tok3.test Testing tokenise_name3 -r -1 on ./names/01.names 2708 Testing tokenise_name3 -r -3 on ./names/01.names 2429 Testing tokenise_name3 -r -5 on ./names/01.names 2264 Testing tokenise_name3 -r -7 on ./names/01.names 2264 Testing tokenise_name3 -r -9 on ./names/01.names 2234 Testing tokenise_name3 -r -11 on ./names/01.names 2449 Testing tokenise_name3 -r -13 on ./names/01.names 2085 Testing tokenise_name3 -r -15 on ./names/01.names 2071 Testing tokenise_name3 -r -17 on ./names/01.names 2070 Testing tokenise_name3 -r -19 on ./names/01.names 2051 Testing tokenise_name3 -r -1 on ./names/02.names 5390 Testing tokenise_name3 -r -3 on ./names/02.names 4955 Testing tokenise_name3 -r -5 on ./names/02.names 4923 Testing tokenise_name3 -r -7 on ./names/02.names 4923 Testing tokenise_name3 -r -9 on ./names/02.names 4918 Testing tokenise_name3 -r -11 on ./names/02.names 4838 Testing tokenise_name3 -r -13 on ./names/02.names 4757 Testing tokenise_name3 -r -15 on ./names/02.names 4743 Testing tokenise_name3 -r -17 on ./names/02.names 4716 Testing tokenise_name3 -r -19 on ./names/02.names 4700 Testing tokenise_name3 -r -1 on ./names/03.names 8854 Testing tokenise_name3 -r -3 on ./names/03.names 7782 Testing tokenise_name3 -r -5 on ./names/03.names 7771 Testing tokenise_name3 -r -7 on ./names/03.names 7771 Testing tokenise_name3 -r -9 on ./names/03.names 7521 Testing tokenise_name3 -r -11 on ./names/03.names 7395 Testing tokenise_name3 -r -13 on ./names/03.names 7252 Testing tokenise_name3 -r -15 on ./names/03.names 7252 Testing tokenise_name3 -r -17 on ./names/03.names 7225 Testing tokenise_name3 -r -19 on ./names/03.names 7075 Testing tokenise_name3 -r -1 on ./names/05.names 3787 Testing tokenise_name3 -r -3 on ./names/05.names 3564 Testing tokenise_name3 -r -5 on ./names/05.names 3536 Testing tokenise_name3 -r -7 on ./names/05.names 3536 Testing tokenise_name3 -r -9 on ./names/05.names 3534 Testing tokenise_name3 -r -11 on ./names/05.names 3411 Testing tokenise_name3 -r -13 on ./names/05.names 3397 Testing tokenise_name3 -r -15 on ./names/05.names 3383 Testing tokenise_name3 -r -17 on ./names/05.names 3383 Testing tokenise_name3 -r -19 on ./names/05.names 3377 Testing tokenise_name3 -r -1 on ./names/08.names 5579 Testing tokenise_name3 -r -3 on ./names/08.names 5274 Testing tokenise_name3 -r -5 on ./names/08.names 5246 Testing tokenise_name3 -r -7 on ./names/08.names 5213 Testing tokenise_name3 -r -9 on ./names/08.names 5160 Testing tokenise_name3 -r -11 on ./names/08.names 4915 Testing tokenise_name3 -r -13 on ./names/08.names 4901 Testing tokenise_name3 -r -15 on ./names/08.names 4887 Testing tokenise_name3 -r -17 on ./names/08.names 4844 Testing tokenise_name3 -r -19 on ./names/08.names 4805 Testing tokenise_name3 -r -1 on ./names/09.names 3740 Testing tokenise_name3 -r -3 on ./names/09.names 3539 Testing tokenise_name3 -r -5 on ./names/09.names 3539 Testing tokenise_name3 -r -7 on ./names/09.names 3528 Testing tokenise_name3 -r -9 on ./names/09.names 3493 Testing tokenise_name3 -r -11 on ./names/09.names 3431 Testing tokenise_name3 -r -13 on ./names/09.names 3394 Testing tokenise_name3 -r -15 on ./names/09.names 3394 Testing tokenise_name3 -r -17 on ./names/09.names 3386 Testing tokenise_name3 -r -19 on ./names/09.names 3366 Testing tokenise_name3 -r -1 on ./names/10.names 5210 Testing tokenise_name3 -r -3 on ./names/10.names 4782 Testing tokenise_name3 -r -5 on ./names/10.names 4752 Testing tokenise_name3 -r -7 on ./names/10.names 4752 Testing tokenise_name3 -r -9 on ./names/10.names 4744 Testing tokenise_name3 -r -11 on ./names/10.names 4566 Testing tokenise_name3 -r -13 on ./names/10.names 4520 Testing tokenise_name3 -r -15 on ./names/10.names 4506 Testing tokenise_name3 -r -17 on ./names/10.names 4494 Testing tokenise_name3 -r -19 on ./names/10.names 4476 Testing tokenise_name3 -r -1 on ./names/20.names 1783 Testing tokenise_name3 -r -3 on ./names/20.names 1668 Testing tokenise_name3 -r -5 on ./names/20.names 1640 Testing tokenise_name3 -r -7 on ./names/20.names 1640 Testing tokenise_name3 -r -9 on ./names/20.names 1632 Testing tokenise_name3 -r -11 on ./names/20.names 1645 Testing tokenise_name3 -r -13 on ./names/20.names 1625 Testing tokenise_name3 -r -15 on ./names/20.names 1611 Testing tokenise_name3 -r -17 on ./names/20.names 1609 Testing tokenise_name3 -r -19 on ./names/20.names 1600 Testing tokenise_name3 -r -1 on ./names/nv.names 5273 Testing tokenise_name3 -r -3 on ./names/nv.names 4968 Testing tokenise_name3 -r -5 on ./names/nv.names 4941 Testing tokenise_name3 -r -7 on ./names/nv.names 4941 Testing tokenise_name3 -r -9 on ./names/nv.names 4937 Testing tokenise_name3 -r -11 on ./names/nv.names 4864 Testing tokenise_name3 -r -13 on ./names/nv.names 4785 Testing tokenise_name3 -r -15 on ./names/nv.names 4772 Testing tokenise_name3 -r -17 on ./names/nv.names 4772 Testing tokenise_name3 -r -19 on ./names/nv.names 4767 Testing tokenise_name3 -r -1 on ./names/nv2.names 1060 Testing tokenise_name3 -r -3 on ./names/nv2.names 891 Testing tokenise_name3 -r -5 on ./names/nv2.names 863 Testing tokenise_name3 -r -7 on ./names/nv2.names 863 Testing tokenise_name3 -r -9 on ./names/nv2.names 855 Testing tokenise_name3 -r -11 on ./names/nv2.names 836 Testing tokenise_name3 -r -13 on ./names/nv2.names 799 Testing tokenise_name3 -r -15 on ./names/nv2.names 785 Testing tokenise_name3 -r -17 on ./names/nv2.names 779 Testing tokenise_name3 -r -19 on ./names/nv2.names 767 Testing tokenise_name3 -r -1 on ./names/rr.names 6605 Testing tokenise_name3 -r -3 on ./names/rr.names 6237 Testing tokenise_name3 -r -5 on ./names/rr.names 6237 Testing tokenise_name3 -r -7 on ./names/rr.names 6237 Testing tokenise_name3 -r -9 on ./names/rr.names 6230 Testing tokenise_name3 -r -11 on ./names/rr.names 6151 Testing tokenise_name3 -r -13 on ./names/rr.names 6025 Testing tokenise_name3 -r -15 on ./names/rr.names 6025 Testing tokenise_name3 -r -17 on ./names/rr.names 6023 Testing tokenise_name3 -r -19 on ./names/rr.names 5973 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -Ihtscodecs -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-hardened-ld-errors -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_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o -llzma -lbz2 -lz -lm -lm -lpthread cd htscodecs/tests && srcdir=. && export srcdir && ./fqzcomp.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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -Ihtscodecs -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-hardened-ld-errors -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_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o -llzma -lbz2 -lz -lm -lm -lpthread cd htscodecs/tests && ./varint test/hts_endian test/test_expr test/test_kfunc test/test_khash test/test_kstring test/test_nibbles -v test/test_str2int test/test_time_funcs test/fieldarith test/fieldarith.sam test/hfile if test "xhfile_libcurl.so hfile_gcs.so hfile_s3.so" != "x"; then \ HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -g ./libhts.so; \ fi if test "xhfile_libcurl.so hfile_gcs.so hfile_s3.so" != "x"; then \ HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -l ./libhts.so; \ fi 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/faidx && ./test-faidx.sh faidx.tst Testing faidx... PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -e faidx.fa.expected.fai PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t fai_line_length -e 24 trailingblank2 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_has_seq -e 1 foo PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_has_seq -e 0 absent PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_iseq -e trailingblank3 3 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_seq_len -e 33 trailingblank1 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_seq_len64 -e 72 trailingblank2 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -e fastqs.fq.expected.fai PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t fai_line_length -e 63 FAKE0005_3 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t fai_line_length -e 144 SRR014849.203935_3 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_has_seq -e 1 SRR014849.203935_3 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_has_seq -e 0 absent PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_iseq -e FAKE0005_1 0 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_seq_len -e 453 FSRRS4401CM938_1 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_seq_len64 -e 309 FSRRS4401AOV6A_4 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai trailingblank2:28-33 trailingblank3:4-5 bar:4-5 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t fai_fetch trailingblank2:28-33 trailingblank3:4-5 bar:4-5 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_fetch_seq64 trailingblank2:28-33 trailingblank3:4-5 bar:4-5 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t fai_adjust_region trailingblank2:28-33 trailingblank3:4-5 bar:4-5 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q FAKE0006_1:4-12 FSRRS4401BE7HA_1:81-120 FAKE0010_2 SRR014849.50939_3:71-90 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t fai_fetch FAKE0006_1:4-12 FSRRS4401BE7HA_1:81-120 FAKE0010_2 SRR014849.50939_3:71-90 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t faidx_fetch_seq64 FAKE0006_1:4-12 FSRRS4401BE7HA_1:81-120 FAKE0010_2 SRR014849.50939_3:71-90 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai FAKE0006_1:4-12 FSRRS4401BE7HA_1:81-120 FAKE0010_2 SRR014849.50939_3:71-90 PASS : $test_faidx -i ce.fa.tmp.gz -f ce.fa.tmp.gz.fai -g ce.fa.tmp.gz.gzi -e ../ce.fa.fai PASS : $test_faidx -i ce.fa.tmp.gz -f ce.fa.tmp.gz.fai -g ce.fa.tmp.gz.gzi CHROMOSOME_I:5001-5125 CHROMOSOME_X:101-225 Expected passes: 25 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 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 | grep -E -cv '^@' PASS : $tv -i 'filter=qlen/(flag*mapq+pos)>5' ../ce#1000.sam | grep -E -cv '^@' PASS : $tv -i 'filter=[NM]>=10 || [MD]=~"A.*A.*A"' -t4 ../ce#1000.sam | grep -E -cv '^@' PASS : $tv -i 'filter=length(seq) != qlen' ../ce#5b.sam | grep -E -cv '^@' PASS : $tv -i 'filter=min(qual) >= 20' ../ce#1000.sam | grep -E -cv '^@' PASS : $tv -i 'filter=max(qual) <= 20' ../ce#1000.sam | grep -E -cv '^@' PASS : $tv -i 'filter=avg(qual) >= 20 && avg(qual) <= 30' ../ce#1000.sam | grep -E -cv '^@' PASS : $tv -i 'filter=sclen>=20' ../realn02.sam | grep -E -v '^@' PASS : $tv -i 'filter=rlen<50' ../realn02.sam | grep -E -v '^@' PASS : $tv -i 'filter=qlen>100' ../realn02.sam | grep -E -v '^@' PASS : $tv -i 'filter=hclen>=4' ../c1#clip.sam | grep -E -v '^@' Expected passes: 18 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 PASS : $tabix -f -p bed bed_file.tbi.tmp.bed.gz -@ 2 PASS : $tabix vcf_file.tbi.tmp.vcf.gz 1:3000151-3000151 --threads 2 Expected passes: 16 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 PASS : $pileup -m mp_overlap1.sam PASS : $pileup -m mp_overlap2.sam Expected passes: 23 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 -i fastq_aux longline.fq 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 -i fastq_umi=RX UMI.fq 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 PASS : $tview -f -o fastq_rnum -o fastq_umi UMI.sam Expected passes: 43 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 : $test_mod MM-explicit.sam PASS : $test_mod -x MM-explicit.sam PASS : $test_mod -f 1 MM-explicit.sam PASS : $test_mod MM-not-all-modded.sam PASS : $pileup_mod < MM-pileup.sam PASS : $pileup_mod < MM-pileup2.sam PASS : $pileup_mod < MM-MNp.sam PASS : $pileup_mod < MM-MNf1.sam (must exit non-zero) PASS : $pileup_mod < MM-MNf2.sam (must exit non-zero) PASS : $test_mod < MM-MNf1.sam (must exit non-zero) PASS : $test_mod < MM-MNf2.sam (must exit non-zero) PASS : $test_mod < MM-bounds+.sam (must exit non-zero) PASS : $test_mod < MM-bounds-.sam (must exit non-zero) PASS : $test_mod -f 1 MM-variants.sam Expected passes: 17 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 cd test/tlen && ./tlen.sh tlen.tst Testing CRAM TLEN auto-creation... PASS : $test_view a7.cram PASS : $test_view a7b.cram PASS : $test_view a8.cram PASS : $test_view a8b.cram PASS : $test_view a9.cram PASS : $test_view a9b.cram PASS : $test_view b7.cram PASS : $test_view b7b.cram PASS : $test_view b8.cram PASS : $test_view b8b.cram PASS : $test_view c7.cram PASS : $test_view c7b.cram PASS : $test_view c8.cram PASS : $test_view c8b.cram PASS : $test_view d7.cram PASS : $test_view d7b.cram PASS : $test_view d4.cram PASS : $test_view d4b.cram PASS : $test_view d4c.cram PASS : $test_view d4d.cram PASS : $test_view d4e.cram PASS : $test_view d4f.cram PASS : $test_view d5.cram PASS : $test_view d5b.cram PASS : $test_view d5c.cram PASS : $test_view d5d.cram PASS : $test_view d5e.cram PASS : $test_view d5f.cram PASS : $test_view a4.cram PASS : $test_view a5.cram Expected passes: 30 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 REF_PATH=: test/sam test/ce.fa test/faidx/faidx.fa test/faidx/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 && \ if test "xhfile_libcurl.so hfile_gcs.so hfile_s3.so" != "x"; then \ REF_PATH=: HTS_PATH=.. ./with-shlib.sh ./test.pl --ref-cache-bin ../ref_cache/ref-cache ${TEST_OPTS:-} ; \ else \ REF_PATH=: ./test.pl --ref-cache-bin ../ref_cache/ref-cache ${TEST_OPTS:-} ; \ fi bgzip round-trip no threads: .. ok bgzip text mode round-trip no threads: .. ok bgzip -b no threads: .. ok bgzip -b -I no threads: .. ok bgzip multifile no threads: .. ok bgzip --output no threads: .. ok bgzip round-trip 4 threads: .. ok bgzip text mode round-trip 4 threads: .. ok bgzip -b 4 threads: .. ok bgzip -b -I 4 threads: .. ok bgzip multifile 4 threads: .. ok bgzip --output 4 threads: .. ok test_index: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view -l 0 -b -m 14 -x /tmp/Y9oItR16Xh/index.bam.csi /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/index.sam > /tmp/Y9oItR16Xh/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_index -c /tmp/Y9oItR16Xh/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view -l 0 -b -m 0 -x /tmp/Y9oItR16Xh/index.bam.bai /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/index.sam > /tmp/Y9oItR16Xh/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_index -b /tmp/Y9oItR16Xh/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view -l 0 -z -m 14 -x /tmp/Y9oItR16Xh/index.sam.gz.csi /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/index.sam > /tmp/Y9oItR16Xh/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_index -c /tmp/Y9oItR16Xh/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view -l 0 -z -m 0 -x /tmp/Y9oItR16Xh/index.sam.gz.bai /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/index.sam > /tmp/Y9oItR16Xh/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_index -b /tmp/Y9oItR16Xh/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view -l 0 -z -m 14 -x /tmp/Y9oItR16Xh/index.sam.gz.csi /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/index_dos.sam > /tmp/Y9oItR16Xh/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_index -c /tmp/Y9oItR16Xh/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view -l 0 -z -m 0 -x /tmp/Y9oItR16Xh/index.sam.gz.bai /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/index_dos.sam > /tmp/Y9oItR16Xh/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_index -b /tmp/Y9oItR16Xh/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view -l 0 -C -x /tmp/Y9oItR16Xh/index.cram.crai /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/index.sam > /tmp/Y9oItR16Xh/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_index /tmp/Y9oItR16Xh/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view -p /tmp/Y9oItR16Xh/index3_rgn.sam /tmp/Y9oItR16Xh/index3.cram CHROMOSOME_I:5000-5100 .. ok test_index: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view -M -p /tmp/Y9oItR16Xh/index3_rgnm.sam /tmp/Y9oItR16Xh/index3.cram CHROMOSOME_I:5000-5100 .. ok test_index: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view -l 0 -b -m 14 -x /tmp/Y9oItR16Xh/index.bcf.csi /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/index.vcf > /tmp/Y9oItR16Xh/index.bcf .. ok test_index: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_index -c /tmp/Y9oItR16Xh/index.bcf .. ok test_index: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view -l 0 -z -m 14 -x /tmp/Y9oItR16Xh/index.vcf.gz.csi /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/index.vcf > /tmp/Y9oItR16Xh/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_index -c /tmp/Y9oItR16Xh/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view -l 0 -z -m 0 -x /tmp/Y9oItR16Xh/index.vcf.gz.tbi /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/index.vcf > /tmp/Y9oItR16Xh/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_index -t /tmp/Y9oItR16Xh/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/tabix /tmp/Y9oItR16Xh/index.vcf.gz##idx##/tmp/Y9oItR16Xh/index.vcf.gz.tbi 1:10000060-10000060 .. ok test_index: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view /tmp/Y9oItR16Xh/index2.bam 1:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view /tmp/Y9oItR16Xh/index2.bam 1:2000000-2000000 .. ok test_index: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view /tmp/Y9oItR16Xh/index2.bam 2:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view /tmp/Y9oItR16Xh/index2.bam 2:2000000-2000000 .. ok test_index: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view -@4 -l 0 -b -m 14 -x /tmp/Y9oItR16Xh/index.bam.csi /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/index.sam > /tmp/Y9oItR16Xh/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_index -c /tmp/Y9oItR16Xh/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view -@4 -l 0 -b -m 0 -x /tmp/Y9oItR16Xh/index.bam.bai /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/index.sam > /tmp/Y9oItR16Xh/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_index -b /tmp/Y9oItR16Xh/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view -@4 -l 0 -z -m 14 -x /tmp/Y9oItR16Xh/index.sam.gz.csi /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/index.sam > /tmp/Y9oItR16Xh/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_index -c /tmp/Y9oItR16Xh/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view -@4 -l 0 -z -m 0 -x /tmp/Y9oItR16Xh/index.sam.gz.bai /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/index.sam > /tmp/Y9oItR16Xh/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_index -b /tmp/Y9oItR16Xh/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view -@4 -l 0 -z -m 14 -x /tmp/Y9oItR16Xh/index.sam.gz.csi /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/index_dos.sam > /tmp/Y9oItR16Xh/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_index -c /tmp/Y9oItR16Xh/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view -@4 -l 0 -z -m 0 -x /tmp/Y9oItR16Xh/index.sam.gz.bai /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/index_dos.sam > /tmp/Y9oItR16Xh/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_index -b /tmp/Y9oItR16Xh/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view -@4 -l 0 -C -x /tmp/Y9oItR16Xh/index.cram.crai /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/index.sam > /tmp/Y9oItR16Xh/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_index /tmp/Y9oItR16Xh/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view -@4 -p /tmp/Y9oItR16Xh/index3_rgn.sam /tmp/Y9oItR16Xh/index3.cram CHROMOSOME_I:5000-5100 .. ok test_index: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view -@4 -M -p /tmp/Y9oItR16Xh/index3_rgnm.sam /tmp/Y9oItR16Xh/index3.cram CHROMOSOME_I:5000-5100 .. ok test_index: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view -@4 -l 0 -b -m 14 -x /tmp/Y9oItR16Xh/index.bcf.csi /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/index.vcf > /tmp/Y9oItR16Xh/index.bcf .. ok test_index: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_index -c /tmp/Y9oItR16Xh/index.bcf .. ok test_index: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view -@4 -l 0 -z -m 14 -x /tmp/Y9oItR16Xh/index.vcf.gz.csi /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/index.vcf > /tmp/Y9oItR16Xh/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_index -c /tmp/Y9oItR16Xh/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view -@4 -l 0 -z -m 0 -x /tmp/Y9oItR16Xh/index.vcf.gz.tbi /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/index.vcf > /tmp/Y9oItR16Xh/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_index -t /tmp/Y9oItR16Xh/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/tabix /tmp/Y9oItR16Xh/index.vcf.gz##idx##/tmp/Y9oItR16Xh/index.vcf.gz.tbi 1:10000060-10000060 .. ok test_index: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view /tmp/Y9oItR16Xh/index2.bam 1:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view /tmp/Y9oItR16Xh/index2.bam 1:2000000-2000000 .. ok test_index: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view /tmp/Y9oItR16Xh/index2.bam 2:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view /tmp/Y9oItR16Xh/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#repeated2.sam, ref xx.fa: ./test_view -S -l0 -b xx#repeated2.sam > xx#repeated2.tmp.bam ./test_view xx#repeated2.tmp.bam > xx#repeated2.tmp.bam.sam_ ./compare_sam.pl xx#repeated2.sam xx#repeated2.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#repeated2.sam > xx#repeated2.tmp.cram [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 100 vs 20 ./test_view -D xx#repeated2.tmp.cram > xx#repeated2.tmp.cram.sam_ [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 100 vs 20 ./compare_sam.pl -nomd xx#repeated2.sam xx#repeated2.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#repeated2.tmp.bam > xx#repeated2.tmp.bam.cram [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 100 vs 20 ./test_view xx#repeated2.tmp.bam.cram > xx#repeated2.tmp.bam.cram.bam.sam_ [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 100 vs 20 ./compare_sam.pl -nomd xx#repeated2.sam xx#repeated2.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#u.sam, ref xx.fa: ./test_view -S -l0 -b xx#u.sam > xx#u.tmp.bam ./test_view xx#u.tmp.bam > xx#u.tmp.bam.sam_ ./compare_sam.pl xx#u.sam xx#u.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#u.sam > xx#u.tmp.cram ./test_view -D xx#u.tmp.cram > xx#u.tmp.cram.sam_ ./compare_sam.pl -nomd xx#u.sam xx#u.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#u.tmp.bam > xx#u.tmp.bam.cram ./test_view xx#u.tmp.bam.cram > xx#u.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#u.sam xx#u.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 BAM records in multiple BGZF blocks: ./test_view -p bgzf_boundaries/bgzf_boundaries1.bam.tmp.sam bgzf_boundaries/bgzf_boundaries1.bam ./compare_sam.pl bgzf_boundaries/bgzf_boundaries1.bam.tmp.sam ce#1.sam ./test_view -p bgzf_boundaries/bgzf_boundaries2.bam.tmp.sam bgzf_boundaries/bgzf_boundaries2.bam ./compare_sam.pl bgzf_boundaries/bgzf_boundaries2.bam.tmp.sam ce#1.sam ./test_view -p bgzf_boundaries/bgzf_boundaries3.bam.tmp.sam bgzf_boundaries/bgzf_boundaries3.bam ./compare_sam.pl bgzf_boundaries/bgzf_boundaries3.bam.tmp.sam ce#1.sam ./test_view -b -l 0 -p bgzf_boundaries/large_rec.tmp.sam.bam bgzf_boundaries/large_rec.tmp.sam ./test_view -p bgzf_boundaries/large_rec.tmp.sam.bam.sam bgzf_boundaries/large_rec.tmp.sam.bam ./compare_sam.pl bgzf_boundaries/large_rec.tmp.sam bgzf_boundaries/large_rec.tmp.sam.bam.sam .. ok test_view testing embed_ref=2: ./test_view -C -p ce#1000_er.tmp.cram ce#1000.sam [W::cram_get_ref] Failed to populate reference "CHROMOSOME_I" [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam ./test_view -C -p c1#bounds_er.tmp.cram c1#bounds.sam [W::cram_get_ref] Failed to populate reference "c1" [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -p c1#bounds_er.tmp.cram.sam c1#bounds_er.tmp.cram ./compare_sam.pl c1#bounds.sam c1#bounds_er.tmp.cram.sam ./test_view -o embed_ref=2 -o seqs_per_slice=3 -o bases_per_slice=1000000 -C -p embed_MD.tmp.cram embed_MD.sam ./test_view -p embed_MD.tmp.cram.sam embed_MD.tmp.cram ./compare_sam.pl embed_MD.sam embed_MD.tmp.cram.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 ./test_view -i reference=ce.fa -M range.cram CHROMOSOME_I:1122-1122 CHROMOSOME_II:1136-1136 CHROMOSOME_II:1241-1241 CHROMOSOME_II:1267-1267 CHROMOSOME_II:1326-1326 CHROMOSOME_II:1345-1345 CHROMOSOME_II:1353-1353 CHROMOSOME_II:1366-1366 CHROMOSOME_II:1416-1416 CHROMOSOME_II:1459-1459 CHROMOSOME_II:1536-1536 > range.tmp ./compare_sam.pl range.tmp range.out2 ./test_view -M range.bam CHROMOSOME_I:1122-1122 CHROMOSOME_II:1136-1136 CHROMOSOME_II:1241-1241 CHROMOSOME_II:1267-1267 CHROMOSOME_II:1326-1326 CHROMOSOME_II:1345-1345 CHROMOSOME_II:1353-1353 CHROMOSOME_II:1366-1366 CHROMOSOME_II:1416-1416 CHROMOSOME_II:1459-1459 CHROMOSOME_II:1536-1536 > range.tmp ./compare_sam.pl range.tmp range.out2 .. 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-1.23-build/htslib-1.23/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 ./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#bounds_er.tmp.cram.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#bounds_er.tmp.cram.sam > c1#bounds_er.tmp.cram.tmp.bam ./test_view -@4 c1#bounds_er.tmp.cram.tmp.bam > c1#bounds_er.tmp.cram.tmp.bam.sam_ ./compare_sam.pl c1#bounds_er.tmp.cram.sam c1#bounds_er.tmp.cram.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#bounds_er.tmp.cram.sam > c1#bounds_er.tmp.cram.tmp.cram ./test_view -@4 -D c1#bounds_er.tmp.cram.tmp.cram > c1#bounds_er.tmp.cram.tmp.cram.sam_ ./compare_sam.pl -nomd c1#bounds_er.tmp.cram.sam c1#bounds_er.tmp.cram.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#bounds_er.tmp.cram.tmp.bam > c1#bounds_er.tmp.cram.tmp.bam.cram ./test_view -@4 c1#bounds_er.tmp.cram.tmp.bam.cram > c1#bounds_er.tmp.cram.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#bounds_er.tmp.cram.sam c1#bounds_er.tmp.cram.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 ./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 ./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 ./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 ./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 ./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#1000_er.tmp.cram.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#1000_er.tmp.cram.sam > ce#1000_er.tmp.cram.tmp.bam ./test_view -@4 ce#1000_er.tmp.cram.tmp.bam > ce#1000_er.tmp.cram.tmp.bam.sam_ ./compare_sam.pl ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1000_er.tmp.cram.sam > ce#1000_er.tmp.cram.tmp.cram ./test_view -@4 -D ce#1000_er.tmp.cram.tmp.cram > ce#1000_er.tmp.cram.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1000_er.tmp.cram.tmp.bam > ce#1000_er.tmp.cram.tmp.bam.cram ./test_view -@4 ce#1000_er.tmp.cram.tmp.bam.cram > ce#1000_er.tmp.cram.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.bam.cram.bam.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 ./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 ./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 ./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 ./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 ./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 ./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 ./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#repeated2.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#repeated2.sam > xx#repeated2.tmp.bam ./test_view -@4 xx#repeated2.tmp.bam > xx#repeated2.tmp.bam.sam_ ./compare_sam.pl xx#repeated2.sam xx#repeated2.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#repeated2.sam > xx#repeated2.tmp.cram [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 100 vs 20 ./test_view -@4 -D xx#repeated2.tmp.cram > xx#repeated2.tmp.cram.sam_ [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 100 vs 20 ./compare_sam.pl -nomd xx#repeated2.sam xx#repeated2.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#repeated2.tmp.bam > xx#repeated2.tmp.bam.cram [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 100 vs 20 ./test_view -@4 xx#repeated2.tmp.bam.cram > xx#repeated2.tmp.bam.cram.bam.sam_ [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 100 vs 20 ./compare_sam.pl -nomd xx#repeated2.sam xx#repeated2.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 ./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#u.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#u.sam > xx#u.tmp.bam ./test_view -@4 xx#u.tmp.bam > xx#u.tmp.bam.sam_ ./compare_sam.pl xx#u.sam xx#u.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#u.sam > xx#u.tmp.cram ./test_view -@4 -D xx#u.tmp.cram > xx#u.tmp.cram.sam_ ./compare_sam.pl -nomd xx#u.sam xx#u.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#u.tmp.bam > xx#u.tmp.bam.cram ./test_view -@4 xx#u.tmp.bam.cram > xx#u.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#u.sam xx#u.tmp.bam.cram.bam.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 BAM records in multiple BGZF blocks: ./test_view -@4 -p bgzf_boundaries/bgzf_boundaries1.bam.tmp.sam bgzf_boundaries/bgzf_boundaries1.bam ./compare_sam.pl bgzf_boundaries/bgzf_boundaries1.bam.tmp.sam ce#1.sam ./test_view -@4 -p bgzf_boundaries/bgzf_boundaries2.bam.tmp.sam bgzf_boundaries/bgzf_boundaries2.bam ./compare_sam.pl bgzf_boundaries/bgzf_boundaries2.bam.tmp.sam ce#1.sam ./test_view -@4 -p bgzf_boundaries/bgzf_boundaries3.bam.tmp.sam bgzf_boundaries/bgzf_boundaries3.bam ./compare_sam.pl bgzf_boundaries/bgzf_boundaries3.bam.tmp.sam ce#1.sam ./test_view -@4 -b -l 0 -p bgzf_boundaries/large_rec.tmp.sam.bam bgzf_boundaries/large_rec.tmp.sam ./test_view -@4 -p bgzf_boundaries/large_rec.tmp.sam.bam.sam bgzf_boundaries/large_rec.tmp.sam.bam ./compare_sam.pl bgzf_boundaries/large_rec.tmp.sam bgzf_boundaries/large_rec.tmp.sam.bam.sam .. ok test_view testing embed_ref=2: ./test_view -@4 -C -p ce#1000_er.tmp.cram ce#1000.sam [W::cram_get_ref] Failed to populate reference "CHROMOSOME_I" [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -@4 -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam ./test_view -@4 -C -p c1#bounds_er.tmp.cram c1#bounds.sam [W::cram_get_ref] Failed to populate reference "c1" [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -@4 -p c1#bounds_er.tmp.cram.sam c1#bounds_er.tmp.cram ./compare_sam.pl c1#bounds.sam c1#bounds_er.tmp.cram.sam ./test_view -@4 -o embed_ref=2 -o seqs_per_slice=3 -o bases_per_slice=1000000 -C -p embed_MD.tmp.cram embed_MD.sam ./test_view -@4 -p embed_MD.tmp.cram.sam embed_MD.tmp.cram ./compare_sam.pl embed_MD.sam embed_MD.tmp.cram.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 ./test_view -@4 -i reference=ce.fa -M range.cram CHROMOSOME_I:1122-1122 CHROMOSOME_II:1136-1136 CHROMOSOME_II:1241-1241 CHROMOSOME_II:1267-1267 CHROMOSOME_II:1326-1326 CHROMOSOME_II:1345-1345 CHROMOSOME_II:1353-1353 CHROMOSOME_II:1366-1366 CHROMOSOME_II:1416-1416 CHROMOSOME_II:1459-1459 CHROMOSOME_II:1536-1536 > range.tmp ./compare_sam.pl range.tmp range.out2 ./test_view -@4 -M range.bam CHROMOSOME_I:1122-1122 CHROMOSOME_II:1136-1136 CHROMOSOME_II:1241-1241 CHROMOSOME_II:1267-1267 CHROMOSOME_II:1326-1326 CHROMOSOME_II:1345-1345 CHROMOSOME_II:1353-1353 CHROMOSOME_II:1366-1366 CHROMOSOME_II:1416-1416 CHROMOSOME_II:1459-1459 CHROMOSOME_II:1536-1536 > range.tmp ./compare_sam.pl range.tmp range.out2 .. 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-1.23-build/htslib-1.23/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-1.23-build/htslib-1.23/test/test-vcf-api /tmp/Y9oItR16Xh/test-vcf-api.bcf .. ok test_bcf2vcf: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/tabix/vcf_file.bcf .. ok test_vcf_sweep: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-vcf-sweep /tmp/Y9oItR16Xh/test-vcf-api.bcf .. ok test_vcf_various: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/htsfile -ch /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-vcf-hdr-in.vcf .. ok test_vcf_various: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/htsfile -c /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/formatcols.vcf .. ok test_vcf_various: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/htsfile -c /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/noroundtrip.vcf .. ok test_vcf_various: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/htsfile -c /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/formatmissing.vcf .. ok test_vcf_various: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/htsfile -c /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/vcf_meta_meta.vcf .. ok test_vcf_various: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/modhdr.vcf.gz chr22:1-2 .. ok test_vcf_44: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/htsfile -c /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/vcf44_1.vcf .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr.pl -t /tmp/Y9oItR16Xh -s 74452500 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr.pl -t /tmp/Y9oItR16Xh -s 34270147 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr.pl -t /tmp/Y9oItR16Xh -s 11108528 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr.pl -t /tmp/Y9oItR16Xh -s 42233895 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr.pl -t /tmp/Y9oItR16Xh -s 8111117 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr.pl -t /tmp/Y9oItR16Xh -s 85644070 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr.pl -t /tmp/Y9oItR16Xh -s 49879942 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr.pl -t /tmp/Y9oItR16Xh -s 47881429 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr.pl -t /tmp/Y9oItR16Xh -s 69081244 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr.pl -t /tmp/Y9oItR16Xh -s 83459376 .. ok test_bcf_sr_no_index: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr --no-index -p all --args /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/bcf-sr/merge.noidx.a.vcf /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/bcf-sr/merge.noidx.b.vcf /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/bcf-sr/merge.noidx.c.vcf 2> /tmp/Y9oItR16Xh/no_index_1.err .. ok test_bcf_sr_no_index: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr --no-index -p all --args /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/bcf-sr/merge.noidx.a.vcf /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/bcf-sr/merge.noidx.hdr_order.vcf > /tmp/Y9oItR16Xh/no_index_2.out 2> /tmp/Y9oItR16Xh/no_index_2.err (expected fail) .. ok test_bcf_sr_no_index: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr --no-index -p all --args /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/bcf-sr/merge.noidx.a.vcf /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/bcf-sr/merge.noidx.rec_order.vcf > /tmp/Y9oItR16Xh/no_index_3.out 2> /tmp/Y9oItR16Xh/no_index_3.err (expected fail) .. ok test_bcf_sr_no_index: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr --no-index -p all --args /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/bcf-sr/merge.noidx.rec_order.vcf /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/bcf-sr/merge.noidx.a.vcf > /tmp/Y9oItR16Xh/no_index_4.out 2> /tmp/Y9oItR16Xh/no_index_4.err (expected fail) .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view -b -p /tmp/Y9oItR16Xh/weird-chr-names.vcf.bcf -x /tmp/Y9oItR16Xh/weird-chr-names.vcf.bcf.csi /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/bcf-sr/weird-chr-names.vcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/Y9oItR16Xh/range_test_1.out.vcf -r '1' --args /tmp/Y9oItR16Xh/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/Y9oItR16Xh/range_test_2.out.vcf -r '1:1-2' --args /tmp/Y9oItR16Xh/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/Y9oItR16Xh/range_test_3.out.vcf -r '1:1,1:2' --args /tmp/Y9oItR16Xh/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/Y9oItR16Xh/range_test_4.out.vcf -r '1:1-1' --args /tmp/Y9oItR16Xh/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/Y9oItR16Xh/range_test_5.out.vcf -r '{1:1}' --args /tmp/Y9oItR16Xh/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/Y9oItR16Xh/range_test_6.out.vcf -r '{1:1}:1-2' --args /tmp/Y9oItR16Xh/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/Y9oItR16Xh/range_test_7.out.vcf -r '{1:1}:1,{1:1}:2' --args /tmp/Y9oItR16Xh/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/Y9oItR16Xh/range_test_8.out.vcf -r '{1:1}:1-1' --args /tmp/Y9oItR16Xh/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/Y9oItR16Xh/range_test_9.out.vcf -r '{1:1-1}' --args /tmp/Y9oItR16Xh/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/Y9oItR16Xh/range_test_10.out.vcf -r '{1:1-1}:1-2' --args /tmp/Y9oItR16Xh/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/Y9oItR16Xh/range_test_11.out.vcf -r '{1:1-1}:1,{1:1-1}:2' --args /tmp/Y9oItR16Xh/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/Y9oItR16Xh/range_test_12.out.vcf -r '{1:1-1}:1-1' --args /tmp/Y9oItR16Xh/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/Y9oItR16Xh/range_test_13.out.vcf -r '{1:1-1}-2' --args /tmp/Y9oItR16Xh/weird-chr-names.vcf.bcf (expected fail) [E::_regions_init_string] Could not parse the region(s): {1:1-1}-2 Failed to set regions .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/Y9oItR16Xh/range_test_14.out.vcf -t '1' --args /tmp/Y9oItR16Xh/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/Y9oItR16Xh/range_test_15.out.vcf -t '1:1-2' --args /tmp/Y9oItR16Xh/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/Y9oItR16Xh/range_test_16.out.vcf -t '1:1,1:2' --args /tmp/Y9oItR16Xh/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/Y9oItR16Xh/range_test_17.out.vcf -t '1:1-1' --args /tmp/Y9oItR16Xh/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/Y9oItR16Xh/range_test_18.out.vcf -t '{1:1}' --args /tmp/Y9oItR16Xh/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/Y9oItR16Xh/range_test_19.out.vcf -t '{1:1}:1-2' --args /tmp/Y9oItR16Xh/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/Y9oItR16Xh/range_test_20.out.vcf -t '{1:1}:1,{1:1}:2' --args /tmp/Y9oItR16Xh/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/Y9oItR16Xh/range_test_21.out.vcf -t '{1:1}:1-1' --args /tmp/Y9oItR16Xh/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/Y9oItR16Xh/range_test_22.out.vcf -t '{1:1-1}' --args /tmp/Y9oItR16Xh/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/Y9oItR16Xh/range_test_23.out.vcf -t '{1:1-1}:1-2' --args /tmp/Y9oItR16Xh/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/Y9oItR16Xh/range_test_24.out.vcf -t '{1:1-1}:1,{1:1-1}:2' --args /tmp/Y9oItR16Xh/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/Y9oItR16Xh/range_test_25.out.vcf -t '{1:1-1}:1-1' --args /tmp/Y9oItR16Xh/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/Y9oItR16Xh/range_test_26.out.vcf -t '{1:1-1}-2' --args /tmp/Y9oItR16Xh/weird-chr-names.vcf.bcf (expected fail) [E::_regions_init_string] Could not parse the region(s): {1:1-1}-2 Failed to set targets .. ok .. ok test_command: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-translate - .. ok test_convert_padded_header: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view -t ce.fa -C /tmp/Y9oItR16Xh/headernul0.bam .. ok test_convert_padded_header: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view -t ce.fa -C /tmp/Y9oItR16Xh/headernul1.bam .. ok test_convert_padded_header: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view -t ce.fa -C /tmp/Y9oItR16Xh/headernul678.bam .. ok test_rebgzip: Alternate zlib/deflate library detected test_rebgzip: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/bgzip -I /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/bgziptest.txt.tmp.gz.gzi -c -g /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/bgziptest.txt .. ok test-logging: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-logging.pl .. ok test_plugin_loading: HTS_PATH=/builddir/build/BUILD/htslib-1.23-build/htslib-1.23 /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/with-shlib.sh /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/htsfile https://localhost:99999/invalid_port .. ok test_realn: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_realn -f /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/realn01.fa -i /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/realn01.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_realn -f /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/realn02.fa -i /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/realn02.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_realn -a -f /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/realn01.fa -i /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/realn01.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_realn -a -f /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/realn02.fa -i /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/realn02.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_realn -e -f /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/realn01.fa -i /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/realn01.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_realn -e -f /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/realn02.fa -i /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/realn02.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_realn -r -f /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/realn02.fa -i /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/realn02-r.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_realn -a -f /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/realn02.fa -i /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/realn02_exp.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_realn -f /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/realn02.fa -i /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/realn02_exp-a.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_realn -f /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/realn03.fa -e -i /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/realn03.sam -o - .. ok test-bcf_set_variant_type: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf_set_variant_type .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -f smpl:overlap --allow-dups -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.1.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.1.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -f smpl:overlap --allow-dups -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.1.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -f smpl:overlap --allow-dups -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -f smpl:overlap -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.1.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.1.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -f smpl:overlap -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.1.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -f smpl:overlap -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -f smpl:overlap -c chr,beg,end -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.1.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.1.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -f smpl:overlap -c chr,beg,end -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.1.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -f smpl:overlap -c chr,beg,end -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -f smpl,value:overlap,value -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.1.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.1.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -f smpl,value:overlap,value -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.1.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -f smpl,value:overlap,value -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -f smpl:overlap -O 0.5 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.1.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.1.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -f smpl:overlap -O 0.5 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.1.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -f smpl:overlap -O 0.5 -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -f smpl:overlap -rO 0.5 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.1.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.1.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -f smpl:overlap -rO 0.5 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.1.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -f smpl:overlap -rO 0.5 -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -f smpl:overlap --allow-dups --max-annots 2 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.1.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.1.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -f smpl:overlap --allow-dups --max-annots 2 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.1.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -f smpl:overlap --allow-dups --max-annots 2 -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.2.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.2.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.2.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.2.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.2.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.2.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4,value:5,value -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.2.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.2.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4,value:5,value -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.2.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4,value:5,value -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.2.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.2.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.2.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -a nbp,frac -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.2.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.2.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -a nbp,frac -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.2.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -a nbp,frac -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups --max-annots 2 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.2.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.2.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups --max-annots 2 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.2.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups --max-annots 2 -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -f smpl:overlap -a nbp,frac -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.3.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.3.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.3.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -f smpl:overlap -a nbp,frac -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.3.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.3.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -f smpl:overlap -a nbp,frac -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.3.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 2,3,4:2,3,4 -m 1:1 -f 1:1 -a nbp,frac -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.4.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.4.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.4.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 2,3,4:2,3,4 -m 1:1 -f 1:1 -a nbp,frac -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.4.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.4.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 2,3,4:2,3,4 -m 1:1 -f 1:1 -a nbp,frac -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.4.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 2,3,4:2,3,4 -a nbp,frac -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.5.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.5.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.5.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 2,3,4:2,3,4 -a nbp,frac -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.5.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.5.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 2,3,4:2,3,4 -a nbp,frac -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.5.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,2:1,2,2 -a nbp -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.6.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.6.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.6.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,2:1,2,2 -a nbp -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.6.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.6.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,2:1,2,2 -a nbp -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.6.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,2:1,2,2 -f overlap -H -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.7.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.7.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.7.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,2:1,2,2 -f overlap -H -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.7.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.7.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,2:1,2,2 -f overlap -H -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.7.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c chr,beg,end:chr,start,end -m sample -f is_tp -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.8.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.8.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.8.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c chr,beg,end:chr,start,end -m sample -f is_tp -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.8.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.8.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c chr,beg,end:chr,start,end -m sample -f is_tp -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.8.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:chr,beg,end -a nbp,frac,cnt -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.9.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.9.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.9.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:chr,beg,end -a nbp,frac,cnt -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.9.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.9.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:chr,beg,end -a nbp,frac,cnt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.9.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -f smpl -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.10.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.10.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -f smpl -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.10.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -f smpl -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.10.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.10.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.10.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -x -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.10.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.10.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -x -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.10.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -x -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -m smpl -f smpl -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.10.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.10.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -m smpl -f smpl -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.10.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -m smpl -f smpl -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -m smpl -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.10.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.10.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -m smpl -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.10.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -m smpl -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -m smpl -x -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.10.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.10.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -m smpl -x -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.10.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -m smpl -x -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.11.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.11.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.11.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -II -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.11.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.11.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -II -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.11.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -II -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:-1 -II -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.11.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.11.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:-1 -II -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.11.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:-1 -II -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.11.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.11.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.11.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.11.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.11.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.11.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -I -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.11.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.11.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -I -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.11.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -I -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -I -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.11.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.11.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -I -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.11.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -I -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d , -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.12.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.12.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.12.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d , -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.12.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.12.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d , -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.12.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d $',:\t' -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.12.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.11.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d $',:\t' -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.12.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.12.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d $',:\t' -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -r -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -r -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -r -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 0.5,0.5 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 0.5,0.5 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 0.5,0.5 -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 0,1 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 0,1 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 0,1 -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 1,0 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 1,0 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 1,0 -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3 -C 11:11 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.14.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.14.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.14.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3 -C 11:11 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.14.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.14.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3 -C 11:11 -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.14.txt .. ok run_annot_tsv: /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3 -C 01:01 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.14.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.14.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.14.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3 -C 01:01 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.14.txt .. ok run_annot_tsv: cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.14.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3 -C 01:01 -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.14.txt .. ok ref-cache: ./test_view -C -p ref_cache/ce_m5.sam.tmp.cram ref_cache/ce_m5.sam ./test_view -p ref_cache/ce_m5.sam.tmp.cram.sam ref_cache/ce_m5.sam.tmp.cram ./compare_sam.pl --nomd ref_cache/ce_m5.sam ref_cache/ce_m5.sam.tmp.cram.sam ./test_view -p ref_cache/ce_m5.sam.tmp.cram.2.sam ref_cache/ce_m5.sam.tmp.cram ./compare_sam.pl --nomd ref_cache/ce_m5.sam ref_cache/ce_m5.sam.tmp.cram.2.sam ./test_view -p ref_cache/ce_m5.sam.tmp.cram.3.sam ref_cache/ce_m5.sam.tmp.cram ./compare_sam.pl --nomd ref_cache/ce_m5.sam ref_cache/ce_m5.sam.tmp.cram.3.sam .. ok Number of tests: total .. 358 passed .. 358 failed .. 0 + RPM_EC=0 ++ jobs -p + exit 0 Processing files: htslib-1.23-1.fc43.aarch64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.jaMDRC + umask 022 + cd /builddir/build/BUILD/htslib-1.23-build + cd htslib-1.23 + DOCDIR=/builddir/build/BUILD/htslib-1.23-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-1.23-build/BUILDROOT/usr/share/doc/htslib + cp -pr /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/NEWS /builddir/build/BUILD/htslib-1.23-build/BUILDROOT/usr/share/doc/htslib + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.MF1KrW + umask 022 + cd /builddir/build/BUILD/htslib-1.23-build + cd htslib-1.23 + LICENSEDIR=/builddir/build/BUILD/htslib-1.23-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-1.23-build/BUILDROOT/usr/share/licenses/htslib + cp -pr /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/LICENSE /builddir/build/BUILD/htslib-1.23-build/BUILDROOT/usr/share/licenses/htslib + RPM_EC=0 ++ jobs -p + exit 0 Provides: htslib = 1.23-1.fc43 htslib(aarch-64) = 1.23-1.fc43 libhts.so.3()(64bit) libhts.so.3(HTSLIB_1.0)(64bit) libhts.so.3(HTSLIB_1.1)(64bit) libhts.so.3(HTSLIB_1.10)(64bit) libhts.so.3(HTSLIB_1.11)(64bit) libhts.so.3(HTSLIB_1.12)(64bit) libhts.so.3(HTSLIB_1.13)(64bit) libhts.so.3(HTSLIB_1.14)(64bit) libhts.so.3(HTSLIB_1.15)(64bit) libhts.so.3(HTSLIB_1.16)(64bit) libhts.so.3(HTSLIB_1.17)(64bit) libhts.so.3(HTSLIB_1.18)(64bit) libhts.so.3(HTSLIB_1.2.1)(64bit) libhts.so.3(HTSLIB_1.20)(64bit) libhts.so.3(HTSLIB_1.21)(64bit) libhts.so.3(HTSLIB_1.22)(64bit) libhts.so.3(HTSLIB_1.23)(64bit) libhts.so.3(HTSLIB_1.3)(64bit) libhts.so.3(HTSLIB_1.4)(64bit) libhts.so.3(HTSLIB_1.5)(64bit) libhts.so.3(HTSLIB_1.6)(64bit) libhts.so.3(HTSLIB_1.7)(64bit) libhts.so.3(HTSLIB_1.9)(64bit) Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: ld-linux-aarch64.so.1()(64bit) ld-linux-aarch64.so.1(GLIBC_2.17)(64bit) libbz2.so.1()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.17)(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_ABI_DT_RELR)(64bit) libcrypto.so.3()(64bit) libcrypto.so.3(OPENSSL_3.0.0)(64bit) libcurl.so.4()(64bit) libhts.so.3()(64bit) libhts.so.3(HTSLIB_1.0)(64bit) libhts.so.3(HTSLIB_1.3)(64bit) libhts.so.3(HTSLIB_1.4)(64bit) libhts.so.3(HTSLIB_1.5)(64bit) libhts.so.3(HTSLIB_1.7)(64bit) liblzma.so.5()(64bit) liblzma.so.5(XZ_5.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.17)(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-1.23-1.fc43.aarch64 Provides: htslib-devel = 1.23-1.fc43 htslib-devel(aarch-64) = 1.23-1.fc43 pkgconfig(htslib) = 1.23 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-1.23-1.fc43.aarch64 Provides: htslib-tools = 1.23-1.fc43 htslib-tools(aarch-64) = 1.23-1.fc43 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: ld-linux-aarch64.so.1()(64bit) ld-linux-aarch64.so.1(GLIBC_2.17)(64bit) libbz2.so.1()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.17)(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_ABI_DT_RELR)(64bit) libcurl.so.4()(64bit) liblzma.so.5()(64bit) liblzma.so.5(XZ_5.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.17)(64bit) libm.so.6(GLIBC_2.29)(64bit) libz.so.1()(64bit) rtld(GNU_HASH) Processing files: htslib-debugsource-1.23-1.fc43.aarch64 Provides: htslib-debugsource = 1.23-1.fc43 htslib-debugsource(aarch-64) = 1.23-1.fc43 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: htslib-debuginfo-1.23-1.fc43.aarch64 Provides: debuginfo(build-id) = 395cf63d36563e65cb10929cf97b9774213f7533 debuginfo(build-id) = 39fda04614aab31471628fb883a4d5a921584241 debuginfo(build-id) = 73b4024805bb6d79c77796065a5ecd31555006f1 debuginfo(build-id) = 99d025123ed02367289cbfb39336492d1f58e2f7 htslib-debuginfo = 1.23-1.fc43 htslib-debuginfo(aarch-64) = 1.23-1.fc43 libhts.so.1.23-1.23-1.fc43.aarch64.debug()(64bit) Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: htslib-debugsource(aarch-64) = 1.23-1.fc43 Processing files: htslib-tools-debuginfo-1.23-1.fc43.aarch64 Provides: debuginfo(build-id) = 13da835c4963761e978f07f2128ef73843c1e986 debuginfo(build-id) = 914cf73e210f6038adc9a7be7627a03f4ee5176f debuginfo(build-id) = d4956fc4b1331c072fa83e38c21392061192bad0 debuginfo(build-id) = dc4a9a00cc54b8bd01b2a32e2d9fcb252c7bfae1 debuginfo(build-id) = ea5ae8bbb22ad5dfc7ef57e4ffcc3d553ea25431 htslib-tools-debuginfo = 1.23-1.fc43 htslib-tools-debuginfo(aarch-64) = 1.23-1.fc43 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: htslib-debugsource(aarch-64) = 1.23-1.fc43 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILD/htslib-1.23-build/BUILDROOT Wrote: /builddir/build/RPMS/htslib-debuginfo-1.23-1.fc43.aarch64.rpm Wrote: /builddir/build/RPMS/htslib-tools-1.23-1.fc43.aarch64.rpm Wrote: /builddir/build/RPMS/htslib-debugsource-1.23-1.fc43.aarch64.rpm Wrote: /builddir/build/RPMS/htslib-devel-1.23-1.fc43.aarch64.rpm Wrote: /builddir/build/RPMS/htslib-1.23-1.fc43.aarch64.rpm Wrote: /builddir/build/RPMS/htslib-tools-debuginfo-1.23-1.fc43.aarch64.rpm Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.jWovaI + umask 022 + cd /builddir/build/BUILD/htslib-1.23-build + test -d /builddir/build/BUILD/htslib-1.23-build + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w /builddir/build/BUILD/htslib-1.23-build + rm -rf /builddir/build/BUILD/htslib-1.23-build + RPM_EC=0 ++ jobs -p + exit 0 Finish: rpmbuild htslib-1.23-1.fc43.src.rpm Finish: build phase for htslib-1.23-1.fc43.src.rpm INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-43-aarch64-1769500621.615308/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-1.23-1.fc43.src.rpm) Config(child) 4 minutes 19 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-debugsource", "epoch": null, "version": "1.23", "release": "1.fc43", "arch": "aarch64" }, { "name": "htslib-tools-debuginfo", "epoch": null, "version": "1.23", "release": "1.fc43", "arch": "aarch64" }, { "name": "htslib", "epoch": null, "version": "1.23", "release": "1.fc43", "arch": "aarch64" }, { "name": "htslib", "epoch": null, "version": "1.23", "release": "1.fc43", "arch": "src" }, { "name": "htslib-debuginfo", "epoch": null, "version": "1.23", "release": "1.fc43", "arch": "aarch64" }, { "name": "htslib-tools", "epoch": null, "version": "1.23", "release": "1.fc43", "arch": "aarch64" }, { "name": "htslib-devel", "epoch": null, "version": "1.23", "release": "1.fc43", "arch": "aarch64" } ] } RPMResults finished