Warning: Permanently added '44.192.129.120' (ED25519) to the list of known hosts. 100 2781k 100 2781k 0 0 139M 0 --:--:-- --:--:-- --:--:-- 142M INFO: Reading stdout from command: md5sum 1.0.11.zip Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-6u3x11z7/mmseq/mmseq.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-6u3x11z7/mmseq --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1717082042.506309 -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-6u3x11z7/mmseq/mmseq.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-6u3x11z7/mmseq --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1717082042.506309 -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-6u3x11z7/mmseq/mmseq.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-1717082042.506309/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-1717082042.506309/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/9c26bea807e0618347302e3ce81d01e58a4d27697bfaf48437ae07f0c2535e7c/merged INFO: umounting image registry.fedoraproject.org/fedora:40 (/var/lib/containers/storage/overlay/9c26bea807e0618347302e3ce81d01e58a4d27697bfaf48437ae07f0c2535e7c/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 80 MB/s | 3.5 MB 00:00 Additional repo http_kojipkgs_fedoraproject_org 69 MB/s | 17 MB 00:00 fedora 28 MB/s | 20 MB 00:00 updates 17 MB/s | 6.7 MB 00:00 Dependencies resolved. =========================================================================================================== Package Arch Version Repository Size =========================================================================================================== Installing: dnf5 x86_64 5.2.2.0-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 692 k replacing dnf.noarch 4.19.2-1.fc40 replacing yum.noarch 4.19.2-1.fc40 dnf5-plugins x86_64 5.2.2.0-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 357 k Upgrading: dnf-data noarch 4.20.0-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 39 k python3-dnf noarch 4.20.0-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 580 k Installing dependencies: fmt x86_64 10.2.1-4.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 125 k libdnf5 x86_64 5.2.2.0-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.0 M libdnf5-cli x86_64 5.2.2.0-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 306 k sdbus-cpp x86_64 1.5.0-2.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 113 k Transaction Summary =========================================================================================================== Install 6 Packages Upgrade 2 Packages Total download size: 3.2 M Downloading Packages: (1/8): dnf5-plugins-5.2.2.0-1.fc41.x86_64.rpm 3.8 MB/s | 357 kB 00:00 (2/8): fmt-10.2.1-4.fc41.x86_64.rpm 1.0 MB/s | 125 kB 00:00 (3/8): libdnf5-5.2.2.0-1.fc41.x86_64.rpm 35 MB/s | 1.0 MB 00:00 (4/8): libdnf5-cli-5.2.2.0-1.fc41.x86_64.rpm 16 MB/s | 306 kB 00:00 (5/8): dnf-data-4.20.0-1.fc41.noarch.rpm 2.2 MB/s | 39 kB 00:00 (6/8): sdbus-cpp-1.5.0-2.fc41.x86_64.rpm 2.4 MB/s | 113 kB 00:00 (7/8): python3-dnf-4.20.0-1.fc41.noarch.rpm 30 MB/s | 580 kB 00:00 (8/8): dnf5-5.2.2.0-1.fc41.x86_64.rpm 3.4 MB/s | 692 kB 00:00 -------------------------------------------------------------------------------- Total 16 MB/s | 3.2 MB 00:00 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Installing : fmt-10.2.1-4.fc41.x86_64 1/12 Installing : libdnf5-5.2.2.0-1.fc41.x86_64 2/12 warning: /etc/dnf/dnf.conf created as /etc/dnf/dnf.conf.rpmnew Installing : libdnf5-cli-5.2.2.0-1.fc41.x86_64 3/12 Installing : sdbus-cpp-1.5.0-2.fc41.x86_64 4/12 Installing : dnf5-5.2.2.0-1.fc41.x86_64 5/12 Upgrading : dnf-data-4.20.0-1.fc41.noarch 6/12 Upgrading : python3-dnf-4.20.0-1.fc41.noarch 7/12 Installing : dnf5-plugins-5.2.2.0-1.fc41.x86_64 8/12 Obsoleting : yum-4.19.2-1.fc40.noarch 9/12 Running scriptlet: dnf-4.19.2-1.fc40.noarch 10/12 Obsoleting : dnf-4.19.2-1.fc40.noarch 10/12 warning: directory /var/cache/dnf: remove failed: Device or resource busy Running scriptlet: dnf-4.19.2-1.fc40.noarch 10/12 Cleanup : python3-dnf-4.19.2-1.fc40.noarch 11/12 Cleanup : dnf-data-4.19.2-1.fc40.noarch 12/12 Running scriptlet: dnf-data-4.19.2-1.fc40.noarch 12/12 Upgraded: dnf-data-4.20.0-1.fc41.noarch python3-dnf-4.20.0-1.fc41.noarch Installed: dnf5-5.2.2.0-1.fc41.x86_64 dnf5-plugins-5.2.2.0-1.fc41.x86_64 fmt-10.2.1-4.fc41.x86_64 libdnf5-5.2.2.0-1.fc41.x86_64 libdnf5-cli-5.2.2.0-1.fc41.x86_64 sdbus-cpp-1.5.0-2.fc41.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_64-1717082042.506309/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-1.6.0-3.fc40.x86_64 python3-dnf-4.20.0-1.fc41.noarch dnf5-5.2.2.0-1.fc41.x86_64 dnf5-plugins-5.2.2.0-1.fc41.x86_64 Start: installing minimal buildroot with dnf5 Updating and loading repositories: updates 100% | 18.2 MiB/s | 7.0 MiB | 00m00s fedora 100% | 29.1 MiB/s | 20.8 MiB | 00m01s Copr repository 100% | 66.4 MiB/s | 3.5 MiB | 00m00s Additional repo http_kojipkgs_fedorapr 100% | 50.0 MiB/s | 17.3 MiB | 00m00s Repositories loaded. Package Arch Version Repository Size Installing group/module packages: bash x86_64 5.2.26-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 8.1 MiB bzip2 x86_64 1.0.8-18.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 91.7 KiB coreutils x86_64 9.5-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 5.5 MiB cpio x86_64 2.15-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.1 MiB diffutils x86_64 3.10-5.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.6 MiB fedora-release-common noarch 41-0.13 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 19.2 KiB findutils x86_64 1:4.9.0-8.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.5 MiB gawk x86_64 5.3.0-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.7 MiB glibc-minimal-langpack x86_64 2.39.9000-18.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 0.0 B grep x86_64 3.11-8.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.0 MiB gzip x86_64 1.13-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 385.0 KiB info x86_64 7.1-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 357.8 KiB patch x86_64 2.7.6-24.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 262.8 KiB redhat-rpm-config noarch 291-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 183.5 KiB rpm-build x86_64 4.19.91-4.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 190.1 KiB sed x86_64 4.9-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 861.5 KiB shadow-utils x86_64 2:4.15.1-5.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 4.1 MiB tar x86_64 2:1.35-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 2.9 MiB unzip x86_64 6.0-63.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 382.8 KiB util-linux x86_64 2.40.1-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 3.7 MiB which x86_64 2.21-41.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 80.2 KiB xz x86_64 1:5.4.6-3.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 2.0 MiB Installing dependencies: add-determinism-nopython x86_64 0.2.0-9.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 2.5 MiB alternatives x86_64 1.27-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 66.3 KiB ansible-srpm-macros noarch 1-15.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 35.7 KiB audit-libs x86_64 4.0.1-2.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 327.3 KiB authselect x86_64 1.5.0-5.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 153.6 KiB authselect-libs x86_64 1.5.0-5.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 818.2 KiB basesystem noarch 11-20.fc40 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1.9.4-6.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 129.4 KiB mpfr x86_64 4.2.1-4.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 828.0 KiB ncurses-base noarch 6.4-12.20240127.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 326.2 KiB ncurses-libs x86_64 6.4-12.20240127.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 963.2 KiB ocaml-srpm-macros noarch 10-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.9 KiB openblas-srpm-macros noarch 2-17.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 112.0 B openldap x86_64 2.6.8-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 636.3 KiB openssl-libs x86_64 1:3.2.1-6.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 7.8 MiB p11-kit x86_64 0.25.3-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 2.2 MiB p11-kit-trust x86_64 0.25.3-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 391.4 KiB package-notes-srpm-macros noarch 0.5-11.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.6 KiB pam x86_64 1.6.1-3.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.8 MiB pam-libs x86_64 1.6.1-3.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 135.0 KiB pcre2 x86_64 10.43-2.fc41.1 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 653.5 KiB pcre2-syntax noarch 10.43-2.fc41.1 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 249.0 KiB perl-srpm-macros noarch 1-53.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 861.0 B pkgconf x86_64 2.1.1-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 82.9 KiB pkgconf-m4 noarch 2.1.1-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 13.9 KiB pkgconf-pkg-config x86_64 2.1.1-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 989.0 B popt x86_64 1.19-6.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 136.9 KiB publicsuffix-list-dafsa noarch 20240107-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 67.5 KiB pyproject-srpm-macros noarch 1.12.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.5 KiB python-srpm-macros noarch 3.12-9.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 50.5 KiB qt5-srpm-macros noarch 5.15.13-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 492.0 B qt6-srpm-macros noarch 6.7.1-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 456.0 B readline x86_64 8.2-8.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 489.2 KiB rpm x86_64 4.19.91-4.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 3.0 MiB rpm-build-libs x86_64 4.19.91-4.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 206.6 KiB rpm-libs x86_64 4.19.91-4.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 709.9 KiB rpm-sequoia x86_64 1.6.0-3.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 2.2 MiB rust-srpm-macros noarch 26.3-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 4.8 KiB setup noarch 2.15.0-3.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 720.7 KiB sqlite-libs x86_64 3.45.3-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.4 MiB systemd-libs x86_64 256~rc3-3.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 2.0 MiB util-linux-core x86_64 2.40.1-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.5 MiB xxhash-libs x86_64 0.8.2-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 88.5 KiB xz-libs x86_64 1:5.4.6-3.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 209.8 KiB zig-srpm-macros noarch 1-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.1 KiB zip x86_64 3.0-40.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 703.2 KiB zlib-ng-compat x86_64 2.1.6-4.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 134.0 KiB zstd x86_64 1.5.6-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.7 MiB Installing groups: Buildsystem building group Transaction Summary: Installing: 155 packages Total size of inbound packages is 53 MiB. Need to download 53 MiB. After this operation 182 MiB will be used (install 182 MiB, remove 0 B). [ 1/155] bzip2-0:1.0.8-18.fc40.x86_64 100% | 818.1 KiB/s | 52.4 KiB | 00m00s [ 2/155] cpio-0:2.15-1.fc40.x86_64 100% | 6.2 MiB/s | 285.1 KiB | 00m00s [ 3/155] bash-0:5.2.26-3.fc40.x86_64 100% | 15.3 MiB/s | 1.8 MiB | 00m00s [ 4/155] fedora-release-common-0:41-0. 100% | 1.1 MiB/s | 22.1 KiB | 00m00s [ 5/155] diffutils-0:3.10-5.fc40.x86_6 100% | 13.8 MiB/s | 396.8 KiB | 00m00s [ 6/155] findutils-1:4.9.0-8.fc40.x86_ 100% | 21.4 MiB/s | 482.5 KiB | 00m00s [ 7/155] gawk-0:5.3.0-3.fc40.x86_64 100% | 42.4 MiB/s | 1.1 MiB | 00m00s [ 8/155] coreutils-0:9.5-1.fc41.x86_64 100% | 6.5 MiB/s | 1.1 MiB | 00m00s [ 9/155] gzip-0:1.13-1.fc40.x86_64 100% | 10.7 MiB/s | 164.0 KiB | 00m00s [ 10/155] grep-0:3.11-8.fc41.x86_64 100% | 13.5 MiB/s | 289.2 KiB | 00m00s [ 11/155] glibc-minimal-langpack-0:2.39 100% | 3.9 MiB/s | 111.6 KiB | 00m00s [ 12/155] redhat-rpm-config-0:291-1.fc4 100% | 5.3 MiB/s | 75.5 KiB | 00m00s [ 13/155] info-0:7.1-2.fc40.x86_64 100% | 6.8 MiB/s | 182.3 KiB | 00m00s [ 14/155] patch-0:2.7.6-24.fc40.x86_64 100% | 5.5 MiB/s | 130.7 KiB | 00m00s [ 15/155] rpm-build-0:4.19.91-4.fc41.x8 100% | 3.6 MiB/s | 74.6 KiB | 00m00s [ 16/155] sed-0:4.9-1.fc40.x86_64 100% | 14.4 MiB/s | 309.2 KiB | 00m00s [ 17/155] shadow-utils-2:4.15.1-5.fc41. 100% | 38.2 MiB/s | 1.3 MiB | 00m00s [ 18/155] tar-2:1.35-3.fc40.x86_64 100% | 31.8 MiB/s | 847.4 KiB | 00m00s [ 19/155] unzip-0:6.0-63.fc40.x86_64 100% | 6.7 MiB/s | 184.5 KiB | 00m00s [ 20/155] util-linux-0:2.40.1-1.fc41.x8 100% | 48.2 MiB/s | 1.2 MiB | 00m00s [ 21/155] which-0:2.21-41.fc40.x86_64 100% | 1.6 MiB/s | 41.4 KiB | 00m00s [ 22/155] xz-1:5.4.6-3.fc41.x86_64 100% | 22.6 MiB/s | 531.9 KiB | 00m00s [ 23/155] fedora-repos-0:41-0.2.noarch 100% | 491.0 KiB/s | 9.3 KiB | 00m00s [ 24/155] coreutils-common-0:9.5-1.fc41 100% | 53.7 MiB/s | 2.1 MiB | 00m00s [ 25/155] glibc-0:2.39.9000-18.fc41.x86 100% | 77.2 MiB/s | 2.2 MiB | 00m00s [ 26/155] glibc-common-0:2.39.9000-18.f 100% | 14.3 MiB/s | 394.3 KiB | 00m00s [ 27/155] rpm-0:4.19.91-4.fc41.x86_64 100% | 24.2 MiB/s | 520.4 KiB | 00m00s [ 28/155] libblkid-0:2.40.1-1.fc41.x86_ 100% | 4.7 MiB/s | 124.3 KiB | 00m00s [ 29/155] libfdisk-0:2.40.1-1.fc41.x86_ 100% | 6.8 MiB/s | 159.2 KiB | 00m00s [ 30/155] libmount-0:2.40.1-1.fc41.x86_ 100% | 5.8 MiB/s | 154.7 KiB | 00m00s [ 31/155] libsmartcols-0:2.40.1-1.fc41. 100% | 3.9 MiB/s | 83.3 KiB | 00m00s [ 32/155] libuuid-0:2.40.1-1.fc41.x86_6 100% | 1.2 MiB/s | 28.5 KiB | 00m00s [ 33/155] xz-libs-1:5.4.6-3.fc41.x86_64 100% | 7.7 MiB/s | 110.2 KiB | 00m00s [ 34/155] util-linux-core-0:2.40.1-1.fc 100% | 23.1 MiB/s | 520.5 KiB | 00m00s [ 35/155] fedora-gpg-keys-0:41-0.2.noar 100% | 5.9 MiB/s | 121.8 KiB | 00m00s [ 36/155] fedora-repos-rawhide-0:41-0.2 100% | 424.1 KiB/s | 8.9 KiB | 00m00s [ 37/155] glibc-gconv-extra-0:2.39.9000 100% | 60.6 MiB/s | 1.6 MiB | 00m00s [ 38/155] rpm-build-libs-0:4.19.91-4.fc 100% | 4.5 MiB/s | 97.7 KiB | 00m00s [ 39/155] rpm-libs-0:4.19.91-4.fc41.x86 100% | 11.1 MiB/s | 307.8 KiB | 00m00s [ 40/155] systemd-libs-0:256~rc3-3.fc41 100% | 35.5 MiB/s | 727.5 KiB | 00m00s [ 41/155] libxcrypt-0:4.4.36-5.fc40.x86 100% | 5.5 MiB/s | 118.1 KiB | 00m00s [ 42/155] libselinux-0:3.6-4.fc40.x86_6 100% | 2.8 MiB/s | 87.5 KiB | 00m00s [ 43/155] ncurses-libs-0:6.4-12.2024012 100% | 15.5 MiB/s | 332.5 KiB | 00m00s [ 44/155] pam-0:1.6.1-3.fc41.x86_64 100% | 23.0 MiB/s | 517.3 KiB | 00m00s [ 45/155] pam-libs-0:1.6.1-3.fc41.x86_6 100% | 2.8 MiB/s | 57.1 KiB | 00m00s [ 46/155] audit-libs-0:4.0.1-2.fc41.x86 100% | 6.1 MiB/s | 125.3 KiB | 00m00s [ 47/155] authselect-libs-0:1.5.0-5.fc4 100% | 10.0 MiB/s | 204.9 KiB | 00m00s [ 48/155] authselect-0:1.5.0-5.fc41.x86 100% | 6.9 MiB/s | 141.1 KiB | 00m00s [ 49/155] libcap-ng-0:0.8.5-1.fc41.x86_ 100% | 1.5 MiB/s | 32.3 KiB | 00m00s [ 50/155] libutempter-0:1.2.1-13.fc40.x 100% | 1.4 MiB/s | 26.4 KiB | 00m00s [ 51/155] readline-0:8.2-8.fc40.x86_64 100% | 10.4 MiB/s | 213.3 KiB | 00m00s [ 52/155] zlib-ng-compat-0:2.1.6-4.fc41 100% | 3.3 MiB/s | 77.2 KiB | 00m00s [ 53/155] libcap-0:2.70-1.fc41.x86_64 100% | 6.0 MiB/s | 86.2 KiB | 00m00s [ 54/155] libacl-0:2.3.2-1.fc40.x86_64 100% | 1.3 MiB/s | 24.4 KiB | 00m00s [ 55/155] bzip2-libs-0:1.0.8-18.fc40.x8 100% | 1.6 MiB/s | 40.9 KiB | 00m00s [ 56/155] libeconf-0:0.6.2-2.fc41.x86_6 100% | 2.2 MiB/s | 32.0 KiB | 00m00s [ 57/155] libattr-0:2.5.2-3.fc40.x86_64 100% | 899.9 KiB/s | 18.0 KiB | 00m00s [ 58/155] libgcc-0:14.1.1-4.fc41.x86_64 100% | 4.8 MiB/s | 128.5 KiB | 00m00s [ 59/155] setup-0:2.15.0-3.fc41.noarch 100% | 6.9 MiB/s | 148.4 KiB | 00m00s [ 60/155] libsemanage-0:3.6-3.fc40.x86_ 100% | 4.9 MiB/s | 116.4 KiB | 00m00s [ 61/155] libzstd-0:1.5.6-1.fc41.x86_64 100% | 15.1 MiB/s | 308.9 KiB | 00m00s [ 62/155] rpm-sequoia-0:1.6.0-3.fc41.x8 100% | 37.6 MiB/s | 846.1 KiB | 00m00s [ 63/155] lua-libs-0:5.4.6-5.fc40.x86_6 100% | 6.4 MiB/s | 131.9 KiB | 00m00s [ 64/155] popt-0:1.19-6.fc40.x86_64 100% | 3.1 MiB/s | 59.6 KiB | 00m00s [ 65/155] libgomp-0:14.1.1-4.fc41.x86_6 100% | 17.1 MiB/s | 349.5 KiB | 00m00s [ 66/155] sqlite-libs-0:3.45.3-1.fc41.x 100% | 31.3 MiB/s | 705.4 KiB | 00m00s [ 67/155] elfutils-libelf-0:0.191-7.fc4 100% | 10.2 MiB/s | 208.5 KiB | 00m00s [ 68/155] elfutils-debuginfod-client-0: 100% | 1.9 MiB/s | 38.2 KiB | 00m00s [ 69/155] elfutils-libs-0:0.191-7.fc41. 100% | 11.0 MiB/s | 258.1 KiB | 00m00s [ 70/155] elfutils-0:0.191-7.fc41.x86_6 100% | 23.3 MiB/s | 524.4 KiB | 00m00s [ 71/155] file-0:5.45-5.fc41.x86_64 100% | 2.5 MiB/s | 49.1 KiB | 00m00s [ 72/155] file-libs-0:5.45-5.fc41.x86_6 100% | 32.4 MiB/s | 763.0 KiB | 00m00s [ 73/155] binutils-gold-0:2.42.50-11.fc 100% | 31.9 MiB/s | 783.1 KiB | 00m00s [ 74/155] binutils-0:2.42.50-11.fc41.x8 100% | 124.6 MiB/s | 6.4 MiB | 00m00s [ 75/155] zstd-0:1.5.6-1.fc41.x86_64 100% | 16.1 MiB/s | 479.3 KiB | 00m00s [ 76/155] pkgconf-pkg-config-0:2.1.1-1. 100% | 760.0 KiB/s | 9.9 KiB | 00m00s [ 77/155] debugedit-0:5.0-16.fc41.x86_6 100% | 3.1 MiB/s | 79.7 KiB | 00m00s [ 78/155] libarchive-0:3.7.4-1.fc41.x86 100% | 19.0 MiB/s | 407.6 KiB | 00m00s [ 79/155] libpkgconf-0:2.1.1-1.fc41.x86 100% | 2.9 MiB/s | 38.0 KiB | 00m00s [ 80/155] pkgconf-m4-0:2.1.1-1.fc41.noa 100% | 739.6 KiB/s | 14.1 KiB | 00m00s [ 81/155] pkgconf-0:2.1.1-1.fc41.x86_64 100% | 1.8 MiB/s | 43.9 KiB | 00m00s [ 82/155] curl-0:8.8.0-1.fc41.x86_64 100% | 13.4 MiB/s | 301.5 KiB | 00m00s [ 83/155] build-reproducibility-srpm-ma 100% | 478.7 KiB/s | 9.1 KiB | 00m00s [ 84/155] add-determinism-nopython-0:0. 100% | 37.8 MiB/s | 890.6 KiB | 00m00s [ 85/155] qt6-srpm-macros-0:6.7.1-1.fc4 100% | 467.2 KiB/s | 8.9 KiB | 00m00s [ 86/155] ansible-srpm-macros-0:1-15.fc 100% | 1.4 MiB/s | 20.9 KiB | 00m00s [ 87/155] forge-srpm-macros-0:0.3.1-1.f 100% | 746.3 KiB/s | 19.4 KiB | 00m00s [ 88/155] fonts-srpm-macros-1:2.0.5-14. 100% | 1.8 MiB/s | 26.5 KiB | 00m00s [ 89/155] efi-srpm-macros-0:5-11.fc40.n 100% | 1.0 MiB/s | 22.3 KiB | 00m00s [ 90/155] dwz-0:0.15-6.fc40.x86_64 100% | 5.2 MiB/s | 137.8 KiB | 00m00s [ 91/155] gnat-srpm-macros-0:6-5.fc40.n 100% | 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zig-srpm-macros-0:1-2.fc40.no 100% | 423.1 KiB/s | 8.0 KiB | 00m00s [105/155] rust-srpm-macros-0:26.3-1.fc4 100% | 625.2 KiB/s | 12.5 KiB | 00m00s [106/155] zip-0:3.0-40.fc40.x86_64 100% | 12.3 MiB/s | 264.8 KiB | 00m00s [107/155] ed-0:1.20.2-1.fc41.x86_64 100% | 4.2 MiB/s | 81.9 KiB | 00m00s [108/155] gdbm-1:1.23-6.fc40.x86_64 100% | 7.2 MiB/s | 147.4 KiB | 00m00s [109/155] gdbm-libs-1:1.23-6.fc40.x86_6 100% | 2.9 MiB/s | 56.2 KiB | 00m00s [110/155] libnsl2-0:2.0.1-1.fc40.x86_64 100% | 1.4 MiB/s | 29.6 KiB | 00m00s [111/155] libpwquality-0:1.4.5-9.fc40.x 100% | 5.6 MiB/s | 108.3 KiB | 00m00s [112/155] libtirpc-0:1.3.4-1.rc3.fc41.x 100% | 4.8 MiB/s | 92.5 KiB | 00m00s [113/155] crypto-policies-0:20240521-1. 100% | 3.3 MiB/s | 64.7 KiB | 00m00s [114/155] openssl-libs-1:3.2.1-6.fc41.x 100% | 82.3 MiB/s | 2.3 MiB | 00m00s [115/155] ncurses-base-0:6.4-12.2024012 100% | 3.1 MiB/s | 63.8 KiB | 00m00s [116/155] ca-certificates-0:2023.2.62_v 100% | 29.0 MiB/s | 862.1 KiB | 00m00s [117/155] 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Installing p11-kit-trust-0:0. 100% | 64.0 MiB/s | 393.1 KiB | 00m00s >>> Running post-install scriptlet: p11-kit-trust-0:0.25.3-4.fc40.x86_64 >>> Stop post-install scriptlet: p11-kit-trust-0:0.25.3-4.fc40.x86_64 [ 97/157] Installing libnghttp2-0:1.62. 100% | 163.3 MiB/s | 167.2 KiB | 00m00s [ 98/157] Installing xxhash-libs-0:0.8. 100% | 0.0 B/s | 89.9 KiB | 00m00s [ 99/157] Installing libbrotli-0:1.1.0- 100% | 406.2 MiB/s | 831.8 KiB | 00m00s [100/157] Installing libtool-ltdl-0:2.4 100% | 0.0 B/s | 67.3 KiB | 00m00s [101/157] Installing rust-srpm-macros-0 100% | 0.0 B/s | 5.6 KiB | 00m00s [102/157] Installing qt5-srpm-macros-0: 100% | 0.0 B/s | 768.0 B | 00m00s [103/157] Installing perl-srpm-macros-0 100% | 0.0 B/s | 1.1 KiB | 00m00s [104/157] Installing package-notes-srpm 100% | 0.0 B/s | 2.0 KiB | 00m00s [105/157] Installing openblas-srpm-macr 100% | 0.0 B/s | 392.0 B | 00m00s [106/157] Installing ocaml-srpm-macros- 100% | 0.0 B/s | 2.2 KiB | 00m00s [107/157] Installing kernel-srpm-macros 100% | 0.0 B/s | 2.3 KiB | 00m00s [108/157] Installing gnat-srpm-macros-0 100% | 0.0 B/s | 1.3 KiB | 00m00s [109/157] Installing ghc-srpm-macros-0: 100% | 0.0 B/s | 1.0 KiB | 00m00s [110/157] Installing fpc-srpm-macros-0: 100% | 0.0 B/s | 420.0 B | 00m00s [111/157] Installing ansible-srpm-macro 100% | 0.0 B/s | 36.2 KiB | 00m00s [112/157] Installing qt6-srpm-macros-0: 100% | 0.0 B/s | 732.0 B | 00m00s [113/157] Installing pkgconf-m4-0:2.1.1 100% | 0.0 B/s | 14.3 KiB | 00m00s [114/157] Installing pkgconf-pkg-config 100% | 0.0 B/s | 1.8 KiB | 00m00s [115/157] Installing coreutils-common-0 100% | 466.3 MiB/s | 11.2 MiB | 00m00s [116/157] Installing openssl-libs-1:3.2 100% | 487.2 MiB/s | 7.8 MiB | 00m00s [117/157] Installing coreutils-0:9.5-1. 100% | 328.8 MiB/s | 5.6 MiB | 00m00s >>> Running pre-install scriptlet: ca-certificates-0:2023.2.62_v7.0.401-6.fc40.n >>> Stop pre-install scriptlet: ca-certificates-0:2023.2.62_v7.0.401-6.fc40.noar [118/157] Installing ca-certificates-0: 100% | 4.5 MiB/s | 2.3 MiB | 00m01s >>> Running post-install scriptlet: ca-certificates-0:2023.2.62_v7.0.401-6.fc40. >>> Stop post-install scriptlet: ca-certificates-0:2023.2.62_v7.0.401-6.fc40.noa [119/157] Installing krb5-libs-0:1.21.2 100% | 327.8 MiB/s | 2.3 MiB | 00m00s [120/157] Installing libarchive-0:3.7.4 100% | 447.5 MiB/s | 916.6 KiB | 00m00s [121/157] Installing libtirpc-0:1.3.4-1 100% | 199.8 MiB/s | 204.6 KiB | 00m00s [122/157] Installing gzip-0:1.13-1.fc40 100% | 190.7 MiB/s | 390.6 KiB | 00m00s [123/157] Installing authselect-libs-0: 100% | 203.4 MiB/s | 833.2 KiB | 00m00s [124/157] Installing authselect-0:1.5.0 100% | 154.2 MiB/s | 157.9 KiB | 00m00s [125/157] Installing cracklib-0:2.9.11- 100% | 81.5 MiB/s | 250.3 KiB | 00m00s [126/157] Installing libpwquality-0:1.4 100% | 140.0 MiB/s | 430.1 KiB | 00m00s [127/157] Installing libnsl2-0:2.0.1-1. 100% | 57.7 MiB/s | 59.0 KiB | 00m00s [128/157] Installing pam-0:1.6.1-3.fc41 100% | 181.9 MiB/s | 1.8 MiB | 00m00s [129/157] Installing libssh-0:0.10.6-6. 100% | 251.7 MiB/s | 515.4 KiB | 00m00s [130/157] Installing rpm-sequoia-0:1.6. 100% | 442.0 MiB/s | 2.2 MiB | 00m00s [131/157] Installing rpm-libs-0:4.19.91 100% | 347.4 MiB/s | 711.4 KiB | 00m00s [132/157] Installing libevent-0:2.1.12- 100% | 292.8 MiB/s | 899.4 KiB | 00m00s [133/157] Installing openldap-0:2.6.8-1 100% | 312.5 MiB/s | 640.0 KiB | 00m00s [134/157] Installing libcurl-0:8.8.0-1. 100% | 394.0 MiB/s | 806.8 KiB | 00m00s [135/157] Installing elfutils-libs-0:0. 100% | 316.4 MiB/s | 648.0 KiB | 00m00s [136/157] Installing elfutils-debuginfo 100% | 65.3 MiB/s | 66.9 KiB | 00m00s [137/157] Installing binutils-gold-0:2. 100% | 203.1 MiB/s | 2.0 MiB | 00m00s >>> Running post-install scriptlet: binutils-gold-0:2.42.50-11.fc41.x86_64 >>> Stop post-install scriptlet: binutils-gold-0:2.42.50-11.fc41.x86_64 [138/157] Installing binutils-0:2.42.50 100% | 430.0 MiB/s | 27.5 MiB | 00m00s >>> Running post-install scriptlet: binutils-0:2.42.50-11.fc41.x86_64 >>> Stop post-install scriptlet: binutils-0:2.42.50-11.fc41.x86_64 [139/157] Installing elfutils-0:0.191-7 100% | 425.4 MiB/s | 2.6 MiB | 00m00s [140/157] Installing gdb-minimal-0:14.2 100% | 453.6 MiB/s | 12.7 MiB | 00m00s [141/157] Installing debugedit-0:5.0-16 100% | 197.3 MiB/s | 202.0 KiB | 00m00s [142/157] Installing rpm-build-libs-0:4 100% | 202.6 MiB/s | 207.5 KiB | 00m00s [143/157] Installing curl-0:8.8.0-1.fc4 100% | 81.0 MiB/s | 746.2 KiB | 00m00s >>> Running pre-install scriptlet: rpm-0:4.19.91-4.fc41.x86_64 >>> Stop pre-install scriptlet: rpm-0:4.19.91-4.fc41.x86_64 [144/157] Installing rpm-0:4.19.91-4.fc 100% | 207.5 MiB/s | 2.5 MiB | 00m00s [145/157] Installing efi-srpm-macros-0: 100% | 0.0 B/s | 41.2 KiB | 00m00s [146/157] Installing lua-srpm-macros-0: 100% | 0.0 B/s | 1.9 KiB | 00m00s [147/157] Installing zig-srpm-macros-0: 100% | 0.0 B/s | 1.7 KiB | 00m00s [148/157] Installing forge-srpm-macros- 100% | 39.4 MiB/s | 40.3 KiB | 00m00s [149/157] Installing fonts-srpm-macros- 100% | 0.0 B/s | 56.5 KiB | 00m00s [150/157] Installing go-srpm-macros-0:3 100% | 0.0 B/s | 62.0 KiB | 00m00s [151/157] Installing python-srpm-macros 100% | 0.0 B/s | 51.7 KiB | 00m00s [152/157] Installing redhat-rpm-config- 100% | 185.6 MiB/s | 190.0 KiB | 00m00s [153/157] Installing rpm-build-0:4.19.9 100% | 194.1 MiB/s | 198.7 KiB | 00m00s [154/157] Installing pyproject-srpm-mac 100% | 2.0 MiB/s | 2.1 KiB | 00m00s [155/157] Installing util-linux-0:2.40. 100% | 208.0 MiB/s | 3.7 MiB | 00m00s >>> Running post-install scriptlet: util-linux-0:2.40.1-1.fc41.x86_64 >>> Stop post-install scriptlet: util-linux-0:2.40.1-1.fc41.x86_64 [156/157] Installing which-0:2.21-41.fc 100% | 80.5 MiB/s | 82.4 KiB | 00m00s [157/157] Installing info-0:7.1-2.fc40. 100% | 505.2 KiB/s | 358.2 KiB | 00m01s >>> Running post-transaction scriptlet: filesystem-0:3.18-9.fc41.x86_64 >>> Stop post-transaction scriptlet: filesystem-0:3.18-9.fc41.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.fc41.x86_64 >>> Stop post-transaction scriptlet: authselect-libs-0:1.5.0-5.fc41.x86_64 >>> Running post-transaction scriptlet: rpm-0:4.19.91-4.fc41.x86_64 >>> Stop post-transaction scriptlet: rpm-0:4.19.91-4.fc41.x86_64 >>> Running trigger-install scriptlet: glibc-common-0:2.39.9000-18.fc41.x86_64 >>> Stop trigger-install scriptlet: glibc-common-0:2.39.9000-18.fc41.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 Warning: skipped PGP checks for 155 package(s). Finish: installing minimal buildroot with dnf5 Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: add-determinism-nopython-0.2.0-9.fc41.x86_64 alternatives-1.27-1.fc41.x86_64 ansible-srpm-macros-1-15.fc41.noarch audit-libs-4.0.1-2.fc41.x86_64 authselect-1.5.0-5.fc41.x86_64 authselect-libs-1.5.0-5.fc41.x86_64 basesystem-11-20.fc40.noarch bash-5.2.26-3.fc40.x86_64 binutils-2.42.50-11.fc41.x86_64 binutils-gold-2.42.50-11.fc41.x86_64 build-reproducibility-srpm-macros-0.2.0-9.fc41.noarch 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-9.5-1.fc41.x86_64 coreutils-common-9.5-1.fc41.x86_64 cpio-2.15-1.fc40.x86_64 cracklib-2.9.11-5.fc40.x86_64 crypto-policies-20240521-1.gitf71d135.fc41.noarch curl-8.8.0-1.fc41.x86_64 cyrus-sasl-lib-2.1.28-22.fc41.x86_64 debugedit-5.0-16.fc41.x86_64 diffutils-3.10-5.fc40.x86_64 dwz-0.15-6.fc40.x86_64 ed-1.20.2-1.fc41.x86_64 efi-srpm-macros-5-11.fc40.noarch elfutils-0.191-7.fc41.x86_64 elfutils-debuginfod-client-0.191-7.fc41.x86_64 elfutils-default-yama-scope-0.191-7.fc41.noarch elfutils-libelf-0.191-7.fc41.x86_64 elfutils-libs-0.191-7.fc41.x86_64 fedora-gpg-keys-41-0.2.noarch fedora-release-41-0.13.noarch fedora-release-common-41-0.13.noarch fedora-release-identity-basic-41-0.13.noarch fedora-repos-41-0.2.noarch fedora-repos-rawhide-41-0.2.noarch file-5.45-5.fc41.x86_64 file-libs-5.45-5.fc41.x86_64 filesystem-3.18-9.fc41.x86_64 findutils-4.9.0-8.fc40.x86_64 fonts-srpm-macros-2.0.5-14.fc40.noarch forge-srpm-macros-0.3.1-1.fc41.noarch fpc-srpm-macros-1.3-12.fc40.noarch gawk-5.3.0-3.fc40.x86_64 gdb-minimal-14.2-9.fc41.x86_64 gdbm-1.23-6.fc40.x86_64 gdbm-libs-1.23-6.fc40.x86_64 ghc-srpm-macros-1.9.1-1.fc41.noarch glibc-2.39.9000-18.fc41.x86_64 glibc-common-2.39.9000-18.fc41.x86_64 glibc-gconv-extra-2.39.9000-18.fc41.x86_64 glibc-minimal-langpack-2.39.9000-18.fc41.x86_64 gmp-6.3.0-1.fc41.x86_64 gnat-srpm-macros-6-5.fc40.noarch go-srpm-macros-3.6.0-1.fc41.noarch grep-3.11-8.fc41.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.fc41.noarch keyutils-libs-1.6.3-3.fc40.x86_64 krb5-libs-1.21.2-5.fc40.x86_64 libacl-2.3.2-1.fc40.x86_64 libarchive-3.7.4-1.fc41.x86_64 libattr-2.5.2-3.fc40.x86_64 libblkid-2.40.1-1.fc41.x86_64 libbrotli-1.1.0-3.fc40.x86_64 libcap-2.70-1.fc41.x86_64 libcap-ng-0.8.5-1.fc41.x86_64 libcom_err-1.47.0-5.fc40.x86_64 libcurl-8.8.0-1.fc41.x86_64 libeconf-0.6.2-2.fc41.x86_64 libevent-2.1.12-13.fc41.x86_64 libfdisk-2.40.1-1.fc41.x86_64 libffi-3.4.6-1.fc41.x86_64 libgcc-14.1.1-4.fc41.x86_64 libgomp-14.1.1-4.fc41.x86_64 libidn2-2.3.7-1.fc40.x86_64 libmount-2.40.1-1.fc41.x86_64 libnghttp2-1.62.0-1.fc41.x86_64 libnsl2-2.0.1-1.fc40.x86_64 libpkgconf-2.1.1-1.fc41.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.fc41.x86_64 libssh-0.10.6-6.fc41.x86_64 libssh-config-0.10.6-6.fc41.noarch libstdc++-14.1.1-4.fc41.x86_64 libtasn1-4.19.0-6.fc40.x86_64 libtirpc-1.3.4-1.rc3.fc41.x86_64 libtool-ltdl-2.4.7-10.fc40.x86_64 libunistring-1.1-7.fc41.x86_64 libutempter-1.2.1-13.fc40.x86_64 libuuid-2.40.1-1.fc41.x86_64 libverto-0.3.2-8.fc40.x86_64 libxcrypt-4.4.36-5.fc40.x86_64 libxml2-2.12.7-1.fc41.x86_64 libzstd-1.5.6-1.fc41.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.fc41.x86_64 ncurses-base-6.4-12.20240127.fc40.noarch ncurses-libs-6.4-12.20240127.fc40.x86_64 ocaml-srpm-macros-10-1.fc41.noarch openblas-srpm-macros-2-17.fc41.noarch openldap-2.6.8-1.fc41.x86_64 openssl-libs-3.2.1-6.fc41.x86_64 p11-kit-0.25.3-4.fc40.x86_64 p11-kit-trust-0.25.3-4.fc40.x86_64 package-notes-srpm-macros-0.5-11.fc40.noarch pam-1.6.1-3.fc41.x86_64 pam-libs-1.6.1-3.fc41.x86_64 patch-2.7.6-24.fc40.x86_64 pcre2-10.43-2.fc41.1.x86_64 pcre2-syntax-10.43-2.fc41.1.noarch perl-srpm-macros-1-53.fc40.noarch pkgconf-2.1.1-1.fc41.x86_64 pkgconf-m4-2.1.1-1.fc41.noarch pkgconf-pkg-config-2.1.1-1.fc41.x86_64 popt-1.19-6.fc40.x86_64 publicsuffix-list-dafsa-20240107-3.fc40.noarch pyproject-srpm-macros-1.12.0-1.fc40.noarch python-srpm-macros-3.12-9.fc41.noarch qt5-srpm-macros-5.15.13-1.fc41.noarch qt6-srpm-macros-6.7.1-1.fc41.noarch readline-8.2-8.fc40.x86_64 redhat-rpm-config-291-1.fc41.noarch rpm-4.19.91-4.fc41.x86_64 rpm-build-4.19.91-4.fc41.x86_64 rpm-build-libs-4.19.91-4.fc41.x86_64 rpm-libs-4.19.91-4.fc41.x86_64 rpm-sequoia-1.6.0-3.fc41.x86_64 rust-srpm-macros-26.3-1.fc41.noarch sed-4.9-1.fc40.x86_64 setup-2.15.0-3.fc41.noarch shadow-utils-4.15.1-5.fc41.x86_64 sqlite-libs-3.45.3-1.fc41.x86_64 systemd-libs-256~rc3-3.fc41.x86_64 tar-1.35-3.fc40.x86_64 unzip-6.0-63.fc40.x86_64 util-linux-2.40.1-1.fc41.x86_64 util-linux-core-2.40.1-1.fc41.x86_64 which-2.21-41.fc40.x86_64 xxhash-libs-0.8.2-2.fc40.x86_64 xz-5.4.6-3.fc41.x86_64 xz-libs-5.4.6-3.fc41.x86_64 zig-srpm-macros-1-2.fc40.noarch zip-3.0-40.fc40.x86_64 zlib-ng-compat-2.1.6-4.fc41.x86_64 zstd-1.5.6-1.fc41.x86_64 Start: buildsrpm Start: rpmbuild -bs Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1706140800 Wrote: /builddir/build/SRPMS/mmseq-1.0.11-19.fc41.src.rpm Finish: rpmbuild -bs cp: preserving permissions for ‘/var/lib/copr-rpmbuild/results/chroot_scan/var/lib/mock/fedora-40-x86_64-1717082042.506309/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_64-1717082042.506309/root/var/log/dnf5.log Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-6u3x11z7/mmseq/mmseq.spec) Config(child) 0 minutes 30 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/mmseq-1.0.11-19.fc41.src.rpm) Config(fedora-40-x86_64) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-40-x86_64-bootstrap-1717082042.506309/root. INFO: reusing tmpfs at /var/lib/mock/fedora-40-x86_64-bootstrap-1717082042.506309/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_64-1717082042.506309/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-1.6.0-3.fc40.x86_64 python3-dnf-4.20.0-1.fc41.noarch dnf5-5.2.2.0-1.fc41.x86_64 dnf5-plugins-5.2.2.0-1.fc41.x86_64 Finish: chroot init Start: build phase for mmseq-1.0.11-19.fc41.src.rpm Start: build setup for mmseq-1.0.11-19.fc41.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1706140800 Wrote: /builddir/build/SRPMS/mmseq-1.0.11-19.fc41.src.rpm Updating and loading repositories: Additional repo http_kojipkgs_fedorapr 100% | 31.0 KiB/s | 4.1 KiB | 00m00s Copr repository 100% | 128.1 KiB/s | 1.5 KiB | 00m00s fedora 100% | 90.8 KiB/s | 24.1 KiB | 00m00s updates 100% | 84.3 KiB/s | 21.1 KiB | 00m00s Repositories loaded. Package Arch Version Repository Size Installing: armadillo-devel x86_64 12.8.1-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 7.3 MiB boost-devel x86_64 1.83.0-5.fc41 copr_base 143.0 MiB flexiblas-devel x86_64 3.4.4-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 4.7 MiB gcc-c++ x86_64 14.1.1-4.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 38.1 MiB gsl-devel x86_64 2.7.1-8.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.6 MiB htslib-devel x86_64 1.15.1-5.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 411.1 KiB make x86_64 1:4.4.1-6.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.8 MiB perl-generators noarch 1.16-5.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 21.8 KiB zlib-ng-compat-devel x86_64 2.1.6-4.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 103.4 KiB Installing dependencies: SuperLU x86_64 6.0.1-5.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 474.3 KiB SuperLU-devel x86_64 6.0.1-5.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 102.2 KiB add-determinism x86_64 0.2.0-9.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 2.6 MiB annobin-docs noarch 12.54-2.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 96.2 KiB annobin-plugin-gcc x86_64 12.54-2.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 974.4 KiB armadillo x86_64 12.8.1-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 90.3 KiB arpack x86_64 3.9.1-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 646.0 KiB arpack-devel x86_64 3.9.1-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 69.1 KiB autoconf noarch 2.72-2.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 2.8 MiB automake noarch 1.16.5-16.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.7 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http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 83.7 KiB perl-vars noarch 1.05-507.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 3.9 KiB python-pip-wheel noarch 24.0-2.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.5 MiB python3 x86_64 3.12.3-2.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 31.5 KiB python3-libs x86_64 3.12.3-2.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 40.9 MiB python3-numpy x86_64 1:1.26.4-4.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 43.9 MiB tzdata noarch 2024a-8.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.7 MiB Transaction Summary: Installing: 159 packages Total size of inbound packages is 172 MiB. Need to download 172 MiB. After this operation 742 MiB will be used (install 742 MiB, remove 0 B). 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perl-B-0:1.88-507.fc41.x86_64 100% | 6.1 MiB/s | 176.1 KiB | 00m00s [130/159] libaec-0:1.1.2-1.fc40.x86_64 100% | 1.6 MiB/s | 37.2 KiB | 00m00s [131/159] libaec-devel-0:1.1.2-1.fc40.x 100% | 492.6 KiB/s | 11.8 KiB | 00m00s [132/159] hdf5-0:1.12.1-15.fc40.x86_64 100% | 65.3 MiB/s | 2.2 MiB | 00m00s [133/159] openblas-0:0.3.26-4.fc40.x86_ 100% | 1.7 MiB/s | 38.6 KiB | 00m00s [134/159] flexiblas-openblas-openmp64-0 100% | 614.5 KiB/s | 17.2 KiB | 00m00s [135/159] openblas-openmp-0:0.3.26-4.fc 100% | 99.2 MiB/s | 5.1 MiB | 00m00s [136/159] perl-Pod-Usage-4:2.03-504.fc4 100% | 1.5 MiB/s | 39.8 KiB | 00m00s [137/159] perl-Pod-Perldoc-0:3.28.01-50 100% | 3.5 MiB/s | 79.4 KiB | 00m00s [138/159] perl-podlators-1:5.01-502.fc4 100% | 4.4 MiB/s | 120.9 KiB | 00m00s [139/159] openblas-openmp64-0:0.3.26-4. 100% | 77.2 MiB/s | 4.9 MiB | 00m00s [140/159] groff-base-0:1.23.0-6.fc40.x8 100% | 46.5 MiB/s | 1.1 MiB | 00m00s [141/159] perl-HTTP-Tiny-0:0.088-5.fc40 100% | 2.0 MiB/s | 55.6 KiB | 00m00s 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41.7 KiB | 00m00s [155/159] perl-libnet-0:3.15-503.fc40.n 100% | 5.2 MiB/s | 122.5 KiB | 00m00s [156/159] perl-URI-0:5.28-1.fc41.noarch 100% | 3.9 MiB/s | 119.6 KiB | 00m00s [157/159] perl-Digest-MD5-0:2.59-3.fc40 100% | 1.8 MiB/s | 35.8 KiB | 00m00s [158/159] perl-FileHandle-0:2.05-507.fc 100% | 743.8 KiB/s | 15.6 KiB | 00m00s [159/159] perl-Digest-0:1.20-502.fc40.n 100% | 912.9 KiB/s | 24.6 KiB | 00m00s -------------------------------------------------------------------------------- [159/159] Total 100% | 112.0 MiB/s | 172.2 MiB | 00m02s Running transaction [ 1/161] Verify package files 100% | 333.0 B/s | 159.0 B | 00m00s [ 2/161] Prepare transaction 100% | 1.5 KiB/s | 159.0 B | 00m00s [ 3/161] Installing boost-system-0:1.8 100% | 0.0 B/s | 17.3 KiB | 00m00s [ 4/161] Installing libgfortran-0:14.1 100% | 420.4 MiB/s | 2.9 MiB | 00m00s [ 5/161] Installing boost-chrono-0:1.8 100% | 0.0 B/s | 38.6 KiB | 00m00s [ 6/161] Installing boost-thread-0:1.8 100% | 134.6 MiB/s | 137.8 KiB | 00m00s 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KiB | 00m00s [ 20/161] Installing boost-wave-0:1.83. 100% | 310.9 MiB/s | 636.7 KiB | 00m00s [ 21/161] Installing hdf5-0:1.12.1-15.f 100% | 440.6 MiB/s | 8.4 MiB | 00m00s [ 22/161] Installing libaec-devel-0:1.1 100% | 0.0 B/s | 12.9 KiB | 00m00s [ 23/161] Installing openblas-openmp-0: 100% | 694.7 MiB/s | 38.9 MiB | 00m00s [ 24/161] Installing openblas-openmp64- 100% | 698.1 MiB/s | 39.1 MiB | 00m00s [ 25/161] Installing flexiblas-netlib-0 100% | 472.1 MiB/s | 10.4 MiB | 00m00s [ 26/161] Installing flexiblas-openblas 100% | 0.0 B/s | 40.1 KiB | 00m00s [ 27/161] Installing flexiblas-0:3.4.4- 100% | 0.0 B/s | 49.7 KiB | 00m00s [ 28/161] Installing flexiblas-openblas 100% | 0.0 B/s | 40.2 KiB | 00m00s [ 29/161] Installing flexiblas-netlib64 100% | 476.9 MiB/s | 10.5 MiB | 00m00s [ 30/161] Installing arpack-0:3.9.1-3.f 100% | 316.5 MiB/s | 648.1 KiB | 00m00s [ 31/161] Installing arpack-devel-0:3.9 100% | 0.0 B/s | 72.1 KiB | 00m00s [ 32/161] Installing flexiblas-devel-0: 100% | 777.9 MiB/s | 4.7 MiB | 00m00s [ 33/161] Installing boost-fiber-0:1.83 100% | 81.8 MiB/s | 83.8 KiB | 00m00s [ 34/161] Installing boost-log-0:1.83.0 100% | 367.8 MiB/s | 1.5 MiB | 00m00s [ 35/161] Installing boost-coroutine-0: 100% | 0.0 B/s | 22.2 KiB | 00m00s [ 36/161] Installing boost-graph-0:1.83 100% | 335.3 MiB/s | 343.3 KiB | 00m00s [ 37/161] Installing cpp-0:14.1.1-4.fc4 100% | 448.2 MiB/s | 35.0 MiB | 00m00s [ 38/161] Installing boost-locale-0:1.8 100% | 296.5 MiB/s | 607.2 KiB | 00m00s [ 39/161] Installing libicu-devel-0:74. 100% | 352.6 MiB/s | 5.6 MiB | 00m00s [ 40/161] Installing boost-type_erasure 100% | 0.0 B/s | 59.2 KiB | 00m00s [ 41/161] Installing boost-timer-0:1.83 100% | 0.0 B/s | 26.1 KiB | 00m00s [ 42/161] Installing ncurses-0:6.4-12.2 100% | 68.1 MiB/s | 627.6 KiB | 00m00s >>> Running pre-install scriptlet: groff-base-0:1.23.0-6.fc40.x86_64 >>> Stop pre-install scriptlet: groff-base-0:1.23.0-6.fc40.x86_64 [ 43/161] Installing groff-base-0:1.23. 100% | 226.9 MiB/s | 3.9 MiB | 00m00s >>> Running post-install scriptlet: groff-base-0:1.23.0-6.fc40.x86_64 >>> Stop post-install scriptlet: groff-base-0:1.23.0-6.fc40.x86_64 [ 44/161] Installing perl-Digest-0:1.20 100% | 0.0 B/s | 37.0 KiB | 00m00s [ 45/161] Installing perl-B-0:1.88-507. 100% | 242.1 MiB/s | 495.7 KiB | 00m00s [ 46/161] Installing perl-FileHandle-0: 100% | 0.0 B/s | 9.8 KiB | 00m00s [ 47/161] Installing perl-Digest-MD5-0: 100% | 60.2 MiB/s | 61.6 KiB | 00m00s [ 48/161] Installing perl-Data-Dumper-0 100% | 110.9 MiB/s | 113.6 KiB | 00m00s [ 49/161] Installing perl-libnet-0:3.15 100% | 287.4 MiB/s | 294.3 KiB | 00m00s [ 50/161] Installing perl-AutoLoader-0: 100% | 0.0 B/s | 20.9 KiB | 00m00s [ 51/161] Installing perl-URI-0:5.28-1. 100% | 122.9 MiB/s | 251.8 KiB | 00m00s [ 52/161] Installing perl-locale-0:1.10 100% | 0.0 B/s | 6.6 KiB | 00m00s [ 53/161] Installing perl-File-Path-0:2 100% | 0.0 B/s | 64.5 KiB | 00m00s [ 54/161] Installing perl-if-0:0.61.000 100% | 0.0 B/s | 6.2 KiB | 00m00s [ 55/161] Installing perl-Mozilla-CA-0: 100% | 0.0 B/s | 10.5 KiB | 00m00s [ 56/161] Installing perl-Time-Local-2: 100% | 0.0 B/s | 70.5 KiB | 00m00s [ 57/161] Installing perl-Pod-Escapes-1 100% | 0.0 B/s | 25.9 KiB | 00m00s [ 58/161] Installing perl-Text-Tabs+Wra 100% | 0.0 B/s | 23.8 KiB | 00m00s [ 59/161] Installing perl-Net-SSLeay-0: 100% | 340.6 MiB/s | 1.4 MiB | 00m00s [ 60/161] Installing perl-IO-Socket-IP- 100% | 98.1 MiB/s | 100.4 KiB | 00m00s [ 61/161] Installing perl-IO-Socket-SSL 100% | 336.4 MiB/s | 689.0 KiB | 00m00s [ 62/161] Installing perl-Class-Struct- 100% | 0.0 B/s | 25.9 KiB | 00m00s [ 63/161] Installing perl-POSIX-0:2.13- 100% | 224.9 MiB/s | 230.3 KiB | 00m00s [ 64/161] Installing perl-File-Temp-1:0 100% | 160.2 MiB/s | 164.0 KiB | 00m00s [ 65/161] Installing perl-IPC-Open3-0:1 100% | 0.0 B/s | 23.3 KiB | 00m00s [ 66/161] Installing perl-Term-ANSIColo 100% | 96.8 MiB/s | 99.1 KiB | 00m00s [ 67/161] Installing perl-Term-Cap-0:1. 100% | 0.0 B/s | 30.5 KiB | 00m00s [ 68/161] Installing perl-Pod-Simple-1: 100% | 278.0 MiB/s | 569.4 KiB | 00m00s [ 69/161] Installing perl-HTTP-Tiny-0:0 100% | 150.6 MiB/s | 154.2 KiB | 00m00s [ 70/161] Installing perl-Socket-4:2.03 100% | 123.1 MiB/s | 126.0 KiB | 00m00s [ 71/161] Installing perl-File-stat-0:1 100% | 0.0 B/s | 13.2 KiB | 00m00s [ 72/161] Installing perl-SelectSaver-0 100% | 0.0 B/s | 2.6 KiB | 00m00s [ 73/161] Installing perl-Symbol-0:1.09 100% | 0.0 B/s | 7.2 KiB | 00m00s [ 74/161] Installing perl-podlators-1:5 100% | 304.7 MiB/s | 312.1 KiB | 00m00s [ 75/161] Installing perl-Pod-Perldoc-0 100% | 164.7 MiB/s | 168.6 KiB | 00m00s [ 76/161] Installing perl-Text-ParseWor 100% | 0.0 B/s | 14.5 KiB | 00m00s [ 77/161] Installing perl-mro-0:1.28-50 100% | 0.0 B/s | 42.6 KiB | 00m00s [ 78/161] Installing perl-overloading-0 100% | 0.0 B/s | 5.5 KiB | 00m00s [ 79/161] Installing perl-Fcntl-0:1.15- 100% | 0.0 B/s | 25.8 KiB | 00m00s [ 80/161] Installing perl-IO-0:1.52-507 100% | 151.5 MiB/s | 155.2 KiB | 00m00s [ 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Installing perl-Carp-0:1.54-5 100% | 0.0 B/s | 47.7 KiB | 00m00s [ 95/161] Installing perl-Exporter-0:5. 100% | 0.0 B/s | 55.5 KiB | 00m00s [ 96/161] Installing perl-PathTools-0:3 100% | 179.8 MiB/s | 184.2 KiB | 00m00s [ 97/161] Installing perl-DynaLoader-0: 100% | 0.0 B/s | 32.5 KiB | 00m00s [ 98/161] Installing perl-Encode-4:3.21 100% | 428.9 MiB/s | 4.7 MiB | 00m00s [ 99/161] Installing perl-libs-4:5.38.2 100% | 320.7 MiB/s | 9.9 MiB | 00m00s [100/161] Installing perl-interpreter-4 100% | 118.6 MiB/s | 121.4 KiB | 00m00s [101/161] Installing perl-threads-1:2.3 100% | 114.4 MiB/s | 117.1 KiB | 00m00s [102/161] Installing perl-threads-share 100% | 83.9 MiB/s | 85.9 KiB | 00m00s [103/161] Installing perl-Thread-Queue- 100% | 0.0 B/s | 30.3 KiB | 00m00s [104/161] Installing perl-macros-4:5.38 100% | 0.0 B/s | 5.8 KiB | 00m00s [105/161] Installing perl-Fedora-VSP-0: 100% | 0.0 B/s | 40.5 KiB | 00m00s [106/161] Installing perl-File-Compare- 100% | 0.0 B/s | 6.0 KiB | 00m00s [107/161] Installing perl-File-Copy-0:2 100% | 0.0 B/s | 20.2 KiB | 00m00s [108/161] Installing perl-File-Find-0:1 100% | 0.0 B/s | 42.4 KiB | 00m00s [109/161] Installing metis-0:5.1.0.3-5. 100% | 318.3 MiB/s | 977.7 KiB | 00m00s [110/161] Installing SuperLU-0:6.0.1-5. 100% | 464.3 MiB/s | 475.4 KiB | 00m00s [111/161] Installing armadillo-0:12.8.1 100% | 0.0 B/s | 91.6 KiB | 00m00s [112/161] Installing cmake-filesystem-0 100% | 7.0 MiB/s | 7.1 KiB | 00m00s [113/161] Installing SuperLU-devel-0:6. 100% | 0.0 B/s | 105.1 KiB | 00m00s [114/161] Installing m4-0:1.4.19-9.fc40 100% | 193.8 MiB/s | 595.2 KiB | 00m00s [115/161] Installing emacs-filesystem-1 100% | 0.0 B/s | 544.0 B | 00m00s [116/161] Installing autoconf-0:2.72-2. 100% | 466.3 MiB/s | 2.8 MiB | 00m00s [117/161] Installing automake-0:1.16.5- 100% | 352.4 MiB/s | 1.8 MiB | 00m00s [118/161] Installing annobin-docs-0:12. 100% | 95.0 MiB/s | 97.3 KiB | 00m00s [119/161] Installing kernel-headers-0:6 100% | 268.7 MiB/s | 6.4 MiB | 00m00s [120/161] Installing gc-0:8.2.2-6.fc40. 100% | 127.6 MiB/s | 261.2 KiB | 00m00s [121/161] Installing guile30-0:3.0.9-1. 100% | 522.7 MiB/s | 52.8 MiB | 00m00s [122/161] Installing make-1:4.4.1-6.fc4 100% | 360.1 MiB/s | 1.8 MiB | 00m00s [123/161] Installing htslib-0:1.15.1-5. 100% | 215.1 MiB/s | 1.1 MiB | 00m00s [124/161] Installing tzdata-0:2024a-8.f 100% | 77.6 MiB/s | 1.9 MiB | 00m00s [125/161] Installing python-pip-wheel-0 100% | 764.0 MiB/s | 1.5 MiB | 00m00s [126/161] Installing mpdecimal-0:2.5.1- 100% | 197.3 MiB/s | 202.0 KiB | 00m00s [127/161] Installing libb2-0:0.98.1-11. 100% | 0.0 B/s | 43.3 KiB | 00m00s [128/161] Installing expat-0:2.6.2-1.fc 100% | 69.1 MiB/s | 282.9 KiB | 00m00s [129/161] Installing python3-libs-0:3.1 100% | 397.4 MiB/s | 41.3 MiB | 00m00s [130/161] Installing python3-0:3.12.3-2 100% | 0.0 B/s | 33.2 KiB | 00m00s [131/161] Installing boost-python3-0:1. 100% | 81.9 MiB/s | 251.5 KiB | 00m00s [132/161] Installing python3-numpy-1:1. 100% | 480.7 MiB/s | 44.2 MiB | 00m00s [133/161] Installing boost-numpy3-0:1.8 100% | 57.3 MiB/s | 58.6 KiB | 00m00s [134/161] Installing glibc-headers-x86- 100% | 228.3 MiB/s | 2.3 MiB | 00m00s [135/161] Installing libxcrypt-devel-0: 100% | 31.8 MiB/s | 32.6 KiB | 00m00s [136/161] Installing glibc-devel-0:2.39 100% | 40.5 MiB/s | 41.4 KiB | 00m00s [137/161] Installing gcc-0:14.1.1-4.fc4 100% | 479.5 MiB/s | 104.1 MiB | 00m00s >>> Running trigger-install scriptlet: redhat-rpm-config-0:291-1.fc41.noarch >>> Stop trigger-install scriptlet: redhat-rpm-config-0:291-1.fc41.noarch [138/161] Installing libquadmath-devel- 100% | 22.7 MiB/s | 23.3 KiB | 00m00s [139/161] Installing gcc-gfortran-0:14. 100% | 442.8 MiB/s | 37.2 MiB | 00m00s [140/161] Installing boost-test-0:1.83. 100% | 312.7 MiB/s | 640.4 KiB | 00m00s [141/161] Installing boost-stacktrace-0 100% | 64.5 MiB/s | 66.0 KiB | 00m00s [142/161] Installing boost-serializatio 100% | 428.8 MiB/s | 439.1 KiB | 00m00s [143/161] Installing boost-random-0:1.8 100% | 0.0 B/s | 30.7 KiB | 00m00s [144/161] Installing boost-program-opti 100% | 267.3 MiB/s | 273.8 KiB | 00m00s [145/161] Installing boost-nowide-0:1.8 100% | 0.0 B/s | 25.8 KiB | 00m00s [146/161] Installing boost-math-0:1.83. 100% | 317.5 MiB/s | 650.3 KiB | 00m00s [147/161] Installing boost-iostreams-0: 100% | 93.5 MiB/s | 95.7 KiB | 00m00s [148/161] Installing boost-contract-0:1 100% | 101.7 MiB/s | 104.2 KiB | 00m00s [149/161] Installing boost-0:1.83.0-5.f 100% | 0.0 B/s | 1.7 KiB | 00m00s [150/161] Installing gsl-0:2.7.1-8.fc41 100% | 403.6 MiB/s | 3.2 MiB | 00m00s [151/161] Installing zlib-ng-compat-dev 100% | 102.0 MiB/s | 104.5 KiB | 00m00s [152/161] Installing hdf5-devel-0:1.12. 100% | 389.7 MiB/s | 3.9 MiB | 00m00s [153/161] Installing armadillo-devel-0: 100% | 437.5 MiB/s | 7.4 MiB | 00m00s [154/161] Installing gsl-devel-0:2.7.1- 100% | 71.8 MiB/s | 1.7 MiB | 00m00s [155/161] Installing boost-devel-0:1.83 100% | 339.0 MiB/s | 145.8 MiB | 00m00s [156/161] Installing gcc-c++-0:14.1.1-4 100% | 453.7 MiB/s | 38.1 MiB | 00m00s [157/161] Installing gcc-plugin-annobin 100% | 4.8 MiB/s | 58.6 KiB | 00m00s >>> Running trigger-install scriptlet: redhat-rpm-config-0:291-1.fc41.noarch >>> Stop trigger-install scriptlet: redhat-rpm-config-0:291-1.fc41.noarch [158/161] Installing annobin-plugin-gcc 100% | 68.1 MiB/s | 976.1 KiB | 00m00s >>> Running trigger-install scriptlet: redhat-rpm-config-0:291-1.fc41.noarch >>> Stop trigger-install scriptlet: redhat-rpm-config-0:291-1.fc41.noarch [159/161] Installing add-determinism-0: 100% | 366.4 MiB/s | 2.6 MiB | 00m00s [160/161] Installing htslib-devel-0:1.1 100% | 405.8 MiB/s | 415.5 KiB | 00m00s [161/161] Installing perl-generators-0: 100% | 132.5 KiB/s | 23.2 KiB | 00m00s >>> Running trigger-install scriptlet: glibc-common-0:2.39.9000-18.fc41.x86_64 >>> Stop trigger-install scriptlet: glibc-common-0:2.39.9000-18.fc41.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 Warning: skipped PGP checks for 159 package(s). Finish: build setup for mmseq-1.0.11-19.fc41.src.rpm Start: rpmbuild mmseq-1.0.11-19.fc41.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1706140800 Executing(%mkbuilddir): /bin/sh -e /var/tmp/rpm-tmp.jAWrqR + umask 022 + cd /builddir/build/BUILD/mmseq-1.0.11-build + test -d /builddir/build/BUILD/mmseq-1.0.11-build + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w /builddir/build/BUILD/mmseq-1.0.11-build + /usr/bin/rm -rf /builddir/build/BUILD/mmseq-1.0.11-build + /usr/bin/mkdir -p /builddir/build/BUILD/mmseq-1.0.11-build + /usr/bin/mkdir -p /builddir/build/BUILD/mmseq-1.0.11-build/SPECPARTS + RPM_EC=0 ++ jobs -p + exit 0 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.P1AEQm + umask 022 + cd /builddir/build/BUILD/mmseq-1.0.11-build + cd /builddir/build/BUILD/mmseq-1.0.11-build + rm -rf mmseq-1.0.11 + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/1.0.11.zip + STATUS=0 + '[' 0 -ne 0 ']' + cd mmseq-1.0.11 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . Patch #2 (mmseq-zlib.patch): + echo 'Patch #2 (mmseq-zlib.patch):' + /usr/bin/patch --no-backup-if-mismatch -f -p1 -b --suffix .mmseq-zlib.patch --fuzz=0 patching file src/Makefile + rm -f bin/offsetGTF-linux bin/postdiff-linux + sed -e s/-lblas/-lflexiblas/g -e s/-llapack/-lflexiblas/g -i src/Makefile + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.Psvppx + umask 022 + cd /builddir/build/BUILD/mmseq-1.0.11-build + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd mmseq-1.0.11 + cd src + make -j4 'CXXFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer' g++ -O3 -c sokal.cc g++ -fopenmp -O3 -c uh.cpp g++ -DVERSION=1.0.11 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fopenmp -O3 hitsio.cpp hitsio.hpp -c hitsio.cpp gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o fasta.o fasta.c g++ -DVERSION=1.0.11 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O3 offsetGTF.cpp -o ../bin/offsetGTF offsetGTF.cpp: In function ‘int main(int, char**)’: offsetGTF.cpp:115:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 115 | while(gff_ind < gff_positions[chrom].size()) { | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ offsetGTF.cpp:117:57: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} and ‘__gnu_cxx::__alloc_traits, int>::value_type’ {aka ‘int’} [-Wsign-compare] 117 | pos + tokens[3].size() - tokens[4].size() >= gff_positions[chrom][gff_ind]) { offsetGTF.cpp:114:11: warning: unused variable ‘curoff’ [-Wunused-variable] 114 | int curoff=offset; | ^~~~~~ offsetGTF.cpp:150:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 150 | while(gff_ind < gff_positions[prevchrom].size()) { | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ offsetGTF.cpp:163:53: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} and ‘__gnu_cxx::__alloc_traits, int>::value_type’ {aka ‘int’} [-Wsign-compare] 163 | pos + tokens[3].size() - tokens[4].size() >= gff_positions[chrom][gff_ind]) { offsetGTF.cpp:177:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 177 | while(gff_ind < gff_positions[chrom].size() && gff_positions[chrom][gff_ind] <= pos) { | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ offsetGTF.cpp:235:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 235 | for(int i=5; i < tokens.size(); i++) { | ~~^~~~~~~~~~~~~~~ offsetGTF.cpp:237:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 237 | if(i < tokens.size()-1) { | ~~^~~~~~~~~~~~~~~~~ offsetGTF.cpp:108:7: warning: unused variable ‘gff_pos’ [-Wunused-variable] 108 | int gff_pos= -1; | ^~~~~~~ g++ -DVERSION=1.0.11 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O3 t2g_hits.cpp -o ../bin/t2g_hits t2g_hits.cpp: In function ‘int main(int, char**)’: t2g_hits.cpp:90:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 90 | for(int i=2; i < tokens.size(); i++) { | ~~^~~~~~~~~~~~~~~ t2g_hits.cpp:112:13: warning: ignoring return value of ‘_FIter std::unique(_FIter, _FIter) [with _FIter = __gnu_cxx::__normal_iterator<__cxx11::basic_string*, vector<__cxx11::basic_string > >]’, declared with attribute ‘nodiscard’ [-Wunused-result] 112 | unique(comb.begin(), comb.end()); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/algorithm:61, from t2g_hits.cpp:27: /usr/include/c++/14/bits/stl_algo.h:891:5: note: declared here 891 | unique(_ForwardIterator __first, _ForwardIterator __last) | ^~~~~~ g++ -DVERSION=1.0.11 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fopenmp -O2 bms.cpp bms.hpp -c bms.cpp hitsio.cpp: In member function ‘void HitsfileWriter::writeHeaderSchema0()’: hitsio.cpp:163:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 163 | for(int i = 0; i < transcriptName.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~ hitsio.cpp: In member function ‘void HitsfileWriter::writeReadMapRecordSchema0()’: hitsio.cpp:184:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 184 | for(int i = 0; i < currentReadTranscripts.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hitsio.cpp: In member function ‘void HitsfileWriter::writeHeaderSchema1()’: hitsio.cpp:24:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 24 | if (VAL > numeric_limits::max()) { \ | ^ hitsio.cpp:191:9: note: in expansion of macro ‘WRITE_UINT’ 191 | WRITE_UINT(ofs, hitsfileSchema); | ^~~~~~~~~~ hitsio.cpp:193:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 193 | for(int i = 0; i < transcriptName.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~ hitsio.cpp:24:17: warning: comparison of integer expressions of different signedness: ‘std::map, int>::mapped_type’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare] 24 | if (VAL > numeric_limits::max()) { \ hitsio.cpp:196:17: note: in expansion of macro ‘WRITE_UINT’ 196 | WRITE_UINT(ofs, transcriptTrueLength[transcriptName[i] ]) | ^~~~~~~~~~ hitsio.cpp: In member function ‘void HitsfileWriter::writeReadMapRecordSchema1()’: hitsio.cpp:236:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 236 | for(int i = 0; i < currentReadTranscripts.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hitsio.cpp: In member function ‘void HitsfileReader::readHeaderSchema1(std::vector >*, std::map, double>*, std::map, int>*, std::map, std::vector > >*, std::vector > >*)’: hitsio.cpp:356:16: warning: unused variable ‘nextStrLen’ [-Wunused-variable] 356 | size_t nextStrLen; | ^~~~~~~~~~ hitsio.cpp: In member function ‘bool HitsfileReader::readReadMapRecordTranscriptID(std::string&)’: hitsio.cpp:447:1: warning: control reaches end of non-void function [-Wreturn-type] 447 | } | ^ g++ -DVERSION=1.0.11 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O3 fasta.o extract_transcripts.cpp -o ../bin/extract_transcripts g++ -DVERSION=1.0.11 -DARMA_64BIT_WORD -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fopenmp -O3 uh.o sokal.o mmcollapse.cpp -o ../bin/mmcollapse -lgsl -lgslcblas -lboost_regex -lhts -lboost_iostreams -lflexiblas -lflexiblas -Wl,--as-needed -lz -lgfortran extract_transcripts.cpp: In function ‘int main(int, char**)’: extract_transcripts.cpp:122:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 122 | for(int i=0; i < tokens2.size(); i++) { | ~~^~~~~~~~~~~~~~~~ extract_transcripts.cpp:169:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 169 | for(int i=0; i < tokens.size(); i++) { | ~~^~~~~~~~~~~~~~~ extract_transcripts.cpp:195:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 195 | for(int i=0; i < it->starts()->size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~ extract_transcripts.cpp:203:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 203 | while(faline < stitch.size()) { | ~~~~~~~^~~~~~~~~~~~~~~ extract_transcripts.cpp:108:7: warning: unused variable ‘line’ [-Wunused-variable] 108 | int line=0; | ^~~~ bms.cpp: In member function ‘arma::Col BMS::m2v(arma::Mat)’: bms.cpp:36:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 36 | for(int i=0; i < P.n_cols; i++) { | ~~^~~~~~~~~~ bms.cpp:37:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 37 | for(int j=0; j < P.n_rows; j++) { | ~~^~~~~~~~~~ bms.cpp: In member function ‘std::vector BMS::meanvar(arma::Col)’: bms.cpp:76:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 76 | for(int i=0;i < v.n_elem; i++) { | ~~^~~~~~~~~~ bms.cpp: In member function ‘void BMS::print(bool)’: bms.cpp:93:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 93 | for(int feature=0; feature < y->n_rows; feature++) { | ~~~~~~~~^~~~~~~~~~~ bms.cpp:97:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 97 | for(int i=0; i < M.n_cols; i++) { | ~~^~~~~~~~~~ bms.cpp:102:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 102 | for(int l=0; l < P[model].n_cols; l++) { | ~~^~~~~~~~~~~~~~~~~ bms.cpp: In member function ‘void BMS::printtune(int)’: bms.cpp:132:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 132 | for(int feature=0; feature < y->n_rows; feature++) { | ~~~~~~~~^~~~~~~~~~~ bms.cpp: In member function ‘void BMS::set_pseudoprior_alpha()’: bms.cpp:185:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 185 | for(int j=0; j < y->n_rows; j++) { | ~~^~~~~~~~~~~ bms.cpp: In member function ‘void BMS::set_pseudoprior_beta()’: bms.cpp:253:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 253 | for(int j=0; j < y->n_rows; j++) { | ~~^~~~~~~~~~~ bms.cpp:255:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 255 | for(int b=0; b < M.n_cols; b++) { | ~~^~~~~~~~~~ bms.cpp: In member function ‘void BMS::set_pseudoprior_eta()’: bms.cpp:332:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 332 | for(int j=0; j < y->n_rows; j++) { | ~~^~~~~~~~~~~ bms.cpp:334:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 334 | for(int c=0; c < P[model].n_cols; c++) { | ~~^~~~~~~~~~~~~~~~~ bms.cpp: In member function ‘void BMS::set_pseudoprior_sigmasq()’: bms.cpp:415:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 415 | for(int j=0; j < y->n_rows; j++) { | ~~^~~~~~~~~~~ bms.cpp: In member function ‘void BMS::set_pseudoprior_lambda()’: bms.cpp:504:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 504 | for(int j=0; j < y->n_rows; j++) { | ~~^~~~~~~~~~~ bms.cpp:506:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 506 | for(int l=0; l < P[model].n_cols; l++) { | ~~^~~~~~~~~~~~~~~~~ bms.cpp: In member function ‘void BMS::set_pseudoprior_rho()’: bms.cpp:559:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 559 | for(int j=0; j < y->n_rows; j++) { | ~~^~~~~~~~~~~ bms.cpp: In member function ‘void BMS::copy_pseudo()’: bms.cpp:582:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 582 | for(int j=0; j < y->n_rows; j++) { | ~~^~~~~~~~~~~ bms.cpp:585:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 585 | for(int c=0; c < P[0].n_cols; c++) { | ~~^~~~~~~~~~~~~ bms.cpp: In member function ‘void BMS::update_alpha(int, int, bool)’: bms.cpp:603:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 603 | for(int j=0; j < y->n_cols; j++) { | ~~^~~~~~~~~~~ bms.cpp:610:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 610 | for(int i=0; i < y->n_cols; i++) { | ~~^~~~~~~~~~~ bms.cpp: In member function ‘void BMS::update_beta(int, int, bool)’: bms.cpp:631:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 631 | for(int j=0; j < y->n_cols; j++) { | ~~^~~~~~~~~~~ bms.cpp:638:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 638 | for(int i=0; i < M.n_cols; i++) { | ~~^~~~~~~~~~ bms.cpp:646:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 646 | for(int i=0; i < M.n_cols; i++) { | ~~^~~~~~~~~~ bms.cpp:651:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 651 | for(int i=0; i < M.n_cols; i++) { | ~~^~~~~~~~~~ bms.cpp: In member function ‘void BMS::update_eta(int, int, bool)’: bms.cpp:663:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 663 | for(int l=0; l < P[model].n_cols; l++) { | ~~^~~~~~~~~~~~~~~~~ bms.cpp:666:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 666 | for(int i=0; i < y->n_cols; i++) { | ~~^~~~~~~~~~~ bms.cpp:673:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 673 | for(int i=0; i < y->n_cols; i++) { | ~~^~~~~~~~~~~ bms.cpp:681:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 681 | for(int l=0; l < P[model].n_cols; l++) { | ~~^~~~~~~~~~~~~~~~~ bms.cpp:686:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 686 | for(int l=0; l < P[model].n_cols; l++) { | ~~^~~~~~~~~~~~~~~~~ bms.cpp: In member function ‘void BMS::update_lambda(int, int, bool)’: bms.cpp:699:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 699 | for(int l=0; l < P[model].n_cols; l++) { | ~~^~~~~~~~~~~~~~~~~ bms.cpp:704:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 704 | for(int l=0; l < P[model].n_cols; l++) { | ~~^~~~~~~~~~~~~~~~~ bms.cpp:711:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 711 | for(int l=0; l < P[model].n_cols; l++) { | ~~^~~~~~~~~~~~~~~~~ bms.cpp: In member function ‘void BMS::update_sigmasq(int, int, bool, bool)’: bms.cpp:729:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 729 | for(int i=0; i < y->n_cols; i++) { | ~~^~~~~~~~~~~ bms.cpp:740:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 740 | for(int i=0; i < y->n_cols; i++) { | ~~^~~~~~~~~~~ bms.cpp:751:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 751 | for(int i=0; i < y->n_cols; i++) { | ~~^~~~~~~~~~~ bms.cpp:763:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 763 | for(int i=0; i < y->n_cols; i++) { | ~~^~~~~~~~~~~ bms.cpp: In member function ‘void BMS::update_sigmasq_RW(int, int, bool, bool)’: bms.cpp:877:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 877 | for(int i=0; i < y->n_cols; i++) { | ~~^~~~~~~~~~~ bms.cpp: In member function ‘double BMS::log_target_posterior(int, int)’: bms.cpp:931:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 931 | for(int i=0; i < y->n_cols; i++) { | ~~^~~~~~~~~~~ bms.cpp:940:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 940 | for(int j=0; j < M.n_cols; j++) { | ~~^~~~~~~~~~ bms.cpp:947:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 947 | for(int l=0; l < P[model].n_cols; l++) { | ~~^~~~~~~~~~~~~~~~~ bms.cpp: In member function ‘double BMS::log_target_pseudo(int, int)’: bms.cpp:968:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 968 | for(int l=0; l < M.n_cols; l++) { | ~~^~~~~~~~~~ bms.cpp:974:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 974 | for(int l=0; l < P[model].n_cols; l++) { | ~~^~~~~~~~~~~~~~~~~ bms.cpp: In member function ‘void BMS::print_pseudo()’: bms.cpp:1086:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 1086 | for(int l=0; l < M.n_cols; l++) { | ~~^~~~~~~~~~ bms.cpp:1089:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 1089 | for(int l=0; l < P[model].n_cols; l++) { | ~~^~~~~~~~~~~~~~~~~ bms.cpp:1100:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 1100 | for(int i=0; i < y->n_rows; i++) { | ~~^~~~~~~~~~~ bms.cpp:1103:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 1103 | for(int l=0; l < M.n_cols; l++) { | ~~^~~~~~~~~~ bms.cpp:1106:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 1106 | for(int l=0; l < P[model].n_cols; l++) { | ~~^~~~~~~~~~~~~~~~~ bms.cpp: In constructor ‘BMS::BMS(const arma::Mat*, const arma::Mat&, arma::Mat, arma::Mat, arma::Mat, arma::Mat, double, double, double, std::string, gsl_rng**, int, bool)’: bms.cpp:1188:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 1188 | for(int i=0; i < y->n_cols; i++) { | ~~^~~~~~~~~~~ bms.cpp:1192:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1192 | if(C(i,model)+1 > _n.size()) { | ~~~~~~~~~~~~~^~~~~~~~~~~ bms.cpp: In member function ‘void BMS::initialise_streams(std::string)’: bms.cpp:1348:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 1348 | for(int i=0; i < M.n_cols; i++) { | ~~^~~~~~~~~~ bms.cpp:1354:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 1354 | for(int i=0; i < M.n_cols; i++) { | ~~^~~~~~~~~~ bms.cpp:1360:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 1360 | for(int i=0; i < P[0].n_cols; i++) { | ~~^~~~~~~~~~~~~ bms.cpp:1366:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 1366 | for(int i=0; i < P[1].n_cols; i++) { | ~~^~~~~~~~~~~~~ bms.cpp:1372:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 1372 | for(int i=0; i < P[0].n_cols; i++) { | ~~^~~~~~~~~~~~~ bms.cpp:1378:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 1378 | for(int i=0; i < P[1].n_cols; i++) { | ~~^~~~~~~~~~~~~ mmcollapse.cpp: In function ‘void get_unidentifiable_transcripts(std::string, std::vector, std::allocator > >&, std::vector, std::allocator > >&, std::vector, std::allocator > >&, std::map, std::map, double> >&, std::map, std::map, double> >&, std::map, std::map, double> >&, std::map, int>&, std::vector, std::allocator > >&, std::map, bool>&)’: mmcollapse.cpp:158:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 158 | for(int i=0; i < tokens.size(); i++) { | ~~^~~~~~~~~~~~~~~ mmcollapse.cpp:213:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 213 | for(int i=0; i < tokens2.size(); i++) isIdent[tokens2[i]]=1; | ~~^~~~~~~~~~~~~~~~ mmcollapse.cpp:259:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 259 | for(int i=0; i < tokens.size(); i++) { | ~~^~~~~~~~~~~~~~~ mmcollapse.cpp: In function ‘void collapse(arma::cube&, std::vector, std::allocator > >&, std::map, int>&, std::vector >)’: mmcollapse.cpp:400:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 400 | for(int s=0; s < R.n_slices; s++) { | ~~^~~~~~~~~~~~ mmcollapse.cpp:401:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 401 | for(int t=0; t < candidates.size(); t++) { | ~~^~~~~~~~~~~~~~~~~~~ mmcollapse.cpp:402:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 402 | for(int j=1; j < indexes.size(); j++) { | ~~^~~~~~~~~~~~~~~~ mmcollapse.cpp:414:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 414 | for(int j=1; j < indexes.size(); j++) { | ~~^~~~~~~~~~~~~~~~ mmcollapse.cpp:417:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 417 | for(int i=0; i < R.n_cols; i++) { | ~~^~~~~~~~~~ mmcollapse.cpp:426:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 426 | for(int i=0; i < indexes.size(); i++) { | ~~^~~~~~~~~~~~~~~~ mmcollapse.cpp:431:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 431 | for(int i=1; i < tset.size(); i++) { | ~~^~~~~~~~~~~~~ mmcollapse.cpp:437:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 437 | for(int i=1; i < indexes.size(); i++) { | ~~^~~~~~~~~~~~~~~~ mmcollapse.cpp: In function ‘std::map join_traces(arma::mat&, std::vector, std::allocator > >&, std::vector, std::allocator > >)’: mmcollapse.cpp:445:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 445 | for(int t=0; t < allnames.size(); t++) tmap[allnames[t]]=t; | ~~^~~~~~~~~~~~~~~~~ mmcollapse.cpp:452:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 452 | for(int c=0; c < candidates.size(); c++) { | ~~^~~~~~~~~~~~~~~~~~~ mmcollapse.cpp:456:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 456 | for(int t=0; t < tokens.size(); t++) { | ~~^~~~~~~~~~~~~~~ mmcollapse.cpp:464:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 464 | for(int t=1; t < indexes.size(); t++) { | ~~^~~~~~~~~~~~~~~~ mmcollapse.cpp:469:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 469 | for(int t=1; t < indexes.size(); t++) { | ~~^~~~~~~~~~~~~~~~ mmcollapse.cpp:476:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 476 | for(int i=0; i < toshed.size(); i++) { | ~~^~~~~~~~~~~~~~~ mmcollapse.cpp: In function ‘void mean_corrs(const arma::cube&, const arma::umat&, arma::mat&, arma::mat&, std::vector >, std::vector >, double)’: mmcollapse.cpp:486:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 486 | for(int v= 0; v < R.n_rows; v++) { | ~~^~~~~~~~~~ mmcollapse.cpp:492:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘arma::uword’ {aka ‘long long unsigned int’} [-Wsign-compare] 492 | for(int i=0; i < u.size(); i++) { | ~~^~~~~~~~~~ mmcollapse.cpp: In function ‘void get_corrs(arma::cube&, arma::mat&, const std::vector, std::allocator > >&, std::map, int>&)’: mmcollapse.cpp:519:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 519 | for(int s=0; s < basenames.size(); s++) { | ~~^~~~~~~~~~~~~~~~~~ mmcollapse.cpp:543:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 543 | for(int t=0; t < tokens.size(); t++) { | ~~^~~~~~~~~~~~~~~ mmcollapse.cpp: In function ‘int main(int, char**)’: mmcollapse.cpp:632:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 632 | for(int i=1; i < basenames.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~ mmcollapse.cpp:691:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 691 | for(int s=0; s < basenames.size(); s++) { | ~~^~~~~~~~~~~~~~~~~~ mmcollapse.cpp:707:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 707 | for(int i=0; i < candidates.size(); i++) ts.push_back(i); | ~~^~~~~~~~~~~~~~~~~~~ mmcollapse.cpp:732:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 732 | for(int i=0 ;i < maxcorrs.size(); i++) { | ~~^~~~~~~~~~~~~~~~~ mmcollapse.cpp:738:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 738 | for(int i=0 ;i < mincorrs.size(); i++) { | ~~^~~~~~~~~~~~~~~~~ mmcollapse.cpp:802:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 802 | for(int i=0 ;i < maxcorrs.size(); i++) { | ~~^~~~~~~~~~~~~~~~~ mmcollapse.cpp:808:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 808 | for(int i=0 ;i < mincorrs.size(); i++) { | ~~^~~~~~~~~~~~~~~~~ mmcollapse.cpp:827:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 827 | for(int s=0; s < basenames.size(); s++) { | ~~^~~~~~~~~~~~~~~~~~ mmcollapse.cpp:852:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 852 | for(int t=0; t < tokens.size(); t++) { | ~~^~~~~~~~~~~~~~~ mmcollapse.cpp:882:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 882 | for(int t=0; t < tokens2.size(); t++) { | ~~^~~~~~~~~~~~~~~~ mmcollapse.cpp:934:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 934 | for(int t=0; t < M.n_cols; t++) { | ~~^~~~~~~~~~ mmcollapse.cpp:963:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 963 | for(int i=1; i < tokens2.size(); i++) { | ~~^~~~~~~~~~~~~~~~ mmcollapse.cpp:976:21: warning: comparison of integer expressions of different signedness: ‘boost::numeric::ublas::compressed_matrix::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 976 | if(MM.size1() < i+1 ) factor1=2; | ~~~~~~~~~~~^~~~~ mmcollapse.cpp:977:21: warning: comparison of integer expressions of different signedness: ‘boost::numeric::ublas::compressed_matrix::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 977 | if(MM.size2() < j+1 ) factor2=2; | ~~~~~~~~~~~^~~~~ mmcollapse.cpp:1010:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1010 | for(int t=0; t < ids.size(); t++) { | ~~^~~~~~~~~~~~ mmcollapse.cpp:1083:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1083 | for(int i=0; i < ids.size(); i++) { | ~~^~~~~~~~~~~~ mmcollapse.cpp:1092:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 1092 | for(int v = 0; v < M.n_cols; v++) { | ~~^~~~~~~~~~ mmcollapse.cpp:840:9: warning: unused variable ‘isident’ [-Wunused-variable] 840 | int isident=0; | ^~~~~~~ hitsio.cpp: In member function ‘void HitsfileWriter::writeHeaderSchema0()’: hitsio.cpp:163:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 163 | for(int i = 0; i < transcriptName.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~ hitsio.cpp: In member function ‘void HitsfileWriter::writeReadMapRecordSchema0()’: hitsio.cpp:184:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 184 | for(int i = 0; i < currentReadTranscripts.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hitsio.cpp: In member function ‘void HitsfileWriter::writeHeaderSchema1()’: hitsio.cpp:24:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 24 | if (VAL > numeric_limits::max()) { \ | ^ hitsio.cpp:191:9: note: in expansion of macro ‘WRITE_UINT’ 191 | WRITE_UINT(ofs, hitsfileSchema); | ^~~~~~~~~~ hitsio.cpp:193:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 193 | for(int i = 0; i < transcriptName.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~ hitsio.cpp:24:17: warning: comparison of integer expressions of different signedness: ‘std::map, int>::mapped_type’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare] 24 | if (VAL > numeric_limits::max()) { \ hitsio.cpp:196:17: note: in expansion of macro ‘WRITE_UINT’ 196 | WRITE_UINT(ofs, transcriptTrueLength[transcriptName[i] ]) | ^~~~~~~~~~ hitsio.cpp: In member function ‘void HitsfileWriter::writeReadMapRecordSchema1()’: hitsio.cpp:236:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 236 | for(int i = 0; i < currentReadTranscripts.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hitsio.cpp: In member function ‘void HitsfileReader::readHeaderSchema1(std::vector >*, std::map, double>*, std::map, int>*, std::map, std::vector > >*, std::vector > >*)’: hitsio.cpp:356:16: warning: unused variable ‘nextStrLen’ [-Wunused-variable] 356 | size_t nextStrLen; | ^~~~~~~~~~ hitsio.cpp: In member function ‘bool HitsfileReader::readReadMapRecordTranscriptID(std::string&)’: hitsio.cpp:447:1: warning: control reaches end of non-void function [-Wreturn-type] 447 | } | ^ g++ -DVERSION=1.0.11 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fopenmp -O3 sokal.o uh.o hitsio.o mmseq.cpp -o ../bin/mmseq -lgsl -lgslcblas -lboost_regex -lhts -lboost_iostreams -lflexiblas -lflexiblas -Wl,--as-needed -lz -lgfortran g++ -DVERSION=1.0.11 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fopenmp -O3 fasta.o hitsio.o bam2hits.cpp -o ../bin/bam2hits -lgsl -lgslcblas -lboost_regex -lhts -lboost_iostreams -lflexiblas -lflexiblas -Wl,--as-needed -lz -lgfortran mmseq.cpp: In function ‘std::vector meanvar(std::vector, double, double)’: mmseq.cpp:130:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 130 | for(int i=0;i < v.size(); i++) { | ~~^~~~~~~~~~ mmseq.cpp: In function ‘int main(int, char**)’: mmseq.cpp:244:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 244 | for(int i=0; i < tokens.size(); i++) { | ~~^~~~~~~~~~~~~~~ mmseq.cpp:423:20: warning: comparison of integer expressions of different signedness: ‘boost::numeric::ublas::compressed_matrix::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 423 | if(M.size1() < m ) factor1=2; | ~~~~~~~~~~^~~ mmseq.cpp:424:20: warning: comparison of integer expressions of different signedness: ‘boost::numeric::ublas::compressed_matrix::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 424 | if(M.size2() < n ) factor2=2; | ~~~~~~~~~~^~~ mmseq.cpp:594:23: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 594 | for(unsigned t=0; t < n; t++) { | ~~^~~ mmseq.cpp:736:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 736 | for(unsigned t=0; t < n; t++) | ~~^~~ mmseq.cpp:765:27: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 765 | for(unsigned t=0; t < n; t++) | ~~^~~ mmseq.cpp:774:11: warning: unused variable ‘threadid’ [-Wunused-variable] 774 | int threadid=OMP_GET_THREAD_NUM; | ^~~~~~~~ mmseq.cpp:829:23: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 829 | for(unsigned t=0; t < n; t++) | ~~^~~ mmseq.cpp:912:27: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 912 | for(unsigned t=0; t < n; t++) { | ~~^~~ mmseq.cpp:940:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 940 | for(int i=0; i < identical_transcripts.size() * trace_length; i++) mu_trace_identical[i]=0; | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mmseq.cpp:961:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::map, std::vector > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 961 | for(int i=0; i < gene2transcripts.size() * trace_length; i++) mu_trace_gene[i]=0; | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1098:23: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 1098 | for(unsigned t=0; t < n; t++) gofs << indexSid[t] << " "; | ~~^~~ mmseq.cpp:1112:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1112 | for(int i=0; i < percentiles.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1136:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1136 | for(int j=0; j < percentiles.size(); j++) { | ~~^~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1144:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1144 | for(int j=0; j < percentiles.size(); j++) { | ~~^~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1149:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1149 | for(int i=0;i < identical_transcripts.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1156:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1156 | for(int j=0; j < percentiles.size(); j++) { | ~~^~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1161:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::map, std::vector > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1161 | for(int i=0;i < gene2transcripts.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1168:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1168 | for(int j=0; j < percentiles.size(); j++) { | ~~^~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1179:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1179 | for(int j=0; j < percentiles.size(); j++) { | ~~^~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1189:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1189 | for(int j=0; j < percentiles.size(); j++) { | ~~^~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1208:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1208 | for(int t=0; t < identical_transcripts.size() ; t++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1212:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::map, std::vector > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1212 | for(int t=0; t < gene2transcripts.size(); t++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1226:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1226 | for(int i=0; i < identical_transcripts.size() ; i++) meanmu_identical[i] /= trace_length; | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1227:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::map, std::vector > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1227 | for(int i=0; i < gene2transcripts.size(); i++) meanmu_gene[i]/= trace_length; | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1330:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1330 | for(int t=0; t < identical_transcripts.size(); t++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1349:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::map, std::vector > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1349 | for(int g=0; g < gene2transcripts.size(); g++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1473:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1473 | for(int i=0; i < percentiles.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1475:9: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1475 | if(i==percentiles.size()-1) { | ~^~~~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1482:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1482 | for(int i=0; i < percentiles.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1484:9: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1484 | if(i==percentiles.size()-1) { | ~^~~~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1506:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1506 | for(int i=0; i < percentiles.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1508:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1508 | if(i==percentiles.size()-1) { | ~^~~~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1514:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1514 | for(int i=0; i < percentiles.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1516:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1516 | if(i==percentiles.size()-1) { | ~^~~~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1536:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1536 | for(int i=0; i < percentiles.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1538:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1538 | if(i==percentiles.size()-1) { | ~^~~~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1544:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1544 | for(int i=0; i < percentiles.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1546:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1546 | if(i==percentiles.size()-1) { | ~^~~~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1560:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1560 | for(int i=0; i < percentiles.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1562:9: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1562 | if(i==percentiles.size()-1) { | ~^~~~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1582:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1582 | for(int i=0; i < percentiles.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1584:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1584 | if(i==percentiles.size()-1) { | ~^~~~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1599:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1599 | for(int i=0; i < percentiles.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1601:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1601 | if(i==percentiles.size()-1) { | ~^~~~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1619:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1619 | for(int i=0; i < percentiles.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1621:9: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1621 | if(i==percentiles.size()-1) { | ~^~~~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1644:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1644 | for(int i=0; i < percentiles.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1646:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1646 | if(i==percentiles.size()-1) { | ~^~~~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1656:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1656 | for(int i=0; i < percentiles.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1658:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1658 | if(i==percentiles.size()-1) { | ~^~~~~~~~~~~~~~~~~~~~~~ mmseq.cpp:308:8: warning: unused variable ‘buf16384’ [-Wunused-variable] 308 | char buf16384[16384]; | ^~~~~~~~ mmseq.cpp:391:8: warning: variable ‘doublehit’ set but not used [-Wunused-but-set-variable] 391 | bool doublehit; | ^~~~~~~~~ bam2hits.cpp: In function ‘void outputMergeHeaders(std::vector&, char, const char*, bool, HitsfileWriter&)’: bam2hits.cpp:109:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 109 | for(int i=0; i < sortedfastas.size()-1; i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~ bam2hits.cpp:119:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 119 | for(int j=0; j < curSet.size()-1; j++) { | ~~^~~~~~~~~~~~~~~~~ bam2hits.cpp:137:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 137 | for(int j=0; j < curSet.size()-1; j++) { | ~~^~~~~~~~~~~~~~~~~ bam2hits.cpp: In function ‘std::vector repetitiveTranscriptFilter(std::vector&, int)’: bam2hits.cpp:218:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 218 | for(int j=0; j < alns.size(); j++) { | ~~^~~~~~~~~~~~~ bam2hits.cpp:219:10: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 219 | if(i < torem.size() && j==torem[i]) { | ~~^~~~~~~~~~~~~~ bam2hits.cpp: In function ‘int main(int, char**)’: bam2hits.cpp:518:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 518 | if(_B != tg[0].size()-2) { | ~~~^~~~~~~~~~~~~~~~~ bam2hits.cpp:520:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 520 | if(_A == tg[0].size()-2) { | ~~~^~~~~~~~~~~~~~~~~ bam2hits.cpp:522:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 522 | if(_A != tg[1].size()-2) { | ~~~^~~~~~~~~~~~~~~~~ bam2hits.cpp:558:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 558 | for(int i=1; i < tokens2.size(); i++) { | ~~^~~~~~~~~~~~~~~~ bam2hits.cpp:609:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 609 | for(int i=0; i < fastas.size(); i++) { | ~~^~~~~~~~~~~~~~~ bam2hits.cpp:645:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 645 | for(int i=0;i < fastas.size(); i++) transcriptCounts[i] /= (double)fastas[i].seq().size(); | ~~^~~~~~~~~~~~~~~ bam2hits.cpp:659:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 659 | for(int i=0; i < fastas.size(); i++) { | ~~^~~~~~~~~~~~~~~ bam2hits.cpp:662:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 662 | for(int j =0; j < fastas[i].seq().size(); j++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~ bam2hits.cpp:663:44: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 663 | int tag = (j <= MSEQ_BEFORE || j >= fastas[i].seq().size()-MSEQ_AFTER) ? -2 : 0; | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bam2hits.cpp:791:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 791 | for(int j=MSEQ_BEFORE + 1; j <= fastas[i].seq().length()-MSEQ_AFTER; j++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bam2hits.cpp:920:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 920 | for(int j=1; j < frequencies.size()-WINDOWFORISIZEMODE + 1; j++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bam2hits.cpp:948:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 948 | for(int i=0; i < testIsizes.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~ bam2hits.cpp:959:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 959 | for(int i=0; i < heights.size(); i++) { | ~~^~~~~~~~~~~~~~~~ bam2hits.cpp:997:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 997 | for(int fl=1; fl <= (it->seq()).size(); fl++) { | ~~~^~~~~~~~~~~~~~~~~~~~~ bam2hits.cpp:1091:56: warning: comparing the result of pointer addition ‘(bam_aux_get(((const bam1_t*)line), ((const char*)"NM")) + ((sizetype)ait.__gnu_cxx::__normal_iterator >::operator->()->Alignment::NM()))’ and NULL [-Waddress] 1091 | ait->NM(ait->NM() + bam_aux_get(line,"NM") == NULL ? 0 : bam_aux2i(bam_aux_get(line,"NM"))); | ^ bms.cpp: In member function ‘arma::Col BMS::m2v(arma::Mat)’: bms.cpp:36:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 36 | for(int i=0; i < P.n_cols; i++) { | ~~^~~~~~~~~~ bms.cpp:37:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 37 | for(int j=0; j < P.n_rows; j++) { | ~~^~~~~~~~~~ bms.cpp: In member function ‘std::vector BMS::meanvar(arma::Col)’: bms.cpp:76:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 76 | for(int i=0;i < v.n_elem; i++) { | ~~^~~~~~~~~~ bms.cpp: In member function ‘void BMS::print(bool)’: bms.cpp:93:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 93 | for(int feature=0; feature < y->n_rows; feature++) { | ~~~~~~~~^~~~~~~~~~~ bms.cpp:97:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 97 | for(int i=0; i < M.n_cols; i++) { | ~~^~~~~~~~~~ bms.cpp:102:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 102 | for(int l=0; l < P[model].n_cols; l++) { | ~~^~~~~~~~~~~~~~~~~ bms.cpp: In member function ‘void BMS::printtune(int)’: bms.cpp:132:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 132 | for(int feature=0; feature < y->n_rows; feature++) { | ~~~~~~~~^~~~~~~~~~~ bms.cpp: In member function ‘void BMS::set_pseudoprior_alpha()’: bms.cpp:185:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 185 | for(int j=0; j < y->n_rows; j++) { | ~~^~~~~~~~~~~ bms.cpp: In member function ‘void BMS::set_pseudoprior_beta()’: bms.cpp:253:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 253 | for(int j=0; j < y->n_rows; j++) { | ~~^~~~~~~~~~~ bms.cpp:255:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 255 | for(int b=0; b < M.n_cols; b++) { | ~~^~~~~~~~~~ bms.cpp: In member function ‘void BMS::set_pseudoprior_eta()’: bms.cpp:332:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 332 | for(int j=0; j < y->n_rows; j++) { | ~~^~~~~~~~~~~ bms.cpp:334:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 334 | for(int c=0; c < P[model].n_cols; c++) { | ~~^~~~~~~~~~~~~~~~~ bms.cpp: In member function ‘void BMS::set_pseudoprior_sigmasq()’: bms.cpp:415:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 415 | for(int j=0; j < y->n_rows; j++) { | ~~^~~~~~~~~~~ bms.cpp: In member function ‘void BMS::set_pseudoprior_lambda()’: bms.cpp:504:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 504 | for(int j=0; j < y->n_rows; j++) { | ~~^~~~~~~~~~~ bms.cpp:506:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 506 | for(int l=0; l < P[model].n_cols; l++) { | ~~^~~~~~~~~~~~~~~~~ bms.cpp: In member function ‘void BMS::set_pseudoprior_rho()’: bms.cpp:559:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 559 | for(int j=0; j < y->n_rows; j++) { | ~~^~~~~~~~~~~ bms.cpp: In member function ‘void BMS::copy_pseudo()’: bms.cpp:582:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 582 | for(int j=0; j < y->n_rows; j++) { | ~~^~~~~~~~~~~ bms.cpp:585:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 585 | for(int c=0; c < P[0].n_cols; c++) { | ~~^~~~~~~~~~~~~ bms.cpp: In member function ‘void BMS::update_alpha(int, int, bool)’: bms.cpp:603:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 603 | for(int j=0; j < y->n_cols; j++) { | ~~^~~~~~~~~~~ bms.cpp:610:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 610 | for(int i=0; i < y->n_cols; i++) { | ~~^~~~~~~~~~~ bms.cpp: In member function ‘void BMS::update_beta(int, int, bool)’: bms.cpp:631:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 631 | for(int j=0; j < y->n_cols; j++) { | ~~^~~~~~~~~~~ bms.cpp:638:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 638 | for(int i=0; i < M.n_cols; i++) { | ~~^~~~~~~~~~ bms.cpp:646:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 646 | for(int i=0; i < M.n_cols; i++) { | ~~^~~~~~~~~~ bms.cpp:651:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 651 | for(int i=0; i < M.n_cols; i++) { | ~~^~~~~~~~~~ bms.cpp: In member function ‘void BMS::update_eta(int, int, bool)’: bms.cpp:663:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 663 | for(int l=0; l < P[model].n_cols; l++) { | ~~^~~~~~~~~~~~~~~~~ bms.cpp:666:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 666 | for(int i=0; i < y->n_cols; i++) { | ~~^~~~~~~~~~~ bms.cpp:673:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 673 | for(int i=0; i < y->n_cols; i++) { | ~~^~~~~~~~~~~ bms.cpp:681:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 681 | for(int l=0; l < P[model].n_cols; l++) { | ~~^~~~~~~~~~~~~~~~~ bms.cpp:686:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 686 | for(int l=0; l < P[model].n_cols; l++) { | ~~^~~~~~~~~~~~~~~~~ bms.cpp: In member function ‘void BMS::update_lambda(int, int, bool)’: bms.cpp:699:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 699 | for(int l=0; l < P[model].n_cols; l++) { | ~~^~~~~~~~~~~~~~~~~ bms.cpp:704:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 704 | for(int l=0; l < P[model].n_cols; l++) { | ~~^~~~~~~~~~~~~~~~~ bms.cpp:711:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 711 | for(int l=0; l < P[model].n_cols; l++) { | ~~^~~~~~~~~~~~~~~~~ bms.cpp: In member function ‘void BMS::update_sigmasq(int, int, bool, bool)’: bms.cpp:729:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 729 | for(int i=0; i < y->n_cols; i++) { | ~~^~~~~~~~~~~ bms.cpp:740:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 740 | for(int i=0; i < y->n_cols; i++) { | ~~^~~~~~~~~~~ bms.cpp:751:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 751 | for(int i=0; i < y->n_cols; i++) { | ~~^~~~~~~~~~~ bms.cpp:763:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 763 | for(int i=0; i < y->n_cols; i++) { | ~~^~~~~~~~~~~ bms.cpp: In member function ‘void BMS::update_sigmasq_RW(int, int, bool, bool)’: bms.cpp:877:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 877 | for(int i=0; i < y->n_cols; i++) { | ~~^~~~~~~~~~~ bms.cpp: In member function ‘double BMS::log_target_posterior(int, int)’: bms.cpp:931:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 931 | for(int i=0; i < y->n_cols; i++) { | ~~^~~~~~~~~~~ bms.cpp:940:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 940 | for(int j=0; j < M.n_cols; j++) { | ~~^~~~~~~~~~ bms.cpp:947:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 947 | for(int l=0; l < P[model].n_cols; l++) { | ~~^~~~~~~~~~~~~~~~~ bms.cpp: In member function ‘double BMS::log_target_pseudo(int, int)’: bms.cpp:968:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 968 | for(int l=0; l < M.n_cols; l++) { | ~~^~~~~~~~~~ bms.cpp:974:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 974 | for(int l=0; l < P[model].n_cols; l++) { | ~~^~~~~~~~~~~~~~~~~ bms.cpp: In member function ‘void BMS::print_pseudo()’: bms.cpp:1086:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 1086 | for(int l=0; l < M.n_cols; l++) { | ~~^~~~~~~~~~ bms.cpp:1089:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 1089 | for(int l=0; l < P[model].n_cols; l++) { | ~~^~~~~~~~~~~~~~~~~ bms.cpp:1100:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 1100 | for(int i=0; i < y->n_rows; i++) { | ~~^~~~~~~~~~~ bms.cpp:1103:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 1103 | for(int l=0; l < M.n_cols; l++) { | ~~^~~~~~~~~~ bms.cpp:1106:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 1106 | for(int l=0; l < P[model].n_cols; l++) { | ~~^~~~~~~~~~~~~~~~~ bms.cpp: In constructor ‘BMS::BMS(const arma::Mat*, const arma::Mat&, arma::Mat, arma::Mat, arma::Mat, arma::Mat, double, double, double, std::string, gsl_rng**, int, bool)’: bms.cpp:1188:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 1188 | for(int i=0; i < y->n_cols; i++) { | ~~^~~~~~~~~~~ bms.cpp:1192:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1192 | if(C(i,model)+1 > _n.size()) { | ~~~~~~~~~~~~~^~~~~~~~~~~ bms.cpp: In member function ‘void BMS::initialise_streams(std::string)’: bms.cpp:1348:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 1348 | for(int i=0; i < M.n_cols; i++) { | ~~^~~~~~~~~~ bms.cpp:1354:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 1354 | for(int i=0; i < M.n_cols; i++) { | ~~^~~~~~~~~~ bms.cpp:1360:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 1360 | for(int i=0; i < P[0].n_cols; i++) { | ~~^~~~~~~~~~~~~ bms.cpp:1366:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 1366 | for(int i=0; i < P[1].n_cols; i++) { | ~~^~~~~~~~~~~~~ bms.cpp:1372:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 1372 | for(int i=0; i < P[0].n_cols; i++) { | ~~^~~~~~~~~~~~~ bms.cpp:1378:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 1378 | for(int i=0; i < P[1].n_cols; i++) { | ~~^~~~~~~~~~~~~ g++ -DVERSION=1.0.11 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fopenmp -O3 hitsio.o hitstools.cpp -o ../bin/hitstools -lgsl -lgslcblas -lboost_regex -lhts -lboost_iostreams -lflexiblas -lflexiblas -Wl,--as-needed -lz -lgfortran hitstools.cpp: In function ‘void convert(char*, std::string)’: hitstools.cpp:51:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 51 | for(int i = 0; i < transcriptName.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~ hitstools.cpp: In function ‘int main(int, char**)’: hitstools.cpp:96:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 96 | for(int i = 0; i < transcriptName.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~ hitstools.cpp:136:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 136 | for(int i = 0; i < transcriptName.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~ g++ -DVERSION=1.0.11 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fopenmp -O2 bms.o mmdiff.cpp -o ../bin/mmdiff -lgsl -lgslcblas -lboost_regex -lhts -lboost_iostreams -lflexiblas -lflexiblas -Wl,--as-needed -lz -lgfortran mmdiff.cpp: In function ‘void parse_mmseq(std::vector, std::allocator > >, std::vector, std::allocator > >&, arma::Mat&, arma::Mat&, arma::Mat&, int, int, double, bool)’: mmdiff.cpp:100:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 100 | for(int i=0; i < filenames.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~ mmdiff.cpp:111:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 111 | for(int j=0; j < tokens.size(); j++) { | ~~^~~~~~~~~~~~~~~ mmdiff.cpp:138:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 138 | if(k + 1 > features.size()) { | ~~~~~~^~~~~~~~~~~~~~~~~ mmdiff.cpp:147:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 147 | if(k+1 > y.n_rows) { | ~~~~^~~~~~~~~~ mmdiff.cpp:152:20: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 152 | if(!useprops && tokens[lmg_ind]=="NA" || useprops && tokens[mp_ind]=="NA") { | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ mmdiff.cpp:173:62: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 173 | if(range_start >=0 && range_end > range_start && range_end < y.n_rows) { | ~~~~~~~~~~^~~~~~~~~~ mmdiff.cpp:94:46: warning: variable ‘mcse_ind’ set but not used [-Wunused-but-set-variable] 94 | int feature_ind=-1, lmg_ind=-1, sd_ind=-1, mcse_ind=-1, iact_ind=-1, mp_ind=-1, sp_ind=-1, uh_ind=-1; | ^~~~~~~~ mmdiff.cpp:94:59: warning: variable ‘iact_ind’ set but not used [-Wunused-but-set-variable] 94 | int feature_ind=-1, lmg_ind=-1, sd_ind=-1, mcse_ind=-1, iact_ind=-1, mp_ind=-1, sp_ind=-1, uh_ind=-1; | ^~~~~~~~ mmdiff.cpp: In function ‘void apply_normalisation(std::vector, std::allocator > >, arma::Mat&, arma::Mat&, double)’: mmdiff.cpp:212:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 212 | for(int i=0; i < uh.n_rows; i++) { | ~~^~~~~~~~~~~ mmdiff.cpp:214:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 214 | for(int j=0; j < uh.n_cols; j++) { | ~~^~~~~~~~~~~ mmdiff.cpp:230:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 230 | for(int i=0; i < use.size(); i++) { | ~~^~~~~~~~~~~~ mmdiff.cpp:232:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 232 | for(int j=0; j < y.n_cols; j++) { | ~~^~~~~~~~~~ mmdiff.cpp:239:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 239 | for(int sample=0; sample < y.n_cols; sample++) { | ~~~~~~~^~~~~~~~~~ mmdiff.cpp:241:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 241 | for(int i=0; i < use.size(); i++) { | ~~^~~~~~~~~~~~ mmdiff.cpp:246:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 246 | for(int i=0; i < y.n_rows; i++) { | ~~^~~~~~~~~~ mmdiff.cpp: In function ‘void apply_permutation(arma::Mat&, arma::Mat&)’: mmdiff.cpp:257:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 257 | for(int j=0; j< y.n_cols; j++) randinds.push_back(j); | ~^~~~~~~~~~ mmdiff.cpp:258:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 258 | for(int i=0; i < y.n_rows; i++) { | ~~^~~~~~~~~~ mmdiff.cpp:259:19: warning: ‘void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator > >]’ is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations] 259 | random_shuffle(randinds.begin(), randinds.end()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/algorithm:61, from mmdiff.cpp:31: /usr/include/c++/14/bits/stl_algo.h:4491:5: note: declared here 4491 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last) | ^~~~~~~~~~~~~~ mmdiff.cpp:260:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 260 | for(int j=0; j < y.n_cols; j++) { | ~~^~~~~~~~~~ mmdiff.cpp: In function ‘void parse_matrices(std::string, arma::Mat&, arma::Mat&, arma::Mat&, arma::Mat&, int)’: mmdiff.cpp:310:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 310 | for(int t=0; t < tokens.size(); t++) { | ~~^~~~~~~~~~~~~~~ mmdiff.cpp: In function ‘int main(int, char**)’: mmdiff.cpp:420:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 420 | for(int i=0; i < arguments.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~ mmdiff.cpp:431:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 431 | for(int i=0; i < arguments.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~ mmdiff.cpp:439:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 439 | while(ss < arguments.size()) { | ~~~^~~~~~~~~~~~~~~~~~ mmdiff.cpp:451:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 451 | if(ss != arguments.size()) { | ~~~^~~~~~~~~~~~~~~~~~~ mmdiff.cpp:578:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 578 | for(int i=0; i < arguments.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~ mmdiff.cpp:640:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 640 | for(int i=0; i < simple_de.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~ mmdiff.cpp:759:17: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 759 | if(inburnin && iter == OUTLEN/10 || !inburnin && iter==tuneiters) { | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ mmdiff.cpp:764:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 764 | for(int feature=0; feature < features.size(); feature++) { | ~~~~~~~~^~~~~~~~~~~~~~~~~ mmdiff.cpp:837:17: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 837 | if(inburnin && iter % subsample_burnin ==0 || !inburnin && iter >= tuneiters && (iter - tuneiters) % subsample_iter == 0) { | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mmdiff.cpp:886:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 886 | for(int l=0; l < M.n_cols; l++) { | ~~^~~~~~~~~~ mmdiff.cpp:898:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 898 | for(int f=0; f < samplenames.size(); f++) { | ~~^~~~~~~~~~~~~~~~~~~~ mmdiff.cpp:902:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const std::__cxx11::basic_string::size_type’ {aka ‘const long unsigned int’} [-Wsign-compare] 902 | found2 = found2==string::npos ? -1 : found2; | ~~~~~~^~~~~~~~~~~~~~ mmdiff.cpp:907:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 907 | for(int f=0; f < samplenames.size(); f++) { | ~~^~~~~~~~~~~~~~~~~~~~ mmdiff.cpp:909:10: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 909 | if(f < samplenames.size()-1) cout << "\t"; | ~~^~~~~~~~~~~~~~~~~~~~~~ mmdiff.cpp:914:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 914 | for(int feature=0; feature < features.size(); feature++) { | ~~~~~~~~^~~~~~~~~~~~~~~~~ mmdiff.cpp:926:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 926 | for(int l=0; l < M.n_cols; l++) { | ~~^~~~~~~~~~ mmdiff.cpp:936:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 936 | for(int f=0; f < samplenames.size(); f++) { | ~~^~~~~~~~~~~~~~~~~~~~ mmdiff.cpp:939:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 939 | for(int f=0; f < samplenames.size(); f++) { | ~~^~~~~~~~~~~~~~~~~~~~ mmdiff.cpp:941:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 941 | if(f < samplenames.size()-1) cout << "\t"; | ~~^~~~~~~~~~~~~~~~~~~~~~ mmdiff.cpp:951:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 951 | for(int feature=0; feature < features.size(); feature++) { | ~~~~~~~~^~~~~~~~~~~~~~~~~ /usr/bin/ld: /tmp/ccCczShB.ltrans0.ltrans.o: in function `main': /builddir/build/BUILD/mmseq-1.0.11-build/mmseq-1.0.11/src/bam2hits.cpp:653:(.text.startup+0x25dd): warning: the use of `tmpnam' is dangerous, better use `mkstemp' + RPM_EC=0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.PnGt0K ++ jobs -p + exit 0 + umask 022 + cd /builddir/build/BUILD/mmseq-1.0.11-build + '[' /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT '!=' / ']' + rm -rf /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT ++ dirname /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT + mkdir -p /builddir/build/BUILD/mmseq-1.0.11-build + mkdir /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd mmseq-1.0.11 + rm -rf /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT + mkdir -p /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/bin + install -p -m 0755 bin/bam2hits /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/bin + install -p -m 0755 bin/extract_transcripts /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/bin + install -p -m 0755 bin/hitstools /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/bin + install -p -m 0755 bin/mmcollapse /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/bin + install -p -m 0755 bin/mmdiff /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/bin + install -p -m 0755 bin/mmseq /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/bin + install -p -m 0755 bin/offsetGTF /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/bin + install -p -m 0755 bin/t2g_hits /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/bin + install -p -m 0755 bin/fastagrep.sh bin/mouse_strain_transcriptome.sh bin/usage.sh /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/bin + install -p -m 0755 bin/filterGTF.rb bin/haploref.rb bin/testregexp.rb /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/bin + install -p -m 0755 bin/ensembl_gtf_to_gff.pl /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/bin + /usr/bin/find-debuginfo -j4 --strict-build-id -m -i --build-id-seed 1.0.11-19.fc41 --unique-debug-suffix -1.0.11-19.fc41.x86_64 --unique-debug-src-base mmseq-1.0.11-19.fc41.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/mmseq-1.0.11-build/mmseq-1.0.11 find-debuginfo: starting Extracting debug info from 8 files DWARF-compressing 8 files sepdebugcrcfix: Updated 8 CRC32s, 0 CRC32s did match. Creating .debug symlinks for symlinks to ELF files Copying sources found by 'debugedit -l' to /usr/src/debug/mmseq-1.0.11-19.fc41.x86_64 542 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 mangling shebang in /usr/bin/ensembl_gtf_to_gff.pl from /usr/bin/env perl to #!/usr/bin/perl mangling shebang in /usr/bin/testregexp.rb from /usr/bin/env ruby to #!/usr/bin/ruby mangling shebang in /usr/bin/haploref.rb from /usr/bin/env ruby to #!/usr/bin/ruby mangling shebang in /usr/bin/filterGTF.rb from /usr/bin/env ruby to #!/usr/bin/ruby mangling shebang in /usr/bin/usage.sh from /bin/bash to #!/usr/bin/bash mangling shebang in /usr/bin/mouse_strain_transcriptome.sh from /bin/sh to #!/usr/bin/sh mangling shebang in /usr/bin/fastagrep.sh from /bin/bash to #!/usr/bin/bash + /usr/lib/rpm/brp-remove-la-files + env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j4 + /usr/lib/rpm/redhat/brp-python-hardlink + /usr/bin/add-determinism --brp -j4 /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT Cannot initialize handler pyc: ModuleNotFoundError: No module named 'marshalparser' [src/multiprocess.rs:66:9] &cmd = Command { program: "/usr/bin/add-determinism", args: [ "/usr/bin/add-determinism", "--socket", "3", "--brp", "--handler", "ar,jar,javadoc", ], env: CommandEnv { clear: false, vars: { "SOURCE_DATE_EPOCH": Some( "1706140800", ), }, }, create_pidfd: false, } Bye! Bye! Bye! Bye! Reading /builddir/build/BUILD/mmseq-1.0.11-build/SPECPARTS/rpm-debuginfo.specpart Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.qCJib3 + umask 022 + cd /builddir/build/BUILD/mmseq-1.0.11-build + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd mmseq-1.0.11 ++ bin/mmseq --version ++ true + test mmseq-1.0.11 = mmseq-1.0.11 + RPM_EC=0 ++ jobs -p + exit 0 Processing files: mmseq-1.0.11-19.fc41.x86_64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.1MYZhU + umask 022 + cd /builddir/build/BUILD/mmseq-1.0.11-build + cd mmseq-1.0.11 + DOCDIR=/builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/share/doc/mmseq + export LC_ALL=C.UTF-8 + LC_ALL=C.UTF-8 + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/share/doc/mmseq + cp -pr /builddir/build/BUILD/mmseq-1.0.11-build/mmseq-1.0.11/README.md /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/share/doc/mmseq + cp -pr /builddir/build/BUILD/mmseq-1.0.11-build/mmseq-1.0.11/COPYING /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/share/doc/mmseq + cp -pr /builddir/build/BUILD/mmseq-1.0.11-build/mmseq-1.0.11/doc /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/share/doc/mmseq + RPM_EC=0 ++ jobs -p + exit 0 Provides: mmseq = 1.0.11-19.fc41 mmseq(x86-64) = 1.0.11-19.fc41 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: /usr/bin/bash /usr/bin/perl /usr/bin/ruby /usr/bin/sh libboost_iostreams.so.1.83.0()(64bit) libboost_regex.so.1.83.0()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.32)(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) libflexiblas.so.3()(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(OMP_1.0)(64bit) libgsl.so.27()(64bit) libgslcblas.so.0()(64bit) libhts.so.3()(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_1.3.8)(64bit) libstdc++.so.6(CXXABI_1.3.9)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.11)(64bit) libstdc++.so.6(GLIBCXX_3.4.15)(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_3.4.9)(64bit) perl(strict) rtld(GNU_HASH) Processing files: mmseq-debugsource-1.0.11-19.fc41.x86_64 Provides: mmseq-debugsource = 1.0.11-19.fc41 mmseq-debugsource(x86-64) = 1.0.11-19.fc41 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: mmseq-debuginfo-1.0.11-19.fc41.x86_64 Provides: debuginfo(build-id) = 608e821f89293d587be852881eacded426e825a9 debuginfo(build-id) = 69a26f047e4932ef7b5540484075b5643f6fe28b debuginfo(build-id) = 7d0ad6b02360a5e3f649a408e1fae1c6e7e1a5c3 debuginfo(build-id) = 867fa41d1c4a81d8e651fa36d4919c06e485abb1 debuginfo(build-id) = bd252e3cf9e07c1861dadecab5c87e272bc68754 debuginfo(build-id) = bef4381a5cada94ba45178dbb6670011aa60a6e8 debuginfo(build-id) = e28d87d7427324b64622eb59c3085d0374682403 debuginfo(build-id) = e91d422f267a543c5caad40c19012fdd51ea2a3f mmseq-debuginfo = 1.0.11-19.fc41 mmseq-debuginfo(x86-64) = 1.0.11-19.fc41 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: mmseq-debugsource(x86-64) = 1.0.11-19.fc41 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT Wrote: /builddir/build/RPMS/mmseq-debugsource-1.0.11-19.fc41.x86_64.rpm Wrote: /builddir/build/RPMS/mmseq-1.0.11-19.fc41.x86_64.rpm Wrote: /builddir/build/RPMS/mmseq-debuginfo-1.0.11-19.fc41.x86_64.rpm Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.ShSZ4c + umask 022 + cd /builddir/build/BUILD/mmseq-1.0.11-build + test -d /builddir/build/BUILD/mmseq-1.0.11-build + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w /builddir/build/BUILD/mmseq-1.0.11-build + rm -rf /builddir/build/BUILD/mmseq-1.0.11-build + RPM_EC=0 ++ jobs -p + exit 0 Finish: rpmbuild mmseq-1.0.11-19.fc41.src.rpm Finish: build phase for mmseq-1.0.11-19.fc41.src.rpm INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-40-x86_64-1717082042.506309/root/var/log/dnf5.log INFO: Done(/var/lib/copr-rpmbuild/results/mmseq-1.0.11-19.fc41.src.rpm) Config(child) 0 minutes 56 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": "mmseq-debuginfo", "epoch": null, "version": "1.0.11", "release": "19.fc41", "arch": "x86_64" }, { "name": "mmseq-debugsource", "epoch": null, "version": "1.0.11", "release": "19.fc41", "arch": "x86_64" }, { "name": "mmseq", "epoch": null, "version": "1.0.11", "release": "19.fc41", "arch": "x86_64" }, { "name": "mmseq", "epoch": null, "version": "1.0.11", "release": "19.fc41", "arch": "src" } ] } RPMResults finished