Warning: Permanently added '34.229.117.115' (ED25519) to the list of known hosts. INFO: Calling: curl -H Pragma: -o htslib-1.15.1.tar.bz2 --location --connect-timeout 60 --retry 3 --retry-delay 10 --remote-time --show-error --fail --retry-all-errors https://copr-dist-git.fedorainfracloud.org/repo/pkgs/trawets/random-al2023-pkg-builds/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 79.9M 0 --:--:-- --:--:-- --:--:-- 80.5M INFO: Reading stdout from command: md5sum htslib-1.15.1.tar.bz2 Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-yinqapun/htslib/htslib.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-yinqapun/htslib --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1704591054.948002 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 5.4 starting (python version = 3.11.3, NVR = mock-5.4-1.fc38), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-yinqapun/htslib/htslib.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-yinqapun/htslib --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1704591054.948002 -r /var/lib/copr-rpmbuild/results/configs/child.cfg Start(bootstrap): init plugins INFO: tmpfs initialized INFO: selinux enabled INFO: chroot_scan: initialized INFO: compress_logs: initialized Finish(bootstrap): init plugins Start: init plugins INFO: tmpfs initialized INFO: selinux enabled INFO: chroot_scan: initialized INFO: compress_logs: initialized Finish: init plugins INFO: Signal handler active Start: run INFO: Start(/var/lib/copr-rpmbuild/workspace/workdir-yinqapun/htslib/htslib.spec) Config(amazonlinux-2023-aarch64) Start: clean chroot Finish: clean chroot Mock Version: 5.4 INFO: Mock Version: 5.4 Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/amazonlinux-2023-aarch64-bootstrap-1704591054.948002/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata INFO: Guessed host environment type: unknown INFO: Using bootstrap image: public.ecr.aws/amazonlinux/amazonlinux:2023 INFO: Pulling image: public.ecr.aws/amazonlinux/amazonlinux:2023 INFO: Copy content of container public.ecr.aws/amazonlinux/amazonlinux:2023 to /var/lib/mock/amazonlinux-2023-aarch64-bootstrap-1704591054.948002/root INFO: Checking that public.ecr.aws/amazonlinux/amazonlinux:2023 image matches host's architecture INFO: mounting public.ecr.aws/amazonlinux/amazonlinux:2023 with podman image mount INFO: image public.ecr.aws/amazonlinux/amazonlinux:2023 as /var/lib/containers/storage/overlay/90b47655dc28817c48ff86404223b17287409bc6bb899cd0b28e2b0c754404da/merged INFO: umounting image public.ecr.aws/amazonlinux/amazonlinux:2023 (/var/lib/containers/storage/overlay/90b47655dc28817c48ff86404223b17287409bc6bb899cd0b28e2b0c754404da/merged) with podman image umount INFO: Package manager dnf detected and used (fallback) INFO: Bootstrap image not marked ready Start(bootstrap): installing dnf tooling No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 1.8 MB/s | 151 kB 00:00 Amazon Linux 2023 repository - aarch64 36 MB/s | 22 MB 00:00 Package python3-dnf-4.12.0-2.amzn2023.0.4.noarch is already installed. Dependencies resolved. ================================================================================ Package Arch Version Repository Size ================================================================================ Installing: python3-dnf-plugins-core noarch 4.1.0-1.amzn2023.0.3 amazonlinux 219 k Installing dependencies: dbus-libs aarch64 1:1.12.28-1.amzn2023.0.1 amazonlinux 152 k python3-dateutil noarch 1:2.8.1-3.amzn2023.0.2 amazonlinux 289 k python3-dbus aarch64 1.2.18-1.amzn2023.0.2 amazonlinux 134 k python3-distro noarch 1.5.0-5.amzn2023.0.2 amazonlinux 36 k python3-setuptools noarch 59.6.0-2.amzn2023.0.4 amazonlinux 940 k python3-six noarch 1.15.0-5.amzn2023.0.2 amazonlinux 36 k systemd-libs aarch64 252.16-1.amzn2023.0.1 amazonlinux 597 k Transaction Summary ================================================================================ Install 8 Packages Total download size: 2.3 M Installed size: 11 M Downloading Packages: (1/8): python3-six-1.15.0-5.amzn2023.0.2.noarch 1.0 MB/s | 36 kB 00:00 (2/8): python3-dateutil-2.8.1-3.amzn2023.0.2.no 6.9 MB/s | 289 kB 00:00 (3/8): python3-distro-1.5.0-5.amzn2023.0.2.noar 6.1 MB/s | 36 kB 00:00 (4/8): python3-setuptools-59.6.0-2.amzn2023.0.4 21 MB/s | 940 kB 00:00 (5/8): python3-dnf-plugins-core-4.1.0-1.amzn202 23 MB/s | 219 kB 00:00 (6/8): systemd-libs-252.16-1.amzn2023.0.1.aarch 50 MB/s | 597 kB 00:00 (7/8): dbus-libs-1.12.28-1.amzn2023.0.1.aarch64 16 MB/s | 152 kB 00:00 (8/8): python3-dbus-1.2.18-1.amzn2023.0.2.aarch 15 MB/s | 134 kB 00:00 -------------------------------------------------------------------------------- Total 6.5 MB/s | 2.3 MB 00:00 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Installing : systemd-libs-252.16-1.amzn2023.0.1.aarch64 1/8 Installing : dbus-libs-1:1.12.28-1.amzn2023.0.1.aarch64 2/8 Installing : python3-dbus-1.2.18-1.amzn2023.0.2.aarch64 3/8 Installing : python3-setuptools-59.6.0-2.amzn2023.0.4.noarch 4/8 Installing : python3-distro-1.5.0-5.amzn2023.0.2.noarch 5/8 Installing : python3-six-1.15.0-5.amzn2023.0.2.noarch 6/8 Installing : python3-dateutil-1:2.8.1-3.amzn2023.0.2.noarch 7/8 Installing : python3-dnf-plugins-core-4.1.0-1.amzn2023.0.3.noarch 8/8 Running scriptlet: python3-dnf-plugins-core-4.1.0-1.amzn2023.0.3.noarch 8/8 Verifying : python3-six-1.15.0-5.amzn2023.0.2.noarch 1/8 Verifying : python3-dateutil-1:2.8.1-3.amzn2023.0.2.noarch 2/8 Verifying : python3-setuptools-59.6.0-2.amzn2023.0.4.noarch 3/8 Verifying : python3-distro-1.5.0-5.amzn2023.0.2.noarch 4/8 Verifying : python3-dnf-plugins-core-4.1.0-1.amzn2023.0.3.noarch 5/8 Verifying : systemd-libs-252.16-1.amzn2023.0.1.aarch64 6/8 Verifying : dbus-libs-1:1.12.28-1.amzn2023.0.1.aarch64 7/8 Verifying : python3-dbus-1.2.18-1.amzn2023.0.2.aarch64 8/8 Installed: dbus-libs-1:1.12.28-1.amzn2023.0.1.aarch64 python3-dateutil-1:2.8.1-3.amzn2023.0.2.noarch python3-dbus-1.2.18-1.amzn2023.0.2.aarch64 python3-distro-1.5.0-5.amzn2023.0.2.noarch python3-dnf-plugins-core-4.1.0-1.amzn2023.0.3.noarch python3-setuptools-59.6.0-2.amzn2023.0.4.noarch python3-six-1.15.0-5.amzn2023.0.2.noarch systemd-libs-252.16-1.amzn2023.0.1.aarch64 Complete! Finish(bootstrap): installing dnf tooling Start(bootstrap): creating root cache Finish(bootstrap): creating root cache Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/amazonlinux-2023-aarch64-1704591054.948002/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin INFO: Package manager dnf detected and used (direct choice) INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-4.16.1.3-12.amzn2023.0.6.aarch64 python3-dnf-4.12.0-2.amzn2023.0.4.noarch python3-dnf-plugins-core-4.1.0-1.amzn2023.0.3.noarch yum-4.12.0-2.amzn2023.0.4.noarch Start: installing minimal buildroot with dnf No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 44 kB/s | 1.5 kB 00:00 Copr repository 2.3 MB/s | 151 kB 00:00 Amazon Linux 2023 repository - aarch64 11 kB/s | 3.6 kB 00:00 Dependencies resolved. ============================================================================================= Package Arch Version Repository Size ============================================================================================= Installing: amazon-rpm-config noarch 228-3.amzn2023.0.2 amazonlinux 74 k bash aarch64 5.2.15-1.amzn2023.0.2 amazonlinux 1.8 M bzip2 aarch64 1.0.8-6.amzn2023.0.2 amazonlinux 53 k coreutils aarch64 8.32-30.amzn2023.0.3 amazonlinux 1.2 M cpio aarch64 2.13-13.amzn2023.0.2 amazonlinux 270 k diffutils aarch64 3.8-1.amzn2023.0.2 amazonlinux 368 k findutils aarch64 1:4.8.0-2.amzn2023.0.2 amazonlinux 541 k gawk aarch64 5.1.0-3.amzn2023.0.3 amazonlinux 984 k glibc-minimal-langpack aarch64 2.34-52.amzn2023.0.7 amazonlinux 33 k grep aarch64 3.8-1.amzn2023.0.4 amazonlinux 282 k gzip aarch64 1.12-1.amzn2023.0.1 amazonlinux 158 k info aarch64 6.7-10.amzn2023.0.2 amazonlinux 224 k patch aarch64 2.7.6-14.amzn2023.0.2 amazonlinux 126 k rpm-build aarch64 4.16.1.3-12.amzn2023.0.6 amazonlinux 92 k sed aarch64 4.8-7.amzn2023.0.2 amazonlinux 295 k system-release noarch 2023.3.20231218-0.amzn2023 amazonlinux 27 k tar aarch64 2:1.34-1.amzn2023.0.3 amazonlinux 869 k unzip aarch64 6.0-57.amzn2023.0.2 amazonlinux 180 k util-linux aarch64 2.37.4-1.amzn2023.0.3 amazonlinux 2.2 M which aarch64 2.21-26.amzn2023.0.2 amazonlinux 42 k xz aarch64 5.2.5-9.amzn2023.0.2 amazonlinux 216 k Installing dependencies: alternatives aarch64 1.15-2.amzn2023.0.2 amazonlinux 36 k amazon-linux-repo-cdn noarch 2023.3.20231218-0.amzn2023 amazonlinux 16 k audit-libs aarch64 3.0.6-1.amzn2023.0.2 amazonlinux 116 k basesystem noarch 11-11.amzn2023.0.2 amazonlinux 7.8 k binutils aarch64 2.39-6.amzn2023.0.10 amazonlinux 4.7 M bzip2-libs aarch64 1.0.8-6.amzn2023.0.2 amazonlinux 44 k ca-certificates noarch 2023.2.62-1.0.amzn2023.0.1 amazonlinux 739 k coreutils-common aarch64 8.32-30.amzn2023.0.3 amazonlinux 2.0 M cracklib aarch64 2.9.6-27.amzn2023.0.2 amazonlinux 83 k crypto-policies noarch 20220428-1.gitdfb10ea.amzn2023.0.2 amazonlinux 60 k curl aarch64 8.3.0-1.amzn2023.0.2 amazonlinux 351 k cyrus-sasl-lib aarch64 2.1.27-18.amzn2023.0.3 amazonlinux 776 k dwz aarch64 0.14-6.amzn2023.0.2 amazonlinux 127 k ed aarch64 1.14.2-10.amzn2023.0.2 amazonlinux 74 k efi-srpm-macros noarch 5-4.amzn2023.0.5 amazonlinux 23 k elfutils aarch64 0.188-3.amzn2023.0.2 amazonlinux 519 k elfutils-debuginfod-client aarch64 0.188-3.amzn2023.0.2 amazonlinux 41 k elfutils-default-yama-scope noarch 0.188-3.amzn2023.0.2 amazonlinux 17 k elfutils-libelf aarch64 0.188-3.amzn2023.0.2 amazonlinux 199 k elfutils-libs aarch64 0.188-3.amzn2023.0.2 amazonlinux 257 k file aarch64 5.39-7.amzn2023.0.4 amazonlinux 50 k file-libs aarch64 5.39-7.amzn2023.0.4 amazonlinux 587 k filesystem aarch64 3.14-5.amzn2023.0.3 amazonlinux 22 k fonts-srpm-macros noarch 1:2.0.5-12.amzn2023.0.2 amazonlinux 27 k gdb-minimal aarch64 12.1-5.amzn2023.0.3 amazonlinux 3.5 M gdbm-libs aarch64 1:1.19-2.amzn2023.0.2 amazonlinux 53 k ghc-srpm-macros noarch 1.5.0-4.amzn2023.0.2 amazonlinux 8.5 k glibc aarch64 2.34-52.amzn2023.0.7 amazonlinux 1.7 M glibc-common aarch64 2.34-52.amzn2023.0.7 amazonlinux 297 k glibc-gconv-extra aarch64 2.34-52.amzn2023.0.7 amazonlinux 1.9 M gmp aarch64 1:6.2.1-2.amzn2023.0.2 amazonlinux 276 k go-srpm-macros noarch 3.3.1-1.amzn2023 copr_base 28 k jansson aarch64 2.14-0.amzn2023 amazonlinux 47 k kernel-srpm-macros noarch 1.0-14.amzn2023.0.2 amazonlinux 10 k keyutils-libs aarch64 1.6.3-1.amzn2023 amazonlinux 33 k krb5-libs aarch64 1.21-3.amzn2023.0.3 amazonlinux 768 k libacl aarch64 2.3.1-2.amzn2023.0.2 amazonlinux 24 k libarchive aarch64 3.5.3-2.amzn2023.0.3 amazonlinux 395 k libattr aarch64 2.5.1-3.amzn2023.0.2 amazonlinux 19 k libblkid aarch64 2.37.4-1.amzn2023.0.3 amazonlinux 106 k libbrotli aarch64 1.0.9-4.amzn2023.0.2 amazonlinux 316 k libcap aarch64 2.48-2.amzn2023.0.3 amazonlinux 68 k libcap-ng aarch64 0.8.2-4.amzn2023.0.2 amazonlinux 33 k libcom_err aarch64 1.46.5-2.amzn2023.0.2 amazonlinux 27 k libcurl aarch64 8.3.0-1.amzn2023.0.2 amazonlinux 339 k libdb aarch64 5.3.28-49.amzn2023.0.2 amazonlinux 731 k libeconf aarch64 0.4.0-1.amzn2023.0.3 amazonlinux 27 k libfdisk aarch64 2.37.4-1.amzn2023.0.3 amazonlinux 149 k libffi aarch64 3.4.4-1.amzn2023.0.1 amazonlinux 37 k libgcc aarch64 11.4.1-2.amzn2023.0.2 amazonlinux 87 k libgomp aarch64 11.4.1-2.amzn2023.0.2 amazonlinux 262 k libidn2 aarch64 2.3.2-1.amzn2023.0.5 amazonlinux 105 k libmount aarch64 2.37.4-1.amzn2023.0.3 amazonlinux 131 k libnghttp2 aarch64 1.57.0-1.amzn2023.0.1 amazonlinux 77 k libpkgconf aarch64 1.8.0-4.amzn2023.0.2 amazonlinux 37 k libpsl aarch64 0.21.1-3.amzn2023.0.2 amazonlinux 61 k libpwquality aarch64 1.4.4-6.amzn2023.0.2 amazonlinux 106 k libselinux aarch64 3.4-5.amzn2023.0.2 amazonlinux 87 k libsemanage aarch64 3.4-5.amzn2023.0.2 amazonlinux 119 k libsepol aarch64 3.4-3.amzn2023.0.3 amazonlinux 311 k libsigsegv aarch64 2.13-2.amzn2023.0.2 amazonlinux 28 k libsmartcols aarch64 2.37.4-1.amzn2023.0.3 amazonlinux 61 k libssh aarch64 0.10.5-1.amzn2023.0.2 amazonlinux 213 k libssh-config noarch 0.10.5-1.amzn2023.0.2 amazonlinux 11 k libstdc++ aarch64 11.4.1-2.amzn2023.0.2 amazonlinux 691 k libtasn1 aarch64 4.19.0-1.amzn2023.0.4 amazonlinux 75 k libunistring aarch64 0.9.10-10.amzn2023.0.2 amazonlinux 493 k libutempter aarch64 1.2.1-4.amzn2023.0.2 amazonlinux 27 k libuuid aarch64 2.37.4-1.amzn2023.0.3 amazonlinux 27 k libverto aarch64 0.3.2-1.amzn2023.0.2 amazonlinux 22 k libxcrypt aarch64 4.4.33-7.amzn2023 amazonlinux 127 k libxml2 aarch64 2.10.4-1.amzn2023.0.6 amazonlinux 691 k libzstd aarch64 1.5.5-1.amzn2023.0.1 amazonlinux 284 k lua-libs aarch64 5.4.4-3.amzn2023.0.2 amazonlinux 214 k lua-srpm-macros noarch 1-4.amzn2023.0.2 amazonlinux 9.2 k lz4-libs aarch64 1.9.4-1.amzn2023.0.2 amazonlinux 73 k mpfr aarch64 4.1.0-7.amzn2023.0.2 amazonlinux 243 k ncurses-base noarch 6.2-4.20200222.amzn2023.0.4 amazonlinux 60 k ncurses-libs aarch64 6.2-4.20200222.amzn2023.0.4 amazonlinux 318 k ocaml-srpm-macros noarch 6-6.amzn2023.0.2 amazonlinux 8.8 k openblas-srpm-macros noarch 2-9.amzn2023.0.2 amazonlinux 8.2 k openldap aarch64 2.4.57-6.amzn2023.0.6 amazonlinux 254 k openssl-libs aarch64 1:3.0.8-1.amzn2023.0.10 amazonlinux 2.1 M p11-kit aarch64 0.24.1-2.amzn2023.0.3 amazonlinux 346 k p11-kit-trust aarch64 0.24.1-2.amzn2023.0.3 amazonlinux 138 k package-notes-srpm-macros noarch 0.4-18.amzn2023.0.5 amazonlinux 13 k pam aarch64 1.5.1-8.amzn2023.0.3 amazonlinux 554 k pcre2 aarch64 10.40-1.amzn2023.0.3 amazonlinux 220 k pcre2-syntax noarch 10.40-1.amzn2023.0.3 amazonlinux 142 k perl-srpm-macros noarch 1-39.amzn2023.0.2 amazonlinux 8.7 k pkgconf aarch64 1.8.0-4.amzn2023.0.2 amazonlinux 43 k pkgconf-m4 noarch 1.8.0-4.amzn2023.0.2 amazonlinux 15 k pkgconf-pkg-config aarch64 1.8.0-4.amzn2023.0.2 amazonlinux 11 k popt aarch64 1.18-6.amzn2023.0.2 amazonlinux 59 k publicsuffix-list-dafsa noarch 20221208-60.amzn2023 amazonlinux 61 k python-srpm-macros noarch 3.9-41.amzn2023.0.5 amazonlinux 22 k readline aarch64 8.1-2.amzn2023.0.2 amazonlinux 212 k rpm aarch64 4.16.1.3-12.amzn2023.0.6 amazonlinux 484 k rpm-build-libs aarch64 4.16.1.3-12.amzn2023.0.6 amazonlinux 87 k rpm-libs aarch64 4.16.1.3-12.amzn2023.0.6 amazonlinux 305 k rust-srpm-macros noarch 21-42.amzn2023.0.2 amazonlinux 10 k setup noarch 2.13.7-3.amzn2023.0.2 amazonlinux 141 k shadow-utils aarch64 2:4.9-12.amzn2023.0.4 amazonlinux 1.1 M sqlite-libs aarch64 3.40.0-1.amzn2023.0.3 amazonlinux 660 k systemd-libs aarch64 252.16-1.amzn2023.0.1 amazonlinux 597 k util-linux-core aarch64 2.37.4-1.amzn2023.0.3 amazonlinux 438 k xxhash-libs aarch64 0.8.0-3.amzn2023.0.2 amazonlinux 32 k xz-libs aarch64 5.2.5-9.amzn2023.0.2 amazonlinux 92 k zip aarch64 3.0-28.amzn2023.0.2 amazonlinux 254 k zlib aarch64 1.2.11-33.amzn2023.0.5 amazonlinux 91 k zstd aarch64 1.5.5-1.amzn2023.0.1 amazonlinux 450 k Transaction Summary ============================================================================================= Install 132 Packages Total size: 45 M Total download size: 28 k Installed size: 284 M Downloading Packages: [SKIPPED] efi-srpm-macros-5-4.amzn2023.0.5.noarch.rpm: Already downloaded [SKIPPED] ghc-srpm-macros-1.5.0-4.amzn2023.0.2.noarch.rpm: Already downloaded [SKIPPED] elfutils-default-yama-scope-0.188-3.amzn2023.0.2.noarch.rpm: Already downloaded [SKIPPED] ncurses-base-6.2-4.20200222.amzn2023.0.4.noarch.rpm: Already downloaded [SKIPPED] openblas-srpm-macros-2-9.amzn2023.0.2.noarch.rpm: Already downloaded [SKIPPED] publicsuffix-list-dafsa-20221208-60.amzn2023.noarch.rpm: Already downloaded [SKIPPED] kernel-srpm-macros-1.0-14.amzn2023.0.2.noarch.rpm: Already downloaded [SKIPPED] pcre2-syntax-10.40-1.amzn2023.0.3.noarch.rpm: Already downloaded [SKIPPED] ocaml-srpm-macros-6-6.amzn2023.0.2.noarch.rpm: Already downloaded [SKIPPED] basesystem-11-11.amzn2023.0.2.noarch.rpm: Already downloaded [SKIPPED] setup-2.13.7-3.amzn2023.0.2.noarch.rpm: Already downloaded [SKIPPED] libssh-config-0.10.5-1.amzn2023.0.2.noarch.rpm: Already downloaded [SKIPPED] amazon-rpm-config-228-3.amzn2023.0.2.noarch.rpm: Already downloaded [SKIPPED] ca-certificates-2023.2.62-1.0.amzn2023.0.1.noarch.rpm: Already downloaded [SKIPPED] python-srpm-macros-3.9-41.amzn2023.0.5.noarch.rpm: Already downloaded [SKIPPED] crypto-policies-20220428-1.gitdfb10ea.amzn2023.0.2.noarch.rpm: Already downloaded [SKIPPED] fonts-srpm-macros-2.0.5-12.amzn2023.0.2.noarch.rpm: Already downloaded [SKIPPED] package-notes-srpm-macros-0.4-18.amzn2023.0.5.noarch.rpm: Already downloaded [SKIPPED] perl-srpm-macros-1-39.amzn2023.0.2.noarch.rpm: Already downloaded [SKIPPED] lua-srpm-macros-1-4.amzn2023.0.2.noarch.rpm: Already downloaded [SKIPPED] system-release-2023.3.20231218-0.amzn2023.noarch.rpm: Already downloaded [SKIPPED] amazon-linux-repo-cdn-2023.3.20231218-0.amzn2023.noarch.rpm: Already downloaded [SKIPPED] rust-srpm-macros-21-42.amzn2023.0.2.noarch.rpm: Already downloaded [SKIPPED] pkgconf-m4-1.8.0-4.amzn2023.0.2.noarch.rpm: Already downloaded [SKIPPED] libzstd-1.5.5-1.amzn2023.0.1.aarch64.rpm: Already downloaded [SKIPPED] mpfr-4.1.0-7.amzn2023.0.2.aarch64.rpm: Already downloaded [SKIPPED] libverto-0.3.2-1.amzn2023.0.2.aarch64.rpm: Already downloaded [SKIPPED] elfutils-libelf-0.188-3.amzn2023.0.2.aarch64.rpm: Already downloaded [SKIPPED] ncurses-libs-6.2-4.20200222.amzn2023.0.4.aarch64.rpm: Already downloaded [SKIPPED] bash-5.2.15-1.amzn2023.0.2.aarch64.rpm: Already downloaded [SKIPPED] diffutils-3.8-1.amzn2023.0.2.aarch64.rpm: Already downloaded [SKIPPED] p11-kit-trust-0.24.1-2.amzn2023.0.3.aarch64.rpm: Already downloaded [SKIPPED] util-linux-core-2.37.4-1.amzn2023.0.3.aarch64.rpm: Already downloaded [SKIPPED] dwz-0.14-6.amzn2023.0.2.aarch64.rpm: Already downloaded [SKIPPED] libbrotli-1.0.9-4.amzn2023.0.2.aarch64.rpm: Already downloaded [SKIPPED] gawk-5.1.0-3.amzn2023.0.3.aarch64.rpm: Already downloaded [SKIPPED] findutils-4.8.0-2.amzn2023.0.2.aarch64.rpm: Already downloaded [SKIPPED] libffi-3.4.4-1.amzn2023.0.1.aarch64.rpm: Already downloaded [SKIPPED] rpm-build-4.16.1.3-12.amzn2023.0.6.aarch64.rpm: 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1.8 kB 00:00 Importing GPG key 0xD832C631: Userid : "Amazon Linux " Fingerprint: B21C 50FA 44A9 9720 EAA7 2F7F E951 904A D832 C631 From : /usr/share/distribution-gpg-keys/amazon-linux/RPM-GPG-KEY-amazon-linux-2023 Key imported successfully Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Running scriptlet: filesystem-3.14-5.amzn2023.0.3.aarch64 1/1 Preparing : 1/1 Installing : libgcc-11.4.1-2.amzn2023.0.2.aarch64 1/132 Running scriptlet: libgcc-11.4.1-2.amzn2023.0.2.aarch64 1/132 Installing : crypto-policies-20220428-1.gitdfb10ea.amzn2023.0 2/132 Running scriptlet: crypto-policies-20220428-1.gitdfb10ea.amzn2023.0 2/132 Installing : coreutils-common-8.32-30.amzn2023.0.3.aarch64 3/132 Installing : pkgconf-m4-1.8.0-4.amzn2023.0.2.noarch 4/132 Installing : rust-srpm-macros-21-42.amzn2023.0.2.noarch 5/132 Installing : perl-srpm-macros-1-39.amzn2023.0.2.noarch 6/132 Installing : libssh-config-0.10.5-1.amzn2023.0.2.noarch 7/132 Installing : ocaml-srpm-macros-6-6.amzn2023.0.2.noarch 8/132 Installing : pcre2-syntax-10.40-1.amzn2023.0.3.noarch 9/132 Installing : kernel-srpm-macros-1.0-14.amzn2023.0.2.noarch 10/132 Installing : publicsuffix-list-dafsa-20221208-60.amzn2023.noa 11/132 Installing : openblas-srpm-macros-2-9.amzn2023.0.2.noarch 12/132 Installing : 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ca-certificates-2023.2.62-1.0.amzn2023.0.1.noarc 89/132 Installing : ca-certificates-2023.2.62-1.0.amzn2023.0.1.noarc 89/132 Running scriptlet: ca-certificates-2023.2.62-1.0.amzn2023.0.1.noarc 89/132 Installing : libblkid-2.37.4-1.amzn2023.0.3.aarch64 90/132 Running scriptlet: libblkid-2.37.4-1.amzn2023.0.3.aarch64 90/132 Installing : krb5-libs-1.21-3.amzn2023.0.3.aarch64 91/132 Installing : libmount-2.37.4-1.amzn2023.0.3.aarch64 92/132 Installing : gzip-1.12-1.amzn2023.0.1.aarch64 93/132 Installing : cracklib-2.9.6-27.amzn2023.0.2.aarch64 94/132 Installing : util-linux-core-2.37.4-1.amzn2023.0.3.aarch64 95/132 Running scriptlet: util-linux-core-2.37.4-1.amzn2023.0.3.aarch64 95/132 Installing : libssh-0.10.5-1.amzn2023.0.2.aarch64 96/132 Installing : libfdisk-2.37.4-1.amzn2023.0.3.aarch64 97/132 Installing : libarchive-3.5.3-2.amzn2023.0.3.aarch64 98/132 Installing : xxhash-libs-0.8.0-3.amzn2023.0.2.aarch64 99/132 Installing : libdb-5.3.28-49.amzn2023.0.2.aarch64 100/132 Installing : pam-1.5.1-8.amzn2023.0.3.aarch64 101/132 Installing : libpwquality-1.4.4-6.amzn2023.0.2.aarch64 102/132 Installing : libnghttp2-1.57.0-1.amzn2023.0.1.aarch64 103/132 Installing : jansson-2.14-0.amzn2023.aarch64 104/132 Installing : libgomp-11.4.1-2.amzn2023.0.2.aarch64 105/132 Installing : gdbm-libs-1:1.19-2.amzn2023.0.2.aarch64 106/132 Installing : cyrus-sasl-lib-2.1.27-18.amzn2023.0.3.aarch64 107/132 Installing : openldap-2.4.57-6.amzn2023.0.6.aarch64 108/132 Installing : libcurl-8.3.0-1.amzn2023.0.2.aarch64 109/132 Installing : curl-8.3.0-1.amzn2023.0.2.aarch64 110/132 Installing : rpm-libs-4.16.1.3-12.amzn2023.0.6.aarch64 111/132 Installing : rpm-4.16.1.3-12.amzn2023.0.6.aarch64 112/132 Installing : efi-srpm-macros-5-4.amzn2023.0.5.noarch 113/132 Installing : lua-srpm-macros-1-4.amzn2023.0.2.noarch 114/132 Installing : elfutils-default-yama-scope-0.188-3.amzn2023.0.2 115/132 Running scriptlet: elfutils-default-yama-scope-0.188-3.amzn2023.0.2 115/132 Installing : elfutils-debuginfod-client-0.188-3.amzn2023.0.2. 116/132 Installing : elfutils-libs-0.188-3.amzn2023.0.2.aarch64 117/132 Installing : elfutils-0.188-3.amzn2023.0.2.aarch64 118/132 Installing : rpm-build-libs-4.16.1.3-12.amzn2023.0.6.aarch64 119/132 Installing : gdb-minimal-12.1-5.amzn2023.0.3.aarch64 120/132 Installing : binutils-2.39-6.amzn2023.0.10.aarch64 121/132 Running scriptlet: binutils-2.39-6.amzn2023.0.10.aarch64 121/132 Installing : package-notes-srpm-macros-0.4-18.amzn2023.0.5.no 122/132 Installing : ghc-srpm-macros-1.5.0-4.amzn2023.0.2.noarch 123/132 Installing : python-srpm-macros-3.9-41.amzn2023.0.5.noarch 124/132 Installing : fonts-srpm-macros-1:2.0.5-12.amzn2023.0.2.noarch 125/132 Installing : amazon-rpm-config-228-3.amzn2023.0.2.noarch 126/132 Running scriptlet: amazon-rpm-config-228-3.amzn2023.0.2.noarch 126/132 Installing : go-srpm-macros-3.3.1-1.amzn2023.noarch 127/132 Installing : pkgconf-1.8.0-4.amzn2023.0.2.aarch64 128/132 Installing : pkgconf-pkg-config-1.8.0-4.amzn2023.0.2.aarch64 129/132 Installing : rpm-build-4.16.1.3-12.amzn2023.0.6.aarch64 130/132 Installing : util-linux-2.37.4-1.amzn2023.0.3.aarch64 131/132 Running scriptlet: util-linux-2.37.4-1.amzn2023.0.3.aarch64 131/132 Installing : which-2.21-26.amzn2023.0.2.aarch64 132/132 Running scriptlet: filesystem-3.14-5.amzn2023.0.3.aarch64 132/132 Running scriptlet: ca-certificates-2023.2.62-1.0.amzn2023.0.1.noarc 132/132 Running scriptlet: pam-1.5.1-8.amzn2023.0.3.aarch64 132/132 Running scriptlet: rpm-4.16.1.3-12.amzn2023.0.6.aarch64 132/132 Running scriptlet: which-2.21-26.amzn2023.0.2.aarch64 132/132 Verifying : go-srpm-macros-3.3.1-1.amzn2023.noarch 1/132 Verifying : efi-srpm-macros-5-4.amzn2023.0.5.noarch 2/132 Verifying : ghc-srpm-macros-1.5.0-4.amzn2023.0.2.noarch 3/132 Verifying : elfutils-default-yama-scope-0.188-3.amzn2023.0.2 4/132 Verifying : ncurses-base-6.2-4.20200222.amzn2023.0.4.noarch 5/132 Verifying : openblas-srpm-macros-2-9.amzn2023.0.2.noarch 6/132 Verifying : publicsuffix-list-dafsa-20221208-60.amzn2023.noa 7/132 Verifying : kernel-srpm-macros-1.0-14.amzn2023.0.2.noarch 8/132 Verifying : pcre2-syntax-10.40-1.amzn2023.0.3.noarch 9/132 Verifying : ocaml-srpm-macros-6-6.amzn2023.0.2.noarch 10/132 Verifying : basesystem-11-11.amzn2023.0.2.noarch 11/132 Verifying : setup-2.13.7-3.amzn2023.0.2.noarch 12/132 Verifying : libssh-config-0.10.5-1.amzn2023.0.2.noarch 13/132 Verifying : amazon-rpm-config-228-3.amzn2023.0.2.noarch 14/132 Verifying : ca-certificates-2023.2.62-1.0.amzn2023.0.1.noarc 15/132 Verifying : python-srpm-macros-3.9-41.amzn2023.0.5.noarch 16/132 Verifying : crypto-policies-20220428-1.gitdfb10ea.amzn2023.0 17/132 Verifying : fonts-srpm-macros-1:2.0.5-12.amzn2023.0.2.noarch 18/132 Verifying : package-notes-srpm-macros-0.4-18.amzn2023.0.5.no 19/132 Verifying : perl-srpm-macros-1-39.amzn2023.0.2.noarch 20/132 Verifying : lua-srpm-macros-1-4.amzn2023.0.2.noarch 21/132 Verifying : system-release-2023.3.20231218-0.amzn2023.noarch 22/132 Verifying : amazon-linux-repo-cdn-2023.3.20231218-0.amzn2023 23/132 Verifying : rust-srpm-macros-21-42.amzn2023.0.2.noarch 24/132 Verifying : pkgconf-m4-1.8.0-4.amzn2023.0.2.noarch 25/132 Verifying : libzstd-1.5.5-1.amzn2023.0.1.aarch64 26/132 Verifying : mpfr-4.1.0-7.amzn2023.0.2.aarch64 27/132 Verifying : libverto-0.3.2-1.amzn2023.0.2.aarch64 28/132 Verifying : elfutils-libelf-0.188-3.amzn2023.0.2.aarch64 29/132 Verifying : ncurses-libs-6.2-4.20200222.amzn2023.0.4.aarch64 30/132 Verifying : bash-5.2.15-1.amzn2023.0.2.aarch64 31/132 Verifying : diffutils-3.8-1.amzn2023.0.2.aarch64 32/132 Verifying : p11-kit-trust-0.24.1-2.amzn2023.0.3.aarch64 33/132 Verifying : util-linux-core-2.37.4-1.amzn2023.0.3.aarch64 34/132 Verifying : dwz-0.14-6.amzn2023.0.2.aarch64 35/132 Verifying : libbrotli-1.0.9-4.amzn2023.0.2.aarch64 36/132 Verifying : gawk-5.1.0-3.amzn2023.0.3.aarch64 37/132 Verifying : findutils-1:4.8.0-2.amzn2023.0.2.aarch64 38/132 Verifying : libffi-3.4.4-1.amzn2023.0.1.aarch64 39/132 Verifying : rpm-build-4.16.1.3-12.amzn2023.0.6.aarch64 40/132 Verifying : bzip2-libs-1.0.8-6.amzn2023.0.2.aarch64 41/132 Verifying : pcre2-10.40-1.amzn2023.0.3.aarch64 42/132 Verifying : popt-1.18-6.amzn2023.0.2.aarch64 43/132 Verifying : elfutils-debuginfod-client-0.188-3.amzn2023.0.2. 44/132 Verifying : keyutils-libs-1.6.3-1.amzn2023.aarch64 45/132 Verifying : gmp-1:6.2.1-2.amzn2023.0.2.aarch64 46/132 Verifying : glibc-common-2.34-52.amzn2023.0.7.aarch64 47/132 Verifying : libsigsegv-2.13-2.amzn2023.0.2.aarch64 48/132 Verifying : readline-8.1-2.amzn2023.0.2.aarch64 49/132 Verifying : elfutils-0.188-3.amzn2023.0.2.aarch64 50/132 Verifying : libeconf-0.4.0-1.amzn2023.0.3.aarch64 51/132 Verifying : libutempter-1.2.1-4.amzn2023.0.2.aarch64 52/132 Verifying : filesystem-3.14-5.amzn2023.0.3.aarch64 53/132 Verifying : coreutils-common-8.32-30.amzn2023.0.3.aarch64 54/132 Verifying : elfutils-libs-0.188-3.amzn2023.0.2.aarch64 55/132 Verifying : libblkid-2.37.4-1.amzn2023.0.3.aarch64 56/132 Verifying : libselinux-3.4-5.amzn2023.0.2.aarch64 57/132 Verifying : audit-libs-3.0.6-1.amzn2023.0.2.aarch64 58/132 Verifying : zlib-1.2.11-33.amzn2023.0.5.aarch64 59/132 Verifying : rpm-build-libs-4.16.1.3-12.amzn2023.0.6.aarch64 60/132 Verifying : unzip-6.0-57.amzn2023.0.2.aarch64 61/132 Verifying : libsmartcols-2.37.4-1.amzn2023.0.3.aarch64 62/132 Verifying : patch-2.7.6-14.amzn2023.0.2.aarch64 63/132 Verifying : cpio-2.13-13.amzn2023.0.2.aarch64 64/132 Verifying : coreutils-8.32-30.amzn2023.0.3.aarch64 65/132 Verifying : tar-2:1.34-1.amzn2023.0.3.aarch64 66/132 Verifying : lua-libs-5.4.4-3.amzn2023.0.2.aarch64 67/132 Verifying : libcap-2.48-2.amzn2023.0.3.aarch64 68/132 Verifying : util-linux-2.37.4-1.amzn2023.0.3.aarch64 69/132 Verifying : libpkgconf-1.8.0-4.amzn2023.0.2.aarch64 70/132 Verifying : libacl-2.3.1-2.amzn2023.0.2.aarch64 71/132 Verifying : systemd-libs-252.16-1.amzn2023.0.1.aarch64 72/132 Verifying : libfdisk-2.37.4-1.amzn2023.0.3.aarch64 73/132 Verifying : libstdc++-11.4.1-2.amzn2023.0.2.aarch64 74/132 Verifying : which-2.21-26.amzn2023.0.2.aarch64 75/132 Verifying : libtasn1-4.19.0-1.amzn2023.0.4.aarch64 76/132 Verifying : file-libs-5.39-7.amzn2023.0.4.aarch64 77/132 Verifying : zip-3.0-28.amzn2023.0.2.aarch64 78/132 Verifying : lz4-libs-1.9.4-1.amzn2023.0.2.aarch64 79/132 Verifying : p11-kit-0.24.1-2.amzn2023.0.3.aarch64 80/132 Verifying : libssh-0.10.5-1.amzn2023.0.2.aarch64 81/132 Verifying : sqlite-libs-3.40.0-1.amzn2023.0.3.aarch64 82/132 Verifying : libcap-ng-0.8.2-4.amzn2023.0.2.aarch64 83/132 Verifying : libattr-2.5.1-3.amzn2023.0.2.aarch64 84/132 Verifying : sed-4.8-7.amzn2023.0.2.aarch64 85/132 Verifying : openldap-2.4.57-6.amzn2023.0.6.aarch64 86/132 Verifying : gdb-minimal-12.1-5.amzn2023.0.3.aarch64 87/132 Verifying : zstd-1.5.5-1.amzn2023.0.1.aarch64 88/132 Verifying : rpm-4.16.1.3-12.amzn2023.0.6.aarch64 89/132 Verifying : libsemanage-3.4-5.amzn2023.0.2.aarch64 90/132 Verifying : glibc-2.34-52.amzn2023.0.7.aarch64 91/132 Verifying : libunistring-0.9.10-10.amzn2023.0.2.aarch64 92/132 Verifying : xxhash-libs-0.8.0-3.amzn2023.0.2.aarch64 93/132 Verifying : libdb-5.3.28-49.amzn2023.0.2.aarch64 94/132 Verifying : pkgconf-1.8.0-4.amzn2023.0.2.aarch64 95/132 Verifying : libcurl-8.3.0-1.amzn2023.0.2.aarch64 96/132 Verifying : libidn2-2.3.2-1.amzn2023.0.5.aarch64 97/132 Verifying : libcom_err-1.46.5-2.amzn2023.0.2.aarch64 98/132 Verifying : bzip2-1.0.8-6.amzn2023.0.2.aarch64 99/132 Verifying : libarchive-3.5.3-2.amzn2023.0.3.aarch64 100/132 Verifying : gzip-1.12-1.amzn2023.0.1.aarch64 101/132 Verifying : curl-8.3.0-1.amzn2023.0.2.aarch64 102/132 Verifying : krb5-libs-1.21-3.amzn2023.0.3.aarch64 103/132 Verifying : libnghttp2-1.57.0-1.amzn2023.0.1.aarch64 104/132 Verifying : libmount-2.37.4-1.amzn2023.0.3.aarch64 105/132 Verifying : xz-libs-5.2.5-9.amzn2023.0.2.aarch64 106/132 Verifying : glibc-gconv-extra-2.34-52.amzn2023.0.7.aarch64 107/132 Verifying : jansson-2.14-0.amzn2023.aarch64 108/132 Verifying : libgomp-11.4.1-2.amzn2023.0.2.aarch64 109/132 Verifying : libuuid-2.37.4-1.amzn2023.0.3.aarch64 110/132 Verifying : glibc-minimal-langpack-2.34-52.amzn2023.0.7.aarc 111/132 Verifying : libsepol-3.4-3.amzn2023.0.3.aarch64 112/132 Verifying : cyrus-sasl-lib-2.1.27-18.amzn2023.0.3.aarch64 113/132 Verifying : pkgconf-pkg-config-1.8.0-4.amzn2023.0.2.aarch64 114/132 Verifying : libpwquality-1.4.4-6.amzn2023.0.2.aarch64 115/132 Verifying : ed-1.14.2-10.amzn2023.0.2.aarch64 116/132 Verifying : shadow-utils-2:4.9-12.amzn2023.0.4.aarch64 117/132 Verifying : libgcc-11.4.1-2.amzn2023.0.2.aarch64 118/132 Verifying : gdbm-libs-1:1.19-2.amzn2023.0.2.aarch64 119/132 Verifying : libxcrypt-4.4.33-7.amzn2023.aarch64 120/132 Verifying : binutils-2.39-6.amzn2023.0.10.aarch64 121/132 Verifying : pam-1.5.1-8.amzn2023.0.3.aarch64 122/132 Verifying : rpm-libs-4.16.1.3-12.amzn2023.0.6.aarch64 123/132 Verifying : grep-3.8-1.amzn2023.0.4.aarch64 124/132 Verifying : libpsl-0.21.1-3.amzn2023.0.2.aarch64 125/132 Verifying : libxml2-2.10.4-1.amzn2023.0.6.aarch64 126/132 Verifying : alternatives-1.15-2.amzn2023.0.2.aarch64 127/132 Verifying : info-6.7-10.amzn2023.0.2.aarch64 128/132 Verifying : file-5.39-7.amzn2023.0.4.aarch64 129/132 Verifying : openssl-libs-1:3.0.8-1.amzn2023.0.10.aarch64 130/132 Verifying : xz-5.2.5-9.amzn2023.0.2.aarch64 131/132 Verifying : cracklib-2.9.6-27.amzn2023.0.2.aarch64 132/132 Installed: alternatives-1.15-2.amzn2023.0.2.aarch64 amazon-linux-repo-cdn-2023.3.20231218-0.amzn2023.noarch amazon-rpm-config-228-3.amzn2023.0.2.noarch audit-libs-3.0.6-1.amzn2023.0.2.aarch64 basesystem-11-11.amzn2023.0.2.noarch bash-5.2.15-1.amzn2023.0.2.aarch64 binutils-2.39-6.amzn2023.0.10.aarch64 bzip2-1.0.8-6.amzn2023.0.2.aarch64 bzip2-libs-1.0.8-6.amzn2023.0.2.aarch64 ca-certificates-2023.2.62-1.0.amzn2023.0.1.noarch coreutils-8.32-30.amzn2023.0.3.aarch64 coreutils-common-8.32-30.amzn2023.0.3.aarch64 cpio-2.13-13.amzn2023.0.2.aarch64 cracklib-2.9.6-27.amzn2023.0.2.aarch64 crypto-policies-20220428-1.gitdfb10ea.amzn2023.0.2.noarch curl-8.3.0-1.amzn2023.0.2.aarch64 cyrus-sasl-lib-2.1.27-18.amzn2023.0.3.aarch64 diffutils-3.8-1.amzn2023.0.2.aarch64 dwz-0.14-6.amzn2023.0.2.aarch64 ed-1.14.2-10.amzn2023.0.2.aarch64 efi-srpm-macros-5-4.amzn2023.0.5.noarch elfutils-0.188-3.amzn2023.0.2.aarch64 elfutils-debuginfod-client-0.188-3.amzn2023.0.2.aarch64 elfutils-default-yama-scope-0.188-3.amzn2023.0.2.noarch elfutils-libelf-0.188-3.amzn2023.0.2.aarch64 elfutils-libs-0.188-3.amzn2023.0.2.aarch64 file-5.39-7.amzn2023.0.4.aarch64 file-libs-5.39-7.amzn2023.0.4.aarch64 filesystem-3.14-5.amzn2023.0.3.aarch64 findutils-1:4.8.0-2.amzn2023.0.2.aarch64 fonts-srpm-macros-1:2.0.5-12.amzn2023.0.2.noarch gawk-5.1.0-3.amzn2023.0.3.aarch64 gdb-minimal-12.1-5.amzn2023.0.3.aarch64 gdbm-libs-1:1.19-2.amzn2023.0.2.aarch64 ghc-srpm-macros-1.5.0-4.amzn2023.0.2.noarch glibc-2.34-52.amzn2023.0.7.aarch64 glibc-common-2.34-52.amzn2023.0.7.aarch64 glibc-gconv-extra-2.34-52.amzn2023.0.7.aarch64 glibc-minimal-langpack-2.34-52.amzn2023.0.7.aarch64 gmp-1:6.2.1-2.amzn2023.0.2.aarch64 go-srpm-macros-3.3.1-1.amzn2023.noarch grep-3.8-1.amzn2023.0.4.aarch64 gzip-1.12-1.amzn2023.0.1.aarch64 info-6.7-10.amzn2023.0.2.aarch64 jansson-2.14-0.amzn2023.aarch64 kernel-srpm-macros-1.0-14.amzn2023.0.2.noarch keyutils-libs-1.6.3-1.amzn2023.aarch64 krb5-libs-1.21-3.amzn2023.0.3.aarch64 libacl-2.3.1-2.amzn2023.0.2.aarch64 libarchive-3.5.3-2.amzn2023.0.3.aarch64 libattr-2.5.1-3.amzn2023.0.2.aarch64 libblkid-2.37.4-1.amzn2023.0.3.aarch64 libbrotli-1.0.9-4.amzn2023.0.2.aarch64 libcap-2.48-2.amzn2023.0.3.aarch64 libcap-ng-0.8.2-4.amzn2023.0.2.aarch64 libcom_err-1.46.5-2.amzn2023.0.2.aarch64 libcurl-8.3.0-1.amzn2023.0.2.aarch64 libdb-5.3.28-49.amzn2023.0.2.aarch64 libeconf-0.4.0-1.amzn2023.0.3.aarch64 libfdisk-2.37.4-1.amzn2023.0.3.aarch64 libffi-3.4.4-1.amzn2023.0.1.aarch64 libgcc-11.4.1-2.amzn2023.0.2.aarch64 libgomp-11.4.1-2.amzn2023.0.2.aarch64 libidn2-2.3.2-1.amzn2023.0.5.aarch64 libmount-2.37.4-1.amzn2023.0.3.aarch64 libnghttp2-1.57.0-1.amzn2023.0.1.aarch64 libpkgconf-1.8.0-4.amzn2023.0.2.aarch64 libpsl-0.21.1-3.amzn2023.0.2.aarch64 libpwquality-1.4.4-6.amzn2023.0.2.aarch64 libselinux-3.4-5.amzn2023.0.2.aarch64 libsemanage-3.4-5.amzn2023.0.2.aarch64 libsepol-3.4-3.amzn2023.0.3.aarch64 libsigsegv-2.13-2.amzn2023.0.2.aarch64 libsmartcols-2.37.4-1.amzn2023.0.3.aarch64 libssh-0.10.5-1.amzn2023.0.2.aarch64 libssh-config-0.10.5-1.amzn2023.0.2.noarch libstdc++-11.4.1-2.amzn2023.0.2.aarch64 libtasn1-4.19.0-1.amzn2023.0.4.aarch64 libunistring-0.9.10-10.amzn2023.0.2.aarch64 libutempter-1.2.1-4.amzn2023.0.2.aarch64 libuuid-2.37.4-1.amzn2023.0.3.aarch64 libverto-0.3.2-1.amzn2023.0.2.aarch64 libxcrypt-4.4.33-7.amzn2023.aarch64 libxml2-2.10.4-1.amzn2023.0.6.aarch64 libzstd-1.5.5-1.amzn2023.0.1.aarch64 lua-libs-5.4.4-3.amzn2023.0.2.aarch64 lua-srpm-macros-1-4.amzn2023.0.2.noarch lz4-libs-1.9.4-1.amzn2023.0.2.aarch64 mpfr-4.1.0-7.amzn2023.0.2.aarch64 ncurses-base-6.2-4.20200222.amzn2023.0.4.noarch ncurses-libs-6.2-4.20200222.amzn2023.0.4.aarch64 ocaml-srpm-macros-6-6.amzn2023.0.2.noarch openblas-srpm-macros-2-9.amzn2023.0.2.noarch openldap-2.4.57-6.amzn2023.0.6.aarch64 openssl-libs-1:3.0.8-1.amzn2023.0.10.aarch64 p11-kit-0.24.1-2.amzn2023.0.3.aarch64 p11-kit-trust-0.24.1-2.amzn2023.0.3.aarch64 package-notes-srpm-macros-0.4-18.amzn2023.0.5.noarch pam-1.5.1-8.amzn2023.0.3.aarch64 patch-2.7.6-14.amzn2023.0.2.aarch64 pcre2-10.40-1.amzn2023.0.3.aarch64 pcre2-syntax-10.40-1.amzn2023.0.3.noarch perl-srpm-macros-1-39.amzn2023.0.2.noarch pkgconf-1.8.0-4.amzn2023.0.2.aarch64 pkgconf-m4-1.8.0-4.amzn2023.0.2.noarch pkgconf-pkg-config-1.8.0-4.amzn2023.0.2.aarch64 popt-1.18-6.amzn2023.0.2.aarch64 publicsuffix-list-dafsa-20221208-60.amzn2023.noarch python-srpm-macros-3.9-41.amzn2023.0.5.noarch readline-8.1-2.amzn2023.0.2.aarch64 rpm-4.16.1.3-12.amzn2023.0.6.aarch64 rpm-build-4.16.1.3-12.amzn2023.0.6.aarch64 rpm-build-libs-4.16.1.3-12.amzn2023.0.6.aarch64 rpm-libs-4.16.1.3-12.amzn2023.0.6.aarch64 rust-srpm-macros-21-42.amzn2023.0.2.noarch sed-4.8-7.amzn2023.0.2.aarch64 setup-2.13.7-3.amzn2023.0.2.noarch shadow-utils-2:4.9-12.amzn2023.0.4.aarch64 sqlite-libs-3.40.0-1.amzn2023.0.3.aarch64 system-release-2023.3.20231218-0.amzn2023.noarch systemd-libs-252.16-1.amzn2023.0.1.aarch64 tar-2:1.34-1.amzn2023.0.3.aarch64 unzip-6.0-57.amzn2023.0.2.aarch64 util-linux-2.37.4-1.amzn2023.0.3.aarch64 util-linux-core-2.37.4-1.amzn2023.0.3.aarch64 which-2.21-26.amzn2023.0.2.aarch64 xxhash-libs-0.8.0-3.amzn2023.0.2.aarch64 xz-5.2.5-9.amzn2023.0.2.aarch64 xz-libs-5.2.5-9.amzn2023.0.2.aarch64 zip-3.0-28.amzn2023.0.2.aarch64 zlib-1.2.11-33.amzn2023.0.5.aarch64 zstd-1.5.5-1.amzn2023.0.1.aarch64 Complete! Finish: installing minimal buildroot with dnf Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: alternatives-1.15-2.amzn2023.0.2.aarch64 amazon-linux-repo-cdn-2023.3.20231218-0.amzn2023.noarch amazon-rpm-config-228-3.amzn2023.0.2.noarch audit-libs-3.0.6-1.amzn2023.0.2.aarch64 basesystem-11-11.amzn2023.0.2.noarch bash-5.2.15-1.amzn2023.0.2.aarch64 binutils-2.39-6.amzn2023.0.10.aarch64 bzip2-1.0.8-6.amzn2023.0.2.aarch64 bzip2-libs-1.0.8-6.amzn2023.0.2.aarch64 ca-certificates-2023.2.62-1.0.amzn2023.0.1.noarch coreutils-8.32-30.amzn2023.0.3.aarch64 coreutils-common-8.32-30.amzn2023.0.3.aarch64 cpio-2.13-13.amzn2023.0.2.aarch64 cracklib-2.9.6-27.amzn2023.0.2.aarch64 crypto-policies-20220428-1.gitdfb10ea.amzn2023.0.2.noarch curl-8.3.0-1.amzn2023.0.2.aarch64 cyrus-sasl-lib-2.1.27-18.amzn2023.0.3.aarch64 diffutils-3.8-1.amzn2023.0.2.aarch64 dwz-0.14-6.amzn2023.0.2.aarch64 ed-1.14.2-10.amzn2023.0.2.aarch64 efi-srpm-macros-5-4.amzn2023.0.5.noarch elfutils-0.188-3.amzn2023.0.2.aarch64 elfutils-debuginfod-client-0.188-3.amzn2023.0.2.aarch64 elfutils-default-yama-scope-0.188-3.amzn2023.0.2.noarch elfutils-libelf-0.188-3.amzn2023.0.2.aarch64 elfutils-libs-0.188-3.amzn2023.0.2.aarch64 file-5.39-7.amzn2023.0.4.aarch64 file-libs-5.39-7.amzn2023.0.4.aarch64 filesystem-3.14-5.amzn2023.0.3.aarch64 findutils-4.8.0-2.amzn2023.0.2.aarch64 fonts-srpm-macros-2.0.5-12.amzn2023.0.2.noarch gawk-5.1.0-3.amzn2023.0.3.aarch64 gdb-minimal-12.1-5.amzn2023.0.3.aarch64 gdbm-libs-1.19-2.amzn2023.0.2.aarch64 ghc-srpm-macros-1.5.0-4.amzn2023.0.2.noarch glibc-2.34-52.amzn2023.0.7.aarch64 glibc-common-2.34-52.amzn2023.0.7.aarch64 glibc-gconv-extra-2.34-52.amzn2023.0.7.aarch64 glibc-minimal-langpack-2.34-52.amzn2023.0.7.aarch64 gmp-6.2.1-2.amzn2023.0.2.aarch64 go-srpm-macros-3.3.1-1.amzn2023.noarch gpg-pubkey-d832c631-6515c85e grep-3.8-1.amzn2023.0.4.aarch64 gzip-1.12-1.amzn2023.0.1.aarch64 info-6.7-10.amzn2023.0.2.aarch64 jansson-2.14-0.amzn2023.aarch64 kernel-srpm-macros-1.0-14.amzn2023.0.2.noarch keyutils-libs-1.6.3-1.amzn2023.aarch64 krb5-libs-1.21-3.amzn2023.0.3.aarch64 libacl-2.3.1-2.amzn2023.0.2.aarch64 libarchive-3.5.3-2.amzn2023.0.3.aarch64 libattr-2.5.1-3.amzn2023.0.2.aarch64 libblkid-2.37.4-1.amzn2023.0.3.aarch64 libbrotli-1.0.9-4.amzn2023.0.2.aarch64 libcap-2.48-2.amzn2023.0.3.aarch64 libcap-ng-0.8.2-4.amzn2023.0.2.aarch64 libcom_err-1.46.5-2.amzn2023.0.2.aarch64 libcurl-8.3.0-1.amzn2023.0.2.aarch64 libdb-5.3.28-49.amzn2023.0.2.aarch64 libeconf-0.4.0-1.amzn2023.0.3.aarch64 libfdisk-2.37.4-1.amzn2023.0.3.aarch64 libffi-3.4.4-1.amzn2023.0.1.aarch64 libgcc-11.4.1-2.amzn2023.0.2.aarch64 libgomp-11.4.1-2.amzn2023.0.2.aarch64 libidn2-2.3.2-1.amzn2023.0.5.aarch64 libmount-2.37.4-1.amzn2023.0.3.aarch64 libnghttp2-1.57.0-1.amzn2023.0.1.aarch64 libpkgconf-1.8.0-4.amzn2023.0.2.aarch64 libpsl-0.21.1-3.amzn2023.0.2.aarch64 libpwquality-1.4.4-6.amzn2023.0.2.aarch64 libselinux-3.4-5.amzn2023.0.2.aarch64 libsemanage-3.4-5.amzn2023.0.2.aarch64 libsepol-3.4-3.amzn2023.0.3.aarch64 libsigsegv-2.13-2.amzn2023.0.2.aarch64 libsmartcols-2.37.4-1.amzn2023.0.3.aarch64 libssh-0.10.5-1.amzn2023.0.2.aarch64 libssh-config-0.10.5-1.amzn2023.0.2.noarch libstdc++-11.4.1-2.amzn2023.0.2.aarch64 libtasn1-4.19.0-1.amzn2023.0.4.aarch64 libunistring-0.9.10-10.amzn2023.0.2.aarch64 libutempter-1.2.1-4.amzn2023.0.2.aarch64 libuuid-2.37.4-1.amzn2023.0.3.aarch64 libverto-0.3.2-1.amzn2023.0.2.aarch64 libxcrypt-4.4.33-7.amzn2023.aarch64 libxml2-2.10.4-1.amzn2023.0.6.aarch64 libzstd-1.5.5-1.amzn2023.0.1.aarch64 lua-libs-5.4.4-3.amzn2023.0.2.aarch64 lua-srpm-macros-1-4.amzn2023.0.2.noarch lz4-libs-1.9.4-1.amzn2023.0.2.aarch64 mpfr-4.1.0-7.amzn2023.0.2.aarch64 ncurses-base-6.2-4.20200222.amzn2023.0.4.noarch ncurses-libs-6.2-4.20200222.amzn2023.0.4.aarch64 ocaml-srpm-macros-6-6.amzn2023.0.2.noarch openblas-srpm-macros-2-9.amzn2023.0.2.noarch openldap-2.4.57-6.amzn2023.0.6.aarch64 openssl-libs-3.0.8-1.amzn2023.0.10.aarch64 p11-kit-0.24.1-2.amzn2023.0.3.aarch64 p11-kit-trust-0.24.1-2.amzn2023.0.3.aarch64 package-notes-srpm-macros-0.4-18.amzn2023.0.5.noarch pam-1.5.1-8.amzn2023.0.3.aarch64 patch-2.7.6-14.amzn2023.0.2.aarch64 pcre2-10.40-1.amzn2023.0.3.aarch64 pcre2-syntax-10.40-1.amzn2023.0.3.noarch perl-srpm-macros-1-39.amzn2023.0.2.noarch pkgconf-1.8.0-4.amzn2023.0.2.aarch64 pkgconf-m4-1.8.0-4.amzn2023.0.2.noarch pkgconf-pkg-config-1.8.0-4.amzn2023.0.2.aarch64 popt-1.18-6.amzn2023.0.2.aarch64 publicsuffix-list-dafsa-20221208-60.amzn2023.noarch python-srpm-macros-3.9-41.amzn2023.0.5.noarch readline-8.1-2.amzn2023.0.2.aarch64 rpm-4.16.1.3-12.amzn2023.0.6.aarch64 rpm-build-4.16.1.3-12.amzn2023.0.6.aarch64 rpm-build-libs-4.16.1.3-12.amzn2023.0.6.aarch64 rpm-libs-4.16.1.3-12.amzn2023.0.6.aarch64 rust-srpm-macros-21-42.amzn2023.0.2.noarch sed-4.8-7.amzn2023.0.2.aarch64 setup-2.13.7-3.amzn2023.0.2.noarch shadow-utils-4.9-12.amzn2023.0.4.aarch64 sqlite-libs-3.40.0-1.amzn2023.0.3.aarch64 system-release-2023.3.20231218-0.amzn2023.noarch systemd-libs-252.16-1.amzn2023.0.1.aarch64 tar-1.34-1.amzn2023.0.3.aarch64 unzip-6.0-57.amzn2023.0.2.aarch64 util-linux-2.37.4-1.amzn2023.0.3.aarch64 util-linux-core-2.37.4-1.amzn2023.0.3.aarch64 which-2.21-26.amzn2023.0.2.aarch64 xxhash-libs-0.8.0-3.amzn2023.0.2.aarch64 xz-5.2.5-9.amzn2023.0.2.aarch64 xz-libs-5.2.5-9.amzn2023.0.2.aarch64 zip-3.0-28.amzn2023.0.2.aarch64 zlib-1.2.11-33.amzn2023.0.5.aarch64 zstd-1.5.5-1.amzn2023.0.1.aarch64 Start: buildsrpm Start: rpmbuild -bs Building target platforms: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1689811200 Wrote: /builddir/build/SRPMS/htslib-1.15.1-3.amzn2023.src.rpm Finish: rpmbuild -bs INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/amazonlinux-2023-aarch64-1704591054.948002/root/var/log/dnf.rpm.log /var/lib/mock/amazonlinux-2023-aarch64-1704591054.948002/root/var/log/dnf.librepo.log /var/lib/mock/amazonlinux-2023-aarch64-1704591054.948002/root/var/log/dnf.log Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-yinqapun/htslib/htslib.spec) Config(child) 0 minutes 21 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot INFO: Start(/var/lib/copr-rpmbuild/results/htslib-1.15.1-3.amzn2023.src.rpm) Config(amazonlinux-2023-aarch64) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/amazonlinux-2023-aarch64-bootstrap-1704591054.948002/root. INFO: reusing tmpfs at /var/lib/mock/amazonlinux-2023-aarch64-bootstrap-1704591054.948002/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/amazonlinux-2023-aarch64-1704591054.948002/root. INFO: calling preinit hooks INFO: enabled root cache Start: unpacking root cache Finish: unpacking root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-4.16.1.3-12.amzn2023.0.6.aarch64 python3-dnf-4.12.0-2.amzn2023.0.4.noarch python3-dnf-plugins-core-4.1.0-1.amzn2023.0.3.noarch yum-4.12.0-2.amzn2023.0.4.noarch Finish: chroot init Start: build phase for htslib-1.15.1-3.amzn2023.src.rpm Start: build setup for htslib-1.15.1-3.amzn2023.src.rpm Building target platforms: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1689811200 Wrote: /builddir/build/SRPMS/htslib-1.15.1-3.amzn2023.src.rpm No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 42 kB/s | 1.5 kB 00:00 Copr repository 2.1 MB/s | 156 kB 00:00 Amazon Linux 2023 repository - aarch64 11 kB/s | 3.6 kB 00:00 Dependencies resolved. ================================================================================ Package Arch Version Repository Size ================================================================================ Installing: bzip2-devel aarch64 1.0.8-6.amzn2023.0.2 amazonlinux 214 k gcc aarch64 11.4.1-2.amzn2023.0.2 amazonlinux 30 M libcurl-devel aarch64 8.3.0-1.amzn2023.0.2 amazonlinux 903 k make aarch64 1:4.3-5.amzn2023.0.2 amazonlinux 530 k openssl-devel aarch64 1:3.0.8-1.amzn2023.0.10 amazonlinux 3.0 M perl-Data-Dumper aarch64 2.174-460.amzn2023.0.2 amazonlinux 55 k perl-FindBin noarch 1.51-477.amzn2023.0.6 amazonlinux 14 k perl-Getopt-Long noarch 1:2.52-2.amzn2023.0.2 amazonlinux 60 k perl-interpreter aarch64 4:5.32.1-477.amzn2023.0.6 amazonlinux 71 k perl-lib aarch64 0.65-477.amzn2023.0.6 amazonlinux 15 k xz-devel aarch64 5.2.5-9.amzn2023.0.2 amazonlinux 53 k zlib-devel aarch64 1.2.11-33.amzn2023.0.5 amazonlinux 45 k Installing dependencies: annobin-docs noarch 10.93-1.amzn2023.0.1 amazonlinux 92 k annobin-plugin-gcc aarch64 10.93-1.amzn2023.0.1 amazonlinux 886 k cpp aarch64 11.4.1-2.amzn2023.0.2 amazonlinux 9.8 M gc aarch64 8.0.4-5.amzn2023.0.2 amazonlinux 102 k glibc-devel aarch64 2.34-52.amzn2023.0.7 amazonlinux 455 k groff-base aarch64 1.22.4-7.amzn2023.0.2 amazonlinux 1.0 M guile22 aarch64 2.2.7-2.amzn2023.0.3 amazonlinux 6.4 M kernel-headers aarch64 6.1.66-91.160.amzn2023 amazonlinux 1.4 M libasan aarch64 11.4.1-2.amzn2023.0.2 amazonlinux 401 k libatomic aarch64 11.4.1-2.amzn2023.0.2 amazonlinux 35 k libmpc aarch64 1.2.1-2.amzn2023.0.2 amazonlinux 63 k libtool-ltdl aarch64 2.4.7-1.amzn2023.0.3 amazonlinux 38 k libubsan aarch64 11.4.1-2.amzn2023.0.2 amazonlinux 183 k libxcrypt-devel aarch64 4.4.33-7.amzn2023 amazonlinux 32 k ncurses aarch64 6.2-4.20200222.amzn2023.0.4 amazonlinux 395 k perl-B aarch64 1.80-477.amzn2023.0.6 amazonlinux 180 k perl-Carp noarch 1.50-458.amzn2023.0.2 amazonlinux 29 k perl-Class-Struct noarch 0.66-477.amzn2023.0.6 amazonlinux 22 k perl-DynaLoader aarch64 1.47-477.amzn2023.0.6 amazonlinux 26 k perl-Encode aarch64 4:3.15-462.amzn2023.0.2 amazonlinux 1.7 M perl-Errno aarch64 1.30-477.amzn2023.0.6 amazonlinux 15 k perl-Exporter noarch 5.74-459.amzn2023.0.2 amazonlinux 31 k perl-Fcntl aarch64 1.13-477.amzn2023.0.6 amazonlinux 21 k perl-File-Basename noarch 2.85-477.amzn2023.0.6 amazonlinux 18 k perl-File-Path noarch 2.18-2.amzn2023.0.2 amazonlinux 36 k perl-File-Temp noarch 1:0.231.100-2.amzn2023.0.2 amazonlinux 60 k perl-File-stat noarch 1.09-477.amzn2023.0.6 amazonlinux 17 k perl-Getopt-Std noarch 1.12-477.amzn2023.0.6 amazonlinux 16 k perl-HTTP-Tiny noarch 0.078-1.amzn2023.0.3 amazonlinux 56 k perl-IO aarch64 1.43-477.amzn2023.0.6 amazonlinux 87 k perl-IPC-Open3 noarch 1.21-477.amzn2023.0.6 amazonlinux 23 k perl-MIME-Base64 aarch64 3.16-2.amzn2023.0.2 amazonlinux 31 k perl-POSIX aarch64 1.94-477.amzn2023.0.6 amazonlinux 97 k perl-PathTools aarch64 3.78-459.amzn2023.0.2 amazonlinux 86 k perl-Pod-Escapes noarch 1:1.07-458.amzn2023.0.2 amazonlinux 20 k perl-Pod-Perldoc noarch 3.28.01-459.amzn2023.0.3 amazonlinux 84 k perl-Pod-Simple noarch 1:3.42-2.amzn2023.0.2 amazonlinux 215 k perl-Pod-Usage noarch 4:2.01-2.amzn2023.0.2 amazonlinux 41 k perl-Scalar-List-Utils aarch64 4:1.56-459.amzn2023.0.2 amazonlinux 71 k perl-SelectSaver noarch 1.02-477.amzn2023.0.6 amazonlinux 12 k perl-Socket aarch64 4:2.032-1.amzn2023.0.2 amazonlinux 55 k perl-Storable aarch64 1:3.21-458.amzn2023.0.2 amazonlinux 94 k perl-Symbol noarch 1.08-477.amzn2023.0.6 amazonlinux 15 k perl-Term-ANSIColor noarch 5.01-459.amzn2023.0.2 amazonlinux 48 k perl-Term-Cap noarch 1.17-458.amzn2023.0.2 amazonlinux 22 k perl-Text-ParseWords noarch 3.30-458.amzn2023.0.2 amazonlinux 17 k perl-Text-Tabs+Wrap noarch 2021.0726-1.amzn2023.0.1 amazonlinux 22 k perl-Time-Local noarch 2:1.300-5.amzn2023.0.2 amazonlinux 34 k perl-constant noarch 1.33-459.amzn2023.0.2 amazonlinux 23 k perl-if noarch 0.60.800-477.amzn2023.0.6 amazonlinux 14 k perl-libs aarch64 4:5.32.1-477.amzn2023.0.6 amazonlinux 2.0 M perl-mro aarch64 1.23-477.amzn2023.0.6 amazonlinux 28 k perl-overload noarch 1.31-477.amzn2023.0.6 amazonlinux 46 k perl-overloading noarch 0.02-477.amzn2023.0.6 amazonlinux 13 k perl-parent noarch 1:0.238-458.amzn2023.0.2 amazonlinux 14 k perl-podlators noarch 1:4.14-458.amzn2023.0.2 amazonlinux 112 k perl-subs noarch 1.03-477.amzn2023.0.6 amazonlinux 12 k perl-vars noarch 1.05-477.amzn2023.0.6 amazonlinux 13 k Transaction Summary ================================================================================ Install 70 Packages Total size: 61 M Total download size: 8.3 M Installed size: 201 M Downloading Packages: [SKIPPED] annobin-docs-10.93-1.amzn2023.0.1.noarch.rpm: Already downloaded [SKIPPED] glibc-devel-2.34-52.amzn2023.0.7.aarch64.rpm: Already downloaded [SKIPPED] gc-8.0.4-5.amzn2023.0.2.aarch64.rpm: Already downloaded [SKIPPED] kernel-headers-6.1.66-91.160.amzn2023.aarch64.rpm: Already downloaded [SKIPPED] gcc-11.4.1-2.amzn2023.0.2.aarch64.rpm: Already downloaded [SKIPPED] libtool-ltdl-2.4.7-1.amzn2023.0.3.aarch64.rpm: Already downloaded [SKIPPED] guile22-2.2.7-2.amzn2023.0.3.aarch64.rpm: Already downloaded [SKIPPED] libasan-11.4.1-2.amzn2023.0.2.aarch64.rpm: Already downloaded [SKIPPED] annobin-plugin-gcc-10.93-1.amzn2023.0.1.aarch64.rpm: Already downloaded [SKIPPED] libubsan-11.4.1-2.amzn2023.0.2.aarch64.rpm: Already downloaded [SKIPPED] libatomic-11.4.1-2.amzn2023.0.2.aarch64.rpm: Already downloaded [SKIPPED] libxcrypt-devel-4.4.33-7.amzn2023.aarch64.rpm: Already downloaded [SKIPPED] cpp-11.4.1-2.amzn2023.0.2.aarch64.rpm: Already downloaded [SKIPPED] libmpc-1.2.1-2.amzn2023.0.2.aarch64.rpm: Already downloaded [SKIPPED] openssl-devel-3.0.8-1.amzn2023.0.10.aarch64.rpm: Already downloaded [SKIPPED] make-4.3-5.amzn2023.0.2.aarch64.rpm: Already downloaded (17/70): perl-podlators-4.14-458.amzn2023.0.2.n 3.2 MB/s | 112 kB 00:00 (18/70): perl-parent-0.238-458.amzn2023.0.2.noa 397 kB/s | 14 kB 00:00 (19/70): perl-Carp-1.50-458.amzn2023.0.2.noarch 740 kB/s | 29 kB 00:00 (20/70): perl-Time-Local-1.300-5.amzn2023.0.2.n 6.4 MB/s | 34 kB 00:00 (21/70): perl-constant-1.33-459.amzn2023.0.2.no 2.8 MB/s | 23 kB 00:00 (22/70): perl-Text-ParseWords-3.30-458.amzn2023 2.4 MB/s | 17 kB 00:00 (23/70): perl-FindBin-1.51-477.amzn2023.0.6.noa 1.7 MB/s | 14 kB 00:00 (24/70): perl-File-Temp-0.231.100-2.amzn2023.0. 9.7 MB/s | 60 kB 00:00 (25/70): perl-Term-ANSIColor-5.01-459.amzn2023. 7.1 MB/s | 48 kB 00:00 (26/70): perl-if-0.60.800-477.amzn2023.0.6.noar 2.4 MB/s | 14 kB 00:00 (27/70): perl-Text-Tabs+Wrap-2021.0726-1.amzn20 6.0 MB/s | 22 kB 00:00 (28/70): perl-Term-Cap-1.17-458.amzn2023.0.2.no 2.5 MB/s | 22 kB 00:00 (29/70): perl-overloading-0.02-477.amzn2023.0.6 2.0 MB/s | 13 kB 00:00 (30/70): perl-Exporter-5.74-459.amzn2023.0.2.no 5.3 MB/s | 31 kB 00:00 (31/70): perl-File-Basename-2.85-477.amzn2023.0 3.6 MB/s | 18 kB 00:00 (32/70): perl-subs-1.03-477.amzn2023.0.6.noarch 2.8 MB/s | 12 kB 00:00 (33/70): perl-File-stat-1.09-477.amzn2023.0.6.n 3.2 MB/s | 17 kB 00:00 (34/70): perl-Getopt-Long-2.52-2.amzn2023.0.2.n 13 MB/s | 60 kB 00:00 (35/70): perl-Getopt-Std-1.12-477.amzn2023.0.6. 4.1 MB/s | 16 kB 00:00 (36/70): perl-Pod-Simple-3.42-2.amzn2023.0.2.no 21 MB/s | 215 kB 00:00 (37/70): perl-IPC-Open3-1.21-477.amzn2023.0.6.n 5.1 MB/s | 23 kB 00:00 (38/70): perl-HTTP-Tiny-0.078-1.amzn2023.0.3.no 12 MB/s | 56 kB 00:00 (39/70): perl-overload-1.31-477.amzn2023.0.6.no 4.2 MB/s | 46 kB 00:00 (40/70): perl-Pod-Usage-2.01-2.amzn2023.0.2.noa 11 MB/s | 41 kB 00:00 (41/70): perl-Pod-Perldoc-3.28.01-459.amzn2023. 16 MB/s | 84 kB 00:00 (42/70): perl-Symbol-1.08-477.amzn2023.0.6.noar 3.1 MB/s | 15 kB 00:00 (43/70): perl-SelectSaver-1.02-477.amzn2023.0.6 3.2 MB/s | 12 kB 00:00 (44/70): perl-vars-1.05-477.amzn2023.0.6.noarch 3.0 MB/s | 13 kB 00:00 (45/70): perl-Pod-Escapes-1.07-458.amzn2023.0.2 4.4 MB/s | 20 kB 00:00 (46/70): perl-File-Path-2.18-2.amzn2023.0.2.noa 6.8 MB/s | 36 kB 00:00 (47/70): perl-Class-Struct-0.66-477.amzn2023.0. 5.3 MB/s | 22 kB 00:00 (48/70): perl-B-1.80-477.amzn2023.0.6.aarch64.r 28 MB/s | 180 kB 00:00 (49/70): xz-devel-5.2.5-9.amzn2023.0.2.aarch64. 8.7 MB/s | 53 kB 00:00 (50/70): ncurses-6.2-4.20200222.amzn2023.0.4.aa 58 MB/s | 395 kB 00:00 (51/70): perl-Scalar-List-Utils-1.56-459.amzn20 11 MB/s | 71 kB 00:00 (52/70): perl-Socket-2.032-1.amzn2023.0.2.aarch 13 MB/s | 55 kB 00:00 (53/70): perl-mro-1.23-477.amzn2023.0.6.aarch64 5.7 MB/s | 28 kB 00:00 (54/70): bzip2-devel-1.0.8-6.amzn2023.0.2.aarch 21 MB/s | 214 kB 00:00 (55/70): perl-POSIX-1.94-477.amzn2023.0.6.aarch 17 MB/s | 97 kB 00:00 (56/70): perl-Storable-3.21-458.amzn2023.0.2.aa 18 MB/s | 94 kB 00:00 (57/70): perl-IO-1.43-477.amzn2023.0.6.aarch64. 14 MB/s | 87 kB 00:00 (58/70): perl-MIME-Base64-3.16-2.amzn2023.0.2.a 3.9 MB/s | 31 kB 00:00 (59/70): perl-interpreter-5.32.1-477.amzn2023.0 11 MB/s | 71 kB 00:00 (60/70): perl-Fcntl-1.13-477.amzn2023.0.6.aarch 3.3 MB/s | 21 kB 00:00 (61/70): groff-base-1.22.4-7.amzn2023.0.2.aarch 84 MB/s | 1.0 MB 00:00 (62/70): perl-libs-5.32.1-477.amzn2023.0.6.aarc 68 MB/s | 2.0 MB 00:00 (63/70): perl-Errno-1.30-477.amzn2023.0.6.aarch 1.3 MB/s | 15 kB 00:00 (64/70): perl-DynaLoader-1.47-477.amzn2023.0.6. 3.8 MB/s | 26 kB 00:00 (65/70): perl-Data-Dumper-2.174-460.amzn2023.0. 11 MB/s | 55 kB 00:00 (66/70): perl-lib-0.65-477.amzn2023.0.6.aarch64 2.4 MB/s | 15 kB 00:00 (67/70): zlib-devel-1.2.11-33.amzn2023.0.5.aarc 6.3 MB/s | 45 kB 00:00 (68/70): perl-Encode-3.15-462.amzn2023.0.2.aarc 113 MB/s | 1.7 MB 00:00 (69/70): perl-PathTools-3.78-459.amzn2023.0.2.a 6.8 MB/s | 86 kB 00:00 (70/70): libcurl-devel-8.3.0-1.amzn2023.0.2.aar 56 MB/s | 903 kB 00:00 -------------------------------------------------------------------------------- Total 16 MB/s | 8.3 MB 00:00 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Installing : libmpc-1.2.1-2.amzn2023.0.2.aarch64 1/70 Installing : cpp-11.4.1-2.amzn2023.0.2.aarch64 2/70 Installing : libatomic-11.4.1-2.amzn2023.0.2.aarch64 3/70 Installing : libubsan-11.4.1-2.amzn2023.0.2.aarch64 4/70 Running scriptlet: groff-base-1.22.4-7.amzn2023.0.2.aarch64 5/70 Installing : groff-base-1.22.4-7.amzn2023.0.2.aarch64 5/70 Running scriptlet: groff-base-1.22.4-7.amzn2023.0.2.aarch64 5/70 Installing : libasan-11.4.1-2.amzn2023.0.2.aarch64 6/70 Installing : libtool-ltdl-2.4.7-1.amzn2023.0.3.aarch64 7/70 Installing : kernel-headers-6.1.66-91.160.amzn2023.aarch64 8/70 Installing : libxcrypt-devel-4.4.33-7.amzn2023.aarch64 9/70 Installing : glibc-devel-2.34-52.amzn2023.0.7.aarch64 10/70 Installing : gc-8.0.4-5.amzn2023.0.2.aarch64 11/70 Installing : guile22-2.2.7-2.amzn2023.0.3.aarch64 12/70 Installing : make-1:4.3-5.amzn2023.0.2.aarch64 13/70 Installing : gcc-11.4.1-2.amzn2023.0.2.aarch64 14/70 Running scriptlet: gcc-11.4.1-2.amzn2023.0.2.aarch64 14/70 Installing : ncurses-6.2-4.20200222.amzn2023.0.4.aarch64 15/70 Installing : perl-if-0.60.800-477.amzn2023.0.6.noarch 16/70 Installing : perl-Text-Tabs+Wrap-2021.0726-1.amzn2023.0.1.noarc 17/70 Installing : perl-Time-Local-2:1.300-5.amzn2023.0.2.noarch 18/70 Installing : perl-Pod-Escapes-1:1.07-458.amzn2023.0.2.noarch 19/70 Installing : perl-File-Path-2.18-2.amzn2023.0.2.noarch 20/70 Installing : perl-Term-ANSIColor-5.01-459.amzn2023.0.2.noarch 21/70 Installing : perl-subs-1.03-477.amzn2023.0.6.noarch 22/70 Installing : perl-Term-Cap-1.17-458.amzn2023.0.2.noarch 23/70 Installing : perl-Class-Struct-0.66-477.amzn2023.0.6.noarch 24/70 Installing : perl-POSIX-1.94-477.amzn2023.0.6.aarch64 25/70 Installing : perl-Pod-Simple-1:3.42-2.amzn2023.0.2.noarch 26/70 Installing : perl-File-Temp-1:0.231.100-2.amzn2023.0.2.noarch 27/70 Installing : perl-IPC-Open3-1.21-477.amzn2023.0.6.noarch 28/70 Installing : perl-HTTP-Tiny-0.078-1.amzn2023.0.3.noarch 29/70 Installing : perl-Symbol-1.08-477.amzn2023.0.6.noarch 30/70 Installing : perl-SelectSaver-1.02-477.amzn2023.0.6.noarch 31/70 Installing : perl-Socket-4:2.032-1.amzn2023.0.2.aarch64 32/70 Installing : perl-File-stat-1.09-477.amzn2023.0.6.noarch 33/70 Installing : perl-Pod-Perldoc-3.28.01-459.amzn2023.0.3.noarch 34/70 Installing : perl-podlators-1:4.14-458.amzn2023.0.2.noarch 35/70 Installing : perl-overloading-0.02-477.amzn2023.0.6.noarch 36/70 Installing : perl-Text-ParseWords-3.30-458.amzn2023.0.2.noarch 37/70 Installing : perl-mro-1.23-477.amzn2023.0.6.aarch64 38/70 Installing : perl-Fcntl-1.13-477.amzn2023.0.6.aarch64 39/70 Installing : perl-IO-1.43-477.amzn2023.0.6.aarch64 40/70 Installing : perl-Pod-Usage-4:2.01-2.amzn2023.0.2.noarch 41/70 Installing : perl-parent-1:0.238-458.amzn2023.0.2.noarch 42/70 Installing : perl-constant-1.33-459.amzn2023.0.2.noarch 43/70 Installing : perl-File-Basename-2.85-477.amzn2023.0.6.noarch 44/70 Installing : perl-Getopt-Std-1.12-477.amzn2023.0.6.noarch 45/70 Installing : perl-vars-1.05-477.amzn2023.0.6.noarch 46/70 Installing : perl-Scalar-List-Utils-4:1.56-459.amzn2023.0.2.aar 47/70 Installing : perl-overload-1.31-477.amzn2023.0.6.noarch 48/70 Installing : perl-MIME-Base64-3.16-2.amzn2023.0.2.aarch64 49/70 Installing : perl-Errno-1.30-477.amzn2023.0.6.aarch64 50/70 Installing : perl-Storable-1:3.21-458.amzn2023.0.2.aarch64 51/70 Installing : perl-Getopt-Long-1:2.52-2.amzn2023.0.2.noarch 52/70 Installing : perl-Carp-1.50-458.amzn2023.0.2.noarch 53/70 Installing : perl-Exporter-5.74-459.amzn2023.0.2.noarch 54/70 Installing : perl-DynaLoader-1.47-477.amzn2023.0.6.aarch64 55/70 Installing : perl-PathTools-3.78-459.amzn2023.0.2.aarch64 56/70 Installing : perl-Encode-4:3.15-462.amzn2023.0.2.aarch64 57/70 Installing : perl-libs-4:5.32.1-477.amzn2023.0.6.aarch64 58/70 Installing : perl-interpreter-4:5.32.1-477.amzn2023.0.6.aarch64 59/70 Installing : perl-B-1.80-477.amzn2023.0.6.aarch64 60/70 Installing : perl-Data-Dumper-2.174-460.amzn2023.0.2.aarch64 61/70 Installing : annobin-docs-10.93-1.amzn2023.0.1.noarch 62/70 Installing : annobin-plugin-gcc-10.93-1.amzn2023.0.1.aarch64 63/70 Running scriptlet: annobin-plugin-gcc-10.93-1.amzn2023.0.1.aarch64 63/70 Installing : perl-FindBin-1.51-477.amzn2023.0.6.noarch 64/70 Installing : perl-lib-0.65-477.amzn2023.0.6.aarch64 65/70 Installing : libcurl-devel-8.3.0-1.amzn2023.0.2.aarch64 66/70 Installing : zlib-devel-1.2.11-33.amzn2023.0.5.aarch64 67/70 Installing : openssl-devel-1:3.0.8-1.amzn2023.0.10.aarch64 68/70 Installing : bzip2-devel-1.0.8-6.amzn2023.0.2.aarch64 69/70 Installing : xz-devel-5.2.5-9.amzn2023.0.2.aarch64 70/70 Running scriptlet: xz-devel-5.2.5-9.amzn2023.0.2.aarch64 70/70 Verifying : perl-podlators-1:4.14-458.amzn2023.0.2.noarch 1/70 Verifying : perl-Carp-1.50-458.amzn2023.0.2.noarch 2/70 Verifying : perl-parent-1:0.238-458.amzn2023.0.2.noarch 3/70 Verifying : perl-Time-Local-2:1.300-5.amzn2023.0.2.noarch 4/70 Verifying : perl-constant-1.33-459.amzn2023.0.2.noarch 5/70 Verifying : perl-Text-ParseWords-3.30-458.amzn2023.0.2.noarch 6/70 Verifying : perl-FindBin-1.51-477.amzn2023.0.6.noarch 7/70 Verifying : perl-File-Temp-1:0.231.100-2.amzn2023.0.2.noarch 8/70 Verifying : perl-Term-ANSIColor-5.01-459.amzn2023.0.2.noarch 9/70 Verifying : perl-if-0.60.800-477.amzn2023.0.6.noarch 10/70 Verifying : perl-Term-Cap-1.17-458.amzn2023.0.2.noarch 11/70 Verifying : perl-Text-Tabs+Wrap-2021.0726-1.amzn2023.0.1.noarc 12/70 Verifying : perl-overloading-0.02-477.amzn2023.0.6.noarch 13/70 Verifying : perl-Exporter-5.74-459.amzn2023.0.2.noarch 14/70 Verifying : perl-File-Basename-2.85-477.amzn2023.0.6.noarch 15/70 Verifying : perl-subs-1.03-477.amzn2023.0.6.noarch 16/70 Verifying : perl-File-stat-1.09-477.amzn2023.0.6.noarch 17/70 Verifying : perl-Pod-Simple-1:3.42-2.amzn2023.0.2.noarch 18/70 Verifying : perl-Getopt-Long-1:2.52-2.amzn2023.0.2.noarch 19/70 Verifying : perl-overload-1.31-477.amzn2023.0.6.noarch 20/70 Verifying : perl-Getopt-Std-1.12-477.amzn2023.0.6.noarch 21/70 Verifying : perl-IPC-Open3-1.21-477.amzn2023.0.6.noarch 22/70 Verifying : perl-HTTP-Tiny-0.078-1.amzn2023.0.3.noarch 23/70 Verifying : perl-Pod-Perldoc-3.28.01-459.amzn2023.0.3.noarch 24/70 Verifying : perl-Pod-Usage-4:2.01-2.amzn2023.0.2.noarch 25/70 Verifying : perl-Symbol-1.08-477.amzn2023.0.6.noarch 26/70 Verifying : perl-SelectSaver-1.02-477.amzn2023.0.6.noarch 27/70 Verifying : perl-vars-1.05-477.amzn2023.0.6.noarch 28/70 Verifying : annobin-docs-10.93-1.amzn2023.0.1.noarch 29/70 Verifying : perl-Pod-Escapes-1:1.07-458.amzn2023.0.2.noarch 30/70 Verifying : perl-File-Path-2.18-2.amzn2023.0.2.noarch 31/70 Verifying : perl-Class-Struct-0.66-477.amzn2023.0.6.noarch 32/70 Verifying : perl-B-1.80-477.amzn2023.0.6.aarch64 33/70 Verifying : xz-devel-5.2.5-9.amzn2023.0.2.aarch64 34/70 Verifying : ncurses-6.2-4.20200222.amzn2023.0.4.aarch64 35/70 Verifying : perl-Scalar-List-Utils-4:1.56-459.amzn2023.0.2.aar 36/70 Verifying : bzip2-devel-1.0.8-6.amzn2023.0.2.aarch64 37/70 Verifying : perl-Socket-4:2.032-1.amzn2023.0.2.aarch64 38/70 Verifying : glibc-devel-2.34-52.amzn2023.0.7.aarch64 39/70 Verifying : perl-mro-1.23-477.amzn2023.0.6.aarch64 40/70 Verifying : gc-8.0.4-5.amzn2023.0.2.aarch64 41/70 Verifying : kernel-headers-6.1.66-91.160.amzn2023.aarch64 42/70 Verifying : perl-POSIX-1.94-477.amzn2023.0.6.aarch64 43/70 Verifying : gcc-11.4.1-2.amzn2023.0.2.aarch64 44/70 Verifying : libtool-ltdl-2.4.7-1.amzn2023.0.3.aarch64 45/70 Verifying : guile22-2.2.7-2.amzn2023.0.3.aarch64 46/70 Verifying : perl-Storable-1:3.21-458.amzn2023.0.2.aarch64 47/70 Verifying : perl-libs-4:5.32.1-477.amzn2023.0.6.aarch64 48/70 Verifying : perl-IO-1.43-477.amzn2023.0.6.aarch64 49/70 Verifying : libasan-11.4.1-2.amzn2023.0.2.aarch64 50/70 Verifying : perl-MIME-Base64-3.16-2.amzn2023.0.2.aarch64 51/70 Verifying : perl-interpreter-4:5.32.1-477.amzn2023.0.6.aarch64 52/70 Verifying : annobin-plugin-gcc-10.93-1.amzn2023.0.1.aarch64 53/70 Verifying : perl-Fcntl-1.13-477.amzn2023.0.6.aarch64 54/70 Verifying : groff-base-1.22.4-7.amzn2023.0.2.aarch64 55/70 Verifying : perl-Errno-1.30-477.amzn2023.0.6.aarch64 56/70 Verifying : perl-DynaLoader-1.47-477.amzn2023.0.6.aarch64 57/70 Verifying : libubsan-11.4.1-2.amzn2023.0.2.aarch64 58/70 Verifying : libatomic-11.4.1-2.amzn2023.0.2.aarch64 59/70 Verifying : libxcrypt-devel-4.4.33-7.amzn2023.aarch64 60/70 Verifying : cpp-11.4.1-2.amzn2023.0.2.aarch64 61/70 Verifying : libmpc-1.2.1-2.amzn2023.0.2.aarch64 62/70 Verifying : perl-Data-Dumper-2.174-460.amzn2023.0.2.aarch64 63/70 Verifying : openssl-devel-1:3.0.8-1.amzn2023.0.10.aarch64 64/70 Verifying : perl-lib-0.65-477.amzn2023.0.6.aarch64 65/70 Verifying : perl-Encode-4:3.15-462.amzn2023.0.2.aarch64 66/70 Verifying : zlib-devel-1.2.11-33.amzn2023.0.5.aarch64 67/70 Verifying : perl-PathTools-3.78-459.amzn2023.0.2.aarch64 68/70 Verifying : libcurl-devel-8.3.0-1.amzn2023.0.2.aarch64 69/70 Verifying : make-1:4.3-5.amzn2023.0.2.aarch64 70/70 Installed: annobin-docs-10.93-1.amzn2023.0.1.noarch annobin-plugin-gcc-10.93-1.amzn2023.0.1.aarch64 bzip2-devel-1.0.8-6.amzn2023.0.2.aarch64 cpp-11.4.1-2.amzn2023.0.2.aarch64 gc-8.0.4-5.amzn2023.0.2.aarch64 gcc-11.4.1-2.amzn2023.0.2.aarch64 glibc-devel-2.34-52.amzn2023.0.7.aarch64 groff-base-1.22.4-7.amzn2023.0.2.aarch64 guile22-2.2.7-2.amzn2023.0.3.aarch64 kernel-headers-6.1.66-91.160.amzn2023.aarch64 libasan-11.4.1-2.amzn2023.0.2.aarch64 libatomic-11.4.1-2.amzn2023.0.2.aarch64 libcurl-devel-8.3.0-1.amzn2023.0.2.aarch64 libmpc-1.2.1-2.amzn2023.0.2.aarch64 libtool-ltdl-2.4.7-1.amzn2023.0.3.aarch64 libubsan-11.4.1-2.amzn2023.0.2.aarch64 libxcrypt-devel-4.4.33-7.amzn2023.aarch64 make-1:4.3-5.amzn2023.0.2.aarch64 ncurses-6.2-4.20200222.amzn2023.0.4.aarch64 openssl-devel-1:3.0.8-1.amzn2023.0.10.aarch64 perl-B-1.80-477.amzn2023.0.6.aarch64 perl-Carp-1.50-458.amzn2023.0.2.noarch perl-Class-Struct-0.66-477.amzn2023.0.6.noarch perl-Data-Dumper-2.174-460.amzn2023.0.2.aarch64 perl-DynaLoader-1.47-477.amzn2023.0.6.aarch64 perl-Encode-4:3.15-462.amzn2023.0.2.aarch64 perl-Errno-1.30-477.amzn2023.0.6.aarch64 perl-Exporter-5.74-459.amzn2023.0.2.noarch perl-Fcntl-1.13-477.amzn2023.0.6.aarch64 perl-File-Basename-2.85-477.amzn2023.0.6.noarch perl-File-Path-2.18-2.amzn2023.0.2.noarch perl-File-Temp-1:0.231.100-2.amzn2023.0.2.noarch perl-File-stat-1.09-477.amzn2023.0.6.noarch perl-FindBin-1.51-477.amzn2023.0.6.noarch perl-Getopt-Long-1:2.52-2.amzn2023.0.2.noarch perl-Getopt-Std-1.12-477.amzn2023.0.6.noarch perl-HTTP-Tiny-0.078-1.amzn2023.0.3.noarch perl-IO-1.43-477.amzn2023.0.6.aarch64 perl-IPC-Open3-1.21-477.amzn2023.0.6.noarch perl-MIME-Base64-3.16-2.amzn2023.0.2.aarch64 perl-POSIX-1.94-477.amzn2023.0.6.aarch64 perl-PathTools-3.78-459.amzn2023.0.2.aarch64 perl-Pod-Escapes-1:1.07-458.amzn2023.0.2.noarch perl-Pod-Perldoc-3.28.01-459.amzn2023.0.3.noarch perl-Pod-Simple-1:3.42-2.amzn2023.0.2.noarch perl-Pod-Usage-4:2.01-2.amzn2023.0.2.noarch perl-Scalar-List-Utils-4:1.56-459.amzn2023.0.2.aarch64 perl-SelectSaver-1.02-477.amzn2023.0.6.noarch perl-Socket-4:2.032-1.amzn2023.0.2.aarch64 perl-Storable-1:3.21-458.amzn2023.0.2.aarch64 perl-Symbol-1.08-477.amzn2023.0.6.noarch perl-Term-ANSIColor-5.01-459.amzn2023.0.2.noarch perl-Term-Cap-1.17-458.amzn2023.0.2.noarch perl-Text-ParseWords-3.30-458.amzn2023.0.2.noarch perl-Text-Tabs+Wrap-2021.0726-1.amzn2023.0.1.noarch perl-Time-Local-2:1.300-5.amzn2023.0.2.noarch perl-constant-1.33-459.amzn2023.0.2.noarch perl-if-0.60.800-477.amzn2023.0.6.noarch perl-interpreter-4:5.32.1-477.amzn2023.0.6.aarch64 perl-lib-0.65-477.amzn2023.0.6.aarch64 perl-libs-4:5.32.1-477.amzn2023.0.6.aarch64 perl-mro-1.23-477.amzn2023.0.6.aarch64 perl-overload-1.31-477.amzn2023.0.6.noarch perl-overloading-0.02-477.amzn2023.0.6.noarch perl-parent-1:0.238-458.amzn2023.0.2.noarch perl-podlators-1:4.14-458.amzn2023.0.2.noarch perl-subs-1.03-477.amzn2023.0.6.noarch perl-vars-1.05-477.amzn2023.0.6.noarch xz-devel-5.2.5-9.amzn2023.0.2.aarch64 zlib-devel-1.2.11-33.amzn2023.0.5.aarch64 Complete! Finish: build setup for htslib-1.15.1-3.amzn2023.src.rpm Start: rpmbuild htslib-1.15.1-3.amzn2023.src.rpm Building target platforms: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1689811200 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.eeQCto + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf htslib-1.15.1 + /usr/bin/bzip2 -dc /builddir/build/SOURCES/htslib-1.15.1.tar.bz2 + /usr/bin/tar -xof - + 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 -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.xcWNGH + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection' + export CFLAGS + CXXFLAGS='-O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection' + export CXXFLAGS + FFLAGS='-O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -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-1.15.1-3.amzn2023.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 1.15.1-3.amzn2023 aarch64 + cd htslib-1.15.1 + CFLAGS='-O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection' + export CFLAGS + CXXFLAGS='-O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection' + export CXXFLAGS + FFLAGS='-O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -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-1.15.1-3.amzn2023.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 2024-01-07 01:31:27.238026834 +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* .* \\(.*\\)$/extern char \\1;/p'\''"#' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + '[' 1 = 1 ']' +++ dirname ./configure ++ find . -name config.guess -o -name config.sub + '[' 1 = 1 ']' + '[' x '!=' 'x-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' ']' ++ find . -name ltmain.sh + ./configure --build=aarch64-amazon-linux-gnu --host=aarch64-amazon-linux-gnu --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/libexec --localstatedir=/var --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info 'CFLAGS=-O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection' 'LDFLAGS=-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-3.amzn2023.aarch64.ld' --prefix=/usr --libdir=/usr/lib64 --enable-plugins '--with-plugin-path=/usr/local/libexec/htslib:$(plugindir)' --enable-gcs --enable-libcurl --enable-s3 configure: WARNING: unrecognized options: --disable-dependency-tracking checking for aarch64-amazon-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-amazon-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-amazon-linux-gnu-pkg-config... /usr/bin/aarch64-amazon-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-amazon-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 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o kfunc.o kfunc.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o kstring.o kstring.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o errmod.o errmod.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o bcf_sr_sort.o bcf_sr_sort.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -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 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -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-1.15.1-3.amzn2023.aarch64.ld -fvisibility=hidden -rdynamic"' >> config_vars.h echo '#define HTS_LIBS "-llzma -lbz2 -lz -lm "' >> config_vars.h gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o bgzf.o bgzf.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o hts_os.o hts_os.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o hts_expr.o hts_expr.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o hfile.o hfile.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o md5.o md5.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o multipart.o multipart.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o probaln.o probaln.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o realn.o realn.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o region.o region.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o header.o header.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o regidx.o regidx.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o vcf_sweep.o vcf_sweep.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o tbx.o tbx.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o textutils.o textutils.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o thread_pool.o thread_pool.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o synced_bcf_reader.o synced_bcf_reader.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o vcfutils.o vcfutils.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/cram_codecs.o cram/cram_codecs.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/cram_decode.o cram/cram_decode.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/cram_external.o cram/cram_external.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o sam.o sam.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/cram_index.o cram/cram_index.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/cram_stats.o cram/cram_stats.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/mFILE.o cram/mFILE.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/cram_encode.o cram/cram_encode.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -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 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/string_alloc.o cram/string_alloc.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o vcf.o vcf.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -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 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -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 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o cram/cram_io.o cram/cram_io.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -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 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -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 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -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 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o kfunc.pico kfunc.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o kstring.pico kstring.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -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 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o errmod.pico errmod.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -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 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o faidx.pico faidx.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o bgzf.pico bgzf.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o hfile.pico hfile.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o hts_os.pico hts_os.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o hts_expr.pico hts_expr.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o md5.pico md5.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o multipart.pico multipart.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o probaln.pico probaln.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o header.pico header.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o realn.pico realn.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o region.pico region.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o regidx.pico regidx.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o vcf_sweep.pico vcf_sweep.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o tbx.pico tbx.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -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 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o textutils.pico textutils.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o thread_pool.pico thread_pool.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o hts.pico hts.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o vcfutils.pico vcfutils.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -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 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -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 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o sam.pico sam.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -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 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -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 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -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 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o cram/mFILE.pico cram/mFILE.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -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 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -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 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o vcf.pico vcf.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -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 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -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 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -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 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -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 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -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 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -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 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -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 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -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 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -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 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -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 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -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 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o bgzip.o bgzip.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o htsfile.o htsfile.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o hfile_gcs.pico hfile_gcs.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -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 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o tabix.o tabix.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/hts_endian.o test/hts_endian.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/fieldarith.o test/fieldarith.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -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 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o hfile_libcurl.pico hfile_libcurl.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/pileup.o test/pileup.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/plugins-dlhts.o test/plugins-dlhts.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/pileup_mod.o test/pileup_mod.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/hfile.o test/hfile.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -fpic -c -o hfile_s3.pico hfile_s3.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_expr.o test/test_expr.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_kfunc.o test/test_kfunc.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_mod.o test/test_mod.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_kstring.o test/test_kstring.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_realn.o test/test_realn.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_bgzf.o test/test_bgzf.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_str2int.o test/test_str2int.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test-regidx.o test/test-regidx.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_index.o test/test_index.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_view.o test/test_view.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -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 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -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 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -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 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -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 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test-vcf-api.o test/test-vcf-api.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/sam.o test/sam.c sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' htslib.pc.tmp > htslib_static.mk sed -e 's#@-includedir@#'`pwd`'#g;s#@-libdir@#'`pwd`'#g' htslib.pc.tmp > htslib-uninstalled.pc gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test-parse-reg.o test/test-parse-reg.c gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fvisibility=hidden -I. -c -o test/test_introspection.o test/test_introspection.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-1.15.1-3.amzn2023.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-1.15.1-3.amzn2023.aarch64.ld -fvisibility=hidden -rdynamic -o test/hts_endian test/hts_endian.o -llzma -lbz2 -lz -lm gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -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 -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-1.15.1-3.amzn2023.aarch64.ld -fvisibility=hidden -rdynamic -o bgzip bgzip.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 12 LTRANS jobs 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-1.15.1-3.amzn2023.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 lto-wrapper: warning: using serial compilation of 15 LTRANS jobs 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-1.15.1-3.amzn2023.aarch64.ld -fvisibility=hidden -rdynamic -o htsfile htsfile.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 15 LTRANS jobs 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-1.15.1-3.amzn2023.aarch64.ld -fvisibility=hidden -rdynamic -o tabix tabix.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 15 LTRANS jobs 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-1.15.1-3.amzn2023.aarch64.ld -fvisibility=hidden -rdynamic -o test/fieldarith test/fieldarith.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 13 LTRANS jobs 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-1.15.1-3.amzn2023.aarch64.ld -fvisibility=hidden -rdynamic -o test/hfile test/hfile.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 13 LTRANS jobs 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-1.15.1-3.amzn2023.aarch64.ld -fvisibility=hidden -rdynamic -o test/pileup test/pileup.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 13 LTRANS jobs 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-1.15.1-3.amzn2023.aarch64.ld -fvisibility=hidden -rdynamic -o test/pileup_mod test/pileup_mod.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 12 LTRANS jobs 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-1.15.1-3.amzn2023.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-1.15.1-3.amzn2023.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-1.15.1-3.amzn2023.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-1.15.1-3.amzn2023.aarch64.ld -fvisibility=hidden -rdynamic -o test/sam test/sam.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 13 LTRANS jobs 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-1.15.1-3.amzn2023.aarch64.ld -fvisibility=hidden -rdynamic -o test/test_bgzf test/test_bgzf.o libhts.a -lz -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 12 LTRANS jobs 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-1.15.1-3.amzn2023.aarch64.ld -fvisibility=hidden -rdynamic -o test/test_mod test/test_mod.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 13 LTRANS jobs 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-1.15.1-3.amzn2023.aarch64.ld -fvisibility=hidden -rdynamic -o test/test_realn test/test_realn.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 13 LTRANS jobs 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-1.15.1-3.amzn2023.aarch64.ld -fvisibility=hidden -rdynamic -o test/test-regidx test/test-regidx.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 13 LTRANS jobs 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-1.15.1-3.amzn2023.aarch64.ld -fvisibility=hidden -rdynamic -o test/test_str2int test/test_str2int.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 12 LTRANS jobs 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-1.15.1-3.amzn2023.aarch64.ld -fvisibility=hidden -rdynamic -o test/test_view test/test_view.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 15 LTRANS jobs 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-1.15.1-3.amzn2023.aarch64.ld -fvisibility=hidden -rdynamic -o test/test_index test/test_index.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 14 LTRANS jobs 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-1.15.1-3.amzn2023.aarch64.ld -fvisibility=hidden -rdynamic -o test/test-vcf-api test/test-vcf-api.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 15 LTRANS jobs 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-1.15.1-3.amzn2023.aarch64.ld -fvisibility=hidden -rdynamic -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 14 LTRANS jobs 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-1.15.1-3.amzn2023.aarch64.ld -fvisibility=hidden -rdynamic -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -lz -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 15 LTRANS jobs 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-1.15.1-3.amzn2023.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-1.15.1-3.amzn2023.aarch64.ld -fvisibility=hidden -rdynamic -o hfile_gcs.so hfile_gcs.pico libhts.so -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/htslib-1.15.1/.package_note-htslib-1.15.1-3.amzn2023.aarch64.ld -fvisibility=hidden -rdynamic -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 15 LTRANS jobs 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-1.15.1-3.amzn2023.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-1.15.1-3.amzn2023.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-1.15.1-3.amzn2023.aarch64.ld -fvisibility=hidden -rdynamic -o test/test-parse-reg test/test-parse-reg.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 13 LTRANS jobs 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-1.15.1-3.amzn2023.aarch64.ld -fvisibility=hidden -rdynamic -o test/test_introspection test/test_introspection.o libhts.a -llzma -lbz2 -lz -lm -lpthread lto-wrapper: warning: using serial compilation of 13 LTRANS jobs + 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.rH7ck7 + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.aarch64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.aarch64 ++ dirname /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.aarch64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.aarch64 + CFLAGS='-O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection' + export CFLAGS + CXXFLAGS='-O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection' + export CXXFLAGS + FFLAGS='-O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -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-1.15.1-3.amzn2023.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-1.15.1-3.amzn2023.aarch64 'INSTALL=/usr/bin/install -p' mkdir -p -m 755 /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.aarch64/usr/bin /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.aarch64/usr/include /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.aarch64/usr/include/htslib /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.aarch64/usr/lib64 /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.aarch64/usr/share/man/man1 /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.aarch64/usr/share/man/man5 /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.aarch64/usr/share/man/man7 /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.aarch64/usr/lib64/pkgconfig if test -n "/usr/libexec/htslib"; then mkdir -p -m 755 /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.aarch64/usr/libexec/htslib; fi /usr/bin/install -p -m 644 libhts.so /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.aarch64/usr/lib64/libhts.so.1.15.1 ln -sf libhts.so.1.15.1 /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.aarch64/usr/lib64/libhts.so ln -sf libhts.so.1.15.1 /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.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-1.15.1-3.amzn2023.aarch64/usr/lib64/pkgconfig/htslib.pc chmod 644 /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.aarch64/usr/lib64/pkgconfig/htslib.pc /usr/bin/install -p bgzip htsfile tabix /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.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-1.15.1-3.amzn2023.aarch64/usr/libexec/htslib; fi /usr/bin/install -p -m 644 htslib/*.h /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.aarch64/usr/include/htslib /usr/bin/install -p -m 644 libhts.a /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.aarch64/usr/lib64/libhts.a /usr/bin/install -p -m 644 bgzip.1 htsfile.1 tabix.1 /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.aarch64/usr/share/man/man1 /usr/bin/install -p -m 644 faidx.5 sam.5 vcf.5 /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.aarch64/usr/share/man/man5 /usr/bin/install -p -m 644 htslib-s3-plugin.7 /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.aarch64/usr/share/man/man7 + pushd /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.aarch64//usr/lib64 ~/build/BUILDROOT/htslib-1.15.1-3.amzn2023.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-1.15.1-3.amzn2023.aarch64 -name '*.la' -delete + rm -f /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.aarch64//usr/lib64/libhts.a + /usr/lib/rpm/find-debuginfo.sh -j4 --strict-build-id -m -i --build-id-seed 1.15.1-3.amzn2023 --unique-debug-suffix -1.15.1-3.amzn2023.aarch64 --unique-debug-src-base htslib-1.15.1-3.amzn2023.aarch64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/htslib-1.15.1 explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.aarch64/usr/bin/bgzip explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.aarch64/usr/bin/tabix explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.aarch64/usr/bin/htsfile explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.aarch64/usr/lib64/libhts.so.1.15.1 extracting debug info from /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.aarch64/usr/bin/tabix extracting debug info from /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.aarch64/usr/bin/htsfile extracting debug info from /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.aarch64/usr/bin/bgzip extracting debug info from /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.aarch64/usr/lib64/libhts.so.1.15.1 explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.aarch64/usr/libexec/htslib/hfile_gcs.so extracting debug info from /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.aarch64/usr/libexec/htslib/hfile_gcs.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.aarch64/usr/libexec/htslib/hfile_s3.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.aarch64/usr/libexec/htslib/hfile_libcurl.so extracting debug info from /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.aarch64/usr/libexec/htslib/hfile_libcurl.so extracting debug info from /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.aarch64/usr/libexec/htslib/hfile_s3.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.aarch64/usr/libexec/htslib/hfile_s3_write.so extracting debug info from /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.aarch64/usr/libexec/htslib/hfile_s3_write.so original debug info size: 12376kB, size after compression: 11652kB /usr/lib/rpm/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-python-bytecompile '' 0 1 Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.rZqlJZ + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection' + export CFLAGS + CXXFLAGS='-O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection' + export CXXFLAGS + FFLAGS='-O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -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-1.15.1-3.amzn2023.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 1.15.1-3.amzn2023 aarch64 + cd htslib-1.15.1 + make test gcc -O2 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -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-1.15.1-3.amzn2023.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 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -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-1.15.1-3.amzn2023.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 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -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-1.15.1-3.amzn2023.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 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -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-1.15.1-3.amzn2023.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 lto-wrapper: warning: using serial compilation of 2 LTRANS jobs 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 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -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-1.15.1-3.amzn2023.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 -ftree-vectorize -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv8.2-a+crypto -mtune=neoverse-n1 -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-1.15.1-3.amzn2023.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/Xj_Ix_uMYK/index.bam.csi /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/Xj_Ix_uMYK/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/Xj_Ix_uMYK/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -b -m 0 -x /tmp/Xj_Ix_uMYK/index.bam.bai /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/Xj_Ix_uMYK/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -b /tmp/Xj_Ix_uMYK/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -z -m 14 -x /tmp/Xj_Ix_uMYK/index.sam.gz.csi /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/Xj_Ix_uMYK/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/Xj_Ix_uMYK/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -z -m 0 -x /tmp/Xj_Ix_uMYK/index.sam.gz.bai /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/Xj_Ix_uMYK/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -b /tmp/Xj_Ix_uMYK/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -z -m 14 -x /tmp/Xj_Ix_uMYK/index.sam.gz.csi /builddir/build/BUILD/htslib-1.15.1/test/index_dos.sam > /tmp/Xj_Ix_uMYK/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/Xj_Ix_uMYK/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -z -m 0 -x /tmp/Xj_Ix_uMYK/index.sam.gz.bai /builddir/build/BUILD/htslib-1.15.1/test/index_dos.sam > /tmp/Xj_Ix_uMYK/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -b /tmp/Xj_Ix_uMYK/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -C -x /tmp/Xj_Ix_uMYK/index.cram.crai /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/Xj_Ix_uMYK/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index /tmp/Xj_Ix_uMYK/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -b -m 14 -x /tmp/Xj_Ix_uMYK/index.bcf.csi /builddir/build/BUILD/htslib-1.15.1/test/index.vcf > /tmp/Xj_Ix_uMYK/index.bcf .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/Xj_Ix_uMYK/index.bcf .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -z -m 14 -x /tmp/Xj_Ix_uMYK/index.vcf.gz.csi /builddir/build/BUILD/htslib-1.15.1/test/index.vcf > /tmp/Xj_Ix_uMYK/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/Xj_Ix_uMYK/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -l 0 -z -m 0 -x /tmp/Xj_Ix_uMYK/index.vcf.gz.tbi /builddir/build/BUILD/htslib-1.15.1/test/index.vcf > /tmp/Xj_Ix_uMYK/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -t /tmp/Xj_Ix_uMYK/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/tabix /tmp/Xj_Ix_uMYK/index.vcf.gz##idx##/tmp/Xj_Ix_uMYK/index.vcf.gz.tbi 1:10000060-10000060 .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view /tmp/Xj_Ix_uMYK/index2.bam 1:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view /tmp/Xj_Ix_uMYK/index2.bam 1:2000000-2000000 .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view /tmp/Xj_Ix_uMYK/index2.bam 2:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view /tmp/Xj_Ix_uMYK/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/Xj_Ix_uMYK/index.bam.csi /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/Xj_Ix_uMYK/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/Xj_Ix_uMYK/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -b -m 0 -x /tmp/Xj_Ix_uMYK/index.bam.bai /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/Xj_Ix_uMYK/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -b /tmp/Xj_Ix_uMYK/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -z -m 14 -x /tmp/Xj_Ix_uMYK/index.sam.gz.csi /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/Xj_Ix_uMYK/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/Xj_Ix_uMYK/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -z -m 0 -x /tmp/Xj_Ix_uMYK/index.sam.gz.bai /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/Xj_Ix_uMYK/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -b /tmp/Xj_Ix_uMYK/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -z -m 14 -x /tmp/Xj_Ix_uMYK/index.sam.gz.csi /builddir/build/BUILD/htslib-1.15.1/test/index_dos.sam > /tmp/Xj_Ix_uMYK/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/Xj_Ix_uMYK/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -z -m 0 -x /tmp/Xj_Ix_uMYK/index.sam.gz.bai /builddir/build/BUILD/htslib-1.15.1/test/index_dos.sam > /tmp/Xj_Ix_uMYK/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -b /tmp/Xj_Ix_uMYK/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -C -x /tmp/Xj_Ix_uMYK/index.cram.crai /builddir/build/BUILD/htslib-1.15.1/test/index.sam > /tmp/Xj_Ix_uMYK/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index /tmp/Xj_Ix_uMYK/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -b -m 14 -x /tmp/Xj_Ix_uMYK/index.bcf.csi /builddir/build/BUILD/htslib-1.15.1/test/index.vcf > /tmp/Xj_Ix_uMYK/index.bcf .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/Xj_Ix_uMYK/index.bcf .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -z -m 14 -x /tmp/Xj_Ix_uMYK/index.vcf.gz.csi /builddir/build/BUILD/htslib-1.15.1/test/index.vcf > /tmp/Xj_Ix_uMYK/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -c /tmp/Xj_Ix_uMYK/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view -@4 -l 0 -z -m 0 -x /tmp/Xj_Ix_uMYK/index.vcf.gz.tbi /builddir/build/BUILD/htslib-1.15.1/test/index.vcf > /tmp/Xj_Ix_uMYK/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_index -t /tmp/Xj_Ix_uMYK/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/tabix /tmp/Xj_Ix_uMYK/index.vcf.gz##idx##/tmp/Xj_Ix_uMYK/index.vcf.gz.tbi 1:10000060-10000060 .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view /tmp/Xj_Ix_uMYK/index2.bam 1:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view /tmp/Xj_Ix_uMYK/index2.bam 1:2000000-2000000 .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view /tmp/Xj_Ix_uMYK/index2.bam 2:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.15.1/test/test_view /tmp/Xj_Ix_uMYK/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/Xj_Ix_uMYK/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/Xj_Ix_uMYK/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/Xj_Ix_uMYK/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/Xj_Ix_uMYK -s 498703816 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/Xj_Ix_uMYK -s 1694069861 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/Xj_Ix_uMYK -s 1171835437 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/Xj_Ix_uMYK -s 1027327191 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/Xj_Ix_uMYK -s 1461929565 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/Xj_Ix_uMYK -s 128550881 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/Xj_Ix_uMYK -s 176284437 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/Xj_Ix_uMYK -s 474472040 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/Xj_Ix_uMYK -s 740158570 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/Xj_Ix_uMYK -s 112436035 .. 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/Xj_Ix_uMYK/headernul0.bam .. ok test_convert_padded_header: /builddir/build/BUILD/htslib-1.15.1/test/test_view -t ce.fa -C /tmp/Xj_Ix_uMYK/headernul1.bam .. ok test_convert_padded_header: /builddir/build/BUILD/htslib-1.15.1/test/test_view -t ce.fa -C /tmp/Xj_Ix_uMYK/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-1.15.1-3.amzn2023.aarch64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.Nw1eMY + umask 022 + cd /builddir/build/BUILD + cd htslib-1.15.1 + DOCDIR=/builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.aarch64/usr/share/doc/htslib + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.aarch64/usr/share/doc/htslib + cp -pr NEWS /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.aarch64/usr/share/doc/htslib + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.dRMw17 + umask 022 + cd /builddir/build/BUILD + cd htslib-1.15.1 + LICENSEDIR=/builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.aarch64/usr/share/licenses/htslib + export LC_ALL=C + LC_ALL=C + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.aarch64/usr/share/licenses/htslib + cp -pr LICENSE /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.aarch64/usr/share/licenses/htslib + RPM_EC=0 ++ jobs -p + exit 0 Provides: htslib = 1.15.1-3.amzn2023 htslib(aarch-64) = 1.15.1-3.amzn2023 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-1.15.1-3.amzn2023.aarch64 Provides: htslib-devel = 1.15.1-3.amzn2023 htslib-devel(aarch-64) = 1.15.1-3.amzn2023 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-1.15.1-3.amzn2023.aarch64 Provides: htslib-tools = 1.15.1-3.amzn2023 htslib-tools(aarch-64) = 1.15.1-3.amzn2023 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-1.15.1-3.amzn2023.aarch64 Provides: htslib-debugsource = 1.15.1-3.amzn2023 htslib-debugsource(aarch-64) = 1.15.1-3.amzn2023 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: htslib-debuginfo-1.15.1-3.amzn2023.aarch64 Provides: debuginfo(build-id) = 9d28d3d3b52fc77f9fd241bd494fe66fb99ec421 debuginfo(build-id) = d12a93ff69b91fe8e3b38f3c51085adbbb021ded debuginfo(build-id) = d696409b3ef6d937a1d5a2c87c6ecc86775b7a40 debuginfo(build-id) = f4e30e844f886b979bcbcb7e097124dc10b05bdc debuginfo(build-id) = fda97090ccf84a5c78e1e95a6ce87a415612ab6a htslib-debuginfo = 1.15.1-3.amzn2023 htslib-debuginfo(aarch-64) = 1.15.1-3.amzn2023 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: htslib-debugsource(aarch-64) = 1.15.1-3.amzn2023 Processing files: htslib-tools-debuginfo-1.15.1-3.amzn2023.aarch64 Provides: debuginfo(build-id) = 2cbcce380bfa8d07fd081538ef8089ab90d6c40f debuginfo(build-id) = 69529a0c04d21f2ba3c68d7b8d6754474d967931 debuginfo(build-id) = a363a112488244469ab8994b1a347cb9d97eb0c1 htslib-tools-debuginfo = 1.15.1-3.amzn2023 htslib-tools-debuginfo(aarch-64) = 1.15.1-3.amzn2023 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: htslib-debugsource(aarch-64) = 1.15.1-3.amzn2023 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.aarch64 Wrote: /builddir/build/RPMS/htslib-tools-1.15.1-3.amzn2023.aarch64.rpm Wrote: /builddir/build/RPMS/htslib-debugsource-1.15.1-3.amzn2023.aarch64.rpm Wrote: /builddir/build/RPMS/htslib-debuginfo-1.15.1-3.amzn2023.aarch64.rpm Wrote: /builddir/build/RPMS/htslib-1.15.1-3.amzn2023.aarch64.rpm Wrote: /builddir/build/RPMS/htslib-devel-1.15.1-3.amzn2023.aarch64.rpm Wrote: /builddir/build/RPMS/htslib-tools-debuginfo-1.15.1-3.amzn2023.aarch64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.Ppbhlo + umask 022 + cd /builddir/build/BUILD + cd htslib-1.15.1 + /usr/bin/rm -rf /builddir/build/BUILDROOT/htslib-1.15.1-3.amzn2023.aarch64 + RPM_EC=0 ++ jobs -p + exit 0 Finish: rpmbuild htslib-1.15.1-3.amzn2023.src.rpm Finish: build phase for htslib-1.15.1-3.amzn2023.src.rpm INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/amazonlinux-2023-aarch64-1704591054.948002/root/var/log/dnf.rpm.log /var/lib/mock/amazonlinux-2023-aarch64-1704591054.948002/root/var/log/dnf.librepo.log /var/lib/mock/amazonlinux-2023-aarch64-1704591054.948002/root/var/log/dnf.log INFO: Done(/var/lib/copr-rpmbuild/results/htslib-1.15.1-3.amzn2023.src.rpm) Config(child) 3 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 RPMResults tool Package info: { "packages": [ { "name": "htslib-tools", "epoch": null, "version": "1.15.1", "release": "3.amzn2023", "arch": "aarch64" }, { "name": "htslib-devel", "epoch": null, "version": "1.15.1", "release": "3.amzn2023", "arch": "aarch64" }, { "name": "htslib", "epoch": null, "version": "1.15.1", "release": "3.amzn2023", "arch": "aarch64" }, { "name": "htslib", "epoch": null, "version": "1.15.1", "release": "3.amzn2023", "arch": "src" }, { "name": "htslib-debugsource", "epoch": null, "version": "1.15.1", "release": "3.amzn2023", "arch": "aarch64" }, { "name": "htslib-tools-debuginfo", "epoch": null, "version": "1.15.1", "release": "3.amzn2023", "arch": "aarch64" }, { "name": "htslib-debuginfo", "epoch": null, "version": "1.15.1", "release": "3.amzn2023", "arch": "aarch64" } ] } RPMResults finished