Warning: Permanently added '54.175.166.117' (ED25519) to the list of known hosts. Running: /usr/bin/copr-rpmbuild --verbose --drop-resultdir --build-id 4732438 --chroot fedora-rawhide-aarch64 --detached Version: 0.61 PID: 7636 Logging PID: 7637 Task: {'appstream': True, 'background': False, 'bootstrap': 'off', 'build_id': 4732438, 'buildroot_pkgs': [], 'chroot': 'fedora-rawhide-aarch64', 'enable_net': False, 'fedora_review': False, 'git_hash': '9dc71172c44886608e8a486ef0e8b669f6ecf6a5', 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/jaruga/staging/htslib', 'isolation': 'default', 'memory_reqs': 2048, 'package_name': 'htslib', 'package_version': '1.15.1-1.fc38', 'project_dirname': 'staging', 'project_name': 'staging', 'project_owner': 'jaruga', 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/jaruga/staging/fedora-rawhide-aarch64/', 'id': 'copr_base', 'name': 'Copr repository'}], 'sandbox': 'jaruga/staging--jaruga', 'source_json': {}, 'source_type': None, 'submitter': 'jaruga', 'tags': [], 'task_id': '4732438-fedora-rawhide-aarch64', 'timeout': 18000, 'uses_devel_repo': False, 'with_opts': [], 'without_opts': []} Running: git clone https://copr-dist-git.fedorainfracloud.org/git/jaruga/staging/htslib /var/lib/copr-rpmbuild/workspace/workdir-m5uvbacp/htslib --depth 500 --no-single-branch --recursive cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/jaruga/staging/htslib', '/var/lib/copr-rpmbuild/workspace/workdir-m5uvbacp/htslib', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-m5uvbacp/htslib'... Running: git checkout 9dc71172c44886608e8a486ef0e8b669f6ecf6a5 cmd: ['git', 'checkout', '9dc71172c44886608e8a486ef0e8b669f6ecf6a5'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-m5uvbacp/htslib rc: 0 stdout: stderr: Note: switching to '9dc71172c44886608e8a486ef0e8b669f6ecf6a5'. 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 9dc7117 automatic import of htslib Running: copr-distgit-client sources cmd: ['copr-distgit-client', 'sources'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-m5uvbacp/htslib rc: 0 stdout: stderr: INFO: Reading stdout from command: git rev-parse --abbrev-ref HEAD INFO: Reading stdout from command: git rev-parse HEAD INFO: Reading sources specification file: sources INFO: Downloading htslib-1.15.1.tar.bz2 /usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated INFO: Calling: curl -H Pragma: -o htslib-1.15.1.tar.bz2 --location --remote-time --show-error --fail https://copr-dist-git.fedorainfracloud.org/repo/pkgs/jaruga/staging/htslib/htslib-1.15.1.tar.bz2/md5/9ea5cff8edcebb01f31dd02bd4d2a082/htslib-1.15.1.tar.bz2 % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 4044k 100 4044k 0 0 68.0M 0 --:--:-- --:--:-- --:--:-- 69.2M INFO: Reading stdout from command: md5sum htslib-1.15.1.tar.bz2 Running (timeout=18000): unbuffer mock --buildsrpm --spec /var/lib/copr-rpmbuild/workspace/workdir-m5uvbacp/htslib/htslib.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-m5uvbacp/htslib --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1660557065.245354 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 3.1 starting (python version = 3.10.4, NVR = mock-3.1-1.fc35)... 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-m5uvbacp/htslib/htslib.spec) Config(fedora-rawhide-aarch64) Start: clean chroot Finish: clean chroot Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-aarch64-1660557065.245354/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin Mock Version: 3.1 INFO: Mock Version: 3.1 Start: dnf install No matches found for the following disable plugin patterns: local, spacewalk, versionlock Updating Subscription Management repositories. Unable to read consumer identity This system is not registered with an entitlement server. You can use subscription-manager to register. Copr repository 164 kB/s | 19 kB 00:00 fedora 17 MB/s | 61 MB 00:03 Dependencies resolved. ================================================================================ Package Arch Version Repo Size ================================================================================ Installing group/module packages: bash aarch64 5.1.16-3.fc37 fedora 1.7 M bzip2 aarch64 1.0.8-12.fc37 fedora 52 k coreutils aarch64 9.1-6.fc37 fedora 1.0 M cpio aarch64 2.13-13.fc37 fedora 274 k diffutils aarch64 3.8-3.fc37 fedora 376 k fedora-release-common noarch 38-0.2 fedora 22 k findutils aarch64 1:4.9.0-2.fc37 fedora 493 k gawk aarch64 5.1.1-4.fc37 fedora 1.0 M glibc-minimal-langpack aarch64 2.36-1.fc37 fedora 81 k grep aarch64 3.7-4.fc37 fedora 270 k gzip aarch64 1.12-2.fc37 fedora 164 k info aarch64 6.8-4.fc37 fedora 220 k patch aarch64 2.7.6-17.fc37 fedora 121 k redhat-rpm-config noarch 227-1.fc37 fedora 80 k rpm-build aarch64 4.18.0-0.beta1.4.fc37 fedora 77 k sed aarch64 4.8-11.fc37 fedora 304 k shadow-utils aarch64 2:4.11.1-4.fc37 fedora 1.1 M tar aarch64 2:1.34-3.fc36 fedora 877 k unzip aarch64 6.0-58.fc37 fedora 182 k util-linux aarch64 2.38.1-1.fc37 fedora 2.3 M which aarch64 2.21-35.fc37 fedora 41 k xz aarch64 5.2.5-10.fc37 fedora 223 k Installing dependencies: alternatives aarch64 1.19-3.fc37 fedora 35 k ansible-srpm-macros noarch 1-6.fc37 fedora 7.5 k audit-libs aarch64 3.0.8-3.fc37 fedora 116 k authselect aarch64 1.4.0-3.fc37 fedora 144 k authselect-libs aarch64 1.4.0-3.fc37 fedora 247 k basesystem noarch 11-14.fc37 fedora 7.0 k binutils aarch64 2.38-24.fc38 fedora 5.8 M binutils-gold aarch64 2.38-24.fc38 fedora 924 k bzip2-libs aarch64 1.0.8-12.fc37 fedora 43 k ca-certificates noarch 2022.2.54-5.fc37 fedora 829 k coreutils-common aarch64 9.1-6.fc37 fedora 2.0 M cracklib aarch64 2.9.6-28.fc36 fedora 93 k crypto-policies noarch 20220802-1.gita99dfd2.fc37 fedora 86 k curl aarch64 7.84.0-2.fc37 fedora 309 k cyrus-sasl-lib aarch64 2.1.28-7.fc37 fedora 777 k debugedit aarch64 5.0-5.fc37 fedora 76 k dwz aarch64 0.14-7.fc37 fedora 126 k ed aarch64 1.18-2.fc37 fedora 78 k efi-srpm-macros noarch 5-6.fc37 fedora 22 k elfutils aarch64 0.187-6.fc37 fedora 522 k elfutils-debuginfod-client aarch64 0.187-6.fc37 fedora 38 k elfutils-default-yama-scope noarch 0.187-6.fc37 fedora 17 k elfutils-libelf aarch64 0.187-6.fc37 fedora 197 k elfutils-libs aarch64 0.187-6.fc37 fedora 256 k fedora-gpg-keys noarch 38-0.2 fedora 125 k fedora-release noarch 38-0.2 fedora 12 k fedora-release-identity-basic noarch 38-0.2 fedora 12 k fedora-repos noarch 38-0.2 fedora 10 k fedora-repos-rawhide noarch 38-0.2 fedora 9.6 k file aarch64 5.42-4.fc37 fedora 49 k file-libs aarch64 5.42-4.fc37 fedora 674 k filesystem aarch64 3.18-2.fc37 fedora 1.1 M fonts-srpm-macros noarch 1:2.0.5-8.fc37 fedora 26 k fpc-srpm-macros noarch 1.3-6.fc37 fedora 7.7 k gdb-minimal aarch64 12.1-4.fc37 fedora 3.5 M gdbm-libs aarch64 1:1.23-2.fc37 fedora 57 k ghc-srpm-macros noarch 1.5.0-7.fc37 fedora 7.8 k glibc aarch64 2.36-1.fc37 fedora 1.8 M glibc-common aarch64 2.36-1.fc37 fedora 355 k glibc-gconv-extra aarch64 2.36-1.fc37 fedora 1.7 M gmp aarch64 1:6.2.1-3.fc37 fedora 265 k gnat-srpm-macros noarch 4-16.fc37 fedora 8.3 k go-srpm-macros noarch 3.1.0-4.fc37 fedora 27 k jansson aarch64 2.13.1-5.fc37 fedora 46 k kernel-srpm-macros noarch 1.0-15.fc37 fedora 9.4 k keyutils-libs aarch64 1.6.1-5.fc37 fedora 31 k krb5-libs aarch64 1.19.2-11.fc37.1 fedora 733 k libacl aarch64 2.3.1-4.fc37 fedora 23 k libarchive aarch64 3.6.1-2.fc37 fedora 392 k libattr aarch64 2.5.1-5.fc37 fedora 18 k libblkid aarch64 2.38.1-1.fc37 fedora 106 k libbrotli aarch64 1.0.9-9.fc37 fedora 318 k libcap aarch64 2.48-5.fc37 fedora 67 k libcap-ng aarch64 0.8.3-3.fc37 fedora 33 k libcom_err aarch64 1.46.5-3.fc37 fedora 25 k libcurl aarch64 7.84.0-2.fc37 fedora 301 k libdb aarch64 5.3.28-53.fc37 fedora 737 k libeconf aarch64 0.4.0-4.fc37 fedora 26 k libevent aarch64 2.1.12-7.fc37 fedora 254 k libfdisk aarch64 2.38.1-1.fc37 fedora 155 k libffi aarch64 3.4.2-9.fc37 fedora 36 k libgcc aarch64 12.1.1-4.fc38 fedora 92 k libgomp aarch64 12.1.1-4.fc38 fedora 290 k libidn2 aarch64 2.3.3-2.fc37 fedora 114 k libmount aarch64 2.38.1-1.fc37 fedora 133 k libnghttp2 aarch64 1.48.0-2.fc37 fedora 73 k libnsl2 aarch64 2.0.0-4.fc37 fedora 30 k libpkgconf aarch64 1.8.0-3.fc37 fedora 36 k libpsl aarch64 0.21.1-6.fc37 fedora 63 k libpwquality aarch64 1.4.4-11.fc37 fedora 116 k libselinux aarch64 3.4-5.fc37 fedora 85 k libsemanage aarch64 3.4-5.fc37 fedora 116 k libsepol aarch64 3.4-3.fc37 fedora 310 k libsigsegv aarch64 2.14-3.fc37 fedora 27 k libsmartcols aarch64 2.38.1-1.fc37 fedora 63 k libssh aarch64 0.9.6-5.fc37 fedora 202 k libssh-config noarch 0.9.6-5.fc37 fedora 7.8 k libstdc++ aarch64 12.1.1-4.fc38 fedora 760 k libtasn1 aarch64 4.18.0-3.fc37 fedora 73 k libtirpc aarch64 1.3.3-0.fc37 fedora 94 k libunistring aarch64 1.0-2.fc37 fedora 543 k libutempter aarch64 1.2.1-7.fc37 fedora 26 k libuuid aarch64 2.38.1-1.fc37 fedora 28 k libverto aarch64 0.3.2-4.fc37 fedora 21 k libxcrypt aarch64 4.4.28-3.fc38 fedora 121 k libxml2 aarch64 2.9.14-3.fc37 fedora 734 k libzstd aarch64 1.5.2-3.fc37 fedora 267 k lua-libs aarch64 5.4.4-4.fc37 fedora 213 k lua-srpm-macros noarch 1-7.fc37 fedora 8.8 k lz4-libs aarch64 1.9.3-5.fc37 fedora 70 k mpfr aarch64 4.1.0-10.fc37 fedora 240 k ncurses-base noarch 6.3-3.20220501.fc37 fedora 86 k ncurses-libs aarch64 6.3-3.20220501.fc37 fedora 318 k nim-srpm-macros noarch 3-7.fc37 fedora 8.4 k ocaml-srpm-macros noarch 7-2.fc37 fedora 13 k openblas-srpm-macros noarch 2-12.fc37 fedora 7.5 k openldap aarch64 2.6.2-5.fc38 fedora 250 k openssl-libs aarch64 1:3.0.5-2.fc37 fedora 2.0 M p11-kit aarch64 0.24.1-3.fc37 fedora 361 k p11-kit-trust aarch64 0.24.1-3.fc37 fedora 138 k package-notes-srpm-macros noarch 0.4-16.fc37 fedora 11 k pam aarch64 1.5.2-14.fc37 fedora 567 k pam-libs aarch64 1.5.2-14.fc37 fedora 58 k pcre aarch64 8.45-1.fc37.2 fedora 184 k pcre2 aarch64 10.40-1.fc37.1 fedora 219 k pcre2-syntax noarch 10.40-1.fc37.1 fedora 142 k perl-srpm-macros noarch 1-46.fc37 fedora 8.3 k pkgconf aarch64 1.8.0-3.fc37 fedora 41 k pkgconf-m4 noarch 1.8.0-3.fc37 fedora 14 k pkgconf-pkg-config aarch64 1.8.0-3.fc37 fedora 10 k popt aarch64 1.19~rc1-3.fc37 fedora 65 k publicsuffix-list-dafsa noarch 20210518-5.fc37 fedora 58 k python-srpm-macros noarch 3.11-4.fc37 fedora 25 k qt5-srpm-macros noarch 5.15.5-2.fc37 fedora 8.1 k readline aarch64 8.1-7.fc37 fedora 209 k rpm aarch64 4.18.0-0.beta1.4.fc37 fedora 565 k rpm-build-libs aarch64 4.18.0-0.beta1.4.fc37 fedora 90 k rpm-libs aarch64 4.18.0-0.beta1.4.fc37 fedora 311 k rpmautospec-rpm-macros noarch 0.3.0-1.fc37 fedora 8.8 k rust-srpm-macros noarch 22-1.fc37 fedora 9.5 k setup noarch 2.14.1-2.fc37 fedora 149 k sqlite-libs aarch64 3.39.2-2.fc37 fedora 658 k systemd-libs aarch64 251.4-51.fc37 fedora 591 k tzdata noarch 2022a-4.fc37 fedora 719 k util-linux-core aarch64 2.38.1-1.fc37 fedora 471 k xxhash-libs aarch64 0.8.1-3.fc37 fedora 33 k xz-libs aarch64 5.2.5-10.fc37 fedora 90 k zip aarch64 3.0-33.fc37 fedora 256 k zlib aarch64 1.2.12-4.fc37 fedora 93 k zstd aarch64 1.5.2-3.fc37 fedora 412 k Installing Groups: Buildsystem building group Transaction Summary ================================================================================ Install 152 Packages Total download size: 50 M Installed size: 204 M Downloading Packages: (1/152): alternatives-1.19-3.fc37.aarch64.rpm 778 kB/s | 35 kB 00:00 (2/152): ansible-srpm-macros-1-6.fc37.noarch.rp 166 kB/s | 7.5 kB 00:00 (3/152): audit-libs-3.0.8-3.fc37.aarch64.rpm 2.4 MB/s | 116 kB 00:00 (4/152): authselect-1.4.0-3.fc37.aarch64.rpm 27 MB/s | 144 kB 00:00 (5/152): basesystem-11-14.fc37.noarch.rpm 2.4 MB/s | 7.0 kB 00:00 (6/152): authselect-libs-1.4.0-3.fc37.aarch64.r 31 MB/s | 247 kB 00:00 (7/152): binutils-gold-2.38-24.fc38.aarch64.rpm 66 MB/s | 924 kB 00:00 (8/152): bash-5.1.16-3.fc37.aarch64.rpm 63 MB/s | 1.7 MB 00:00 (9/152): bzip2-1.0.8-12.fc37.aarch64.rpm 4.8 MB/s | 52 kB 00:00 (10/152): bzip2-libs-1.0.8-12.fc37.aarch64.rpm 6.6 MB/s | 43 kB 00:00 (11/152): ca-certificates-2022.2.54-5.fc37.noar 60 MB/s | 829 kB 00:00 (12/152): coreutils-9.1-6.fc37.aarch64.rpm 59 MB/s | 1.0 MB 00:00 (13/152): coreutils-common-9.1-6.fc37.aarch64.r 74 MB/s | 2.0 MB 00:00 (14/152): cpio-2.13-13.fc37.aarch64.rpm 13 MB/s | 274 kB 00:00 (15/152): cracklib-2.9.6-28.fc36.aarch64.rpm 9.6 MB/s | 93 kB 00:00 (16/152): crypto-policies-20220802-1.gita99dfd2 11 MB/s | 86 kB 00:00 (17/152): curl-7.84.0-2.fc37.aarch64.rpm 58 MB/s | 309 kB 00:00 (18/152): cyrus-sasl-lib-2.1.28-7.fc37.aarch64. 86 MB/s | 777 kB 00:00 (19/152): debugedit-5.0-5.fc37.aarch64.rpm 9.7 MB/s | 76 kB 00:00 (20/152): diffutils-3.8-3.fc37.aarch64.rpm 54 MB/s | 376 kB 00:00 (21/152): dwz-0.14-7.fc37.aarch64.rpm 20 MB/s | 126 kB 00:00 (22/152): ed-1.18-2.fc37.aarch64.rpm 16 MB/s | 78 kB 00:00 (23/152): efi-srpm-macros-5-6.fc37.noarch.rpm 5.4 MB/s | 22 kB 00:00 (24/152): elfutils-debuginfod-client-0.187-6.fc 15 MB/s | 38 kB 00:00 (25/152): elfutils-default-yama-scope-0.187-6.f 5.2 MB/s | 17 kB 00:00 (26/152): elfutils-0.187-6.fc37.aarch64.rpm 35 MB/s | 522 kB 00:00 (27/152): elfutils-libelf-0.187-6.fc37.aarch64. 34 MB/s | 197 kB 00:00 (28/152): elfutils-libs-0.187-6.fc37.aarch64.rp 45 MB/s | 256 kB 00:00 (29/152): fedora-gpg-keys-38-0.2.noarch.rpm 19 MB/s | 125 kB 00:00 (30/152): fedora-release-38-0.2.noarch.rpm 2.6 MB/s | 12 kB 00:00 (31/152): fedora-release-common-38-0.2.noarch.r 7.8 MB/s | 22 kB 00:00 (32/152): fedora-release-identity-basic-38-0.2. 5.6 MB/s | 12 kB 00:00 (33/152): fedora-repos-38-0.2.noarch.rpm 4.8 MB/s | 10 kB 00:00 (34/152): fedora-repos-rawhide-38-0.2.noarch.rp 3.8 MB/s | 9.6 kB 00:00 (35/152): binutils-2.38-24.fc38.aarch64.rpm 34 MB/s | 5.8 MB 00:00 (36/152): file-5.42-4.fc37.aarch64.rpm 2.9 MB/s | 49 kB 00:00 (37/152): file-libs-5.42-4.fc37.aarch64.rpm 32 MB/s | 674 kB 00:00 (38/152): filesystem-3.18-2.fc37.aarch64.rpm 58 MB/s | 1.1 MB 00:00 (39/152): findutils-4.9.0-2.fc37.aarch64.rpm 30 MB/s | 493 kB 00:00 (40/152): fonts-srpm-macros-2.0.5-8.fc37.noarch 2.9 MB/s | 26 kB 00:00 (41/152): fpc-srpm-macros-1.3-6.fc37.noarch.rpm 1.6 MB/s | 7.7 kB 00:00 (42/152): gdbm-libs-1.23-2.fc37.aarch64.rpm 9.4 MB/s | 57 kB 00:00 (43/152): ghc-srpm-macros-1.5.0-7.fc37.noarch.r 834 kB/s | 7.8 kB 00:00 (44/152): gawk-5.1.1-4.fc37.aarch64.rpm 21 MB/s | 1.0 MB 00:00 (45/152): glibc-2.36-1.fc37.aarch64.rpm 49 MB/s | 1.8 MB 00:00 (46/152): glibc-common-2.36-1.fc37.aarch64.rpm 14 MB/s | 355 kB 00:00 (47/152): glibc-gconv-extra-2.36-1.fc37.aarch64 59 MB/s | 1.7 MB 00:00 (48/152): glibc-minimal-langpack-2.36-1.fc37.aa 3.8 MB/s | 81 kB 00:00 (49/152): gdb-minimal-12.1-4.fc37.aarch64.rpm 32 MB/s | 3.5 MB 00:00 (50/152): gmp-6.2.1-3.fc37.aarch64.rpm 17 MB/s | 265 kB 00:00 (51/152): gnat-srpm-macros-4-16.fc37.noarch.rpm 872 kB/s | 8.3 kB 00:00 (52/152): go-srpm-macros-3.1.0-4.fc37.noarch.rp 12 MB/s | 27 kB 00:00 (53/152): gzip-1.12-2.fc37.aarch64.rpm 46 MB/s | 164 kB 00:00 (54/152): grep-3.7-4.fc37.aarch64.rpm 35 MB/s | 270 kB 00:00 (55/152): jansson-2.13.1-5.fc37.aarch64.rpm 13 MB/s | 46 kB 00:00 (56/152): info-6.8-4.fc37.aarch64.rpm 23 MB/s | 220 kB 00:00 (57/152): kernel-srpm-macros-1.0-15.fc37.noarch 2.6 MB/s | 9.4 kB 00:00 (58/152): keyutils-libs-1.6.1-5.fc37.aarch64.rp 11 MB/s | 31 kB 00:00 (59/152): libacl-2.3.1-4.fc37.aarch64.rpm 8.1 MB/s | 23 kB 00:00 (60/152): libarchive-3.6.1-2.fc37.aarch64.rpm 49 MB/s | 392 kB 00:00 (61/152): krb5-libs-1.19.2-11.fc37.1.aarch64.rp 59 MB/s | 733 kB 00:00 (62/152): libattr-2.5.1-5.fc37.aarch64.rpm 2.8 MB/s | 18 kB 00:00 (63/152): libblkid-2.38.1-1.fc37.aarch64.rpm 24 MB/s | 106 kB 00:00 (64/152): libbrotli-1.0.9-9.fc37.aarch64.rpm 67 MB/s | 318 kB 00:00 (65/152): libcap-2.48-5.fc37.aarch64.rpm 13 MB/s | 67 kB 00:00 (66/152): libcap-ng-0.8.3-3.fc37.aarch64.rpm 7.6 MB/s | 33 kB 00:00 (67/152): libcom_err-1.46.5-3.fc37.aarch64.rpm 3.8 MB/s | 25 kB 00:00 (68/152): libcurl-7.84.0-2.fc37.aarch64.rpm 41 MB/s | 301 kB 00:00 (69/152): libdb-5.3.28-53.fc37.aarch64.rpm 65 MB/s | 737 kB 00:00 (70/152): libeconf-0.4.0-4.fc37.aarch64.rpm 7.9 MB/s | 26 kB 00:00 (71/152): libevent-2.1.12-7.fc37.aarch64.rpm 36 MB/s | 254 kB 00:00 (72/152): libffi-3.4.2-9.fc37.aarch64.rpm 12 MB/s | 36 kB 00:00 (73/152): libfdisk-2.38.1-1.fc37.aarch64.rpm 21 MB/s | 155 kB 00:00 (74/152): libgcc-12.1.1-4.fc38.aarch64.rpm 21 MB/s | 92 kB 00:00 (75/152): libidn2-2.3.3-2.fc37.aarch64.rpm 21 MB/s | 114 kB 00:00 (76/152): libgomp-12.1.1-4.fc38.aarch64.rpm 31 MB/s | 290 kB 00:00 (77/152): libmount-2.38.1-1.fc37.aarch64.rpm 31 MB/s | 133 kB 00:00 (78/152): libnghttp2-1.48.0-2.fc37.aarch64.rpm 20 MB/s | 73 kB 00:00 (79/152): libpkgconf-1.8.0-3.fc37.aarch64.rpm 16 MB/s | 36 kB 00:00 (80/152): libnsl2-2.0.0-4.fc37.aarch64.rpm 7.1 MB/s | 30 kB 00:00 (81/152): libpsl-0.21.1-6.fc37.aarch64.rpm 19 MB/s | 63 kB 00:00 (82/152): libpwquality-1.4.4-11.fc37.aarch64.rp 35 MB/s | 116 kB 00:00 (83/152): libsemanage-3.4-5.fc37.aarch64.rpm 35 MB/s | 116 kB 00:00 (84/152): libselinux-3.4-5.fc37.aarch64.rpm 16 MB/s | 85 kB 00:00 (85/152): libsepol-3.4-3.fc37.aarch64.rpm 56 MB/s | 310 kB 00:00 (86/152): libsigsegv-2.14-3.fc37.aarch64.rpm 4.7 MB/s | 27 kB 00:00 (87/152): libsmartcols-2.38.1-1.fc37.aarch64.rp 15 MB/s | 63 kB 00:00 (88/152): libssh-0.9.6-5.fc37.aarch64.rpm 47 MB/s | 202 kB 00:00 (89/152): libssh-config-0.9.6-5.fc37.noarch.rpm 2.3 MB/s | 7.8 kB 00:00 (90/152): libtasn1-4.18.0-3.fc37.aarch64.rpm 19 MB/s | 73 kB 00:00 (91/152): libtirpc-1.3.3-0.fc37.aarch64.rpm 23 MB/s | 94 kB 00:00 (92/152): libstdc++-12.1.1-4.fc38.aarch64.rpm 68 MB/s | 760 kB 00:00 (93/152): libunistring-1.0-2.fc37.aarch64.rpm 78 MB/s | 543 kB 00:00 (94/152): libutempter-1.2.1-7.fc37.aarch64.rpm 3.7 MB/s | 26 kB 00:00 (95/152): libuuid-2.38.1-1.fc37.aarch64.rpm 7.8 MB/s | 28 kB 00:00 (96/152): libverto-0.3.2-4.fc37.aarch64.rpm 9.4 MB/s | 21 kB 00:00 (97/152): libxcrypt-4.4.28-3.fc38.aarch64.rpm 29 MB/s | 121 kB 00:00 (98/152): libxml2-2.9.14-3.fc37.aarch64.rpm 71 MB/s | 734 kB 00:00 (99/152): libzstd-1.5.2-3.fc37.aarch64.rpm 30 MB/s | 267 kB 00:00 (100/152): lua-libs-5.4.4-4.fc37.aarch64.rpm 38 MB/s | 213 kB 00:00 (101/152): lua-srpm-macros-1-7.fc37.noarch.rpm 3.1 MB/s | 8.8 kB 00:00 (102/152): lz4-libs-1.9.3-5.fc37.aarch64.rpm 22 MB/s | 70 kB 00:00 (103/152): mpfr-4.1.0-10.fc37.aarch64.rpm 49 MB/s | 240 kB 00:00 (104/152): ncurses-libs-6.3-3.20220501.fc37.aar 66 MB/s | 318 kB 00:00 (105/152): nim-srpm-macros-3-7.fc37.noarch.rpm 2.2 MB/s | 8.4 kB 00:00 (106/152): ncurses-base-6.3-3.20220501.fc37.noa 11 MB/s | 86 kB 00:00 (107/152): ocaml-srpm-macros-7-2.fc37.noarch.rp 6.5 MB/s | 13 kB 00:00 (108/152): openblas-srpm-macros-2-12.fc37.noarc 2.0 MB/s | 7.5 kB 00:00 (109/152): openldap-2.6.2-5.fc38.aarch64.rpm 21 MB/s | 250 kB 00:00 (110/152): openssl-libs-3.0.5-2.fc37.aarch64.rp 108 MB/s | 2.0 MB 00:00 (111/152): p11-kit-0.24.1-3.fc37.aarch64.rpm 31 MB/s | 361 kB 00:00 (112/152): p11-kit-trust-0.24.1-3.fc37.aarch64. 17 MB/s | 138 kB 00:00 (113/152): package-notes-srpm-macros-0.4-16.fc3 1.7 MB/s | 11 kB 00:00 (114/152): pam-1.5.2-14.fc37.aarch64.rpm 72 MB/s | 567 kB 00:00 (115/152): pam-libs-1.5.2-14.fc37.aarch64.rpm 8.3 MB/s | 58 kB 00:00 (116/152): patch-2.7.6-17.fc37.aarch64.rpm 39 MB/s | 121 kB 00:00 (117/152): pcre2-10.40-1.fc37.1.aarch64.rpm 39 MB/s | 219 kB 00:00 (118/152): pcre-8.45-1.fc37.2.aarch64.rpm 21 MB/s | 184 kB 00:00 (119/152): pcre2-syntax-10.40-1.fc37.1.noarch.r 32 MB/s | 142 kB 00:00 (120/152): perl-srpm-macros-1-46.fc37.noarch.rp 1.7 MB/s | 8.3 kB 00:00 (121/152): pkgconf-1.8.0-3.fc37.aarch64.rpm 9.6 MB/s | 41 kB 00:00 (122/152): pkgconf-m4-1.8.0-3.fc37.noarch.rpm 3.2 MB/s | 14 kB 00:00 (123/152): pkgconf-pkg-config-1.8.0-3.fc37.aarc 4.3 MB/s | 10 kB 00:00 (124/152): popt-1.19~rc1-3.fc37.aarch64.rpm 18 MB/s | 65 kB 00:00 (125/152): publicsuffix-list-dafsa-20210518-5.f 15 MB/s | 58 kB 00:00 (126/152): python-srpm-macros-3.11-4.fc37.noarc 7.7 MB/s | 25 kB 00:00 (127/152): qt5-srpm-macros-5.15.5-2.fc37.noarch 2.0 MB/s | 8.1 kB 00:00 (128/152): redhat-rpm-config-227-1.fc37.noarch. 19 MB/s | 80 kB 00:00 (129/152): readline-8.1-7.fc37.aarch64.rpm 31 MB/s | 209 kB 00:00 (130/152): rpm-build-4.18.0-0.beta1.4.fc37.aarc 27 MB/s | 77 kB 00:00 (131/152): rpm-4.18.0-0.beta1.4.fc37.aarch64.rp 68 MB/s | 565 kB 00:00 (132/152): rpm-build-libs-4.18.0-0.beta1.4.fc37 12 MB/s | 90 kB 00:00 (133/152): rpm-libs-4.18.0-0.beta1.4.fc37.aarch 48 MB/s | 311 kB 00:00 (134/152): rpmautospec-rpm-macros-0.3.0-1.fc37. 3.8 MB/s | 8.8 kB 00:00 (135/152): rust-srpm-macros-22-1.fc37.noarch.rp 2.8 MB/s | 9.5 kB 00:00 (136/152): sed-4.8-11.fc37.aarch64.rpm 55 MB/s | 304 kB 00:00 (137/152): setup-2.14.1-2.fc37.noarch.rpm 30 MB/s | 149 kB 00:00 (138/152): shadow-utils-4.11.1-4.fc37.aarch64.r 109 MB/s | 1.1 MB 00:00 (139/152): systemd-libs-251.4-51.fc37.aarch64.r 49 MB/s | 591 kB 00:00 (140/152): sqlite-libs-3.39.2-2.fc37.aarch64.rp 35 MB/s | 658 kB 00:00 (141/152): tar-1.34-3.fc36.aarch64.rpm 61 MB/s | 877 kB 00:00 (142/152): tzdata-2022a-4.fc37.noarch.rpm 73 MB/s | 719 kB 00:00 (143/152): unzip-6.0-58.fc37.aarch64.rpm 29 MB/s | 182 kB 00:00 (144/152): util-linux-core-2.38.1-1.fc37.aarch6 64 MB/s | 471 kB 00:00 (145/152): which-2.21-35.fc37.aarch64.rpm 6.5 MB/s | 41 kB 00:00 (146/152): xxhash-libs-0.8.1-3.fc37.aarch64.rpm 7.9 MB/s | 33 kB 00:00 (147/152): util-linux-2.38.1-1.fc37.aarch64.rpm 71 MB/s | 2.3 MB 00:00 (148/152): xz-5.2.5-10.fc37.aarch64.rpm 12 MB/s | 223 kB 00:00 (149/152): xz-libs-5.2.5-10.fc37.aarch64.rpm 7.1 MB/s | 90 kB 00:00 (150/152): zip-3.0-33.fc37.aarch64.rpm 50 MB/s | 256 kB 00:00 (151/152): zlib-1.2.12-4.fc37.aarch64.rpm 16 MB/s | 93 kB 00:00 (152/152): zstd-1.5.2-3.fc37.aarch64.rpm 39 MB/s | 412 kB 00:00 -------------------------------------------------------------------------------- Total 71 MB/s | 50 MB 00:00 fedora 1.6 MB/s | 1.6 kB 00:00 Importing GPG key 0xEB10B464: Userid : "Fedora (38) " Fingerprint: 6A51 BBAB BA3D 5467 B617 1221 809A 8D7C EB10 B464 From : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-38-primary Key imported successfully fedora 1.6 MB/s | 1.6 kB 00:00 GPG key at file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-38-primary (0xEB10B464) is already installed fedora 1.6 MB/s | 1.6 kB 00:00 Importing GPG key 0x5323552A: Userid : "Fedora (37) " Fingerprint: ACB5 EE4E 831C 74BB 7C16 8D27 F55A D3FB 5323 552A From : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-37-primary Key imported successfully Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Running scriptlet: filesystem-3.18-2.fc37.aarch64 1/1 Preparing : 1/1 Installing : libgcc-12.1.1-4.fc38.aarch64 1/152 Running scriptlet: libgcc-12.1.1-4.fc38.aarch64 1/152 Installing : crypto-policies-20220802-1.gita99dfd2.fc37.noarc 2/152 Running scriptlet: crypto-policies-20220802-1.gita99dfd2.fc37.noarc 2/152 Installing : fedora-release-identity-basic-38-0.2.noarch 3/152 Installing : tzdata-2022a-4.fc37.noarch 4/152 Installing : rust-srpm-macros-22-1.fc37.noarch 5/152 Installing : qt5-srpm-macros-5.15.5-2.fc37.noarch 6/152 Installing : publicsuffix-list-dafsa-20210518-5.fc37.noarch 7/152 Installing : pkgconf-m4-1.8.0-3.fc37.noarch 8/152 Installing : perl-srpm-macros-1-46.fc37.noarch 9/152 Installing : pcre2-syntax-10.40-1.fc37.1.noarch 10/152 Installing : openblas-srpm-macros-2-12.fc37.noarch 11/152 Installing : ocaml-srpm-macros-7-2.fc37.noarch 12/152 Installing : nim-srpm-macros-3-7.fc37.noarch 13/152 Installing : ncurses-base-6.3-3.20220501.fc37.noarch 14/152 Installing : libssh-config-0.9.6-5.fc37.noarch 15/152 Installing : kernel-srpm-macros-1.0-15.fc37.noarch 16/152 Installing : gnat-srpm-macros-4-16.fc37.noarch 17/152 Installing : ghc-srpm-macros-1.5.0-7.fc37.noarch 18/152 Installing : fpc-srpm-macros-1.3-6.fc37.noarch 19/152 Installing : fedora-gpg-keys-38-0.2.noarch 20/152 Installing : fedora-release-38-0.2.noarch 21/152 Installing : fedora-release-common-38-0.2.noarch 22/152 Installing : fedora-repos-rawhide-38-0.2.noarch 23/152 Installing : fedora-repos-38-0.2.noarch 24/152 Installing : setup-2.14.1-2.fc37.noarch 25/152 warning: /etc/hosts created as /etc/hosts.rpmnew Running scriptlet: setup-2.14.1-2.fc37.noarch 25/152 Installing : filesystem-3.18-2.fc37.aarch64 26/152 Installing : basesystem-11-14.fc37.noarch 27/152 Installing : glibc-gconv-extra-2.36-1.fc37.aarch64 28/152 Running scriptlet: glibc-gconv-extra-2.36-1.fc37.aarch64 28/152 Installing : glibc-minimal-langpack-2.36-1.fc37.aarch64 29/152 Installing : glibc-common-2.36-1.fc37.aarch64 30/152 Running scriptlet: glibc-2.36-1.fc37.aarch64 31/152 Installing : glibc-2.36-1.fc37.aarch64 31/152 Running scriptlet: glibc-2.36-1.fc37.aarch64 31/152 Installing : ncurses-libs-6.3-3.20220501.fc37.aarch64 32/152 Installing : bash-5.1.16-3.fc37.aarch64 33/152 Running scriptlet: bash-5.1.16-3.fc37.aarch64 33/152 Installing : zlib-1.2.12-4.fc37.aarch64 34/152 Installing : xz-libs-5.2.5-10.fc37.aarch64 35/152 Installing : bzip2-libs-1.0.8-12.fc37.aarch64 36/152 Installing : elfutils-libelf-0.187-6.fc37.aarch64 37/152 Installing : libstdc++-12.1.1-4.fc38.aarch64 38/152 Installing : libuuid-2.38.1-1.fc37.aarch64 39/152 Installing : libzstd-1.5.2-3.fc37.aarch64 40/152 Installing : popt-1.19~rc1-3.fc37.aarch64 41/152 Installing : libblkid-2.38.1-1.fc37.aarch64 42/152 Installing : readline-8.1-7.fc37.aarch64 43/152 Installing : gmp-1:6.2.1-3.fc37.aarch64 44/152 Installing : libattr-2.5.1-5.fc37.aarch64 45/152 Installing : libacl-2.3.1-4.fc37.aarch64 46/152 Installing : libcap-2.48-5.fc37.aarch64 47/152 Installing : libxcrypt-4.4.28-3.fc38.aarch64 48/152 Installing : lz4-libs-1.9.3-5.fc37.aarch64 49/152 Installing : systemd-libs-251.4-51.fc37.aarch64 50/152 Installing : mpfr-4.1.0-10.fc37.aarch64 51/152 Installing : dwz-0.14-7.fc37.aarch64 52/152 Installing : unzip-6.0-58.fc37.aarch64 53/152 Installing : file-libs-5.42-4.fc37.aarch64 54/152 Installing : file-5.42-4.fc37.aarch64 55/152 Installing : sqlite-libs-3.39.2-2.fc37.aarch64 56/152 Installing : alternatives-1.19-3.fc37.aarch64 57/152 Installing : libcap-ng-0.8.3-3.fc37.aarch64 58/152 Installing : audit-libs-3.0.8-3.fc37.aarch64 59/152 Installing : libcom_err-1.46.5-3.fc37.aarch64 60/152 Installing : libeconf-0.4.0-4.fc37.aarch64 61/152 Installing : pam-libs-1.5.2-14.fc37.aarch64 62/152 Installing : libsepol-3.4-3.fc37.aarch64 63/152 Installing : libsmartcols-2.38.1-1.fc37.aarch64 64/152 Installing : libunistring-1.0-2.fc37.aarch64 65/152 Installing : libidn2-2.3.3-2.fc37.aarch64 66/152 Installing : lua-libs-5.4.4-4.fc37.aarch64 67/152 Installing : libpsl-0.21.1-6.fc37.aarch64 68/152 Installing : zip-3.0-33.fc37.aarch64 69/152 Installing : zstd-1.5.2-3.fc37.aarch64 70/152 Installing : libfdisk-2.38.1-1.fc37.aarch64 71/152 Installing : bzip2-1.0.8-12.fc37.aarch64 72/152 Installing : libxml2-2.9.14-3.fc37.aarch64 73/152 Installing : ed-1.18-2.fc37.aarch64 74/152 Installing : elfutils-default-yama-scope-0.187-6.fc37.noarch 75/152 Running scriptlet: elfutils-default-yama-scope-0.187-6.fc37.noarch 75/152 Installing : package-notes-srpm-macros-0.4-16.fc37.noarch 76/152 Installing : cpio-2.13-13.fc37.aarch64 77/152 Installing : diffutils-3.8-3.fc37.aarch64 78/152 Installing : gdbm-libs-1:1.23-2.fc37.aarch64 79/152 Installing : cyrus-sasl-lib-2.1.28-7.fc37.aarch64 80/152 Installing : jansson-2.13.1-5.fc37.aarch64 81/152 Installing : keyutils-libs-1.6.1-5.fc37.aarch64 82/152 Installing : libbrotli-1.0.9-9.fc37.aarch64 83/152 Installing : libdb-5.3.28-53.fc37.aarch64 84/152 Installing : libffi-3.4.2-9.fc37.aarch64 85/152 Installing : p11-kit-0.24.1-3.fc37.aarch64 86/152 Installing : libgomp-12.1.1-4.fc38.aarch64 87/152 Installing : libnghttp2-1.48.0-2.fc37.aarch64 88/152 Installing : libpkgconf-1.8.0-3.fc37.aarch64 89/152 Installing : pkgconf-1.8.0-3.fc37.aarch64 90/152 Installing : pkgconf-pkg-config-1.8.0-3.fc37.aarch64 91/152 Installing : libsigsegv-2.14-3.fc37.aarch64 92/152 Installing : gawk-5.1.1-4.fc37.aarch64 93/152 Installing : libtasn1-4.18.0-3.fc37.aarch64 94/152 Installing : p11-kit-trust-0.24.1-3.fc37.aarch64 95/152 Running scriptlet: p11-kit-trust-0.24.1-3.fc37.aarch64 95/152 Installing : libverto-0.3.2-4.fc37.aarch64 96/152 Installing : pcre-8.45-1.fc37.2.aarch64 97/152 Installing : grep-3.7-4.fc37.aarch64 98/152 Installing : xz-5.2.5-10.fc37.aarch64 99/152 Installing : pcre2-10.40-1.fc37.1.aarch64 100/152 Installing : libselinux-3.4-5.fc37.aarch64 101/152 Installing : sed-4.8-11.fc37.aarch64 102/152 Installing : findutils-1:4.9.0-2.fc37.aarch64 103/152 Installing : libmount-2.38.1-1.fc37.aarch64 104/152 Installing : util-linux-core-2.38.1-1.fc37.aarch64 105/152 Installing : libsemanage-3.4-5.fc37.aarch64 106/152 Installing : shadow-utils-2:4.11.1-4.fc37.aarch64 107/152 Running scriptlet: libutempter-1.2.1-7.fc37.aarch64 108/152 Installing : libutempter-1.2.1-7.fc37.aarch64 108/152 Installing : patch-2.7.6-17.fc37.aarch64 109/152 Installing : tar-2:1.34-3.fc36.aarch64 110/152 Installing : xxhash-libs-0.8.1-3.fc37.aarch64 111/152 Installing : coreutils-common-9.1-6.fc37.aarch64 112/152 Installing : openssl-libs-1:3.0.5-2.fc37.aarch64 113/152 Installing : coreutils-9.1-6.fc37.aarch64 114/152 Running scriptlet: ca-certificates-2022.2.54-5.fc37.noarch 115/152 Installing : ca-certificates-2022.2.54-5.fc37.noarch 115/152 Running scriptlet: ca-certificates-2022.2.54-5.fc37.noarch 115/152 Installing : krb5-libs-1.19.2-11.fc37.1.aarch64 116/152 Installing : libtirpc-1.3.3-0.fc37.aarch64 117/152 Running scriptlet: authselect-libs-1.4.0-3.fc37.aarch64 118/152 Installing : authselect-libs-1.4.0-3.fc37.aarch64 118/152 Installing : gzip-1.12-2.fc37.aarch64 119/152 Installing : cracklib-2.9.6-28.fc36.aarch64 120/152 Installing : libpwquality-1.4.4-11.fc37.aarch64 121/152 Installing : authselect-1.4.0-3.fc37.aarch64 122/152 Installing : libnsl2-2.0.0-4.fc37.aarch64 123/152 Installing : pam-1.5.2-14.fc37.aarch64 124/152 Installing : libssh-0.9.6-5.fc37.aarch64 125/152 Installing : libarchive-3.6.1-2.fc37.aarch64 126/152 Installing : libevent-2.1.12-7.fc37.aarch64 127/152 Installing : openldap-2.6.2-5.fc38.aarch64 128/152 Installing : libcurl-7.84.0-2.fc37.aarch64 129/152 Installing : elfutils-libs-0.187-6.fc37.aarch64 130/152 Installing : elfutils-debuginfod-client-0.187-6.fc37.aarch64 131/152 Installing : binutils-gold-2.38-24.fc38.aarch64 132/152 Installing : binutils-2.38-24.fc38.aarch64 133/152 Running scriptlet: binutils-2.38-24.fc38.aarch64 133/152 Installing : elfutils-0.187-6.fc37.aarch64 134/152 Installing : gdb-minimal-12.1-4.fc37.aarch64 135/152 Installing : debugedit-5.0-5.fc37.aarch64 136/152 Installing : curl-7.84.0-2.fc37.aarch64 137/152 Running scriptlet: rpm-4.18.0-0.beta1.4.fc37.aarch64 138/152 Installing : rpm-4.18.0-0.beta1.4.fc37.aarch64 138/152 Installing : rpm-libs-4.18.0-0.beta1.4.fc37.aarch64 139/152 Installing : rpm-build-libs-4.18.0-0.beta1.4.fc37.aarch64 140/152 Installing : efi-srpm-macros-5-6.fc37.noarch 141/152 Installing : lua-srpm-macros-1-7.fc37.noarch 142/152 Installing : rpmautospec-rpm-macros-0.3.0-1.fc37.noarch 143/152 Installing : ansible-srpm-macros-1-6.fc37.noarch 144/152 Installing : fonts-srpm-macros-1:2.0.5-8.fc37.noarch 145/152 Installing : go-srpm-macros-3.1.0-4.fc37.noarch 146/152 Installing : python-srpm-macros-3.11-4.fc37.noarch 147/152 Installing : redhat-rpm-config-227-1.fc37.noarch 148/152 Installing : rpm-build-4.18.0-0.beta1.4.fc37.aarch64 149/152 Installing : util-linux-2.38.1-1.fc37.aarch64 150/152 Installing : which-2.21-35.fc37.aarch64 151/152 Installing : info-6.8-4.fc37.aarch64 152/152 Running scriptlet: filesystem-3.18-2.fc37.aarch64 152/152 Running scriptlet: ca-certificates-2022.2.54-5.fc37.noarch 152/152 Running scriptlet: authselect-libs-1.4.0-3.fc37.aarch64 152/152 Running scriptlet: rpm-4.18.0-0.beta1.4.fc37.aarch64 152/152 Running scriptlet: info-6.8-4.fc37.aarch64 152/152 Verifying : alternatives-1.19-3.fc37.aarch64 1/152 Verifying : ansible-srpm-macros-1-6.fc37.noarch 2/152 Verifying : audit-libs-3.0.8-3.fc37.aarch64 3/152 Verifying : authselect-1.4.0-3.fc37.aarch64 4/152 Verifying : authselect-libs-1.4.0-3.fc37.aarch64 5/152 Verifying : basesystem-11-14.fc37.noarch 6/152 Verifying : bash-5.1.16-3.fc37.aarch64 7/152 Verifying : binutils-2.38-24.fc38.aarch64 8/152 Verifying : binutils-gold-2.38-24.fc38.aarch64 9/152 Verifying : bzip2-1.0.8-12.fc37.aarch64 10/152 Verifying : bzip2-libs-1.0.8-12.fc37.aarch64 11/152 Verifying : ca-certificates-2022.2.54-5.fc37.noarch 12/152 Verifying : coreutils-9.1-6.fc37.aarch64 13/152 Verifying : coreutils-common-9.1-6.fc37.aarch64 14/152 Verifying : cpio-2.13-13.fc37.aarch64 15/152 Verifying : cracklib-2.9.6-28.fc36.aarch64 16/152 Verifying : crypto-policies-20220802-1.gita99dfd2.fc37.noarc 17/152 Verifying : curl-7.84.0-2.fc37.aarch64 18/152 Verifying : cyrus-sasl-lib-2.1.28-7.fc37.aarch64 19/152 Verifying : debugedit-5.0-5.fc37.aarch64 20/152 Verifying : diffutils-3.8-3.fc37.aarch64 21/152 Verifying : dwz-0.14-7.fc37.aarch64 22/152 Verifying : ed-1.18-2.fc37.aarch64 23/152 Verifying : efi-srpm-macros-5-6.fc37.noarch 24/152 Verifying : elfutils-0.187-6.fc37.aarch64 25/152 Verifying : elfutils-debuginfod-client-0.187-6.fc37.aarch64 26/152 Verifying : elfutils-default-yama-scope-0.187-6.fc37.noarch 27/152 Verifying : elfutils-libelf-0.187-6.fc37.aarch64 28/152 Verifying : elfutils-libs-0.187-6.fc37.aarch64 29/152 Verifying : fedora-gpg-keys-38-0.2.noarch 30/152 Verifying : fedora-release-38-0.2.noarch 31/152 Verifying : fedora-release-common-38-0.2.noarch 32/152 Verifying : fedora-release-identity-basic-38-0.2.noarch 33/152 Verifying : fedora-repos-38-0.2.noarch 34/152 Verifying : fedora-repos-rawhide-38-0.2.noarch 35/152 Verifying : file-5.42-4.fc37.aarch64 36/152 Verifying : file-libs-5.42-4.fc37.aarch64 37/152 Verifying : filesystem-3.18-2.fc37.aarch64 38/152 Verifying : findutils-1:4.9.0-2.fc37.aarch64 39/152 Verifying : fonts-srpm-macros-1:2.0.5-8.fc37.noarch 40/152 Verifying : fpc-srpm-macros-1.3-6.fc37.noarch 41/152 Verifying : gawk-5.1.1-4.fc37.aarch64 42/152 Verifying : gdb-minimal-12.1-4.fc37.aarch64 43/152 Verifying : gdbm-libs-1:1.23-2.fc37.aarch64 44/152 Verifying : ghc-srpm-macros-1.5.0-7.fc37.noarch 45/152 Verifying : glibc-2.36-1.fc37.aarch64 46/152 Verifying : glibc-common-2.36-1.fc37.aarch64 47/152 Verifying : glibc-gconv-extra-2.36-1.fc37.aarch64 48/152 Verifying : glibc-minimal-langpack-2.36-1.fc37.aarch64 49/152 Verifying : gmp-1:6.2.1-3.fc37.aarch64 50/152 Verifying : gnat-srpm-macros-4-16.fc37.noarch 51/152 Verifying : go-srpm-macros-3.1.0-4.fc37.noarch 52/152 Verifying : grep-3.7-4.fc37.aarch64 53/152 Verifying : gzip-1.12-2.fc37.aarch64 54/152 Verifying : info-6.8-4.fc37.aarch64 55/152 Verifying : jansson-2.13.1-5.fc37.aarch64 56/152 Verifying : kernel-srpm-macros-1.0-15.fc37.noarch 57/152 Verifying : keyutils-libs-1.6.1-5.fc37.aarch64 58/152 Verifying : krb5-libs-1.19.2-11.fc37.1.aarch64 59/152 Verifying : libacl-2.3.1-4.fc37.aarch64 60/152 Verifying : libarchive-3.6.1-2.fc37.aarch64 61/152 Verifying : libattr-2.5.1-5.fc37.aarch64 62/152 Verifying : libblkid-2.38.1-1.fc37.aarch64 63/152 Verifying : libbrotli-1.0.9-9.fc37.aarch64 64/152 Verifying : libcap-2.48-5.fc37.aarch64 65/152 Verifying : libcap-ng-0.8.3-3.fc37.aarch64 66/152 Verifying : libcom_err-1.46.5-3.fc37.aarch64 67/152 Verifying : libcurl-7.84.0-2.fc37.aarch64 68/152 Verifying : libdb-5.3.28-53.fc37.aarch64 69/152 Verifying : libeconf-0.4.0-4.fc37.aarch64 70/152 Verifying : libevent-2.1.12-7.fc37.aarch64 71/152 Verifying : libfdisk-2.38.1-1.fc37.aarch64 72/152 Verifying : libffi-3.4.2-9.fc37.aarch64 73/152 Verifying : libgcc-12.1.1-4.fc38.aarch64 74/152 Verifying : libgomp-12.1.1-4.fc38.aarch64 75/152 Verifying : libidn2-2.3.3-2.fc37.aarch64 76/152 Verifying : libmount-2.38.1-1.fc37.aarch64 77/152 Verifying : libnghttp2-1.48.0-2.fc37.aarch64 78/152 Verifying : libnsl2-2.0.0-4.fc37.aarch64 79/152 Verifying : libpkgconf-1.8.0-3.fc37.aarch64 80/152 Verifying : libpsl-0.21.1-6.fc37.aarch64 81/152 Verifying : libpwquality-1.4.4-11.fc37.aarch64 82/152 Verifying : libselinux-3.4-5.fc37.aarch64 83/152 Verifying : libsemanage-3.4-5.fc37.aarch64 84/152 Verifying : libsepol-3.4-3.fc37.aarch64 85/152 Verifying : libsigsegv-2.14-3.fc37.aarch64 86/152 Verifying : libsmartcols-2.38.1-1.fc37.aarch64 87/152 Verifying : libssh-0.9.6-5.fc37.aarch64 88/152 Verifying : libssh-config-0.9.6-5.fc37.noarch 89/152 Verifying : libstdc++-12.1.1-4.fc38.aarch64 90/152 Verifying : libtasn1-4.18.0-3.fc37.aarch64 91/152 Verifying : libtirpc-1.3.3-0.fc37.aarch64 92/152 Verifying : libunistring-1.0-2.fc37.aarch64 93/152 Verifying : libutempter-1.2.1-7.fc37.aarch64 94/152 Verifying : libuuid-2.38.1-1.fc37.aarch64 95/152 Verifying : libverto-0.3.2-4.fc37.aarch64 96/152 Verifying : libxcrypt-4.4.28-3.fc38.aarch64 97/152 Verifying : libxml2-2.9.14-3.fc37.aarch64 98/152 Verifying : libzstd-1.5.2-3.fc37.aarch64 99/152 Verifying : lua-libs-5.4.4-4.fc37.aarch64 100/152 Verifying : lua-srpm-macros-1-7.fc37.noarch 101/152 Verifying : lz4-libs-1.9.3-5.fc37.aarch64 102/152 Verifying : mpfr-4.1.0-10.fc37.aarch64 103/152 Verifying : ncurses-base-6.3-3.20220501.fc37.noarch 104/152 Verifying : ncurses-libs-6.3-3.20220501.fc37.aarch64 105/152 Verifying : nim-srpm-macros-3-7.fc37.noarch 106/152 Verifying : ocaml-srpm-macros-7-2.fc37.noarch 107/152 Verifying : openblas-srpm-macros-2-12.fc37.noarch 108/152 Verifying : openldap-2.6.2-5.fc38.aarch64 109/152 Verifying : openssl-libs-1:3.0.5-2.fc37.aarch64 110/152 Verifying : p11-kit-0.24.1-3.fc37.aarch64 111/152 Verifying : p11-kit-trust-0.24.1-3.fc37.aarch64 112/152 Verifying : package-notes-srpm-macros-0.4-16.fc37.noarch 113/152 Verifying : pam-1.5.2-14.fc37.aarch64 114/152 Verifying : pam-libs-1.5.2-14.fc37.aarch64 115/152 Verifying : patch-2.7.6-17.fc37.aarch64 116/152 Verifying : pcre-8.45-1.fc37.2.aarch64 117/152 Verifying : pcre2-10.40-1.fc37.1.aarch64 118/152 Verifying : pcre2-syntax-10.40-1.fc37.1.noarch 119/152 Verifying : perl-srpm-macros-1-46.fc37.noarch 120/152 Verifying : pkgconf-1.8.0-3.fc37.aarch64 121/152 Verifying : pkgconf-m4-1.8.0-3.fc37.noarch 122/152 Verifying : pkgconf-pkg-config-1.8.0-3.fc37.aarch64 123/152 Verifying : popt-1.19~rc1-3.fc37.aarch64 124/152 Verifying : publicsuffix-list-dafsa-20210518-5.fc37.noarch 125/152 Verifying : python-srpm-macros-3.11-4.fc37.noarch 126/152 Verifying : qt5-srpm-macros-5.15.5-2.fc37.noarch 127/152 Verifying : readline-8.1-7.fc37.aarch64 128/152 Verifying : redhat-rpm-config-227-1.fc37.noarch 129/152 Verifying : rpm-4.18.0-0.beta1.4.fc37.aarch64 130/152 Verifying : rpm-build-4.18.0-0.beta1.4.fc37.aarch64 131/152 Verifying : rpm-build-libs-4.18.0-0.beta1.4.fc37.aarch64 132/152 Verifying : rpm-libs-4.18.0-0.beta1.4.fc37.aarch64 133/152 Verifying : rpmautospec-rpm-macros-0.3.0-1.fc37.noarch 134/152 Verifying : rust-srpm-macros-22-1.fc37.noarch 135/152 Verifying : sed-4.8-11.fc37.aarch64 136/152 Verifying : setup-2.14.1-2.fc37.noarch 137/152 Verifying : shadow-utils-2:4.11.1-4.fc37.aarch64 138/152 Verifying : sqlite-libs-3.39.2-2.fc37.aarch64 139/152 Verifying : systemd-libs-251.4-51.fc37.aarch64 140/152 Verifying : tar-2:1.34-3.fc36.aarch64 141/152 Verifying : tzdata-2022a-4.fc37.noarch 142/152 Verifying : unzip-6.0-58.fc37.aarch64 143/152 Verifying : util-linux-2.38.1-1.fc37.aarch64 144/152 Verifying : util-linux-core-2.38.1-1.fc37.aarch64 145/152 Verifying : which-2.21-35.fc37.aarch64 146/152 Verifying : xxhash-libs-0.8.1-3.fc37.aarch64 147/152 Verifying : xz-5.2.5-10.fc37.aarch64 148/152 Verifying : xz-libs-5.2.5-10.fc37.aarch64 149/152 Verifying : zip-3.0-33.fc37.aarch64 150/152 Verifying : zlib-1.2.12-4.fc37.aarch64 151/152 Verifying : zstd-1.5.2-3.fc37.aarch64 152/152 Installed products updated. Installed: alternatives-1.19-3.fc37.aarch64 ansible-srpm-macros-1-6.fc37.noarch audit-libs-3.0.8-3.fc37.aarch64 authselect-1.4.0-3.fc37.aarch64 authselect-libs-1.4.0-3.fc37.aarch64 basesystem-11-14.fc37.noarch bash-5.1.16-3.fc37.aarch64 binutils-2.38-24.fc38.aarch64 binutils-gold-2.38-24.fc38.aarch64 bzip2-1.0.8-12.fc37.aarch64 bzip2-libs-1.0.8-12.fc37.aarch64 ca-certificates-2022.2.54-5.fc37.noarch coreutils-9.1-6.fc37.aarch64 coreutils-common-9.1-6.fc37.aarch64 cpio-2.13-13.fc37.aarch64 cracklib-2.9.6-28.fc36.aarch64 crypto-policies-20220802-1.gita99dfd2.fc37.noarch curl-7.84.0-2.fc37.aarch64 cyrus-sasl-lib-2.1.28-7.fc37.aarch64 debugedit-5.0-5.fc37.aarch64 diffutils-3.8-3.fc37.aarch64 dwz-0.14-7.fc37.aarch64 ed-1.18-2.fc37.aarch64 efi-srpm-macros-5-6.fc37.noarch elfutils-0.187-6.fc37.aarch64 elfutils-debuginfod-client-0.187-6.fc37.aarch64 elfutils-default-yama-scope-0.187-6.fc37.noarch elfutils-libelf-0.187-6.fc37.aarch64 elfutils-libs-0.187-6.fc37.aarch64 fedora-gpg-keys-38-0.2.noarch fedora-release-38-0.2.noarch fedora-release-common-38-0.2.noarch fedora-release-identity-basic-38-0.2.noarch fedora-repos-38-0.2.noarch fedora-repos-rawhide-38-0.2.noarch file-5.42-4.fc37.aarch64 file-libs-5.42-4.fc37.aarch64 filesystem-3.18-2.fc37.aarch64 findutils-1:4.9.0-2.fc37.aarch64 fonts-srpm-macros-1:2.0.5-8.fc37.noarch fpc-srpm-macros-1.3-6.fc37.noarch gawk-5.1.1-4.fc37.aarch64 gdb-minimal-12.1-4.fc37.aarch64 gdbm-libs-1:1.23-2.fc37.aarch64 ghc-srpm-macros-1.5.0-7.fc37.noarch glibc-2.36-1.fc37.aarch64 glibc-common-2.36-1.fc37.aarch64 glibc-gconv-extra-2.36-1.fc37.aarch64 glibc-minimal-langpack-2.36-1.fc37.aarch64 gmp-1:6.2.1-3.fc37.aarch64 gnat-srpm-macros-4-16.fc37.noarch go-srpm-macros-3.1.0-4.fc37.noarch grep-3.7-4.fc37.aarch64 gzip-1.12-2.fc37.aarch64 info-6.8-4.fc37.aarch64 jansson-2.13.1-5.fc37.aarch64 kernel-srpm-macros-1.0-15.fc37.noarch keyutils-libs-1.6.1-5.fc37.aarch64 krb5-libs-1.19.2-11.fc37.1.aarch64 libacl-2.3.1-4.fc37.aarch64 libarchive-3.6.1-2.fc37.aarch64 libattr-2.5.1-5.fc37.aarch64 libblkid-2.38.1-1.fc37.aarch64 libbrotli-1.0.9-9.fc37.aarch64 libcap-2.48-5.fc37.aarch64 libcap-ng-0.8.3-3.fc37.aarch64 libcom_err-1.46.5-3.fc37.aarch64 libcurl-7.84.0-2.fc37.aarch64 libdb-5.3.28-53.fc37.aarch64 libeconf-0.4.0-4.fc37.aarch64 libevent-2.1.12-7.fc37.aarch64 libfdisk-2.38.1-1.fc37.aarch64 libffi-3.4.2-9.fc37.aarch64 libgcc-12.1.1-4.fc38.aarch64 libgomp-12.1.1-4.fc38.aarch64 libidn2-2.3.3-2.fc37.aarch64 libmount-2.38.1-1.fc37.aarch64 libnghttp2-1.48.0-2.fc37.aarch64 libnsl2-2.0.0-4.fc37.aarch64 libpkgconf-1.8.0-3.fc37.aarch64 libpsl-0.21.1-6.fc37.aarch64 libpwquality-1.4.4-11.fc37.aarch64 libselinux-3.4-5.fc37.aarch64 libsemanage-3.4-5.fc37.aarch64 libsepol-3.4-3.fc37.aarch64 libsigsegv-2.14-3.fc37.aarch64 libsmartcols-2.38.1-1.fc37.aarch64 libssh-0.9.6-5.fc37.aarch64 libssh-config-0.9.6-5.fc37.noarch libstdc++-12.1.1-4.fc38.aarch64 libtasn1-4.18.0-3.fc37.aarch64 libtirpc-1.3.3-0.fc37.aarch64 libunistring-1.0-2.fc37.aarch64 libutempter-1.2.1-7.fc37.aarch64 libuuid-2.38.1-1.fc37.aarch64 libverto-0.3.2-4.fc37.aarch64 libxcrypt-4.4.28-3.fc38.aarch64 libxml2-2.9.14-3.fc37.aarch64 libzstd-1.5.2-3.fc37.aarch64 lua-libs-5.4.4-4.fc37.aarch64 lua-srpm-macros-1-7.fc37.noarch lz4-libs-1.9.3-5.fc37.aarch64 mpfr-4.1.0-10.fc37.aarch64 ncurses-base-6.3-3.20220501.fc37.noarch ncurses-libs-6.3-3.20220501.fc37.aarch64 nim-srpm-macros-3-7.fc37.noarch ocaml-srpm-macros-7-2.fc37.noarch openblas-srpm-macros-2-12.fc37.noarch openldap-2.6.2-5.fc38.aarch64 openssl-libs-1:3.0.5-2.fc37.aarch64 p11-kit-0.24.1-3.fc37.aarch64 p11-kit-trust-0.24.1-3.fc37.aarch64 package-notes-srpm-macros-0.4-16.fc37.noarch pam-1.5.2-14.fc37.aarch64 pam-libs-1.5.2-14.fc37.aarch64 patch-2.7.6-17.fc37.aarch64 pcre-8.45-1.fc37.2.aarch64 pcre2-10.40-1.fc37.1.aarch64 pcre2-syntax-10.40-1.fc37.1.noarch perl-srpm-macros-1-46.fc37.noarch pkgconf-1.8.0-3.fc37.aarch64 pkgconf-m4-1.8.0-3.fc37.noarch pkgconf-pkg-config-1.8.0-3.fc37.aarch64 popt-1.19~rc1-3.fc37.aarch64 publicsuffix-list-dafsa-20210518-5.fc37.noarch python-srpm-macros-3.11-4.fc37.noarch qt5-srpm-macros-5.15.5-2.fc37.noarch readline-8.1-7.fc37.aarch64 redhat-rpm-config-227-1.fc37.noarch rpm-4.18.0-0.beta1.4.fc37.aarch64 rpm-build-4.18.0-0.beta1.4.fc37.aarch64 rpm-build-libs-4.18.0-0.beta1.4.fc37.aarch64 rpm-libs-4.18.0-0.beta1.4.fc37.aarch64 rpmautospec-rpm-macros-0.3.0-1.fc37.noarch rust-srpm-macros-22-1.fc37.noarch sed-4.8-11.fc37.aarch64 setup-2.14.1-2.fc37.noarch shadow-utils-2:4.11.1-4.fc37.aarch64 sqlite-libs-3.39.2-2.fc37.aarch64 systemd-libs-251.4-51.fc37.aarch64 tar-2:1.34-3.fc36.aarch64 tzdata-2022a-4.fc37.noarch unzip-6.0-58.fc37.aarch64 util-linux-2.38.1-1.fc37.aarch64 util-linux-core-2.38.1-1.fc37.aarch64 which-2.21-35.fc37.aarch64 xxhash-libs-0.8.1-3.fc37.aarch64 xz-5.2.5-10.fc37.aarch64 xz-libs-5.2.5-10.fc37.aarch64 zip-3.0-33.fc37.aarch64 zlib-1.2.12-4.fc37.aarch64 zstd-1.5.2-3.fc37.aarch64 Complete! Finish: dnf install Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: gpg-pubkey-eb10b464-6202d9c6 libacl-2.3.1-4.fc37.aarch64 qt5-srpm-macros-5.15.5-2.fc37.noarch zlib-1.2.12-4.fc37.aarch64 zstd-1.5.2-3.fc37.aarch64 zip-3.0-33.fc37.aarch64 fedora-gpg-keys-38-0.2.noarch libtirpc-1.3.3-0.fc37.aarch64 libidn2-2.3.3-2.fc37.aarch64 pam-1.5.2-14.fc37.aarch64 libarchive-3.6.1-2.fc37.aarch64 binutils-2.38-24.fc38.aarch64 cyrus-sasl-lib-2.1.28-7.fc37.aarch64 rpm-4.18.0-0.beta1.4.fc37.aarch64 perl-srpm-macros-1-46.fc37.noarch binutils-gold-2.38-24.fc38.aarch64 xz-5.2.5-10.fc37.aarch64 openblas-srpm-macros-2-12.fc37.noarch libxcrypt-4.4.28-3.fc38.aarch64 audit-libs-3.0.8-3.fc37.aarch64 libsmartcols-2.38.1-1.fc37.aarch64 libstdc++-12.1.1-4.fc38.aarch64 mpfr-4.1.0-10.fc37.aarch64 libcom_err-1.46.5-3.fc37.aarch64 bzip2-1.0.8-12.fc37.aarch64 tzdata-2022a-4.fc37.noarch libsemanage-3.4-5.fc37.aarch64 libuuid-2.38.1-1.fc37.aarch64 nim-srpm-macros-3-7.fc37.noarch gzip-1.12-2.fc37.aarch64 libssh-config-0.9.6-5.fc37.noarch file-libs-5.42-4.fc37.aarch64 setup-2.14.1-2.fc37.noarch glibc-common-2.36-1.fc37.aarch64 libevent-2.1.12-7.fc37.aarch64 popt-1.19~rc1-3.fc37.aarch64 basesystem-11-14.fc37.noarch libpkgconf-1.8.0-3.fc37.aarch64 libnsl2-2.0.0-4.fc37.aarch64 fedora-release-identity-basic-38-0.2.noarch gnat-srpm-macros-4-16.fc37.noarch libnghttp2-1.48.0-2.fc37.aarch64 libunistring-1.0-2.fc37.aarch64 fedora-repos-38-0.2.noarch libxml2-2.9.14-3.fc37.aarch64 cpio-2.13-13.fc37.aarch64 go-srpm-macros-3.1.0-4.fc37.noarch elfutils-debuginfod-client-0.187-6.fc37.aarch64 xxhash-libs-0.8.1-3.fc37.aarch64 ocaml-srpm-macros-7-2.fc37.noarch crypto-policies-20220802-1.gita99dfd2.fc37.noarch libgcc-12.1.1-4.fc38.aarch64 libcap-ng-0.8.3-3.fc37.aarch64 pkgconf-pkg-config-1.8.0-3.fc37.aarch64 ncurses-libs-6.3-3.20220501.fc37.aarch64 authselect-1.4.0-3.fc37.aarch64 shadow-utils-4.11.1-4.fc37.aarch64 ca-certificates-2022.2.54-5.fc37.noarch ghc-srpm-macros-1.5.0-7.fc37.noarch gpg-pubkey-5323552a-6112bcdc libtasn1-4.18.0-3.fc37.aarch64 p11-kit-trust-0.24.1-3.fc37.aarch64 rpm-build-4.18.0-0.beta1.4.fc37.aarch64 gdb-minimal-12.1-4.fc37.aarch64 elfutils-0.187-6.fc37.aarch64 glibc-gconv-extra-2.36-1.fc37.aarch64 curl-7.84.0-2.fc37.aarch64 lz4-libs-1.9.3-5.fc37.aarch64 elfutils-libs-0.187-6.fc37.aarch64 libgomp-12.1.1-4.fc38.aarch64 xz-libs-5.2.5-10.fc37.aarch64 info-6.8-4.fc37.aarch64 efi-srpm-macros-5-6.fc37.noarch bzip2-libs-1.0.8-12.fc37.aarch64 openssl-libs-3.0.5-2.fc37.aarch64 pam-libs-1.5.2-14.fc37.aarch64 krb5-libs-1.19.2-11.fc37.1.aarch64 ansible-srpm-macros-1-6.fc37.noarch dwz-0.14-7.fc37.aarch64 rust-srpm-macros-22-1.fc37.noarch findutils-4.9.0-2.fc37.aarch64 libmount-2.38.1-1.fc37.aarch64 glibc-minimal-langpack-2.36-1.fc37.aarch64 libfdisk-2.38.1-1.fc37.aarch64 patch-2.7.6-17.fc37.aarch64 libdb-5.3.28-53.fc37.aarch64 alternatives-1.19-3.fc37.aarch64 sed-4.8-11.fc37.aarch64 libsepol-3.4-3.fc37.aarch64 fedora-release-common-38-0.2.noarch sqlite-libs-3.39.2-2.fc37.aarch64 libeconf-0.4.0-4.fc37.aarch64 tar-1.34-3.fc36.aarch64 coreutils-9.1-6.fc37.aarch64 bash-5.1.16-3.fc37.aarch64 cracklib-2.9.6-28.fc36.aarch64 libblkid-2.38.1-1.fc37.aarch64 grep-3.7-4.fc37.aarch64 package-notes-srpm-macros-0.4-16.fc37.noarch readline-8.1-7.fc37.aarch64 pcre2-10.40-1.fc37.1.aarch64 rpm-build-libs-4.18.0-0.beta1.4.fc37.aarch64 libffi-3.4.2-9.fc37.aarch64 lua-srpm-macros-1-7.fc37.noarch redhat-rpm-config-227-1.fc37.noarch python-srpm-macros-3.11-4.fc37.noarch pcre-8.45-1.fc37.2.aarch64 libpwquality-1.4.4-11.fc37.aarch64 gdbm-libs-1.23-2.fc37.aarch64 libpsl-0.21.1-6.fc37.aarch64 lua-libs-5.4.4-4.fc37.aarch64 publicsuffix-list-dafsa-20210518-5.fc37.noarch coreutils-common-9.1-6.fc37.aarch64 ncurses-base-6.3-3.20220501.fc37.noarch libcap-2.48-5.fc37.aarch64 keyutils-libs-1.6.1-5.fc37.aarch64 fedora-repos-rawhide-38-0.2.noarch libssh-0.9.6-5.fc37.aarch64 libselinux-3.4-5.fc37.aarch64 unzip-6.0-58.fc37.aarch64 authselect-libs-1.4.0-3.fc37.aarch64 openldap-2.6.2-5.fc38.aarch64 pkgconf-1.8.0-3.fc37.aarch64 jansson-2.13.1-5.fc37.aarch64 gawk-5.1.1-4.fc37.aarch64 diffutils-3.8-3.fc37.aarch64 debugedit-5.0-5.fc37.aarch64 p11-kit-0.24.1-3.fc37.aarch64 file-5.42-4.fc37.aarch64 filesystem-3.18-2.fc37.aarch64 which-2.21-35.fc37.aarch64 fpc-srpm-macros-1.3-6.fc37.noarch libcurl-7.84.0-2.fc37.aarch64 fedora-release-38-0.2.noarch rpm-libs-4.18.0-0.beta1.4.fc37.aarch64 libsigsegv-2.14-3.fc37.aarch64 gmp-6.2.1-3.fc37.aarch64 ed-1.18-2.fc37.aarch64 util-linux-core-2.38.1-1.fc37.aarch64 elfutils-libelf-0.187-6.fc37.aarch64 fonts-srpm-macros-2.0.5-8.fc37.noarch libverto-0.3.2-4.fc37.aarch64 pkgconf-m4-1.8.0-3.fc37.noarch libutempter-1.2.1-7.fc37.aarch64 glibc-2.36-1.fc37.aarch64 libattr-2.5.1-5.fc37.aarch64 util-linux-2.38.1-1.fc37.aarch64 elfutils-default-yama-scope-0.187-6.fc37.noarch kernel-srpm-macros-1.0-15.fc37.noarch libbrotli-1.0.9-9.fc37.aarch64 pcre2-syntax-10.40-1.fc37.1.noarch systemd-libs-251.4-51.fc37.aarch64 rpmautospec-rpm-macros-0.3.0-1.fc37.noarch libzstd-1.5.2-3.fc37.aarch64 Start: buildsrpm Start: rpmbuild -bs Building target platforms: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1660521600 Wrote: /builddir/build/SRPMS/htslib-1.15.1-1.fc38.src.rpm Finish: rpmbuild -bs INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-aarch64-1660557065.245354/root/var/log/dnf.rpm.log /var/lib/mock/fedora-rawhide-aarch64-1660557065.245354/root/var/log/dnf.librepo.log /var/lib/mock/fedora-rawhide-aarch64-1660557065.245354/root/var/log/dnf.log Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-m5uvbacp/htslib/htslib.spec) Config(child) 1 minutes 10 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot Finish: run Running (timeout=18000): unbuffer mock --rebuild /var/lib/copr-rpmbuild/results/htslib-1.15.1-1.fc38.src.rpm --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1660557065.245354 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 3.1 starting (python version = 3.10.4, NVR = mock-3.1-1.fc35)... Start: init plugins INFO: tmpfs initialized INFO: selinux enabled INFO: chroot_scan: initialized INFO: compress_logs: initialized Finish: init plugins INFO: Signal handler active Start: run INFO: Start(/var/lib/copr-rpmbuild/results/htslib-1.15.1-1.fc38.src.rpm) Config(fedora-rawhide-aarch64) Start: clean chroot Finish: clean chroot Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-aarch64-1660557065.245354/root. INFO: calling preinit hooks INFO: enabled root cache Start: unpacking root cache Finish: unpacking root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin Mock Version: 3.1 INFO: Mock Version: 3.1 Start: dnf update No matches found for the following disable plugin patterns: local, spacewalk, versionlock Updating Subscription Management repositories. Unable to read consumer identity This system is not registered with an entitlement server. You can use subscription-manager to register. Copr repository 77 kB/s | 3.3 kB 00:00 fedora 153 kB/s | 12 kB 00:00 Dependencies resolved. Nothing to do. Complete! Finish: dnf update Finish: chroot init Start: build phase for htslib-1.15.1-1.fc38.src.rpm Start: build setup for htslib-1.15.1-1.fc38.src.rpm Building target platforms: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1660521600 Wrote: /builddir/build/SRPMS/htslib-1.15.1-1.fc38.src.rpm No matches found for the following disable plugin patterns: local, spacewalk, versionlock Updating Subscription Management repositories. Unable to read consumer identity This system is not registered with an entitlement server. You can use subscription-manager to register. Copr repository 129 kB/s | 3.3 kB 00:00 fedora 179 kB/s | 12 kB 00:00 Dependencies resolved. ================================================================================ Package Arch Version Repo Size ================================================================================ Installing: bzip2-devel aarch64 1.0.8-12.fc37 fedora 214 k gcc aarch64 12.1.1-4.fc38 fedora 29 M libcurl-devel aarch64 7.84.0-2.fc37 fedora 977 k make aarch64 1:4.3-11.fc37 fedora 537 k openssl-devel aarch64 1:3.0.5-2.fc37 fedora 3.1 M perl-Data-Dumper aarch64 2.184-490.fc37 fedora 55 k perl-FindBin noarch 1.53-491.fc37 fedora 18 k perl-Getopt-Long noarch 1:2.52-489.fc37 fedora 60 k perl-interpreter aarch64 4:5.36.0-491.fc37 fedora 76 k perl-lib aarch64 0.65-491.fc37 fedora 19 k xz-devel aarch64 5.2.5-10.fc37 fedora 57 k zlib-devel aarch64 1.2.12-4.fc37 fedora 44 k Installing dependencies: annobin-docs noarch 10.81-1.fc38 fedora 91 k annobin-plugin-gcc aarch64 10.81-1.fc38 fedora 882 k cpp aarch64 12.1.1-4.fc38 fedora 9.2 M gc aarch64 8.0.6-4.fc37 fedora 102 k gcc-plugin-annobin aarch64 12.1.1-4.fc38 fedora 50 k glibc-devel aarch64 2.36-1.fc37 fedora 583 k groff-base aarch64 1.22.4-10.fc37 fedora 1.0 M guile22 aarch64 2.2.7-6.fc37 fedora 6.5 M kernel-headers aarch64 5.19.0-1.fc37 fedora 1.5 M libasan aarch64 12.1.1-4.fc38 fedora 421 k libatomic aarch64 12.1.1-4.fc38 fedora 41 k libmpc aarch64 1.2.1-5.fc37 fedora 62 k libtool-ltdl aarch64 2.4.7-2.fc37 fedora 37 k libubsan aarch64 12.1.1-4.fc38 fedora 190 k libxcrypt-devel aarch64 4.4.28-3.fc38 fedora 28 k ncurses aarch64 6.3-3.20220501.fc37 fedora 409 k perl-B aarch64 1.83-491.fc37 fedora 187 k perl-Carp noarch 1.52-489.fc37 fedora 29 k perl-Class-Struct noarch 0.66-491.fc37 fedora 26 k perl-DynaLoader aarch64 1.52-491.fc37 fedora 30 k perl-Encode aarch64 4:3.19-491.fc37 fedora 1.7 M perl-Errno aarch64 1.36-491.fc37 fedora 19 k perl-Exporter noarch 5.77-489.fc37 fedora 31 k perl-Fcntl aarch64 1.15-491.fc37 fedora 25 k perl-File-Basename noarch 2.85-491.fc37 fedora 22 k perl-File-Path noarch 2.18-489.fc37 fedora 35 k perl-File-Temp noarch 1:0.231.100-489.fc37 fedora 59 k perl-File-stat noarch 1.12-491.fc37 fedora 22 k perl-Getopt-Std noarch 1.13-491.fc37 fedora 20 k perl-HTTP-Tiny noarch 0.082-1.fc37 fedora 55 k perl-IO aarch64 1.50-491.fc37 fedora 96 k perl-IPC-Open3 noarch 1.22-491.fc37 fedora 27 k perl-MIME-Base64 aarch64 3.16-489.fc37 fedora 30 k perl-POSIX aarch64 2.03-491.fc37 fedora 102 k perl-PathTools aarch64 3.84-489.fc37 fedora 90 k perl-Pod-Escapes noarch 1:1.07-489.fc37 fedora 20 k perl-Pod-Perldoc noarch 3.28.01-490.fc37 fedora 90 k perl-Pod-Simple noarch 1:3.43-490.fc37 fedora 225 k perl-Pod-Usage noarch 4:2.03-3.fc37 fedora 40 k perl-Scalar-List-Utils aarch64 5:1.63-489.fc38 fedora 71 k perl-SelectSaver noarch 1.02-491.fc37 fedora 16 k perl-Socket aarch64 4:2.035-2.fc37 fedora 55 k perl-Storable aarch64 1:3.26-489.fc37 fedora 95 k perl-Symbol noarch 1.09-491.fc37 fedora 19 k perl-Term-ANSIColor noarch 5.01-490.fc37 fedora 48 k perl-Term-Cap noarch 1.17-489.fc37 fedora 22 k perl-Text-ParseWords noarch 3.31-489.fc37 fedora 16 k perl-Text-Tabs+Wrap noarch 2021.0814-489.fc37 fedora 22 k perl-Time-Local noarch 2:1.300-489.fc37 fedora 33 k perl-constant noarch 1.33-490.fc37 fedora 23 k perl-if noarch 0.61.000-491.fc37 fedora 18 k perl-libs aarch64 4:5.36.0-491.fc37 fedora 2.2 M perl-mro aarch64 1.26-491.fc37 fedora 33 k perl-overload noarch 1.35-491.fc37 fedora 50 k perl-overloading noarch 0.02-491.fc37 fedora 17 k perl-parent noarch 1:0.238-489.fc37 fedora 14 k perl-podlators noarch 1:4.14-489.fc37 fedora 116 k perl-subs noarch 1.04-491.fc37 fedora 16 k perl-vars noarch 1.05-491.fc37 fedora 17 k Transaction Summary ================================================================================ Install 71 Packages Total download size: 60 M Installed size: 195 M Downloading Packages: (1/71): bzip2-devel-1.0.8-12.fc37.aarch64.rpm 4.1 MB/s | 214 kB 00:00 (2/71): annobin-docs-10.81-1.fc38.noarch.rpm 1.6 MB/s | 91 kB 00:00 (3/71): annobin-plugin-gcc-10.81-1.fc38.aarch64 15 MB/s | 882 kB 00:00 (4/71): gc-8.0.6-4.fc37.aarch64.rpm 15 MB/s | 102 kB 00:00 (5/71): gcc-plugin-annobin-12.1.1-4.fc38.aarch6 13 MB/s | 50 kB 00:00 (6/71): glibc-devel-2.36-1.fc37.aarch64.rpm 37 MB/s | 583 kB 00:00 (7/71): groff-base-1.22.4-10.fc37.aarch64.rpm 49 MB/s | 1.0 MB 00:00 (8/71): guile22-2.2.7-6.fc37.aarch64.rpm 53 MB/s | 6.5 MB 00:00 (9/71): cpp-12.1.1-4.fc38.aarch64.rpm 43 MB/s | 9.2 MB 00:00 (10/71): kernel-headers-5.19.0-1.fc37.aarch64.r 26 MB/s | 1.5 MB 00:00 (11/71): libasan-12.1.1-4.fc38.aarch64.rpm 12 MB/s | 421 kB 00:00 (12/71): libatomic-12.1.1-4.fc38.aarch64.rpm 3.0 MB/s | 41 kB 00:00 (13/71): libmpc-1.2.1-5.fc37.aarch64.rpm 9.7 MB/s | 62 kB 00:00 (14/71): libtool-ltdl-2.4.7-2.fc37.aarch64.rpm 4.9 MB/s | 37 kB 00:00 (15/71): libcurl-devel-7.84.0-2.fc37.aarch64.rp 35 MB/s | 977 kB 00:00 (16/71): libubsan-12.1.1-4.fc38.aarch64.rpm 18 MB/s | 190 kB 00:00 (17/71): libxcrypt-devel-4.4.28-3.fc38.aarch64. 4.6 MB/s | 28 kB 00:00 (18/71): make-4.3-11.fc37.aarch64.rpm 47 MB/s | 537 kB 00:00 (19/71): ncurses-6.3-3.20220501.fc37.aarch64.rp 33 MB/s | 409 kB 00:00 (20/71): perl-B-1.83-491.fc37.aarch64.rpm 17 MB/s | 187 kB 00:00 (21/71): perl-Carp-1.52-489.fc37.noarch.rpm 2.9 MB/s | 29 kB 00:00 (22/71): perl-Class-Struct-0.66-491.fc37.noarch 2.4 MB/s | 26 kB 00:00 (23/71): perl-Data-Dumper-2.184-490.fc37.aarch6 6.1 MB/s | 55 kB 00:00 (24/71): openssl-devel-3.0.5-2.fc37.aarch64.rpm 52 MB/s | 3.1 MB 00:00 (25/71): perl-DynaLoader-1.52-491.fc37.aarch64. 2.6 MB/s | 30 kB 00:00 (26/71): perl-Errno-1.36-491.fc37.aarch64.rpm 2.5 MB/s | 19 kB 00:00 (27/71): perl-Exporter-5.77-489.fc37.noarch.rpm 4.0 MB/s | 31 kB 00:00 (28/71): gcc-12.1.1-4.fc38.aarch64.rpm 63 MB/s | 29 MB 00:00 (29/71): perl-Encode-3.19-491.fc37.aarch64.rpm 19 MB/s | 1.7 MB 00:00 (30/71): perl-Fcntl-1.15-491.fc37.aarch64.rpm 393 kB/s | 25 kB 00:00 (31/71): perl-File-Basename-2.85-491.fc37.noarc 7.4 MB/s | 22 kB 00:00 (32/71): perl-File-Path-2.18-489.fc37.noarch.rp 7.8 MB/s | 35 kB 00:00 (33/71): perl-File-Temp-0.231.100-489.fc37.noar 12 MB/s | 59 kB 00:00 (34/71): perl-File-stat-1.12-491.fc37.noarch.rp 4.8 MB/s | 22 kB 00:00 (35/71): perl-FindBin-1.53-491.fc37.noarch.rpm 5.6 MB/s | 18 kB 00:00 (36/71): perl-Getopt-Long-2.52-489.fc37.noarch. 10 MB/s | 60 kB 00:00 (37/71): perl-Getopt-Std-1.13-491.fc37.noarch.r 5.8 MB/s | 20 kB 00:00 (38/71): perl-HTTP-Tiny-0.082-1.fc37.noarch.rpm 12 MB/s | 55 kB 00:00 (39/71): perl-MIME-Base64-3.16-489.fc37.aarch64 5.8 MB/s | 30 kB 00:00 (40/71): perl-IO-1.50-491.fc37.aarch64.rpm 11 MB/s | 96 kB 00:00 (41/71): perl-IPC-Open3-1.22-491.fc37.noarch.rp 2.7 MB/s | 27 kB 00:00 (42/71): perl-POSIX-2.03-491.fc37.aarch64.rpm 23 MB/s | 102 kB 00:00 (43/71): perl-PathTools-3.84-489.fc37.aarch64.r 18 MB/s | 90 kB 00:00 (44/71): perl-Pod-Escapes-1.07-489.fc37.noarch. 4.8 MB/s | 20 kB 00:00 (45/71): perl-Pod-Perldoc-3.28.01-490.fc37.noar 22 MB/s | 90 kB 00:00 (46/71): perl-Pod-Usage-2.03-3.fc37.noarch.rpm 8.2 MB/s | 40 kB 00:00 (47/71): perl-Pod-Simple-3.43-490.fc37.noarch.r 33 MB/s | 225 kB 00:00 (48/71): perl-SelectSaver-1.02-491.fc37.noarch. 5.5 MB/s | 16 kB 00:00 (49/71): perl-Scalar-List-Utils-1.63-489.fc38.a 10 MB/s | 71 kB 00:00 (50/71): perl-Socket-2.035-2.fc37.aarch64.rpm 9.7 MB/s | 55 kB 00:00 (51/71): perl-Symbol-1.09-491.fc37.noarch.rpm 5.3 MB/s | 19 kB 00:00 (52/71): perl-Storable-3.26-489.fc37.aarch64.rp 15 MB/s | 95 kB 00:00 (53/71): perl-Term-ANSIColor-5.01-490.fc37.noar 12 MB/s | 48 kB 00:00 (54/71): perl-Term-Cap-1.17-489.fc37.noarch.rpm 6.0 MB/s | 22 kB 00:00 (55/71): perl-Text-ParseWords-3.31-489.fc37.noa 4.5 MB/s | 16 kB 00:00 (56/71): perl-Text-Tabs+Wrap-2021.0814-489.fc37 6.6 MB/s | 22 kB 00:00 (57/71): perl-Time-Local-1.300-489.fc37.noarch. 9.1 MB/s | 33 kB 00:00 (58/71): perl-constant-1.33-490.fc37.noarch.rpm 6.6 MB/s | 23 kB 00:00 (59/71): perl-if-0.61.000-491.fc37.noarch.rpm 5.1 MB/s | 18 kB 00:00 (60/71): perl-interpreter-5.36.0-491.fc37.aarch 18 MB/s | 76 kB 00:00 (61/71): perl-lib-0.65-491.fc37.aarch64.rpm 4.2 MB/s | 19 kB 00:00 (62/71): perl-mro-1.26-491.fc37.aarch64.rpm 9.8 MB/s | 33 kB 00:00 (63/71): perl-overload-1.35-491.fc37.noarch.rpm 13 MB/s | 50 kB 00:00 (64/71): perl-overloading-0.02-491.fc37.noarch. 5.1 MB/s | 17 kB 00:00 (65/71): perl-parent-0.238-489.fc37.noarch.rpm 4.6 MB/s | 14 kB 00:00 (66/71): perl-podlators-4.14-489.fc37.noarch.rp 19 MB/s | 116 kB 00:00 (67/71): perl-subs-1.04-491.fc37.noarch.rpm 4.2 MB/s | 16 kB 00:00 (68/71): perl-vars-1.05-491.fc37.noarch.rpm 4.6 MB/s | 17 kB 00:00 (69/71): perl-libs-5.36.0-491.fc37.aarch64.rpm 67 MB/s | 2.2 MB 00:00 (70/71): xz-devel-5.2.5-10.fc37.aarch64.rpm 5.6 MB/s | 57 kB 00:00 (71/71): zlib-devel-1.2.12-4.fc37.aarch64.rpm 7.3 MB/s | 44 kB 00:00 -------------------------------------------------------------------------------- Total 65 MB/s | 60 MB 00:00 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Installing : libmpc-1.2.1-5.fc37.aarch64 1/71 Installing : cpp-12.1.1-4.fc38.aarch64 2/71 Installing : ncurses-6.3-3.20220501.fc37.aarch64 3/71 Installing : libubsan-12.1.1-4.fc38.aarch64 4/71 Installing : libtool-ltdl-2.4.7-2.fc37.aarch64 5/71 Installing : libatomic-12.1.1-4.fc38.aarch64 6/71 Installing : libasan-12.1.1-4.fc38.aarch64 7/71 Installing : kernel-headers-5.19.0-1.fc37.aarch64 8/71 Installing : libxcrypt-devel-4.4.28-3.fc38.aarch64 9/71 Installing : glibc-devel-2.36-1.fc37.aarch64 10/71 Running scriptlet: groff-base-1.22.4-10.fc37.aarch64 11/71 Installing : groff-base-1.22.4-10.fc37.aarch64 11/71 Running scriptlet: groff-base-1.22.4-10.fc37.aarch64 11/71 Installing : perl-Text-Tabs+Wrap-2021.0814-489.fc37.noarch 12/71 Installing : perl-if-0.61.000-491.fc37.noarch 13/71 Installing : perl-Time-Local-2:1.300-489.fc37.noarch 14/71 Installing : perl-File-Path-2.18-489.fc37.noarch 15/71 Installing : perl-Pod-Escapes-1:1.07-489.fc37.noarch 16/71 Installing : perl-Class-Struct-0.66-491.fc37.noarch 17/71 Installing : perl-POSIX-2.03-491.fc37.aarch64 18/71 Installing : perl-Term-ANSIColor-5.01-490.fc37.noarch 19/71 Installing : perl-IPC-Open3-1.22-491.fc37.noarch 20/71 Installing : perl-HTTP-Tiny-0.082-1.fc37.noarch 21/71 Installing : perl-subs-1.04-491.fc37.noarch 22/71 Installing : perl-File-Temp-1:0.231.100-489.fc37.noarch 23/71 Installing : perl-Term-Cap-1.17-489.fc37.noarch 24/71 Installing : perl-Pod-Simple-1:3.43-490.fc37.noarch 25/71 Installing : perl-Socket-4:2.035-2.fc37.aarch64 26/71 Installing : perl-SelectSaver-1.02-491.fc37.noarch 27/71 Installing : perl-Symbol-1.09-491.fc37.noarch 28/71 Installing : perl-File-stat-1.12-491.fc37.noarch 29/71 Installing : perl-podlators-1:4.14-489.fc37.noarch 30/71 Installing : perl-Pod-Perldoc-3.28.01-490.fc37.noarch 31/71 Installing : perl-Fcntl-1.15-491.fc37.aarch64 32/71 Installing : perl-Text-ParseWords-3.31-489.fc37.noarch 33/71 Installing : perl-mro-1.26-491.fc37.aarch64 34/71 Installing : perl-IO-1.50-491.fc37.aarch64 35/71 Installing : perl-overloading-0.02-491.fc37.noarch 36/71 Installing : perl-Pod-Usage-4:2.03-3.fc37.noarch 37/71 Installing : perl-Errno-1.36-491.fc37.aarch64 38/71 Installing : perl-File-Basename-2.85-491.fc37.noarch 39/71 Installing : perl-Getopt-Std-1.13-491.fc37.noarch 40/71 Installing : perl-MIME-Base64-3.16-489.fc37.aarch64 41/71 Installing : perl-Scalar-List-Utils-5:1.63-489.fc38.aarch64 42/71 Installing : perl-constant-1.33-490.fc37.noarch 43/71 Installing : perl-Storable-1:3.26-489.fc37.aarch64 44/71 Installing : perl-overload-1.35-491.fc37.noarch 45/71 Installing : perl-parent-1:0.238-489.fc37.noarch 46/71 Installing : perl-vars-1.05-491.fc37.noarch 47/71 Installing : perl-Getopt-Long-1:2.52-489.fc37.noarch 48/71 Installing : perl-Carp-1.52-489.fc37.noarch 49/71 Installing : perl-Exporter-5.77-489.fc37.noarch 50/71 Installing : perl-PathTools-3.84-489.fc37.aarch64 51/71 Installing : perl-DynaLoader-1.52-491.fc37.aarch64 52/71 Installing : perl-Encode-4:3.19-491.fc37.aarch64 53/71 Installing : perl-libs-4:5.36.0-491.fc37.aarch64 54/71 Installing : perl-interpreter-4:5.36.0-491.fc37.aarch64 55/71 Installing : perl-Data-Dumper-2.184-490.fc37.aarch64 56/71 Installing : perl-B-1.83-491.fc37.aarch64 57/71 Installing : gc-8.0.6-4.fc37.aarch64 58/71 Installing : guile22-2.2.7-6.fc37.aarch64 59/71 Installing : make-1:4.3-11.fc37.aarch64 60/71 Installing : gcc-12.1.1-4.fc38.aarch64 61/71 Running scriptlet: gcc-12.1.1-4.fc38.aarch64 61/71 Installing : annobin-docs-10.81-1.fc38.noarch 62/71 Installing : annobin-plugin-gcc-10.81-1.fc38.aarch64 63/71 Running scriptlet: annobin-plugin-gcc-10.81-1.fc38.aarch64 63/71 Installing : gcc-plugin-annobin-12.1.1-4.fc38.aarch64 64/71 Installing : perl-FindBin-1.53-491.fc37.noarch 65/71 Installing : perl-lib-0.65-491.fc37.aarch64 66/71 Installing : zlib-devel-1.2.12-4.fc37.aarch64 67/71 Installing : xz-devel-5.2.5-10.fc37.aarch64 68/71 Installing : openssl-devel-1:3.0.5-2.fc37.aarch64 69/71 Installing : libcurl-devel-7.84.0-2.fc37.aarch64 70/71 Installing : bzip2-devel-1.0.8-12.fc37.aarch64 71/71 Running scriptlet: bzip2-devel-1.0.8-12.fc37.aarch64 71/71 Verifying : annobin-docs-10.81-1.fc38.noarch 1/71 Verifying : annobin-plugin-gcc-10.81-1.fc38.aarch64 2/71 Verifying : bzip2-devel-1.0.8-12.fc37.aarch64 3/71 Verifying : cpp-12.1.1-4.fc38.aarch64 4/71 Verifying : gc-8.0.6-4.fc37.aarch64 5/71 Verifying : gcc-12.1.1-4.fc38.aarch64 6/71 Verifying : gcc-plugin-annobin-12.1.1-4.fc38.aarch64 7/71 Verifying : glibc-devel-2.36-1.fc37.aarch64 8/71 Verifying : groff-base-1.22.4-10.fc37.aarch64 9/71 Verifying : guile22-2.2.7-6.fc37.aarch64 10/71 Verifying : kernel-headers-5.19.0-1.fc37.aarch64 11/71 Verifying : libasan-12.1.1-4.fc38.aarch64 12/71 Verifying : libatomic-12.1.1-4.fc38.aarch64 13/71 Verifying : libcurl-devel-7.84.0-2.fc37.aarch64 14/71 Verifying : libmpc-1.2.1-5.fc37.aarch64 15/71 Verifying : libtool-ltdl-2.4.7-2.fc37.aarch64 16/71 Verifying : libubsan-12.1.1-4.fc38.aarch64 17/71 Verifying : libxcrypt-devel-4.4.28-3.fc38.aarch64 18/71 Verifying : make-1:4.3-11.fc37.aarch64 19/71 Verifying : ncurses-6.3-3.20220501.fc37.aarch64 20/71 Verifying : openssl-devel-1:3.0.5-2.fc37.aarch64 21/71 Verifying : perl-B-1.83-491.fc37.aarch64 22/71 Verifying : perl-Carp-1.52-489.fc37.noarch 23/71 Verifying : perl-Class-Struct-0.66-491.fc37.noarch 24/71 Verifying : perl-Data-Dumper-2.184-490.fc37.aarch64 25/71 Verifying : perl-DynaLoader-1.52-491.fc37.aarch64 26/71 Verifying : perl-Encode-4:3.19-491.fc37.aarch64 27/71 Verifying : perl-Errno-1.36-491.fc37.aarch64 28/71 Verifying : perl-Exporter-5.77-489.fc37.noarch 29/71 Verifying : perl-Fcntl-1.15-491.fc37.aarch64 30/71 Verifying : perl-File-Basename-2.85-491.fc37.noarch 31/71 Verifying : perl-File-Path-2.18-489.fc37.noarch 32/71 Verifying : perl-File-Temp-1:0.231.100-489.fc37.noarch 33/71 Verifying : perl-File-stat-1.12-491.fc37.noarch 34/71 Verifying : perl-FindBin-1.53-491.fc37.noarch 35/71 Verifying : perl-Getopt-Long-1:2.52-489.fc37.noarch 36/71 Verifying : perl-Getopt-Std-1.13-491.fc37.noarch 37/71 Verifying : perl-HTTP-Tiny-0.082-1.fc37.noarch 38/71 Verifying : perl-IO-1.50-491.fc37.aarch64 39/71 Verifying : perl-IPC-Open3-1.22-491.fc37.noarch 40/71 Verifying : perl-MIME-Base64-3.16-489.fc37.aarch64 41/71 Verifying : perl-POSIX-2.03-491.fc37.aarch64 42/71 Verifying : perl-PathTools-3.84-489.fc37.aarch64 43/71 Verifying : perl-Pod-Escapes-1:1.07-489.fc37.noarch 44/71 Verifying : perl-Pod-Perldoc-3.28.01-490.fc37.noarch 45/71 Verifying : perl-Pod-Simple-1:3.43-490.fc37.noarch 46/71 Verifying : perl-Pod-Usage-4:2.03-3.fc37.noarch 47/71 Verifying : perl-Scalar-List-Utils-5:1.63-489.fc38.aarch64 48/71 Verifying : perl-SelectSaver-1.02-491.fc37.noarch 49/71 Verifying : perl-Socket-4:2.035-2.fc37.aarch64 50/71 Verifying : perl-Storable-1:3.26-489.fc37.aarch64 51/71 Verifying : perl-Symbol-1.09-491.fc37.noarch 52/71 Verifying : perl-Term-ANSIColor-5.01-490.fc37.noarch 53/71 Verifying : perl-Term-Cap-1.17-489.fc37.noarch 54/71 Verifying : perl-Text-ParseWords-3.31-489.fc37.noarch 55/71 Verifying : perl-Text-Tabs+Wrap-2021.0814-489.fc37.noarch 56/71 Verifying : perl-Time-Local-2:1.300-489.fc37.noarch 57/71 Verifying : perl-constant-1.33-490.fc37.noarch 58/71 Verifying : perl-if-0.61.000-491.fc37.noarch 59/71 Verifying : perl-interpreter-4:5.36.0-491.fc37.aarch64 60/71 Verifying : perl-lib-0.65-491.fc37.aarch64 61/71 Verifying : perl-libs-4:5.36.0-491.fc37.aarch64 62/71 Verifying : perl-mro-1.26-491.fc37.aarch64 63/71 Verifying : perl-overload-1.35-491.fc37.noarch 64/71 Verifying : perl-overloading-0.02-491.fc37.noarch 65/71 Verifying : perl-parent-1:0.238-489.fc37.noarch 66/71 Verifying : perl-podlators-1:4.14-489.fc37.noarch 67/71 Verifying : perl-subs-1.04-491.fc37.noarch 68/71 Verifying : perl-vars-1.05-491.fc37.noarch 69/71 Verifying : xz-devel-5.2.5-10.fc37.aarch64 70/71 Verifying : zlib-devel-1.2.12-4.fc37.aarch64 71/71 Installed products updated. Installed: annobin-docs-10.81-1.fc38.noarch annobin-plugin-gcc-10.81-1.fc38.aarch64 bzip2-devel-1.0.8-12.fc37.aarch64 cpp-12.1.1-4.fc38.aarch64 gc-8.0.6-4.fc37.aarch64 gcc-12.1.1-4.fc38.aarch64 gcc-plugin-annobin-12.1.1-4.fc38.aarch64 glibc-devel-2.36-1.fc37.aarch64 groff-base-1.22.4-10.fc37.aarch64 guile22-2.2.7-6.fc37.aarch64 kernel-headers-5.19.0-1.fc37.aarch64 libasan-12.1.1-4.fc38.aarch64 libatomic-12.1.1-4.fc38.aarch64 libcurl-devel-7.84.0-2.fc37.aarch64 libmpc-1.2.1-5.fc37.aarch64 libtool-ltdl-2.4.7-2.fc37.aarch64 libubsan-12.1.1-4.fc38.aarch64 libxcrypt-devel-4.4.28-3.fc38.aarch64 make-1:4.3-11.fc37.aarch64 ncurses-6.3-3.20220501.fc37.aarch64 openssl-devel-1:3.0.5-2.fc37.aarch64 perl-B-1.83-491.fc37.aarch64 perl-Carp-1.52-489.fc37.noarch perl-Class-Struct-0.66-491.fc37.noarch perl-Data-Dumper-2.184-490.fc37.aarch64 perl-DynaLoader-1.52-491.fc37.aarch64 perl-Encode-4:3.19-491.fc37.aarch64 perl-Errno-1.36-491.fc37.aarch64 perl-Exporter-5.77-489.fc37.noarch perl-Fcntl-1.15-491.fc37.aarch64 perl-File-Basename-2.85-491.fc37.noarch perl-File-Path-2.18-489.fc37.noarch perl-File-Temp-1:0.231.100-489.fc37.noarch perl-File-stat-1.12-491.fc37.noarch perl-FindBin-1.53-491.fc37.noarch perl-Getopt-Long-1:2.52-489.fc37.noarch perl-Getopt-Std-1.13-491.fc37.noarch perl-HTTP-Tiny-0.082-1.fc37.noarch perl-IO-1.50-491.fc37.aarch64 perl-IPC-Open3-1.22-491.fc37.noarch perl-MIME-Base64-3.16-489.fc37.aarch64 perl-POSIX-2.03-491.fc37.aarch64 perl-PathTools-3.84-489.fc37.aarch64 perl-Pod-Escapes-1:1.07-489.fc37.noarch perl-Pod-Perldoc-3.28.01-490.fc37.noarch perl-Pod-Simple-1:3.43-490.fc37.noarch perl-Pod-Usage-4:2.03-3.fc37.noarch perl-Scalar-List-Utils-5:1.63-489.fc38.aarch64 perl-SelectSaver-1.02-491.fc37.noarch perl-Socket-4:2.035-2.fc37.aarch64 perl-Storable-1:3.26-489.fc37.aarch64 perl-Symbol-1.09-491.fc37.noarch perl-Term-ANSIColor-5.01-490.fc37.noarch perl-Term-Cap-1.17-489.fc37.noarch perl-Text-ParseWords-3.31-489.fc37.noarch perl-Text-Tabs+Wrap-2021.0814-489.fc37.noarch perl-Time-Local-2:1.300-489.fc37.noarch perl-constant-1.33-490.fc37.noarch perl-if-0.61.000-491.fc37.noarch perl-interpreter-4:5.36.0-491.fc37.aarch64 perl-lib-0.65-491.fc37.aarch64 perl-libs-4:5.36.0-491.fc37.aarch64 perl-mro-1.26-491.fc37.aarch64 perl-overload-1.35-491.fc37.noarch perl-overloading-0.02-491.fc37.noarch perl-parent-1:0.238-489.fc37.noarch perl-podlators-1:4.14-489.fc37.noarch perl-subs-1.04-491.fc37.noarch perl-vars-1.05-491.fc37.noarch xz-devel-5.2.5-10.fc37.aarch64 zlib-devel-1.2.12-4.fc37.aarch64 Complete! Finish: build setup for htslib-1.15.1-1.fc38.src.rpm Start: rpmbuild htslib-1.15.1-1.fc38.src.rpm Building target platforms: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1660521600 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.ww7CAe + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf htslib-1.15.1 + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/htslib-1.15.1.tar.bz2 + STATUS=0 + '[' 0 -ne 0 ']' + cd htslib-1.15.1 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + echo 'Patch #0 (htslib-1.15.1-gcc12.patch):' Patch #0 (htslib-1.15.1-gcc12.patch): + /usr/bin/patch --no-backup-if-mismatch -f -p1 --fuzz=0 patching file htscodecs/htscodecs/rANS_word.h + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.0H3ljd + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules' + export FCFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-1.fc38.aarch64.ld' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + '[' -f /usr/lib/rpm/generate-rpm-note.sh ']' + /usr/lib/rpm/generate-rpm-note.sh htslib 1.15.1-1.fc38 aarch64 + cd htslib-1.15.1 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules' + export FCFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-1.fc38.aarch64.ld' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + '[' '-flto=auto -ffat-lto-objectsx' '!=' x ']' ++ find . -type f -name configure -print + for file in $(find . -type f -name configure -print) + /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\) = /__attribute__ ((used)) char (*f) () = /g' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\);/__attribute__ ((used)) char (*f) ();/g' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed -r --in-place=.backup 's/^char \$2 \(\);/__attribute__ ((used)) char \$2 ();/g' ./configure + diff -u ./configure.backup ./configure --- ./configure.backup 2022-04-07 15:42:52.000000000 +0000 +++ ./configure 2022-08-15 09:52:41.858405478 +0000 @@ -1697,7 +1697,7 @@ #ifdef __cplusplus extern "C" #endif -char $2 (); +__attribute__ ((used)) char $2 (); /* The GNU C library defines this for functions which it implements to always fail with ENOSYS. Some functions are actually named something starting with __ and the normal name is an alias. */ + /usr/bin/sed --in-place=.backup '1{$!N;$!N};$!N;s/int x = 1;\nint y = 0;\nint z;\nint nan;/volatile int x = 1; volatile int y = 0; volatile int z, nan;/;P;D' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed --in-place=.backup 's#^lt_cv_sys_global_symbol_to_cdecl=.*#lt_cv_sys_global_symbol_to_cdecl="sed -n -e '\''s/^T .* \\(.*\\)$/extern int \\1();/p'\'' -e '\''s/^$symcode* .* \\(.*\\)$/extern char \\1;/p'\''"#' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + '[' 1 = 1 ']' +++ dirname ./configure ++ find . -name config.guess -o -name config.sub + '[' 1 = 1 ']' + '[' x '!=' 'x-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' ']' ++ find . -name ltmain.sh + ./configure --build=aarch64-redhat-linux-gnu --host=aarch64-redhat-linux-gnu --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/libexec --localstatedir=/var --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info 'CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection' 'LDFLAGS=-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-1.fc38.aarch64.ld' --prefix=/usr --libdir=/usr/lib64 --enable-plugins '--with-plugin-path=/usr/local/libexec/htslib:$(plugindir)' --enable-gcs --enable-libcurl --enable-s3 configure: WARNING: unrecognized options: --disable-dependency-tracking checking for aarch64-redhat-linux-gnu-gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for aarch64-redhat-linux-gnu-ranlib... no checking for ranlib... ranlib checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for aarch64-redhat-linux-gnu-pkg-config... /usr/bin/aarch64-redhat-linux-gnu-pkg-config checking pkg-config is at least version 0.9.0... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking shared library type for aarch64-redhat-linux-gnu... plain .so checking whether the compiler accepts -fvisibility=hidden... yes checking how to run the C preprocessor... gcc -E checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... yes checking for getpagesize... yes checking for working mmap... yes checking for gmtime_r... yes checking for fsync... yes checking for drand48... yes checking for srand48_deterministic... no checking whether fdatasync is declared... yes checking for fdatasync... yes checking for library containing dlsym... none required checking whether the compiler accepts -rdynamic... yes checking for library containing log... -lm checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing recv... none required checking for bzlib.h... yes checking for BZ2_bzBuffToBuffCompress in -lbz2... yes checking for lzma.h... yes checking for lzma_easy_buffer_encode in -llzma... yes checking whether htscodecs files are present... yes checking for libdeflate.h... no checking for libdeflate_deflate_compress in -ldeflate... no checking for curl/curl.h... yes checking for curl_easy_pause in -lcurl... yes checking for CCHmac... no checking for library containing HMAC... -lcrypto checking for library containing regcomp... none required checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes configure: creating ./config.status config.status: creating config.mk config.status: creating htslib.pc.tmp config.status: creating config.h config.status: linking htscodecs_bundled.mk to htscodecs.mk configure: WARNING: unrecognized options: --disable-dependency-tracking + /usr/bin/make -O -j4 V=1 VERBOSE=1 gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o kfunc.o kfunc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o kstring.o kstring.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o errmod.o errmod.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o bcf_sr_sort.o bcf_sr_sort.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o faidx.o faidx.c echo '#define HTS_VERSION_TEXT "1.15.1"' > version.h echo '#define HTS_CC "gcc"' > config_vars.h echo '#define HTS_CPPFLAGS ""' >> config_vars.h echo '#define HTS_CFLAGS "-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden"' >> config_vars.h echo '#define HTS_LDFLAGS "-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-1.fc38.aarch64.ld -fvisibility=hidden -rdynamic"' >> config_vars.h echo '#define HTS_LIBS "-llzma -lbz2 -lz -lm "' >> config_vars.h gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o bgzf.o bgzf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o hts_os.o hts_os.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o hts_expr.o hts_expr.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o md5.o md5.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o hfile.o hfile.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o multipart.o multipart.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o probaln.o probaln.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o realn.o realn.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o region.o region.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o header.o header.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o regidx.o regidx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o vcf_sweep.o vcf_sweep.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o tbx.o tbx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o textutils.o textutils.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o thread_pool.o thread_pool.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o synced_bcf_reader.o synced_bcf_reader.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o vcfutils.o vcfutils.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/cram_codecs.o cram/cram_codecs.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/cram_decode.o cram/cram_decode.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/cram_external.o cram/cram_external.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o sam.o sam.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/cram_index.o cram/cram_index.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/cram_stats.o cram/cram_stats.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/cram_encode.o cram/cram_encode.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/mFILE.o cram/mFILE.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/open_trace_file.o cram/open_trace_file.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/string_alloc.o cram/string_alloc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o vcf.o vcf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/cram_io.o cram/cram_io.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o kfunc.pico kfunc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -DPLUGINPATH=\"/usr/local/libexec/htslib:/usr/libexec/htslib\" -c -o plugin.o plugin.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o kstring.pico kstring.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o errmod.pico errmod.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o bcf_sr_sort.pico bcf_sr_sort.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o faidx.pico faidx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o bgzf.pico bgzf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o hfile.pico hfile.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o hts_os.pico hts_os.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o hts_expr.pico hts_expr.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o md5.pico md5.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o multipart.pico multipart.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o probaln.pico probaln.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o header.pico header.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o realn.pico realn.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o region.pico region.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o regidx.pico regidx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o vcf_sweep.pico vcf_sweep.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o tbx.pico tbx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o synced_bcf_reader.pico synced_bcf_reader.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o textutils.pico textutils.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o thread_pool.pico thread_pool.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o hts.pico hts.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o vcfutils.pico vcfutils.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o cram/cram_codecs.pico cram/cram_codecs.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o sam.pico sam.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o cram/cram_decode.pico cram/cram_decode.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o cram/cram_external.pico cram/cram_external.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o cram/cram_index.pico cram/cram_index.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o cram/cram_stats.pico cram/cram_stats.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o cram/mFILE.pico cram/mFILE.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o cram/open_trace_file.pico cram/open_trace_file.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o vcf.pico vcf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o cram/pooled_alloc.pico cram/pooled_alloc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o cram/string_alloc.pico cram/string_alloc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o cram/cram_encode.pico cram/cram_encode.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/htscodecs.pico htscodecs/htscodecs/htscodecs.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/pack.pico htscodecs/htscodecs/pack.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/arith_dynamic.pico htscodecs/htscodecs/arith_dynamic.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/fqzcomp_qual.pico htscodecs/htscodecs/fqzcomp_qual.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o cram/cram_io.pico cram/cram_io.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rle.pico htscodecs/htscodecs/rle.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -DPLUGINPATH=\"/usr/local/libexec/htslib:/usr/libexec/htslib\" -fpic -c -o plugin.pico plugin.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rANS_static.pico htscodecs/htscodecs/rANS_static.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rANS_static4x16pr.pico htscodecs/htscodecs/rANS_static4x16pr.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o bgzip.o bgzip.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o htsfile.o htsfile.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o hfile_gcs.pico hfile_gcs.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o tabix.o tabix.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/tokenise_name3.pico htscodecs/htscodecs/tokenise_name3.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/hts_endian.o test/hts_endian.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o hfile_s3_write.pico hfile_s3_write.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o hfile_libcurl.pico hfile_libcurl.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/fieldarith.o test/fieldarith.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/pileup.o test/pileup.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/pileup_mod.o test/pileup_mod.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/plugins-dlhts.o test/plugins-dlhts.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/hfile.o test/hfile.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o hfile_s3.pico hfile_s3.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_kfunc.o test/test_kfunc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_expr.o test/test_expr.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_mod.o test/test_mod.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_realn.o test/test_realn.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_kstring.o test/test_kstring.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_bgzf.o test/test_bgzf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_str2int.o test/test_str2int.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test-regidx.o test/test-regidx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_index.o test/test_index.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_view.o test/test_view.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/fuzz/hts_open_fuzzer.o test/fuzz/hts_open_fuzzer.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test-bcf-sr.o test/test-bcf-sr.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test-bcf-translate.o test/test-bcf-translate.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test-vcf-api.o test/test-vcf-api.c sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' htslib.pc.tmp > htslib_static.mk gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test-parse-reg.o test/test-parse-reg.c sed -e 's#@-includedir@#'`pwd`'#g;s#@-libdir@#'`pwd`'#g' htslib.pc.tmp > htslib-uninstalled.pc gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_introspection.o test/test_introspection.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/sam.o test/sam.c gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-1.fc38.aarch64.ld -fvisibility=hidden -rdynamic -o test/plugins-dlhts test/plugins-dlhts.o -llzma -lbz2 -lz -lm gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-1.fc38.aarch64.ld -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o hts.o hts.c ar -rc libhts.a kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o plugin.o ranlib libhts.a gcc -shared -Wl,-soname,libhts.so.3 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-1.fc38.aarch64.ld -fvisibility=hidden -rdynamic -o libhts.so kfunc.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico header.pico hfile.pico hts.pico hts_expr.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico region.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_stats.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/string_alloc.pico htscodecs/htscodecs/arith_dynamic.pico htscodecs/htscodecs/fqzcomp_qual.pico htscodecs/htscodecs/htscodecs.pico htscodecs/htscodecs/pack.pico htscodecs/htscodecs/rANS_static4x16pr.pico htscodecs/htscodecs/rANS_static.pico htscodecs/htscodecs/rle.pico htscodecs/htscodecs/tokenise_name3.pico plugin.pico -llzma -lbz2 -lz -lm -lpthread ln -sf libhts.so libhts.so.3 gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-1.fc38.aarch64.ld -fvisibility=hidden -rdynamic -o bgzip bgzip.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-1.fc38.aarch64.ld -fvisibility=hidden -rdynamic -o tabix tabix.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-1.fc38.aarch64.ld -fvisibility=hidden -rdynamic -o htsfile htsfile.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-1.fc38.aarch64.ld -fvisibility=hidden -rdynamic -o test/fieldarith test/fieldarith.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-1.fc38.aarch64.ld -fvisibility=hidden -rdynamic -o test/hfile test/hfile.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-1.fc38.aarch64.ld -fvisibility=hidden -rdynamic -o test/pileup test/pileup.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-1.fc38.aarch64.ld -fvisibility=hidden -rdynamic -o test/test_expr test/test_expr.o libhts.a -lz -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-1.fc38.aarch64.ld -fvisibility=hidden -rdynamic -o test/pileup_mod test/pileup_mod.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-1.fc38.aarch64.ld -fvisibility=hidden -rdynamic -o test/test_kfunc test/test_kfunc.o libhts.a -lz -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-1.fc38.aarch64.ld -fvisibility=hidden -rdynamic -o test/test_kstring test/test_kstring.o libhts.a -lz -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-1.fc38.aarch64.ld -fvisibility=hidden -rdynamic -o test/sam test/sam.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-1.fc38.aarch64.ld -fvisibility=hidden -rdynamic -o test/test_bgzf test/test_bgzf.o libhts.a -lz -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-1.fc38.aarch64.ld -fvisibility=hidden -rdynamic -o test/test_mod test/test_mod.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-1.fc38.aarch64.ld -fvisibility=hidden -rdynamic -o test/test_realn test/test_realn.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-1.fc38.aarch64.ld -fvisibility=hidden -rdynamic -o test/test_str2int test/test_str2int.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-1.fc38.aarch64.ld -fvisibility=hidden -rdynamic -o test/test-regidx test/test-regidx.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-1.fc38.aarch64.ld -fvisibility=hidden -rdynamic -o test/test_view test/test_view.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-1.fc38.aarch64.ld -fvisibility=hidden -rdynamic -o test/test_index test/test_index.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-1.fc38.aarch64.ld -fvisibility=hidden -rdynamic -o test/test-vcf-api test/test-vcf-api.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-1.fc38.aarch64.ld -fvisibility=hidden -rdynamic -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-1.fc38.aarch64.ld -fvisibility=hidden -rdynamic -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-1.fc38.aarch64.ld -fvisibility=hidden -rdynamic -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -lz -llzma -lbz2 -lz -lm -lpthread gcc -shared -Wl,-E -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-1.fc38.aarch64.ld -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,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-1.fc38.aarch64.ld -fvisibility=hidden -rdynamic -o hfile_libcurl.so hfile_libcurl.pico libhts.so -llzma -lbz2 -lz -lm -lcurl -lpthread gcc -shared -Wl,-E -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-1.fc38.aarch64.ld -fvisibility=hidden -rdynamic -o hfile_s3_write.so hfile_s3_write.pico libhts.so -llzma -lbz2 -lz -lm -lcrypto -lcurl -lpthread gcc -shared -Wl,-E -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-1.fc38.aarch64.ld -fvisibility=hidden -rdynamic -o hfile_s3.so hfile_s3.pico libhts.so -llzma -lbz2 -lz -lm -lcrypto -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-1.fc38.aarch64.ld -fvisibility=hidden -rdynamic -o test/test-parse-reg test/test-parse-reg.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-1.fc38.aarch64.ld -fvisibility=hidden -rdynamic -o test/test_introspection test/test_introspection.o libhts.a -llzma -lbz2 -lz -lm -lpthread + sed -i -E '/^(Libs|Requires)\.private:/d' htslib.pc.tmp + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.YhaVcq + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.aarch64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.aarch64 ++ dirname /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.aarch64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.aarch64 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules' + export FCFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-1.fc38.aarch64.ld' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd htslib-1.15.1 + /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.aarch64 'INSTALL=/usr/bin/install -p' mkdir -p -m 755 /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.aarch64/usr/bin /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.aarch64/usr/include /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.aarch64/usr/include/htslib /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.aarch64/usr/lib64 /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.aarch64/usr/share/man/man1 /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.aarch64/usr/share/man/man5 /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.aarch64/usr/share/man/man7 /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.aarch64/usr/lib64/pkgconfig if test -n "/usr/libexec/htslib"; then mkdir -p -m 755 /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.aarch64/usr/libexec/htslib; fi /usr/bin/install -p -m 644 libhts.so /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.aarch64/usr/lib64/libhts.so.1.15.1 ln -sf libhts.so.1.15.1 /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.aarch64/usr/lib64/libhts.so ln -sf libhts.so.1.15.1 /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.aarch64/usr/lib64/libhts.so.3 sed -e 's#@-includedir@#/usr/include#g;s#@-libdir@#/usr/lib64#g;s#@-PACKAGE_VERSION@#1.15.1#g' htslib.pc.tmp > /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.aarch64/usr/lib64/pkgconfig/htslib.pc chmod 644 /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.aarch64/usr/lib64/pkgconfig/htslib.pc /usr/bin/install -p bgzip htsfile tabix /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.aarch64/usr/bin if test -n "hfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so"; then /usr/bin/install -p hfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.aarch64/usr/libexec/htslib; fi /usr/bin/install -p -m 644 htslib/*.h /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.aarch64/usr/include/htslib /usr/bin/install -p -m 644 libhts.a /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.aarch64/usr/lib64/libhts.a /usr/bin/install -p -m 644 bgzip.1 htsfile.1 tabix.1 /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.aarch64/usr/share/man/man1 /usr/bin/install -p -m 644 faidx.5 sam.5 vcf.5 /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.aarch64/usr/share/man/man5 /usr/bin/install -p -m 644 htslib-s3-plugin.7 /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.aarch64/usr/share/man/man7 + pushd /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.aarch64//usr/lib64 ~/build/BUILDROOT/htslib-1.15.1-1.fc38.aarch64/usr/lib64 ~/build/BUILD/htslib-1.15.1 + chmod 755 libhts.so.1.15.1 + popd ~/build/BUILD/htslib-1.15.1 + find /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.aarch64 -name '*.la' -delete + rm -f /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.aarch64//usr/lib64/libhts.a + /usr/bin/find-debuginfo -j4 --strict-build-id -m -i --build-id-seed 1.15.1-1.fc38 --unique-debug-suffix -1.15.1-1.fc38.aarch64 --unique-debug-src-base htslib-1.15.1-1.fc38.aarch64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/htslib-1.15.1 extracting debug info from /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.aarch64/usr/bin/bgzip extracting debug info from /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.aarch64/usr/bin/htsfile extracting debug info from /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.aarch64/usr/bin/tabix extracting debug info from /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.aarch64/usr/lib64/libhts.so.1.15.1 extracting debug info from /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.aarch64/usr/libexec/htslib/hfile_gcs.so extracting debug info from /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.aarch64/usr/libexec/htslib/hfile_libcurl.so extracting debug info from /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.aarch64/usr/libexec/htslib/hfile_s3.so extracting debug info from /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.aarch64/usr/libexec/htslib/hfile_s3_write.so original debug info size: 12004kB, size after compression: 11284kB /usr/bin/sepdebugcrcfix: Updated 8 CRC32s, 0 CRC32s did match. 5259 blocks + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + /usr/lib/rpm/brp-compress + /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/check-rpaths + /usr/lib/rpm/redhat/brp-mangle-shebangs + /usr/lib/rpm/brp-remove-la-files + /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 + /usr/lib/rpm/redhat/brp-python-hardlink Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.RfXxbn + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules' + export FCFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-1.fc38.aarch64.ld' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + '[' -f /usr/lib/rpm/generate-rpm-note.sh ']' + /usr/lib/rpm/generate-rpm-note.sh htslib 1.15.1-1.fc38 aarch64 + cd htslib-1.15.1 + make test gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -Ihtscodecs -D_POSIX_C_SOURCE=200112L -c -o htscodecs/tests/rANS_static_test.o htscodecs/tests/rANS_static_test.c gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-1.fc38.aarch64.ld -fvisibility=hidden -rdynamic -o htscodecs/tests/rans4x8 htscodecs/tests/rANS_static_test.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o -llzma -lbz2 -lz -lm -lm -lpthread cd htscodecs/tests && srcdir=. && export srcdir && ./rans4x8.test Testing rans4x8 -r -o0 on ./dat/q4 11674 Testing rans4x8 -r -o1 on ./dat/q4 10870 Testing rans4x8 -r -o0 on ./dat/q40+dir 50258 Testing rans4x8 -r -o1 on ./dat/q40+dir 50537 Testing rans4x8 -r -o0 on ./dat/q8 33099 Testing rans4x8 -r -o1 on ./dat/q8 31428 Testing rans4x8 -r -o0 on ./dat/qvar 32997 Testing rans4x8 -r -o1 on ./dat/qvar 32832 gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -Ihtscodecs -D_POSIX_C_SOURCE=200112L -c -o htscodecs/tests/rANS_static4x16pr_test.o htscodecs/tests/rANS_static4x16pr_test.c gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-1.fc38.aarch64.ld -fvisibility=hidden -rdynamic -o htscodecs/tests/rans4x16pr htscodecs/tests/rANS_static4x16pr_test.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o -llzma -lbz2 -lz -lm -lm -lpthread cd htscodecs/tests && srcdir=. && export srcdir && ./rans4x16.test Testing rans4x16 -r -o0 on ./dat/q4 11660 Testing rans4x16 -r -o1 on ./dat/q4 10848 Testing rans4x16 -r -o64 on ./dat/q4 12878 Testing rans4x16 -r -o65 on ./dat/q4 10672 Testing rans4x16 -r -o128 on ./dat/q4 10902 Testing rans4x16 -r -o129 on ./dat/q4 10890 Testing rans4x16 -r -o192 on ./dat/q4 11225 Testing rans4x16 -r -o193 on ./dat/q4 10825 Testing rans4x16 -r -o8 on ./dat/q4 11731 Testing rans4x16 -r -o9 on ./dat/q4 11111 Testing rans4x16 -r -o0 on ./dat/q40+dir 50247 Testing rans4x16 -r -o1 on ./dat/q40+dir 49449 Testing rans4x16 -r -o8 on ./dat/q40+dir 50072 Testing rans4x16 -r -o9 on ./dat/q40+dir 50072 Testing rans4x16 -r -o0 on ./dat/q8 33088 Testing rans4x16 -r -o1 on ./dat/q8 31372 Testing rans4x16 -r -o64 on ./dat/q8 33458 Testing rans4x16 -r -o65 on ./dat/q8 31025 Testing rans4x16 -r -o128 on ./dat/q8 32237 Testing rans4x16 -r -o129 on ./dat/q8 31258 Testing rans4x16 -r -o192 on ./dat/q8 32024 Testing rans4x16 -r -o193 on ./dat/q8 31146 Testing rans4x16 -r -o0 on ./dat/qvar 32987 Testing rans4x16 -r -o1 on ./dat/qvar 32261 gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -Ihtscodecs -D_POSIX_C_SOURCE=200112L -c -o htscodecs/tests/arith_dynamic_test.o htscodecs/tests/arith_dynamic_test.c gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-1.fc38.aarch64.ld -fvisibility=hidden -rdynamic -o htscodecs/tests/arith_dynamic htscodecs/tests/arith_dynamic_test.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o -llzma -lbz2 -lz -lm -lm -lpthread cd htscodecs/tests && srcdir=. && export srcdir && ./arith.test Testing arith_dynamic -r -o0 on ./dat/q4 11615 Testing arith_dynamic -r -o1 on ./dat/q4 10831 Testing arith_dynamic -r -o64 on ./dat/q4 13360 Testing arith_dynamic -r -o65 on ./dat/q4 10484 Testing arith_dynamic -r -o128 on ./dat/q4 10774 Testing arith_dynamic -r -o129 on ./dat/q4 10329 Testing arith_dynamic -r -o192 on ./dat/q4 11095 Testing arith_dynamic -r -o193 on ./dat/q4 10283 Testing arith_dynamic -r -o8 on ./dat/q4 11448 Testing arith_dynamic -r -o9 on ./dat/q4 11083 Testing arith_dynamic -r -o0 on ./dat/q40+dir 49949 Testing arith_dynamic -r -o1 on ./dat/q40+dir 49034 Testing arith_dynamic -r -o64 on ./dat/q40+dir 51242 Testing arith_dynamic -r -o65 on ./dat/q40+dir 49061 Testing arith_dynamic -r -o8 on ./dat/q40+dir 49820 Testing arith_dynamic -r -o9 on ./dat/q40+dir 49448 Testing arith_dynamic -r -o0 on ./dat/q8 32752 Testing arith_dynamic -r -o1 on ./dat/q8 31331 Testing arith_dynamic -r -o64 on ./dat/q8 35211 Testing arith_dynamic -r -o65 on ./dat/q8 30907 Testing arith_dynamic -r -o128 on ./dat/q8 32063 Testing arith_dynamic -r -o129 on ./dat/q8 31084 Testing arith_dynamic -r -o192 on ./dat/q8 32267 Testing arith_dynamic -r -o193 on ./dat/q8 30931 Testing arith_dynamic -r -o0 on ./dat/qvar 32597 Testing arith_dynamic -r -o1 on ./dat/qvar 31982 Testing arith_dynamic -r -o64 on ./dat/qvar 33237 Testing arith_dynamic -r -o65 on ./dat/qvar 31993 gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -Ihtscodecs -D_POSIX_C_SOURCE=200112L -c -o htscodecs/tests/tokenise_name3_test.o htscodecs/tests/tokenise_name3_test.c gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-1.fc38.aarch64.ld -fvisibility=hidden -rdynamic -o htscodecs/tests/tokenise_name3 htscodecs/tests/tokenise_name3_test.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o -llzma -lbz2 -lz -lm -lm -lpthread cd htscodecs/tests && srcdir=. && export srcdir && ./tok3.test Testing tokenise_name3 -r -1 on ./names/01.names 3392 Testing tokenise_name3 -r -3 on ./names/01.names 2471 Testing tokenise_name3 -r -5 on ./names/01.names 2283 Testing tokenise_name3 -r -7 on ./names/01.names 2234 Testing tokenise_name3 -r -9 on ./names/01.names 2234 Testing tokenise_name3 -r -11 on ./names/01.names 3151 Testing tokenise_name3 -r -13 on ./names/01.names 2424 Testing tokenise_name3 -r -15 on ./names/01.names 2061 Testing tokenise_name3 -r -17 on ./names/01.names 2051 Testing tokenise_name3 -r -19 on ./names/01.names 2049 Testing tokenise_name3 -r -1 on ./names/02.names 6633 Testing tokenise_name3 -r -3 on ./names/02.names 4983 Testing tokenise_name3 -r -5 on ./names/02.names 4942 Testing tokenise_name3 -r -7 on ./names/02.names 4922 Testing tokenise_name3 -r -9 on ./names/02.names 4918 Testing tokenise_name3 -r -11 on ./names/02.names 6087 Testing tokenise_name3 -r -13 on ./names/02.names 4797 Testing tokenise_name3 -r -15 on ./names/02.names 4714 Testing tokenise_name3 -r -17 on ./names/02.names 4695 Testing tokenise_name3 -r -19 on ./names/02.names 4695 Testing tokenise_name3 -r -1 on ./names/03.names 10557 Testing tokenise_name3 -r -3 on ./names/03.names 7822 Testing tokenise_name3 -r -5 on ./names/03.names 7557 Testing tokenise_name3 -r -7 on ./names/03.names 7521 Testing tokenise_name3 -r -9 on ./names/03.names 7521 Testing tokenise_name3 -r -11 on ./names/03.names 9294 Testing tokenise_name3 -r -13 on ./names/03.names 7291 Testing tokenise_name3 -r -15 on ./names/03.names 7125 Testing tokenise_name3 -r -17 on ./names/03.names 7069 Testing tokenise_name3 -r -19 on ./names/03.names 7068 Testing tokenise_name3 -r -1 on ./names/05.names 5098 Testing tokenise_name3 -r -3 on ./names/05.names 3600 Testing tokenise_name3 -r -5 on ./names/05.names 3551 Testing tokenise_name3 -r -7 on ./names/05.names 3534 Testing tokenise_name3 -r -9 on ./names/05.names 3534 Testing tokenise_name3 -r -11 on ./names/05.names 4648 Testing tokenise_name3 -r -13 on ./names/05.names 3405 Testing tokenise_name3 -r -15 on ./names/05.names 3381 Testing tokenise_name3 -r -17 on ./names/05.names 3377 Testing tokenise_name3 -r -19 on ./names/05.names 3377 Testing tokenise_name3 -r -1 on ./names/08.names 6841 Testing tokenise_name3 -r -3 on ./names/08.names 5291 Testing tokenise_name3 -r -5 on ./names/08.names 5206 Testing tokenise_name3 -r -7 on ./names/08.names 5160 Testing tokenise_name3 -r -9 on ./names/08.names 5160 Testing tokenise_name3 -r -11 on ./names/08.names 6374 Testing tokenise_name3 -r -13 on ./names/08.names 4895 Testing tokenise_name3 -r -15 on ./names/08.names 4851 Testing tokenise_name3 -r -17 on ./names/08.names 4805 Testing tokenise_name3 -r -19 on ./names/08.names 4805 Testing tokenise_name3 -r -1 on ./names/09.names 5339 Testing tokenise_name3 -r -3 on ./names/09.names 3598 Testing tokenise_name3 -r -5 on ./names/09.names 3527 Testing tokenise_name3 -r -7 on ./names/09.names 3493 Testing tokenise_name3 -r -9 on ./names/09.names 3493 Testing tokenise_name3 -r -11 on ./names/09.names 4861 Testing tokenise_name3 -r -13 on ./names/09.names 3427 Testing tokenise_name3 -r -15 on ./names/09.names 3391 Testing tokenise_name3 -r -17 on ./names/09.names 3366 Testing tokenise_name3 -r -19 on ./names/09.names 3366 Testing tokenise_name3 -r -1 on ./names/10.names 6458 Testing tokenise_name3 -r -3 on ./names/10.names 4843 Testing tokenise_name3 -r -5 on ./names/10.names 4799 Testing tokenise_name3 -r -7 on ./names/10.names 4746 Testing tokenise_name3 -r -9 on ./names/10.names 4744 Testing tokenise_name3 -r -11 on ./names/10.names 5785 Testing tokenise_name3 -r -13 on ./names/10.names 4567 Testing tokenise_name3 -r -15 on ./names/10.names 4492 Testing tokenise_name3 -r -17 on ./names/10.names 4472 Testing tokenise_name3 -r -19 on ./names/10.names 4472 Testing tokenise_name3 -r -1 on ./names/20.names 2511 Testing tokenise_name3 -r -3 on ./names/20.names 1701 Testing tokenise_name3 -r -5 on ./names/20.names 1659 Testing tokenise_name3 -r -7 on ./names/20.names 1632 Testing tokenise_name3 -r -9 on ./names/20.names 1632 Testing tokenise_name3 -r -11 on ./names/20.names 2319 Testing tokenise_name3 -r -13 on ./names/20.names 1629 Testing tokenise_name3 -r -15 on ./names/20.names 1605 Testing tokenise_name3 -r -17 on ./names/20.names 1600 Testing tokenise_name3 -r -19 on ./names/20.names 1600 Testing tokenise_name3 -r -1 on ./names/nv.names 6816 Testing tokenise_name3 -r -3 on ./names/nv.names 4989 Testing tokenise_name3 -r -5 on ./names/nv.names 4972 Testing tokenise_name3 -r -7 on ./names/nv.names 4937 Testing tokenise_name3 -r -9 on ./names/nv.names 4937 Testing tokenise_name3 -r -11 on ./names/nv.names 6084 Testing tokenise_name3 -r -13 on ./names/nv.names 4825 Testing tokenise_name3 -r -15 on ./names/nv.names 4771 Testing tokenise_name3 -r -17 on ./names/nv.names 4767 Testing tokenise_name3 -r -19 on ./names/nv.names 4767 Testing tokenise_name3 -r -1 on ./names/nv2.names 1181 Testing tokenise_name3 -r -3 on ./names/nv2.names 903 Testing tokenise_name3 -r -5 on ./names/nv2.names 879 Testing tokenise_name3 -r -7 on ./names/nv2.names 846 Testing tokenise_name3 -r -9 on ./names/nv2.names 846 Testing tokenise_name3 -r -11 on ./names/nv2.names 891 Testing tokenise_name3 -r -13 on ./names/nv2.names 836 Testing tokenise_name3 -r -15 on ./names/nv2.names 764 Testing tokenise_name3 -r -17 on ./names/nv2.names 747 Testing tokenise_name3 -r -19 on ./names/nv2.names 747 Testing tokenise_name3 -r -1 on ./names/rr.names 8788 Testing tokenise_name3 -r -3 on ./names/rr.names 6290 Testing tokenise_name3 -r -5 on ./names/rr.names 6252 Testing tokenise_name3 -r -7 on ./names/rr.names 6230 Testing tokenise_name3 -r -9 on ./names/rr.names 6230 Testing tokenise_name3 -r -11 on ./names/rr.names 8319 Testing tokenise_name3 -r -13 on ./names/rr.names 6066 Testing tokenise_name3 -r -15 on ./names/rr.names 5972 Testing tokenise_name3 -r -17 on ./names/rr.names 5963 Testing tokenise_name3 -r -19 on ./names/rr.names 5963 gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -Ihtscodecs -D_POSIX_C_SOURCE=200112L -c -o htscodecs/tests/fqzcomp_qual_test.o htscodecs/tests/fqzcomp_qual_test.c gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-1.fc38.aarch64.ld -fvisibility=hidden -rdynamic -o htscodecs/tests/fqzcomp_qual htscodecs/tests/fqzcomp_qual_test.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o -llzma -lbz2 -lz -lm -lm -lpthread cd htscodecs/tests && srcdir=. && export srcdir && ./fqzcomp.test Testing fqzcomp_qual -r -s 0 on ./dat/q4 9307 Testing fqzcomp_qual -r -s 1 on ./dat/q4 9618 Testing fqzcomp_qual -r -s 2 on ./dat/q4 9453 Testing fqzcomp_qual -r -s 3 on ./dat/q4 10481 Testing fqzcomp_qual -r -s 0 on ./dat/q40+dir 47674 Testing fqzcomp_qual -r -s 1 on ./dat/q40+dir 45016 Testing fqzcomp_qual -r -s 2 on ./dat/q40+dir 47760 Testing fqzcomp_qual -r -s 3 on ./dat/q40+dir 48583 Testing fqzcomp_qual -r -s 0 on ./dat/q8 30012 Testing fqzcomp_qual -r -s 1 on ./dat/q8 33742 Testing fqzcomp_qual -r -s 2 on ./dat/q8 30982 Testing fqzcomp_qual -r -s 3 on ./dat/q8 31709 Testing fqzcomp_qual -r -s 0 on ./dat/qvar 32868 Testing fqzcomp_qual -r -s 1 on ./dat/qvar 35007 Testing fqzcomp_qual -r -s 2 on ./dat/qvar 32400 Testing fqzcomp_qual -r -s 3 on ./dat/qvar 32073 gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -Ihtscodecs -D_POSIX_C_SOURCE=200112L -c -o htscodecs/tests/varint_test.o htscodecs/tests/varint_test.c gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-1.fc38.aarch64.ld -fvisibility=hidden -rdynamic -o htscodecs/tests/varint htscodecs/tests/varint_test.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o -llzma -lbz2 -lz -lm -lm -lpthread cd htscodecs/tests && ./varint test/hts_endian test/test_expr test/test_kfunc test/test_kstring test/test_str2int test/fieldarith test/fieldarith.sam test/hfile HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -g ./libhts.so HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -l ./libhts.so test/test_bgzf test/bgziptest.txt test/test-parse-reg -t test/colons.bam Expected error: [E::hts_parse_region] Range is ambiguous. Use {chr1:100-200} or {chr1}:100-200 instead Expected error: [E::hts_parse_region] Range is ambiguous. Use {chr1:100-200,chr3} or {chr1}:100-200,chr3 instead Expected error: [E::hts_parse_region] Mismatching braces in "{chr1" Expected error: [E::hts_parse_region] Unexpected string "x" after region Expected error: [E::hts_parse_region] Unexpected string "y" after region Expected error: [E::hts_parse_region] Unexpected string "chr3" after region cd test/sam_filter && ./filter.sh filter.tst Testing sam_filter... PASS : $tv -i 'filter=qname =~ "\.1" && cigar =~ "D"' ../ce#1000.sam PASS : $tv -i 'filter=rname=="CHROMOSOME_II"' ../ce#5b.sam PASS : $tv -i 'filter=rname=~"CHROMOSOME_II"' ../ce#5b.sam PASS : $tv -i 'filter=cigar=~"D"' ../ce#1000.sam PASS : $tv -i 'filter=seq =~ "(AT){2}"' ../ce#1000.sam PASS : $tv -i 'filter=library=="x"' ../xx#rg.sam PASS : $tv -i 'filter=library!="x"' ../xx#rg.sam PASS : $tv -i 'filter=pos % 23 == 11' ../ce#1000.sam |egrep -cv '^@' PASS : $tv -i 'filter=qlen/(flag*mapq+pos)>5' ../ce#1000.sam |egrep -cv '^@' PASS : $tv -i 'filter=[NM]>=10 || [MD]=~"A.*A.*A"' -t4 ../ce#1000.sam |egrep -cv '^@' PASS : $tv -i 'filter=length(seq) != qlen' ../ce#5b.sam | egrep -cv '^@' PASS : $tv -i 'filter=min(qual) >= 20' ../ce#1000.sam | egrep -cv '^@' PASS : $tv -i 'filter=max(qual) <= 20' ../ce#1000.sam | egrep -cv '^@' PASS : $tv -i 'filter=avg(qual) >= 20 && avg(qual) <= 30' ../ce#1000.sam | egrep -cv '^@' Expected passes: 14 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 cd test/tabix && ./test-tabix.sh tabix.tst Testing tabix... PASS : $tabix -f -p vcf vcf_file.tbi.tmp.vcf.gz PASS : $tabix vcf_file.tbi.tmp.vcf.gz 1:3000151-3000151 PASS : $tabix vcf_file.tbi.tmp.vcf.gz 2:3199812-3199812 PASS : $tabix -f -C -p vcf vcf_file.csi.tmp.vcf.gz PASS : $tabix vcf_file.csi.tmp.vcf.gz 1:3000151-3000151 PASS : $tabix vcf_file.csi.tmp.vcf.gz 2:3199812-3199812 PASS : $tabix -f -p vcf large_chr.tmp.vcf.gz (must exit non-zero) PASS : $tabix -f -C -p vcf large_chr.tmp.vcf.gz PASS : $tabix large_chr.tmp.vcf.gz chr20:1-2147483647 PASS : $tabix -f -p bed bed_file.tbi.tmp.bed.gz PASS : $tabix bed_file.tbi.tmp.bed.gz Y:100200-100200 PASS : $tabix -f -p gff gff_file.tbi.tmp.gff.gz PASS : $tabix gff_file.tbi.tmp.gff.gz X:2934832-2935190 PASS : $tabix --separate-regions bed_file.tbi.tmp.bed.gz X:1100-1400 Y:100000-100550 Z:100000-100005 Expected passes: 14 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 cd test/mpileup && ./test-pileup.sh mpileup.tst Testing (m)pileup... PASS : $pileup mp_D.sam PASS : $pileup -m mp_D.sam PASS : $pileup mp_DI.sam PASS : $pileup -m mp_DI.sam PASS : $pileup mp_I.sam PASS : $pileup -m mp_I.sam PASS : $pileup mp_P.sam PASS : $pileup -m mp_P.sam PASS : $pileup mp_ID.sam PASS : $pileup -m mp_ID.sam PASS : $pileup mp_N.sam PASS : $pileup -m mp_N.sam PASS : $pileup mp_N2.sam PASS : $pileup -m mp_N2.sam PASS : $pileup c1#pad1.sam PASS : $pileup -m c1#pad1.sam PASS : $pileup c1#pad2.sam PASS : $pileup -m c1#pad2.sam PASS : $pileup c1#pad3.sam PASS : $pileup -m c1#pad3.sam PASS : $pileup -m small.bam Expected passes: 21 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 cd test/fastq && ./test-fastq.sh Testing fastq support PASS : $tview minimal.fq PASS : $tview minimal.fa PASS : $tview multiline.fq PASS : $tview multiline.fa PASS : $tview single.fq PASS : $tview single.fa PASS : $tview -i fastq_aux single.fq PASS : $tview -i fastq_aux single.fa PASS : $tview interleaved.fq PASS : $tview interleaved.fa PASS : $tview -i fastq_aux interleaved.fq PASS : $tview -i fastq_aux interleaved.fa PASS : $tview -i fastq_casava interleaved_casava.fq PASS : $tview -i fastq_barcode=OX -i fastq_casava interleaved_casava.fq PASS : $tview -i fastq_casava interleaved_casava.fa PASS : $tview -i fastq_barcode=OX -i fastq_casava interleaved_casava.fa PASS : $tview -i fastq_casava filter_casava.fq PASS : $tview -i fastq_casava filter_casava.fa PASS : $tview -i fastq_aux r1.fq PASS : $tview -i fastq_aux r2.fq PASS : $tview -i fastq_aux r1.fa PASS : $tview -i fastq_aux r2.fa PASS : $tview -i fastq_name2 name2.fq PASS : $tview -i fastq_name2 name2.fa PASS : $tview -f minimal.sam PASS : $tview -F minimal.sam PASS : $tview -f -o fastq_aux single_aux.sam PASS : $tview -F -o fastq_aux single_aux.sam PASS : $tview -f -o fastq_aux -o fastq_rnum inter_aux.sam PASS : $tview -F -o fastq_aux -o fastq_rnum inter_aux.sam PASS : $tview -f -o fastq_casava inter_casava.sam PASS : $tview -f -o fastq_barcode=OX -o fastq_casava inter_casavaOX.sam PASS : $tview -F -o fastq_casava inter_casava.sam PASS : $tview -F -o fastq_barcode=OX -o fastq_casava inter_casavaOX.sam PASS : $tview -f -o fastq_casava filter_casava.sam PASS : $tview -F -o fastq_casava filter_casava.sam PASS : $tview -f -o fastq_aux -o fastq_rnum r1.sam PASS : $tview -f -o fastq_aux -o fastq_rnum r2.sam PASS : $tview -F -o fastq_aux -o fastq_rnum r1.sam PASS : $tview -F -o fastq_aux -o fastq_rnum r2.sam Expected passes: 40 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 cd test/base_mods && ./base-mods.sh base-mods.tst Testing base-modifications... PASS : $test_mod MM-chebi.sam PASS : $test_mod MM-double.sam PASS : $test_mod MM-multi.sam PASS : $pileup_mod < MM-pileup.sam PASS : $pileup_mod < MM-pileup2.sam Expected passes: 5 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 REF_PATH=: test/sam test/ce.fa test/faidx.fa test/fastqs.fq (Expect trailing 'x' message for " -1,001x") [W::hts_parse_decimal] Ignoring unknown characters after -1,001[x] (Expect trailing 'k' message for "1.5e+3k") [W::hts_parse_decimal] Ignoring unknown characters after 1.5e+3[k] (Expect dropped fraction message for "12.3456k") [W::hts_parse_decimal] Discarding fractional part of 12.3456k [W::hts_parse_decimal] Discarding fractional part of 12.3456k (Expect invalid numeric message for "A") [W::hts_parse_decimal] Invalid numeric value A[truncated] (Expect invalid numeric message for "G") [W::hts_parse_decimal] Invalid numeric value G[truncated] (Expect invalid numeric message for " +/-") [W::hts_parse_decimal] Invalid numeric value +/-[truncated] (Expect invalid numeric message for " -.e+9999") [W::hts_parse_decimal] Invalid numeric value -.e+9999[truncated] test/test-regidx cd test && REF_PATH=: ./test.pl ${TEST_OPTS:-} "my" variable @p masks earlier declaration in same scope at ./test.pl line 617. bgzip round-trip no threads: .. ok bgzip -b no threads: .. ok bgzip -b -I no threads: .. ok bgzip round-trip 4 threads: .. ok bgzip -b 4 threads: .. ok bgzip -b -I 4 threads: .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -b -m 14 -x /tmp/xEkWqSjgSa/index.bam.csi /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/xEkWqSjgSa/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/xEkWqSjgSa/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -b -m 0 -x /tmp/xEkWqSjgSa/index.bam.bai /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/xEkWqSjgSa/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -b /tmp/xEkWqSjgSa/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -z -m 14 -x /tmp/xEkWqSjgSa/index.sam.gz.csi /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/xEkWqSjgSa/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/xEkWqSjgSa/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -z -m 0 -x /tmp/xEkWqSjgSa/index.sam.gz.bai /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/xEkWqSjgSa/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -b /tmp/xEkWqSjgSa/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -z -m 14 -x /tmp/xEkWqSjgSa/index.sam.gz.csi /builddir/build/BUILD/htslib-1.15.1/test/index_dos.sam > /tmp/xEkWqSjgSa/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/xEkWqSjgSa/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -z -m 0 -x /tmp/xEkWqSjgSa/index.sam.gz.bai /builddir/build/BUILD/htslib-1.15.1/test/index_dos.sam > /tmp/xEkWqSjgSa/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -b /tmp/xEkWqSjgSa/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -C -x /tmp/xEkWqSjgSa/index.cram.crai /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/xEkWqSjgSa/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index /tmp/xEkWqSjgSa/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -b -m 14 -x /tmp/xEkWqSjgSa/index.bcf.csi /builddir/build/BUILD/htslib-1.15.1/test/index.vcf > /tmp/xEkWqSjgSa/index.bcf .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/xEkWqSjgSa/index.bcf .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -z -m 14 -x /tmp/xEkWqSjgSa/index.vcf.gz.csi /builddir/build/BUILD/htslib-1.15.1/test/index.vcf > /tmp/xEkWqSjgSa/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/xEkWqSjgSa/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -z -m 0 -x /tmp/xEkWqSjgSa/index.vcf.gz.tbi /builddir/build/BUILD/htslib-1.15.1/test/index.vcf > /tmp/xEkWqSjgSa/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -t /tmp/xEkWqSjgSa/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/tabix /tmp/xEkWqSjgSa/index.vcf.gz##idx##/tmp/xEkWqSjgSa/index.vcf.gz.tbi 1:10000060-10000060 .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view /tmp/xEkWqSjgSa/index2.bam 1:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view /tmp/xEkWqSjgSa/index2.bam 1:2000000-2000000 .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view /tmp/xEkWqSjgSa/index2.bam 2:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view /tmp/xEkWqSjgSa/index2.bam 2:2000000-2000000 .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -b -m 14 -x /tmp/xEkWqSjgSa/index.bam.csi /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/xEkWqSjgSa/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/xEkWqSjgSa/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -b -m 0 -x /tmp/xEkWqSjgSa/index.bam.bai /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/xEkWqSjgSa/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -b /tmp/xEkWqSjgSa/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -z -m 14 -x /tmp/xEkWqSjgSa/index.sam.gz.csi /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/xEkWqSjgSa/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/xEkWqSjgSa/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -z -m 0 -x /tmp/xEkWqSjgSa/index.sam.gz.bai /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/xEkWqSjgSa/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -b /tmp/xEkWqSjgSa/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -z -m 14 -x /tmp/xEkWqSjgSa/index.sam.gz.csi /builddir/build/BUILD/htslib-1.15.1/test/index_dos.sam > /tmp/xEkWqSjgSa/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/xEkWqSjgSa/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -z -m 0 -x /tmp/xEkWqSjgSa/index.sam.gz.bai /builddir/build/BUILD/htslib-1.15.1/test/index_dos.sam > /tmp/xEkWqSjgSa/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -b /tmp/xEkWqSjgSa/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -C -x /tmp/xEkWqSjgSa/index.cram.crai /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/xEkWqSjgSa/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index /tmp/xEkWqSjgSa/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -b -m 14 -x /tmp/xEkWqSjgSa/index.bcf.csi /builddir/build/BUILD/htslib-1.15.1/test/index.vcf > /tmp/xEkWqSjgSa/index.bcf .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/xEkWqSjgSa/index.bcf .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -z -m 14 -x /tmp/xEkWqSjgSa/index.vcf.gz.csi /builddir/build/BUILD/htslib-1.15.1/test/index.vcf > /tmp/xEkWqSjgSa/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/xEkWqSjgSa/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -z -m 0 -x /tmp/xEkWqSjgSa/index.vcf.gz.tbi /builddir/build/BUILD/htslib-1.15.1/test/index.vcf > /tmp/xEkWqSjgSa/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -t /tmp/xEkWqSjgSa/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/tabix /tmp/xEkWqSjgSa/index.vcf.gz##idx##/tmp/xEkWqSjgSa/index.vcf.gz.tbi 1:10000060-10000060 .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view /tmp/xEkWqSjgSa/index2.bam 1:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view /tmp/xEkWqSjgSa/index2.bam 1:2000000-2000000 .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view /tmp/xEkWqSjgSa/index2.bam 2:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view /tmp/xEkWqSjgSa/index2.bam 2:2000000-2000000 .. ok test_view testing multi-ref CRAM modes: ./test_view -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=-1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ ./test_view -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=0 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ ./test_view -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ .. ok test_view testing multi-ref CRAM modes: ./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=-1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ ./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=0 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ ./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ .. ok test_view testing auxf#values.sam, ref auxf.fa: ./test_view -S -l0 -b auxf#values.sam > auxf#values.tmp.bam ./test_view auxf#values.tmp.bam > auxf#values.tmp.bam.sam_ ./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_ ./test_view -t auxf.fa -S -C -o VERSION=2.1 auxf#values.sam > auxf#values.tmp.cram ./test_view -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ ./test_view -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram ./test_view auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_ ./test_view -i reference=auxf.fa auxf#values_java.cram > auxf#values_java.tmp.sam_ ./compare_sam.pl -Baux -nomd auxf#values.sam auxf#values_java.tmp.sam_ .. ok test_view testing c1#bounds.sam, ref c1.fa: ./test_view -S -l0 -b c1#bounds.sam > c1#bounds.tmp.bam ./test_view c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_ ./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#bounds.sam > c1#bounds.tmp.cram ./test_view -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram ./test_view c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#clip.sam, ref c1.fa: ./test_view -S -l0 -b c1#clip.sam > c1#clip.tmp.bam ./test_view c1#clip.tmp.bam > c1#clip.tmp.bam.sam_ ./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#clip.sam > c1#clip.tmp.cram ./test_view -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.bam > c1#clip.tmp.bam.cram ./test_view c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#noseq.sam, ref c1.fa: ./test_view -S -l0 -b c1#noseq.sam > c1#noseq.tmp.bam ./test_view c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_ ./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#noseq.sam > c1#noseq.tmp.cram ./test_view -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram ./test_view c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad1.sam, ref c1.fa: ./test_view -S -l0 -b c1#pad1.sam > c1#pad1.tmp.bam ./test_view c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_ ./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad1.sam > c1#pad1.tmp.cram ./test_view -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram ./test_view c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad2.sam, ref c1.fa: ./test_view -S -l0 -b c1#pad2.sam > c1#pad2.tmp.bam ./test_view c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_ ./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad2.sam > c1#pad2.tmp.cram ./test_view -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram ./test_view c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad3.sam, ref c1.fa: ./test_view -S -l0 -b c1#pad3.sam > c1#pad3.tmp.bam ./test_view c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_ ./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad3.sam > c1#pad3.tmp.cram ./test_view -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram ./test_view c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#unknown.sam, ref c1.fa: ./test_view -S -l0 -b c1#unknown.sam > c1#unknown.tmp.bam ./test_view c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_ ./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#unknown.sam > c1#unknown.tmp.cram ./test_view -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram ./test_view c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_ .. ok test_view testing c2#pad.sam, ref c2.fa: ./test_view -S -l0 -b c2#pad.sam > c2#pad.tmp.bam ./test_view c2#pad.tmp.bam > c2#pad.tmp.bam.sam_ ./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_ ./test_view -t c2.fa -S -C -o VERSION=2.1 c2#pad.sam > c2#pad.tmp.cram ./test_view -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_ ./test_view -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.bam > c2#pad.tmp.bam.cram ./test_view c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#1.sam, ref ce.fa: ./test_view -S -l0 -b ce#1.sam > ce#1.tmp.bam ./test_view ce#1.tmp.bam > ce#1.tmp.bam.sam_ ./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#1.sam > ce#1.tmp.cram ./test_view -D ce#1.tmp.cram > ce#1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#1.tmp.bam > ce#1.tmp.bam.cram ./test_view ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#1000.sam, ref ce.fa: ./test_view -S -b ce#1000.sam > ce#1000.tmp.bam ./test_view ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ ./test_view -S -l0 -b ce#1000.sam > ce#1000.tmp.bam ./test_view ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#1000.sam > ce#1000.tmp.cram ./test_view -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1000.sam > ce#1000.tmp.cram ./test_view -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.bam > ce#1000.tmp.bam.cram ./test_view ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#2.sam, ref ce.fa: ./test_view -S -l0 -b ce#2.sam > ce#2.tmp.bam ./test_view ce#2.tmp.bam > ce#2.tmp.bam.sam_ ./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#2.sam > ce#2.tmp.cram ./test_view -D ce#2.tmp.cram > ce#2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#2.tmp.bam > ce#2.tmp.bam.cram ./test_view ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#5.sam, ref ce.fa: ./test_view -S -l0 -b ce#5.sam > ce#5.tmp.bam ./test_view ce#5.tmp.bam > ce#5.tmp.bam.sam_ ./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#5.sam > ce#5.tmp.cram ./test_view -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#5.tmp.bam > ce#5.tmp.bam.cram ./test_view ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#5b.sam, ref ce.fa: ./test_view -S -l0 -b ce#5b.sam > ce#5b.tmp.bam ./test_view ce#5b.tmp.bam > ce#5b.tmp.bam.sam_ ./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#5b.sam > ce#5b.tmp.cram ./test_view -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.bam > ce#5b.tmp.bam.cram ./test_view ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_ ./test_view -i reference=ce.fa ce#5b_java.cram > ce#5b_java.tmp.sam_ ./compare_sam.pl -Baux -nomd ce#5b.sam ce#5b_java.tmp.sam_ .. ok test_view testing ce#large_seq.sam, ref ce.fa: ./test_view -S -l0 -b ce#large_seq.sam > ce#large_seq.tmp.bam ./test_view ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_ ./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#large_seq.sam > ce#large_seq.tmp.cram ./test_view -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram ./test_view ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#supp.sam, ref ce.fa: ./test_view -S -l0 -b ce#supp.sam > ce#supp.tmp.bam ./test_view ce#supp.tmp.bam > ce#supp.tmp.bam.sam_ ./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#supp.sam > ce#supp.tmp.cram ./test_view -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.bam > ce#supp.tmp.bam.cram ./test_view ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#tag_depadded.sam, ref ce.fa: ./test_view -S -l0 -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam ./test_view ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_ ./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram ./test_view -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram ./test_view ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#tag_padded.sam, ref ce.fa: ./test_view -S -l0 -b ce#tag_padded.sam > ce#tag_padded.tmp.bam ./test_view ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_ ./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#tag_padded.sam > ce#tag_padded.tmp.cram ./test_view -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram ./test_view ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#unmap.sam, ref ce.fa: ./test_view -S -l0 -b ce#unmap.sam > ce#unmap.tmp.bam ./test_view ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_ ./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap.sam > ce#unmap.tmp.cram ./test_view -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram ./test_view ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#unmap1.sam, ref ce.fa: ./test_view -S -l0 -b ce#unmap1.sam > ce#unmap1.tmp.bam ./test_view ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_ ./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap1.sam > ce#unmap1.tmp.cram ./test_view -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram ./test_view ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#unmap2.sam, ref ce.fa: ./test_view -S -l0 -b ce#unmap2.sam > ce#unmap2.tmp.bam ./test_view ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_ ./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap2.sam > ce#unmap2.tmp.cram ./test_view -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram ./test_view ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_ .. ok test_view testing md#1.sam, ref md.fa: ./test_view -S -l0 -b md#1.sam > md#1.tmp.bam ./test_view md#1.tmp.bam > md#1.tmp.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.sam_ ./test_view -t md.fa -S -C -o VERSION=2.1 md#1.sam > md#1.tmp.cram ./test_view -D md#1.tmp.cram > md#1.tmp.cram.sam_ ./compare_sam.pl md#1.sam md#1.tmp.cram.sam_ ./test_view -t md.fa -C -o VERSION=3.0 md#1.tmp.bam > md#1.tmp.bam.cram ./test_view md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#blank.sam, ref xx.fa: ./test_view -S -l0 -b xx#blank.sam > xx#blank.tmp.bam ./test_view xx#blank.tmp.bam > xx#blank.tmp.bam.sam_ ./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#blank.sam > xx#blank.tmp.cram ./test_view -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.bam > xx#blank.tmp.bam.cram ./test_view xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#large_aux.sam, ref xx.fa: ./test_view -S -l0 -b xx#large_aux.sam > xx#large_aux.tmp.bam ./test_view xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_ ./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#large_aux.sam > xx#large_aux.tmp.cram ./test_view -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram ./test_view xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_ ./test_view -i reference=xx.fa xx#large_aux_java.cram > xx#large_aux_java.tmp.sam_ [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 30 vs 20 ./compare_sam.pl -Baux -nomd xx#large_aux.sam xx#large_aux_java.tmp.sam_ .. ok test_view testing xx#large_aux2.sam, ref xx.fa: ./test_view -S -l0 -b xx#large_aux2.sam > xx#large_aux2.tmp.bam ./test_view xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_ ./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#large_aux2.sam > xx#large_aux2.tmp.cram ./test_view -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram ./test_view xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#MD.sam, ref xx.fa: ./test_view -S -l0 -b xx#MD.sam > xx#MD.tmp.bam ./test_view xx#MD.tmp.bam > xx#MD.tmp.bam.sam_ ./compare_sam.pl xx#MD.sam xx#MD.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#MD.sam > xx#MD.tmp.cram ./test_view -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.bam > xx#MD.tmp.bam.cram ./test_view xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#MD2.sam, ref xx.fa: ./test_view -S -l0 -b xx#MD2.sam > xx#MD2.tmp.bam ./test_view xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_ ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#MD2.sam > xx#MD2.tmp.cram ./test_view -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram ./test_view xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#minimal.sam, ref xx.fa: ./test_view -S -l0 -b xx#minimal.sam > xx#minimal.tmp.bam ./test_view xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_ ./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#minimal.sam > xx#minimal.tmp.cram ./test_view -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram ./test_view xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#pair.sam, ref xx.fa: ./test_view -S -l0 -b xx#pair.sam > xx#pair.tmp.bam ./test_view xx#pair.tmp.bam > xx#pair.tmp.bam.sam_ ./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#pair.sam > xx#pair.tmp.cram ./test_view -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.bam > xx#pair.tmp.bam.cram ./test_view xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#repeated.sam, ref xx.fa: ./test_view -S -l0 -b xx#repeated.sam > xx#repeated.tmp.bam ./test_view xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_ ./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#repeated.sam > xx#repeated.tmp.cram ./test_view -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram ./test_view xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#rg.sam, ref xx.fa: ./test_view -S -l0 -b xx#rg.sam > xx#rg.tmp.bam ./test_view xx#rg.tmp.bam > xx#rg.tmp.bam.sam_ ./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#rg.sam > xx#rg.tmp.cram ./test_view -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.bam > xx#rg.tmp.bam.cram ./test_view xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#tlen.sam, ref xx.fa: ./test_view -S -l0 -b xx#tlen.sam > xx#tlen.tmp.bam ./test_view xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_ ./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#tlen.sam > xx#tlen.tmp.cram ./test_view -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram ./test_view xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#tlen2.sam, ref xx.fa: ./test_view -S -l0 -b xx#tlen2.sam > xx#tlen2.tmp.bam ./test_view xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_ ./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#tlen2.sam > xx#tlen2.tmp.cram ./test_view -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram ./test_view xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#triplet.sam, ref xx.fa: ./test_view -S -l0 -b xx#triplet.sam > xx#triplet.tmp.bam ./test_view xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_ ./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#triplet.sam > xx#triplet.tmp.cram ./test_view -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram ./test_view xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#unsorted.sam, ref xx.fa: ./test_view -S -l0 -b xx#unsorted.sam > xx#unsorted.tmp.bam ./test_view xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_ ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#unsorted.sam > xx#unsorted.tmp.cram ./test_view -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram ./test_view xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_ .. ok test_view testing region queries: ./test_view -i reference=ce.fa range.cram CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp ./compare_sam.pl range.tmp range.out ./test_view range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp ./compare_sam.pl range.tmp range.out .. ok test_view testing BAM files with absent @SQ lines: ./test_view -p no_hdr_sq_1.tmp.sam no_hdr_sq_1.bam ./compare_sam.pl no_hdr_sq_1.tmp.sam no_hdr_sq_1.expected.sam ./test_view -p no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.bam CHROMOSOME_I ./compare_sam.pl no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.expected.sam .. ok test_view testing large (> 2Gbases) positions: ./test_view -z -p longrefs/longref.tmp.sam.gz -x longrefs/longref.tmp.sam.gz.csi.otf -m 14 longrefs/longref.sam ./test_view -p longrefs/longref.tmp.sam_ longrefs/longref.tmp.sam.gz ./compare_sam.pl longrefs/longref.sam longrefs/longref.tmp.sam_ test_view: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c longrefs/longref.tmp.sam.gz .. ok ./test_view -p longrefs/longref_itr.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 ./compare_sam.pl longrefs/longref_itr.expected.sam longrefs/longref_itr.tmp.sam ./test_view -M -p longrefs/longref_multi.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 CHROMOSOME_I:10000000100-10000000110 ./compare_sam.pl longrefs/longref_multi.expected.sam longrefs/longref_multi.tmp.sam .. ok test_view testing auxf#values.sam, ref auxf.fa: ./test_view -@4 -S -l0 -b auxf#values.sam > auxf#values.tmp.bam ./test_view -@4 auxf#values.tmp.bam > auxf#values.tmp.bam.sam_ ./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_ ./test_view -@4 -t auxf.fa -S -C -o VERSION=2.1 auxf#values.sam > auxf#values.tmp.cram ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ ./test_view -@4 -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram ./test_view -@4 auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_ ./test_view -@4 -t auxf.fa -S -l7 -C -o VERSION=3.1 -o archive auxf#values.sam > auxf#values.tmp.cram [W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ ./test_view -@4 -t auxf.fa -S -l7 -C -o VERSION=4.0 -o archive auxf#values.sam > auxf#values.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ ./test_view -@4 -i reference=auxf.fa auxf#values_java.cram > auxf#values_java.tmp.sam_ ./compare_sam.pl -Baux -nomd auxf#values.sam auxf#values_java.tmp.sam_ .. ok test_view testing c1#bounds.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#bounds.sam > c1#bounds.tmp.bam ./test_view -@4 c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_ ./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#bounds.sam > c1#bounds.tmp.cram ./test_view -@4 -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram ./test_view -@4 c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#clip.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#clip.sam > c1#clip.tmp.bam ./test_view -@4 c1#clip.tmp.bam > c1#clip.tmp.bam.sam_ ./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#clip.sam > c1#clip.tmp.cram ./test_view -@4 -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.bam > c1#clip.tmp.bam.cram ./test_view -@4 c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#noseq.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#noseq.sam > c1#noseq.tmp.bam ./test_view -@4 c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_ ./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#noseq.sam > c1#noseq.tmp.cram ./test_view -@4 -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram ./test_view -@4 c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad1.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#pad1.sam > c1#pad1.tmp.bam ./test_view -@4 c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_ ./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad1.sam > c1#pad1.tmp.cram ./test_view -@4 -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram ./test_view -@4 c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad2.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#pad2.sam > c1#pad2.tmp.bam ./test_view -@4 c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_ ./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad2.sam > c1#pad2.tmp.cram ./test_view -@4 -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram ./test_view -@4 c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad3.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#pad3.sam > c1#pad3.tmp.bam ./test_view -@4 c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_ ./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad3.sam > c1#pad3.tmp.cram ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram ./test_view -@4 c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_ ./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=3.1 -o archive c1#pad3.sam > c1#pad3.tmp.cram [W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ ./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=4.0 -o archive c1#pad3.sam > c1#pad3.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ .. ok test_view testing c1#unknown.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#unknown.sam > c1#unknown.tmp.bam ./test_view -@4 c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_ ./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#unknown.sam > c1#unknown.tmp.cram ./test_view -@4 -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram ./test_view -@4 c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_ .. ok test_view testing c2#pad.sam, ref c2.fa: ./test_view -@4 -S -l0 -b c2#pad.sam > c2#pad.tmp.bam ./test_view -@4 c2#pad.tmp.bam > c2#pad.tmp.bam.sam_ ./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_ ./test_view -@4 -t c2.fa -S -C -o VERSION=2.1 c2#pad.sam > c2#pad.tmp.cram ./test_view -@4 -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_ ./test_view -@4 -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.bam > c2#pad.tmp.bam.cram ./test_view -@4 c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#1.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#1.sam > ce#1.tmp.bam ./test_view -@4 ce#1.tmp.bam > ce#1.tmp.bam.sam_ ./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1.sam > ce#1.tmp.cram ./test_view -@4 -D ce#1.tmp.cram > ce#1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1.tmp.bam > ce#1.tmp.bam.cram ./test_view -@4 ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#1000.sam, ref ce.fa: ./test_view -@4 -S -b ce#1000.sam > ce#1000.tmp.bam ./test_view -@4 ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ ./test_view -@4 -S -l0 -b ce#1000.sam > ce#1000.tmp.bam ./test_view -@4 ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1000.sam > ce#1000.tmp.cram ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1000.sam > ce#1000.tmp.cram ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.bam > ce#1000.tmp.bam.cram ./test_view -@4 ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.ms ./test_view -@4 ce#1000.tmp.bam.cram.ms > ce#1000.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#1000.sam > ce#1000.tmp.cram [W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o normal ce#1000.sam > ce#1000.tmp.cram [W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o small ce#1000.sam > ce#1000.tmp.cram [W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#1000.sam > ce#1000.tmp.cram [W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#1000.sam > ce#1000.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ .. ok test_view testing ce#2.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#2.sam > ce#2.tmp.bam ./test_view -@4 ce#2.tmp.bam > ce#2.tmp.bam.sam_ ./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#2.sam > ce#2.tmp.cram ./test_view -@4 -D ce#2.tmp.cram > ce#2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#2.tmp.bam > ce#2.tmp.bam.cram ./test_view -@4 ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#5.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#5.sam > ce#5.tmp.bam ./test_view -@4 ce#5.tmp.bam > ce#5.tmp.bam.sam_ ./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#5.sam > ce#5.tmp.cram ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5.tmp.bam > ce#5.tmp.bam.cram ./test_view -@4 ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.ms ./test_view -@4 ce#5.tmp.bam.cram.ms > ce#5.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#5.sam > ce#5.tmp.cram [W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#5.sam > ce#5.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ .. ok test_view testing ce#5b.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#5b.sam > ce#5b.tmp.bam ./test_view -@4 ce#5b.tmp.bam > ce#5b.tmp.bam.sam_ ./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#5b.sam > ce#5b.tmp.cram ./test_view -@4 -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.bam > ce#5b.tmp.bam.cram ./test_view -@4 ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.ms ./test_view -@4 ce#5b.tmp.bam.cram.ms > ce#5b.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.sam_ ./test_view -@4 -i reference=ce.fa ce#5b_java.cram > ce#5b_java.tmp.sam_ ./compare_sam.pl -Baux -nomd ce#5b.sam ce#5b_java.tmp.sam_ .. ok test_view testing ce#large_seq.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#large_seq.sam > ce#large_seq.tmp.bam ./test_view -@4 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_ ./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#large_seq.sam > ce#large_seq.tmp.cram ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram ./test_view -@4 ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#large_seq.sam > ce#large_seq.tmp.cram [W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o fast ce#large_seq.sam > ce#large_seq.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o normal ce#large_seq.sam > ce#large_seq.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o small ce#large_seq.sam > ce#large_seq.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#large_seq.sam > ce#large_seq.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ .. ok test_view testing ce#supp.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#supp.sam > ce#supp.tmp.bam ./test_view -@4 ce#supp.tmp.bam > ce#supp.tmp.bam.sam_ ./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#supp.sam > ce#supp.tmp.cram ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.bam > ce#supp.tmp.bam.cram ./test_view -@4 ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#supp.sam > ce#supp.tmp.cram [W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#supp.sam > ce#supp.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ .. ok test_view testing ce#tag_depadded.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam ./test_view -@4 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_ ./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram ./test_view -@4 -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram ./test_view -@4 ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#tag_padded.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#tag_padded.sam > ce#tag_padded.tmp.bam ./test_view -@4 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_ ./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#tag_padded.sam > ce#tag_padded.tmp.cram ./test_view -@4 -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram ./test_view -@4 ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#unmap.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#unmap.sam > ce#unmap.tmp.bam ./test_view -@4 ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_ ./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap.sam > ce#unmap.tmp.cram ./test_view -@4 -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram ./test_view -@4 ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.ms ./test_view -@4 ce#unmap.tmp.bam.cram.ms > ce#unmap.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.sam_ .. ok test_view testing ce#unmap1.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#unmap1.sam > ce#unmap1.tmp.bam ./test_view -@4 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_ ./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap1.sam > ce#unmap1.tmp.cram ./test_view -@4 -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram ./test_view -@4 ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.ms ./test_view -@4 ce#unmap1.tmp.bam.cram.ms > ce#unmap1.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.sam_ .. ok test_view testing ce#unmap2.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#unmap2.sam > ce#unmap2.tmp.bam ./test_view -@4 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_ ./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap2.sam > ce#unmap2.tmp.cram ./test_view -@4 -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram ./test_view -@4 ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.ms ./test_view -@4 ce#unmap2.tmp.bam.cram.ms > ce#unmap2.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.sam_ .. ok test_view testing md#1.sam, ref md.fa: ./test_view -@4 -S -l0 -b md#1.sam > md#1.tmp.bam ./test_view -@4 md#1.tmp.bam > md#1.tmp.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.sam_ ./test_view -@4 -t md.fa -S -C -o VERSION=2.1 md#1.sam > md#1.tmp.cram ./test_view -@4 -D md#1.tmp.cram > md#1.tmp.cram.sam_ ./compare_sam.pl md#1.sam md#1.tmp.cram.sam_ ./test_view -@4 -t md.fa -C -o VERSION=3.0 md#1.tmp.bam > md#1.tmp.bam.cram ./test_view -@4 md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#blank.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#blank.sam > xx#blank.tmp.bam ./test_view -@4 xx#blank.tmp.bam > xx#blank.tmp.bam.sam_ ./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#blank.sam > xx#blank.tmp.cram ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.bam > xx#blank.tmp.bam.cram ./test_view -@4 xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.ms ./test_view -@4 xx#blank.tmp.bam.cram.ms > xx#blank.tmp.bam.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#blank.sam > xx#blank.tmp.cram [W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#blank.sam > xx#blank.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ .. ok test_view testing xx#large_aux.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#large_aux.sam > xx#large_aux.tmp.bam ./test_view -@4 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_ ./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#large_aux.sam > xx#large_aux.tmp.cram ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram ./test_view -@4 xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#large_aux.sam > xx#large_aux.tmp.cram [W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o fast xx#large_aux.sam > xx#large_aux.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o normal xx#large_aux.sam > xx#large_aux.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o small xx#large_aux.sam > xx#large_aux.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#large_aux.sam > xx#large_aux.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -i reference=xx.fa xx#large_aux_java.cram > xx#large_aux_java.tmp.sam_ [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 30 vs 20 ./compare_sam.pl -Baux -nomd xx#large_aux.sam xx#large_aux_java.tmp.sam_ .. ok test_view testing xx#large_aux2.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#large_aux2.sam > xx#large_aux2.tmp.bam ./test_view -@4 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_ ./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#large_aux2.sam > xx#large_aux2.tmp.cram ./test_view -@4 -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram ./test_view -@4 xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#MD.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#MD.sam > xx#MD.tmp.bam ./test_view -@4 xx#MD.tmp.bam > xx#MD.tmp.bam.sam_ ./compare_sam.pl xx#MD.sam xx#MD.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#MD.sam > xx#MD.tmp.cram ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.bam > xx#MD.tmp.bam.cram ./test_view -@4 xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#MD.sam > xx#MD.tmp.cram [W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#MD.sam > xx#MD.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ .. ok test_view testing xx#MD2.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#MD2.sam > xx#MD2.tmp.bam ./test_view -@4 xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_ ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#MD2.sam > xx#MD2.tmp.cram ./test_view -@4 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram ./test_view -@4 xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#minimal.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#minimal.sam > xx#minimal.tmp.bam ./test_view -@4 xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_ ./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#minimal.sam > xx#minimal.tmp.cram ./test_view -@4 -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram ./test_view -@4 xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.ms ./test_view -@4 xx#minimal.tmp.bam.cram.ms > xx#minimal.tmp.bam.cram.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.sam_ .. ok test_view testing xx#pair.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#pair.sam > xx#pair.tmp.bam ./test_view -@4 xx#pair.tmp.bam > xx#pair.tmp.bam.sam_ ./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#pair.sam > xx#pair.tmp.cram ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.bam > xx#pair.tmp.bam.cram ./test_view -@4 xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#pair.sam > xx#pair.tmp.cram [W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#pair.sam > xx#pair.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ .. ok test_view testing xx#repeated.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#repeated.sam > xx#repeated.tmp.bam ./test_view -@4 xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_ ./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#repeated.sam > xx#repeated.tmp.cram ./test_view -@4 -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram ./test_view -@4 xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#rg.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#rg.sam > xx#rg.tmp.bam ./test_view -@4 xx#rg.tmp.bam > xx#rg.tmp.bam.sam_ ./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#rg.sam > xx#rg.tmp.cram ./test_view -@4 -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.bam > xx#rg.tmp.bam.cram ./test_view -@4 xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#tlen.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#tlen.sam > xx#tlen.tmp.bam ./test_view -@4 xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_ ./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#tlen.sam > xx#tlen.tmp.cram ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram ./test_view -@4 xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.ms ./test_view -@4 xx#tlen.tmp.bam.cram.ms > xx#tlen.tmp.bam.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#tlen.sam > xx#tlen.tmp.cram [W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#tlen.sam > xx#tlen.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ .. ok test_view testing xx#tlen2.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#tlen2.sam > xx#tlen2.tmp.bam ./test_view -@4 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_ ./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#tlen2.sam > xx#tlen2.tmp.cram ./test_view -@4 -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram ./test_view -@4 xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.ms ./test_view -@4 xx#tlen2.tmp.bam.cram.ms > xx#tlen2.tmp.bam.cram.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.sam_ .. ok test_view testing xx#triplet.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#triplet.sam > xx#triplet.tmp.bam ./test_view -@4 xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_ ./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#triplet.sam > xx#triplet.tmp.cram ./test_view -@4 -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram ./test_view -@4 xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.ms ./test_view -@4 xx#triplet.tmp.bam.cram.ms > xx#triplet.tmp.bam.cram.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.sam_ .. ok test_view testing xx#unsorted.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#unsorted.sam > xx#unsorted.tmp.bam ./test_view -@4 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_ ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#unsorted.sam > xx#unsorted.tmp.cram ./test_view -@4 -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram ./test_view -@4 xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_ .. ok test_view testing region queries: ./test_view -@4 -i reference=ce.fa range.cram CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp ./compare_sam.pl range.tmp range.out ./test_view -@4 range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp ./compare_sam.pl range.tmp range.out .. ok test_view testing BAM files with absent @SQ lines: ./test_view -@4 -p no_hdr_sq_1.tmp.sam no_hdr_sq_1.bam ./compare_sam.pl no_hdr_sq_1.tmp.sam no_hdr_sq_1.expected.sam ./test_view -@4 -p no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.bam CHROMOSOME_I ./compare_sam.pl no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.expected.sam .. ok test_view testing large (> 2Gbases) positions: ./test_view -@4 -z -p longrefs/longref.tmp.sam.gz -x longrefs/longref.tmp.sam.gz.csi.otf -m 14 longrefs/longref.sam ./test_view -@4 -p longrefs/longref.tmp.sam_ longrefs/longref.tmp.sam.gz ./compare_sam.pl longrefs/longref.sam longrefs/longref.tmp.sam_ test_view: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c longrefs/longref.tmp.sam.gz .. ok ./test_view -@4 -p longrefs/longref_itr.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 ./compare_sam.pl longrefs/longref_itr.expected.sam longrefs/longref_itr.tmp.sam ./test_view -@4 -M -p longrefs/longref_multi.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 CHROMOSOME_I:10000000100-10000000110 ./compare_sam.pl longrefs/longref_multi.expected.sam longrefs/longref_multi.tmp.sam .. ok test_MD testing xx#MD.sam, ref xx.fa: ./test_view -o store_nm=1 -o store_md=1 -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram ./test_view -i decode_md=0 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl xx#MD.sam xx#MD.tmp.cram.sam_ ./test_view -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram ./test_view -i decode_md=0 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -partialmd=2 xx#MD.sam xx#MD.tmp.cram.sam_ Checking for MD/NM in xx#MD.sam ./test_view -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram ./test_view -i decode_md=1 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -partialmd=1 xx#MD.sam xx#MD.tmp.cram.sam_ .. ok test_MD testing xx#MD2.sam, ref xx.fa: ./test_view -o store_nm=1 -o store_md=1 -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram ./test_view -i decode_md=0 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.cram.sam_ ./test_view -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram ./test_view -i decode_md=0 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl -partialmd=2 xx#MD2.sam xx#MD2.tmp.cram.sam_ ./test_view -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram ./test_view -i decode_md=1 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl -partialmd=1 xx#MD2.sam xx#MD2.tmp.cram.sam_ .. ok test_vcf_api: /builddir/build/BUILD/htslib-1.15.1/test/test-vcf-api /tmp/xEkWqSjgSa/test-vcf-api.bcf [W::bcf_record_check] Bad BCF record at 1:1: No REF allele [E::bcf_index_build3] TBI indices for BCF files are not supported [E::idx_find_and_load] Could not retrieve index file for '/tmp/xEkWqSjgSa/test-vcf-api.bcf' .. ok test_bcf2vcf: /builddir/build/BUILD/htslib-1.15.1/test/test_view /builddir/build/BUILD/htslib-1.15.1/test/tabix/vcf_file.bcf .. ok test_vcf_sweep: /builddir/build/BUILD/htslib-1.15.1/test/test-vcf-sweep /tmp/xEkWqSjgSa/test-vcf-api.bcf .. ok test_vcf_various: /builddir/build/BUILD/htslib-1.15.1/htsfile -ch /builddir/build/BUILD/htslib-1.15.1/test/test-vcf-hdr-in.vcf .. ok test_vcf_various: /builddir/build/BUILD/htslib-1.15.1/htsfile -c /builddir/build/BUILD/htslib-1.15.1/test/formatcols.vcf .. ok test_vcf_various: /builddir/build/BUILD/htslib-1.15.1/htsfile -c /builddir/build/BUILD/htslib-1.15.1/test/noroundtrip.vcf .. ok test_vcf_various: /builddir/build/BUILD/htslib-1.15.1/htsfile -c /builddir/build/BUILD/htslib-1.15.1/test/formatmissing.vcf .. ok test_vcf_various: /builddir/build/BUILD/htslib-1.15.1/htsfile -c /builddir/build/BUILD/htslib-1.15.1/test/vcf_meta_meta.vcf .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/xEkWqSjgSa -s 411380026 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/xEkWqSjgSa -s 624621403 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/xEkWqSjgSa -s 111066191 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/xEkWqSjgSa -s 825430351 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/xEkWqSjgSa -s 1055902473 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/xEkWqSjgSa -s 411953603 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/xEkWqSjgSa -s 436604114 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/xEkWqSjgSa -s 336248074 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/xEkWqSjgSa -s 970897358 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/xEkWqSjgSa -s 1488713639 .. ok test_command: /builddir/build/BUILD/htslib-1.15.1/test/test-bcf-translate - .. ok test_convert_padded_header: /builddir/build/BUILD/htslib-1.15.1/test/test_view -t ce.fa -C /tmp/xEkWqSjgSa/headernul0.bam .. ok test_convert_padded_header: /builddir/build/BUILD/htslib-1.15.1/test/test_view -t ce.fa -C /tmp/xEkWqSjgSa/headernul1.bam .. ok test_convert_padded_header: /builddir/build/BUILD/htslib-1.15.1/test/test_view -t ce.fa -C /tmp/xEkWqSjgSa/headernul678.bam .. ok test_rebgzip: /builddir/build/BUILD/htslib-1.15.1/bgzip -I /builddir/build/BUILD/htslib-1.15.1/test/bgziptest.txt.gz.gzi -c -g /builddir/build/BUILD/htslib-1.15.1/test/bgziptest.txt .. ok test-logging: /builddir/build/BUILD/htslib-1.15.1/test/test-logging.pl .. ok test_plugin_loading: HTS_PATH=/builddir/build/BUILD/htslib-1.15.1 /builddir/build/BUILD/htslib-1.15.1/test/with-shlib.sh /builddir/build/BUILD/htslib-1.15.1/htsfile https://localhost:99999/invalid_port .. ok test_realn: /builddir/build/BUILD/htslib-1.15.1/test/test_realn -f /builddir/build/BUILD/htslib-1.15.1/test/realn01.fa -i /builddir/build/BUILD/htslib-1.15.1/test/realn01.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.15.1/test/test_realn -f /builddir/build/BUILD/htslib-1.15.1/test/realn02.fa -i /builddir/build/BUILD/htslib-1.15.1/test/realn02.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.15.1/test/test_realn -a -f /builddir/build/BUILD/htslib-1.15.1/test/realn01.fa -i /builddir/build/BUILD/htslib-1.15.1/test/realn01.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.15.1/test/test_realn -a -f /builddir/build/BUILD/htslib-1.15.1/test/realn02.fa -i /builddir/build/BUILD/htslib-1.15.1/test/realn02.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.15.1/test/test_realn -e -f /builddir/build/BUILD/htslib-1.15.1/test/realn01.fa -i /builddir/build/BUILD/htslib-1.15.1/test/realn01.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.15.1/test/test_realn -e -f /builddir/build/BUILD/htslib-1.15.1/test/realn02.fa -i /builddir/build/BUILD/htslib-1.15.1/test/realn02.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.15.1/test/test_realn -r -f /builddir/build/BUILD/htslib-1.15.1/test/realn02.fa -i /builddir/build/BUILD/htslib-1.15.1/test/realn02-r.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.15.1/test/test_realn -a -f /builddir/build/BUILD/htslib-1.15.1/test/realn02.fa -i /builddir/build/BUILD/htslib-1.15.1/test/realn02_exp.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.15.1/test/test_realn -f /builddir/build/BUILD/htslib-1.15.1/test/realn02.fa -i /builddir/build/BUILD/htslib-1.15.1/test/realn02_exp-a.sam -o - .. ok Number of tests: total .. 172 passed .. 172 failed .. 0 + RPM_EC=0 ++ jobs -p + exit 0 Processing files: htslib-1.15.1-1.fc38.aarch64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.gErzff + umask 022 + cd /builddir/build/BUILD + cd htslib-1.15.1 + DOCDIR=/builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.aarch64/usr/share/doc/htslib + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.aarch64/usr/share/doc/htslib + cp -pr NEWS /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.aarch64/usr/share/doc/htslib + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.MH01NB + umask 022 + cd /builddir/build/BUILD + cd htslib-1.15.1 + LICENSEDIR=/builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.aarch64/usr/share/licenses/htslib + export LC_ALL=C + LC_ALL=C + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.aarch64/usr/share/licenses/htslib + cp -pr LICENSE /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.aarch64/usr/share/licenses/htslib + RPM_EC=0 ++ jobs -p + exit 0 Provides: htslib = 1.15.1-1.fc38 htslib(aarch-64) = 1.15.1-1.fc38 libhts.so.3()(64bit) Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: 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) libcrypto.so.3()(64bit) libcrypto.so.3(OPENSSL_3.0.0)(64bit) libcurl.so.4()(64bit) libhts.so.3()(64bit) liblzma.so.5()(64bit) liblzma.so.5(XZ_5.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.17)(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-1.15.1-1.fc38.aarch64 Provides: htslib-devel = 1.15.1-1.fc38 htslib-devel(aarch-64) = 1.15.1-1.fc38 pkgconfig(htslib) = 1.15.1 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: /usr/bin/pkg-config libhts.so.3()(64bit) Processing files: htslib-tools-1.15.1-1.fc38.aarch64 Provides: htslib-tools = 1.15.1-1.fc38 htslib-tools(aarch-64) = 1.15.1-1.fc38 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: 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) liblzma.so.5()(64bit) liblzma.so.5(XZ_5.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.29)(64bit) libz.so.1()(64bit) rtld(GNU_HASH) Processing files: htslib-debugsource-1.15.1-1.fc38.aarch64 Provides: htslib-debugsource = 1.15.1-1.fc38 htslib-debugsource(aarch-64) = 1.15.1-1.fc38 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: htslib-debuginfo-1.15.1-1.fc38.aarch64 Provides: debuginfo(build-id) = 202e00b06ebfd183a1aa09c089e3205c3c57cc61 debuginfo(build-id) = 2ef57e6a275f552453a3988a88cbb3f15be78702 debuginfo(build-id) = 346710f878305f1a2a4636c18e2cf90c2457e2c0 debuginfo(build-id) = 496a3ee6af4f7ccd0af26dd66358fbe1c77ae35c debuginfo(build-id) = 7d3156f55da17c515ae826d835d470f0ee2a0d84 htslib-debuginfo = 1.15.1-1.fc38 htslib-debuginfo(aarch-64) = 1.15.1-1.fc38 libhts.so.1.15.1-1.15.1-1.fc38.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) = 1.15.1-1.fc38 Processing files: htslib-tools-debuginfo-1.15.1-1.fc38.aarch64 Provides: debuginfo(build-id) = 5624864bf19c3ea019a58269c68dd0fefcf8179b debuginfo(build-id) = 6c8b8b3cce6a3bcac35be143f61ae1e5b84a90c8 debuginfo(build-id) = fba11139a486f3676f097e39059ed73bf78439e4 htslib-tools-debuginfo = 1.15.1-1.fc38 htslib-tools-debuginfo(aarch-64) = 1.15.1-1.fc38 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: htslib-debugsource(aarch-64) = 1.15.1-1.fc38 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.aarch64 Wrote: /builddir/build/RPMS/htslib-tools-1.15.1-1.fc38.aarch64.rpm Wrote: /builddir/build/RPMS/htslib-debuginfo-1.15.1-1.fc38.aarch64.rpm Wrote: /builddir/build/RPMS/htslib-debugsource-1.15.1-1.fc38.aarch64.rpm Wrote: /builddir/build/RPMS/htslib-1.15.1-1.fc38.aarch64.rpm Wrote: /builddir/build/RPMS/htslib-devel-1.15.1-1.fc38.aarch64.rpm Wrote: /builddir/build/RPMS/htslib-tools-debuginfo-1.15.1-1.fc38.aarch64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.b7fLwn + umask 022 + cd /builddir/build/BUILD + cd htslib-1.15.1 + /usr/bin/rm -rf /builddir/build/BUILDROOT/htslib-1.15.1-1.fc38.aarch64 + RPM_EC=0 ++ jobs -p + exit 0 Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.3KUveq + umask 022 + cd /builddir/build/BUILD + rm -rf htslib-1.15.1 htslib-1.15.1.gemspec + RPM_EC=0 ++ jobs -p + exit 0 Finish: rpmbuild htslib-1.15.1-1.fc38.src.rpm Finish: build phase for htslib-1.15.1-1.fc38.src.rpm INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-aarch64-1660557065.245354/root/var/log/dnf.rpm.log /var/lib/mock/fedora-rawhide-aarch64-1660557065.245354/root/var/log/dnf.librepo.log /var/lib/mock/fedora-rawhide-aarch64-1660557065.245354/root/var/log/dnf.log INFO: Done(/var/lib/copr-rpmbuild/results/htslib-1.15.1-1.fc38.src.rpm) Config(child) 8 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 Finish: run Running RPMResults tool