Warning: Permanently added '2620:52:3:1:dead:beef:cafe:c10d' (ED25519) to the list of known hosts. You can reproduce this build on your computer by running: sudo dnf install copr-rpmbuild /usr/bin/copr-rpmbuild --verbose --drop-resultdir --task-url https://copr.fedorainfracloud.org/backend/get-build-task/8061640-fedora-40-x86_64 --chroot fedora-40-x86_64 Version: 0.73 PID: 8670 Logging PID: 8671 Task: {'allow_user_ssh': False, 'appstream': False, 'background': False, 'build_id': 8061640, 'buildroot_pkgs': [], 'chroot': 'fedora-40-x86_64', 'enable_net': False, 'fedora_review': False, 'git_hash': '99deaf2976d5e2a7dd69e5d010840ab4dff6f7b4', 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/mttmartin/star/star', 'isolation': 'default', 'memory_reqs': 2048, 'package_name': 'star', 'package_version': '2.7.11b-1', 'project_dirname': 'star', 'project_name': 'star', 'project_owner': 'mttmartin', 'repo_priority': None, 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/mttmartin/star/fedora-40-x86_64/', 'id': 'copr_base', 'name': 'Copr repository', 'priority': None}], 'sandbox': 'mttmartin/star--mttmartin', 'source_json': {}, 'source_type': None, 'ssh_public_keys': None, 'submitter': 'mttmartin', 'tags': [], 'task_id': '8061640-fedora-40-x86_64', 'timeout': 18000, 'uses_devel_repo': False, 'with_opts': [], 'without_opts': []} Running: git clone https://copr-dist-git.fedorainfracloud.org/git/mttmartin/star/star /var/lib/copr-rpmbuild/workspace/workdir-jriai2_s/star --depth 500 --no-single-branch --recursive cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/mttmartin/star/star', '/var/lib/copr-rpmbuild/workspace/workdir-jriai2_s/star', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-jriai2_s/star'... Running: git checkout 99deaf2976d5e2a7dd69e5d010840ab4dff6f7b4 -- cmd: ['git', 'checkout', '99deaf2976d5e2a7dd69e5d010840ab4dff6f7b4', '--'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-jriai2_s/star rc: 0 stdout: stderr: Note: switching to '99deaf2976d5e2a7dd69e5d010840ab4dff6f7b4'. You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by switching back to a branch. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -c with the switch command. Example: git switch -c Or undo this operation with: git switch - Turn off this advice by setting config variable advice.detachedHead to false HEAD is now at 99deaf2 automatic import of star Running: copr-distgit-client sources /usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated INFO: Calling: curl -H Pragma: -o 2.7.11b.tar.gz --location --connect-timeout 60 --retry 3 --retry-delay 10 --remote-time --show-error --fail --retry-all-errors https://copr-dist-git.fedorainfracloud.org/repo/pkgs/mttmartin/star/star/2.7.11b.tar.gz/md5/9e21d9930989b1be3ffc50b818489d55/2.7.11b.tar.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 11.8M 100 11.8M 0 0 54.2M 0 --:--:-- --:--:-- --:--:-- 54.0M INFO: Reading stdout from command: md5sum 2.7.11b.tar.gz Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-jriai2_s/star/star.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-jriai2_s/star --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1727101652.169710 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 5.6 starting (python version = 3.12.1, NVR = mock-5.6-1.fc39), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-jriai2_s/star/star.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-jriai2_s/star --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1727101652.169710 -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-jriai2_s/star/star.spec) Config(fedora-40-x86_64) Start: clean chroot Finish: clean chroot Mock Version: 5.6 INFO: Mock Version: 5.6 Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-40-x86_64-bootstrap-1727101652.169710/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata INFO: Guessed host environment type: unknown INFO: Using bootstrap image: registry.fedoraproject.org/fedora:40 INFO: Pulling image: registry.fedoraproject.org/fedora:40 INFO: Copy content of container registry.fedoraproject.org/fedora:40 to /var/lib/mock/fedora-40-x86_64-bootstrap-1727101652.169710/root INFO: Checking that registry.fedoraproject.org/fedora:40 image matches host's architecture INFO: mounting registry.fedoraproject.org/fedora:40 with podman image mount INFO: image registry.fedoraproject.org/fedora:40 as /var/lib/containers/storage/overlay/35313cbf22428fc3de2eb9fcc887733f6447c6c4ff0cdb2dc6fdd571184ce4c3/merged INFO: umounting image registry.fedoraproject.org/fedora:40 (/var/lib/containers/storage/overlay/35313cbf22428fc3de2eb9fcc887733f6447c6c4ff0cdb2dc6fdd571184ce4c3/merged) with podman image umount INFO: Using 'dnf' instead of 'dnf5' for bootstrap chroot INFO: Package manager dnf detected and used (fallback) INFO: Bootstrap image not marked ready Start(bootstrap): installing dnf5 tooling No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 18 kB/s | 1.8 kB 00:00 fedora 289 kB/s | 20 MB 01:10 updates 7.8 MB/s | 10 MB 00:01 Dependencies resolved. ================================================================================ Package Architecture Version Repository Size ================================================================================ Installing: dnf5 x86_64 5.1.17-2.fc40 updates 700 k dnf5-plugins x86_64 5.1.17-2.fc40 updates 358 k Installing dependencies: fmt x86_64 10.2.1-4.fc40 fedora 125 k libdnf5 x86_64 5.1.17-2.fc40 updates 999 k libdnf5-cli x86_64 5.1.17-2.fc40 updates 231 k sdbus-cpp x86_64 1.4.0-2.fc40 fedora 110 k Transaction Summary ================================================================================ Install 6 Packages Total download size: 2.5 M Installed size: 6.9 M Downloading Packages: (1/6): fmt-10.2.1-4.fc40.x86_64.rpm 1.1 MB/s | 125 kB 00:00 (2/6): sdbus-cpp-1.4.0-2.fc40.x86_64.rpm 930 kB/s | 110 kB 00:00 (3/6): libdnf5-5.1.17-2.fc40.x86_64.rpm 2.0 MB/s | 999 kB 00:00 (4/6): libdnf5-cli-5.1.17-2.fc40.x86_64.rpm 2.1 MB/s | 231 kB 00:00 (5/6): dnf5-5.1.17-2.fc40.x86_64.rpm 706 kB/s | 700 kB 00:00 (6/6): dnf5-plugins-5.1.17-2.fc40.x86_64.rpm 341 kB/s | 358 kB 00:01 -------------------------------------------------------------------------------- Total 2.0 MB/s | 2.5 MB 00:01 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Installing : fmt-10.2.1-4.fc40.x86_64 1/6 Installing : libdnf5-5.1.17-2.fc40.x86_64 2/6 Installing : libdnf5-cli-5.1.17-2.fc40.x86_64 3/6 Installing : sdbus-cpp-1.4.0-2.fc40.x86_64 4/6 Installing : dnf5-5.1.17-2.fc40.x86_64 5/6 Installing : dnf5-plugins-5.1.17-2.fc40.x86_64 6/6 Running scriptlet: dnf5-plugins-5.1.17-2.fc40.x86_64 6/6 Installed: dnf5-5.1.17-2.fc40.x86_64 dnf5-plugins-5.1.17-2.fc40.x86_64 fmt-10.2.1-4.fc40.x86_64 libdnf5-5.1.17-2.fc40.x86_64 libdnf5-cli-5.1.17-2.fc40.x86_64 sdbus-cpp-1.4.0-2.fc40.x86_64 Complete! INFO: Switching package manager from dnf to the dnf5 (direct choice) Finish(bootstrap): installing dnf5 tooling Start(bootstrap): creating root cache Finish(bootstrap): creating root cache Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-40-x86_64-1727101652.169710/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin INFO: Package manager dnf5 detected and used (direct choice) INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-4.19.1.1-1.fc40.x86_64 rpm-sequoia-1.7.0-1.fc40.x86_64 python3-dnf-4.21.1-1.fc40.noarch yum-4.21.1-1.fc40.noarch dnf5-5.1.17-2.fc40.x86_64 dnf5-plugins-5.1.17-2.fc40.x86_64 Start: installing minimal buildroot with dnf5 Updating and loading repositories: updates 100% | 25.1 MiB/s | 10.9 MiB | 00m00s fedora 100% | 10.9 MiB/s | 20.8 MiB | 00m02s Copr repository 100% | 35.9 KiB/s | 3.3 KiB | 00m00s Repositories loaded. Package Arch Version Repository Size Installing group/module packages: bash x86_64 5.2.26-3.fc40 fedora 8.1 MiB bzip2 x86_64 1.0.8-18.fc40 fedora 91.7 KiB coreutils x86_64 9.4-7.fc40 updates 5.8 MiB cpio x86_64 2.15-1.fc40 fedora 1.1 MiB diffutils x86_64 3.10-5.fc40 fedora 1.6 MiB fedora-release-common noarch 40-39 updates 19.1 KiB findutils x86_64 1:4.9.0-9.fc40 updates 1.5 MiB gawk x86_64 5.3.0-3.fc40 fedora 1.7 MiB glibc-minimal-langpack x86_64 2.39-22.fc40 updates 0.0 B grep x86_64 3.11-7.fc40 fedora 1.0 MiB gzip x86_64 1.13-1.fc40 fedora 385.0 KiB info x86_64 7.1-2.fc40 fedora 357.8 KiB patch x86_64 2.7.6-24.fc40 fedora 262.8 KiB redhat-rpm-config noarch 288-1.fc40 updates 185.2 KiB rpm-build x86_64 4.19.1.1-1.fc40 fedora 173.7 KiB sed x86_64 4.9-1.fc40 fedora 861.5 KiB shadow-utils x86_64 2:4.15.1-3.fc40 updates 4.1 MiB tar x86_64 2:1.35-3.fc40 fedora 2.9 MiB unzip x86_64 6.0-63.fc40 fedora 382.8 KiB util-linux x86_64 2.40.1-1.fc40 updates 3.7 MiB which x86_64 2.21-41.fc40 fedora 80.2 KiB xz x86_64 1:5.4.6-3.fc40 fedora 2.0 MiB Installing dependencies: alternatives x86_64 1.27-1.fc40 updates 66.3 KiB ansible-srpm-macros noarch 1-14.fc40 fedora 35.7 KiB audit-libs x86_64 4.0.2-1.fc40 updates 327.4 KiB authselect x86_64 1.5.0-5.fc40 fedora 153.6 KiB authselect-libs x86_64 1.5.0-5.fc40 fedora 818.3 KiB basesystem noarch 11-20.fc40 fedora 0.0 B binutils x86_64 2.41-37.fc40 updates 26.4 MiB binutils-gold x86_64 2.41-37.fc40 updates 2.0 MiB bzip2-libs x86_64 1.0.8-18.fc40 fedora 80.7 KiB ca-certificates noarch 2023.2.62_v7.0.401-6.fc40 fedora 2.3 MiB coreutils-common x86_64 9.4-7.fc40 updates 11.4 MiB cracklib x86_64 2.9.11-5.fc40 fedora 238.9 KiB crypto-policies noarch 20240725-1.git28d3e2d.fc40 updates 153.3 KiB curl x86_64 8.6.0-10.fc40 updates 738.6 KiB cyrus-sasl-lib x86_64 2.1.28-19.fc40 fedora 2.3 MiB debugedit x86_64 5.0-14.fc40 fedora 199.0 KiB dwz x86_64 0.15-6.fc40 fedora 290.9 KiB ed x86_64 1.20.2-1.fc40 updates 146.9 KiB efi-srpm-macros noarch 5-11.fc40 fedora 40.1 KiB elfutils x86_64 0.191-4.fc40 fedora 2.5 MiB elfutils-debuginfod-client x86_64 0.191-4.fc40 fedora 64.9 KiB elfutils-default-yama-scope noarch 0.191-4.fc40 fedora 1.8 KiB elfutils-libelf x86_64 0.191-4.fc40 fedora 1.2 MiB elfutils-libs x86_64 0.191-4.fc40 fedora 646.1 KiB fedora-gpg-keys noarch 40-2 updates 124.7 KiB fedora-release noarch 40-39 updates 0.0 B fedora-release-identity-basic noarch 40-39 updates 654.0 B fedora-repos noarch 40-2 updates 4.9 KiB file x86_64 5.45-4.fc40 fedora 103.5 KiB file-libs x86_64 5.45-4.fc40 fedora 9.9 MiB filesystem x86_64 3.18-8.fc40 fedora 106.0 B fonts-srpm-macros noarch 1:2.0.5-14.fc40 fedora 55.3 KiB forge-srpm-macros noarch 0.3.2-1.fc40 updates 39.0 KiB fpc-srpm-macros noarch 1.3-12.fc40 fedora 144.0 B gdb-minimal x86_64 15.1-1.fc40 updates 13.0 MiB gdbm x86_64 1:1.23-6.fc40 fedora 460.9 KiB gdbm-libs x86_64 1:1.23-6.fc40 fedora 121.9 KiB ghc-srpm-macros noarch 1.9-1.fc40 fedora 716.0 B glibc x86_64 2.39-22.fc40 updates 6.6 MiB glibc-common x86_64 2.39-22.fc40 updates 1.0 MiB glibc-gconv-extra x86_64 2.39-22.fc40 updates 7.8 MiB gmp x86_64 1:6.2.1-8.fc40 fedora 794.6 KiB gnat-srpm-macros noarch 6-5.fc40 fedora 1.0 KiB go-srpm-macros noarch 3.5.0-1.fc40 fedora 60.6 KiB jansson x86_64 2.13.1-9.fc40 fedora 88.3 KiB kernel-srpm-macros noarch 1.0-23.fc40 fedora 1.9 KiB keyutils-libs x86_64 1.6.3-3.fc40 fedora 54.4 KiB krb5-libs x86_64 1.21.3-1.fc40 updates 2.3 MiB libacl x86_64 2.3.2-1.fc40 fedora 40.0 KiB libarchive x86_64 3.7.2-4.fc40 updates 914.6 KiB libattr x86_64 2.5.2-3.fc40 fedora 28.5 KiB libblkid x86_64 2.40.1-1.fc40 updates 258.5 KiB libbrotli x86_64 1.1.0-3.fc40 fedora 829.5 KiB libcap x86_64 2.69-8.fc40 updates 219.8 KiB libcap-ng x86_64 0.8.4-4.fc40 fedora 73.1 KiB libcom_err x86_64 1.47.0-5.fc40 fedora 67.2 KiB libcurl x86_64 8.6.0-10.fc40 updates 776.8 KiB libeconf x86_64 0.6.2-2.fc40 updates 58.0 KiB libevent x86_64 2.1.12-12.fc40 fedora 895.6 KiB libfdisk x86_64 2.40.1-1.fc40 updates 362.9 KiB libffi x86_64 3.4.4-7.fc40 fedora 81.6 KiB libgcc x86_64 14.2.1-3.fc40 updates 274.6 KiB libgomp x86_64 14.2.1-3.fc40 updates 523.6 KiB libidn2 x86_64 2.3.7-1.fc40 fedora 329.1 KiB libmount x86_64 2.40.1-1.fc40 updates 351.8 KiB libnghttp2 x86_64 1.59.0-3.fc40 updates 166.1 KiB libnsl2 x86_64 2.0.1-1.fc40 fedora 57.9 KiB libpkgconf x86_64 2.1.1-2.fc40 updates 74.2 KiB libpsl x86_64 0.21.5-3.fc40 fedora 80.5 KiB libpwquality x86_64 1.4.5-9.fc40 fedora 417.8 KiB libselinux x86_64 3.6-4.fc40 fedora 173.0 KiB libsemanage x86_64 3.6-3.fc40 fedora 293.5 KiB libsepol x86_64 3.6-3.fc40 fedora 802.0 KiB libsmartcols x86_64 2.40.1-1.fc40 updates 180.4 KiB libssh x86_64 0.10.6-5.fc40 fedora 509.3 KiB libssh-config noarch 0.10.6-5.fc40 fedora 277.0 B libstdc++ x86_64 14.2.1-3.fc40 updates 2.8 MiB libtasn1 x86_64 4.19.0-6.fc40 fedora 175.7 KiB libtirpc x86_64 1.3.5-0.fc40 updates 202.7 KiB libtool-ltdl x86_64 2.4.7-10.fc40 fedora 66.2 KiB libunistring x86_64 1.1-7.fc40 fedora 1.7 MiB libutempter x86_64 1.2.1-13.fc40 fedora 57.7 KiB libuuid x86_64 2.40.1-1.fc40 updates 37.4 KiB libverto x86_64 0.3.2-8.fc40 fedora 29.5 KiB libxcrypt x86_64 4.4.36-5.fc40 fedora 262.8 KiB libxml2 x86_64 2.12.8-1.fc40 updates 1.7 MiB libzstd x86_64 1.5.6-1.fc40 updates 787.9 KiB lua-libs x86_64 5.4.6-5.fc40 fedora 281.1 KiB lua-srpm-macros noarch 1-13.fc40 fedora 1.3 KiB lz4-libs x86_64 1.9.4-6.fc40 fedora 129.4 KiB mpfr x86_64 4.2.1-4.fc40 updates 832.0 KiB ncurses-base noarch 6.4-12.20240127.fc40 fedora 326.2 KiB ncurses-libs x86_64 6.4-12.20240127.fc40 fedora 963.2 KiB ocaml-srpm-macros noarch 9-3.fc40 fedora 1.9 KiB openblas-srpm-macros noarch 2-16.fc40 fedora 104.0 B openldap x86_64 2.6.7-1.fc40 fedora 635.1 KiB openssl-libs x86_64 1:3.2.2-3.fc40 updates 7.8 MiB p11-kit x86_64 0.25.5-1.fc40 updates 2.2 MiB p11-kit-trust x86_64 0.25.5-1.fc40 updates 391.4 KiB package-notes-srpm-macros noarch 0.5-11.fc40 fedora 1.6 KiB pam x86_64 1.6.1-3.fc40 updates 1.8 MiB pam-libs x86_64 1.6.1-3.fc40 updates 135.0 KiB pcre2 x86_64 10.44-1.fc40 updates 653.5 KiB pcre2-syntax noarch 10.44-1.fc40 updates 251.6 KiB perl-srpm-macros noarch 1-53.fc40 fedora 861.0 B pkgconf x86_64 2.1.1-2.fc40 updates 82.9 KiB pkgconf-m4 noarch 2.1.1-2.fc40 updates 13.9 KiB pkgconf-pkg-config x86_64 2.1.1-2.fc40 updates 989.0 B popt x86_64 1.19-6.fc40 fedora 136.9 KiB publicsuffix-list-dafsa noarch 20240107-3.fc40 fedora 67.5 KiB pyproject-srpm-macros noarch 1.13.0-1.fc40 updates 1.5 KiB python-srpm-macros noarch 3.12-8.fc40 updates 50.6 KiB qt5-srpm-macros noarch 5.15.15-1.fc40 updates 500.0 B qt6-srpm-macros noarch 6.7.2-2.fc40 updates 456.0 B readline x86_64 8.2-8.fc40 fedora 489.2 KiB rpm x86_64 4.19.1.1-1.fc40 fedora 3.0 MiB rpm-build-libs x86_64 4.19.1.1-1.fc40 fedora 198.4 KiB rpm-libs x86_64 4.19.1.1-1.fc40 fedora 709.9 KiB rpm-sequoia x86_64 1.7.0-1.fc40 updates 2.4 MiB rust-srpm-macros noarch 26.3-1.fc40 updates 4.8 KiB setup noarch 2.14.5-2.fc40 fedora 720.4 KiB sqlite-libs x86_64 3.45.1-2.fc40 fedora 1.4 MiB systemd-libs x86_64 255.12-1.fc40 updates 1.9 MiB util-linux-core x86_64 2.40.1-1.fc40 updates 1.5 MiB xxhash-libs x86_64 0.8.2-2.fc40 fedora 88.5 KiB xz-libs x86_64 1:5.4.6-3.fc40 fedora 209.8 KiB zig-srpm-macros noarch 1-2.fc40 fedora 1.1 KiB zip x86_64 3.0-40.fc40 fedora 703.2 KiB zlib-ng-compat x86_64 2.1.7-2.fc40 updates 134.0 KiB zstd x86_64 1.5.6-1.fc40 updates 1.7 MiB Installing groups: Buildsystem building group Transaction Summary: Installing: 152 packages Total size of inbound packages is 53 MiB. Need to download 53 MiB. After this operation 179 MiB will be used (install 179 MiB, remove 0 B). [ 1/152] bzip2-0:1.0.8-18.fc40.x86_64 100% | 523.6 KiB/s | 52.4 KiB | 00m00s [ 2/152] cpio-0:2.15-1.fc40.x86_64 100% | 2.1 MiB/s | 292.2 KiB | 00m00s [ 3/152] diffutils-0:3.10-5.fc40.x86_6 100% | 6.8 MiB/s | 405.6 KiB | 00m00s [ 4/152] grep-0:3.11-7.fc40.x86_64 100% | 6.8 MiB/s | 300.2 KiB | 00m00s [ 5/152] bash-0:5.2.26-3.fc40.x86_64 100% | 9.9 MiB/s | 1.8 MiB | 00m00s [ 6/152] gzip-0:1.13-1.fc40.x86_64 100% | 4.5 MiB/s | 170.6 KiB | 00m00s [ 7/152] info-0:7.1-2.fc40.x86_64 100% | 9.4 MiB/s | 182.3 KiB | 00m00s [ 8/152] patch-0:2.7.6-24.fc40.x86_64 100% | 7.1 MiB/s | 130.7 KiB | 00m00s [ 9/152] rpm-build-0:4.19.1.1-1.fc40.x 100% | 4.8 MiB/s | 78.2 KiB | 00m00s [ 10/152] sed-0:4.9-1.fc40.x86_64 100% | 15.5 MiB/s | 318.2 KiB | 00m00s [ 11/152] tar-2:1.35-3.fc40.x86_64 100% | 31.0 MiB/s | 856.6 KiB | 00m00s [ 12/152] unzip-0:6.0-63.fc40.x86_64 100% | 10.0 MiB/s | 184.5 KiB | 00m00s [ 13/152] which-0:2.21-41.fc40.x86_64 100% | 2.5 MiB/s | 41.4 KiB | 00m00s [ 14/152] xz-1:5.4.6-3.fc40.x86_64 100% | 23.7 MiB/s | 557.4 KiB | 00m00s [ 15/152] fedora-release-common-0:40-39 100% | 146.8 KiB/s | 21.3 KiB | 00m00s [ 16/152] gawk-0:5.3.0-3.fc40.x86_64 100% | 36.9 MiB/s | 1.1 MiB | 00m00s [ 17/152] glibc-minimal-langpack-0:2.39 100% | 1.0 MiB/s | 106.3 KiB | 00m00s [ 18/152] findutils-1:4.9.0-9.fc40.x86_ 100% | 1.7 MiB/s | 491.4 KiB | 00m00s [ 19/152] coreutils-0:9.4-7.fc40.x86_64 100% | 3.5 MiB/s | 1.1 MiB | 00m00s [ 20/152] redhat-rpm-config-0:288-1.fc4 100% | 1.7 MiB/s | 82.1 KiB | 00m00s [ 21/152] filesystem-0:3.18-8.fc40.x86_ 100% | 36.2 MiB/s | 1.1 MiB | 00m00s [ 22/152] ncurses-libs-0:6.4-12.2024012 100% | 14.1 MiB/s | 332.5 KiB | 00m00s [ 23/152] util-linux-0:2.40.1-1.fc40.x8 100% | 17.5 MiB/s | 1.2 MiB | 00m00s [ 24/152] bzip2-libs-0:1.0.8-18.fc40.x8 100% | 2.5 MiB/s | 40.9 KiB | 00m00s [ 25/152] shadow-utils-2:4.15.1-3.fc40. 100% | 12.8 MiB/s | 1.3 MiB | 00m00s [ 26/152] libattr-0:2.5.2-3.fc40.x86_64 100% | 1.1 MiB/s | 18.0 KiB | 00m00s [ 27/152] libselinux-0:3.6-4.fc40.x86_6 100% | 4.3 MiB/s | 87.5 KiB | 00m00s [ 28/152] debugedit-0:5.0-14.fc40.x86_6 100% | 4.0 MiB/s | 78.7 KiB | 00m00s [ 29/152] elfutils-0:0.191-4.fc40.x86_6 100% | 21.6 MiB/s | 531.3 KiB | 00m00s [ 30/152] elfutils-libelf-0:0.191-4.fc4 100% | 10.8 MiB/s | 209.8 KiB | 00m00s [ 31/152] file-0:5.45-4.fc40.x86_64 100% | 1.6 MiB/s | 49.0 KiB | 00m00s [ 32/152] popt-0:1.19-6.fc40.x86_64 100% | 3.6 MiB/s | 66.7 KiB | 00m00s [ 33/152] readline-0:8.2-8.fc40.x86_64 100% | 11.0 MiB/s | 213.3 KiB | 00m00s [ 34/152] rpm-0:4.19.1.1-1.fc40.x86_64 100% | 22.9 MiB/s | 540.1 KiB | 00m00s [ 35/152] rpm-build-libs-0:4.19.1.1-1.f 100% | 3.6 MiB/s | 95.0 KiB | 00m00s [ 36/152] rpm-libs-0:4.19.1.1-1.fc40.x8 100% | 15.1 MiB/s | 308.9 KiB | 00m00s [ 37/152] libacl-0:2.3.2-1.fc40.x86_64 100% | 1.5 MiB/s | 24.4 KiB | 00m00s [ 38/152] xz-libs-1:5.4.6-3.fc40.x86_64 100% | 6.3 MiB/s | 110.0 KiB | 00m00s [ 39/152] gmp-1:6.2.1-8.fc40.x86_64 100% | 15.3 MiB/s | 312.5 KiB | 00m00s [ 40/152] ansible-srpm-macros-0:1-14.fc 100% | 1.3 MiB/s | 20.8 KiB | 00m00s [ 41/152] coreutils-common-0:9.4-7.fc40 100% | 31.6 MiB/s | 2.1 MiB | 00m00s [ 42/152] dwz-0:0.15-6.fc40.x86_64 100% | 6.7 MiB/s | 137.8 KiB | 00m00s [ 43/152] efi-srpm-macros-0:5-11.fc40.n 100% | 1.4 MiB/s | 22.3 KiB | 00m00s [ 44/152] fonts-srpm-macros-1:2.0.5-14. 100% | 1.6 MiB/s | 26.5 KiB | 00m00s [ 45/152] fpc-srpm-macros-0:1.3-12.fc40 100% | 489.6 KiB/s | 7.8 KiB | 00m00s [ 46/152] ghc-srpm-macros-0:1.9-1.fc40. 100% | 546.8 KiB/s | 8.7 KiB | 00m00s [ 47/152] glibc-common-0:2.39-22.fc40.x 100% | 3.7 MiB/s | 390.4 KiB | 00m00s [ 48/152] gnat-srpm-macros-0:6-5.fc40.n 100% | 519.0 KiB/s | 8.8 KiB | 00m00s [ 49/152] go-srpm-macros-0:3.5.0-1.fc40 100% | 888.6 KiB/s | 27.5 KiB | 00m00s [ 50/152] kernel-srpm-macros-0:1.0-23.f 100% | 608.0 KiB/s | 9.7 KiB | 00m00s [ 51/152] lua-srpm-macros-0:1-13.fc40.n 100% | 582.0 KiB/s | 8.7 KiB | 00m00s [ 52/152] ocaml-srpm-macros-0:9-3.fc40. 100% | 567.1 KiB/s | 9.1 KiB | 00m00s [ 53/152] openblas-srpm-macros-0:2-16.f 100% | 441.2 KiB/s | 7.5 KiB | 00m00s [ 54/152] package-notes-srpm-macros-0:0 100% | 320.8 KiB/s | 9.9 KiB | 00m00s [ 55/152] perl-srpm-macros-0:1-53.fc40. 100% | 523.9 KiB/s | 8.4 KiB | 00m00s [ 56/152] zig-srpm-macros-0:1-2.fc40.no 100% | 535.9 KiB/s | 8.0 KiB | 00m00s [ 57/152] zip-0:3.0-40.fc40.x86_64 100% | 13.6 MiB/s | 264.8 KiB | 00m00s [ 58/152] libsemanage-0:3.6-3.fc40.x86_ 100% | 5.7 MiB/s | 116.4 KiB | 00m00s [ 59/152] libxcrypt-0:4.4.36-5.fc40.x86 100% | 5.8 MiB/s | 118.1 KiB | 00m00s [ 60/152] setup-0:2.14.5-2.fc40.noarch 100% | 8.0 MiB/s | 154.7 KiB | 00m00s [ 61/152] libcap-ng-0:0.8.4-4.fc40.x86_ 100% | 1.0 MiB/s | 32.6 KiB | 00m00s [ 62/152] libutempter-0:1.2.1-13.fc40.x 100% | 1.4 MiB/s | 26.4 KiB | 00m00s [ 63/152] util-linux-core-0:2.40.1-1.fc 100% | 13.8 MiB/s | 537.0 KiB | 00m00s [ 64/152] ncurses-base-0:6.4-12.2024012 100% | 5.1 MiB/s | 88.8 KiB | 00m00s [ 65/152] libsepol-0:3.6-3.fc40.x86_64 100% | 15.8 MiB/s | 340.1 KiB | 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14.2 MiB/s | 553.4 KiB | 00m00s [105/152] authselect-0:1.5.0-5.fc40.x86 100% | 7.5 MiB/s | 146.2 KiB | 00m00s [106/152] pam-libs-0:1.6.1-3.fc40.x86_6 100% | 1.7 MiB/s | 57.1 KiB | 00m00s [107/152] gdbm-libs-1:1.23-6.fc40.x86_6 100% | 3.2 MiB/s | 56.2 KiB | 00m00s [108/152] libnsl2-0:2.0.1-1.fc40.x86_64 100% | 1.8 MiB/s | 29.6 KiB | 00m00s [109/152] libpwquality-0:1.4.5-9.fc40.x 100% | 6.5 MiB/s | 119.7 KiB | 00m00s [110/152] authselect-libs-0:1.5.0-5.fc4 100% | 11.2 MiB/s | 218.6 KiB | 00m00s [111/152] cracklib-0:2.9.11-5.fc40.x86_ 100% | 5.3 MiB/s | 92.5 KiB | 00m00s [112/152] libeconf-0:0.6.2-2.fc40.x86_6 100% | 968.5 KiB/s | 32.0 KiB | 00m00s [113/152] ca-certificates-0:2023.2.62_v 100% | 31.2 MiB/s | 862.1 KiB | 00m00s [114/152] pyproject-srpm-macros-0:1.13. 100% | 390.1 KiB/s | 12.9 KiB | 00m00s [115/152] python-srpm-macros-0:3.12-8.f 100% | 708.7 KiB/s | 23.4 KiB | 00m00s [116/152] openssl-libs-1:3.2.2-3.fc40.x 100% | 33.5 MiB/s | 2.3 MiB | 00m00s [117/152] qt5-srpm-macros-0:5.15.15-1.f 100% | 278.2 KiB/s | 8.9 KiB | 00m00s [118/152] qt6-srpm-macros-0:6.7.2-2.fc4 100% | 272.7 KiB/s | 9.0 KiB | 00m00s [119/152] rust-srpm-macros-0:26.3-1.fc4 100% | 379.1 KiB/s | 12.5 KiB | 00m00s [120/152] libcom_err-0:1.47.0-5.fc40.x8 100% | 1.5 MiB/s | 25.4 KiB | 00m00s [121/152] gdbm-1:1.23-6.fc40.x86_64 100% | 7.1 MiB/s | 152.5 KiB | 00m00s [122/152] libtirpc-0:1.3.5-0.fc40.x86_6 100% | 2.8 MiB/s | 94.1 KiB | 00m00s [123/152] keyutils-libs-0:1.6.3-3.fc40. 100% | 1.6 MiB/s | 31.5 KiB | 00m00s [124/152] crypto-policies-0:20240725-1. 100% | 2.8 MiB/s | 99.2 KiB | 00m00s [125/152] krb5-libs-0:1.21.3-1.fc40.x86 100% | 18.5 MiB/s | 757.0 KiB | 00m00s [126/152] libverto-0:0.3.2-8.fc40.x86_6 100% | 586.8 KiB/s | 20.5 KiB | 00m00s [127/152] libxml2-0:2.12.8-1.fc40.x86_6 100% | 17.2 MiB/s | 687.1 KiB | 00m00s [128/152] fedora-repos-0:40-2.noarch 100% | 287.4 KiB/s | 9.5 KiB | 00m00s [129/152] fedora-gpg-keys-0:40-2.noarch 100% | 3.8 MiB/s | 132.1 KiB | 00m00s 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KiB | 00m00s [143/152] gdb-minimal-0:15.1-1.fc40.x86 100% | 32.9 MiB/s | 4.3 MiB | 00m00s [144/152] openldap-0:2.6.7-1.fc40.x86_6 100% | 9.2 MiB/s | 254.3 KiB | 00m00s [145/152] libunistring-0:1.1-7.fc40.x86 100% | 23.2 MiB/s | 545.5 KiB | 00m00s [146/152] publicsuffix-list-dafsa-0:202 100% | 3.5 MiB/s | 58.1 KiB | 00m00s [147/152] libssh-config-0:0.10.6-5.fc40 100% | 501.6 KiB/s | 9.0 KiB | 00m00s [148/152] cyrus-sasl-lib-0:2.1.28-19.fc 100% | 29.6 MiB/s | 789.3 KiB | 00m00s [149/152] libevent-0:2.1.12-12.fc40.x86 100% | 10.9 MiB/s | 257.2 KiB | 00m00s [150/152] libtool-ltdl-0:2.4.7-10.fc40. 100% | 2.2 MiB/s | 36.2 KiB | 00m00s [151/152] libnghttp2-0:1.59.0-3.fc40.x8 100% | 2.2 MiB/s | 75.3 KiB | 00m00s [152/152] fedora-release-identity-basic 100% | 257.6 KiB/s | 11.6 KiB | 00m00s -------------------------------------------------------------------------------- [152/152] Total 100% | 25.3 MiB/s | 52.8 MiB | 00m02s Running transaction Importing PGP key 0xA15B79CC: Userid : "Fedora (40) " Fingerprint: 115DF9AEF857853EE8445D0A0727707EA15B79CC From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-40-primary The key was successfully imported. [ 1/154] Verify package files 100% | 713.0 B/s | 152.0 B | 00m00s >>> Running pre-transaction scriptlet: filesystem-0:3.18-8.fc40.x86_64 >>> Stop pre-transaction scriptlet: filesystem-0:3.18-8.fc40.x86_64 [ 2/154] Prepare transaction 100% | 1.8 KiB/s | 152.0 B | 00m00s [ 3/154] Installing libgcc-0:14.2.1-3. 100% | 89.9 MiB/s | 276.3 KiB | 00m00s >>> Running post-install scriptlet: libgcc-0:14.2.1-3.fc40.x86_64 >>> Stop post-install scriptlet: libgcc-0:14.2.1-3.fc40.x86_64 [ 4/154] Installing crypto-policies-0: 100% | 16.5 MiB/s | 185.9 KiB | 00m00s >>> Running post-install scriptlet: crypto-policies-0:20240725-1.git28d3e2d.fc40 >>> Stop post-install scriptlet: crypto-policies-0:20240725-1.git28d3e2d.fc40.no [ 5/154] Installing fedora-release-ide 100% | 890.6 KiB/s | 912.0 B | 00m00s [ 6/154] Installing fedora-gpg-keys-0: 100% | 20.7 MiB/s | 169.7 KiB | 00m00s [ 7/154] Installing fedora-repos-0:40- 100% | 5.6 MiB/s | 5.7 KiB | 00m00s [ 8/154] Installing fedora-release-com 100% | 11.4 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| 156.0 MiB/s | 638.9 KiB | 00m00s [131/154] Installing libcurl-0:8.6.0-10 100% | 189.9 MiB/s | 777.9 KiB | 00m00s [132/154] Installing elfutils-libs-0:0. 100% | 210.9 MiB/s | 648.0 KiB | 00m00s [133/154] Installing elfutils-debuginfo 100% | 32.7 MiB/s | 66.9 KiB | 00m00s [134/154] Installing binutils-gold-0:2. 100% | 101.5 MiB/s | 2.0 MiB | 00m00s >>> Running post-install scriptlet: binutils-gold-0:2.41-37.fc40.x86_64 >>> Stop post-install scriptlet: binutils-gold-0:2.41-37.fc40.x86_64 [135/154] Installing binutils-0:2.41-37 100% | 258.9 MiB/s | 26.4 MiB | 00m00s >>> Running post-install scriptlet: binutils-0:2.41-37.fc40.x86_64 >>> Stop post-install scriptlet: binutils-0:2.41-37.fc40.x86_64 [136/154] Installing elfutils-0:0.191-4 100% | 213.1 MiB/s | 2.6 MiB | 00m00s [137/154] Installing gdb-minimal-0:15.1 100% | 316.9 MiB/s | 13.0 MiB | 00m00s [138/154] Installing debugedit-0:5.0-14 100% | 98.5 MiB/s | 201.7 KiB | 00m00s [139/154] Installing rpm-build-libs-0:4 100% | 97.3 MiB/s | 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[151/154] Installing pyproject-srpm-mac 100% | 1.0 MiB/s | 2.1 KiB | 00m00s [152/154] Installing util-linux-0:2.40. 100% | 91.3 MiB/s | 3.7 MiB | 00m00s >>> Running post-install scriptlet: util-linux-0:2.40.1-1.fc40.x86_64 >>> Stop post-install scriptlet: util-linux-0:2.40.1-1.fc40.x86_64 [153/154] Installing which-0:2.21-41.fc 100% | 40.3 MiB/s | 82.4 KiB | 00m00s [154/154] Installing info-0:7.1-2.fc40. 100% | 282.7 KiB/s | 358.2 KiB | 00m01s >>> Running post-transaction scriptlet: filesystem-0:3.18-8.fc40.x86_64 >>> Stop post-transaction scriptlet: filesystem-0:3.18-8.fc40.x86_64 >>> Running post-transaction scriptlet: ca-certificates-0:2023.2.62_v7.0.401-6.f >>> Stop post-transaction scriptlet: ca-certificates-0:2023.2.62_v7.0.401-6.fc40 >>> Running post-transaction scriptlet: authselect-libs-0:1.5.0-5.fc40.x86_64 >>> Stop post-transaction scriptlet: authselect-libs-0:1.5.0-5.fc40.x86_64 >>> Running post-transaction scriptlet: rpm-0:4.19.1.1-1.fc40.x86_64 >>> Stop post-transaction scriptlet: rpm-0:4.19.1.1-1.fc40.x86_64 >>> Running trigger-install scriptlet: glibc-common-0:2.39-22.fc40.x86_64 >>> Stop trigger-install scriptlet: glibc-common-0:2.39-22.fc40.x86_64 >>> Running trigger-install scriptlet: info-0:7.1-2.fc40.x86_64 >>> Stop trigger-install scriptlet: info-0:7.1-2.fc40.x86_64 Finish: installing minimal buildroot with dnf5 Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: alternatives-1.27-1.fc40.x86_64 ansible-srpm-macros-1-14.fc40.noarch audit-libs-4.0.2-1.fc40.x86_64 authselect-1.5.0-5.fc40.x86_64 authselect-libs-1.5.0-5.fc40.x86_64 basesystem-11-20.fc40.noarch bash-5.2.26-3.fc40.x86_64 binutils-2.41-37.fc40.x86_64 binutils-gold-2.41-37.fc40.x86_64 bzip2-1.0.8-18.fc40.x86_64 bzip2-libs-1.0.8-18.fc40.x86_64 ca-certificates-2023.2.62_v7.0.401-6.fc40.noarch coreutils-9.4-7.fc40.x86_64 coreutils-common-9.4-7.fc40.x86_64 cpio-2.15-1.fc40.x86_64 cracklib-2.9.11-5.fc40.x86_64 crypto-policies-20240725-1.git28d3e2d.fc40.noarch curl-8.6.0-10.fc40.x86_64 cyrus-sasl-lib-2.1.28-19.fc40.x86_64 debugedit-5.0-14.fc40.x86_64 diffutils-3.10-5.fc40.x86_64 dwz-0.15-6.fc40.x86_64 ed-1.20.2-1.fc40.x86_64 efi-srpm-macros-5-11.fc40.noarch elfutils-0.191-4.fc40.x86_64 elfutils-debuginfod-client-0.191-4.fc40.x86_64 elfutils-default-yama-scope-0.191-4.fc40.noarch elfutils-libelf-0.191-4.fc40.x86_64 elfutils-libs-0.191-4.fc40.x86_64 fedora-gpg-keys-40-2.noarch fedora-release-40-39.noarch fedora-release-common-40-39.noarch fedora-release-identity-basic-40-39.noarch fedora-repos-40-2.noarch file-5.45-4.fc40.x86_64 file-libs-5.45-4.fc40.x86_64 filesystem-3.18-8.fc40.x86_64 findutils-4.9.0-9.fc40.x86_64 fonts-srpm-macros-2.0.5-14.fc40.noarch forge-srpm-macros-0.3.2-1.fc40.noarch fpc-srpm-macros-1.3-12.fc40.noarch gawk-5.3.0-3.fc40.x86_64 gdb-minimal-15.1-1.fc40.x86_64 gdbm-1.23-6.fc40.x86_64 gdbm-libs-1.23-6.fc40.x86_64 ghc-srpm-macros-1.9-1.fc40.noarch glibc-2.39-22.fc40.x86_64 glibc-common-2.39-22.fc40.x86_64 glibc-gconv-extra-2.39-22.fc40.x86_64 glibc-minimal-langpack-2.39-22.fc40.x86_64 gmp-6.2.1-8.fc40.x86_64 gnat-srpm-macros-6-5.fc40.noarch go-srpm-macros-3.5.0-1.fc40.noarch gpg-pubkey-a15b79cc-63d04c2c grep-3.11-7.fc40.x86_64 gzip-1.13-1.fc40.x86_64 info-7.1-2.fc40.x86_64 jansson-2.13.1-9.fc40.x86_64 kernel-srpm-macros-1.0-23.fc40.noarch keyutils-libs-1.6.3-3.fc40.x86_64 krb5-libs-1.21.3-1.fc40.x86_64 libacl-2.3.2-1.fc40.x86_64 libarchive-3.7.2-4.fc40.x86_64 libattr-2.5.2-3.fc40.x86_64 libblkid-2.40.1-1.fc40.x86_64 libbrotli-1.1.0-3.fc40.x86_64 libcap-2.69-8.fc40.x86_64 libcap-ng-0.8.4-4.fc40.x86_64 libcom_err-1.47.0-5.fc40.x86_64 libcurl-8.6.0-10.fc40.x86_64 libeconf-0.6.2-2.fc40.x86_64 libevent-2.1.12-12.fc40.x86_64 libfdisk-2.40.1-1.fc40.x86_64 libffi-3.4.4-7.fc40.x86_64 libgcc-14.2.1-3.fc40.x86_64 libgomp-14.2.1-3.fc40.x86_64 libidn2-2.3.7-1.fc40.x86_64 libmount-2.40.1-1.fc40.x86_64 libnghttp2-1.59.0-3.fc40.x86_64 libnsl2-2.0.1-1.fc40.x86_64 libpkgconf-2.1.1-2.fc40.x86_64 libpsl-0.21.5-3.fc40.x86_64 libpwquality-1.4.5-9.fc40.x86_64 libselinux-3.6-4.fc40.x86_64 libsemanage-3.6-3.fc40.x86_64 libsepol-3.6-3.fc40.x86_64 libsmartcols-2.40.1-1.fc40.x86_64 libssh-0.10.6-5.fc40.x86_64 libssh-config-0.10.6-5.fc40.noarch libstdc++-14.2.1-3.fc40.x86_64 libtasn1-4.19.0-6.fc40.x86_64 libtirpc-1.3.5-0.fc40.x86_64 libtool-ltdl-2.4.7-10.fc40.x86_64 libunistring-1.1-7.fc40.x86_64 libutempter-1.2.1-13.fc40.x86_64 libuuid-2.40.1-1.fc40.x86_64 libverto-0.3.2-8.fc40.x86_64 libxcrypt-4.4.36-5.fc40.x86_64 libxml2-2.12.8-1.fc40.x86_64 libzstd-1.5.6-1.fc40.x86_64 lua-libs-5.4.6-5.fc40.x86_64 lua-srpm-macros-1-13.fc40.noarch lz4-libs-1.9.4-6.fc40.x86_64 mpfr-4.2.1-4.fc40.x86_64 ncurses-base-6.4-12.20240127.fc40.noarch ncurses-libs-6.4-12.20240127.fc40.x86_64 ocaml-srpm-macros-9-3.fc40.noarch openblas-srpm-macros-2-16.fc40.noarch openldap-2.6.7-1.fc40.x86_64 openssl-libs-3.2.2-3.fc40.x86_64 p11-kit-0.25.5-1.fc40.x86_64 p11-kit-trust-0.25.5-1.fc40.x86_64 package-notes-srpm-macros-0.5-11.fc40.noarch pam-1.6.1-3.fc40.x86_64 pam-libs-1.6.1-3.fc40.x86_64 patch-2.7.6-24.fc40.x86_64 pcre2-10.44-1.fc40.x86_64 pcre2-syntax-10.44-1.fc40.noarch perl-srpm-macros-1-53.fc40.noarch pkgconf-2.1.1-2.fc40.x86_64 pkgconf-m4-2.1.1-2.fc40.noarch pkgconf-pkg-config-2.1.1-2.fc40.x86_64 popt-1.19-6.fc40.x86_64 publicsuffix-list-dafsa-20240107-3.fc40.noarch pyproject-srpm-macros-1.13.0-1.fc40.noarch python-srpm-macros-3.12-8.fc40.noarch qt5-srpm-macros-5.15.15-1.fc40.noarch qt6-srpm-macros-6.7.2-2.fc40.noarch readline-8.2-8.fc40.x86_64 redhat-rpm-config-288-1.fc40.noarch rpm-4.19.1.1-1.fc40.x86_64 rpm-build-4.19.1.1-1.fc40.x86_64 rpm-build-libs-4.19.1.1-1.fc40.x86_64 rpm-libs-4.19.1.1-1.fc40.x86_64 rpm-sequoia-1.7.0-1.fc40.x86_64 rust-srpm-macros-26.3-1.fc40.noarch sed-4.9-1.fc40.x86_64 setup-2.14.5-2.fc40.noarch shadow-utils-4.15.1-3.fc40.x86_64 sqlite-libs-3.45.1-2.fc40.x86_64 systemd-libs-255.12-1.fc40.x86_64 tar-1.35-3.fc40.x86_64 unzip-6.0-63.fc40.x86_64 util-linux-2.40.1-1.fc40.x86_64 util-linux-core-2.40.1-1.fc40.x86_64 which-2.21-41.fc40.x86_64 xxhash-libs-0.8.2-2.fc40.x86_64 xz-5.4.6-3.fc40.x86_64 xz-libs-5.4.6-3.fc40.x86_64 zig-srpm-macros-1-2.fc40.noarch zip-3.0-40.fc40.x86_64 zlib-ng-compat-2.1.7-2.fc40.x86_64 zstd-1.5.6-1.fc40.x86_64 Start: buildsrpm Start: rpmbuild -bs Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1727049600 Wrote: /builddir/build/SRPMS/star-2.7.11b-1.fc40.src.rpm Finish: rpmbuild -bs cp: preserving permissions for ‘/var/lib/copr-rpmbuild/results/chroot_scan/var/lib/mock/fedora-40-x86_64-1727101652.169710/root/var/log’: No such file or directory INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-40-x86_64-1727101652.169710/root/var/log/dnf5.log Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-jriai2_s/star/star.spec) Config(child) 1 minutes 54 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/star-2.7.11b-1.fc40.src.rpm) Config(fedora-40-x86_64) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-40-x86_64-bootstrap-1727101652.169710/root. INFO: reusing tmpfs at /var/lib/mock/fedora-40-x86_64-bootstrap-1727101652.169710/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-40-x86_64-1727101652.169710/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-4.19.1.1-1.fc40.x86_64 rpm-sequoia-1.7.0-1.fc40.x86_64 python3-dnf-4.21.1-1.fc40.noarch yum-4.21.1-1.fc40.noarch dnf5-5.1.17-2.fc40.x86_64 dnf5-plugins-5.1.17-2.fc40.x86_64 Finish: chroot init Start: build phase for star-2.7.11b-1.fc40.src.rpm Start: build setup for star-2.7.11b-1.fc40.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1727049600 Wrote: /builddir/build/SRPMS/star-2.7.11b-1.fc40.src.rpm Updating and loading repositories: updates 100% | 646.7 KiB/s | 24.6 KiB | 00m00s fedora 100% | 388.0 KiB/s | 30.7 KiB | 00m00s Copr repository 100% | 52.3 KiB/s | 1.5 KiB | 00m00s Repositories loaded. Package Arch Version Repository Size Installing: gcc-c++ x86_64 14.2.1-3.fc40 updates 38.2 MiB make x86_64 1:4.4.1-6.fc40 fedora 1.8 MiB xxd x86_64 2:9.1.719-1.fc40 updates 41.1 KiB zlib-ng-compat-devel x86_64 2.1.7-2.fc40 updates 106.8 KiB Installing dependencies: annobin-docs noarch 12.60-1.fc40 updates 96.2 KiB annobin-plugin-gcc x86_64 12.60-1.fc40 updates 976.2 KiB cmake-filesystem x86_64 3.28.2-1.fc40 fedora 0.0 B cpp x86_64 14.2.1-3.fc40 updates 35.0 MiB gc x86_64 8.2.2-6.fc40 fedora 258.7 KiB gcc x86_64 14.2.1-3.fc40 updates 104.3 MiB gcc-plugin-annobin x86_64 14.2.1-3.fc40 updates 57.1 KiB glibc-devel x86_64 2.39-22.fc40 updates 35.8 KiB glibc-headers-x86 noarch 2.39-22.fc40 updates 2.2 MiB guile30 x86_64 3.0.7-12.fc40 fedora 51.5 MiB kernel-headers x86_64 6.10.3-200.fc40 updates 6.3 MiB libmpc x86_64 1.3.1-5.fc40 fedora 164.7 KiB libstdc++-devel x86_64 14.2.1-3.fc40 updates 15.4 MiB libxcrypt-devel x86_64 4.4.36-5.fc40 fedora 30.3 KiB Transaction Summary: Installing: 18 packages Total size of inbound packages is 78 MiB. Need to download 78 MiB. After this operation 256 MiB will be used (install 256 MiB, remove 0 B). [ 1/18] make-1:4.4.1-6.fc40.x86_64 100% | 3.4 MiB/s | 587.6 KiB | 00m00s [ 2/18] xxd-2:9.1.719-1.fc40.x86_64 100% | 119.3 KiB/s | 36.2 KiB | 00m00s [ 3/18] zlib-ng-compat-devel-0:2.1.7-2. 100% | 114.3 KiB/s | 37.9 KiB | 00m00s [ 4/18] gcc-c++-0:14.2.1-3.fc40.x86_64 100% | 22.8 MiB/s | 14.2 MiB | 00m01s [ 5/18] libmpc-0:1.3.1-5.fc40.x86_64 100% | 756.8 KiB/s | 71.1 KiB | 00m00s [ 6/18] cmake-filesystem-0:3.28.2-1.fc4 100% | 923.0 KiB/s | 17.5 KiB | 00m00s [ 7/18] gc-0:8.2.2-6.fc40.x86_64 100% | 3.1 MiB/s | 110.2 KiB | 00m00s [ 8/18] cpp-0:14.2.1-3.fc40.x86_64 100% | 46.0 MiB/s | 12.0 MiB | 00m00s [ 9/18] gcc-plugin-annobin-0:14.2.1-3.f 100% | 2.4 MiB/s | 55.1 KiB | 00m00s [10/18] libstdc++-devel-0:14.2.1-3.fc40 100% | 30.9 MiB/s | 2.8 MiB | 00m00s [11/18] annobin-plugin-gcc-0:12.60-1.fc 100% | 26.2 MiB/s | 966.0 KiB | 00m00s [12/18] annobin-docs-0:12.60-1.fc40.noa 100% | 3.5 MiB/s | 89.5 KiB | 00m00s [13/18] glibc-devel-0:2.39-22.fc40.x86_ 100% | 4.9 MiB/s | 115.6 KiB | 00m00s [14/18] glibc-headers-x86-0:2.39-22.fc4 100% | 19.8 MiB/s | 609.6 KiB | 00m00s [15/18] libxcrypt-devel-0:4.4.36-5.fc40 100% | 1.9 MiB/s | 28.6 KiB | 00m00s [16/18] kernel-headers-0:6.10.3-200.fc4 100% | 35.6 MiB/s | 1.6 MiB | 00m00s [17/18] gcc-0:14.2.1-3.fc40.x86_64 100% | 35.4 MiB/s | 37.0 MiB | 00m01s [18/18] guile30-0:3.0.7-12.fc40.x86_64 100% | 3.1 MiB/s | 8.1 MiB | 00m03s -------------------------------------------------------------------------------- [18/18] Total 100% | 26.1 MiB/s | 78.3 MiB | 00m03s Running transaction [ 1/20] Verify package files 100% | 71.0 B/s | 18.0 B | 00m00s [ 2/20] Prepare transaction 100% | 400.0 B/s | 18.0 B | 00m00s [ 3/20] Installing libmpc-0:1.3.1-5.fc4 100% | 81.2 MiB/s | 166.2 KiB | 00m00s [ 4/20] Installing cpp-0:14.2.1-3.fc40. 100% | 294.1 MiB/s | 35.0 MiB | 00m00s [ 5/20] Installing kernel-headers-0:6.1 100% | 115.2 MiB/s | 6.4 MiB | 00m00s [ 6/20] Installing glibc-headers-x86-0: 100% | 98.1 MiB/s | 2.3 MiB | 00m00s [ 7/20] Installing libxcrypt-devel-0:4. 100% | 15.9 MiB/s | 32.6 KiB | 00m00s [ 8/20] Installing glibc-devel-0:2.39-2 100% | 19.2 MiB/s | 39.3 KiB | 00m00s [ 9/20] Installing annobin-docs-0:12.60 100% | 31.7 MiB/s | 97.4 KiB | 00m00s [10/20] Installing libstdc++-devel-0:14 100% | 219.1 MiB/s | 15.6 MiB | 00m00s [11/20] Installing gc-0:8.2.2-6.fc40.x8 100% | 63.8 MiB/s | 261.2 KiB | 00m00s [12/20] Installing guile30-0:3.0.7-12.f 100% | 320.4 MiB/s | 51.6 MiB | 00m00s [13/20] Installing make-1:4.4.1-6.fc40. 100% | 180.0 MiB/s | 1.8 MiB | 00m00s [14/20] Installing gcc-0:14.2.1-3.fc40. 100% | 316.3 MiB/s | 104.4 MiB | 00m00s >>> Running trigger-install scriptlet: redhat-rpm-config-0:288-1.fc40.noarch >>> Stop trigger-install scriptlet: redhat-rpm-config-0:288-1.fc40.noarch [15/20] Installing cmake-filesystem-0:3 100% | 2.3 MiB/s | 7.1 KiB | 00m00s [16/20] Installing zlib-ng-compat-devel 100% | 105.8 MiB/s | 108.3 KiB | 00m00s [17/20] Installing gcc-c++-0:14.2.1-3.f 100% | 307.8 MiB/s | 38.2 MiB | 00m00s [18/20] Installing gcc-plugin-annobin-0 100% | 2.7 MiB/s | 58.6 KiB | 00m00s >>> Running trigger-install scriptlet: redhat-rpm-config-0:288-1.fc40.noarch >>> Stop trigger-install scriptlet: redhat-rpm-config-0:288-1.fc40.noarch [19/20] Installing annobin-plugin-gcc-0 100% | 38.2 MiB/s | 977.9 KiB | 00m00s >>> Running trigger-install scriptlet: redhat-rpm-config-0:288-1.fc40.noarch >>> Stop trigger-install scriptlet: redhat-rpm-config-0:288-1.fc40.noarch [20/20] Installing xxd-2:9.1.719-1.fc40 100% | 265.5 KiB/s | 42.2 KiB | 00m00s >>> Running trigger-install scriptlet: glibc-common-0:2.39-22.fc40.x86_64 >>> Stop trigger-install scriptlet: glibc-common-0:2.39-22.fc40.x86_64 >>> Running trigger-install scriptlet: info-0:7.1-2.fc40.x86_64 >>> Stop trigger-install scriptlet: info-0:7.1-2.fc40.x86_64 Finish: build setup for star-2.7.11b-1.fc40.src.rpm Start: rpmbuild star-2.7.11b-1.fc40.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1727049600 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.roS5Nj + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf STAR-2.7.11b/source + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/2.7.11b.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + cd STAR-2.7.11b/source + rm -rf /builddir/build/BUILD/STAR-2.7.11b/source-SPECPARTS + /usr/bin/mkdir -p /builddir/build/BUILD/STAR-2.7.11b/source-SPECPARTS + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.yrBmfy + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd STAR-2.7.11b/source + /usr/bin/make -O -j2 V=1 VERBOSE=1 /usr/bin/make -C htslib lib-static xxd -i parametersDefault > parametersDefault.xxd make[1]: Entering directory '/builddir/build/BUILD/STAR-2.7.11b/source/htslib' gcc -g -Wall -O2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -DSAMTOOLS=1 -c -o kfunc.o kfunc.c make[1]: Leaving directory '/builddir/build/BUILD/STAR-2.7.11b/source/htslib' make[1]: Entering directory '/builddir/build/BUILD/STAR-2.7.11b/source/htslib' gcc -g -Wall -O2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -DSAMTOOLS=1 -c -o knetfile.o knetfile.c make[1]: Leaving directory '/builddir/build/BUILD/STAR-2.7.11b/source/htslib' make[1]: Entering directory '/builddir/build/BUILD/STAR-2.7.11b/source/htslib' gcc -g -Wall -O2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -DSAMTOOLS=1 -c -o kstring.o kstring.c make[1]: Leaving directory '/builddir/build/BUILD/STAR-2.7.11b/source/htslib' make[1]: Entering directory '/builddir/build/BUILD/STAR-2.7.11b/source/htslib' gcc -g -Wall -O2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -DSAMTOOLS=1 -c -o faidx.o faidx.c make[1]: Leaving directory '/builddir/build/BUILD/STAR-2.7.11b/source/htslib' faidx.c: In function ‘fai_load’: faidx.c:265:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 265 | else | ^~~~ faidx.c:268:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 268 | if (fp == 0) { | ^~ make[1]: Entering directory '/builddir/build/BUILD/STAR-2.7.11b/source/htslib' gcc -g -Wall -O2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -DSAMTOOLS=1 -c -o bgzf.o bgzf.c make[1]: Leaving directory '/builddir/build/BUILD/STAR-2.7.11b/source/htslib' bgzf.c: In function ‘bgzf_write’: bgzf.c:733:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 733 | if ( !fp->is_compressed ) | ^~ bgzf.c:736:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 736 | const uint8_t *input = (const uint8_t*)data; | ^~~~~ make[1]: Entering directory '/builddir/build/BUILD/STAR-2.7.11b/source/htslib' gcc -g -Wall -O2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -DSAMTOOLS=1 -c -o hfile_net.o hfile_net.c make[1]: Leaving directory '/builddir/build/BUILD/STAR-2.7.11b/source/htslib' make[1]: Entering directory '/builddir/build/BUILD/STAR-2.7.11b/source/htslib' echo '#define HTS_VERSION "0.0.1"' > version.h make[1]: Leaving directory '/builddir/build/BUILD/STAR-2.7.11b/source/htslib' make[1]: Entering directory '/builddir/build/BUILD/STAR-2.7.11b/source/htslib' gcc -g -Wall -O2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -DSAMTOOLS=1 -c -o hfile.o hfile.c make[1]: Leaving directory '/builddir/build/BUILD/STAR-2.7.11b/source/htslib' make[1]: Entering directory '/builddir/build/BUILD/STAR-2.7.11b/source/htslib' gcc -g -Wall -O2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -DSAMTOOLS=1 -c -o synced_bcf_reader.o synced_bcf_reader.c make[1]: Leaving directory '/builddir/build/BUILD/STAR-2.7.11b/source/htslib' make[1]: Entering directory '/builddir/build/BUILD/STAR-2.7.11b/source/htslib' gcc -g -Wall -O2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -DSAMTOOLS=1 -c -o vcf_sweep.o vcf_sweep.c make[1]: Leaving directory '/builddir/build/BUILD/STAR-2.7.11b/source/htslib' make[1]: Entering directory '/builddir/build/BUILD/STAR-2.7.11b/source/htslib' gcc -g -Wall -O2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -DSAMTOOLS=1 -c -o tbx.o tbx.c make[1]: Leaving directory '/builddir/build/BUILD/STAR-2.7.11b/source/htslib' tbx.c: In function ‘tbx_seqnames’: tbx.c:285:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 285 | for (tid=0; tidnext = t); | ^ cram/sam_header.c: In function ‘sam_hdr_vadd’: cram/sam_header.c:449:16: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 449 | assert(p->next = t); | ^ make[1]: Entering directory '/builddir/build/BUILD/STAR-2.7.11b/source/htslib' gcc -g -Wall -O2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -DSAMTOOLS=1 -c -o hts.o hts.c make[1]: Leaving directory '/builddir/build/BUILD/STAR-2.7.11b/source/htslib' make[1]: Entering directory '/builddir/build/BUILD/STAR-2.7.11b/source/htslib' ar -rc libhts.a kfunc.o knetfile.o kstring.o bgzf.o faidx.o hfile.o hfile_net.o hts.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/md5.o cram/open_trace_file.o cram/pooled_alloc.o cram/sam_header.o cram/string_alloc.o cram/thread_pool.o cram/vlen.o cram/zfio.o ranlib libhts.a make[1]: Leaving directory '/builddir/build/BUILD/STAR-2.7.11b/source/htslib' echo BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp funPrimaryAlignMark.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp systemFunctions.cpp twoPassRunPass1.cpp bam_cat.c BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp funPrimaryAlignMark.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp systemFunctions.cpp twoPassRunPass1.cpp bam_cat.c 'rm' -f ./Depend.list g++ -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -MM BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp funPrimaryAlignMark.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp systemFunctions.cpp twoPassRunPass1.cpp bam_cat.c parametersDefault.xxd htslib >> Depend.list g++: warning: parametersDefault.xxd: linker input file unused because linking not done g++: warning: htslib: linker input file unused because linking not done 'rm' -f STAR.o Parameters.o g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer systemFunctions.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer funPrimaryAlignMark.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer SoloFeature_collapseUMI_Graph.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ParametersClip_initialize.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer SoloFeature_collapseUMIall.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ClipCR4.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ClipMate_clip.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ClipMate_clipChunk.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ClipMate_initialize.cpp cd opal && \ g++ -c -I./ -std=c++11 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -mavx2 opal.cpp In file included from /usr/lib/gcc/x86_64-redhat-linux/14/include/immintrin.h:43, from ./simde_avx2.h:3556, from opal.cpp:10: In function ‘_mm256_store_si256’, inlined from ‘searchDatabase_, 0>(unsigned char*, int, unsigned char**, int, int*, int, int, int*, int, OpalSearchResult**, int, bool*, int)int’ at opal.cpp:854:28: /usr/lib/gcc/x86_64-redhat-linux/14/include/avxintrin.h:923:8: warning: ‘H’ may be used uninitialized [-Wmaybe-uninitialized] 923 | *__P = __A; | ~~~~~^~~~~ opal.cpp: In function ‘searchDatabase_, 0>(unsigned char*, int, unsigned char**, int, int*, int, int, int*, int, OpalSearchResult**, int, bool*, int)int’: opal.cpp:739:17: note: ‘H’ was declared here 739 | __mxxxi H; | ^ In file included from /usr/lib/gcc/x86_64-redhat-linux/14/include/immintrin.h:53: In function ‘_mm256_max_epi8’, inlined from ‘Simd::max(long long __vector(4) const&, long long __vector(4) const&)’ at opal.cpp:561:91, inlined from ‘searchDatabase_, 1>(unsigned char*, int, unsigned char**, int, int*, int, int, int*, int, OpalSearchResult**, int, bool*, int)int’ at opal.cpp:776:32: /usr/lib/gcc/x86_64-redhat-linux/14/include/avx2intrin.h:351:44: warning: ‘H’ may be used uninitialized [-Wmaybe-uninitialized] 351 | return (__m256i)__builtin_ia32_pmaxsb256 ((__v32qi)__A, (__v32qi)__B); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ opal.cpp: In function ‘searchDatabase_, 1>(unsigned char*, int, unsigned char**, int, int*, int, int, int*, int, OpalSearchResult**, int, bool*, int)int’: opal.cpp:739:17: note: ‘H’ was declared here 739 | __mxxxi H; | ^ In function ‘_mm256_max_epi8’, inlined from ‘Simd::max(long long __vector(4) const&, long long __vector(4) const&)’ at opal.cpp:561:91, inlined from ‘searchDatabase_, 2>(unsigned char*, int, unsigned char**, int, int*, int, int, int*, int, OpalSearchResult**, int, bool*, int)int’ at opal.cpp:776:32: /usr/lib/gcc/x86_64-redhat-linux/14/include/avx2intrin.h:351:44: warning: ‘H’ may be used uninitialized [-Wmaybe-uninitialized] 351 | return (__m256i)__builtin_ia32_pmaxsb256 ((__v32qi)__A, (__v32qi)__B); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ opal.cpp: In function ‘searchDatabase_, 2>(unsigned char*, int, unsigned char**, int, int*, int, int, int*, int, OpalSearchResult**, int, bool*, int)int’: opal.cpp:739:17: note: ‘H’ was declared here 739 | __mxxxi H; | ^ In function ‘_mm256_store_si256’, inlined from ‘searchDatabase_, 0>(unsigned char*, int, unsigned char**, int, int*, int, int, int*, int, OpalSearchResult**, int, bool*, int)int’ at opal.cpp:854:28: /usr/lib/gcc/x86_64-redhat-linux/14/include/avxintrin.h:923:8: warning: ‘H’ may be used uninitialized [-Wmaybe-uninitialized] 923 | *__P = __A; | ~~~~~^~~~~ opal.cpp: In function ‘searchDatabase_, 0>(unsigned char*, int, unsigned char**, int, int*, int, int, int*, int, OpalSearchResult**, int, bool*, int)int’: opal.cpp:739:17: note: ‘H’ was declared here 739 | __mxxxi H; | ^ In function ‘_mm256_max_epi16’, inlined from ‘Simd::max(long long __vector(4) const&, long long __vector(4) const&)’ at opal.cpp:574:92, inlined from ‘searchDatabase_, 1>(unsigned char*, int, unsigned char**, int, int*, int, int, int*, int, OpalSearchResult**, int, bool*, int)int’ at opal.cpp:776:32: /usr/lib/gcc/x86_64-redhat-linux/14/include/avx2intrin.h:358:44: warning: ‘H’ may be used uninitialized [-Wmaybe-uninitialized] 358 | return (__m256i)__builtin_ia32_pmaxsw256 ((__v16hi)__A, (__v16hi)__B); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ opal.cpp: In function ‘searchDatabase_, 1>(unsigned char*, int, unsigned char**, int, int*, int, int, int*, int, OpalSearchResult**, int, bool*, int)int’: opal.cpp:739:17: note: ‘H’ was declared here 739 | __mxxxi H; | ^ In function ‘_mm256_max_epi16’, inlined from ‘Simd::max(long long __vector(4) const&, long long __vector(4) const&)’ at opal.cpp:574:92, inlined from ‘searchDatabase_, 2>(unsigned char*, int, unsigned char**, int, int*, int, int, int*, int, OpalSearchResult**, int, bool*, int)int’ at opal.cpp:776:32: /usr/lib/gcc/x86_64-redhat-linux/14/include/avx2intrin.h:358:44: warning: ‘H’ may be used uninitialized [-Wmaybe-uninitialized] 358 | return (__m256i)__builtin_ia32_pmaxsw256 ((__v16hi)__A, (__v16hi)__B); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ opal.cpp: In function ‘searchDatabase_, 2>(unsigned char*, int, unsigned char**, int, int*, int, int, int*, int, OpalSearchResult**, int, bool*, int)int’: opal.cpp:739:17: note: ‘H’ was declared here 739 | __mxxxi H; | ^ In function ‘searchDatabase_, 0>(unsigned char*, int, unsigned char**, int, int*, int, int, int*, int, OpalSearchResult**, int, bool*, int)int’, inlined from ‘searchDatabase<0>(unsigned char*, int, unsigned char**, int, int*, int, int, int*, int, OpalSearchResult**, int, bool*, int)int’ at opal.cpp:1013:21, inlined from ‘opalSearchDatabase’ at opal.cpp:1457:46: opal.cpp:861:35: warning: ‘overflowed’ may be used uninitialized [-Wmaybe-uninitialized] 861 | if (overflowed[i] || currDbSeqsLengths[i] == 0) { // If sequence ended | ~~~~~~~~~~^ opal.cpp: In function ‘opalSearchDatabase’: opal.cpp:794:14: note: ‘overflowed’ declared here 794 | bool overflowed[SIMD::numSeqs]; | ^~~~~~~~~~ In function ‘_mm256_max_epi32’, inlined from ‘Simd::max(long long __vector(4) const&, long long __vector(4) const&)’ at opal.cpp:587:92, inlined from ‘searchDatabase_, 1>(unsigned char*, int, unsigned char**, int, int*, int, int, int*, int, OpalSearchResult**, int, bool*, int)int’ at opal.cpp:776:32, inlined from ‘searchDatabase<1>(unsigned char*, int, unsigned char**, int, int*, int, int, int*, int, OpalSearchResult**, int, bool*, int)int’ at opal.cpp:1013:21, inlined from ‘opalSearchDatabase’ at opal.cpp:1461:46: /usr/lib/gcc/x86_64-redhat-linux/14/include/avx2intrin.h:365:44: warning: ‘H’ may be used uninitialized [-Wmaybe-uninitialized] 365 | return (__m256i)__builtin_ia32_pmaxsd256 ((__v8si)__A, (__v8si)__B); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ opal.cpp: In function ‘opalSearchDatabase’: opal.cpp:739:17: note: ‘H’ was declared here 739 | __mxxxi H; | ^ In function ‘searchDatabase_, 1>(unsigned char*, int, unsigned char**, int, int*, int, int, int*, int, OpalSearchResult**, int, bool*, int)int’, inlined from ‘searchDatabase<1>(unsigned char*, int, unsigned char**, int, int*, int, int, int*, int, OpalSearchResult**, int, bool*, int)int’ at opal.cpp:1013:21, inlined from ‘opalSearchDatabase’ at opal.cpp:1461:46: opal.cpp:830:57: warning: ‘overflowed’ may be used uninitialized [-Wmaybe-uninitialized] 830 | if (currDbSeqsPos[i] != 0 && !overflowed[i]) { // If not null sequence or overflowed | ~~~~~~~~~~^ opal.cpp: In function ‘opalSearchDatabase’: opal.cpp:794:14: note: ‘overflowed’ declared here 794 | bool overflowed[SIMD::numSeqs]; | ^~~~~~~~~~ In function ‘searchDatabase_, 1>(unsigned char*, int, unsigned char**, int, int*, int, int, int*, int, OpalSearchResult**, int, bool*, int)int’, inlined from ‘searchDatabase<1>(unsigned char*, int, unsigned char**, int, int*, int, int, int*, int, OpalSearchResult**, int, bool*, int)int’ at opal.cpp:1013:21, inlined from ‘opalSearchDatabase’ at opal.cpp:1461:46: opal.cpp:861:35: warning: ‘overflowed’ may be used uninitialized [-Wmaybe-uninitialized] 861 | if (overflowed[i] || currDbSeqsLengths[i] == 0) { // If sequence ended | ~~~~~~~~~~^ opal.cpp: In function ‘opalSearchDatabase’: opal.cpp:794:14: note: ‘overflowed’ declared here 794 | bool overflowed[SIMD::numSeqs]; | ^~~~~~~~~~ In function ‘_mm256_max_epi32’, inlined from ‘Simd::max(long long __vector(4) const&, long long __vector(4) const&)’ at opal.cpp:587:92, inlined from ‘searchDatabase_, 2>(unsigned char*, int, unsigned char**, int, int*, int, int, int*, int, OpalSearchResult**, int, bool*, int)int’ at opal.cpp:776:32, inlined from ‘searchDatabase<2>(unsigned char*, int, unsigned char**, int, int*, int, int, int*, int, OpalSearchResult**, int, bool*, int)int’ at opal.cpp:1013:21, inlined from ‘opalSearchDatabase’ at opal.cpp:1465:46: /usr/lib/gcc/x86_64-redhat-linux/14/include/avx2intrin.h:365:44: warning: ‘H’ may be used uninitialized [-Wmaybe-uninitialized] 365 | return (__m256i)__builtin_ia32_pmaxsd256 ((__v8si)__A, (__v8si)__B); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ opal.cpp: In function ‘opalSearchDatabase’: opal.cpp:739:17: note: ‘H’ was declared here 739 | __mxxxi H; | ^ In function ‘searchDatabase_, 2>(unsigned char*, int, unsigned char**, int, int*, int, int, int*, int, OpalSearchResult**, int, bool*, int)int’, inlined from ‘searchDatabase<2>(unsigned char*, int, unsigned char**, int, int*, int, int, int*, int, OpalSearchResult**, int, bool*, int)int’ at opal.cpp:1013:21, inlined from ‘opalSearchDatabase’ at opal.cpp:1465:46: opal.cpp:830:57: warning: ‘overflowed’ may be used uninitialized [-Wmaybe-uninitialized] 830 | if (currDbSeqsPos[i] != 0 && !overflowed[i]) { // If not null sequence or overflowed | ~~~~~~~~~~^ opal.cpp: In function ‘opalSearchDatabase’: opal.cpp:794:14: note: ‘overflowed’ declared here 794 | bool overflowed[SIMD::numSeqs]; | ^~~~~~~~~~ In function ‘searchDatabase_, 2>(unsigned char*, int, unsigned char**, int, int*, int, int, int*, int, OpalSearchResult**, int, bool*, int)int’, inlined from ‘searchDatabase<2>(unsigned char*, int, unsigned char**, int, int*, int, int, int*, int, OpalSearchResult**, int, bool*, int)int’ at opal.cpp:1013:21, inlined from ‘opalSearchDatabase’ at opal.cpp:1465:46: opal.cpp:861:35: warning: ‘overflowed’ may be used uninitialized [-Wmaybe-uninitialized] 861 | if (overflowed[i] || currDbSeqsLengths[i] == 0) { // If sequence ended | ~~~~~~~~~~^ opal.cpp: In function ‘opalSearchDatabase’: opal.cpp:794:14: note: ‘overflowed’ declared here 794 | bool overflowed[SIMD::numSeqs]; | ^~~~~~~~~~ In function ‘_mm256_store_si256’, inlined from ‘searchDatabase_, 0>(unsigned char*, int, unsigned char**, int, int*, int, int, int*, int, OpalSearchResult**, int, bool*, int)int’ at opal.cpp:854:28, inlined from ‘searchDatabase<0>(unsigned char*, int, unsigned char**, int, int*, int, int, int*, int, OpalSearchResult**, int, bool*, int)int’ at opal.cpp:1013:21, inlined from ‘opalSearchDatabase’ at opal.cpp:1457:46: /usr/lib/gcc/x86_64-redhat-linux/14/include/avxintrin.h:923:8: warning: ‘H’ may be used uninitialized [-Wmaybe-uninitialized] 923 | *__P = __A; | ~~~~~^~~~~ opal.cpp: In function ‘opalSearchDatabase’: opal.cpp:739:17: note: ‘H’ was declared here 739 | __mxxxi H; | ^ g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer SoloFeature_loadRawMatrix.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer soloInputFeatureUMI.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer SoloFeature_emptyDrops_CR.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer SoloFeature_countSmartSeq.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer SoloFeature_redistributeReadsByCB.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer SoloFeature_sumThreads.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer SoloFeature_quantTranscript.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer SoloFeature_countVelocyto.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer SoloFeature_countCBgeneUMI.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer Transcriptome_classifyAlign.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer SoloFeature_cellFiltering.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer SoloFeature_statsOutput.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer SoloBarcode.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer bamSortByCoordinate.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer SoloRead.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer SoloRead_record.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer SoloReadBarcode.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ParametersSolo.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer SoloBarcode_extractBarcode.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer SoloReadBarcode_getCBandUMI.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer SoloReadFeature.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer SoloReadFeature_record.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer SoloReadFeature_inputRecords.cpp SoloReadFeature_inputRecords.cpp: In member function ‘void SoloReadFeature::inputRecords(unsigned int**, unsigned int, std::vector&, std::vector&, SoloReadFlagClass&, std::vector&, std::vector&)’: SoloReadFeature_inputRecords.cpp:21:12: warning: unused variable ‘nReadsIn’ [-Wunused-variable] 21 | uint64 nReadsIn = 0; | ^~~~~~~~ g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer Solo.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer SoloFeature.cpp In file included from SoloFeature.cpp:1: SoloFeature.h: In constructor ‘SoloFeature::SoloFeature(Parameters&, ReadAlignChunk**, Transcriptome&, int, SoloReadBarcode*, SoloFeature**)’: SoloFeature.h:36:17: warning: ‘SoloFeature::featureType’ will be initialized after [-Wreorder] 36 | const int32 featureType; | ^~~~~~~~~~~ SoloFeature.h:24:19: warning: ‘SoloFeature** SoloFeature::soloFeatAll’ [-Wreorder] 24 | SoloFeature **soloFeatAll; | ^~~~~~~~~~~ SoloFeature.cpp:4:1: warning: when initialized here [-Wreorder] 4 | SoloFeature::SoloFeature(Parameters &Pin, ReadAlignChunk **RAchunk, Transcriptome &inTrans, int32 feTy, SoloReadBarcode *readBarSumIn, SoloFeature **soloFeatAll) | ^~~~~~~~~~~ g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer SoloFeature_processRecords.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer SoloFeature_outputResults.cpp SoloFeature_outputResults.cpp: In member function ‘void SoloFeature::outputResults(bool, std::string)’: SoloFeature_outputResults.cpp:51:23: warning: ignoring return value of ‘char* getcwd(char*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 51 | getcwd(cwd,4096); | ~~~~~~^~~~~~~~~~ g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer SoloFeature_addBAMtags.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ReadAlign_transformGenome.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer Transcript_convertGenomeCigar.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer Genome_transformGenome.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer twoPassRunPass1.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer samHeaders.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer Genome_genomeLoad.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer Genome_genomeOutLoad.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer Transcript_transformGenome.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ReadAlign_outputSpliceGraphSAM.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ReadAlign_mapOneReadSpliceGraph.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer SpliceGraph.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer SpliceGraph_swTraceBack.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer SpliceGraph_swScoreSpliced.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer sjAlignSplit.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer SpliceGraph_findSuperTr.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer GTF_transcriptGeneSJ.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer GTF.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer SuperTranscriptome.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer GTF_superTranscript.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ReadAlign_outputAlignments.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ReadAlign.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer SharedMemory.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer PackedArray.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer SuffixArrayFuns.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer STAR.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer Parameters_samAttributes.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer InOutStreams.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer SequenceFuns.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer Genome.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ParametersGenome.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer Stats.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer Parameters.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer Transcript.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer Transcript_alignScore.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer Transcript_generateCigarP.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer Transcript_variationAdjust.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer Chain.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ReadAlign_waspMap.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer Variation.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ReadAlign_storeAligns.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ReadAlign_stitchPieces.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ReadAlign_multMapSelect.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ReadAlign_mapOneRead.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer readLoad.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ReadAlignChunk.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ReadAlignChunk_processChunks.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ReadAlignChunk_mapChunk.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer OutSJ.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer outputSJ.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer blocksOverlap.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer sysRemoveDir.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ThreadControl.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer binarySearch2.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ReadAlign_maxMappableLength2strands.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ReadAlign_outputTranscriptSJ.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ReadAlign_outputTranscriptSAM.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ReadAlign_outputTranscriptCIGARp.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ReadAlign_createExtendWindowsWithAlign.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ReadAlign_assignAlignToWindow.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ReadAlign_oneRead.cpp ReadAlign_oneRead.cpp: In member function ‘ReadAlign::oneRead()’: ReadAlign_oneRead.cpp:23:21: warning: ‘(*readStatus.0_153)[0]’ may be used uninitialized [-Wmaybe-uninitialized] 23 | if (readStatus[0]==-1) {//finished with the stream | ~~~~~~~~~~~~^ g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ReadAlign_stitchWindowSeeds.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ReadAlign_peOverlapMergeMap.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ReadAlign_mappedFilter.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ParametersChimeric_initialize.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ReadAlign_chimericDetection.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ReadAlign_chimericDetectionOldOutput.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ReadAlign_chimericDetectionOld.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ChimericDetection.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ChimericDetection_chimericDetectionMult.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ReadAlign_chimericDetectionPEmerged.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer extendAlign.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer stitchWindowAligns.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer stitchAlignToTranscript.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ChimericAlign_chimericJunctionOutput.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ChimericAlign_chimericStitching.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ChimericAlign_chimericBAMoutput.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer genomeParametersWrite.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer genomeScanFastaFiles.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer Genome_genomeGenerate.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer genomeSAindex.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer Genome_insertSequences.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer funCompareUintAndSuffixes.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer funCompareUintAndSuffixesMemcmp.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer TimeFunctions.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer insertSeqSA.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ErrorWarning.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer stringSubstituteAll.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer streamFuns.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer Transcriptome_quantAlign.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer Transcriptome.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer Transcriptome_geneFullAlignOverlap.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer Quantifications.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ReadAlign_quantTranscriptome.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer Transcriptome_geneCountsAddAlign.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer sjdbLoadFromFiles.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer sjdbLoadFromStream.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer sjdbPrepare.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer sjdbBuildIndex.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer mapThreadsSpawn.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer sjdbInsertJunctions.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer Parameters_readSAMheader.cpp Parameters_readSAMheader.cpp: In member function ‘void Parameters::readSAMheader(std::string, std::vector >)’: Parameters_readSAMheader.cpp:32:15: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 32 | system(com1.c_str()); | ~~~~~~^~~~~~~~~~~~~~ g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer Parameters_readFilesInit.cpp g++ -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer bam_cat.c g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer serviceFuns.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer BAMfunctions.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer BAMoutput.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer BAMbinSortByCoordinate.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ReadAlign_alignBAM.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer signalFromBAM.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer bamRemoveDuplicates.cpp g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer BAMbinSortUnmapped.cpp g++ -o STAR -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 e412c7496d704480b1b7ead5391d7e2f:/builddir/build/BUILD/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer systemFunctions.o funPrimaryAlignMark.o SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o SoloFeature_loadRawMatrix.o SoloFeature_emptyDrops_CR.o soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o SoloFeature_quantTranscript.o SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o Transcriptome_geneFullAlignOverlap_ExonOverIntron.o Transcriptome_alignExonOverlap.cpp SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -Lhtslib -Bstatic -lhts -Bdynamic -lz -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes In function ‘copy’, inlined from ‘__ct ’ at /usr/include/c++/14/bits/basic_string.h:688:23, inlined from ‘operator+’ at /usr/include/c++/14/bits/basic_string.h:3735:43, inlined from ‘redistributeReadsByCB’ at SoloFeature_redistributeReadsByCB.cpp:48:136, inlined from ‘countSmartSeq’ at SoloFeature_countSmartSeq.cpp:20:26: /usr/include/c++/14/bits/char_traits.h:427:56: warning: ‘__builtin_memcpy’ writing 39 bytes into a region of size 16 overflows the destination [-Wstringop-overflow=] 427 | return static_cast(__builtin_memcpy(__s1, __s2, __n)); | ^ SoloFeature_redistributeReadsByCB.cpp: In member function ‘countSmartSeq’: SoloFeature_redistributeReadsByCB.cpp:48:136: note: at offset 16 into destination object ‘’ of size 32 48 | redistrFilesStreams[ii] = &fstrOpen(P.outFileTmp + "solo"+SoloFeatureTypes::Names[featureType]+"_redistr_"+std::to_string(ii), ERROR_OUT, P, true); | ^ BAMbinSortUnmapped.cpp: In function ‘BAMbinSortUnmapped’: BAMbinSortUnmapped.cpp:30:59: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 30 | ifstream *bamInStream = new ifstream [bamInFile.size()]; | ^ /usr/include/c++/14/new:133:26: note: in a call to allocation function ‘operator new []’ declared here 133 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘copy’, inlined from ‘__ct ’ at /usr/include/c++/14/bits/basic_string.h:688:23, inlined from ‘operator+’ at /usr/include/c++/14/bits/basic_string.h:3735:43, inlined from ‘outputResults’ at SoloFeature_outputResults.cpp:104:62: /usr/include/c++/14/bits/char_traits.h:427:56: warning: ‘__builtin_memcpy’ writing 31 bytes into a region of size 16 overflows the destination [-Wstringop-overflow=] 427 | return static_cast(__builtin_memcpy(__s1, __s2, __n)); | ^ SoloFeature_outputResults.cpp: In member function ‘outputResults’: SoloFeature_outputResults.cpp:104:62: note: at offset 16 into destination object ‘’ of size 32 104 | ofstream &countMatrixStream=ofstrOpen(matrixFileName,ERROR_OUT, P); | ^ In function ‘copy’, inlined from ‘__ct ’ at /usr/include/c++/14/bits/basic_string.h:688:23, inlined from ‘operator+’ at /usr/include/c++/14/bits/basic_string.h:3735:43, inlined from ‘statsOutput’ at SoloFeature_statsOutput.cpp:8:60: /usr/include/c++/14/bits/char_traits.h:427:56: warning: ‘__builtin_memcpy’ writing 29 bytes into a region of size 16 overflows the destination [-Wstringop-overflow=] 427 | return static_cast(__builtin_memcpy(__s1, __s2, __n)); | ^ SoloFeature_statsOutput.cpp: In member function ‘statsOutput’: SoloFeature_statsOutput.cpp:8:60: note: at offset 16 into destination object ‘’ of size 32 8 | ofstream &strOut=ofstrOpen(outputPrefix+"Summary.csv", ERROR_OUT, P); | ^ In function ‘copy’, inlined from ‘__ct ’ at /usr/include/c++/14/bits/basic_string.h:688:23, inlined from ‘operator+’ at /usr/include/c++/14/bits/basic_string.h:3735:43, inlined from ‘statsOutput’ at SoloFeature_statsOutput.cpp:75:85: /usr/include/c++/14/bits/char_traits.h:427:56: warning: ‘__builtin_memcpy’ writing 29 bytes into a region of size 16 overflows the destination [-Wstringop-overflow=] 427 | return static_cast(__builtin_memcpy(__s1, __s2, __n)); | ^ SoloFeature_statsOutput.cpp: In member function ‘statsOutput’: SoloFeature_statsOutput.cpp:75:85: note: at offset 16 into destination object ‘’ of size 32 75 | ofstream &strOutUMIperCell = ofstrOpen(outputPrefix+"UMIperCellSorted.txt", ERROR_OUT, P); | ^ In function ‘copy’, inlined from ‘__ct ’ at /usr/include/c++/14/bits/basic_string.h:688:23, inlined from ‘operator+’ at /usr/include/c++/14/bits/basic_string.h:3735:43, inlined from ‘statsOutput’ at SoloFeature_statsOutput.cpp:89:68: /usr/include/c++/14/bits/char_traits.h:427:56: warning: ‘__builtin_memcpy’ writing 29 bytes into a region of size 16 overflows the destination [-Wstringop-overflow=] 427 | return static_cast(__builtin_memcpy(__s1, __s2, __n)); | ^ SoloFeature_statsOutput.cpp: In member function ‘statsOutput’: SoloFeature_statsOutput.cpp:89:68: note: at offset 16 into destination object ‘’ of size 32 89 | ofstream &strOut=ofstrOpen(outputPrefix+"CellReads.stats", ERROR_OUT, P); | ^ In function ‘copy’, inlined from ‘__ct ’ at /usr/include/c++/14/bits/basic_string.h:688:23, inlined from ‘operator+’ at /usr/include/c++/14/bits/basic_string.h:3735:43, inlined from ‘__ct_base ’ at SoloReadFeature.cpp:22:119: /usr/include/c++/14/bits/char_traits.h:427:56: warning: ‘__builtin_memcpy’ writing 21 bytes into a region of size 16 overflows the destination [-Wstringop-overflow=] 427 | return static_cast(__builtin_memcpy(__s1, __s2, __n)); | ^ SoloReadFeature.cpp: In member function ‘__ct_base ’: SoloReadFeature.cpp:22:119: note: at offset 16 into destination object ‘’ of size 32 22 | streamReads = &fstrOpen(P.outFileTmp+"/solo"+SoloFeatureTypes::Names[featureType]+'_'+std::to_string(iChunk), ERROR_OUT, P, false); | ^ In function ‘copy’, inlined from ‘__ct ’ at /usr/include/c++/14/bits/basic_string.h:688:23, inlined from ‘operator+’ at /usr/include/c++/14/bits/basic_string.h:3735:43, inlined from ‘processRecords’ at SoloFeature_processRecords.cpp:30:70, inlined from ‘processAndOutput’ at Solo.cpp:82:41: /usr/include/c++/14/bits/char_traits.h:427:56: warning: ‘__builtin_memcpy’ writing 32 bytes into a region of size 16 overflows the destination [-Wstringop-overflow=] 427 | return static_cast(__builtin_memcpy(__s1, __s2, __n)); | ^ SoloFeature_processRecords.cpp: In member function ‘processAndOutput’: SoloFeature_processRecords.cpp:30:70: note: at offset 16 into destination object ‘’ of size 32 30 | ifstream &sjIn = ifstrOpen(P.outFileTmp+"SJ.start_gap.tsv", ERROR_OUT, "SOLUTION: re-run STAR", P); | ^ In function ‘copy’, inlined from ‘__ct ’ at /usr/include/c++/14/bits/basic_string.h:688:23, inlined from ‘operator+’ at /usr/include/c++/14/bits/basic_string.h:3735:43, inlined from ‘processRecords’ at SoloFeature_processRecords.cpp:64:70, inlined from ‘processAndOutput’ at Solo.cpp:82:41: /usr/include/c++/14/bits/char_traits.h:427:56: warning: ‘__builtin_memcpy’ writing 32 bytes into a region of size 16 overflows the destination [-Wstringop-overflow=] 427 | return static_cast(__builtin_memcpy(__s1, __s2, __n)); | ^ SoloFeature_processRecords.cpp: In member function ‘processAndOutput’: SoloFeature_processRecords.cpp:64:70: note: at offset 16 into destination object ‘’ of size 32 64 | ofstream *statsStream = &ofstrOpen(outputPrefix+"Features.stats",ERROR_OUT, P); | ^ + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.zrmcOp + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/star-2.7.11b-1.fc40.x86_64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/star-2.7.11b-1.fc40.x86_64 ++ dirname /builddir/build/BUILDROOT/star-2.7.11b-1.fc40.x86_64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/star-2.7.11b-1.fc40.x86_64 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd STAR-2.7.11b/source + mkdir -p /builddir/build/BUILDROOT/star-2.7.11b-1.fc40.x86_64/usr/bin + install -p -m 755 STAR /builddir/build/BUILDROOT/star-2.7.11b-1.fc40.x86_64/usr/bin/STAR + /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 2.7.11b-1.fc40 --unique-debug-suffix -2.7.11b-1.fc40.x86_64 --unique-debug-src-base star-2.7.11b-1.fc40.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/STAR-2.7.11b/source find-debuginfo: starting Extracting debug info from 1 files DWARF-compressing 1 files sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match. Creating .debug symlinks for symlinks to ELF files Copying sources found by 'debugedit -l' to /usr/src/debug/star-2.7.11b-1.fc40.x86_64 4504 blocks find-debuginfo: done + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + /usr/lib/rpm/brp-compress + /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/check-rpaths + /usr/lib/rpm/redhat/brp-mangle-shebangs *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/ChimericDetection.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/ChimericDetection.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/GTF.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/GTF.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/GTF_superTranscript.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/GTF_transcriptGeneSJ.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/Genome.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/Genome.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/Genome_genomeGenerate.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/Genome_genomeLoad.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/Genome_genomeOutLoad.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/Genome_transformGenome.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/IncludeDefine.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/Parameters.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/Parameters.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/ParametersChimeric_initialize.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/ParametersGenome.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/ParametersSolo.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/ParametersSolo.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/ReadAlign.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/ReadAlign.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/ReadAlignChunk_processChunks.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/ReadAlign_mapOneReadSpliceGraph.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/ReadAlign_oneRead.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/ReadAlign_outputAlignments.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/ReadAlign_outputSpliceGraphSAM.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/ReadAlign_outputTranscriptSAM.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/ReadAlign_stitchPieces.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/ReadAlign_stitchWindowSeeds.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/ReadAlign_transformGenome.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/STAR.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/Solo.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/SoloBarcode_extractBarcode.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/SoloFeature.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/SoloFeature.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/SoloFeature_countCBgeneUMI.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/SoloFeature_processRecords.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/SoloFeature_quantTranscript.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/SoloRead.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/SoloRead.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/SoloReadBarcode.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/SoloReadBarcode_getCBandUMI.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/SoloReadFeature.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/SoloReadFeature.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/SoloReadFeature_inputRecords.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/SoloReadFeature_record.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/SoloRead_record.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/SpliceGraph.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/SpliceGraph.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/SpliceGraph_findSuperTr.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/SpliceGraph_swScoreSpliced.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/SpliceGraph_swTraceBack.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/SuperTranscriptome.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/SuperTranscriptome.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/Transcript.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/Transcript_convertGenomeCigar.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/Transcriptome.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/Transcriptome.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/Transcriptome_classifyAlign.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/Transcriptome_quantAlign.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/genomeParametersWrite.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/sjAlignSplit.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/sjAlignSplit.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/sjdbPrepare.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/stitchWindowAligns.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/star-2.7.11b-1.fc40.x86_64/stitchWindowAligns.h is executable but has no shebang, removing executable bit + /usr/lib/rpm/brp-remove-la-files + env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j2 + /usr/lib/rpm/redhat/brp-python-hardlink Processing files: star-2.7.11b-1.fc40.x86_64 Provides: star = 2.7.11b-1.fc40 star(x86-64) = 2.7.11b-1.fc40 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.15)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.2)(64bit) libc.so.6(GLIBC_2.3.3)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.38)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.7)(64bit) libc.so.6(GLIBC_ABI_DT_RELR)(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgcc_s.so.1(GCC_3.3.1)(64bit) libgomp.so.1()(64bit) libgomp.so.1(GOMP_1.0)(64bit) libgomp.so.1(GOMP_4.0)(64bit) libgomp.so.1(GOMP_4.5)(64bit) libgomp.so.1(OMP_1.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.29)(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.15)(64bit) libstdc++.so.6(CXXABI_1.3.5)(64bit) libstdc++.so.6(CXXABI_1.3.8)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.11)(64bit) libstdc++.so.6(GLIBCXX_3.4.18)(64bit) libstdc++.so.6(GLIBCXX_3.4.20)(64bit) libstdc++.so.6(GLIBCXX_3.4.21)(64bit) libstdc++.so.6(GLIBCXX_3.4.26)(64bit) libstdc++.so.6(GLIBCXX_3.4.29)(64bit) libstdc++.so.6(GLIBCXX_3.4.30)(64bit) libstdc++.so.6(GLIBCXX_3.4.32)(64bit) libstdc++.so.6(GLIBCXX_3.4.5)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) libz.so.1()(64bit) libz.so.1(ZLIB_1.2.0)(64bit) rtld(GNU_HASH) Processing files: star-debugsource-2.7.11b-1.fc40.x86_64 Provides: star-debugsource = 2.7.11b-1.fc40 star-debugsource(x86-64) = 2.7.11b-1.fc40 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: star-debuginfo-2.7.11b-1.fc40.x86_64 Provides: debuginfo(build-id) = ed415174beb4549a4ed539ec38277c0412fc26b1 star-debuginfo = 2.7.11b-1.fc40 star-debuginfo(x86-64) = 2.7.11b-1.fc40 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: star-debugsource(x86-64) = 2.7.11b-1.fc40 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/star-2.7.11b-1.fc40.x86_64 Wrote: /builddir/build/RPMS/star-debugsource-2.7.11b-1.fc40.x86_64.rpm Wrote: /builddir/build/RPMS/star-2.7.11b-1.fc40.x86_64.rpm Wrote: /builddir/build/RPMS/star-debuginfo-2.7.11b-1.fc40.x86_64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.beSocD + umask 022 + cd /builddir/build/BUILD + cd STAR-2.7.11b/source + /usr/bin/rm -rf /builddir/build/BUILDROOT/star-2.7.11b-1.fc40.x86_64 + RPM_EC=0 ++ jobs -p + exit 0 Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.XVjRRE + umask 022 + cd /builddir/build/BUILD + rm -rf /builddir/build/BUILD/STAR-2.7.11b/source-SPECPARTS + rm -rf STAR-2.7.11b/source STAR-2.7.11b/source.gemspec + RPM_EC=0 ++ jobs -p + exit 0 Finish: rpmbuild star-2.7.11b-1.fc40.src.rpm Finish: build phase for star-2.7.11b-1.fc40.src.rpm INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-40-x86_64-1727101652.169710/root/var/log/dnf5.log INFO: Done(/var/lib/copr-rpmbuild/results/star-2.7.11b-1.fc40.src.rpm) Config(child) 3 minutes 4 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": "star-debuginfo", "epoch": null, "version": "2.7.11b", "release": "1.fc40", "arch": "x86_64" }, { "name": "star-debugsource", "epoch": null, "version": "2.7.11b", "release": "1.fc40", "arch": "x86_64" }, { "name": "star", "epoch": null, "version": "2.7.11b", "release": "1.fc40", "arch": "x86_64" }, { "name": "star", "epoch": null, "version": "2.7.11b", "release": "1.fc40", "arch": "src" } ] } RPMResults finished