Warning: Permanently added '2620:52:3:1:dead:beef:cafe:c119' (ED25519) to the list of known hosts. cmd: ['copr-distgit-client', 'sources'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-z0z6lht3/mmseq rc: 0 stdout: stderr: INFO: Reading stdout from command: git rev-parse --abbrev-ref HEAD INFO: Reading stdout from command: git rev-parse HEAD INFO: Reading sources specification file: sources INFO: Downloading 1.0.11.zip INFO: Reading stdout from command: curl --help all INFO: Calling: curl -H Pragma: -o 1.0.11.zip --location --connect-timeout 60 --retry 3 --retry-delay 10 --remote-time --show-error --fail --retry-all-errors https://copr-dist-git.fedorainfracloud.org/repo/pkgs/ppalka/boost-1.83-all-arches/mmseq/1.0.11.zip/md5/c727916d339d7a2111523800b621ce2b/1.0.11.zip % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 2781k 100 2781k 0 0 18.8M 0 --:--:-- --:--:-- --:--:-- 18.8M INFO: Reading stdout from command: md5sum 1.0.11.zip Running (timeout=115200): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-z0z6lht3/mmseq/mmseq.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-z0z6lht3/mmseq --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1702420456.496724 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 5.2 starting (python version = 3.11.3, NVR = mock-5.2-1.fc38), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-z0z6lht3/mmseq/mmseq.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-z0z6lht3/mmseq --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1702420456.496724 -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-z0z6lht3/mmseq/mmseq.spec) Config(fedora-rawhide-x86_64) Start: clean chroot Finish: clean chroot Mock Version: 5.2 INFO: Mock Version: 5.2 Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1702420456.496724/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:rawhide INFO: Pulling image: registry.fedoraproject.org/fedora:rawhide INFO: Copy content of container registry.fedoraproject.org/fedora:rawhide to /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1702420456.496724/root INFO: Checking that registry.fedoraproject.org/fedora:rawhide image matches host's architecture INFO: mounting registry.fedoraproject.org/fedora:rawhide with podman image mount INFO: image registry.fedoraproject.org/fedora:rawhide as /var/lib/containers/storage/overlay/ef7f879f9a7c8f3b179a505bc57c531f411bc8d830c8c86540e47c3fe4f37c04/merged INFO: umounting image registry.fedoraproject.org/fedora:rawhide (/var/lib/containers/storage/overlay/ef7f879f9a7c8f3b179a505bc57c531f411bc8d830c8c86540e47c3fe4f37c04/merged) with podman image umount INFO: Package manager dnf detected and used (fallback) INFO: Bootstrap image not marked ready Start(bootstrap): installing dnf tooling No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 12 MB/s | 1.7 MB 00:00 fedora 12 MB/s | 72 MB 00:06 Package python3-dnf-4.18.2-1.fc40.noarch is already installed. Dependencies resolved. ================================================================================ Package Arch Version Repository Size ================================================================================ Installing: python3-dnf-plugins-core noarch 4.4.4-1.fc40 fedora 317 k Installing dependencies: dbus-libs x86_64 1:1.14.10-1.fc40 fedora 155 k python3-dateutil noarch 1:2.8.2-11.fc40 fedora 356 k python3-dbus x86_64 1.3.2-4.fc39 fedora 157 k python3-distro noarch 1.8.0-6.fc39 fedora 49 k python3-six noarch 1.16.0-12.fc39 fedora 41 k python3-systemd x86_64 235-5.fc39 fedora 107 k Transaction Summary ================================================================================ Install 7 Packages Total download size: 1.2 M Installed size: 3.6 M Downloading Packages: (1/7): dbus-libs-1.14.10-1.fc40.x86_64.rpm 232 kB/s | 155 kB 00:00 (2/7): python3-dbus-1.3.2-4.fc39.x86_64.rpm 230 kB/s | 157 kB 00:00 (3/7): python3-distro-1.8.0-6.fc39.noarch.rpm 359 kB/s | 49 kB 00:00 (4/7): python3-dateutil-2.8.2-11.fc40.noarch.rp 438 kB/s | 356 kB 00:00 (5/7): python3-six-1.16.0-12.fc39.noarch.rpm 308 kB/s | 41 kB 00:00 (6/7): python3-systemd-235-5.fc39.x86_64.rpm 803 kB/s | 107 kB 00:00 (7/7): python3-dnf-plugins-core-4.4.4-1.fc40.no 1.1 MB/s | 317 kB 00:00 -------------------------------------------------------------------------------- Total 1.2 MB/s | 1.2 MB 00:00 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Installing : python3-systemd-235-5.fc39.x86_64 1/7 Installing : python3-six-1.16.0-12.fc39.noarch 2/7 Installing : python3-dateutil-1:2.8.2-11.fc40.noarch 3/7 Installing : python3-distro-1.8.0-6.fc39.noarch 4/7 Installing : dbus-libs-1:1.14.10-1.fc40.x86_64 5/7 Installing : python3-dbus-1.3.2-4.fc39.x86_64 6/7 Installing : python3-dnf-plugins-core-4.4.4-1.fc40.noarch 7/7 Running scriptlet: python3-dnf-plugins-core-4.4.4-1.fc40.noarch 7/7 Installed: dbus-libs-1:1.14.10-1.fc40.x86_64 python3-dateutil-1:2.8.2-11.fc40.noarch python3-dbus-1.3.2-4.fc39.x86_64 python3-distro-1.8.0-6.fc39.noarch python3-dnf-plugins-core-4.4.4-1.fc40.noarch python3-six-1.16.0-12.fc39.noarch python3-systemd-235-5.fc39.x86_64 Complete! Finish(bootstrap): installing dnf tooling Start(bootstrap): creating root cache Finish(bootstrap): creating root cache Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-1702420456.496724/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin INFO: Package manager dnf detected and used (direct choice) Start: installing minimal buildroot with dnf No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 30 kB/s | 1.5 kB 00:00 Copr repository 7.9 MB/s | 1.7 MB 00:00 fedora 521 kB/s | 21 kB 00:00 Dependencies resolved. ================================================================================ Package Arch Version Repo Size ================================================================================ Installing group/module packages: bash x86_64 5.2.21-2.fc40 fedora 1.8 M bzip2 x86_64 1.0.8-16.fc39 fedora 52 k coreutils x86_64 9.4-1.fc40 fedora 1.1 M cpio x86_64 2.14-5.fc40 fedora 280 k diffutils x86_64 3.10-3.fc39 fedora 398 k fedora-release-common noarch 40-0.20 fedora 20 k findutils x86_64 1:4.9.0-6.fc40 fedora 492 k gawk x86_64 5.2.2-2.fc39 fedora 1.1 M glibc-minimal-langpack x86_64 2.38.9000-26.fc40 fedora 85 k grep x86_64 3.11-5.fc40 fedora 298 k gzip x86_64 1.12-6.fc39 fedora 166 k info x86_64 7.1-1.fc40 fedora 184 k patch x86_64 2.7.6-22.fc39 fedora 125 k redhat-rpm-config noarch 271-1.fc40 fedora 81 k rpm-build x86_64 4.19.0-3.fc40 fedora 79 k sed x86_64 4.8-14.fc39 fedora 306 k shadow-utils x86_64 2:4.14.0-2.fc40 fedora 1.3 M tar x86_64 2:1.35-2.fc40 fedora 864 k unzip x86_64 6.0-62.fc39 fedora 184 k util-linux x86_64 2.39.2-1.fc40 fedora 1.2 M which x86_64 2.21-40.fc39 fedora 42 k xz x86_64 5.4.5-1.fc40 fedora 557 k Installing dependencies: alternatives x86_64 1.25-1.fc39 fedora 39 k ansible-srpm-macros noarch 1-11.fc39 fedora 21 k audit-libs x86_64 3.1.2-5.fc40 fedora 117 k authselect x86_64 1.4.3-1.fc40 fedora 149 k authselect-libs x86_64 1.4.3-1.fc40 fedora 249 k basesystem noarch 11-18.fc39 fedora 7.2 k binutils x86_64 2.41-16.fc40 fedora 6.3 M binutils-gold x86_64 2.41-16.fc40 fedora 797 k bzip2-libs x86_64 1.0.8-16.fc39 fedora 41 k ca-certificates noarch 2023.2.62_v7.0.401-4.fc40 fedora 863 k coreutils-common x86_64 9.4-1.fc40 fedora 2.1 M cracklib x86_64 2.9.11-2.fc39 fedora 94 k crypto-policies noarch 20231204-1.git1e3a2e4.fc40 fedora 100 k curl x86_64 8.5.0-1.fc40 fedora 373 k cyrus-sasl-lib x86_64 2.1.28-11.fc39 fedora 793 k debugedit x86_64 5.0-12.fc40 fedora 78 k dwz x86_64 0.15-3.fc39 fedora 134 k ed x86_64 1.19-4.fc39 fedora 79 k efi-srpm-macros noarch 5-9.fc39 fedora 22 k elfutils x86_64 0.190-4.fc40 fedora 550 k elfutils-debuginfod-client x86_64 0.190-4.fc40 fedora 38 k elfutils-default-yama-scope noarch 0.190-4.fc40 fedora 13 k elfutils-libelf x86_64 0.190-4.fc40 fedora 194 k elfutils-libs x86_64 0.190-4.fc40 fedora 259 k fedora-gpg-keys noarch 40-0.2 fedora 130 k fedora-release noarch 40-0.20 fedora 9.3 k fedora-release-identity-basic noarch 40-0.20 fedora 10 k fedora-repos noarch 40-0.2 fedora 9.3 k fedora-repos-rawhide noarch 40-0.2 fedora 8.9 k file x86_64 5.45-1.fc40 fedora 49 k file-libs x86_64 5.45-1.fc40 fedora 763 k filesystem x86_64 3.18-6.fc39 fedora 1.1 M fonts-srpm-macros noarch 1:2.0.5-12.fc39 fedora 26 k forge-srpm-macros noarch 0.2.0-1.fc40 fedora 18 k fpc-srpm-macros noarch 1.3-8.fc39 fedora 7.4 k gdb-minimal x86_64 14.1-1.fc40 fedora 4.3 M gdbm x86_64 1:1.23-4.fc39 fedora 155 k gdbm-libs x86_64 1:1.23-4.fc39 fedora 56 k ghc-srpm-macros noarch 1.6.1-3.fc40 fedora 8.1 k glibc x86_64 2.38.9000-26.fc40 fedora 2.2 M glibc-common x86_64 2.38.9000-26.fc40 fedora 367 k glibc-gconv-extra x86_64 2.38.9000-26.fc40 fedora 1.7 M gmp x86_64 1:6.2.1-5.fc39 fedora 313 k gnat-srpm-macros noarch 6-3.fc39 fedora 8.8 k go-srpm-macros noarch 3.3.1-1.fc40 fedora 28 k jansson x86_64 2.13.1-7.fc39 fedora 44 k kernel-srpm-macros noarch 1.0-20.fc39 fedora 10 k keyutils-libs x86_64 1.6.1-7.fc39 fedora 31 k krb5-libs x86_64 1.21.2-2.fc40 fedora 765 k libacl x86_64 2.3.1-11.fc40 fedora 24 k libarchive x86_64 3.7.2-1.fc40 fedora 408 k libattr x86_64 2.5.1-9.fc40 fedora 18 k libblkid x86_64 2.39.2-1.fc40 fedora 116 k libbrotli x86_64 1.1.0-1.fc40 fedora 336 k libcap x86_64 2.69-1.fc40 fedora 83 k libcap-ng x86_64 0.8.3-8.fc40 fedora 32 k libcom_err x86_64 1.47.0-2.fc39 fedora 26 k libcurl x86_64 8.5.0-1.fc40 fedora 345 k libeconf x86_64 0.5.2-1.fc40 fedora 30 k libevent x86_64 2.1.12-9.fc39 fedora 258 k libfdisk x86_64 2.39.2-1.fc40 fedora 162 k libffi x86_64 3.4.4-4.fc39 fedora 40 k libgcc x86_64 13.2.1-6.fc40 fedora 112 k libgomp x86_64 13.2.1-6.fc40 fedora 321 k libidn2 x86_64 2.3.4-3.fc39 fedora 117 k libmount x86_64 2.39.2-1.fc40 fedora 154 k libnghttp2 x86_64 1.58.0-1.fc40 fedora 76 k libnsl2 x86_64 2.0.0-6.fc39 fedora 30 k libpkgconf x86_64 1.9.5-2.fc39 fedora 38 k libpsl x86_64 0.21.2-4.fc39 fedora 63 k libpwquality x86_64 1.4.5-6.fc39 fedora 120 k libselinux x86_64 3.6-0.rc2.1.fc40 fedora 88 k libsemanage x86_64 3.6-0.rc2.1.fc40 fedora 116 k libsepol x86_64 3.6-0.rc2.1.fc40 fedora 340 k libsigsegv x86_64 2.14-5.fc39 fedora 27 k libsmartcols x86_64 2.39.2-1.fc40 fedora 67 k libssh x86_64 0.10.5-2.fc39 fedora 211 k libssh-config noarch 0.10.5-2.fc39 fedora 9.2 k libstdc++ x86_64 13.2.1-6.fc40 fedora 865 k libtasn1 x86_64 4.19.0-3.fc39 fedora 74 k libtirpc x86_64 1.3.4-0.fc40 fedora 94 k libunistring x86_64 1.1-5.fc40 fedora 543 k libutempter x86_64 1.2.1-10.fc39 fedora 26 k libuuid x86_64 2.39.2-1.fc40 fedora 28 k libverto x86_64 0.3.2-6.fc39 fedora 20 k libxcrypt x86_64 4.4.36-2.fc39 fedora 119 k libxml2 x86_64 2.12.2-2.fc40 fedora 691 k libzstd x86_64 1.5.5-4.fc39 fedora 309 k lua-libs x86_64 5.4.6-3.fc39 fedora 133 k lua-srpm-macros noarch 1-9.fc39 fedora 8.6 k lz4-libs x86_64 1.9.4-4.fc39 fedora 67 k mpfr x86_64 4.2.1-1.fc40 fedora 343 k ncurses-base noarch 6.4-8.20231001.fc40 fedora 88 k ncurses-libs x86_64 6.4-8.20231001.fc40 fedora 338 k ocaml-srpm-macros noarch 9-1.fc40 fedora 9.0 k openblas-srpm-macros noarch 2-14.fc39 fedora 7.5 k openldap x86_64 2.6.6-1.fc39 fedora 255 k openssl-libs x86_64 1:3.1.4-1.fc40 fedora 2.2 M p11-kit x86_64 0.25.3-1.fc40 fedora 522 k p11-kit-trust x86_64 0.25.3-1.fc40 fedora 142 k package-notes-srpm-macros noarch 0.5-9.fc39 fedora 11 k pam x86_64 1.5.3-8.fc40 fedora 547 k pam-libs x86_64 1.5.3-8.fc40 fedora 57 k pcre2 x86_64 10.42-2.fc40 fedora 233 k pcre2-syntax noarch 10.42-2.fc40 fedora 143 k perl-srpm-macros noarch 1-51.fc39 fedora 8.0 k pkgconf x86_64 1.9.5-2.fc39 fedora 42 k pkgconf-m4 noarch 1.9.5-2.fc39 fedora 14 k pkgconf-pkg-config x86_64 1.9.5-2.fc39 fedora 9.6 k popt x86_64 1.19-3.fc39 fedora 66 k publicsuffix-list-dafsa noarch 20230812-1.fc40 fedora 57 k pyproject-srpm-macros noarch 1.10.0-1.fc40 fedora 14 k python-srpm-macros noarch 3.12-5.fc40 fedora 25 k qt5-srpm-macros noarch 5.15.11-1.fc40 fedora 8.3 k qt6-srpm-macros noarch 6.6.1-1.fc40 fedora 8.6 k readline x86_64 8.2-4.fc39 fedora 213 k rpm x86_64 4.19.0-3.fc40 fedora 537 k rpm-build-libs x86_64 4.19.0-3.fc40 fedora 96 k rpm-libs x86_64 4.19.0-3.fc40 fedora 313 k rpm-sequoia x86_64 1.5.0-2.fc40 fedora 879 k rust-srpm-macros noarch 25.2-2.fc40 fedora 13 k setup noarch 2.14.5-1.fc40 fedora 155 k sqlite-libs x86_64 3.44.2-1.fc40 fedora 693 k systemd-libs x86_64 255-1.fc40 fedora 702 k util-linux-core x86_64 2.39.2-1.fc40 fedora 493 k xxhash-libs x86_64 0.8.2-1.fc39 fedora 37 k xz-libs x86_64 5.4.5-1.fc40 fedora 108 k zip x86_64 3.0-39.fc40 fedora 266 k zlib x86_64 1.2.13-5.fc40 fedora 94 k zstd x86_64 1.5.5-4.fc39 fedora 482 k Installing Groups: Buildsystem building group Transaction Summary ================================================================================ Install 152 Packages Total size: 52 M Installed size: 180 M Downloading Packages: [SKIPPED] alternatives-1.25-1.fc39.x86_64.rpm: Already downloaded [SKIPPED] ansible-srpm-macros-1-11.fc39.noarch.rpm: Already downloaded [SKIPPED] audit-libs-3.1.2-5.fc40.x86_64.rpm: Already downloaded [SKIPPED] authselect-1.4.3-1.fc40.x86_64.rpm: Already downloaded [SKIPPED] authselect-libs-1.4.3-1.fc40.x86_64.rpm: Already downloaded [SKIPPED] basesystem-11-18.fc39.noarch.rpm: Already downloaded [SKIPPED] bash-5.2.21-2.fc40.x86_64.rpm: Already downloaded [SKIPPED] binutils-2.41-16.fc40.x86_64.rpm: Already downloaded [SKIPPED] binutils-gold-2.41-16.fc40.x86_64.rpm: Already downloaded [SKIPPED] bzip2-1.0.8-16.fc39.x86_64.rpm: Already downloaded [SKIPPED] bzip2-libs-1.0.8-16.fc39.x86_64.rpm: Already downloaded [SKIPPED] ca-certificates-2023.2.62_v7.0.401-4.fc40.noarch.rpm: Already downloaded [SKIPPED] coreutils-9.4-1.fc40.x86_64.rpm: Already downloaded [SKIPPED] coreutils-common-9.4-1.fc40.x86_64.rpm: Already downloaded [SKIPPED] cpio-2.14-5.fc40.x86_64.rpm: Already downloaded [SKIPPED] cracklib-2.9.11-2.fc39.x86_64.rpm: Already downloaded [SKIPPED] crypto-policies-20231204-1.git1e3a2e4.fc40.noarch.rpm: Already downloaded [SKIPPED] curl-8.5.0-1.fc40.x86_64.rpm: Already downloaded [SKIPPED] cyrus-sasl-lib-2.1.28-11.fc39.x86_64.rpm: Already downloaded [SKIPPED] debugedit-5.0-12.fc40.x86_64.rpm: Already downloaded [SKIPPED] diffutils-3.10-3.fc39.x86_64.rpm: Already downloaded [SKIPPED] dwz-0.15-3.fc39.x86_64.rpm: Already downloaded [SKIPPED] ed-1.19-4.fc39.x86_64.rpm: Already downloaded [SKIPPED] efi-srpm-macros-5-9.fc39.noarch.rpm: Already downloaded [SKIPPED] elfutils-0.190-4.fc40.x86_64.rpm: Already downloaded [SKIPPED] elfutils-debuginfod-client-0.190-4.fc40.x86_64.rpm: Already downloaded [SKIPPED] elfutils-default-yama-scope-0.190-4.fc40.noarch.rpm: Already downloaded [SKIPPED] elfutils-libelf-0.190-4.fc40.x86_64.rpm: Already downloaded [SKIPPED] elfutils-libs-0.190-4.fc40.x86_64.rpm: Already downloaded [SKIPPED] fedora-gpg-keys-40-0.2.noarch.rpm: Already downloaded [SKIPPED] fedora-release-40-0.20.noarch.rpm: Already downloaded [SKIPPED] fedora-release-common-40-0.20.noarch.rpm: Already downloaded [SKIPPED] fedora-release-identity-basic-40-0.20.noarch.rpm: Already downloaded [SKIPPED] fedora-repos-40-0.2.noarch.rpm: Already downloaded [SKIPPED] fedora-repos-rawhide-40-0.2.noarch.rpm: Already downloaded [SKIPPED] file-5.45-1.fc40.x86_64.rpm: Already downloaded [SKIPPED] file-libs-5.45-1.fc40.x86_64.rpm: Already downloaded [SKIPPED] filesystem-3.18-6.fc39.x86_64.rpm: Already downloaded [SKIPPED] findutils-4.9.0-6.fc40.x86_64.rpm: Already downloaded [SKIPPED] fonts-srpm-macros-2.0.5-12.fc39.noarch.rpm: Already downloaded [SKIPPED] forge-srpm-macros-0.2.0-1.fc40.noarch.rpm: Already downloaded [SKIPPED] fpc-srpm-macros-1.3-8.fc39.noarch.rpm: Already downloaded [SKIPPED] gawk-5.2.2-2.fc39.x86_64.rpm: Already downloaded [SKIPPED] gdb-minimal-14.1-1.fc40.x86_64.rpm: Already downloaded [SKIPPED] gdbm-1.23-4.fc39.x86_64.rpm: Already downloaded [SKIPPED] gdbm-libs-1.23-4.fc39.x86_64.rpm: Already downloaded [SKIPPED] ghc-srpm-macros-1.6.1-3.fc40.noarch.rpm: Already downloaded [SKIPPED] glibc-2.38.9000-26.fc40.x86_64.rpm: Already downloaded [SKIPPED] glibc-common-2.38.9000-26.fc40.x86_64.rpm: Already downloaded [SKIPPED] glibc-gconv-extra-2.38.9000-26.fc40.x86_64.rpm: Already downloaded [SKIPPED] glibc-minimal-langpack-2.38.9000-26.fc40.x86_64.rpm: Already downloaded [SKIPPED] gmp-6.2.1-5.fc39.x86_64.rpm: Already downloaded [SKIPPED] gnat-srpm-macros-6-3.fc39.noarch.rpm: Already downloaded [SKIPPED] go-srpm-macros-3.3.1-1.fc40.noarch.rpm: Already downloaded [SKIPPED] grep-3.11-5.fc40.x86_64.rpm: Already downloaded [SKIPPED] gzip-1.12-6.fc39.x86_64.rpm: Already downloaded [SKIPPED] info-7.1-1.fc40.x86_64.rpm: Already downloaded [SKIPPED] jansson-2.13.1-7.fc39.x86_64.rpm: Already downloaded [SKIPPED] kernel-srpm-macros-1.0-20.fc39.noarch.rpm: Already downloaded [SKIPPED] keyutils-libs-1.6.1-7.fc39.x86_64.rpm: Already downloaded [SKIPPED] krb5-libs-1.21.2-2.fc40.x86_64.rpm: Already downloaded [SKIPPED] libacl-2.3.1-11.fc40.x86_64.rpm: Already downloaded [SKIPPED] libarchive-3.7.2-1.fc40.x86_64.rpm: Already downloaded [SKIPPED] libattr-2.5.1-9.fc40.x86_64.rpm: Already downloaded [SKIPPED] libblkid-2.39.2-1.fc40.x86_64.rpm: Already downloaded [SKIPPED] libbrotli-1.1.0-1.fc40.x86_64.rpm: Already downloaded [SKIPPED] libcap-2.69-1.fc40.x86_64.rpm: Already downloaded [SKIPPED] libcap-ng-0.8.3-8.fc40.x86_64.rpm: Already downloaded [SKIPPED] libcom_err-1.47.0-2.fc39.x86_64.rpm: Already downloaded [SKIPPED] libcurl-8.5.0-1.fc40.x86_64.rpm: Already downloaded [SKIPPED] libeconf-0.5.2-1.fc40.x86_64.rpm: Already downloaded [SKIPPED] libevent-2.1.12-9.fc39.x86_64.rpm: Already downloaded [SKIPPED] libfdisk-2.39.2-1.fc40.x86_64.rpm: Already downloaded [SKIPPED] libffi-3.4.4-4.fc39.x86_64.rpm: Already downloaded [SKIPPED] libgcc-13.2.1-6.fc40.x86_64.rpm: Already downloaded [SKIPPED] libgomp-13.2.1-6.fc40.x86_64.rpm: Already downloaded [SKIPPED] libidn2-2.3.4-3.fc39.x86_64.rpm: Already downloaded [SKIPPED] libmount-2.39.2-1.fc40.x86_64.rpm: Already downloaded [SKIPPED] libnghttp2-1.58.0-1.fc40.x86_64.rpm: Already downloaded 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/usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-40-primary Key imported successfully fedora 1.6 MB/s | 1.6 kB 00:00 GPG key at file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-40-primary (0xA15B79CC) is already installed fedora 1.6 MB/s | 1.6 kB 00:00 Importing GPG key 0x18B8E74C: Userid : "Fedora (39) " Fingerprint: E8F2 3996 F232 1864 0CB4 4CBE 75CF 5AC4 18B8 E74C From : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-39-primary Key imported successfully Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. 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gdb-minimal-14.1-1.fc40.x86_64 133/152 Installing : debugedit-5.0-12.fc40.x86_64 134/152 Installing : curl-8.5.0-1.fc40.x86_64 135/152 Installing : rpm-sequoia-1.5.0-2.fc40.x86_64 136/152 Installing : rpm-libs-4.19.0-3.fc40.x86_64 137/152 Running scriptlet: rpm-4.19.0-3.fc40.x86_64 138/152 Installing : rpm-4.19.0-3.fc40.x86_64 138/152 Installing : efi-srpm-macros-5-9.fc39.noarch 139/152 Installing : lua-srpm-macros-1-9.fc39.noarch 140/152 Installing : rpm-build-libs-4.19.0-3.fc40.x86_64 141/152 Installing : ansible-srpm-macros-1-11.fc39.noarch 142/152 Installing : fonts-srpm-macros-1:2.0.5-12.fc39.noarch 143/152 Installing : forge-srpm-macros-0.2.0-1.fc40.noarch 144/152 Installing : go-srpm-macros-3.3.1-1.fc40.noarch 145/152 Installing : python-srpm-macros-3.12-5.fc40.noarch 146/152 Installing : redhat-rpm-config-271-1.fc40.noarch 147/152 Installing : rpm-build-4.19.0-3.fc40.x86_64 148/152 Installing : pyproject-srpm-macros-1.10.0-1.fc40.noarch 149/152 Installing : util-linux-2.39.2-1.fc40.x86_64 150/152 Installing : which-2.21-40.fc39.x86_64 151/152 Installing : info-7.1-1.fc40.x86_64 152/152 Running scriptlet: filesystem-3.18-6.fc39.x86_64 152/152 Running scriptlet: ca-certificates-2023.2.62_v7.0.401-4.fc40.noarch 152/152 Running scriptlet: authselect-libs-1.4.3-1.fc40.x86_64 152/152 Running scriptlet: rpm-4.19.0-3.fc40.x86_64 152/152 Running scriptlet: info-7.1-1.fc40.x86_64 152/152 Installed: alternatives-1.25-1.fc39.x86_64 ansible-srpm-macros-1-11.fc39.noarch audit-libs-3.1.2-5.fc40.x86_64 authselect-1.4.3-1.fc40.x86_64 authselect-libs-1.4.3-1.fc40.x86_64 basesystem-11-18.fc39.noarch bash-5.2.21-2.fc40.x86_64 binutils-2.41-16.fc40.x86_64 binutils-gold-2.41-16.fc40.x86_64 bzip2-1.0.8-16.fc39.x86_64 bzip2-libs-1.0.8-16.fc39.x86_64 ca-certificates-2023.2.62_v7.0.401-4.fc40.noarch coreutils-9.4-1.fc40.x86_64 coreutils-common-9.4-1.fc40.x86_64 cpio-2.14-5.fc40.x86_64 cracklib-2.9.11-2.fc39.x86_64 crypto-policies-20231204-1.git1e3a2e4.fc40.noarch curl-8.5.0-1.fc40.x86_64 cyrus-sasl-lib-2.1.28-11.fc39.x86_64 debugedit-5.0-12.fc40.x86_64 diffutils-3.10-3.fc39.x86_64 dwz-0.15-3.fc39.x86_64 ed-1.19-4.fc39.x86_64 efi-srpm-macros-5-9.fc39.noarch elfutils-0.190-4.fc40.x86_64 elfutils-debuginfod-client-0.190-4.fc40.x86_64 elfutils-default-yama-scope-0.190-4.fc40.noarch elfutils-libelf-0.190-4.fc40.x86_64 elfutils-libs-0.190-4.fc40.x86_64 fedora-gpg-keys-40-0.2.noarch fedora-release-40-0.20.noarch fedora-release-common-40-0.20.noarch fedora-release-identity-basic-40-0.20.noarch fedora-repos-40-0.2.noarch fedora-repos-rawhide-40-0.2.noarch file-5.45-1.fc40.x86_64 file-libs-5.45-1.fc40.x86_64 filesystem-3.18-6.fc39.x86_64 findutils-1:4.9.0-6.fc40.x86_64 fonts-srpm-macros-1:2.0.5-12.fc39.noarch forge-srpm-macros-0.2.0-1.fc40.noarch fpc-srpm-macros-1.3-8.fc39.noarch gawk-5.2.2-2.fc39.x86_64 gdb-minimal-14.1-1.fc40.x86_64 gdbm-1:1.23-4.fc39.x86_64 gdbm-libs-1:1.23-4.fc39.x86_64 ghc-srpm-macros-1.6.1-3.fc40.noarch glibc-2.38.9000-26.fc40.x86_64 glibc-common-2.38.9000-26.fc40.x86_64 glibc-gconv-extra-2.38.9000-26.fc40.x86_64 glibc-minimal-langpack-2.38.9000-26.fc40.x86_64 gmp-1:6.2.1-5.fc39.x86_64 gnat-srpm-macros-6-3.fc39.noarch go-srpm-macros-3.3.1-1.fc40.noarch grep-3.11-5.fc40.x86_64 gzip-1.12-6.fc39.x86_64 info-7.1-1.fc40.x86_64 jansson-2.13.1-7.fc39.x86_64 kernel-srpm-macros-1.0-20.fc39.noarch keyutils-libs-1.6.1-7.fc39.x86_64 krb5-libs-1.21.2-2.fc40.x86_64 libacl-2.3.1-11.fc40.x86_64 libarchive-3.7.2-1.fc40.x86_64 libattr-2.5.1-9.fc40.x86_64 libblkid-2.39.2-1.fc40.x86_64 libbrotli-1.1.0-1.fc40.x86_64 libcap-2.69-1.fc40.x86_64 libcap-ng-0.8.3-8.fc40.x86_64 libcom_err-1.47.0-2.fc39.x86_64 libcurl-8.5.0-1.fc40.x86_64 libeconf-0.5.2-1.fc40.x86_64 libevent-2.1.12-9.fc39.x86_64 libfdisk-2.39.2-1.fc40.x86_64 libffi-3.4.4-4.fc39.x86_64 libgcc-13.2.1-6.fc40.x86_64 libgomp-13.2.1-6.fc40.x86_64 libidn2-2.3.4-3.fc39.x86_64 libmount-2.39.2-1.fc40.x86_64 libnghttp2-1.58.0-1.fc40.x86_64 libnsl2-2.0.0-6.fc39.x86_64 libpkgconf-1.9.5-2.fc39.x86_64 libpsl-0.21.2-4.fc39.x86_64 libpwquality-1.4.5-6.fc39.x86_64 libselinux-3.6-0.rc2.1.fc40.x86_64 libsemanage-3.6-0.rc2.1.fc40.x86_64 libsepol-3.6-0.rc2.1.fc40.x86_64 libsigsegv-2.14-5.fc39.x86_64 libsmartcols-2.39.2-1.fc40.x86_64 libssh-0.10.5-2.fc39.x86_64 libssh-config-0.10.5-2.fc39.noarch libstdc++-13.2.1-6.fc40.x86_64 libtasn1-4.19.0-3.fc39.x86_64 libtirpc-1.3.4-0.fc40.x86_64 libunistring-1.1-5.fc40.x86_64 libutempter-1.2.1-10.fc39.x86_64 libuuid-2.39.2-1.fc40.x86_64 libverto-0.3.2-6.fc39.x86_64 libxcrypt-4.4.36-2.fc39.x86_64 libxml2-2.12.2-2.fc40.x86_64 libzstd-1.5.5-4.fc39.x86_64 lua-libs-5.4.6-3.fc39.x86_64 lua-srpm-macros-1-9.fc39.noarch lz4-libs-1.9.4-4.fc39.x86_64 mpfr-4.2.1-1.fc40.x86_64 ncurses-base-6.4-8.20231001.fc40.noarch ncurses-libs-6.4-8.20231001.fc40.x86_64 ocaml-srpm-macros-9-1.fc40.noarch openblas-srpm-macros-2-14.fc39.noarch openldap-2.6.6-1.fc39.x86_64 openssl-libs-1:3.1.4-1.fc40.x86_64 p11-kit-0.25.3-1.fc40.x86_64 p11-kit-trust-0.25.3-1.fc40.x86_64 package-notes-srpm-macros-0.5-9.fc39.noarch pam-1.5.3-8.fc40.x86_64 pam-libs-1.5.3-8.fc40.x86_64 patch-2.7.6-22.fc39.x86_64 pcre2-10.42-2.fc40.x86_64 pcre2-syntax-10.42-2.fc40.noarch perl-srpm-macros-1-51.fc39.noarch pkgconf-1.9.5-2.fc39.x86_64 pkgconf-m4-1.9.5-2.fc39.noarch pkgconf-pkg-config-1.9.5-2.fc39.x86_64 popt-1.19-3.fc39.x86_64 publicsuffix-list-dafsa-20230812-1.fc40.noarch pyproject-srpm-macros-1.10.0-1.fc40.noarch python-srpm-macros-3.12-5.fc40.noarch qt5-srpm-macros-5.15.11-1.fc40.noarch qt6-srpm-macros-6.6.1-1.fc40.noarch readline-8.2-4.fc39.x86_64 redhat-rpm-config-271-1.fc40.noarch rpm-4.19.0-3.fc40.x86_64 rpm-build-4.19.0-3.fc40.x86_64 rpm-build-libs-4.19.0-3.fc40.x86_64 rpm-libs-4.19.0-3.fc40.x86_64 rpm-sequoia-1.5.0-2.fc40.x86_64 rust-srpm-macros-25.2-2.fc40.noarch sed-4.8-14.fc39.x86_64 setup-2.14.5-1.fc40.noarch shadow-utils-2:4.14.0-2.fc40.x86_64 sqlite-libs-3.44.2-1.fc40.x86_64 systemd-libs-255-1.fc40.x86_64 tar-2:1.35-2.fc40.x86_64 unzip-6.0-62.fc39.x86_64 util-linux-2.39.2-1.fc40.x86_64 util-linux-core-2.39.2-1.fc40.x86_64 which-2.21-40.fc39.x86_64 xxhash-libs-0.8.2-1.fc39.x86_64 xz-5.4.5-1.fc40.x86_64 xz-libs-5.4.5-1.fc40.x86_64 zip-3.0-39.fc40.x86_64 zlib-1.2.13-5.fc40.x86_64 zstd-1.5.5-4.fc39.x86_64 Complete! Finish: installing minimal buildroot with dnf Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: alternatives-1.25-1.fc39.x86_64 ansible-srpm-macros-1-11.fc39.noarch audit-libs-3.1.2-5.fc40.x86_64 authselect-1.4.3-1.fc40.x86_64 authselect-libs-1.4.3-1.fc40.x86_64 basesystem-11-18.fc39.noarch bash-5.2.21-2.fc40.x86_64 binutils-2.41-16.fc40.x86_64 binutils-gold-2.41-16.fc40.x86_64 bzip2-1.0.8-16.fc39.x86_64 bzip2-libs-1.0.8-16.fc39.x86_64 ca-certificates-2023.2.62_v7.0.401-4.fc40.noarch coreutils-9.4-1.fc40.x86_64 coreutils-common-9.4-1.fc40.x86_64 cpio-2.14-5.fc40.x86_64 cracklib-2.9.11-2.fc39.x86_64 crypto-policies-20231204-1.git1e3a2e4.fc40.noarch curl-8.5.0-1.fc40.x86_64 cyrus-sasl-lib-2.1.28-11.fc39.x86_64 debugedit-5.0-12.fc40.x86_64 diffutils-3.10-3.fc39.x86_64 dwz-0.15-3.fc39.x86_64 ed-1.19-4.fc39.x86_64 efi-srpm-macros-5-9.fc39.noarch elfutils-0.190-4.fc40.x86_64 elfutils-debuginfod-client-0.190-4.fc40.x86_64 elfutils-default-yama-scope-0.190-4.fc40.noarch elfutils-libelf-0.190-4.fc40.x86_64 elfutils-libs-0.190-4.fc40.x86_64 fedora-gpg-keys-40-0.2.noarch fedora-release-40-0.20.noarch fedora-release-common-40-0.20.noarch fedora-release-identity-basic-40-0.20.noarch fedora-repos-40-0.2.noarch fedora-repos-rawhide-40-0.2.noarch file-5.45-1.fc40.x86_64 file-libs-5.45-1.fc40.x86_64 filesystem-3.18-6.fc39.x86_64 findutils-4.9.0-6.fc40.x86_64 fonts-srpm-macros-2.0.5-12.fc39.noarch forge-srpm-macros-0.2.0-1.fc40.noarch fpc-srpm-macros-1.3-8.fc39.noarch gawk-5.2.2-2.fc39.x86_64 gdb-minimal-14.1-1.fc40.x86_64 gdbm-1.23-4.fc39.x86_64 gdbm-libs-1.23-4.fc39.x86_64 ghc-srpm-macros-1.6.1-3.fc40.noarch glibc-2.38.9000-26.fc40.x86_64 glibc-common-2.38.9000-26.fc40.x86_64 glibc-gconv-extra-2.38.9000-26.fc40.x86_64 glibc-minimal-langpack-2.38.9000-26.fc40.x86_64 gmp-6.2.1-5.fc39.x86_64 gnat-srpm-macros-6-3.fc39.noarch go-srpm-macros-3.3.1-1.fc40.noarch gpg-pubkey-18b8e74c-62f2920f gpg-pubkey-a15b79cc-63d04c2c grep-3.11-5.fc40.x86_64 gzip-1.12-6.fc39.x86_64 info-7.1-1.fc40.x86_64 jansson-2.13.1-7.fc39.x86_64 kernel-srpm-macros-1.0-20.fc39.noarch keyutils-libs-1.6.1-7.fc39.x86_64 krb5-libs-1.21.2-2.fc40.x86_64 libacl-2.3.1-11.fc40.x86_64 libarchive-3.7.2-1.fc40.x86_64 libattr-2.5.1-9.fc40.x86_64 libblkid-2.39.2-1.fc40.x86_64 libbrotli-1.1.0-1.fc40.x86_64 libcap-2.69-1.fc40.x86_64 libcap-ng-0.8.3-8.fc40.x86_64 libcom_err-1.47.0-2.fc39.x86_64 libcurl-8.5.0-1.fc40.x86_64 libeconf-0.5.2-1.fc40.x86_64 libevent-2.1.12-9.fc39.x86_64 libfdisk-2.39.2-1.fc40.x86_64 libffi-3.4.4-4.fc39.x86_64 libgcc-13.2.1-6.fc40.x86_64 libgomp-13.2.1-6.fc40.x86_64 libidn2-2.3.4-3.fc39.x86_64 libmount-2.39.2-1.fc40.x86_64 libnghttp2-1.58.0-1.fc40.x86_64 libnsl2-2.0.0-6.fc39.x86_64 libpkgconf-1.9.5-2.fc39.x86_64 libpsl-0.21.2-4.fc39.x86_64 libpwquality-1.4.5-6.fc39.x86_64 libselinux-3.6-0.rc2.1.fc40.x86_64 libsemanage-3.6-0.rc2.1.fc40.x86_64 libsepol-3.6-0.rc2.1.fc40.x86_64 libsigsegv-2.14-5.fc39.x86_64 libsmartcols-2.39.2-1.fc40.x86_64 libssh-0.10.5-2.fc39.x86_64 libssh-config-0.10.5-2.fc39.noarch libstdc++-13.2.1-6.fc40.x86_64 libtasn1-4.19.0-3.fc39.x86_64 libtirpc-1.3.4-0.fc40.x86_64 libunistring-1.1-5.fc40.x86_64 libutempter-1.2.1-10.fc39.x86_64 libuuid-2.39.2-1.fc40.x86_64 libverto-0.3.2-6.fc39.x86_64 libxcrypt-4.4.36-2.fc39.x86_64 libxml2-2.12.2-2.fc40.x86_64 libzstd-1.5.5-4.fc39.x86_64 lua-libs-5.4.6-3.fc39.x86_64 lua-srpm-macros-1-9.fc39.noarch lz4-libs-1.9.4-4.fc39.x86_64 mpfr-4.2.1-1.fc40.x86_64 ncurses-base-6.4-8.20231001.fc40.noarch ncurses-libs-6.4-8.20231001.fc40.x86_64 ocaml-srpm-macros-9-1.fc40.noarch openblas-srpm-macros-2-14.fc39.noarch openldap-2.6.6-1.fc39.x86_64 openssl-libs-3.1.4-1.fc40.x86_64 p11-kit-0.25.3-1.fc40.x86_64 p11-kit-trust-0.25.3-1.fc40.x86_64 package-notes-srpm-macros-0.5-9.fc39.noarch pam-1.5.3-8.fc40.x86_64 pam-libs-1.5.3-8.fc40.x86_64 patch-2.7.6-22.fc39.x86_64 pcre2-10.42-2.fc40.x86_64 pcre2-syntax-10.42-2.fc40.noarch perl-srpm-macros-1-51.fc39.noarch pkgconf-1.9.5-2.fc39.x86_64 pkgconf-m4-1.9.5-2.fc39.noarch pkgconf-pkg-config-1.9.5-2.fc39.x86_64 popt-1.19-3.fc39.x86_64 publicsuffix-list-dafsa-20230812-1.fc40.noarch pyproject-srpm-macros-1.10.0-1.fc40.noarch python-srpm-macros-3.12-5.fc40.noarch qt5-srpm-macros-5.15.11-1.fc40.noarch qt6-srpm-macros-6.6.1-1.fc40.noarch readline-8.2-4.fc39.x86_64 redhat-rpm-config-271-1.fc40.noarch rpm-4.19.0-3.fc40.x86_64 rpm-build-4.19.0-3.fc40.x86_64 rpm-build-libs-4.19.0-3.fc40.x86_64 rpm-libs-4.19.0-3.fc40.x86_64 rpm-sequoia-1.5.0-2.fc40.x86_64 rust-srpm-macros-25.2-2.fc40.noarch sed-4.8-14.fc39.x86_64 setup-2.14.5-1.fc40.noarch shadow-utils-4.14.0-2.fc40.x86_64 sqlite-libs-3.44.2-1.fc40.x86_64 systemd-libs-255-1.fc40.x86_64 tar-1.35-2.fc40.x86_64 unzip-6.0-62.fc39.x86_64 util-linux-2.39.2-1.fc40.x86_64 util-linux-core-2.39.2-1.fc40.x86_64 which-2.21-40.fc39.x86_64 xxhash-libs-0.8.2-1.fc39.x86_64 xz-5.4.5-1.fc40.x86_64 xz-libs-5.4.5-1.fc40.x86_64 zip-3.0-39.fc40.x86_64 zlib-1.2.13-5.fc40.x86_64 zstd-1.5.5-4.fc39.x86_64 Start: buildsrpm Start: rpmbuild -bs warning: %patchN is deprecated (1 usages found), use %patch N (or %patch -P N) Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1689811200 Wrote: /builddir/build/SRPMS/mmseq-1.0.11-16.fc40.src.rpm RPM build warnings: %patchN is deprecated (1 usages found), use %patch N (or %patch -P N) Finish: rpmbuild -bs INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-x86_64-1702420456.496724/root/var/log/dnf.rpm.log /var/lib/mock/fedora-rawhide-x86_64-1702420456.496724/root/var/log/dnf.librepo.log /var/lib/mock/fedora-rawhide-x86_64-1702420456.496724/root/var/log/dnf.log Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-z0z6lht3/mmseq/mmseq.spec) Config(child) 0 minutes 48 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-1.0.11-16.fc40.src.rpm) Config(fedora-rawhide-x86_64) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1702420456.496724/root. INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1702420456.496724/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-rawhide-x86_64-1702420456.496724/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 Finish: chroot init INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-4.19.0-3.fc40.x86_64 rpm-sequoia-1.5.0-2.fc40.x86_64 python3-dnf-4.18.2-1.fc40.noarch python3-dnf-plugins-core-4.4.4-1.fc40.noarch yum-4.18.2-1.fc40.noarch Start: build phase for mmseq-1.0.11-16.fc40.src.rpm Start: build setup for mmseq-1.0.11-16.fc40.src.rpm warning: %patchN is deprecated (1 usages found), use %patch N (or %patch -P N) Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1689811200 Wrote: /builddir/build/SRPMS/mmseq-1.0.11-16.fc40.src.rpm RPM build warnings: %patchN is deprecated (1 usages found), use %patch N (or %patch -P N) No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 33 kB/s | 1.5 kB 00:00 fedora 528 kB/s | 21 kB 00:00 Dependencies resolved. ================================================================================ Package Arch Version Repository Size ================================================================================ Installing: armadillo-devel x86_64 10.8.2-5.fc39 fedora 2.2 M boost-devel x86_64 1.83.0-0.fc40 copr_base 12 M flexiblas-devel x86_64 3.3.1-5.fc39 fedora 117 k gcc-c++ x86_64 13.2.1-6.fc40 fedora 13 M gsl-devel x86_64 2.7.1-5.fc39 fedora 653 k htslib-devel x86_64 1.15.1-3.fc39 fedora 105 k make x86_64 1:4.4.1-2.fc39 fedora 589 k perl-generators noarch 1.16-3.fc39 fedora 16 k zlib-devel x86_64 1.2.13-5.fc40 fedora 45 k Installing dependencies: SuperLU x86_64 6.0.1-1.fc40 fedora 186 k SuperLU-devel x86_64 6.0.1-1.fc40 fedora 27 k annobin-docs noarch 12.33-1.fc40 fedora 91 k annobin-plugin-gcc x86_64 12.33-1.fc40 fedora 958 k armadillo x86_64 10.8.2-5.fc39 fedora 34 k arpack x86_64 3.9.1-1.fc40 fedora 211 k arpack-devel x86_64 3.9.1-1.fc40 fedora 22 k autoconf noarch 2.71-7.fc40 fedora 733 k automake noarch 1.16.5-14.fc40 fedora 697 k boost x86_64 1.83.0-0.fc40 copr_base 14 k boost-atomic x86_64 1.83.0-0.fc40 copr_base 20 k boost-chrono x86_64 1.83.0-0.fc40 copr_base 26 k boost-container x86_64 1.83.0-0.fc40 copr_base 40 k boost-context x86_64 1.83.0-0.fc40 copr_base 17 k boost-contract x86_64 1.83.0-0.fc40 copr_base 46 k boost-coroutine x86_64 1.83.0-0.fc40 copr_base 21 k boost-date-time x86_64 1.83.0-0.fc40 copr_base 16 k boost-fiber x86_64 1.83.0-0.fc40 copr_base 42 k boost-filesystem x86_64 1.83.0-0.fc40 copr_base 68 k boost-graph x86_64 1.83.0-0.fc40 copr_base 152 k boost-iostreams x86_64 1.83.0-0.fc40 copr_base 42 k boost-json x86_64 1.83.0-0.fc40 copr_base 143 k boost-locale x86_64 1.83.0-0.fc40 copr_base 212 k boost-log x86_64 1.83.0-0.fc40 copr_base 493 k boost-math x86_64 1.83.0-0.fc40 copr_base 218 k boost-nowide x86_64 1.83.0-0.fc40 copr_base 21 k boost-numpy3 x86_64 1.83.0-0.fc40 copr_base 30 k boost-program-options x86_64 1.83.0-0.fc40 copr_base 110 k boost-python3 x86_64 1.83.0-0.fc40 copr_base 97 k boost-random x86_64 1.83.0-0.fc40 copr_base 25 k boost-regex x86_64 1.83.0-0.fc40 copr_base 112 k boost-serialization x86_64 1.83.0-0.fc40 copr_base 135 k boost-stacktrace x86_64 1.83.0-0.fc40 copr_base 31 k boost-system x86_64 1.83.0-0.fc40 copr_base 16 k boost-test x86_64 1.83.0-0.fc40 copr_base 240 k boost-thread x86_64 1.83.0-0.fc40 copr_base 62 k boost-timer x86_64 1.83.0-0.fc40 copr_base 22 k boost-type_erasure x86_64 1.83.0-0.fc40 copr_base 34 k boost-wave x86_64 1.83.0-0.fc40 copr_base 225 k cmake-filesystem x86_64 3.27.7-1.fc40 fedora 19 k cpp x86_64 13.2.1-6.fc40 fedora 11 M emacs-filesystem noarch 1:29.1-14.fc40 fedora 7.4 k expat x86_64 2.5.0-3.fc39 fedora 110 k flexiblas x86_64 3.3.1-5.fc39 fedora 33 k flexiblas-netlib x86_64 3.3.1-5.fc39 fedora 3.1 M flexiblas-netlib64 x86_64 3.3.1-5.fc39 fedora 3.0 M flexiblas-openblas-openmp x86_64 3.3.1-5.fc39 fedora 17 k flexiblas-openblas-openmp64 x86_64 3.3.1-5.fc39 fedora 17 k gc x86_64 8.2.2-4.fc39 fedora 110 k gcc x86_64 13.2.1-6.fc40 fedora 34 M gcc-gfortran x86_64 13.2.1-6.fc40 fedora 12 M gcc-plugin-annobin x86_64 13.2.1-6.fc40 fedora 50 k glibc-devel x86_64 2.38.9000-26.fc40 fedora 100 k glibc-headers-x86 noarch 2.38.9000-26.fc40 fedora 585 k groff-base x86_64 1.23.0-3.fc40 fedora 1.1 M gsl x86_64 2.7.1-5.fc39 fedora 1.1 M guile22 x86_64 2.2.7-9.fc39 fedora 6.5 M hdf5 x86_64 1.12.1-15.fc40 fedora 2.2 M hdf5-devel x86_64 1.12.1-15.fc40 fedora 1.3 M htslib x86_64 1.15.1-3.fc39 fedora 490 k kernel-headers x86_64 6.7.0-0.rc5.41.fc40 fedora 1.6 M libaec x86_64 1.0.6-5.fc39 fedora 42 k libaec-devel x86_64 1.0.6-5.fc39 fedora 12 k libb2 x86_64 0.98.1-9.fc39 fedora 25 k libgfortran x86_64 13.2.1-6.fc40 fedora 906 k libicu x86_64 73.2-2.fc39 fedora 11 M libicu-devel x86_64 73.2-2.fc39 fedora 924 k libmpc x86_64 1.3.1-3.fc39 fedora 70 k libquadmath x86_64 13.2.1-6.fc40 fedora 198 k libquadmath-devel x86_64 13.2.1-6.fc40 fedora 39 k libstdc++-devel x86_64 13.2.1-6.fc40 fedora 2.6 M libtool-ltdl x86_64 2.4.7-8.fc40 fedora 36 k libxcrypt-devel x86_64 4.4.36-2.fc39 fedora 30 k m4 x86_64 1.4.19-7.fc40 fedora 303 k metis x86_64 5.1.0.3-2.fc39 fedora 572 k mpdecimal x86_64 2.5.1-7.fc39 fedora 89 k ncurses x86_64 6.4-8.20231001.fc40 fedora 418 k openblas x86_64 0.3.25-1.fc40 fedora 38 k openblas-openmp x86_64 0.3.25-1.fc40 fedora 5.0 M openblas-openmp64 x86_64 0.3.25-1.fc40 fedora 4.9 M perl-AutoLoader noarch 5.74-503.fc40 fedora 21 k perl-B x86_64 1.88-503.fc40 fedora 177 k perl-Carp noarch 1.54-500.fc39 fedora 29 k perl-Class-Struct noarch 0.68-503.fc40 fedora 22 k perl-Data-Dumper x86_64 2.188-501.fc39 fedora 56 k perl-Digest noarch 1.20-500.fc39 fedora 25 k perl-Digest-MD5 x86_64 2.58-501.fc40 fedora 35 k perl-DynaLoader x86_64 1.54-503.fc40 fedora 26 k perl-Encode x86_64 4:3.20-501.fc40 fedora 1.7 M perl-Errno x86_64 1.37-503.fc40 fedora 15 k perl-Exporter noarch 5.77-500.fc39 fedora 31 k perl-Fcntl x86_64 1.15-503.fc40 fedora 21 k perl-Fedora-VSP noarch 0.001-32.fc39 fedora 23 k perl-File-Basename noarch 2.86-503.fc40 fedora 17 k perl-File-Compare noarch 1.100.700-503.fc40 fedora 13 k perl-File-Copy noarch 2.41-503.fc40 fedora 20 k perl-File-Find noarch 1.43-503.fc40 fedora 26 k perl-File-Path noarch 2.18-501.fc40 fedora 35 k perl-File-Temp noarch 1:0.231.100-501.fc40 fedora 59 k perl-File-stat noarch 1.13-503.fc40 fedora 17 k perl-FileHandle noarch 2.05-503.fc40 fedora 16 k perl-Getopt-Long noarch 1:2.57-1.fc40 fedora 63 k perl-Getopt-Std noarch 1.13-503.fc40 fedora 16 k perl-HTTP-Tiny noarch 0.088-3.fc39 fedora 56 k perl-IO x86_64 1.52-503.fc40 fedora 82 k perl-IO-Socket-IP noarch 0.42-1.fc39 fedora 42 k perl-IO-Socket-SSL noarch 2.084-1.fc40 fedora 225 k perl-IPC-Open3 noarch 1.22-503.fc40 fedora 22 k perl-MIME-Base64 x86_64 3.16-501.fc40 fedora 29 k perl-Mozilla-CA noarch 20230821-1.fc40 fedora 13 k perl-Net-SSLeay x86_64 1.92-10.fc39 fedora 360 k perl-POSIX x86_64 2.13-503.fc40 fedora 97 k perl-PathTools x86_64 3.89-500.fc39 fedora 87 k perl-Pod-Escapes noarch 1:1.07-501.fc40 fedora 19 k perl-Pod-Perldoc noarch 3.28.01-501.fc39 fedora 86 k perl-Pod-Simple noarch 1:3.45-4.fc39 fedora 218 k perl-Pod-Usage noarch 4:2.03-500.fc39 fedora 39 k perl-Scalar-List-Utils x86_64 5:1.63-500.fc39 fedora 72 k perl-SelectSaver noarch 1.02-503.fc40 fedora 12 k perl-Socket x86_64 4:2.037-3.fc39 fedora 55 k perl-Storable x86_64 1:3.32-500.fc39 fedora 99 k perl-Symbol noarch 1.09-503.fc40 fedora 14 k perl-Term-ANSIColor noarch 5.01-502.fc40 fedora 47 k perl-Term-Cap noarch 1.18-500.fc39 fedora 22 k perl-Text-ParseWords noarch 3.31-500.fc39 fedora 16 k perl-Text-Tabs+Wrap noarch 2023.0511-3.fc39 fedora 22 k perl-Thread-Queue noarch 3.14-501.fc40 fedora 21 k perl-Time-Local noarch 2:1.350-3.fc39 fedora 34 k perl-URI noarch 5.21-1.fc40 fedora 125 k perl-base noarch 2.27-503.fc40 fedora 16 k perl-constant noarch 1.33-501.fc39 fedora 22 k perl-if noarch 0.61.000-503.fc40 fedora 14 k perl-interpreter x86_64 4:5.38.2-503.fc40 fedora 72 k perl-libnet noarch 3.15-501.fc39 fedora 129 k perl-libs x86_64 4:5.38.2-503.fc40 fedora 2.3 M perl-locale noarch 1.10-503.fc40 fedora 14 k perl-macros noarch 4:5.38.2-503.fc40 fedora 13 k perl-mro x86_64 1.28-503.fc40 fedora 29 k perl-overload noarch 1.37-503.fc40 fedora 46 k perl-overloading noarch 0.02-503.fc40 fedora 13 k perl-parent noarch 1:0.241-500.fc39 fedora 14 k perl-podlators noarch 1:5.01-500.fc39 fedora 125 k perl-threads x86_64 1:2.36-500.fc39 fedora 58 k perl-threads-shared x86_64 1.68-500.fc39 fedora 45 k perl-vars noarch 1.05-503.fc40 fedora 13 k python-pip-wheel noarch 23.2.1-1.fc39 fedora 1.5 M python3 x86_64 3.12.1-1.fc40 fedora 26 k python3-libs x86_64 3.12.1-1.fc40 fedora 9.2 M python3-numpy x86_64 1:1.26.0-2.fc40 fedora 7.5 M tzdata noarch 2023c-4.fc40 fedora 717 k Transaction Summary ================================================================================ Install 159 Packages Total size: 165 M Total download size: 28 M Installed size: 713 M Downloading Packages: [SKIPPED] boost-1.83.0-0.fc40.x86_64.rpm: Already downloaded [SKIPPED] boost-atomic-1.83.0-0.fc40.x86_64.rpm: Already downloaded [SKIPPED] boost-chrono-1.83.0-0.fc40.x86_64.rpm: Already downloaded [SKIPPED] boost-container-1.83.0-0.fc40.x86_64.rpm: Already downloaded [SKIPPED] boost-context-1.83.0-0.fc40.x86_64.rpm: Already downloaded [SKIPPED] boost-contract-1.83.0-0.fc40.x86_64.rpm: Already downloaded [SKIPPED] boost-coroutine-1.83.0-0.fc40.x86_64.rpm: Already downloaded [SKIPPED] boost-date-time-1.83.0-0.fc40.x86_64.rpm: Already downloaded [SKIPPED] boost-devel-1.83.0-0.fc40.x86_64.rpm: Already downloaded [SKIPPED] boost-fiber-1.83.0-0.fc40.x86_64.rpm: Already downloaded [SKIPPED] boost-filesystem-1.83.0-0.fc40.x86_64.rpm: Already downloaded [SKIPPED] boost-graph-1.83.0-0.fc40.x86_64.rpm: Already 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boost-test-1.83.0-0.fc40.x86_64.rpm: Already downloaded [SKIPPED] boost-thread-1.83.0-0.fc40.x86_64.rpm: Already downloaded [SKIPPED] boost-timer-1.83.0-0.fc40.x86_64.rpm: Already downloaded [SKIPPED] boost-type_erasure-1.83.0-0.fc40.x86_64.rpm: Already downloaded [SKIPPED] boost-wave-1.83.0-0.fc40.x86_64.rpm: Already downloaded [SKIPPED] annobin-docs-12.33-1.fc40.noarch.rpm: Already downloaded [SKIPPED] annobin-plugin-gcc-12.33-1.fc40.x86_64.rpm: Already downloaded [SKIPPED] autoconf-2.71-7.fc40.noarch.rpm: Already downloaded [SKIPPED] automake-1.16.5-14.fc40.noarch.rpm: Already downloaded [SKIPPED] cpp-13.2.1-6.fc40.x86_64.rpm: Already downloaded [SKIPPED] emacs-filesystem-29.1-14.fc40.noarch.rpm: Already downloaded [SKIPPED] expat-2.5.0-3.fc39.x86_64.rpm: Already downloaded [SKIPPED] flexiblas-3.3.1-5.fc39.x86_64.rpm: Already downloaded [SKIPPED] flexiblas-netlib-3.3.1-5.fc39.x86_64.rpm: Already downloaded [SKIPPED] flexiblas-openblas-openmp-3.3.1-5.fc39.x86_64.rpm: Already 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flexiblas-openblas-openmp64-3.3.1-5.fc39.x86_64 gc-8.2.2-4.fc39.x86_64 gcc-13.2.1-6.fc40.x86_64 gcc-c++-13.2.1-6.fc40.x86_64 gcc-gfortran-13.2.1-6.fc40.x86_64 gcc-plugin-annobin-13.2.1-6.fc40.x86_64 glibc-devel-2.38.9000-26.fc40.x86_64 glibc-headers-x86-2.38.9000-26.fc40.noarch groff-base-1.23.0-3.fc40.x86_64 gsl-2.7.1-5.fc39.x86_64 gsl-devel-2.7.1-5.fc39.x86_64 guile22-2.2.7-9.fc39.x86_64 hdf5-1.12.1-15.fc40.x86_64 hdf5-devel-1.12.1-15.fc40.x86_64 htslib-1.15.1-3.fc39.x86_64 htslib-devel-1.15.1-3.fc39.x86_64 kernel-headers-6.7.0-0.rc5.41.fc40.x86_64 libaec-1.0.6-5.fc39.x86_64 libaec-devel-1.0.6-5.fc39.x86_64 libb2-0.98.1-9.fc39.x86_64 libgfortran-13.2.1-6.fc40.x86_64 libicu-73.2-2.fc39.x86_64 libicu-devel-73.2-2.fc39.x86_64 libmpc-1.3.1-3.fc39.x86_64 libquadmath-13.2.1-6.fc40.x86_64 libquadmath-devel-13.2.1-6.fc40.x86_64 libstdc++-devel-13.2.1-6.fc40.x86_64 libtool-ltdl-2.4.7-8.fc40.x86_64 libxcrypt-devel-4.4.36-2.fc39.x86_64 m4-1.4.19-7.fc40.x86_64 make-1:4.4.1-2.fc39.x86_64 metis-5.1.0.3-2.fc39.x86_64 mpdecimal-2.5.1-7.fc39.x86_64 ncurses-6.4-8.20231001.fc40.x86_64 openblas-0.3.25-1.fc40.x86_64 openblas-openmp-0.3.25-1.fc40.x86_64 openblas-openmp64-0.3.25-1.fc40.x86_64 perl-AutoLoader-5.74-503.fc40.noarch perl-B-1.88-503.fc40.x86_64 perl-Carp-1.54-500.fc39.noarch perl-Class-Struct-0.68-503.fc40.noarch perl-Data-Dumper-2.188-501.fc39.x86_64 perl-Digest-1.20-500.fc39.noarch perl-Digest-MD5-2.58-501.fc40.x86_64 perl-DynaLoader-1.54-503.fc40.x86_64 perl-Encode-4:3.20-501.fc40.x86_64 perl-Errno-1.37-503.fc40.x86_64 perl-Exporter-5.77-500.fc39.noarch perl-Fcntl-1.15-503.fc40.x86_64 perl-Fedora-VSP-0.001-32.fc39.noarch perl-File-Basename-2.86-503.fc40.noarch perl-File-Compare-1.100.700-503.fc40.noarch perl-File-Copy-2.41-503.fc40.noarch perl-File-Find-1.43-503.fc40.noarch perl-File-Path-2.18-501.fc40.noarch perl-File-Temp-1:0.231.100-501.fc40.noarch perl-File-stat-1.13-503.fc40.noarch perl-FileHandle-2.05-503.fc40.noarch perl-Getopt-Long-1:2.57-1.fc40.noarch perl-Getopt-Std-1.13-503.fc40.noarch perl-HTTP-Tiny-0.088-3.fc39.noarch perl-IO-1.52-503.fc40.x86_64 perl-IO-Socket-IP-0.42-1.fc39.noarch perl-IO-Socket-SSL-2.084-1.fc40.noarch perl-IPC-Open3-1.22-503.fc40.noarch perl-MIME-Base64-3.16-501.fc40.x86_64 perl-Mozilla-CA-20230821-1.fc40.noarch perl-Net-SSLeay-1.92-10.fc39.x86_64 perl-POSIX-2.13-503.fc40.x86_64 perl-PathTools-3.89-500.fc39.x86_64 perl-Pod-Escapes-1:1.07-501.fc40.noarch perl-Pod-Perldoc-3.28.01-501.fc39.noarch perl-Pod-Simple-1:3.45-4.fc39.noarch perl-Pod-Usage-4:2.03-500.fc39.noarch perl-Scalar-List-Utils-5:1.63-500.fc39.x86_64 perl-SelectSaver-1.02-503.fc40.noarch perl-Socket-4:2.037-3.fc39.x86_64 perl-Storable-1:3.32-500.fc39.x86_64 perl-Symbol-1.09-503.fc40.noarch perl-Term-ANSIColor-5.01-502.fc40.noarch perl-Term-Cap-1.18-500.fc39.noarch perl-Text-ParseWords-3.31-500.fc39.noarch perl-Text-Tabs+Wrap-2023.0511-3.fc39.noarch perl-Thread-Queue-3.14-501.fc40.noarch perl-Time-Local-2:1.350-3.fc39.noarch perl-URI-5.21-1.fc40.noarch perl-base-2.27-503.fc40.noarch perl-constant-1.33-501.fc39.noarch perl-generators-1.16-3.fc39.noarch perl-if-0.61.000-503.fc40.noarch perl-interpreter-4:5.38.2-503.fc40.x86_64 perl-libnet-3.15-501.fc39.noarch perl-libs-4:5.38.2-503.fc40.x86_64 perl-locale-1.10-503.fc40.noarch perl-macros-4:5.38.2-503.fc40.noarch perl-mro-1.28-503.fc40.x86_64 perl-overload-1.37-503.fc40.noarch perl-overloading-0.02-503.fc40.noarch perl-parent-1:0.241-500.fc39.noarch perl-podlators-1:5.01-500.fc39.noarch perl-threads-1:2.36-500.fc39.x86_64 perl-threads-shared-1.68-500.fc39.x86_64 perl-vars-1.05-503.fc40.noarch python-pip-wheel-23.2.1-1.fc39.noarch python3-3.12.1-1.fc40.x86_64 python3-libs-3.12.1-1.fc40.x86_64 python3-numpy-1:1.26.0-2.fc40.x86_64 tzdata-2023c-4.fc40.noarch zlib-devel-1.2.13-5.fc40.x86_64 Complete! Finish: build setup for mmseq-1.0.11-16.fc40.src.rpm Start: rpmbuild mmseq-1.0.11-16.fc40.src.rpm warning: %patchN is deprecated (1 usages found), use %patch N (or %patch -P N) Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1689811200 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.oWZXa4 + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/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 + rm -rf /builddir/build/BUILD/mmseq-1.0.11-SPECPARTS + /usr/bin/mkdir -p /builddir/build/BUILD/mmseq-1.0.11-SPECPARTS + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + echo 'Patch #2 (mmseq-zlib.patch):' 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.wUbZLb + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -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 -j2 'CXXFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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; | ^~~~~~~ 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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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++) { | ~~^~~~~~~~~~~~~~~ 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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fopenmp -O2 bms.cpp bms.hpp -c bms.cpp 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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 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; | ^~~~~~~~~ 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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 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"))); | ^ 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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O3 fasta.o extract_transcripts.cpp -o ../bin/extract_transcripts 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; | ^~~~ 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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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++/13/algorithm:61, from mmdiff.cpp:31: /usr/include/c++/13/bits/stl_algo.h:4581:5: note: declared here 4581 | 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/cc8O7r4T.ltrans0.ltrans.o: in function `main': /builddir/build/BUILD/mmseq-1.0.11/src/bam2hits.cpp:653:(.text.startup+0x3ef6): warning: the use of `tmpnam' is dangerous, better use `mkstemp' + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.NTs7n2 + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.x86_64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.x86_64 ++ dirname /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.x86_64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.x86_64 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -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/BUILDROOT/mmseq-1.0.11-16.fc40.x86_64 + mkdir -p /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.x86_64/usr/bin + install -p -m 0755 bin/bam2hits /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.x86_64/usr/bin + install -p -m 0755 bin/extract_transcripts /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.x86_64/usr/bin + install -p -m 0755 bin/hitstools /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.x86_64/usr/bin + install -p -m 0755 bin/mmcollapse /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.x86_64/usr/bin + install -p -m 0755 bin/mmdiff /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.x86_64/usr/bin + install -p -m 0755 bin/mmseq /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.x86_64/usr/bin + install -p -m 0755 bin/offsetGTF /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.x86_64/usr/bin + install -p -m 0755 bin/t2g_hits /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.x86_64/usr/bin + install -p -m 0755 bin/fastagrep.sh bin/mouse_strain_transcriptome.sh bin/usage.sh /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.x86_64/usr/bin + install -p -m 0755 bin/filterGTF.rb bin/haploref.rb bin/testregexp.rb /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.x86_64/usr/bin + install -p -m 0755 bin/ensembl_gtf_to_gff.pl /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.x86_64/usr/bin + /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 1.0.11-16.fc40 --unique-debug-suffix -1.0.11-16.fc40.x86_64 --unique-debug-src-base mmseq-1.0.11-16.fc40.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 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-1.0.11-16.fc40.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 -j2 + /usr/lib/rpm/redhat/brp-python-hardlink Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.G45oW0 + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -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-1.0.11-16.fc40.x86_64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.uCcxCM + umask 022 + cd /builddir/build/BUILD + cd mmseq-1.0.11 + DOCDIR=/builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.x86_64/usr/share/doc/mmseq + export LC_ALL= + LC_ALL= + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.x86_64/usr/share/doc/mmseq + cp -pr /builddir/build/BUILD/mmseq-1.0.11/README.md /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.x86_64/usr/share/doc/mmseq + cp -pr /builddir/build/BUILD/mmseq-1.0.11/COPYING /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.x86_64/usr/share/doc/mmseq + cp -pr /builddir/build/BUILD/mmseq-1.0.11/doc /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.x86_64/usr/share/doc/mmseq + RPM_EC=0 ++ jobs -p + exit 0 Provides: mmseq = 1.0.11-16.fc40 mmseq(x86-64) = 1.0.11-16.fc40 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_1.3.8)(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-1.0.11-16.fc40.x86_64 Provides: mmseq-debugsource = 1.0.11-16.fc40 mmseq-debugsource(x86-64) = 1.0.11-16.fc40 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: mmseq-debuginfo-1.0.11-16.fc40.x86_64 Provides: debuginfo(build-id) = 2e51359e6496da1d81def892de38d2f2aafe4395 debuginfo(build-id) = 6c230e63e0fc68b4b9e72a5084777ffea5c9065a debuginfo(build-id) = 746ac224e49c5543f4f8059761a339ffbbe48e5f debuginfo(build-id) = 7cd8d0145f47ff34a4db92e0e952d7460360aff9 debuginfo(build-id) = c03be22d03d2f835ed801a54321bdca4cb0217e1 debuginfo(build-id) = c1693aee50634a8869b9597c027ad4ad30f77b9c debuginfo(build-id) = c61a0aa090ea5a23af17a2c35e12bdee2a3d313a debuginfo(build-id) = efca92d44633f97e8889abad3a6737b8b03d9f4a mmseq-debuginfo = 1.0.11-16.fc40 mmseq-debuginfo(x86-64) = 1.0.11-16.fc40 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: mmseq-debugsource(x86-64) = 1.0.11-16.fc40 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.x86_64 Wrote: /builddir/build/RPMS/mmseq-1.0.11-16.fc40.x86_64.rpm Wrote: /builddir/build/RPMS/mmseq-debugsource-1.0.11-16.fc40.x86_64.rpm Wrote: /builddir/build/RPMS/mmseq-debuginfo-1.0.11-16.fc40.x86_64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.sKEgFM + umask 022 + cd /builddir/build/BUILD + cd mmseq-1.0.11 + /usr/bin/rm -rf /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.x86_64 + RPM_EC=0 ++ jobs -p + exit 0 Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.hFBpmj + umask 022 + cd /builddir/build/BUILD + rm -rf /builddir/build/BUILD/mmseq-1.0.11-SPECPARTS + rm -rf mmseq-1.0.11 mmseq-1.0.11.gemspec + RPM_EC=0 ++ jobs -p + exit 0 RPM build warnings: %patchN is deprecated (1 usages found), use %patch N (or %patch -P N) Finish: rpmbuild mmseq-1.0.11-16.fc40.src.rpm Finish: build phase for mmseq-1.0.11-16.fc40.src.rpm INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-x86_64-1702420456.496724/root/var/log/dnf.rpm.log /var/lib/mock/fedora-rawhide-x86_64-1702420456.496724/root/var/log/dnf.librepo.log /var/lib/mock/fedora-rawhide-x86_64-1702420456.496724/root/var/log/dnf.log INFO: Done(/var/lib/copr-rpmbuild/results/mmseq-1.0.11-16.fc40.src.rpm) Config(child) 1 minutes 33 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", "epoch": null, "version": "1.0.11", "release": "16.fc40", "arch": "src" }, { "name": "mmseq-debuginfo", "epoch": null, "version": "1.0.11", "release": "16.fc40", "arch": "x86_64" }, { "name": "mmseq-debugsource", "epoch": null, "version": "1.0.11", "release": "16.fc40", "arch": "x86_64" }, { "name": "mmseq", "epoch": null, "version": "1.0.11", "release": "16.fc40", "arch": "x86_64" } ] } RPMResults finished