Warning: Permanently added '3.87.17.89' (ED25519) to the list of known hosts. Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-awwvmkn_/mmseq/mmseq.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-awwvmkn_/mmseq --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1738534972.753496 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 6.0 starting (python version = 3.13.0, NVR = mock-6.0-1.fc41), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-awwvmkn_/mmseq/mmseq.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-awwvmkn_/mmseq --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1738534972.753496 -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-awwvmkn_/mmseq/mmseq.spec) Config(fedora-41-x86_64) Start: clean chroot Finish: clean chroot Mock Version: 6.0 INFO: Mock Version: 6.0 Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-41-x86_64-bootstrap-1738534972.753496/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 container image: registry.fedoraproject.org/fedora:41 INFO: Pulling image: registry.fedoraproject.org/fedora:41 INFO: Tagging container image as mock-bootstrap-f2f32b96-bcb9-4c51-9c82-1efd6ab27e41 INFO: Checking that a432b057a522737c229d2aac9b029f55bf2a44eb3f423e4e4ece2acb8a304652 image matches host's architecture INFO: Copy content of container a432b057a522737c229d2aac9b029f55bf2a44eb3f423e4e4ece2acb8a304652 to /var/lib/mock/fedora-41-x86_64-bootstrap-1738534972.753496/root INFO: mounting a432b057a522737c229d2aac9b029f55bf2a44eb3f423e4e4ece2acb8a304652 with podman image mount INFO: image a432b057a522737c229d2aac9b029f55bf2a44eb3f423e4e4ece2acb8a304652 as /var/lib/containers/storage/overlay/c9636add90844f42998958a532f08e880f2904e56e7e03e6d453e29ae1b586c4/merged INFO: umounting image a432b057a522737c229d2aac9b029f55bf2a44eb3f423e4e4ece2acb8a304652 (/var/lib/containers/storage/overlay/c9636add90844f42998958a532f08e880f2904e56e7e03e6d453e29ae1b586c4/merged) with podman image umount INFO: Removing image mock-bootstrap-f2f32b96-bcb9-4c51-9c82-1efd6ab27e41 INFO: Package manager dnf5 detected and used (fallback) INFO: Not updating bootstrap chroot, bootstrap_image_ready=True 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-41-x86_64-1738534972.753496/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin INFO: Package manager dnf5 detected and used (direct choice) INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-4.20.0-1.fc41.x86_64 rpm-sequoia-1.7.0-3.fc41.x86_64 dnf5-5.2.8.1-3.fc41.x86_64 dnf5-plugins-5.2.8.1-3.fc41.x86_64 Start: installing minimal buildroot with dnf5 Updating and loading repositories: updates 100% | 292.7 KiB/s | 29.9 KiB | 00m00s fedora 100% | 188.4 KiB/s | 31.8 KiB | 00m00s Copr repository 100% | 102.5 KiB/s | 1.5 KiB | 00m00s Additional repo http_kojipkgs_fedorapr 100% | 212.7 KiB/s | 3.8 KiB | 00m00s Copr repository 100% | 67.0 MiB/s | 3.4 MiB | 00m00s Repositories loaded. 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ocaml-srpm-macros noarch 10-4.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.9 KiB openblas-srpm-macros noarch 2-19.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 112.0 B openldap x86_64 2.6.9-3.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 655.1 KiB openssl-libs x86_64 1:3.2.2-14.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 7.8 MiB p11-kit x86_64 0.25.5-5.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 2.2 MiB p11-kit-trust x86_64 0.25.5-5.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 395.5 KiB package-notes-srpm-macros noarch 0.5-13.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.6 KiB pam x86_64 1.7.0-4.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.6 MiB pam-libs x86_64 1.7.0-4.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 126.7 KiB pcre2 x86_64 10.44-1.fc42.2 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 649.3 KiB pcre2-syntax noarch 10.44-1.fc42.2 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 251.6 KiB perl-srpm-macros noarch 1-57.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 861.0 B pkgconf x86_64 2.3.0-2.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 88.5 KiB pkgconf-m4 noarch 2.3.0-2.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 14.4 KiB pkgconf-pkg-config x86_64 2.3.0-2.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 989.0 B popt x86_64 1.19-8.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 132.8 KiB publicsuffix-list-dafsa noarch 20250116-1.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 68.5 KiB pyproject-srpm-macros noarch 1.16.4-2.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.9 KiB python-srpm-macros noarch 3.13-4.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 51.0 KiB qt5-srpm-macros noarch 5.15.15-1.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 500.0 B qt6-srpm-macros noarch 6.8.1-5.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 456.0 B readline x86_64 8.2-12.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 485.0 KiB rpm x86_64 4.20.0-8.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 3.0 MiB rpm-build-libs x86_64 4.20.0-8.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 202.6 KiB rpm-libs x86_64 4.20.0-8.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 721.8 KiB rpm-sequoia x86_64 1.7.0-4.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 2.4 MiB rust-srpm-macros noarch 26.3-4.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 4.8 KiB setup noarch 2.15.0-10.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 720.7 KiB sqlite-libs x86_64 3.47.2-2.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.5 MiB systemd x86_64 257.2-17.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 17.4 MiB systemd-libs x86_64 257.2-17.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 2.2 MiB systemd-pam x86_64 257.2-17.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.1 MiB systemd-rpm-macros noarch 257.2-17.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 10.7 KiB util-linux-core x86_64 2.40.4-2.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.4 MiB xxhash-libs x86_64 0.8.3-2.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 90.2 KiB xz-libs x86_64 1:5.6.3-3.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 218.3 KiB zig-srpm-macros noarch 1-4.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.1 KiB zip x86_64 3.0-43.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 698.5 KiB zlib-ng-compat x86_64 2.2.3-2.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 137.6 KiB zstd x86_64 1.5.6-3.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.7 MiB Installing groups: Buildsystem building group Transaction Summary: Installing: 163 packages Total size of inbound packages is 59 MiB. Need to download 4 MiB. After this operation, 197 MiB extra will be used (install 197 MiB, remove 0 B). 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B/s | 74.8 KiB | 00m00s [ 50/165] Installing audit-libs-0:4.0.3 100% | 345.1 MiB/s | 353.4 KiB | 00m00s [ 51/165] Installing pam-libs-0:1.7.0-4 100% | 126.1 MiB/s | 129.1 KiB | 00m00s [ 52/165] Installing libcap-0:2.73-2.fc 100% | 17.3 MiB/s | 212.1 KiB | 00m00s [ 53/165] Installing systemd-libs-0:257 100% | 373.9 MiB/s | 2.2 MiB | 00m00s [ 54/165] Installing libattr-0:2.5.2-5. 100% | 0.0 B/s | 28.1 KiB | 00m00s [ 55/165] Installing libacl-0:2.3.2-3.f 100% | 0.0 B/s | 39.2 KiB | 00m00s [ 56/165] Installing gdbm-libs-1:1.23-9 100% | 128.5 MiB/s | 131.6 KiB | 00m00s [ 57/165] Installing mpfr-0:4.2.1-6.fc4 100% | 407.0 MiB/s | 833.6 KiB | 00m00s [ 58/165] Installing gawk-0:5.3.1-1.fc4 100% | 113.0 MiB/s | 1.7 MiB | 00m00s [ 59/165] Installing dwz-0:0.15-9.fc42. 100% | 26.0 MiB/s | 292.4 KiB | 00m00s [ 60/165] Installing libfdisk-0:2.40.4- 100% | 364.7 MiB/s | 373.5 KiB | 00m00s [ 61/165] Installing unzip-0:6.0-66.fc4 100% | 35.0 MiB/s | 393.8 KiB | 00m00s [ 62/165] Installing file-libs-0:5.45-9 100% | 764.5 MiB/s | 9.9 MiB | 00m00s [ 63/165] Installing file-0:5.45-9.fc42 100% | 6.4 MiB/s | 104.8 KiB | 00m00s [ 64/165] Installing crypto-policies-0: 100% | 40.0 MiB/s | 163.7 KiB | 00m00s [ 65/165] Installing libsmartcols-0:2.4 100% | 177.2 MiB/s | 181.4 KiB | 00m00s [ 66/165] Installing libsepol-0:3.8-1.f 100% | 403.8 MiB/s | 827.0 KiB | 00m00s [ 67/165] Installing lua-libs-0:5.4.7-2 100% | 275.5 MiB/s | 282.1 KiB | 00m00s [ 68/165] Installing alternatives-0:1.3 100% | 6.0 MiB/s | 67.7 KiB | 00m00s [ 69/165] Installing libcom_err-0:1.47. 100% | 0.0 B/s | 68.2 KiB | 00m00s [ 70/165] Installing pcre2-0:10.44-1.fc 100% | 317.7 MiB/s | 650.7 KiB | 00m00s [ 71/165] Installing libselinux-0:3.8-1 100% | 189.8 MiB/s | 194.3 KiB | 00m00s [ 72/165] Installing grep-0:3.11-10.fc4 100% | 71.7 MiB/s | 1.0 MiB | 00m00s [ 73/165] Installing sed-0:4.9-4.fc42.x 100% | 65.0 MiB/s | 865.5 KiB | 00m00s [ 74/165] Installing findutils-1:4.10.0 100% | 124.9 MiB/s | 1.9 MiB | 00m00s [ 75/165] Installing libmount-0:2.40.4- 100% | 348.9 MiB/s | 357.2 KiB | 00m00s [ 76/165] Installing util-linux-core-0: 100% | 95.1 MiB/s | 1.4 MiB | 00m00s [ 77/165] Installing xz-1:5.6.3-3.fc42. 100% | 87.8 MiB/s | 1.2 MiB | 00m00s [ 78/165] Installing lz4-libs-0:1.10.0- 100% | 154.7 MiB/s | 158.5 KiB | 00m00s [ 79/165] Installing libffi-0:3.4.6-5.f 100% | 0.0 B/s | 83.7 KiB | 00m00s [ 80/165] Installing libtasn1-0:4.19.0- 100% | 173.2 MiB/s | 177.4 KiB | 00m00s [ 81/165] Installing p11-kit-0:0.25.5-5 100% | 128.5 MiB/s | 2.2 MiB | 00m00s [ 82/165] Installing libunistring-0:1.1 100% | 431.7 MiB/s | 1.7 MiB | 00m00s [ 83/165] Installing libidn2-0:2.3.7-3. 100% | 163.6 MiB/s | 335.0 KiB | 00m00s [ 84/165] Installing libpsl-0:0.21.5-5. 100% | 0.0 B/s | 77.5 KiB | 00m00s [ 85/165] Installing p11-kit-trust-0:0. 100% | 21.6 MiB/s | 397.2 KiB | 00m00s [ 86/165] Installing zstd-0:1.5.6-3.fc4 100% | 113.0 MiB/s | 1.7 MiB | 00m00s [ 87/165] Installing tar-2:1.35-5.fc42. 100% | 164.6 MiB/s | 3.0 MiB | 00m00s [ 88/165] Installing libsemanage-0:3.8- 100% | 151.5 MiB/s | 310.2 KiB | 00m00s [ 89/165] Installing shadow-utils-2:4.1 100% | 154.6 MiB/s | 4.0 MiB | 00m00s [ 90/165] Installing zip-0:3.0-43.fc42. 100% | 57.2 MiB/s | 702.4 KiB | 00m00s [ 91/165] Installing gdbm-1:1.23-9.fc42 100% | 37.9 MiB/s | 465.2 KiB | 00m00s [ 92/165] Installing cyrus-sasl-lib-0:2 100% | 144.0 MiB/s | 2.3 MiB | 00m00s [ 93/165] Installing bzip2-0:1.0.8-20.f 100% | 9.2 MiB/s | 103.8 KiB | 00m00s [ 94/165] Installing libxml2-0:2.12.9-2 100% | 122.0 MiB/s | 1.7 MiB | 00m00s [ 95/165] Installing sqlite-libs-0:3.47 100% | 376.1 MiB/s | 1.5 MiB | 00m00s [ 96/165] Installing add-determinism-0: 100% | 153.5 MiB/s | 2.5 MiB | 00m00s [ 97/165] Installing build-reproducibil 100% | 0.0 B/s | 1.0 KiB | 00m00s [ 98/165] Installing filesystem-srpm-ma 100% | 0.0 B/s | 38.9 KiB | 00m00s [ 99/165] Installing ed-0:1.21-2.fc42.x 100% | 13.2 MiB/s | 148.8 KiB | 00m00s [100/165] Installing patch-0:2.7.6-26.f 100% | 23.1 MiB/s | 260.2 KiB | 00m00s [101/165] Installing elfutils-default-y 100% | 408.6 KiB/s | 2.0 KiB | 00m00s [102/165] Installing elfutils-libs-0:0. 100% | 330.4 MiB/s | 676.7 KiB | 00m00s [103/165] Installing dbus-common-1:1.16 100% | 3.3 MiB/s | 13.6 KiB | 00m00s [104/165] Installing cpio-0:2.15-2.fc41 100% | 73.3 MiB/s | 1.1 MiB | 00m00s [105/165] Installing diffutils-0:3.10-9 100% | 106.0 MiB/s | 1.6 MiB | 00m00s [106/165] Installing libgomp-0:15.0.1-0 100% | 524.4 MiB/s | 537.0 KiB | 00m00s [107/165] Installing jansson-0:2.14-2.f 100% | 0.0 B/s | 94.4 KiB | 00m00s [108/165] Installing libpkgconf-0:2.3.0 100% | 0.0 B/s | 79.2 KiB | 00m00s [109/165] Installing pkgconf-0:2.3.0-2. 100% | 8.9 MiB/s | 91.0 KiB | 00m00s [110/165] Installing pkgconf-pkg-config 100% | 177.3 KiB/s | 1.8 KiB | 00m00s [111/165] Installing keyutils-libs-0:1. 100% | 0.0 B/s | 59.7 KiB | 00m00s [112/165] Installing libverto-0:0.3.2-1 100% | 0.0 B/s | 27.2 KiB | 00m00s [113/165] Installing json-c-0:0.18-2.fc 100% | 0.0 B/s | 88.0 KiB | 00m00s [114/165] Installing libseccomp-0:2.5.5 100% | 171.1 MiB/s | 175.2 KiB | 00m00s [115/165] Installing expat-0:2.6.4-2.fc 100% | 12.5 MiB/s | 294.9 KiB | 00m00s [116/165] Installing dbus-broker-0:36-5 100% | 21.6 MiB/s | 397.6 KiB | 00m00s [117/165] Installing dbus-1:1.16.0-3.fc 100% | 0.0 B/s | 124.0 B | 00m00s [118/165] Installing xxhash-libs-0:0.8. 100% | 89.4 MiB/s | 91.6 KiB | 00m00s [119/165] Installing libnghttp2-0:1.64. 100% | 167.5 MiB/s | 171.5 KiB | 00m00s [120/165] Installing libbrotli-0:1.1.0- 100% | 274.6 MiB/s | 843.6 KiB | 00m00s [121/165] Installing libtool-ltdl-0:2.5 100% | 69.6 MiB/s | 71.2 KiB | 00m00s [122/165] Installing coreutils-common-0 100% | 429.0 MiB/s | 11.2 MiB | 00m00s [123/165] Installing openssl-libs-1:3.2 100% | 435.3 MiB/s | 7.8 MiB | 00m00s [124/165] Installing coreutils-0:9.6-1. 100% | 179.0 MiB/s | 5.5 MiB | 00m00s [125/165] Installing ca-certificates-0: 100% | 2.2 MiB/s | 2.4 MiB | 00m01s [126/165] Installing krb5-libs-0:1.21.3 100% | 287.5 MiB/s | 2.3 MiB | 00m00s [127/165] Installing libarchive-0:3.7.7 100% | 306.2 MiB/s | 940.6 KiB | 00m00s [128/165] Installing libtirpc-0:1.3.6-1 100% | 196.0 MiB/s | 200.7 KiB | 00m00s [129/165] Installing gzip-0:1.13-3.fc42 100% | 32.4 MiB/s | 398.4 KiB | 00m00s [130/165] Installing authselect-libs-0: 100% | 203.9 MiB/s | 835.0 KiB | 00m00s [131/165] Installing cracklib-0:2.9.11- 100% | 19.1 MiB/s | 253.7 KiB | 00m00s [132/165] Installing libpwquality-0:1.4 100% | 29.4 MiB/s | 421.6 KiB | 00m00s [133/165] Installing libnsl2-0:2.0.1-3. 100% | 57.6 MiB/s | 59.0 KiB | 00m00s [134/165] Installing pam-0:1.7.0-4.fc42 100% | 80.7 MiB/s | 1.7 MiB | 00m00s [135/165] Installing util-linux-0:2.40. 100% | 111.7 MiB/s | 3.5 MiB | 00m00s [136/165] Installing systemd-pam-0:257. 100% | 222.5 MiB/s | 1.1 MiB | 00m00s [137/165] Installing systemd-0:257.2-17 100% | 125.2 MiB/s | 17.5 MiB | 00m00s >>> Running post-install scriptlet: systemd-0:257.2-17.fc42.x86_64 >>> Finished post-install scriptlet: systemd-0:257.2-17.fc42.x86_64 >>> Scriptlet output: >>> Creating group 'systemd-journal' with GID 190. >>> Creating group 'systemd-oom' with GID 999. >>> Creating user 'systemd-oom' (systemd Userspace OOM Killer) with UID 999 and >>> [138/165] Installing libssh-0:0.11.1-4. 100% | 277.1 MiB/s | 567.5 KiB | 00m00s [139/165] Installing rpm-sequoia-0:1.7. 100% | 402.4 MiB/s | 2.4 MiB | 00m00s [140/165] Installing rpm-libs-0:4.20.0- 100% | 353.2 MiB/s | 723.3 KiB | 00m00s [141/165] Installing rpm-build-libs-0:4 100% | 198.7 MiB/s | 203.4 KiB | 00m00s [142/165] Installing libevent-0:2.1.12- 100% | 295.2 MiB/s | 906.9 KiB | 00m00s [143/165] Installing openldap-0:2.6.9-3 100% | 321.7 MiB/s | 658.9 KiB | 00m00s [144/165] Installing libcurl-0:8.11.1-3 100% | 411.7 MiB/s | 843.1 KiB | 00m00s [145/165] Installing elfutils-debuginfo 100% | 7.0 MiB/s | 86.2 KiB | 00m00s [146/165] Installing elfutils-0:0.192-8 100% | 158.1 MiB/s | 2.7 MiB | 00m00s [147/165] Installing binutils-0:2.43.50 100% | 344.7 MiB/s | 25.9 MiB | 00m00s [148/165] Installing gdb-minimal-0:15.2 100% | 310.6 MiB/s | 13.0 MiB | 00m00s [149/165] Installing debugedit-0:5.1-4. 100% | 18.0 MiB/s | 203.1 KiB | 00m00s [150/165] Installing curl-0:8.11.1-3.fc 100% | 23.5 MiB/s | 457.1 KiB | 00m00s [151/165] Installing rpm-0:4.20.0-8.fc4 100% | 103.7 MiB/s | 2.5 MiB | 00m00s [152/165] Installing efi-srpm-macros-0: 100% | 0.0 B/s | 41.1 KiB | 00m00s [153/165] Installing lua-srpm-macros-0: 100% | 0.0 B/s | 1.9 KiB | 00m00s [154/165] Installing zig-srpm-macros-0: 100% | 0.0 B/s | 1.7 KiB | 00m00s [155/165] Installing forge-srpm-macros- 100% | 0.0 B/s | 40.3 KiB | 00m00s [156/165] Installing go-srpm-macros-0:3 100% | 0.0 B/s | 62.0 KiB | 00m00s [157/165] Installing fonts-srpm-macros- 100% | 0.0 B/s | 57.0 KiB | 00m00s [158/165] Installing python-srpm-macros 100% | 0.0 B/s | 52.2 KiB | 00m00s [159/165] Installing redhat-rpm-config- 100% | 94.5 MiB/s | 193.5 KiB | 00m00s [160/165] Installing rpm-build-0:4.20.0 100% | 14.1 MiB/s | 173.7 KiB | 00m00s [161/165] Installing pyproject-srpm-mac 100% | 0.0 B/s | 2.5 KiB | 00m00s [162/165] Installing authselect-0:1.5.0 100% | 14.2 MiB/s | 160.4 KiB | 00m00s [163/165] Installing which-0:2.22-2.fc4 100% | 8.3 MiB/s | 85.3 KiB | 00m00s [164/165] Installing info-0:7.2-3.fc42. 100% | 31.8 MiB/s | 358.3 KiB | 00m00s [165/165] Installing systemd-rpm-macros 100% | 7.5 KiB/s | 11.3 KiB | 00m01s Warning: skipped OpenPGP checks for 163 packages from repository: http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch Complete! Finish: installing minimal buildroot with dnf5 Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: add-determinism-0.5.0-2.fc42.x86_64 alternatives-1.31-3.fc42.x86_64 ansible-srpm-macros-1-17.1.fc42.noarch audit-libs-4.0.3-2.fc42.x86_64 authselect-1.5.0-9.fc42.x86_64 authselect-libs-1.5.0-9.fc42.x86_64 basesystem-11-22.fc42.noarch bash-5.2.37-1.fc42.x86_64 binutils-2.43.50-12.fc42.x86_64 build-reproducibility-srpm-macros-0.5.0-2.fc42.noarch bzip2-1.0.8-20.fc42.x86_64 bzip2-libs-1.0.8-20.fc42.x86_64 ca-certificates-2024.2.69_v8.0.401-5.fc42.noarch coreutils-9.6-1.fc42.x86_64 coreutils-common-9.6-1.fc42.x86_64 cpio-2.15-2.fc41.x86_64 cracklib-2.9.11-7.fc42.x86_64 crypto-policies-20250124-1.git4d262e7.fc42.noarch curl-8.11.1-3.fc42.x86_64 cyrus-sasl-lib-2.1.28-30.fc42.x86_64 dbus-1.16.0-3.fc42.x86_64 dbus-broker-36-5.fc42.x86_64 dbus-common-1.16.0-3.fc42.noarch debugedit-5.1-4.fc42.x86_64 diffutils-3.10-9.fc42.x86_64 dwz-0.15-9.fc42.x86_64 ed-1.21-2.fc42.x86_64 efi-srpm-macros-6-2.fc42.noarch elfutils-0.192-8.fc42.x86_64 elfutils-debuginfod-client-0.192-8.fc42.x86_64 elfutils-default-yama-scope-0.192-8.fc42.noarch elfutils-libelf-0.192-8.fc42.x86_64 elfutils-libs-0.192-8.fc42.x86_64 expat-2.6.4-2.fc42.x86_64 fedora-gpg-keys-42-0.4.noarch fedora-release-42-0.16.noarch fedora-release-common-42-0.16.noarch fedora-release-identity-basic-42-0.16.noarch fedora-repos-42-0.4.noarch fedora-repos-rawhide-42-0.4.noarch file-5.45-9.fc42.x86_64 file-libs-5.45-9.fc42.x86_64 filesystem-3.18-36.fc42.x86_64 filesystem-srpm-macros-3.18-36.fc42.noarch findutils-4.10.0-5.fc42.x86_64 fonts-srpm-macros-2.0.5-21.fc42.noarch forge-srpm-macros-0.4.0-2.fc42.noarch fpc-srpm-macros-1.3-14.fc42.noarch gawk-5.3.1-1.fc42.x86_64 gdb-minimal-15.2-7.fc42.x86_64 gdbm-1.23-9.fc42.x86_64 gdbm-libs-1.23-9.fc42.x86_64 ghc-srpm-macros-1.9.2-2.fc42.noarch glibc-2.40.9000-35.fc42.x86_64 glibc-common-2.40.9000-35.fc42.x86_64 glibc-gconv-extra-2.40.9000-35.fc42.x86_64 glibc-minimal-langpack-2.40.9000-35.fc42.x86_64 gmp-6.3.0-2.fc41.x86_64 gnat-srpm-macros-6-7.fc42.noarch go-srpm-macros-3.6.0-6.fc42.noarch grep-3.11-10.fc42.x86_64 gzip-1.13-3.fc42.x86_64 info-7.2-3.fc42.x86_64 jansson-2.14-2.fc42.x86_64 json-c-0.18-2.fc42.x86_64 kernel-srpm-macros-1.0-25.fc42.noarch keyutils-libs-1.6.3-5.fc42.x86_64 krb5-libs-1.21.3-5.fc42.x86_64 libacl-2.3.2-3.fc42.x86_64 libarchive-3.7.7-2.fc42.x86_64 libattr-2.5.2-5.fc42.x86_64 libblkid-2.40.4-2.fc42.x86_64 libbrotli-1.1.0-6.fc42.x86_64 libcap-2.73-2.fc42.x86_64 libcap-ng-0.8.5-4.fc42.x86_64 libcom_err-1.47.2-3.fc42.x86_64 libcurl-8.11.1-3.fc42.x86_64 libeconf-0.7.5-2.fc42.x86_64 libevent-2.1.12-15.fc42.x86_64 libfdisk-2.40.4-2.fc42.x86_64 libffi-3.4.6-5.fc42.x86_64 libgcc-15.0.1-0.6.fc42.x86_64 libgomp-15.0.1-0.6.fc42.x86_64 libidn2-2.3.7-3.fc42.x86_64 libmount-2.40.4-2.fc42.x86_64 libnghttp2-1.64.0-3.fc42.x86_64 libnsl2-2.0.1-3.fc42.x86_64 libpkgconf-2.3.0-2.fc42.x86_64 libpsl-0.21.5-5.fc42.x86_64 libpwquality-1.4.5-12.fc42.x86_64 libseccomp-2.5.5-2.fc41.x86_64 libselinux-3.8-1.fc42.x86_64 libsemanage-3.8-1.fc42.x86_64 libsepol-3.8-1.fc42.x86_64 libsmartcols-2.40.4-2.fc42.x86_64 libssh-0.11.1-4.fc42.x86_64 libssh-config-0.11.1-4.fc42.noarch libstdc++-15.0.1-0.6.fc42.x86_64 libtasn1-4.19.0-11.fc42.x86_64 libtirpc-1.3.6-1.rc3.fc42.2.x86_64 libtool-ltdl-2.5.4-4.fc42.x86_64 libunistring-1.1-9.fc42.x86_64 libuuid-2.40.4-2.fc42.x86_64 libverto-0.3.2-10.fc42.x86_64 libxcrypt-4.4.38-4.fc42.x86_64 libxml2-2.12.9-2.fc42.x86_64 libzstd-1.5.6-3.fc42.x86_64 lua-libs-5.4.7-2.fc42.x86_64 lua-srpm-macros-1-15.fc42.noarch lz4-libs-1.10.0-2.fc42.x86_64 mpfr-4.2.1-6.fc42.x86_64 ncurses-base-6.5-5.20250125.fc42.noarch ncurses-libs-6.5-5.20250125.fc42.x86_64 ocaml-srpm-macros-10-4.fc42.noarch openblas-srpm-macros-2-19.fc42.noarch openldap-2.6.9-3.fc42.x86_64 openssl-libs-3.2.2-14.fc42.x86_64 p11-kit-0.25.5-5.fc42.x86_64 p11-kit-trust-0.25.5-5.fc42.x86_64 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systemd-pam-257.2-17.fc42.x86_64 systemd-rpm-macros-257.2-17.fc42.noarch tar-1.35-5.fc42.x86_64 unzip-6.0-66.fc42.x86_64 util-linux-2.40.4-2.fc42.x86_64 util-linux-core-2.40.4-2.fc42.x86_64 which-2.22-2.fc42.x86_64 xxhash-libs-0.8.3-2.fc42.x86_64 xz-5.6.3-3.fc42.x86_64 xz-libs-5.6.3-3.fc42.x86_64 zig-srpm-macros-1-4.fc42.noarch zip-3.0-43.fc42.x86_64 zlib-ng-compat-2.2.3-2.fc42.x86_64 zstd-1.5.6-3.fc42.x86_64 Start: buildsrpm Start: rpmbuild -bs Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1738454400 Wrote: /builddir/build/SRPMS/mmseq-1.0.11-23.fc42.src.rpm Finish: rpmbuild -bs INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-41-x86_64-1738534972.753496/root/var/log/dnf5.log INFO: chroot_scan: creating tarball /var/lib/copr-rpmbuild/results/chroot_scan.tar.gz /bin/tar: Removing leading `/' from member names Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-awwvmkn_/mmseq/mmseq.spec) Config(child) 0 minutes 11 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-1.0.11-23.fc42.src.rpm) Config(fedora-41-x86_64) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-41-x86_64-bootstrap-1738534972.753496/root. INFO: reusing tmpfs at /var/lib/mock/fedora-41-x86_64-bootstrap-1738534972.753496/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-41-x86_64-1738534972.753496/root. INFO: calling preinit hooks INFO: enabled root cache Start: unpacking root cache Finish: unpacking root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-4.20.0-1.fc41.x86_64 rpm-sequoia-1.7.0-3.fc41.x86_64 dnf5-5.2.8.1-3.fc41.x86_64 dnf5-plugins-5.2.8.1-3.fc41.x86_64 Finish: chroot init Start: build phase for mmseq-1.0.11-23.fc42.src.rpm Start: build setup for mmseq-1.0.11-23.fc42.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1738454400 Wrote: /builddir/build/SRPMS/mmseq-1.0.11-23.fc42.src.rpm Updating and loading repositories: fedora 100% | 558.5 KiB/s | 31.8 KiB | 00m00s updates 100% | 497.6 KiB/s | 29.9 KiB | 00m00s Copr repository 100% | 96.1 KiB/s | 1.5 KiB | 00m00s Additional repo http_kojipkgs_fedorapr 100% | 212.7 KiB/s | 3.8 KiB | 00m00s Repositories loaded. 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http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 29.3 KiB perl-Text-ParseWords noarch 3.31-512.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 13.6 KiB perl-Text-Tabs+Wrap noarch 2024.001-512.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 22.6 KiB perl-Time-Local noarch 2:1.350-512.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 68.9 KiB perl-URI noarch 5.31-2.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 257.0 KiB perl-base noarch 2.27-515.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 12.5 KiB perl-constant noarch 1.33-513.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 26.2 KiB perl-if noarch 0.61.000-515.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 5.8 KiB perl-interpreter x86_64 4:5.40.1-515.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 118.1 KiB perl-libnet noarch 3.15-513.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 289.4 KiB perl-libs x86_64 4:5.40.1-515.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 9.8 MiB perl-locale noarch 1.12-515.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 6.5 KiB perl-macros noarch 4:5.40.1-515.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 5.5 KiB perl-mro x86_64 1.29-515.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 41.5 KiB perl-overload noarch 1.37-515.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 71.5 KiB perl-overloading noarch 0.02-515.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 4.8 KiB perl-parent noarch 1:0.244-2.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 10.3 KiB perl-podlators noarch 1:6.0.2-3.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 317.5 KiB perl-vars noarch 1.05-515.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 3.9 KiB python-pip-wheel noarch 24.3.1-2.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.2 MiB python3 x86_64 3.13.1-3.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 27.6 KiB python3-libs x86_64 3.13.1-3.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 39.9 MiB python3-numpy x86_64 1:2.2.2-2.fc42 copr_base 40.1 MiB python3-numpy-f2py x86_64 1:2.2.2-2.fc42 copr_base 2.0 MiB tzdata noarch 2024b-2.fc42 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.6 MiB Transaction Summary: Installing: 145 packages Total size of inbound packages is 168 MiB. Need to download 38 MiB. After this operation, 705 MiB extra will be used (install 705 MiB, remove 0 B). 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MiB/s | 35.2 KiB | 00m00s [129/145] perl-Term-ANSIColor-0:5.01-51 100% | 6.7 MiB/s | 47.7 KiB | 00m00s [130/145] perl-Term-Cap-0:1.18-512.fc42 100% | 3.6 MiB/s | 22.2 KiB | 00m00s [131/145] ncurses-0:6.5-5.20250125.fc42 100% | 45.5 MiB/s | 419.8 KiB | 00m00s [132/145] perl-Pod-Escapes-1:1.07-512.f 100% | 2.4 MiB/s | 19.8 KiB | 00m00s [133/145] perl-Text-Tabs+Wrap-0:2024.00 100% | 2.7 MiB/s | 21.8 KiB | 00m00s [134/145] perl-if-0:0.61.000-515.fc42.n 100% | 2.3 MiB/s | 14.0 KiB | 00m00s [135/145] perl-AutoLoader-0:5.74-515.fc 100% | 4.1 MiB/s | 21.2 KiB | 00m00s [136/145] perl-locale-0:1.12-515.fc42.n 100% | 2.2 MiB/s | 13.6 KiB | 00m00s [137/145] perl-IO-Socket-IP-0:0.43-2.fc 100% | 6.9 MiB/s | 42.4 KiB | 00m00s [138/145] perl-Data-Dumper-0:2.189-513. 100% | 5.5 MiB/s | 56.7 KiB | 00m00s [139/145] perl-URI-0:5.31-2.fc42.noarch 100% | 12.4 MiB/s | 127.1 KiB | 00m00s [140/145] perl-MIME-Base32-0:1.303-23.f 100% | 2.5 MiB/s | 20.5 KiB | 00m00s [141/145] perl-Digest-MD5-0:2.59-6.fc42 100% | 5.9 MiB/s | 36.0 KiB | 00m00s [142/145] perl-B-0:1.89-515.fc42.x86_64 100% | 28.8 MiB/s | 177.0 KiB | 00m00s [143/145] perl-libnet-0:3.15-513.fc42.n 100% | 17.1 MiB/s | 122.9 KiB | 00m00s [144/145] perl-FileHandle-0:2.05-515.fc 100% | 3.0 MiB/s | 15.5 KiB | 00m00s [145/145] perl-Digest-0:1.20-512.fc42.n 100% | 4.1 MiB/s | 24.9 KiB | 00m00s -------------------------------------------------------------------------------- [145/145] Total 100% | 84.7 MiB/s | 37.9 MiB | 00m00s Running transaction [ 1/147] Verify package files 100% | 296.0 B/s | 145.0 B | 00m00s [ 2/147] Prepare transaction 100% | 1.3 KiB/s | 145.0 B | 00m00s [ 3/147] Installing boost-system-0:1.8 100% | 12.9 MiB/s | 13.2 KiB | 00m00s [ 4/147] Installing libgfortran-0:15.0 100% | 473.1 MiB/s | 3.3 MiB | 00m00s [ 5/147] Installing boost-chrono-0:1.8 100% | 0.0 B/s | 38.5 KiB | 00m00s [ 6/147] Installing boost-thread-0:1.8 100% | 130.6 MiB/s | 133.7 KiB | 00m00s [ 7/147] Installing libicu-0:76.1-4.fc 100% | 422.5 MiB/s | 36.3 MiB | 00m00s [ 8/147] Installing libmpc-0:1.3.1-7.f 100% | 162.2 MiB/s | 166.1 KiB | 00m00s [ 9/147] Installing libquadmath-0:15.0 100% | 311.7 MiB/s | 319.2 KiB | 00m00s [ 10/147] Installing boost-regex-0:1.83 100% | 281.6 MiB/s | 288.3 KiB | 00m00s [ 11/147] Installing boost-context-0:1. 100% | 0.0 B/s | 13.4 KiB | 00m00s [ 12/147] Installing boost-atomic-0:1.8 100% | 0.0 B/s | 21.9 KiB | 00m00s [ 13/147] Installing boost-filesystem-0 100% | 141.2 MiB/s | 144.6 KiB | 00m00s [ 14/147] Installing openblas-0:0.3.29- 100% | 110.8 MiB/s | 113.5 KiB | 00m00s [ 15/147] Installing libaec-0:1.1.3-2.f 100% | 98.0 MiB/s | 100.3 KiB | 00m00s [ 16/147] Installing boost-date-time-0: 100% | 0.0 B/s | 13.2 KiB | 00m00s [ 17/147] Installing boost-container-0: 100% | 0.0 B/s | 66.4 KiB | 00m00s [ 18/147] Installing cmake-filesystem-0 100% | 3.7 MiB/s | 7.6 KiB | 00m00s [ 19/147] Installing libstdc++-devel-0: 100% | 421.4 MiB/s | 16.0 MiB | 00m00s [ 20/147] Installing zlib-ng-compat-dev 100% | 106.0 MiB/s | 108.5 KiB | 00m00s [ 21/147] Installing boost-json-0:1.83. 100% | 326.2 MiB/s | 334.1 KiB | 00m00s [ 22/147] Installing boost-wave-0:1.83. 100% | 418.6 MiB/s | 857.2 KiB | 00m00s [ 23/147] Installing hdf5-0:1.14.5-2.fc 100% | 254.5 MiB/s | 7.1 MiB | 00m00s [ 24/147] Installing libaec-devel-0:1.1 100% | 0.0 B/s | 13.5 KiB | 00m00s [ 25/147] Installing openblas-openmp64- 100% | 674.7 MiB/s | 43.9 MiB | 00m00s [ 26/147] Installing openblas-openmp-0: 100% | 672.6 MiB/s | 43.7 MiB | 00m00s [ 27/147] Installing flexiblas-0:3.4.4- 100% | 0.0 B/s | 49.7 KiB | 00m00s [ 28/147] Installing flexiblas-openblas 100% | 43.0 MiB/s | 44.1 KiB | 00m00s [ 29/147] Installing flexiblas-netlib-0 100% | 303.9 MiB/s | 10.6 MiB | 00m00s [ 30/147] Installing flexiblas-openblas 100% | 0.0 B/s | 44.1 KiB | 00m00s [ 31/147] Installing flexiblas-netlib64 100% | 306.9 MiB/s | 10.7 MiB | 00m00s [ 32/147] Installing arpack-0:3.9.1-6.f 100% | 318.3 MiB/s | 651.8 KiB | 00m00s [ 33/147] Installing armadillo-0:12.8.1 100% | 85.2 MiB/s | 87.3 KiB | 00m00s [ 34/147] Installing arpack-devel-0:3.9 100% | 70.4 MiB/s | 72.1 KiB | 00m00s [ 35/147] Installing flexiblas-devel-0: 100% | 280.2 MiB/s | 4.8 MiB | 00m00s [ 36/147] Installing boost-fiber-0:1.83 100% | 77.8 MiB/s | 79.7 KiB | 00m00s [ 37/147] Installing boost-log-0:1.83.0 100% | 371.6 MiB/s | 1.5 MiB | 00m00s [ 38/147] Installing boost-coroutine-0: 100% | 0.0 B/s | 22.1 KiB | 00m00s [ 39/147] Installing boost-graph-0:1.83 100% | 343.5 MiB/s | 351.7 KiB | 00m00s [ 40/147] Installing cpp-0:15.0.1-0.6.f 100% | 372.5 MiB/s | 38.0 MiB | 00m00s [ 41/147] Installing libicu-devel-0:76. 100% | 220.6 MiB/s | 5.1 MiB | 00m00s [ 42/147] Installing boost-locale-0:1.8 100% | 300.2 MiB/s | 614.8 KiB | 00m00s [ 43/147] Installing boost-type_erasure 100% | 53.9 MiB/s | 55.2 KiB | 00m00s [ 44/147] Installing boost-timer-0:1.83 100% | 0.0 B/s | 22.0 KiB | 00m00s [ 45/147] Installing annobin-docs-0:12. 100% | 0.0 B/s | 99.8 KiB | 00m00s [ 46/147] Installing ncurses-0:6.5-5.20 100% | 30.0 MiB/s | 614.7 KiB | 00m00s [ 47/147] Installing groff-base-0:1.23. 100% | 125.6 MiB/s | 3.9 MiB | 00m00s [ 48/147] Installing perl-Digest-0:1.20 100% | 36.2 MiB/s | 37.1 KiB | 00m00s [ 49/147] Installing perl-B-0:1.89-515. 100% | 244.8 MiB/s | 501.3 KiB | 00m00s [ 50/147] Installing perl-FileHandle-0: 100% | 0.0 B/s | 9.8 KiB | 00m00s [ 51/147] Installing perl-Digest-MD5-0: 100% | 60.1 MiB/s | 61.6 KiB | 00m00s [ 52/147] Installing perl-MIME-Base32-0 100% | 0.0 B/s | 32.2 KiB | 00m00s [ 53/147] Installing perl-Data-Dumper-0 100% | 114.7 MiB/s | 117.5 KiB | 00m00s [ 54/147] Installing perl-libnet-0:3.15 100% | 287.8 MiB/s | 294.7 KiB | 00m00s [ 55/147] Installing perl-AutoLoader-0: 100% | 0.0 B/s | 20.9 KiB | 00m00s [ 56/147] Installing perl-IO-Socket-IP- 100% | 99.8 MiB/s | 102.2 KiB | 00m00s [ 57/147] Installing perl-URI-0:5.31-2. 100% | 131.7 MiB/s | 269.6 KiB | 00m00s [ 58/147] Installing perl-Time-Local-2: 100% | 0.0 B/s | 70.6 KiB | 00m00s [ 59/147] Installing perl-File-Path-0:2 100% | 0.0 B/s | 64.5 KiB | 00m00s [ 60/147] Installing perl-Pod-Escapes-1 100% | 0.0 B/s | 25.9 KiB | 00m00s [ 61/147] Installing perl-Text-Tabs+Wra 100% | 0.0 B/s | 23.9 KiB | 00m00s [ 62/147] Installing perl-if-0:0.61.000 100% | 0.0 B/s | 6.2 KiB | 00m00s [ 63/147] Installing perl-locale-0:1.12 100% | 0.0 B/s | 6.9 KiB | 00m00s [ 64/147] Installing perl-Net-SSLeay-0: 100% | 271.7 MiB/s | 1.4 MiB | 00m00s [ 65/147] Installing perl-IO-Socket-SSL 100% | 345.4 MiB/s | 707.4 KiB | 00m00s [ 66/147] Installing perl-Class-Struct- 100% | 0.0 B/s | 25.9 KiB | 00m00s [ 67/147] Installing perl-Term-ANSIColo 100% | 0.0 B/s | 99.2 KiB | 00m00s [ 68/147] Installing perl-Term-Cap-0:1. 100% | 0.0 B/s | 30.6 KiB | 00m00s [ 69/147] Installing perl-File-Temp-1:0 100% | 160.2 MiB/s | 164.1 KiB | 00m00s [ 70/147] Installing perl-IPC-Open3-0:1 100% | 0.0 B/s | 23.3 KiB | 00m00s [ 71/147] Installing perl-POSIX-0:2.20- 100% | 226.7 MiB/s | 232.2 KiB | 00m00s [ 72/147] Installing perl-Pod-Simple-1: 100% | 278.5 MiB/s | 570.4 KiB | 00m00s [ 73/147] Installing perl-HTTP-Tiny-0:0 100% | 152.8 MiB/s | 156.4 KiB | 00m00s [ 74/147] Installing perl-Socket-4:2.03 100% | 119.1 MiB/s | 122.0 KiB | 00m00s [ 75/147] Installing perl-SelectSaver-0 100% | 0.0 B/s | 2.6 KiB | 00m00s [ 76/147] Installing perl-Symbol-0:1.09 100% | 0.0 B/s | 7.2 KiB | 00m00s [ 77/147] Installing perl-File-stat-0:1 100% | 0.0 B/s | 13.1 KiB | 00m00s [ 78/147] Installing perl-podlators-1:6 100% | 26.2 MiB/s | 321.4 KiB | 00m00s [ 79/147] Installing perl-Pod-Perldoc-0 100% | 15.0 MiB/s | 169.2 KiB | 00m00s [ 80/147] Installing perl-mro-0:1.29-51 100% | 0.0 B/s | 42.6 KiB | 00m00s [ 81/147] Installing perl-overloading-0 100% | 0.0 B/s | 5.5 KiB | 00m00s [ 82/147] Installing perl-Fcntl-0:1.18- 100% | 0.0 B/s | 50.0 KiB | 00m00s [ 83/147] Installing perl-Text-ParseWor 100% | 0.0 B/s | 14.6 KiB | 00m00s [ 84/147] Installing perl-base-0:2.27-5 100% | 0.0 B/s | 12.9 KiB | 00m00s [ 85/147] Installing perl-IO-0:1.55-515 100% | 147.6 MiB/s | 151.1 KiB | 00m00s [ 86/147] Installing perl-Pod-Usage-4:2 100% | 7.7 MiB/s | 86.3 KiB | 00m00s [ 87/147] Installing perl-Errno-0:1.38- 100% | 0.0 B/s | 8.7 KiB | 00m00s [ 88/147] Installing perl-Scalar-List-U 100% | 145.1 MiB/s | 148.5 KiB | 00m00s [ 89/147] Installing perl-constant-0:1. 100% | 0.0 B/s | 27.4 KiB | 00m00s [ 90/147] Installing perl-Getopt-Std-0: 100% | 0.0 B/s | 11.7 KiB | 00m00s [ 91/147] Installing perl-MIME-Base64-0 100% | 43.2 MiB/s | 44.3 KiB | 00m00s [ 92/147] Installing perl-parent-1:0.24 100% | 0.0 B/s | 11.0 KiB | 00m00s [ 93/147] Installing perl-vars-0:1.05-5 100% | 0.0 B/s | 4.3 KiB | 00m00s [ 94/147] Installing perl-overload-0:1. 100% | 0.0 B/s | 71.9 KiB | 00m00s [ 95/147] Installing perl-Storable-1:3. 100% | 228.4 MiB/s | 233.9 KiB | 00m00s [ 96/147] Installing perl-Getopt-Long-1 100% | 143.8 MiB/s | 147.2 KiB | 00m00s [ 97/147] Installing perl-File-Basename 100% | 0.0 B/s | 14.6 KiB | 00m00s [ 98/147] Installing perl-Carp-0:1.54-5 100% | 0.0 B/s | 47.7 KiB | 00m00s [ 99/147] Installing perl-Exporter-0:5. 100% | 0.0 B/s | 55.6 KiB | 00m00s [100/147] Installing perl-PathTools-0:3 100% | 180.2 MiB/s | 184.5 KiB | 00m00s [101/147] Installing perl-DynaLoader-0: 100% | 0.0 B/s | 32.5 KiB | 00m00s [102/147] Installing perl-Encode-4:3.21 100% | 204.1 MiB/s | 4.7 MiB | 00m00s [103/147] Installing perl-libs-4:5.40.1 100% | 300.2 MiB/s | 9.9 MiB | 00m00s [104/147] Installing perl-interpreter-4 100% | 10.6 MiB/s | 119.8 KiB | 00m00s [105/147] Installing perl-macros-4:5.40 100% | 0.0 B/s | 5.8 KiB | 00m00s [106/147] Installing perl-Fedora-VSP-0: 100% | 19.8 MiB/s | 40.6 KiB | 00m00s [107/147] Installing tzdata-0:2024b-2.f 100% | 64.9 MiB/s | 1.9 MiB | 00m00s [108/147] Installing python-pip-wheel-0 100% | 622.1 MiB/s | 1.2 MiB | 00m00s [109/147] Installing mpdecimal-0:2.5.1- 100% | 197.2 MiB/s | 201.9 KiB | 00m00s [110/147] Installing libb2-0:0.98.1-13. 100% | 15.4 MiB/s | 47.2 KiB | 00m00s 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433.7 MiB/s | 111.0 MiB | 00m00s [137/147] Installing libquadmath-devel- 100% | 22.9 MiB/s | 23.4 KiB | 00m00s [138/147] Installing gcc-gfortran-0:15. 100% | 373.7 MiB/s | 40.4 MiB | 00m00s [139/147] Installing hdf5-devel-0:1.14. 100% | 173.2 MiB/s | 3.3 MiB | 00m00s [140/147] Installing armadillo-devel-0: 100% | 195.7 MiB/s | 7.4 MiB | 00m00s [141/147] Installing boost-devel-0:1.83 100% | 307.5 MiB/s | 145.8 MiB | 00m00s [142/147] Installing gcc-c++-0:15.0.1-0 100% | 375.3 MiB/s | 41.3 MiB | 00m00s [143/147] Installing gcc-plugin-annobin 100% | 4.8 MiB/s | 58.8 KiB | 00m00s [144/147] Installing annobin-plugin-gcc 100% | 64.7 MiB/s | 993.5 KiB | 00m00s [145/147] Installing gsl-devel-0:2.7.1- 100% | 87.0 MiB/s | 1.7 MiB | 00m00s [146/147] Installing htslib-devel-0:1.1 100% | 67.6 MiB/s | 415.5 KiB | 00m00s [147/147] Installing perl-generators-0: 100% | 144.0 KiB/s | 23.2 KiB | 00m00s Warning: skipped OpenPGP checks for 145 packages from repositories: copr_base, http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch Complete! Finish: build setup for mmseq-1.0.11-23.fc42.src.rpm Start: rpmbuild mmseq-1.0.11-23.fc42.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1738454400 Executing(%mkbuilddir): /bin/sh -e /var/tmp/rpm-tmp.Utx8tk + umask 022 + cd /builddir/build/BUILD/mmseq-1.0.11-build + test -d /builddir/build/BUILD/mmseq-1.0.11-build + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w /builddir/build/BUILD/mmseq-1.0.11-build + /usr/bin/rm -rf /builddir/build/BUILD/mmseq-1.0.11-build + /usr/bin/mkdir -p /builddir/build/BUILD/mmseq-1.0.11-build + /usr/bin/mkdir -p /builddir/build/BUILD/mmseq-1.0.11-build/SPECPARTS + RPM_EC=0 ++ jobs -p + exit 0 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.yhtu7C + umask 022 + cd /builddir/build/BUILD/mmseq-1.0.11-build + cd /builddir/build/BUILD/mmseq-1.0.11-build + rm -rf mmseq-1.0.11 + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/1.0.11.zip + STATUS=0 + '[' 0 -ne 0 ']' + cd mmseq-1.0.11 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . Patch #2 (mmseq-zlib.patch): + echo 'Patch #2 (mmseq-zlib.patch):' + /usr/bin/patch --no-backup-if-mismatch -f -p1 -b --suffix .mmseq-zlib.patch --fuzz=0 patching file src/Makefile + rm -f bin/offsetGTF-linux bin/postdiff-linux + sed -e s/-lblas/-lflexiblas/g -e s/-llapack/-lflexiblas/g -i src/Makefile + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.T7OZWZ + umask 022 + cd /builddir/build/BUILD/mmseq-1.0.11-build + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd mmseq-1.0.11 + cd src + make -j4 'CXXFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer' g++ -O3 -c sokal.cc g++ -fopenmp -O3 -c uh.cpp g++ -DVERSION=1.0.11 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fopenmp -O3 hitsio.cpp hitsio.hpp -c hitsio.cpp gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o fasta.o fasta.c g++ -DVERSION=1.0.11 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O3 offsetGTF.cpp -o ../bin/offsetGTF offsetGTF.cpp: In function ‘int main(int, char**)’: offsetGTF.cpp:115:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 115 | while(gff_ind < gff_positions[chrom].size()) { | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ offsetGTF.cpp:117:57: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} and ‘__gnu_cxx::__alloc_traits, int>::value_type’ {aka ‘int’} [-Wsign-compare] 117 | pos + tokens[3].size() - tokens[4].size() >= gff_positions[chrom][gff_ind]) { offsetGTF.cpp:114:11: warning: unused variable ‘curoff’ [-Wunused-variable] 114 | int curoff=offset; | ^~~~~~ offsetGTF.cpp:150:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 150 | while(gff_ind < gff_positions[prevchrom].size()) { | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ offsetGTF.cpp:163:53: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} and ‘__gnu_cxx::__alloc_traits, int>::value_type’ {aka ‘int’} [-Wsign-compare] 163 | pos + tokens[3].size() - tokens[4].size() >= gff_positions[chrom][gff_ind]) { offsetGTF.cpp:177:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 177 | while(gff_ind < gff_positions[chrom].size() && gff_positions[chrom][gff_ind] <= pos) { | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ offsetGTF.cpp:235:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 235 | for(int i=5; i < tokens.size(); i++) { | ~~^~~~~~~~~~~~~~~ offsetGTF.cpp:237:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 237 | if(i < tokens.size()-1) { | ~~^~~~~~~~~~~~~~~~~ offsetGTF.cpp:108:7: warning: unused variable ‘gff_pos’ [-Wunused-variable] 108 | int gff_pos= -1; | ^~~~~~~ g++ -DVERSION=1.0.11 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O3 t2g_hits.cpp -o ../bin/t2g_hits t2g_hits.cpp: In function ‘int main(int, char**)’: t2g_hits.cpp:90:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 90 | for(int i=2; i < tokens.size(); i++) { | ~~^~~~~~~~~~~~~~~ t2g_hits.cpp:112:13: warning: ignoring return value of ‘_FIter std::unique(_FIter, _FIter) [with _FIter = __gnu_cxx::__normal_iterator<__cxx11::basic_string*, vector<__cxx11::basic_string > >]’, declared with attribute ‘nodiscard’ [-Wunused-result] 112 | unique(comb.begin(), comb.end()); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/15/algorithm:63, from t2g_hits.cpp:27: /usr/include/c++/15/bits/stl_algo.h:875:5: note: declared here 875 | unique(_ForwardIterator __first, _ForwardIterator __last) | ^~~~~~ g++ -DVERSION=1.0.11 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fopenmp -O2 bms.cpp bms.hpp -c bms.cpp hitsio.cpp: In member function ‘void HitsfileWriter::writeHeaderSchema0()’: hitsio.cpp:163:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 163 | for(int i = 0; i < transcriptName.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~ hitsio.cpp: In member function ‘void HitsfileWriter::writeReadMapRecordSchema0()’: hitsio.cpp:184:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 184 | for(int i = 0; i < currentReadTranscripts.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hitsio.cpp: In member function ‘void HitsfileWriter::writeHeaderSchema1()’: hitsio.cpp:24:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 24 | if (VAL > numeric_limits::max()) { \ | ^ hitsio.cpp:191:9: note: in expansion of macro ‘WRITE_UINT’ 191 | WRITE_UINT(ofs, hitsfileSchema); | ^~~~~~~~~~ hitsio.cpp:193:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 193 | for(int i = 0; i < transcriptName.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~ hitsio.cpp:24:17: warning: comparison of integer expressions of different signedness: ‘std::map, int>::mapped_type’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare] 24 | if (VAL > numeric_limits::max()) { \ hitsio.cpp:196:17: note: in expansion of macro ‘WRITE_UINT’ 196 | WRITE_UINT(ofs, transcriptTrueLength[transcriptName[i] ]) | ^~~~~~~~~~ hitsio.cpp: In member function ‘void HitsfileWriter::writeReadMapRecordSchema1()’: hitsio.cpp:236:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 236 | for(int i = 0; i < currentReadTranscripts.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hitsio.cpp: In member function ‘void HitsfileReader::readHeaderSchema1(std::vector >*, std::map, double>*, std::map, int>*, std::map, std::vector > >*, std::vector > >*)’: hitsio.cpp:356:16: warning: unused variable ‘nextStrLen’ [-Wunused-variable] 356 | size_t nextStrLen; | ^~~~~~~~~~ hitsio.cpp: In member function ‘bool HitsfileReader::readReadMapRecordTranscriptID(std::string&)’: hitsio.cpp:447:1: warning: control reaches end of non-void function [-Wreturn-type] 447 | } | ^ g++ -DVERSION=1.0.11 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O3 fasta.o extract_transcripts.cpp -o ../bin/extract_transcripts 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++) { | ~~^~~~~~~~~~~~~ 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 -DARMA_64BIT_WORD -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fopenmp -O3 uh.o sokal.o mmcollapse.cpp -o ../bin/mmcollapse -lgsl -lgslcblas -lboost_regex -lhts -lboost_iostreams -lflexiblas -lflexiblas -Wl,--as-needed -lz -lgfortran mmcollapse.cpp: In function ‘void get_unidentifiable_transcripts(std::string, std::vector, std::allocator > >&, std::vector, std::allocator > >&, std::vector, std::allocator > >&, std::map, std::map, double> >&, std::map, std::map, double> >&, std::map, std::map, double> >&, std::map, int>&, std::vector, std::allocator > >&, std::map, bool>&)’: mmcollapse.cpp:158:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 158 | for(int i=0; i < tokens.size(); i++) { | ~~^~~~~~~~~~~~~~~ mmcollapse.cpp:213:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 213 | for(int i=0; i < tokens2.size(); i++) isIdent[tokens2[i]]=1; | ~~^~~~~~~~~~~~~~~~ mmcollapse.cpp:259:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 259 | for(int i=0; i < tokens.size(); i++) { | ~~^~~~~~~~~~~~~~~ mmcollapse.cpp: In function ‘void collapse(arma::cube&, std::vector, std::allocator > >&, std::map, int>&, std::vector >)’: mmcollapse.cpp:400:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 400 | for(int s=0; s < R.n_slices; s++) { | ~~^~~~~~~~~~~~ mmcollapse.cpp:401:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 401 | for(int t=0; t < candidates.size(); t++) { | ~~^~~~~~~~~~~~~~~~~~~ mmcollapse.cpp:402:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 402 | for(int j=1; j < indexes.size(); j++) { | ~~^~~~~~~~~~~~~~~~ mmcollapse.cpp:414:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 414 | for(int j=1; j < indexes.size(); j++) { | ~~^~~~~~~~~~~~~~~~ mmcollapse.cpp:417:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 417 | for(int i=0; i < R.n_cols; i++) { | ~~^~~~~~~~~~ mmcollapse.cpp:426:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 426 | for(int i=0; i < indexes.size(); i++) { | ~~^~~~~~~~~~~~~~~~ mmcollapse.cpp:431:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 431 | for(int i=1; i < tset.size(); i++) { | ~~^~~~~~~~~~~~~ mmcollapse.cpp:437:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 437 | for(int i=1; i < indexes.size(); i++) { | ~~^~~~~~~~~~~~~~~~ mmcollapse.cpp: In function ‘std::map join_traces(arma::mat&, std::vector, std::allocator > >&, std::vector, std::allocator > >)’: mmcollapse.cpp:445:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 445 | for(int t=0; t < allnames.size(); t++) tmap[allnames[t]]=t; | ~~^~~~~~~~~~~~~~~~~ mmcollapse.cpp:452:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 452 | for(int c=0; c < candidates.size(); c++) { | ~~^~~~~~~~~~~~~~~~~~~ mmcollapse.cpp:456:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 456 | for(int t=0; t < tokens.size(); t++) { | ~~^~~~~~~~~~~~~~~ mmcollapse.cpp:464:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 464 | for(int t=1; t < indexes.size(); t++) { | ~~^~~~~~~~~~~~~~~~ mmcollapse.cpp:469:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 469 | for(int t=1; t < indexes.size(); t++) { | ~~^~~~~~~~~~~~~~~~ mmcollapse.cpp:476:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 476 | for(int i=0; i < toshed.size(); i++) { | ~~^~~~~~~~~~~~~~~ mmcollapse.cpp: In function ‘void mean_corrs(const arma::cube&, const arma::umat&, arma::mat&, arma::mat&, std::vector >, std::vector >, double)’: mmcollapse.cpp:486:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 486 | for(int v= 0; v < R.n_rows; v++) { | ~~^~~~~~~~~~ mmcollapse.cpp:492:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘arma::uword’ {aka ‘long long unsigned int’} [-Wsign-compare] 492 | for(int i=0; i < u.size(); i++) { | ~~^~~~~~~~~~ mmcollapse.cpp: In function ‘void get_corrs(arma::cube&, arma::mat&, const std::vector, std::allocator > >&, std::map, int>&)’: mmcollapse.cpp:519:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 519 | for(int s=0; s < basenames.size(); s++) { | ~~^~~~~~~~~~~~~~~~~~ mmcollapse.cpp:543:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 543 | for(int t=0; t < tokens.size(); t++) { | ~~^~~~~~~~~~~~~~~ mmcollapse.cpp: In function ‘int main(int, char**)’: mmcollapse.cpp:632:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 632 | for(int i=1; i < basenames.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~ mmcollapse.cpp:691:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 691 | for(int s=0; s < basenames.size(); s++) { | ~~^~~~~~~~~~~~~~~~~~ mmcollapse.cpp:707:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 707 | for(int i=0; i < candidates.size(); i++) ts.push_back(i); | ~~^~~~~~~~~~~~~~~~~~~ mmcollapse.cpp:732:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 732 | for(int i=0 ;i < maxcorrs.size(); i++) { | ~~^~~~~~~~~~~~~~~~~ mmcollapse.cpp:738:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 738 | for(int i=0 ;i < mincorrs.size(); i++) { | ~~^~~~~~~~~~~~~~~~~ mmcollapse.cpp:802:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 802 | for(int i=0 ;i < maxcorrs.size(); i++) { | ~~^~~~~~~~~~~~~~~~~ mmcollapse.cpp:808:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 808 | for(int i=0 ;i < mincorrs.size(); i++) { | ~~^~~~~~~~~~~~~~~~~ mmcollapse.cpp:827:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 827 | for(int s=0; s < basenames.size(); s++) { | ~~^~~~~~~~~~~~~~~~~~ mmcollapse.cpp:852:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 852 | for(int t=0; t < tokens.size(); t++) { | ~~^~~~~~~~~~~~~~~ mmcollapse.cpp:882:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 882 | for(int t=0; t < tokens2.size(); t++) { | ~~^~~~~~~~~~~~~~~~ mmcollapse.cpp:934:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 934 | for(int t=0; t < M.n_cols; t++) { | ~~^~~~~~~~~~ mmcollapse.cpp:963:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 963 | for(int i=1; i < tokens2.size(); i++) { | ~~^~~~~~~~~~~~~~~~ mmcollapse.cpp:976:21: warning: comparison of integer expressions of different signedness: ‘boost::numeric::ublas::compressed_matrix::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 976 | if(MM.size1() < i+1 ) factor1=2; | ~~~~~~~~~~~^~~~~ mmcollapse.cpp:977:21: warning: comparison of integer expressions of different signedness: ‘boost::numeric::ublas::compressed_matrix::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 977 | if(MM.size2() < j+1 ) factor2=2; | ~~~~~~~~~~~^~~~~ mmcollapse.cpp:1010:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1010 | for(int t=0; t < ids.size(); t++) { | ~~^~~~~~~~~~~~ mmcollapse.cpp:1083:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1083 | for(int i=0; i < ids.size(); i++) { | ~~^~~~~~~~~~~~ mmcollapse.cpp:1092:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 1092 | for(int v = 0; v < M.n_cols; v++) { | ~~^~~~~~~~~~ mmcollapse.cpp:840:9: warning: unused variable ‘isident’ [-Wunused-variable] 840 | int isident=0; | ^~~~~~~ hitsio.cpp: In member function ‘void HitsfileWriter::writeHeaderSchema0()’: hitsio.cpp:163:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 163 | for(int i = 0; i < transcriptName.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~ hitsio.cpp: In member function ‘void HitsfileWriter::writeReadMapRecordSchema0()’: hitsio.cpp:184:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 184 | for(int i = 0; i < currentReadTranscripts.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hitsio.cpp: In member function ‘void HitsfileWriter::writeHeaderSchema1()’: hitsio.cpp:24:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 24 | if (VAL > numeric_limits::max()) { \ | ^ hitsio.cpp:191:9: note: in expansion of macro ‘WRITE_UINT’ 191 | WRITE_UINT(ofs, hitsfileSchema); | ^~~~~~~~~~ hitsio.cpp:193:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 193 | for(int i = 0; i < transcriptName.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~ hitsio.cpp:24:17: warning: comparison of integer expressions of different signedness: ‘std::map, int>::mapped_type’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare] 24 | if (VAL > numeric_limits::max()) { \ hitsio.cpp:196:17: note: in expansion of macro ‘WRITE_UINT’ 196 | WRITE_UINT(ofs, transcriptTrueLength[transcriptName[i] ]) | ^~~~~~~~~~ hitsio.cpp: In member function ‘void HitsfileWriter::writeReadMapRecordSchema1()’: hitsio.cpp:236:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 236 | for(int i = 0; i < currentReadTranscripts.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hitsio.cpp: In member function ‘void HitsfileReader::readHeaderSchema1(std::vector >*, std::map, double>*, std::map, int>*, std::map, std::vector > >*, std::vector > >*)’: hitsio.cpp:356:16: warning: unused variable ‘nextStrLen’ [-Wunused-variable] 356 | size_t nextStrLen; | ^~~~~~~~~~ hitsio.cpp: In member function ‘bool HitsfileReader::readReadMapRecordTranscriptID(std::string&)’: hitsio.cpp:447:1: warning: control reaches end of non-void function [-Wreturn-type] 447 | } | ^ g++ -DVERSION=1.0.11 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fopenmp -O3 sokal.o uh.o hitsio.o mmseq.cpp -o ../bin/mmseq -lgsl -lgslcblas -lboost_regex -lhts -lboost_iostreams -lflexiblas -lflexiblas -Wl,--as-needed -lz -lgfortran g++ -DVERSION=1.0.11 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fopenmp -O3 fasta.o hitsio.o bam2hits.cpp -o ../bin/bam2hits -lgsl -lgslcblas -lboost_regex -lhts -lboost_iostreams -lflexiblas -lflexiblas -Wl,--as-needed -lz -lgfortran mmseq.cpp: In function ‘std::vector meanvar(std::vector, double, double)’: mmseq.cpp:130:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 130 | for(int i=0;i < v.size(); i++) { | ~~^~~~~~~~~~ mmseq.cpp: In function ‘int main(int, char**)’: mmseq.cpp:244:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 244 | for(int i=0; i < tokens.size(); i++) { | ~~^~~~~~~~~~~~~~~ mmseq.cpp:423:20: warning: comparison of integer expressions of different signedness: ‘boost::numeric::ublas::compressed_matrix::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 423 | if(M.size1() < m ) factor1=2; | ~~~~~~~~~~^~~ mmseq.cpp:424:20: warning: comparison of integer expressions of different signedness: ‘boost::numeric::ublas::compressed_matrix::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 424 | if(M.size2() < n ) factor2=2; | ~~~~~~~~~~^~~ mmseq.cpp:594:23: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 594 | for(unsigned t=0; t < n; t++) { | ~~^~~ mmseq.cpp:736:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 736 | for(unsigned t=0; t < n; t++) | ~~^~~ mmseq.cpp:765:27: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 765 | for(unsigned t=0; t < n; t++) | ~~^~~ mmseq.cpp:774:11: warning: unused variable ‘threadid’ [-Wunused-variable] 774 | int threadid=OMP_GET_THREAD_NUM; | ^~~~~~~~ mmseq.cpp:829:23: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 829 | for(unsigned t=0; t < n; t++) | ~~^~~ mmseq.cpp:912:27: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 912 | for(unsigned t=0; t < n; t++) { | ~~^~~ mmseq.cpp:940:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 940 | for(int i=0; i < identical_transcripts.size() * trace_length; i++) mu_trace_identical[i]=0; | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mmseq.cpp:961:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::map, std::vector > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 961 | for(int i=0; i < gene2transcripts.size() * trace_length; i++) mu_trace_gene[i]=0; | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1098:23: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 1098 | for(unsigned t=0; t < n; t++) gofs << indexSid[t] << " "; | ~~^~~ mmseq.cpp:1112:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1112 | for(int i=0; i < percentiles.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1136:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1136 | for(int j=0; j < percentiles.size(); j++) { | ~~^~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1144:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1144 | for(int j=0; j < percentiles.size(); j++) { | ~~^~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1149:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1149 | for(int i=0;i < identical_transcripts.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1156:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1156 | for(int j=0; j < percentiles.size(); j++) { | ~~^~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1161:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::map, std::vector > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1161 | for(int i=0;i < gene2transcripts.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1168:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1168 | for(int j=0; j < percentiles.size(); j++) { | ~~^~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1179:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1179 | for(int j=0; j < percentiles.size(); j++) { | ~~^~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1189:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1189 | for(int j=0; j < percentiles.size(); j++) { | ~~^~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1208:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1208 | for(int t=0; t < identical_transcripts.size() ; t++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1212:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::map, std::vector > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1212 | for(int t=0; t < gene2transcripts.size(); t++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1226:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1226 | for(int i=0; i < identical_transcripts.size() ; i++) meanmu_identical[i] /= trace_length; | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1227:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::map, std::vector > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1227 | for(int i=0; i < gene2transcripts.size(); i++) meanmu_gene[i]/= trace_length; | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1330:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1330 | for(int t=0; t < identical_transcripts.size(); t++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1349:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::map, std::vector > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1349 | for(int g=0; g < gene2transcripts.size(); g++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1473:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1473 | for(int i=0; i < percentiles.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1475:9: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1475 | if(i==percentiles.size()-1) { | ~^~~~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1482:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1482 | for(int i=0; i < percentiles.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1484:9: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1484 | if(i==percentiles.size()-1) { | ~^~~~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1506:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1506 | for(int i=0; i < percentiles.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1508:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1508 | if(i==percentiles.size()-1) { | ~^~~~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1514:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1514 | for(int i=0; i < percentiles.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1516:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1516 | if(i==percentiles.size()-1) { | ~^~~~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1536:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1536 | for(int i=0; i < percentiles.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1538:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1538 | if(i==percentiles.size()-1) { | ~^~~~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1544:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1544 | for(int i=0; i < percentiles.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1546:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1546 | if(i==percentiles.size()-1) { | ~^~~~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1560:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1560 | for(int i=0; i < percentiles.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1562:9: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1562 | if(i==percentiles.size()-1) { | ~^~~~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1582:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1582 | for(int i=0; i < percentiles.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1584:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1584 | if(i==percentiles.size()-1) { | ~^~~~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1599:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1599 | for(int i=0; i < percentiles.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1601:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1601 | if(i==percentiles.size()-1) { | ~^~~~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1619:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1619 | for(int i=0; i < percentiles.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1621:9: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1621 | if(i==percentiles.size()-1) { | ~^~~~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1644:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1644 | for(int i=0; i < percentiles.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1646:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1646 | if(i==percentiles.size()-1) { | ~^~~~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1656:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1656 | for(int i=0; i < percentiles.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~ mmseq.cpp:1658:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1658 | if(i==percentiles.size()-1) { | ~^~~~~~~~~~~~~~~~~~~~~~ mmseq.cpp:308:8: warning: unused variable ‘buf16384’ [-Wunused-variable] 308 | char buf16384[16384]; | ^~~~~~~~ mmseq.cpp:391:8: warning: variable ‘doublehit’ set but not used [-Wunused-but-set-variable] 391 | bool doublehit; | ^~~~~~~~~ bam2hits.cpp: In function ‘void outputMergeHeaders(std::vector&, char, const char*, bool, HitsfileWriter&)’: bam2hits.cpp:109:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 109 | for(int i=0; i < sortedfastas.size()-1; i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~ bam2hits.cpp:119:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 119 | for(int j=0; j < curSet.size()-1; j++) { | ~~^~~~~~~~~~~~~~~~~ bam2hits.cpp:137:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 137 | for(int j=0; j < curSet.size()-1; j++) { | ~~^~~~~~~~~~~~~~~~~ bam2hits.cpp: In function ‘std::vector repetitiveTranscriptFilter(std::vector&, int)’: bam2hits.cpp:218:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 218 | for(int j=0; j < alns.size(); j++) { | ~~^~~~~~~~~~~~~ bam2hits.cpp:219:10: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 219 | if(i < torem.size() && j==torem[i]) { | ~~^~~~~~~~~~~~~~ bam2hits.cpp: In function ‘int main(int, char**)’: bam2hits.cpp:518:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 518 | if(_B != tg[0].size()-2) { | ~~~^~~~~~~~~~~~~~~~~ bam2hits.cpp:520:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 520 | if(_A == tg[0].size()-2) { | ~~~^~~~~~~~~~~~~~~~~ bam2hits.cpp:522:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 522 | if(_A != tg[1].size()-2) { | ~~~^~~~~~~~~~~~~~~~~ bam2hits.cpp:558:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 558 | for(int i=1; i < tokens2.size(); i++) { | ~~^~~~~~~~~~~~~~~~ bam2hits.cpp:609:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 609 | for(int i=0; i < fastas.size(); i++) { | ~~^~~~~~~~~~~~~~~ bam2hits.cpp:645:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 645 | for(int i=0;i < fastas.size(); i++) transcriptCounts[i] /= (double)fastas[i].seq().size(); | ~~^~~~~~~~~~~~~~~ bam2hits.cpp:659:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 659 | for(int i=0; i < fastas.size(); i++) { | ~~^~~~~~~~~~~~~~~ bam2hits.cpp:662:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 662 | for(int j =0; j < fastas[i].seq().size(); j++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~ bam2hits.cpp:663:44: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 663 | int tag = (j <= MSEQ_BEFORE || j >= fastas[i].seq().size()-MSEQ_AFTER) ? -2 : 0; | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bam2hits.cpp:791:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 791 | for(int j=MSEQ_BEFORE + 1; j <= fastas[i].seq().length()-MSEQ_AFTER; j++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bam2hits.cpp:920:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 920 | for(int j=1; j < frequencies.size()-WINDOWFORISIZEMODE + 1; j++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bam2hits.cpp:948:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 948 | for(int i=0; i < testIsizes.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~ bam2hits.cpp:959:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 959 | for(int i=0; i < heights.size(); i++) { | ~~^~~~~~~~~~~~~~~~ bam2hits.cpp:997:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 997 | for(int fl=1; fl <= (it->seq()).size(); fl++) { | ~~~^~~~~~~~~~~~~~~~~~~~~ bam2hits.cpp:1091:56: warning: comparing the result of pointer addition ‘(bam_aux_get(((const bam1_t*)line), ((const char*)"NM")) + ((sizetype)ait.__gnu_cxx::__normal_iterator >::operator->()->Alignment::NM()))’ and NULL [-Waddress] 1091 | ait->NM(ait->NM() + bam_aux_get(line,"NM") == NULL ? 0 : bam_aux2i(bam_aux_get(line,"NM"))); | ^ bms.cpp: In member function ‘arma::Col BMS::m2v(arma::Mat)’: bms.cpp:36:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 36 | for(int i=0; i < P.n_cols; i++) { | ~~^~~~~~~~~~ bms.cpp:37:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 37 | for(int j=0; j < P.n_rows; j++) { | ~~^~~~~~~~~~ bms.cpp: In member function ‘std::vector BMS::meanvar(arma::Col)’: bms.cpp:76:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 76 | for(int i=0;i < v.n_elem; i++) { | ~~^~~~~~~~~~ bms.cpp: In member function ‘void BMS::print(bool)’: bms.cpp:93:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 93 | for(int feature=0; feature < y->n_rows; feature++) { | ~~~~~~~~^~~~~~~~~~~ bms.cpp:97:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 97 | for(int i=0; i < M.n_cols; i++) { | ~~^~~~~~~~~~ bms.cpp:102:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 102 | for(int l=0; l < P[model].n_cols; l++) { | ~~^~~~~~~~~~~~~~~~~ bms.cpp: In member function ‘void BMS::printtune(int)’: bms.cpp:132:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 132 | for(int feature=0; feature < y->n_rows; feature++) { | ~~~~~~~~^~~~~~~~~~~ bms.cpp: In member function ‘void BMS::set_pseudoprior_alpha()’: bms.cpp:185:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 185 | for(int j=0; j < y->n_rows; j++) { | ~~^~~~~~~~~~~ bms.cpp: In member function ‘void BMS::set_pseudoprior_beta()’: bms.cpp:253:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 253 | for(int j=0; j < y->n_rows; j++) { | ~~^~~~~~~~~~~ bms.cpp:255:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 255 | for(int b=0; b < M.n_cols; b++) { | ~~^~~~~~~~~~ bms.cpp: In member function ‘void BMS::set_pseudoprior_eta()’: bms.cpp:332:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 332 | for(int j=0; j < y->n_rows; j++) { | ~~^~~~~~~~~~~ bms.cpp:334:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 334 | for(int c=0; c < P[model].n_cols; c++) { | ~~^~~~~~~~~~~~~~~~~ bms.cpp: In member function ‘void BMS::set_pseudoprior_sigmasq()’: bms.cpp:415:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 415 | for(int j=0; j < y->n_rows; j++) { | ~~^~~~~~~~~~~ bms.cpp: In member function ‘void BMS::set_pseudoprior_lambda()’: bms.cpp:504:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 504 | for(int j=0; j < y->n_rows; j++) { | ~~^~~~~~~~~~~ bms.cpp:506:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 506 | for(int l=0; l < P[model].n_cols; l++) { | ~~^~~~~~~~~~~~~~~~~ bms.cpp: In member function ‘void BMS::set_pseudoprior_rho()’: bms.cpp:559:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 559 | for(int j=0; j < y->n_rows; j++) { | ~~^~~~~~~~~~~ bms.cpp: In member function ‘void BMS::copy_pseudo()’: bms.cpp:582:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 582 | for(int j=0; j < y->n_rows; j++) { | ~~^~~~~~~~~~~ bms.cpp:585:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 585 | for(int c=0; c < P[0].n_cols; c++) { | ~~^~~~~~~~~~~~~ bms.cpp: In member function ‘void BMS::update_alpha(int, int, bool)’: bms.cpp:603:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 603 | for(int j=0; j < y->n_cols; j++) { | ~~^~~~~~~~~~~ bms.cpp:610:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 610 | for(int i=0; i < y->n_cols; i++) { | ~~^~~~~~~~~~~ bms.cpp: In member function ‘void BMS::update_beta(int, int, bool)’: bms.cpp:631:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 631 | for(int j=0; j < y->n_cols; j++) { | ~~^~~~~~~~~~~ bms.cpp:638:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 638 | for(int i=0; i < M.n_cols; i++) { | ~~^~~~~~~~~~ bms.cpp:646:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 646 | for(int i=0; i < M.n_cols; i++) { | ~~^~~~~~~~~~ bms.cpp:651:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 651 | for(int i=0; i < M.n_cols; i++) { | ~~^~~~~~~~~~ bms.cpp: In member function ‘void BMS::update_eta(int, int, bool)’: bms.cpp:663:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 663 | for(int l=0; l < P[model].n_cols; l++) { | ~~^~~~~~~~~~~~~~~~~ bms.cpp:666:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 666 | for(int i=0; i < y->n_cols; i++) { | ~~^~~~~~~~~~~ bms.cpp:673:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 673 | for(int i=0; i < y->n_cols; i++) { | ~~^~~~~~~~~~~ bms.cpp:681:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 681 | for(int l=0; l < P[model].n_cols; l++) { | ~~^~~~~~~~~~~~~~~~~ bms.cpp:686:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 686 | for(int l=0; l < P[model].n_cols; l++) { | ~~^~~~~~~~~~~~~~~~~ bms.cpp: In member function ‘void BMS::update_lambda(int, int, bool)’: bms.cpp:699:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 699 | for(int l=0; l < P[model].n_cols; l++) { | ~~^~~~~~~~~~~~~~~~~ bms.cpp:704:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 704 | for(int l=0; l < P[model].n_cols; l++) { | ~~^~~~~~~~~~~~~~~~~ bms.cpp:711:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 711 | for(int l=0; l < P[model].n_cols; l++) { | ~~^~~~~~~~~~~~~~~~~ bms.cpp: In member function ‘void BMS::update_sigmasq(int, int, bool, bool)’: bms.cpp:729:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 729 | for(int i=0; i < y->n_cols; i++) { | ~~^~~~~~~~~~~ bms.cpp:740:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 740 | for(int i=0; i < y->n_cols; i++) { | ~~^~~~~~~~~~~ bms.cpp:751:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 751 | for(int i=0; i < y->n_cols; i++) { | ~~^~~~~~~~~~~ bms.cpp:763:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 763 | for(int i=0; i < y->n_cols; i++) { | ~~^~~~~~~~~~~ bms.cpp: In member function ‘void BMS::update_sigmasq_RW(int, int, bool, bool)’: bms.cpp:877:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 877 | for(int i=0; i < y->n_cols; i++) { | ~~^~~~~~~~~~~ bms.cpp: In member function ‘double BMS::log_target_posterior(int, int)’: bms.cpp:931:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 931 | for(int i=0; i < y->n_cols; i++) { | ~~^~~~~~~~~~~ bms.cpp:940:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 940 | for(int j=0; j < M.n_cols; j++) { | ~~^~~~~~~~~~ bms.cpp:947:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 947 | for(int l=0; l < P[model].n_cols; l++) { | ~~^~~~~~~~~~~~~~~~~ bms.cpp: In member function ‘double BMS::log_target_pseudo(int, int)’: bms.cpp:968:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 968 | for(int l=0; l < M.n_cols; l++) { | ~~^~~~~~~~~~ bms.cpp:974:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 974 | for(int l=0; l < P[model].n_cols; l++) { | ~~^~~~~~~~~~~~~~~~~ bms.cpp: In member function ‘void BMS::print_pseudo()’: bms.cpp:1086:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 1086 | for(int l=0; l < M.n_cols; l++) { | ~~^~~~~~~~~~ bms.cpp:1089:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 1089 | for(int l=0; l < P[model].n_cols; l++) { | ~~^~~~~~~~~~~~~~~~~ bms.cpp:1100:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 1100 | for(int i=0; i < y->n_rows; i++) { | ~~^~~~~~~~~~~ bms.cpp:1103:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 1103 | for(int l=0; l < M.n_cols; l++) { | ~~^~~~~~~~~~ bms.cpp:1106:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 1106 | for(int l=0; l < P[model].n_cols; l++) { | ~~^~~~~~~~~~~~~~~~~ bms.cpp: In constructor ‘BMS::BMS(const arma::Mat*, const arma::Mat&, arma::Mat, arma::Mat, arma::Mat, arma::Mat, double, double, double, std::string, gsl_rng**, int, bool)’: bms.cpp:1188:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 1188 | for(int i=0; i < y->n_cols; i++) { | ~~^~~~~~~~~~~ bms.cpp:1192:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1192 | if(C(i,model)+1 > _n.size()) { | ~~~~~~~~~~~~~^~~~~~~~~~~ bms.cpp: In member function ‘void BMS::initialise_streams(std::string)’: bms.cpp:1348:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 1348 | for(int i=0; i < M.n_cols; i++) { | ~~^~~~~~~~~~ bms.cpp:1354:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 1354 | for(int i=0; i < M.n_cols; i++) { | ~~^~~~~~~~~~ bms.cpp:1360:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 1360 | for(int i=0; i < P[0].n_cols; i++) { | ~~^~~~~~~~~~~~~ bms.cpp:1366:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 1366 | for(int i=0; i < P[1].n_cols; i++) { | ~~^~~~~~~~~~~~~ bms.cpp:1372:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 1372 | for(int i=0; i < P[0].n_cols; i++) { | ~~^~~~~~~~~~~~~ bms.cpp:1378:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 1378 | for(int i=0; i < P[1].n_cols; i++) { | ~~^~~~~~~~~~~~~ g++ -DVERSION=1.0.11 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fopenmp -O3 hitsio.o hitstools.cpp -o ../bin/hitstools -lgsl -lgslcblas -lboost_regex -lhts -lboost_iostreams -lflexiblas -lflexiblas -Wl,--as-needed -lz -lgfortran hitstools.cpp: In function ‘void convert(char*, std::string)’: hitstools.cpp:51:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 51 | for(int i = 0; i < transcriptName.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~ hitstools.cpp: In function ‘int main(int, char**)’: hitstools.cpp:96:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 96 | for(int i = 0; i < transcriptName.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~ hitstools.cpp:136:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 136 | for(int i = 0; i < transcriptName.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~ g++ -DVERSION=1.0.11 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fopenmp -O2 bms.o mmdiff.cpp -o ../bin/mmdiff -lgsl -lgslcblas -lboost_regex -lhts -lboost_iostreams -lflexiblas -lflexiblas -Wl,--as-needed -lz -lgfortran mmdiff.cpp: In function ‘void parse_mmseq(std::vector, std::allocator > >, std::vector, std::allocator > >&, arma::Mat&, arma::Mat&, arma::Mat&, int, int, double, bool)’: mmdiff.cpp:100:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 100 | for(int i=0; i < filenames.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~ mmdiff.cpp:111:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 111 | for(int j=0; j < tokens.size(); j++) { | ~~^~~~~~~~~~~~~~~ mmdiff.cpp:138:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 138 | if(k + 1 > features.size()) { | ~~~~~~^~~~~~~~~~~~~~~~~ mmdiff.cpp:147:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 147 | if(k+1 > y.n_rows) { | ~~~~^~~~~~~~~~ mmdiff.cpp:152:20: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 152 | if(!useprops && tokens[lmg_ind]=="NA" || useprops && tokens[mp_ind]=="NA") { | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ mmdiff.cpp:173:62: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 173 | if(range_start >=0 && range_end > range_start && range_end < y.n_rows) { | ~~~~~~~~~~^~~~~~~~~~ mmdiff.cpp:94:46: warning: variable ‘mcse_ind’ set but not used [-Wunused-but-set-variable] 94 | int feature_ind=-1, lmg_ind=-1, sd_ind=-1, mcse_ind=-1, iact_ind=-1, mp_ind=-1, sp_ind=-1, uh_ind=-1; | ^~~~~~~~ mmdiff.cpp:94:59: warning: variable ‘iact_ind’ set but not used [-Wunused-but-set-variable] 94 | int feature_ind=-1, lmg_ind=-1, sd_ind=-1, mcse_ind=-1, iact_ind=-1, mp_ind=-1, sp_ind=-1, uh_ind=-1; | ^~~~~~~~ mmdiff.cpp: In function ‘void apply_normalisation(std::vector, std::allocator > >, arma::Mat&, arma::Mat&, double)’: mmdiff.cpp:212:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 212 | for(int i=0; i < uh.n_rows; i++) { | ~~^~~~~~~~~~~ mmdiff.cpp:214:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 214 | for(int j=0; j < uh.n_cols; j++) { | ~~^~~~~~~~~~~ mmdiff.cpp:230:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 230 | for(int i=0; i < use.size(); i++) { | ~~^~~~~~~~~~~~ mmdiff.cpp:232:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 232 | for(int j=0; j < y.n_cols; j++) { | ~~^~~~~~~~~~ mmdiff.cpp:239:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 239 | for(int sample=0; sample < y.n_cols; sample++) { | ~~~~~~~^~~~~~~~~~ mmdiff.cpp:241:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 241 | for(int i=0; i < use.size(); i++) { | ~~^~~~~~~~~~~~ mmdiff.cpp:246:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 246 | for(int i=0; i < y.n_rows; i++) { | ~~^~~~~~~~~~ mmdiff.cpp: In function ‘void apply_permutation(arma::Mat&, arma::Mat&)’: mmdiff.cpp:257:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 257 | for(int j=0; j< y.n_cols; j++) randinds.push_back(j); | ~^~~~~~~~~~ mmdiff.cpp:258:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 258 | for(int i=0; i < y.n_rows; i++) { | ~~^~~~~~~~~~ mmdiff.cpp:259:19: warning: ‘void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator > >]’ is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations] 259 | random_shuffle(randinds.begin(), randinds.end()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/15/algorithm:63, from mmdiff.cpp:31: /usr/include/c++/15/bits/stl_algo.h:4509:5: note: declared here 4509 | 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++) { | ~~~~~~~~^~~~~~~~~~~~~~~~~ bms.cpp: In member function ‘initialise_streams’: bms.cpp:1408:30: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 1408 | ofs = new ofstream[nstreams]; | ^ /usr/include/c++/15/new:140:26: note: in a call to allocation function ‘operator new []’ declared here 140 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) | ^ /usr/bin/ld: /tmp/ccrJq0RK.ltrans1.ltrans.o: in function `main': /builddir/build/BUILD/mmseq-1.0.11-build/mmseq-1.0.11/src/bam2hits.cpp:653:(.text.startup+0x528d): 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.qAm4uo + umask 022 + cd /builddir/build/BUILD/mmseq-1.0.11-build + '[' /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT '!=' / ']' + rm -rf /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT ++ dirname /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT + mkdir -p /builddir/build/BUILD/mmseq-1.0.11-build + mkdir /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd mmseq-1.0.11 + rm -rf /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT + mkdir -p /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/bin + install -p -m 0755 bin/bam2hits /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/bin + install -p -m 0755 bin/extract_transcripts /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/bin + install -p -m 0755 bin/hitstools /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/bin + install -p -m 0755 bin/mmcollapse /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/bin + install -p -m 0755 bin/mmdiff /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/bin + install -p -m 0755 bin/mmseq /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/bin + install -p -m 0755 bin/offsetGTF /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/bin + install -p -m 0755 bin/t2g_hits /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/bin + install -p -m 0755 bin/fastagrep.sh bin/mouse_strain_transcriptome.sh bin/usage.sh /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/bin + install -p -m 0755 bin/filterGTF.rb bin/haploref.rb bin/testregexp.rb /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/bin + install -p -m 0755 bin/ensembl_gtf_to_gff.pl /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/bin + /usr/bin/find-debuginfo -j4 --strict-build-id -m -i --build-id-seed 1.0.11-23.fc42 --unique-debug-suffix -1.0.11-23.fc42.x86_64 --unique-debug-src-base mmseq-1.0.11-23.fc42.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/mmseq-1.0.11-build/mmseq-1.0.11 find-debuginfo: starting Extracting debug info from 8 files DWARF-compressing 8 files sepdebugcrcfix: Updated 8 CRC32s, 0 CRC32s did match. Creating .debug symlinks for symlinks to ELF files Copying sources found by 'debugedit -l' to /usr/src/debug/mmseq-1.0.11-23.fc42.x86_64 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/fastagrep.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/usage.sh from /bin/bash to #!/usr/bin/bash mangling shebang in /usr/bin/filterGTF.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/testregexp.rb from /usr/bin/env ruby to #!/usr/bin/ruby mangling shebang in /usr/bin/ensembl_gtf_to_gff.pl from /usr/bin/env perl to #!/usr/bin/perl + /usr/lib/rpm/brp-remove-la-files + env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j4 + /usr/lib/rpm/redhat/brp-python-hardlink + /usr/bin/add-determinism --brp -j4 /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT Scanned 12 directories and 40 files, processed 0 inodes, 0 modified (0 replaced + 0 rewritten), 0 unsupported format, 0 errors Reading /builddir/build/BUILD/mmseq-1.0.11-build/SPECPARTS/rpm-debuginfo.specpart Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.Vd3lPL + umask 022 + cd /builddir/build/BUILD/mmseq-1.0.11-build + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd mmseq-1.0.11 ++ bin/mmseq --version ++ true + test mmseq-1.0.11 = mmseq-1.0.11 + RPM_EC=0 ++ jobs -p + exit 0 Processing files: mmseq-1.0.11-23.fc42.x86_64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.ttdCD2 + umask 022 + cd /builddir/build/BUILD/mmseq-1.0.11-build + cd mmseq-1.0.11 + DOCDIR=/builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/share/doc/mmseq + export LC_ALL=C.UTF-8 + LC_ALL=C.UTF-8 + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/share/doc/mmseq + cp -pr /builddir/build/BUILD/mmseq-1.0.11-build/mmseq-1.0.11/README.md /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/share/doc/mmseq + cp -pr /builddir/build/BUILD/mmseq-1.0.11-build/mmseq-1.0.11/COPYING /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/share/doc/mmseq + cp -pr /builddir/build/BUILD/mmseq-1.0.11-build/mmseq-1.0.11/doc /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/share/doc/mmseq + RPM_EC=0 ++ jobs -p + exit 0 Provides: mmseq = 1.0.11-23.fc42 mmseq(x86-64) = 1.0.11-23.fc42 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: /usr/bin/bash /usr/bin/perl /usr/bin/ruby /usr/bin/sh libboost_iostreams.so.1.83.0()(64bit) libboost_regex.so.1.83.0()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.32)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.38)(64bit) libc.so.6(GLIBC_2.4)(64bit) libflexiblas.so.3()(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgcc_s.so.1(GCC_3.3.1)(64bit) libgomp.so.1()(64bit) libgomp.so.1(GOMP_1.0)(64bit) libgomp.so.1(GOMP_4.0)(64bit) libgomp.so.1(OMP_1.0)(64bit) libgsl.so.27()(64bit) libgslcblas.so.0()(64bit) libhts.so.3()(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.29)(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.15)(64bit) libstdc++.so.6(CXXABI_1.3.8)(64bit) libstdc++.so.6(CXXABI_1.3.9)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.11)(64bit) libstdc++.so.6(GLIBCXX_3.4.15)(64bit) libstdc++.so.6(GLIBCXX_3.4.20)(64bit) libstdc++.so.6(GLIBCXX_3.4.21)(64bit) libstdc++.so.6(GLIBCXX_3.4.26)(64bit) libstdc++.so.6(GLIBCXX_3.4.29)(64bit) libstdc++.so.6(GLIBCXX_3.4.30)(64bit) libstdc++.so.6(GLIBCXX_3.4.32)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) perl(strict) rtld(GNU_HASH) Processing files: mmseq-debugsource-1.0.11-23.fc42.x86_64 Provides: mmseq-debugsource = 1.0.11-23.fc42 mmseq-debugsource(x86-64) = 1.0.11-23.fc42 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: mmseq-debuginfo-1.0.11-23.fc42.x86_64 Provides: debuginfo(build-id) = 2a3677e2f3988783756ebd1cc7f6b3d17721f15d debuginfo(build-id) = 60f811b4051f4f76dc5f0e4636f18a7723c9798d debuginfo(build-id) = 7621b1d3385648cd1503a0c30ea75bad45638e99 debuginfo(build-id) = 92256ecc2e20b3c471bbcb8965ad7f5dcfaeba6c debuginfo(build-id) = 9af485dc649c9fbfa3eff0b25b9db99d511ce2d4 debuginfo(build-id) = b00a1b4a0263b35a38886694ff4a028cf742cea8 debuginfo(build-id) = c3debccb3b380989ed9ecc4a3a4f7d50ddd9f0f4 debuginfo(build-id) = e1d55844b80845735c53afd212fb0b1923237e5c mmseq-debuginfo = 1.0.11-23.fc42 mmseq-debuginfo(x86-64) = 1.0.11-23.fc42 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: mmseq-debugsource(x86-64) = 1.0.11-23.fc42 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT Wrote: /builddir/build/RPMS/mmseq-debugsource-1.0.11-23.fc42.x86_64.rpm Wrote: /builddir/build/RPMS/mmseq-1.0.11-23.fc42.x86_64.rpm Wrote: /builddir/build/RPMS/mmseq-debuginfo-1.0.11-23.fc42.x86_64.rpm Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.ACkVZ7 + umask 022 + cd /builddir/build/BUILD/mmseq-1.0.11-build + test -d /builddir/build/BUILD/mmseq-1.0.11-build + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w /builddir/build/BUILD/mmseq-1.0.11-build + rm -rf /builddir/build/BUILD/mmseq-1.0.11-build + RPM_EC=0 ++ jobs -p + exit 0 Finish: rpmbuild mmseq-1.0.11-23.fc42.src.rpm Finish: build phase for mmseq-1.0.11-23.fc42.src.rpm INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-41-x86_64-1738534972.753496/root/var/log/dnf5.log INFO: chroot_scan: creating tarball /var/lib/copr-rpmbuild/results/chroot_scan.tar.gz /bin/tar: Removing leading `/' from member names INFO: Done(/var/lib/copr-rpmbuild/results/mmseq-1.0.11-23.fc42.src.rpm) Config(child) 1 minutes 1 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-debugsource", "epoch": null, "version": "1.0.11", "release": "23.fc42", "arch": "x86_64" }, { "name": "mmseq", "epoch": null, "version": "1.0.11", "release": "23.fc42", "arch": "x86_64" }, { "name": "mmseq", "epoch": null, "version": "1.0.11", "release": "23.fc42", "arch": "src" }, { "name": "mmseq-debuginfo", "epoch": null, "version": "1.0.11", "release": "23.fc42", "arch": "x86_64" } ] } RPMResults finished