Warning: Permanently added '2620:52:3:1:dead:beef:cafe:c114' (ED25519) to the list of known hosts. cmd: ['dist-git-client', 'sources'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-x3f6vag2/lagan rc: 0 stdout: stderr: INFO: Reading stdout from command: git rev-parse --abbrev-ref HEAD INFO: Reading stdout from command: git rev-parse HEAD INFO: Reading sources specification file: sources INFO: Downloading lagan20.tar.gz INFO: Reading stdout from command: curl --help all INFO: Calling: curl -H Pragma: -o lagan20.tar.gz --location --connect-timeout 60 --retry 3 --retry-delay 10 --remote-time --show-error --fail --retry-all-errors https://copr-dist-git.fedorainfracloud.org/repo/pkgs/dmalcolm/gcc-15-smoketest-3/lagan/lagan20.tar.gz/md5/da0948fbd76c2c92ae587d3a5db510fa/lagan20.tar.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 575k 100 575k 0 0 6605k 0 --:--:-- --:--:-- --:--:-- 6689k INFO: Reading stdout from command: md5sum lagan20.tar.gz Running (timeout=115200): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-x3f6vag2/lagan/lagan.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-x3f6vag2/lagan --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1734698755.945548 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 5.9 starting (python version = 3.13.0, NVR = mock-5.9-1.fc41), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-x3f6vag2/lagan/lagan.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-x3f6vag2/lagan --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1734698755.945548 -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-x3f6vag2/lagan/lagan.spec) Config(fedora-rawhide-x86_64) Start: clean chroot Finish: clean chroot Mock Version: 5.9 INFO: Mock Version: 5.9 Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1734698755.945548/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata INFO: Guessed host environment type: unknown INFO: Using bootstrap image: registry.fedoraproject.org/fedora:rawhide INFO: Pulling image: registry.fedoraproject.org/fedora:rawhide INFO: Copy content of container registry.fedoraproject.org/fedora:rawhide to /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1734698755.945548/root INFO: Checking that registry.fedoraproject.org/fedora:rawhide image matches host's architecture INFO: mounting registry.fedoraproject.org/fedora:rawhide with podman image mount INFO: image registry.fedoraproject.org/fedora:rawhide as /var/lib/containers/storage/overlay/c63836126604101f4382c0dc8749b882248c46a9701ec5ec9c0c0332b86e8b71/merged INFO: umounting image registry.fedoraproject.org/fedora:rawhide (/var/lib/containers/storage/overlay/c63836126604101f4382c0dc8749b882248c46a9701ec5ec9c0c0332b86e8b71/merged) with podman image umount 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-rawhide-x86_64-1734698755.945548/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.fc42.x86_64 rpm-sequoia-1.7.0-3.fc42.x86_64 dnf5-5.2.8.1-2.fc42.x86_64 dnf5-plugins-5.2.8.1-2.fc42.x86_64 Start: installing minimal buildroot with dnf5 Updating and loading repositories: fedora 100% | 1.1 MiB/s | 28.1 KiB | 00m00s Copr repository 100% | 49.6 KiB/s | 1.5 KiB | 00m00s Additional repo https_fedorapeople_org 100% | 28.3 KiB/s | 1.5 KiB | 00m00s Copr repository 100% | 29.6 MiB/s | 4.2 MiB | 00m00s Repositories loaded. Package Arch Version Repository Size Installing group/module packages: bash x86_64 5.2.37-1.fc42 fedora 8.2 MiB bzip2 x86_64 1.0.8-19.fc42 copr_base 96.9 KiB coreutils x86_64 9.5-11.fc42 copr_base 5.5 MiB cpio x86_64 2.15-2.fc41 fedora 1.1 MiB diffutils x86_64 3.10-8.fc42 copr_base 1.6 MiB fedora-release-common noarch 42-0.11 fedora 19.8 KiB findutils x86_64 1:4.10.0-4.fc42 copr_base 1.9 MiB gawk x86_64 5.3.0-4.fc41 fedora 1.7 MiB glibc-minimal-langpack x86_64 2.40.9000-24.fc42 copr_base 0.0 B grep x86_64 3.11-9.fc42 copr_base 1.0 MiB gzip x86_64 1.13-2.fc42 copr_base 391.0 KiB info x86_64 7.1.1-2.fc42 fedora 361.8 KiB patch x86_64 2.7.6-25.fc41 fedora 266.7 KiB redhat-rpm-config noarch 300-1.no_annobin.0.fc42 copr_base 186.6 KiB rpm-build x86_64 4.20.0-1.fc42 fedora 194.3 KiB sed x86_64 4.9-3.fc41 fedora 861.5 KiB shadow-utils x86_64 2:4.17.0~rc1-1.fc42 fedora 4.1 MiB tar x86_64 2:1.35-4.fc41 fedora 2.9 MiB unzip x86_64 6.0-65.fc42 fedora 398.2 KiB util-linux x86_64 2.40.2-8.fc42 fedora 3.7 MiB which x86_64 2.21-42.fc41 fedora 80.2 KiB xz x86_64 1:5.6.3-2.fc42 fedora 1.2 MiB Installing dependencies: add-determinism x86_64 0.4.3-1.fc42 fedora 2.4 MiB alternatives x86_64 1.31-1.fc42 fedora 64.8 KiB ansible-srpm-macros noarch 1-16.fc41 fedora 35.7 KiB audit-libs x86_64 4.0.2-1.fc42 copr_base 331.3 KiB authselect x86_64 1.5.0-8.fc42 copr_base 156.0 KiB authselect-libs x86_64 1.5.0-8.fc42 copr_base 820.0 KiB basesystem noarch 11-21.fc41 fedora 0.0 B binutils x86_64 2.43.50-9.fc42 copr_base 25.6 MiB build-reproducibility-srpm-macros noarch 0.4.3-1.fc42 fedora 735.0 B bzip2-libs x86_64 1.0.8-19.fc42 copr_base 83.2 KiB ca-certificates noarch 2024.2.69_v8.0.401-3.fc42 fedora 2.6 MiB coreutils-common x86_64 9.5-11.fc42 copr_base 11.2 MiB cracklib x86_64 2.9.11-6.fc42 copr_base 238.1 KiB crypto-policies noarch 20241128-1.gitbb7b0b0.fc42 fedora 137.3 KiB curl x86_64 8.11.1-2.fc42 copr_base 452.0 KiB cyrus-sasl-lib x86_64 2.1.28-27.fc41 fedora 2.3 MiB debugedit x86_64 5.1-2.fc42 copr_base 197.7 KiB dwz x86_64 0.15-8.fc42 copr_base 295.7 KiB ed x86_64 1.20.2-2.fc41 fedora 146.9 KiB efi-srpm-macros noarch 5-13.fc42 fedora 40.2 KiB elfutils x86_64 0.192-7.fc42 copr_base 2.6 MiB elfutils-debuginfod-client x86_64 0.192-7.fc42 copr_base 81.4 KiB elfutils-default-yama-scope noarch 0.192-7.fc42 copr_base 1.8 KiB elfutils-libelf x86_64 0.192-7.fc42 copr_base 1.2 MiB elfutils-libs x86_64 0.192-7.fc42 copr_base 662.9 KiB fedora-gpg-keys noarch 42-0.3 fedora 126.4 KiB fedora-release noarch 42-0.11 fedora 0.0 B fedora-release-identity-basic noarch 42-0.11 fedora 719.0 B fedora-repos noarch 42-0.3 fedora 4.9 KiB fedora-repos-rawhide noarch 42-0.3 fedora 2.2 KiB file x86_64 5.45-8.fc42 fedora 103.7 KiB file-libs x86_64 5.45-8.fc42 fedora 9.9 MiB filesystem x86_64 3.18-29.fc42 fedora 106.0 B filesystem-srpm-macros noarch 3.18-29.fc42 fedora 36.1 KiB fonts-srpm-macros noarch 1:2.0.5-17.fc41 fedora 55.8 KiB forge-srpm-macros noarch 0.4.0-1.fc42 fedora 38.9 KiB fpc-srpm-macros noarch 1.3-13.fc41 fedora 144.0 B gdb-minimal x86_64 15.2-4.fc42 copr_base 12.8 MiB gdbm x86_64 1:1.23-7.fc41 fedora 460.9 KiB gdbm-libs x86_64 1:1.23-7.fc41 fedora 121.9 KiB ghc-srpm-macros noarch 1.9.2-1.fc42 fedora 779.0 B glibc x86_64 2.40.9000-24.fc42 copr_base 6.5 MiB glibc-common x86_64 2.40.9000-24.fc42 copr_base 1.0 MiB glibc-gconv-extra x86_64 2.40.9000-24.fc42 copr_base 8.0 MiB gmp x86_64 1:6.3.0-2.fc41 fedora 811.4 KiB gnat-srpm-macros noarch 6-6.fc41 fedora 1.0 KiB go-srpm-macros noarch 3.6.0-5.fc42 fedora 60.8 KiB jansson x86_64 2.14-1.fc42 copr_base 90.8 KiB json-c x86_64 0.18-1.fc42 copr_base 83.7 KiB kernel-srpm-macros noarch 1.0-24.fc41 fedora 1.9 KiB keyutils-libs x86_64 1.6.3-4.fc42 copr_base 56.8 KiB krb5-libs x86_64 1.21.3-3.fc42 copr_base 2.3 MiB libacl x86_64 2.3.2-2.fc42 copr_base 38.3 KiB libarchive x86_64 3.7.7-1.fc42 fedora 932.3 KiB libattr x86_64 2.5.2-4.fc41 fedora 28.5 KiB libblkid x86_64 2.40.2-8.fc42 fedora 262.5 KiB libbrotli x86_64 1.1.0-5.fc42 copr_base 836.4 KiB libcap x86_64 2.71-1.fc42 fedora 210.8 KiB libcap-ng x86_64 0.8.5-3.fc41 fedora 69.2 KiB libcom_err x86_64 1.47.1-6.fc42 fedora 67.2 KiB libcurl x86_64 8.11.1-2.fc42 copr_base 829.3 KiB libeconf x86_64 0.7.5-1.fc42 fedora 66.7 KiB libevent x86_64 2.1.12-14.fc41 fedora 895.7 KiB libfdisk x86_64 2.40.2-8.fc42 fedora 362.9 KiB libffi x86_64 3.4.6-3.fc42 fedora 86.4 KiB libgcc x86_64 15.0.0-0.2.fc42 https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch 266.9 KiB libgomp x86_64 15.0.0-0.2.fc42 https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch 529.3 KiB libidn2 x86_64 2.3.7-2.fc41 fedora 329.1 KiB libmount x86_64 2.40.2-8.fc42 fedora 355.8 KiB libnghttp2 x86_64 1.64.0-1.fc42 fedora 174.5 KiB libnsl2 x86_64 2.0.1-2.fc41 fedora 57.9 KiB libpkgconf x86_64 2.3.0-1.fc42 fedora 78.2 KiB libpsl x86_64 0.21.5-4.fc41 fedora 80.5 KiB libpwquality x86_64 1.4.5-11.fc41 fedora 417.8 KiB libselinux x86_64 3.8-0.rc3.1.fc42 fedora 191.6 KiB libsemanage x86_64 3.8-0.rc3.1.fc42 fedora 305.3 KiB libsepol x86_64 3.8-0.rc3.1.fc42 fedora 812.3 KiB libsmartcols x86_64 2.40.2-8.fc42 fedora 180.4 KiB libssh x86_64 0.11.1-1.fc42 fedora 569.6 KiB libssh-config noarch 0.11.1-1.fc42 fedora 277.0 B libstdc++ x86_64 15.0.0-0.2.fc42 https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch 2.7 MiB libtasn1 x86_64 4.19.0-9.fc41 fedora 175.7 KiB libtirpc x86_64 1.3.6-1.fc42 fedora 205.5 KiB libtool-ltdl x86_64 2.5.4-1.fc42 copr_base 68.1 KiB libunistring x86_64 1.1-8.fc41 fedora 1.7 MiB libuuid x86_64 2.40.2-8.fc42 fedora 41.4 KiB libverto x86_64 0.3.2-9.fc41 fedora 29.5 KiB libxcrypt x86_64 4.4.36-11.fc42 fedora 271.4 KiB libxml2 x86_64 2.12.8-2.fc41 fedora 1.7 MiB libzstd x86_64 1.5.6-2.fc41 fedora 795.9 KiB lua-libs x86_64 5.4.7-1.fc42 fedora 285.0 KiB lua-srpm-macros noarch 1-14.fc41 fedora 1.3 KiB lz4-libs x86_64 1.10.0-1.fc41 fedora 145.5 KiB mpfr x86_64 4.2.1-5.fc41 fedora 832.1 KiB ncurses-base noarch 6.5-2.20240629.fc41 fedora 326.3 KiB ncurses-libs x86_64 6.5-2.20240629.fc41 fedora 975.2 KiB ocaml-srpm-macros noarch 10-3.fc41 fedora 1.9 KiB openblas-srpm-macros noarch 2-18.fc41 fedora 112.0 B openldap x86_64 2.6.8-6.fc42 fedora 647.4 KiB openssl-libs x86_64 1:3.2.2-8.fc42 fedora 7.8 MiB p11-kit x86_64 0.25.5-4.fc42 fedora 2.2 MiB p11-kit-trust x86_64 0.25.5-4.fc42 fedora 403.8 KiB package-notes-srpm-macros noarch 0.5-12.fc41 fedora 1.6 KiB pam x86_64 1.7.0-3.fc42 fedora 1.8 MiB pam-libs x86_64 1.7.0-3.fc42 fedora 139.4 KiB pcre2 x86_64 10.44-1.fc41.1 fedora 653.5 KiB pcre2-syntax noarch 10.44-1.fc41.1 fedora 251.6 KiB perl-srpm-macros noarch 1-56.fc41 fedora 861.0 B pkgconf x86_64 2.3.0-1.fc42 fedora 88.6 KiB pkgconf-m4 noarch 2.3.0-1.fc42 fedora 14.4 KiB pkgconf-pkg-config x86_64 2.3.0-1.fc42 fedora 989.0 B popt x86_64 1.19-7.fc41 fedora 136.9 KiB publicsuffix-list-dafsa noarch 20240107-4.fc41 fedora 67.5 KiB pyproject-srpm-macros noarch 1.16.3-1.fc42 fedora 1.9 KiB python-srpm-macros noarch 3.13-3.fc41 fedora 51.0 KiB qt5-srpm-macros noarch 5.15.15-1.fc42 fedora 500.0 B qt6-srpm-macros noarch 6.8.1-4.fc42 fedora 456.0 B readline x86_64 8.2-11.fc42 fedora 493.1 KiB rpm x86_64 4.20.0-1.fc42 fedora 3.1 MiB rpm-build-libs x86_64 4.20.0-1.fc42 fedora 206.7 KiB rpm-libs x86_64 4.20.0-1.fc42 fedora 726.1 KiB rpm-sequoia x86_64 1.7.0-3.fc42 fedora 2.3 MiB rust-srpm-macros noarch 26.3-3.fc42 fedora 4.8 KiB setup noarch 2.15.0-5.fc41 fedora 720.7 KiB sqlite-libs x86_64 3.47.2-1.fc42 fedora 1.4 MiB systemd-libs x86_64 257-1.fc42 fedora 2.2 MiB util-linux-core x86_64 2.40.2-8.fc42 fedora 1.5 MiB xxhash-libs x86_64 0.8.2-4.fc42 fedora 88.4 KiB xz-libs x86_64 1:5.6.3-2.fc42 fedora 218.4 KiB zig-srpm-macros noarch 1-3.fc41 fedora 1.1 KiB zip x86_64 3.0-42.fc42 fedora 695.9 KiB zlib-ng-compat x86_64 2.2.2-1.fc42 fedora 134.0 KiB zstd x86_64 1.5.6-2.fc41 fedora 1.7 MiB Installing groups: Buildsystem building group Transaction Summary: Installing: 155 packages Total size of inbound packages is 51 MiB. Need to download 540 KiB. After this operation, 178 MiB extra will be used (install 178 MiB, remove 0 B). [1/1] tar-2:1.35-4.fc41.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [1/1] Total 100% | 0.0 B/s | 0.0 B | 00m00s [1/2] rpm-build-0:4.20.0-1.fc42.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [2/2] Total 100% | 0.0 B/s | 0.0 B | 00m00s [1/3] unzip-0:6.0-65.fc42.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [3/3] Total 100% | 0.0 B/s | 0.0 B | 00m00s [1/4] cpio-0:2.15-2.fc41.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [4/4] Total 100% | 0.0 B/s | 0.0 B | 00m00s [1/5] which-0:2.21-42.fc41.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded 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-------------------------------------------------------------------------------- [155/155] Total 100% | 0.0 B/s | 0.0 B | 00m00s Running transaction Importing OpenPGP key 0x105EF944: UserID : "Fedora (42) " Fingerprint: B0F4950458F69E1150C6C5EDC8AC4916105EF944 From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-42-primary The key was successfully imported. Importing OpenPGP key 0x105EF944: UserID : "Fedora (42) " Fingerprint: B0F4950458F69E1150C6C5EDC8AC4916105EF944 From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-42-primary The key was successfully imported. Importing OpenPGP key 0xE99D6AD1: UserID : "Fedora (41) " Fingerprint: 466CF2D8B60BC3057AA9453ED0622462E99D6AD1 From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-41-primary The key was successfully imported. Importing OpenPGP key 0x31645531: UserID : "Fedora (43) " Fingerprint: C6E7F081CF80E13146676E88829B606631645531 From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-43-primary The key was successfully imported. 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52.2 KiB | 00m00s [151/157] Installing redhat-rpm-config- 100% | 47.2 MiB/s | 193.2 KiB | 00m00s [152/157] Installing rpm-build-0:4.20.0 100% | 39.6 MiB/s | 202.9 KiB | 00m00s [153/157] Installing pyproject-srpm-mac 100% | 1.2 MiB/s | 2.5 KiB | 00m00s [154/157] Installing util-linux-0:2.40. 100% | 79.0 MiB/s | 3.7 MiB | 00m00s [155/157] Installing authselect-0:1.5.0 100% | 39.2 MiB/s | 160.4 KiB | 00m00s [156/157] Installing which-0:2.21-42.fc 100% | 40.2 MiB/s | 82.4 KiB | 00m00s [157/157] Installing info-0:7.1.1-2.fc4 100% | 139.4 KiB/s | 362.2 KiB | 00m03s Warning: skipped OpenPGP checks for 38 packages from repositories: copr_base, https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_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-0.4.3-1.fc42.x86_64 alternatives-1.31-1.fc42.x86_64 ansible-srpm-macros-1-16.fc41.noarch audit-libs-4.0.2-1.fc42.x86_64 authselect-1.5.0-8.fc42.x86_64 authselect-libs-1.5.0-8.fc42.x86_64 basesystem-11-21.fc41.noarch bash-5.2.37-1.fc42.x86_64 binutils-2.43.50-9.fc42.x86_64 build-reproducibility-srpm-macros-0.4.3-1.fc42.noarch bzip2-1.0.8-19.fc42.x86_64 bzip2-libs-1.0.8-19.fc42.x86_64 ca-certificates-2024.2.69_v8.0.401-3.fc42.noarch coreutils-9.5-11.fc42.x86_64 coreutils-common-9.5-11.fc42.x86_64 cpio-2.15-2.fc41.x86_64 cracklib-2.9.11-6.fc42.x86_64 crypto-policies-20241128-1.gitbb7b0b0.fc42.noarch curl-8.11.1-2.fc42.x86_64 cyrus-sasl-lib-2.1.28-27.fc41.x86_64 debugedit-5.1-2.fc42.x86_64 diffutils-3.10-8.fc42.x86_64 dwz-0.15-8.fc42.x86_64 ed-1.20.2-2.fc41.x86_64 efi-srpm-macros-5-13.fc42.noarch elfutils-0.192-7.fc42.x86_64 elfutils-debuginfod-client-0.192-7.fc42.x86_64 elfutils-default-yama-scope-0.192-7.fc42.noarch elfutils-libelf-0.192-7.fc42.x86_64 elfutils-libs-0.192-7.fc42.x86_64 fedora-gpg-keys-42-0.3.noarch fedora-release-42-0.11.noarch fedora-release-common-42-0.11.noarch fedora-release-identity-basic-42-0.11.noarch fedora-repos-42-0.3.noarch fedora-repos-rawhide-42-0.3.noarch file-5.45-8.fc42.x86_64 file-libs-5.45-8.fc42.x86_64 filesystem-3.18-29.fc42.x86_64 filesystem-srpm-macros-3.18-29.fc42.noarch findutils-4.10.0-4.fc42.x86_64 fonts-srpm-macros-2.0.5-17.fc41.noarch forge-srpm-macros-0.4.0-1.fc42.noarch fpc-srpm-macros-1.3-13.fc41.noarch gawk-5.3.0-4.fc41.x86_64 gdb-minimal-15.2-4.fc42.x86_64 gdbm-1.23-7.fc41.x86_64 gdbm-libs-1.23-7.fc41.x86_64 ghc-srpm-macros-1.9.2-1.fc42.noarch glibc-2.40.9000-24.fc42.x86_64 glibc-common-2.40.9000-24.fc42.x86_64 glibc-gconv-extra-2.40.9000-24.fc42.x86_64 glibc-minimal-langpack-2.40.9000-24.fc42.x86_64 gmp-6.3.0-2.fc41.x86_64 gnat-srpm-macros-6-6.fc41.noarch go-srpm-macros-3.6.0-5.fc42.noarch gpg-pubkey-105ef944-65ca83d1 gpg-pubkey-31645531-66b6dccf gpg-pubkey-e99d6ad1-64d2612c grep-3.11-9.fc42.x86_64 gzip-1.13-2.fc42.x86_64 info-7.1.1-2.fc42.x86_64 jansson-2.14-1.fc42.x86_64 json-c-0.18-1.fc42.x86_64 kernel-srpm-macros-1.0-24.fc41.noarch keyutils-libs-1.6.3-4.fc42.x86_64 krb5-libs-1.21.3-3.fc42.x86_64 libacl-2.3.2-2.fc42.x86_64 libarchive-3.7.7-1.fc42.x86_64 libattr-2.5.2-4.fc41.x86_64 libblkid-2.40.2-8.fc42.x86_64 libbrotli-1.1.0-5.fc42.x86_64 libcap-2.71-1.fc42.x86_64 libcap-ng-0.8.5-3.fc41.x86_64 libcom_err-1.47.1-6.fc42.x86_64 libcurl-8.11.1-2.fc42.x86_64 libeconf-0.7.5-1.fc42.x86_64 libevent-2.1.12-14.fc41.x86_64 libfdisk-2.40.2-8.fc42.x86_64 libffi-3.4.6-3.fc42.x86_64 libgcc-15.0.0-0.2.fc42.x86_64 libgomp-15.0.0-0.2.fc42.x86_64 libidn2-2.3.7-2.fc41.x86_64 libmount-2.40.2-8.fc42.x86_64 libnghttp2-1.64.0-1.fc42.x86_64 libnsl2-2.0.1-2.fc41.x86_64 libpkgconf-2.3.0-1.fc42.x86_64 libpsl-0.21.5-4.fc41.x86_64 libpwquality-1.4.5-11.fc41.x86_64 libselinux-3.8-0.rc3.1.fc42.x86_64 libsemanage-3.8-0.rc3.1.fc42.x86_64 libsepol-3.8-0.rc3.1.fc42.x86_64 libsmartcols-2.40.2-8.fc42.x86_64 libssh-0.11.1-1.fc42.x86_64 libssh-config-0.11.1-1.fc42.noarch libstdc++-15.0.0-0.2.fc42.x86_64 libtasn1-4.19.0-9.fc41.x86_64 libtirpc-1.3.6-1.fc42.x86_64 libtool-ltdl-2.5.4-1.fc42.x86_64 libunistring-1.1-8.fc41.x86_64 libuuid-2.40.2-8.fc42.x86_64 libverto-0.3.2-9.fc41.x86_64 libxcrypt-4.4.36-11.fc42.x86_64 libxml2-2.12.8-2.fc41.x86_64 libzstd-1.5.6-2.fc41.x86_64 lua-libs-5.4.7-1.fc42.x86_64 lua-srpm-macros-1-14.fc41.noarch lz4-libs-1.10.0-1.fc41.x86_64 mpfr-4.2.1-5.fc41.x86_64 ncurses-base-6.5-2.20240629.fc41.noarch ncurses-libs-6.5-2.20240629.fc41.x86_64 ocaml-srpm-macros-10-3.fc41.noarch openblas-srpm-macros-2-18.fc41.noarch openldap-2.6.8-6.fc42.x86_64 openssl-libs-3.2.2-8.fc42.x86_64 p11-kit-0.25.5-4.fc42.x86_64 p11-kit-trust-0.25.5-4.fc42.x86_64 package-notes-srpm-macros-0.5-12.fc41.noarch pam-1.7.0-3.fc42.x86_64 pam-libs-1.7.0-3.fc42.x86_64 patch-2.7.6-25.fc41.x86_64 pcre2-10.44-1.fc41.1.x86_64 pcre2-syntax-10.44-1.fc41.1.noarch perl-srpm-macros-1-56.fc41.noarch pkgconf-2.3.0-1.fc42.x86_64 pkgconf-m4-2.3.0-1.fc42.noarch pkgconf-pkg-config-2.3.0-1.fc42.x86_64 popt-1.19-7.fc41.x86_64 publicsuffix-list-dafsa-20240107-4.fc41.noarch pyproject-srpm-macros-1.16.3-1.fc42.noarch python-srpm-macros-3.13-3.fc41.noarch qt5-srpm-macros-5.15.15-1.fc42.noarch qt6-srpm-macros-6.8.1-4.fc42.noarch readline-8.2-11.fc42.x86_64 redhat-rpm-config-300-1.no_annobin.0.fc42.noarch rpm-4.20.0-1.fc42.x86_64 rpm-build-4.20.0-1.fc42.x86_64 rpm-build-libs-4.20.0-1.fc42.x86_64 rpm-libs-4.20.0-1.fc42.x86_64 rpm-sequoia-1.7.0-3.fc42.x86_64 rust-srpm-macros-26.3-3.fc42.noarch sed-4.9-3.fc41.x86_64 setup-2.15.0-5.fc41.noarch shadow-utils-4.17.0~rc1-1.fc42.x86_64 sqlite-libs-3.47.2-1.fc42.x86_64 systemd-libs-257-1.fc42.x86_64 tar-1.35-4.fc41.x86_64 unzip-6.0-65.fc42.x86_64 util-linux-2.40.2-8.fc42.x86_64 util-linux-core-2.40.2-8.fc42.x86_64 which-2.21-42.fc41.x86_64 xxhash-libs-0.8.2-4.fc42.x86_64 xz-5.6.3-2.fc42.x86_64 xz-libs-5.6.3-2.fc42.x86_64 zig-srpm-macros-1-3.fc41.noarch zip-3.0-42.fc42.x86_64 zlib-ng-compat-2.2.2-1.fc42.x86_64 zstd-1.5.6-2.fc41.x86_64 Start: buildsrpm Start: rpmbuild -bs Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1721260800 Wrote: /builddir/build/SRPMS/lagan-2.0-42.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-rawhide-x86_64-1734698755.945548/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-x3f6vag2/lagan/lagan.spec) Config(child) 0 minutes 17 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/lagan-2.0-42.fc42.src.rpm) Config(fedora-rawhide-x86_64) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1734698755.945548/root. INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1734698755.945548/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-1734698755.945548/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.fc42.x86_64 rpm-sequoia-1.7.0-3.fc42.x86_64 dnf5-5.2.8.1-2.fc42.x86_64 dnf5-plugins-5.2.8.1-2.fc42.x86_64 Finish: chroot init Start: build phase for lagan-2.0-42.fc42.src.rpm Start: build setup for lagan-2.0-42.fc42.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1721260800 Wrote: /builddir/build/SRPMS/lagan-2.0-42.fc42.src.rpm Updating and loading repositories: Additional repo https_fedorapeople_org 100% | 21.2 KiB/s | 1.5 KiB | 00m00s Copr repository 100% | 35.7 KiB/s | 1.5 KiB | 00m00s fedora 100% | 825.4 KiB/s | 28.1 KiB | 00m00s Copr repository 100% | 28.0 MiB/s | 4.2 MiB | 00m00s Repositories loaded. Package Arch Version Repository Size Installing: gcc-c++ x86_64 15.0.0-0.2.fc42 https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch 40.7 MiB make x86_64 1:4.4.1-9.fc42 fedora 1.8 MiB perl-generators noarch 1.16-6.fc41 fedora 21.8 KiB Installing dependencies: annobin-docs noarch 12.79-1.fc42 copr_base 98.6 KiB annobin-plugin-gcc x86_64 12.79-1.fc42 copr_base 989.3 KiB cpp x86_64 15.0.0-0.2.fc42 https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch 37.5 MiB gcc x86_64 15.0.0-0.2.fc42 https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch 109.9 MiB gcc-plugin-annobin x86_64 15.0.0-0.2.fc42 https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch 59.6 KiB glibc-devel x86_64 2.40.9000-24.fc42 copr_base 2.3 MiB groff-base x86_64 1.23.0-7.fc42 copr_base 3.8 MiB kernel-headers x86_64 6.13.0-0.rc3.29.fc42 fedora 6.5 MiB libmpc x86_64 1.3.1-6.fc41 fedora 164.7 KiB libstdc++-devel x86_64 15.0.0-0.2.fc42 https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch 15.7 MiB libxcrypt-devel x86_64 4.4.36-11.fc42 fedora 30.5 KiB ncurses x86_64 6.5-2.20240629.fc41 fedora 627.3 KiB perl-AutoLoader noarch 5.74-512.fc42 fedora 20.5 KiB perl-B x86_64 1.89-512.fc42 fedora 498.0 KiB perl-Carp noarch 1.54-511.fc41 fedora 46.6 KiB perl-Class-Struct noarch 0.68-512.fc42 fedora 25.4 KiB perl-Data-Dumper x86_64 2.189-512.fc41 fedora 111.7 KiB perl-Digest noarch 1.20-511.fc41 fedora 35.3 KiB perl-Digest-MD5 x86_64 2.59-5.fc41 fedora 59.8 KiB perl-DynaLoader x86_64 1.56-512.fc42 fedora 32.1 KiB perl-Encode x86_64 4:3.21-511.fc41 fedora 4.7 MiB perl-Errno x86_64 1.38-512.fc42 fedora 8.4 KiB perl-Exporter noarch 5.78-511.fc41 fedora 54.3 KiB perl-Fcntl x86_64 1.18-512.fc42 fedora 49.0 KiB perl-Fedora-VSP noarch 0.001-35.fc41 fedora 39.7 KiB perl-File-Basename noarch 2.86-512.fc42 fedora 14.0 KiB perl-File-Path noarch 2.18-511.fc41 fedora 63.5 KiB perl-File-Temp noarch 1:0.231.100-511.fc41 fedora 162.3 KiB perl-File-stat noarch 1.14-512.fc42 fedora 12.5 KiB perl-FileHandle noarch 2.05-512.fc42 fedora 9.3 KiB perl-Getopt-Long noarch 1:2.58-2.fc41 fedora 144.5 KiB perl-Getopt-Std noarch 1.14-512.fc42 fedora 11.2 KiB perl-HTTP-Tiny noarch 0.090-1.fc42 fedora 154.4 KiB perl-IO x86_64 1.55-512.fc42 fedora 151.1 KiB perl-IO-Socket-IP noarch 0.43-1.fc42 fedora 100.3 KiB perl-IO-Socket-SSL noarch 2.089-1.fc42 fedora 703.3 KiB perl-IPC-Open3 noarch 1.22-512.fc42 fedora 22.5 KiB perl-MIME-Base32 noarch 1.303-21.fc41 fedora 30.7 KiB perl-MIME-Base64 x86_64 3.16-511.fc41 fedora 46.1 KiB perl-Net-SSLeay x86_64 1.94-7.fc41 fedora 1.3 MiB perl-POSIX x86_64 2.20-512.fc42 fedora 235.1 KiB perl-PathTools x86_64 3.91-511.fc41 fedora 180.0 KiB perl-Pod-Escapes noarch 1:1.07-511.fc41 fedora 24.9 KiB perl-Pod-Perldoc noarch 3.28.01-512.fc41 fedora 163.7 KiB perl-Pod-Simple noarch 1:3.45-511.fc41 fedora 560.9 KiB perl-Pod-Usage noarch 4:2.03-511.fc41 fedora 84.8 KiB perl-Scalar-List-Utils x86_64 5:1.68-1.fc42 fedora 148.9 KiB perl-SelectSaver noarch 1.02-512.fc42 fedora 2.2 KiB perl-Socket x86_64 4:2.038-511.fc41 fedora 124.0 KiB perl-Storable x86_64 1:3.32-511.fc41 fedora 232.4 KiB perl-Symbol noarch 1.09-512.fc42 fedora 6.8 KiB perl-Term-ANSIColor noarch 5.01-512.fc41 fedora 97.5 KiB perl-Term-Cap noarch 1.18-511.fc41 fedora 29.3 KiB perl-Text-ParseWords noarch 3.31-511.fc41 fedora 13.6 KiB perl-Text-Tabs+Wrap noarch 2024.001-511.fc41 fedora 22.6 KiB perl-Time-Local noarch 2:1.350-511.fc41 fedora 69.0 KiB perl-URI noarch 5.31-1.fc42 fedora 257.0 KiB perl-base noarch 2.27-512.fc42 fedora 12.5 KiB perl-constant noarch 1.33-512.fc41 fedora 26.2 KiB perl-if noarch 0.61.000-512.fc42 fedora 5.8 KiB perl-interpreter x86_64 4:5.40.0-512.fc42 fedora 122.3 KiB perl-libnet noarch 3.15-512.fc41 fedora 289.4 KiB perl-libs x86_64 4:5.40.0-512.fc42 fedora 9.9 MiB perl-locale noarch 1.12-512.fc42 fedora 6.5 KiB perl-macros noarch 4:5.40.0-512.fc42 fedora 5.5 KiB perl-mro x86_64 1.29-512.fc42 fedora 45.6 KiB perl-overload noarch 1.37-512.fc42 fedora 71.5 KiB perl-overloading noarch 0.02-512.fc42 fedora 4.8 KiB perl-parent noarch 1:0.244-1.fc42 fedora 10.3 KiB perl-podlators noarch 1:6.0.2-2.fc41 fedora 317.5 KiB perl-vars noarch 1.05-512.fc42 fedora 3.9 KiB Transaction Summary: Installing: 74 packages Total size of inbound packages is 80 MiB. Need to download 8 MiB. After this operation, 242 MiB extra will be used (install 242 MiB, remove 0 B). [1/1] make-1:4.4.1-9.fc42.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [1/1] Total 100% | 0.0 B/s | 0.0 B | 00m00s [1/3] gcc-c++-0:15.0.0-0.2.fc42.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [2/8] gcc-0:15.0.0-0.2.fc42.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [3/9] libstdc++-devel-0:15.0.0-0.2.fc42 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 4/10] libmpc-0:1.3.1-6.fc41.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 5/14] cpp-0:15.0.0-0.2.fc42.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 6/69] glibc-devel-0:2.40.9000-24.fc42 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 7/70] libxcrypt-devel-0:4.4.36-11.fc4 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 8/71] kernel-headers-0:6.13.0-0.rc3.2 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 9/72] gcc-plugin-annobin-0:15.0.0-0.2 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359.9 KiB/s | 13.0 KiB | 00m00s [22/74] perl-Errno-0:1.38-512.fc42.x86_ 100% | 573.4 KiB/s | 14.9 KiB | 00m00s [23/74] perl-constant-0:1.33-512.fc41.n 100% | 767.7 KiB/s | 23.0 KiB | 00m00s [24/74] perl-Scalar-List-Utils-5:1.68-1 100% | 1.0 MiB/s | 74.2 KiB | 00m00s [25/74] perl-libs-4:5.40.0-512.fc42.x86 100% | 12.0 MiB/s | 2.3 MiB | 00m00s [26/74] perl-Getopt-Long-1:2.58-2.fc41. 100% | 1.4 MiB/s | 63.9 KiB | 00m00s [27/74] perl-Getopt-Std-0:1.14-512.fc42 100% | 579.5 KiB/s | 15.6 KiB | 00m00s [28/74] perl-MIME-Base64-0:3.16-511.fc4 100% | 965.9 KiB/s | 29.9 KiB | 00m00s [29/74] perl-Storable-1:3.32-511.fc41.x 100% | 3.1 MiB/s | 98.4 KiB | 00m00s [30/74] perl-parent-1:0.244-1.fc42.noar 100% | 582.4 KiB/s | 15.1 KiB | 00m00s [31/74] perl-overload-0:1.37-512.fc42.n 100% | 722.2 KiB/s | 45.5 KiB | 00m00s [32/74] perl-Pod-Usage-4:2.03-511.fc41. 100% | 1.4 MiB/s | 40.0 KiB | 00m00s [33/74] perl-Encode-4:3.21-511.fc41.x86 100% | 5.4 MiB/s | 1.1 MiB | 00m00s [34/74] 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Finish: build setup for lagan-2.0-42.fc42.src.rpm Start: rpmbuild lagan-2.0-42.fc42.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1721260800 Executing(%mkbuilddir): /bin/sh -e /var/tmp/rpm-tmp.oIbegZ + umask 022 + cd /builddir/build/BUILD/lagan-2.0-build + test -d /builddir/build/BUILD/lagan-2.0-build + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w /builddir/build/BUILD/lagan-2.0-build + /usr/bin/rm -rf /builddir/build/BUILD/lagan-2.0-build + /usr/bin/mkdir -p /builddir/build/BUILD/lagan-2.0-build + /usr/bin/mkdir -p /builddir/build/BUILD/lagan-2.0-build/SPECPARTS + RPM_EC=0 ++ jobs -p + exit 0 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.jNGo2f + umask 022 + cd /builddir/build/BUILD/lagan-2.0-build + cd /builddir/build/BUILD/lagan-2.0-build + rm -rf lagan20 + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/lagan20.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + cd lagan20 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . Patch #0 (lagan20-chris.patch): + echo 'Patch #0 (lagan20-chris.patch):' + /usr/bin/patch --no-backup-if-mismatch -f -p1 -b --suffix .chris --fuzz=0 patching file Readmes/README.FIRST patching file Readmes/README.shuffle patching file Readmes/README.chaos patching file Readmes/README.lagan patching file src/utils/scorealign.c patching file src/utils/Glue.cpp patching file src/utils/mrun.pl patching file src/utils/mrunfile.pl patching file src/utils/mrunpairs.pl patching file src/utils/mviz.pl patching file src/mlagan.c patching file src/prolagan.c patching file src/slagan-mfa.pl patching file src/supermap.pl patching file src/xmfa2mfa.pl patching file utils/mrunpairs.pl patching file utils/draft.pl patching file utils/mrunfile.pl patching file utils/mviz.pl patching file utils/mrun.pl patching file slagan.pl patching file lagan.pl patching file rechaos.pl patching file slagan-mfa.pl patching file supermap.pl patching file xmfa2mfa.pl patching file src/glocal/rightinfluence.cpp patching file src/glocal/score.cpp Patch #1 (lagan20-gcc10.patch): + echo 'Patch #1 (lagan20-gcc10.patch):' + /usr/bin/patch --no-backup-if-mismatch -f -p1 -b --suffix .gcc10 --fuzz=0 patching file src/multial.c patching file src/order.c patching file src/utils/scorecontigs.c Hunk #1 succeeded at 258 (offset -1 lines). Patch #2 (lagan-c99.patch): + echo 'Patch #2 (lagan-c99.patch):' + /usr/bin/patch --no-backup-if-mismatch -f -p1 --fuzz=0 patching file src/multial.h patching file src/order.c + sed -i 's/^CC .*$/CC = gcc $(RPM_OPT_FLAGS)/; s/^CPP .*$/CPP = g++ $(RPM_OPT_FLAGS)/' Makefile + sed -i 's|getenv ("LAGAN_DIR")|"/usr/lib64/lagan"|g' src/anchors.c src/diagmatrix.c src/fchaos.c src/filebuffer.c src/global.c src/mempage.c src/mlagan.c src/multial.c src/order.c src/prolagan.c src/skiplist.c src/sortlist.c src/thrtrie.c src/translate.c src/utils/bin2bl.c src/utils/bin2mf.c src/utils/cextract.c src/utils/contigorder.c src/utils/cstat.c src/utils/fa2xfa.c src/utils/getbounds.c src/utils/getcontigpos.c src/utils/getlength.c src/utils/getoverlap.c src/utils/overlay.c src/utils/rc.c src/utils/scorealign.c src/utils/scorecontigs.c src/utils/seqmerge.c + sed -i 's|getenv ("LAGAN_DIR")|"/usr/lib64/lagan"|g' src/utils/Glue.cpp src/utils/dotplot.cpp + sed -i 's|$ENV{LAGAN_DIR}|"/usr/lib64/lagan"|g' anal_gloc.pl lagan.pl rechaos.pl slagan-mfa.pl slagan.pl supermap.pl xmfa2mfa.pl src/anal_gloc.pl src/lagan.pl src/rechaos.pl src/slagan-mfa.pl src/slagan.pl src/supermap.pl src/xmfa2mfa.pl utils/cmerge2.pl utils/draft.pl utils/flipchaos.pl utils/mextract.pl utils/mf2bin.pl utils/mpretty.pl utils/mproject.pl utils/mrun.pl utils/mrunfile.pl utils/mrunpairs.pl utils/msplit.pl utils/mviz.pl src/utils/cmerge2.pl src/utils/draft.pl src/utils/mextract.pl src/utils/mf2bin.pl src/utils/mpretty.pl src/utils/mproject.pl src/utils/mrun.pl src/utils/mrunfile.pl src/utils/mrunpairs.pl src/utils/mviz.pl + sed -i 's|$LAGAN_DIR|/usr/lib64/lagan|g' Readmes/README.shuffle src/anchors.c src/diagmatrix.c src/fchaos.c src/filebuffer.c src/global.c src/mempage.c src/mlagan.c src/multial.c src/order.c src/prolagan.c src/skiplist.c src/sortlist.c src/thrtrie.c src/translate.c + sed -i s/getline/GetLine/g src/anchors.c + sed -i 's/^inline /inline __attribute__ ((always_inline)) /' src/fchaos.c + sed -i '//a#include ' src/filebuffer.c + sed -i '//a#include ' src/utils/scorecontigs.c + sed -i '//a#include ' src/utils/overlay.c + sed -i '//a#include ' src/utils/cstat.c + sed -i 's/^int indeces/extern int indeces/' src/thrtrie.h + sed -i '/^int nnodes=0;/aint indeces[256];' src/thrtrie.c + rm prolagan + chmod -x src/glocal/Makefile src/glocal/default.score src/glocal/glocal src/glocal/glocal.cpp src/glocal/glocal.h src/glocal/io.cpp src/glocal/io.h src/glocal/leftinfluence.cpp src/glocal/leftinfluence.h src/glocal/rightinfluence.cpp src/glocal/rightinfluence.cpp.chris src/glocal/rightinfluence.h src/glocal/score.cpp src/glocal/score.cpp.chris src/glocal/score.h src/glocal/structs.h src/glocal/test.score + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.SxvKbg + umask 022 + cd /builddir/build/BUILD/lagan-2.0-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 lagan20 + make -j2 'CFLAGS=-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' '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' (cd src; make) make[1]: Entering directory '/builddir/build/BUILD/lagan-2.0-build/lagan20/src' gcc -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 -o ../anchors anchors.c skiplist.c gcc -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 -o ../chaos fchaos.c thrtrie.c skiplist.c global.c translate.c filebuffer.c -lm -DCHAOS__FLAG anchors.c: In function ‘hptrcomp’: anchors.c:49:7: warning: unused variable ‘jt’ [-Wunused-variable] 49 | int jt = ((hptr*)p2)->isstart; | ^~ anchors.c: In function ‘doOutput’: anchors.c:171:17: warning: unused variable ‘bestscore’ [-Wunused-variable] 171 | int chl=0, i, bestscore=-1; | ^~~~~~~~~ anchors.c:171:14: warning: unused variable ‘i’ [-Wunused-variable] 171 | int chl=0, i, bestscore=-1; | ^ anchors.c:168:7: warning: variable ‘len’ set but not used [-Wunused-but-set-variable] 168 | int len; | ^~~ anchors.c: In function ‘GetLine’: anchors.c:232:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 232 | fgets(temp, 1024, infile); | ^~~~~~~~~~~~~~~~~~~~~~~~~ fchaos.c: In function ‘removeDups’: fchaos.c:302:24: warning: unused variable ‘temp’ [-Wunused-variable] 302 | hll *i, *j, *jprev, *temp; | ^~~~ fchaos.c: In function ‘readfile’: fchaos.c:357:25: warning: too many arguments for format [-Wformat-extra-args] 357 | fprintf(stderr, "WARNING %c converted to N\n", currchar, alpha); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fchaos.c: In function ‘chain’: fchaos.c:401:16: warning: unused variable ‘d2’ [-Wunused-variable] 401 | int i, d1=0, d2=0; | ^~ fchaos.c:401:10: warning: unused variable ‘d1’ [-Wunused-variable] 401 | int i, d1=0, d2=0; | ^~ fchaos.c:401:7: warning: unused variable ‘i’ [-Wunused-variable] 401 | int i, d1=0, d2=0; | ^ fchaos.c: In function ‘findPrev’: fchaos.c:440:7: warning: unused variable ‘doneset’ [-Wunused-variable] 440 | int doneset = 0; | ^~~~~~~ fchaos.c: In function ‘doAlgo’: fchaos.c:543:24: warning: unused variable ‘bestdbaseloc’ [-Wunused-variable] 543 | int bestqueryloc=-1, bestdbaseloc=-1, numhits; | ^~~~~~~~~~~~ fchaos.c:543:7: warning: unused variable ‘bestqueryloc’ [-Wunused-variable] 543 | int bestqueryloc=-1, bestdbaseloc=-1, numhits; | ^~~~~~~~~~~~ fchaos.c:542:9: warning: unused variable ‘bestscore’ [-Wunused-variable] 542 | float bestscore=-1, baseval; | ^~~~~~~~~ fchaos.c: In function ‘main’: fchaos.c:885:7: warning: unused variable ‘i’ [-Wunused-variable] 885 | int i; | ^ fchaos.c: In function ‘saveScore’: fchaos.c:970:7: warning: unused variable ‘temp’ [-Wunused-variable] 970 | int temp; | ^~~~ fchaos.c: In function ‘savenfreeLList’: fchaos.c:1137:9: warning: variable ‘j’ set but not used [-Wunused-but-set-variable] 1137 | int i,j; | ^ fchaos.c: In function ‘readfile’: fchaos.c:344:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 344 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ fchaos.c: In function ‘readSubstMatrix’: fchaos.c:622:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 622 | fscanf (file, "%d", &(substmatrix[(unsigned char) symbs[i]][(unsigned char) symbs[j]])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fchaos.c:627:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 627 | fscanf (file, "%d", &gappenstart); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fchaos.c:628:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 628 | fscanf (file, "%d", &gappenext); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ anchors.c: In function ‘findBestChain’: anchors.c:164:10: warning: ‘bestptr’ may be used uninitialized [-Wmaybe-uninitialized] 164 | return (hll*)bestptr->myelem; | ^~~~~~~~~~~~~~~~~~~~~ anchors.c:126:15: note: ‘bestptr’ was declared here 126 | sle* help, *bestptr; | ^~~~~~~ skiplist.c: In function ‘printSLE’: skiplist.c:12:19: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 3 has type ‘void *’ [-Wformat=] 12 | printf(" %d %x\n", tbp->index, tbp->myelem); | ~^ ~~~~~~~~~~~ | | | | unsigned int void * | %p skiplist.c: In function ‘makeSkLst’: skiplist.c:33:7: warning: unused variable ‘i’ [-Wunused-variable] 33 | int i; | ^ skiplist.c: In function ‘SLinsert’: skiplist.c:100:37: warning: unused variable ‘tbe’ [-Wunused-variable] 100 | sle* prev = SLfind(trgt, index), *tbe; | ^~~ gcc -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 -o ../order order.c diagmatrix.c filebuffer.c order.c: In function ‘readAncFile’: order.c:238:35: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 238 | if ((tt->seq1start >= s1start && tt->seq1end <= s1end || s1start == 0 && s1end == 0) && | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ order.c:239:35: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 239 | (tt->seq2start >= s2start && tt->seq2end <= s2end || s2start == 0 && s2end == 0)){ | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ order.c: In function ‘mkBarrel’: order.c:275:7: warning: unused variable ‘incr’ [-Wunused-variable] 275 | int incr; | ^~~~ order.c: In function ‘getChain’: order.c:487:7: warning: unused variable ‘temp’ [-Wunused-variable] 487 | int temp; | ^~~~ order.c: In function ‘saveNeck’: order.c:562:6: warning: unused variable ‘second’ [-Wunused-variable] 562 | *second = DMgetDiagStart(mydm, neckdiag, &size2, &x2, &y2); | ^~~~~~ order.c:561:9: warning: unused variable ‘first’ [-Wunused-variable] 561 | alel *first = DMgetDiagStart(mydm, neckdiag-1, &size1, &x1, &y1), | ^~~~~ order.c: In function ‘joinAligns’: order.c:587:10: warning: unused variable ‘n’ [-Wunused-variable] 587 | align *n = a->nextalign, *t; | ^ order.c: In function ‘printBinAlign’: order.c:719:23: warning: array subscript has type ‘char’ [-Wchar-subscripts] 719 | left = lets[seq1[s1++]]; | ~~~~^~~~~~ order.c:721:24: warning: array subscript has type ‘char’ [-Wchar-subscripts] 721 | right = lets[seq2[s2++]]; | ~~~~^~~~~~ order.c: In function ‘printMFAAlign’: order.c:774:27: warning: unused variable ‘nlets’ [-Wunused-variable] 774 | int nm=0, nga=0, ngb=0, nlets=0; | ^~~~~ order.c:774:7: warning: unused variable ‘nm’ [-Wunused-variable] 774 | int nm=0, nga=0, ngb=0, nlets=0; | ^~ order.c: In function ‘printXMFAAlign’: order.c:806:27: warning: unused variable ‘nlets’ [-Wunused-variable] 806 | int nm=0, nga=0, ngb=0, nlets=0; | ^~~~~ order.c:806:7: warning: unused variable ‘nm’ [-Wunused-variable] 806 | int nm=0, nga=0, ngb=0, nlets=0; | ^~ order.c: In function ‘readfile’: order.c:62:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 62 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ order.c: In function ‘readSubstMatrix’: order.c:146:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 146 | fscanf (file, "%d", &(substmatrix[(unsigned char) symbs[i]][(unsigned char) symbs[j]])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ order.c:150:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 150 | fscanf (file, "%d", &gapstart); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ order.c:151:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 151 | fscanf (file, "%d", &gapcont); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ order.c: In function ‘printBinAlign’: order.c:726:1: warning: control reaches end of non-void function [-Wreturn-type] 726 | } | ^ order.c: In function ‘printTextAlign’: order.c:770:1: warning: control reaches end of non-void function [-Wreturn-type] 770 | } | ^ order.c: In function ‘printMFAAlign’: order.c:802:1: warning: control reaches end of non-void function [-Wreturn-type] 802 | } | ^ order.c: In function ‘printXMFAAlign’: order.c:834:1: warning: control reaches end of non-void function [-Wreturn-type] 834 | } | ^ fchaos.c: In function ‘doTranslated’: fchaos.c:865:7: warning: ‘temp’ may be used uninitialized [-Wmaybe-uninitialized] 865 | procPairs(currquery, currdbase); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fchaos.c:805:32: note: ‘temp’ was declared here 805 | seq *currquery, *currdbase, *temp; | ^~~~ fchaos.c: In function ‘main’: fchaos.c:955:7: warning: ‘temp’ may be used uninitialized [-Wmaybe-uninitialized] 955 | procPairs(currquery, currdbase); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fchaos.c:882:32: note: ‘temp’ was declared here 882 | seq *currquery, *currdbase, *temp; | ^~~~ thrtrie.c: In function ‘makeAlpha’: thrtrie.c:34:15: warning: array subscript has type ‘char’ [-Wchar-subscripts] 34 | indeces[*alpha] = i; | ^~~~~~ thrtrie.c:36:19: warning: array subscript has type ‘char’ [-Wchar-subscripts] 36 | else indeces [*alpha] = i++; | ^~~~~~ thrtrie.c: In function ‘lookup’: thrtrie.c:43:17: warning: array subscript has type ‘char’ [-Wchar-subscripts] 43 | return indeces[c]; | ^ thrtrie.c: In function ‘insertString’: thrtrie.c:175:10: warning: unused variable ‘j’ [-Wunused-variable] 175 | int i, j, wordlen = root->height, letprev, letcurr; | ^ In file included from thrtrie.c:14: mempage.c: In function ‘MPallfree’: mempage.c:48:1: warning: control reaches end of non-void function [-Wreturn-type] 48 | } | ^ diagmatrix.c: In function ‘DMsetPtr’: diagmatrix.c:155:8: warning: unused variable ‘res’ [-Wunused-variable] 155 | char res; | ^~~ diagmatrix.c:154:19: warning: unused variable ‘loc’ [-Wunused-variable] 154 | int dn = x+y-1, loc; | ^~~ skiplist.c: In function ‘printSLE’: skiplist.c:12:19: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 3 has type ‘void *’ [-Wformat=] 12 | printf(" %d %x\n", tbp->index, tbp->myelem); | ~^ ~~~~~~~~~~~ | | | | unsigned int void * | %p skiplist.c: In function ‘makeSkLst’: skiplist.c:33:7: warning: unused variable ‘i’ [-Wunused-variable] 33 | int i; | ^ skiplist.c: In function ‘SLinsert’: skiplist.c:100:37: warning: unused variable ‘tbe’ [-Wunused-variable] 100 | sle* prev = SLfind(trgt, index), *tbe; | ^~~ global.c: In function ‘ismatch’: global.c:12:17: warning: array subscript has type ‘char’ [-Wchar-subscripts] 12 | return indeces[a] == indeces[b]; | ^ global.c:12:31: warning: array subscript has type ‘char’ [-Wchar-subscripts] 12 | return indeces[a] == indeces[b]; | ^ global.c: In function ‘global’: global.c:34:31: warning: unused variable ‘score’ [-Wunused-variable] 34 | int mm = end2 - start2 + 1, score; | ^~~~~ global.c: In function ‘printalign’: global.c:172:1: warning: control reaches end of non-void function [-Wreturn-type] 172 | } | ^ translate.c: In function ‘toPeptide’: translate.c:9:10: warning: unused variable ‘j’ [-Wunused-variable] 9 | int i, j, sum=0, mask = 0; | ^ gcc -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 -o ../mlagan mlagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG mlagan.c: In function ‘hptrcomp’: mlagan.c:38:7: warning: unused variable ‘jt’ [-Wunused-variable] 38 | int jt = ((hptr*)p2)->isstart; | ^~ mlagan.c: In function ‘readfile’: mlagan.c:93:25: warning: too many arguments for format [-Wformat-extra-args] 93 | fprintf(stderr, "Warning: %c converted to 'N'\n", currchar, alpha); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mlagan.c: In function ‘getAnchsFromFile’: mlagan.c:161:29: warning: unused variable ‘first’ [-Wunused-variable] 161 | hll *myres = 0, *tt = 0, *first = 0; | ^~~~~ mlagan.c: In function ‘generateAnchors’: mlagan.c:213:8: warning: unused variable ‘flip’ [-Wunused-variable] 213 | char flip = 0; | ^~~~ mlagan.c:211:10: warning: unused variable ‘temp’ [-Wunused-variable] 211 | align* temp; | ^~~~ mlagan.c: In function ‘remakeHLL’: mlagan.c:310:10: warning: unused variable ‘bestscore’ [-Wunused-variable] 310 | int i, bestscore=-1; | ^~~~~~~~~ mlagan.c:310:7: warning: unused variable ‘i’ [-Wunused-variable] 310 | int i, bestscore=-1; | ^ mlagan.c:309:20: warning: unused variable ‘t3’ [-Wunused-variable] 309 | hll *temp, *t2, *t3; | ^~ mlagan.c:309:15: warning: unused variable ‘t2’ [-Wunused-variable] 309 | hll *temp, *t2, *t3; | ^~ mlagan.c:307:7: warning: unused variable ‘len’ [-Wunused-variable] 307 | int len; | ^~~ mlagan.c: In function ‘iterativeImprovement’: mlagan.c:485:10: warning: unused variable ‘readd’ [-Wunused-variable] 485 | align *readd, *old, *new; | ^~~~~ mlagan.c:483:12: warning: unused variable ‘oldscore’ [-Wunused-variable] 483 | int i=0, oldscore, cutoff; | ^~~~~~~~ mlagan.c: In function ‘treeToRPN’: mlagan.c:528:16: warning: unused variable ‘j’ [-Wunused-variable] 528 | int i=0; int j, k; | ^ mlagan.c: In function ‘main’: mlagan.c:942:8: warning: unused variable ‘command’ [-Wunused-variable] 942 | char command[256]; | ^~~~~~~ mlagan.c:941:24: warning: unused variable ‘y’ [-Wunused-variable] 941 | int i = 1, j = 1, x, y; | ^ mlagan.c:941:21: warning: unused variable ‘x’ [-Wunused-variable] 941 | int i = 1, j = 1, x, y; | ^ mlagan.c:939:14: warning: unused variable ‘seqfile’ [-Wunused-variable] 939 | FileBuffer seqfile; | ^~~~~~~ mlagan.c: In function ‘readfile’: mlagan.c:79:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 79 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ mlagan.c: In function ‘treeToRPN’: mlagan.c:565:1: warning: control reaches end of non-void function [-Wreturn-type] 565 | } | ^ mlagan.c: In function ‘buildTree’: mlagan.c:662:8: warning: ‘result’ may be used uninitialized [-Wmaybe-uninitialized] 662 | if (names[i] != result) | ^ mlagan.c:599:9: note: ‘result’ was declared here 599 | char *result, *temp; | ^~~~~~ gcc -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 -o ../prolagan prolagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG prolagan.c: In function ‘hptrcomp’: prolagan.c:41:7: warning: unused variable ‘jt’ [-Wunused-variable] 41 | int jt = ((hptr*)p2)->isstart; | ^~ prolagan.c: In function ‘readfile’: prolagan.c:93:25: warning: too many arguments for format [-Wformat-extra-args] 93 | fprintf(stderr, "Warning: %c converted to 'N'\n", currchar, alpha); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ prolagan.c: In function ‘appendAlignProfile’: prolagan.c:163:9: warning: unused variable ‘j’ [-Wunused-variable] 163 | int i,j,k; | ^ prolagan.c: In function ‘readProfile’: prolagan.c:198:11: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 198 | while ( myseq = FileRead( with_gaps,0,0,VER_MLAGAN )) { | ^~~~~ prolagan.c: In function ‘getAnchsFromFile’: prolagan.c:246:29: warning: unused variable ‘first’ [-Wunused-variable] 246 | hll *myres = 0, *tt = 0, *first = 0; | ^~~~~ prolagan.c: In function ‘generateAnchors’: prolagan.c:298:8: warning: unused variable ‘flip’ [-Wunused-variable] 298 | char flip = 0; | ^~~~ prolagan.c:296:10: warning: unused variable ‘temp’ [-Wunused-variable] 296 | align* temp; | ^~~~ prolagan.c: In function ‘remakeHLL’: prolagan.c:395:10: warning: unused variable ‘bestscore’ [-Wunused-variable] 395 | int i, bestscore=-1; | ^~~~~~~~~ prolagan.c:395:7: warning: unused variable ‘i’ [-Wunused-variable] 395 | int i, bestscore=-1; | ^ prolagan.c:394:20: warning: unused variable ‘t3’ [-Wunused-variable] 394 | hll *temp, *t2, *t3; | ^~ prolagan.c:394:15: warning: unused variable ‘t2’ [-Wunused-variable] 394 | hll *temp, *t2, *t3; | ^~ prolagan.c:392:7: warning: unused variable ‘len’ [-Wunused-variable] 392 | int len; | ^~~ prolagan.c: In function ‘processAnchors’: prolagan.c:539:36: warning: unused variable ‘uni’ [-Wunused-variable] 539 | align *first, *second, *result, *uni; | ^~~ prolagan.c: In function ‘iterativeImprovement’: prolagan.c:587:10: warning: unused variable ‘readd’ [-Wunused-variable] 587 | align *readd, *old, *new; | ^~~~~ prolagan.c:585:12: warning: unused variable ‘oldscore’ [-Wunused-variable] 585 | int i=0, oldscore, cutoff; | ^~~~~~~~ prolagan.c: In function ‘treeToRPN’: prolagan.c:630:16: warning: unused variable ‘j’ [-Wunused-variable] 630 | int i=0; int j, k; | ^ prolagan.c: In function ‘main’: prolagan.c:966:8: warning: unused variable ‘table’ [-Wunused-variable] 966 | hll* table[MAX_SEQ][MAX_SEQ]; | ^~~~~ prolagan.c:960:8: warning: unused variable ‘command’ [-Wunused-variable] 960 | char command[256]; | ^~~~~~~ prolagan.c:954:14: warning: unused variable ‘seqfile’ [-Wunused-variable] 954 | FileBuffer seqfile; | ^~~~~~~ prolagan.c: In function ‘readfile’: prolagan.c:79:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 79 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ prolagan.c: In function ‘treeToRPN’: prolagan.c:667:1: warning: control reaches end of non-void function [-Wreturn-type] 667 | } | ^ multial.c: In function ‘getAnchsFromAlign’: multial.c:104:9: warning: unused variable ‘peakfrac’ [-Wunused-variable] 104 | float peakfrac; | ^~~~~~~~ multial.c:103:19: warning: unused variable ‘isfrst’ [-Wunused-variable] 103 | char ingap = 0, isfrst = 1; | ^~~~~~ multial.c:99:30: warning: unused variable ‘peakscore’ [-Wunused-variable] 99 | int currscore=0, oldscore, peakscore; | ^~~~~~~~~ multial.c:99:20: warning: unused variable ‘oldscore’ [-Wunused-variable] 99 | int currscore=0, oldscore, peakscore; | ^~~~~~~~ multial.c: In function ‘unifyAlign’: multial.c:188:28: warning: unused variable ‘tgc’ [-Wunused-variable] 188 | int s1 = 0, s2 = 0, tgs, tgc; | ^~~ multial.c:188:23: warning: unused variable ‘tgs’ [-Wunused-variable] 188 | int s1 = 0, s2 = 0, tgs, tgc; | ^~~ multial.c:187:19: warning: unused variable ‘brcount’ [-Wunused-variable] 187 | int i,j,k, cbc, brcount; | ^~~~~~~ multial.c:187:14: warning: unused variable ‘cbc’ [-Wunused-variable] 187 | int i,j,k, cbc, brcount; | ^~~ multial.c: In function ‘getChain’: multial.c:247:7: warning: unused variable ‘temp’ [-Wunused-variable] 247 | int temp; | ^~~~ multial.c: In function ‘saveNeck’: multial.c:358:6: warning: unused variable ‘second’ [-Wunused-variable] 358 | *second = DMgetDiagStart(mydm, neckdiag, &size2, &x2, &y2); | ^~~~~~ multial.c:357:9: warning: unused variable ‘first’ [-Wunused-variable] 357 | alel *first = DMgetDiagStart(mydm, neckdiag-1, &size1, &x1, &y1), | ^~~~~ multial.c: In function ‘joinAligns’: multial.c:381:10: warning: unused variable ‘n’ [-Wunused-variable] 381 | align *n = a->nextalign, *t; | ^ multial.c: In function ‘openGap’: multial.c:594:25: warning: unused variable ‘i’ [-Wunused-variable] 594 | int alopen, pen, sav, i; | ^ multial.c:594:15: warning: unused variable ‘pen’ [-Wunused-variable] 594 | int alopen, pen, sav, i; | ^~~ multial.c: In function ‘mkBarrel’: multial.c:615:7: warning: unused variable ‘incr’ [-Wunused-variable] 615 | int incr; | ^~~~ multial.c: In function ‘doNW’: multial.c:811:20: warning: variable ‘oldneck’ set but not used [-Wunused-but-set-variable] 811 | int numNecks =0, oldneck =0; | ^~~~~~~ multial.c:808:8: warning: unused variable ‘rh’ [-Wunused-variable] 808 | char rh, ptr=0, isneck; | ^~ multial.c:807:14: warning: unused variable ‘b’ [-Wunused-variable] 807 | align* a, *b; | ^ multial.c:805:11: warning: unused variable ‘prevgap’ [-Wunused-variable] 805 | int tt, prevgap; | ^~~~~~~ multial.c:805:7: warning: unused variable ‘tt’ [-Wunused-variable] 805 | int tt, prevgap; | ^~ multial.c:804:7: warning: unused variable ‘gapend’ [-Wunused-variable] 804 | int gapend[3]; | ^~~~~~ multial.c: In function ‘removeSeqByName’: multial.c:1062:8: warning: variable ‘removed’ set but not used [-Wunused-but-set-variable] 1062 | seq *removed; | ^~~~~~~ multial.c: In function ‘getSeqNum’: multial.c:1073:8: warning: unused variable ‘removed’ [-Wunused-variable] 1073 | seq *removed; | ^~~~~~~ multial.c: In function ‘remapHLLs’: multial.c:1262:24: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 1262 | if (which == 0 && anchs->seq1end - anchs->seq1start < ANCHOR_LENGTH_CUTOFF || | ^ multial.c:1104:43: warning: unused variable ‘olen’ [-Wunused-variable] 1104 | int mybp, i, *searchint, stmybp, mylen, olen, osize; | ^~~~ multial.c: In function ‘hllJoin’: multial.c:1352:10: warning: unused variable ‘j’ [-Wunused-variable] 1352 | int i, j; | ^ multial.c:1352:7: warning: unused variable ‘i’ [-Wunused-variable] 1352 | int i, j; | ^ multial.c: In function ‘minHLL’: multial.c:1368:10: warning: unused variable ‘j’ [-Wunused-variable] 1368 | int i, j; | ^ multial.c: In function ‘mergeHLLs’: multial.c:1408:10: warning: unused variable ‘j’ [-Wunused-variable] 1408 | int i, j, mscore; | ^ multial.c:1408:7: warning: unused variable ‘i’ [-Wunused-variable] 1408 | int i, j, mscore; | ^ multial.c: In function ‘printTextAlign’: multial.c:1466:7: warning: unused variable ‘nlets’ [-Wunused-variable] 1466 | int nlets=0; | ^~~~~ multial.c:1465:13: warning: unused variable ‘s2’ [-Wunused-variable] 1465 | int s1=0, s2=0, c, k, i; | ^~ multial.c:1465:7: warning: unused variable ‘s1’ [-Wunused-variable] 1465 | int s1=0, s2=0, c, k, i; | ^~ multial.c: In function ‘printFASTAAlign’: multial.c:1525:7: warning: unused variable ‘nlets’ [-Wunused-variable] 1525 | int nlets=0; | ^~~~~ multial.c:1524:13: warning: unused variable ‘s2’ [-Wunused-variable] 1524 | int s1=0, s2=0, c, k, i; | ^~ multial.c:1524:7: warning: unused variable ‘s1’ [-Wunused-variable] 1524 | int s1=0, s2=0, c, k, i; | ^~ multial.c: In function ‘printXMFAAlign’: multial.c:1553:7: warning: unused variable ‘nlets’ [-Wunused-variable] 1553 | int nlets=0; | ^~~~~ multial.c:1552:13: warning: unused variable ‘s2’ [-Wunused-variable] 1552 | int s1=0, s2=0, c, k, i; | ^~ multial.c:1552:7: warning: unused variable ‘s1’ [-Wunused-variable] 1552 | int s1=0, s2=0, c, k, i; | ^~ multial.c: At top level: multial.c:581:10: warning: ‘gapcache’ is static but used in inline function ‘endGap2’ which is not static 581 | return gapcache[(v((a->numseq - a->cnts[CNTS_GS][ai] - a->cnts[CNTS_GC][ai]) + b->cnts[CNTS_GE][bi])<<12) | | ^~~~~~~~ multial.c:576:10: warning: ‘gapcache’ is static but used in inline function ‘endGap1’ which is not static 576 | return gapcache[(v((b->numseq - b->cnts[CNTS_GS][bi] - b->cnts[CNTS_GC][bi]) + a->cnts[CNTS_GE][ai]) << 12) | | ^~~~~~~~ multial.c:570:10: warning: ‘gapcache’ is static but used in inline function ‘endGap0’ which is not static 570 | return gapcache[(v(a->cnts[CNTS_GE][ai]+b->cnts[CNTS_GE][bi])<<12) | | ^~~~~~~~ multial.c:563:10: warning: ‘matchcache’ is static but used in inline function ‘scoreOpp’ which is not static 563 | return matchcache[v(other->cnts[0][ow]) | | ^~~~~~~~~~ multial.c: In function ‘scoreLocal’: multial.c:84:1: warning: control reaches end of non-void function [-Wreturn-type] 84 | } | ^ multial.c: In function ‘readSubstMatrix’: multial.c:478:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 478 | fscanf (file, "%d", &k); | ^~~~~~~~~~~~~~~~~~~~~~~ multial.c:486:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 486 | fscanf (file, "%d", &gapstart); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multial.c:487:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 487 | fscanf (file, "%d", &gapcont); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multial.c: In function ‘removeSeqByName’: multial.c:1068:1: warning: control reaches end of non-void function [-Wreturn-type] 1068 | } | ^ multial.c: In function ‘printTextAlign’: multial.c:1521:1: warning: control reaches end of non-void function [-Wreturn-type] 1521 | } | ^ multial.c: In function ‘printFASTAAlign’: multial.c:1549:1: warning: control reaches end of non-void function [-Wreturn-type] 1549 | } | ^ multial.c: In function ‘printXMFAAlign’: multial.c:1579:1: warning: control reaches end of non-void function [-Wreturn-type] 1579 | } | ^ multial.c: In function ‘getAnchsFromAlign’: multial.c:104:9: warning: unused variable ‘peakfrac’ [-Wunused-variable] 104 | float peakfrac; | ^~~~~~~~ multial.c:103:19: warning: unused variable ‘isfrst’ [-Wunused-variable] 103 | char ingap = 0, isfrst = 1; | ^~~~~~ multial.c:99:30: warning: unused variable ‘peakscore’ [-Wunused-variable] 99 | int currscore=0, oldscore, peakscore; | ^~~~~~~~~ multial.c:99:20: warning: unused variable ‘oldscore’ [-Wunused-variable] 99 | int currscore=0, oldscore, peakscore; | ^~~~~~~~ multial.c: In function ‘unifyAlign’: multial.c:188:28: warning: unused variable ‘tgc’ [-Wunused-variable] 188 | int s1 = 0, s2 = 0, tgs, tgc; | ^~~ multial.c:188:23: warning: unused variable ‘tgs’ [-Wunused-variable] 188 | int s1 = 0, s2 = 0, tgs, tgc; | ^~~ multial.c:187:19: warning: unused variable ‘brcount’ [-Wunused-variable] 187 | int i,j,k, cbc, brcount; | ^~~~~~~ multial.c:187:14: warning: unused variable ‘cbc’ [-Wunused-variable] 187 | int i,j,k, cbc, brcount; | ^~~ multial.c: In function ‘getChain’: multial.c:247:7: warning: unused variable ‘temp’ [-Wunused-variable] 247 | int temp; | ^~~~ multial.c: In function ‘saveNeck’: multial.c:358:6: warning: unused variable ‘second’ [-Wunused-variable] 358 | *second = DMgetDiagStart(mydm, neckdiag, &size2, &x2, &y2); | ^~~~~~ multial.c:357:9: warning: unused variable ‘first’ [-Wunused-variable] 357 | alel *first = DMgetDiagStart(mydm, neckdiag-1, &size1, &x1, &y1), | ^~~~~ multial.c: In function ‘joinAligns’: multial.c:381:10: warning: unused variable ‘n’ [-Wunused-variable] 381 | align *n = a->nextalign, *t; | ^ multial.c: In function ‘openGap’: multial.c:594:25: warning: unused variable ‘i’ [-Wunused-variable] 594 | int alopen, pen, sav, i; | ^ multial.c:594:15: warning: unused variable ‘pen’ [-Wunused-variable] 594 | int alopen, pen, sav, i; | ^~~ multial.c: In function ‘mkBarrel’: multial.c:615:7: warning: unused variable ‘incr’ [-Wunused-variable] 615 | int incr; | ^~~~ multial.c: In function ‘doNW’: multial.c:811:20: warning: variable ‘oldneck’ set but not used [-Wunused-but-set-variable] 811 | int numNecks =0, oldneck =0; | ^~~~~~~ multial.c:808:8: warning: unused variable ‘rh’ [-Wunused-variable] 808 | char rh, ptr=0, isneck; | ^~ multial.c:807:14: warning: unused variable ‘b’ [-Wunused-variable] 807 | align* a, *b; | ^ multial.c:805:11: warning: unused variable ‘prevgap’ [-Wunused-variable] 805 | int tt, prevgap; | ^~~~~~~ multial.c:805:7: warning: unused variable ‘tt’ [-Wunused-variable] 805 | int tt, prevgap; | ^~ multial.c:804:7: warning: unused variable ‘gapend’ [-Wunused-variable] 804 | int gapend[3]; | ^~~~~~ multial.c: In function ‘removeSeqByName’: multial.c:1062:8: warning: variable ‘removed’ set but not used [-Wunused-but-set-variable] 1062 | seq *removed; | ^~~~~~~ multial.c: In function ‘getSeqNum’: multial.c:1073:8: warning: unused variable ‘removed’ [-Wunused-variable] 1073 | seq *removed; | ^~~~~~~ multial.c: In function ‘remapHLLs’: multial.c:1262:24: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 1262 | if (which == 0 && anchs->seq1end - anchs->seq1start < ANCHOR_LENGTH_CUTOFF || | ^ multial.c:1104:43: warning: unused variable ‘olen’ [-Wunused-variable] 1104 | int mybp, i, *searchint, stmybp, mylen, olen, osize; | ^~~~ multial.c: In function ‘hllJoin’: multial.c:1352:10: warning: unused variable ‘j’ [-Wunused-variable] 1352 | int i, j; | ^ multial.c:1352:7: warning: unused variable ‘i’ [-Wunused-variable] 1352 | int i, j; | ^ multial.c: In function ‘minHLL’: multial.c:1368:10: warning: unused variable ‘j’ [-Wunused-variable] 1368 | int i, j; | ^ multial.c: In function ‘mergeHLLs’: multial.c:1408:10: warning: unused variable ‘j’ [-Wunused-variable] 1408 | int i, j, mscore; | ^ multial.c:1408:7: warning: unused variable ‘i’ [-Wunused-variable] 1408 | int i, j, mscore; | ^ multial.c: In function ‘printTextAlign’: multial.c:1466:7: warning: unused variable ‘nlets’ [-Wunused-variable] 1466 | int nlets=0; | ^~~~~ multial.c:1465:13: warning: unused variable ‘s2’ [-Wunused-variable] 1465 | int s1=0, s2=0, c, k, i; | ^~ multial.c:1465:7: warning: unused variable ‘s1’ [-Wunused-variable] 1465 | int s1=0, s2=0, c, k, i; | ^~ multial.c: In function ‘printFASTAAlign’: multial.c:1525:7: warning: unused variable ‘nlets’ [-Wunused-variable] 1525 | int nlets=0; | ^~~~~ multial.c:1524:13: warning: unused variable ‘s2’ [-Wunused-variable] 1524 | int s1=0, s2=0, c, k, i; | ^~ multial.c:1524:7: warning: unused variable ‘s1’ [-Wunused-variable] 1524 | int s1=0, s2=0, c, k, i; | ^~ multial.c: In function ‘printXMFAAlign’: multial.c:1553:7: warning: unused variable ‘nlets’ [-Wunused-variable] 1553 | int nlets=0; | ^~~~~ multial.c:1552:13: warning: unused variable ‘s2’ [-Wunused-variable] 1552 | int s1=0, s2=0, c, k, i; | ^~ multial.c:1552:7: warning: unused variable ‘s1’ [-Wunused-variable] 1552 | int s1=0, s2=0, c, k, i; | ^~ multial.c: At top level: multial.c:581:10: warning: ‘gapcache’ is static but used in inline function ‘endGap2’ which is not static 581 | return gapcache[(v((a->numseq - a->cnts[CNTS_GS][ai] - a->cnts[CNTS_GC][ai]) + b->cnts[CNTS_GE][bi])<<12) | | ^~~~~~~~ multial.c:576:10: warning: ‘gapcache’ is static but used in inline function ‘endGap1’ which is not static 576 | return gapcache[(v((b->numseq - b->cnts[CNTS_GS][bi] - b->cnts[CNTS_GC][bi]) + a->cnts[CNTS_GE][ai]) << 12) | | ^~~~~~~~ multial.c:570:10: warning: ‘gapcache’ is static but used in inline function ‘endGap0’ which is not static 570 | return gapcache[(v(a->cnts[CNTS_GE][ai]+b->cnts[CNTS_GE][bi])<<12) | | ^~~~~~~~ multial.c:563:10: warning: ‘matchcache’ is static but used in inline function ‘scoreOpp’ which is not static 563 | return matchcache[v(other->cnts[0][ow]) | | ^~~~~~~~~~ multial.c: In function ‘scoreLocal’: multial.c:84:1: warning: control reaches end of non-void function [-Wreturn-type] 84 | } | ^ multial.c: In function ‘readSubstMatrix’: multial.c:478:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 478 | fscanf (file, "%d", &k); | ^~~~~~~~~~~~~~~~~~~~~~~ multial.c:486:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 486 | fscanf (file, "%d", &gapstart); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multial.c:487:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 487 | fscanf (file, "%d", &gapcont); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multial.c: In function ‘removeSeqByName’: multial.c:1068:1: warning: control reaches end of non-void function [-Wreturn-type] 1068 | } | ^ multial.c: In function ‘printTextAlign’: multial.c:1521:1: warning: control reaches end of non-void function [-Wreturn-type] 1521 | } | ^ multial.c: In function ‘printFASTAAlign’: multial.c:1549:1: warning: control reaches end of non-void function [-Wreturn-type] 1549 | } | ^ multial.c: In function ‘printXMFAAlign’: multial.c:1579:1: warning: control reaches end of non-void function [-Wreturn-type] 1579 | } | ^ diagmatrix.c: In function ‘DMsetPtr’: diagmatrix.c:155:8: warning: unused variable ‘res’ [-Wunused-variable] 155 | char res; | ^~~ diagmatrix.c:154:19: warning: unused variable ‘loc’ [-Wunused-variable] 154 | int dn = x+y-1, loc; | ^~~ skiplist.c: In function ‘printSLE’: skiplist.c:12:19: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 3 has type ‘void *’ [-Wformat=] 12 | printf(" %d %x\n", tbp->index, tbp->myelem); | ~^ ~~~~~~~~~~~ | | | | unsigned int void * | %p skiplist.c: In function ‘makeSkLst’: skiplist.c:33:7: warning: unused variable ‘i’ [-Wunused-variable] 33 | int i; | ^ skiplist.c: In function ‘SLinsert’: skiplist.c:100:37: warning: unused variable ‘tbe’ [-Wunused-variable] 100 | sle* prev = SLfind(trgt, index), *tbe; | ^~~ diagmatrix.c: In function ‘DMsetPtr’: diagmatrix.c:155:8: warning: unused variable ‘res’ [-Wunused-variable] 155 | char res; | ^~~ diagmatrix.c:154:19: warning: unused variable ‘loc’ [-Wunused-variable] 154 | int dn = x+y-1, loc; | ^~~ skiplist.c: In function ‘printSLE’: skiplist.c:12:19: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 3 has type ‘void *’ [-Wformat=] 12 | printf(" %d %x\n", tbp->index, tbp->myelem); | ~^ ~~~~~~~~~~~ | | | | unsigned int void * | %p skiplist.c: In function ‘makeSkLst’: skiplist.c:33:7: warning: unused variable ‘i’ [-Wunused-variable] 33 | int i; | ^ skiplist.c: In function ‘SLinsert’: skiplist.c:100:37: warning: unused variable ‘tbe’ [-Wunused-variable] 100 | sle* prev = SLfind(trgt, index), *tbe; | ^~~ gcc -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 -o ../utils/bin2mf utils/bin2mf.c gcc -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 -o ../utils/bin2bl utils/bin2bl.c utils/bin2bl.c: In function ‘main’: utils/bin2bl.c:52:6: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 52 | if (argv[1][0] == '-') | ^ utils/bin2bl.c:22:7: warning: unused variable ‘width’ [-Wunused-variable] 22 | int width = 60; | ^~~~~ gcc -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 -o ../utils/cextract utils/cextract.c utils/cextract.c: In function ‘getLength’: utils/cextract.c:16:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ utils/cextract.c: In function ‘readfile’: utils/cextract.c:41:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 41 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -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 -o ../utils/cstat utils/cstat.c utils/cextract.c:59:8: warning: ‘ch’ may be used uninitialized [-Wmaybe-uninitialized] 59 | if (ch == '>') ungetc (ch, file); | ^ utils/cextract.c:29:22: note: ‘ch’ was declared here 29 | char buffer[1024], ch; | ^~ utils/cstat.c: In function ‘main’: utils/cstat.c:235:7: warning: unused variable ‘i’ [-Wunused-variable] 235 | int i; | ^ utils/cstat.c: In function ‘cntlets’: utils/cstat.c:45:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ utils/cstat.c: In function ‘readseq’: utils/cstat.c:68:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 68 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ gcc -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 -o ../utils/contigorder utils/contigorder.c utils/contigorder.c: In function ‘getFileInfo’: utils/contigorder.c:15:57: warning: format ‘%s’ expects a matching ‘char *’ argument [-Wformat=] 15 | fprintf (stderr, "contigorder: Error opening file: %s\n"); | ~^ | | | char * utils/contigorder.c:26:25: warning: unknown conversion type character ‘&’ in format [-Wformat=] 26 | fscanf (file, "%&d", &dummy); | ^ utils/contigorder.c:26:23: warning: too many arguments for format [-Wformat-extra-args] 26 | fscanf (file, "%&d", &dummy); | ^~~~~ utils/contigorder.c: In function ‘getScores’: utils/contigorder.c:52:57: warning: format ‘%s’ expects a matching ‘char *’ argument [-Wformat=] 52 | fprintf (stderr, "contigorder: Error opening file: %s\n"); | ~^ | | | char * utils/contigorder.c: In function ‘solveOrder’: utils/contigorder.c:176:30: warning: unused variable ‘ptr’ [-Wunused-variable] 176 | int **best, *first, *last, ptr, newScore, **scoreOf; | ^~~ utils/contigorder.c: In function ‘getFileInfo’: utils/contigorder.c:19:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 19 | fscanf (file, "numContigs = %d\n", numContigs); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/contigorder.c:20:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 20 | fscanf (file, "seqLen = %d\n", seqLen); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/contigorder.c:26:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | fscanf (file, "%&d", &dummy); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/contigorder.c: In function ‘getScores’: utils/contigorder.c:56:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 56 | fscanf (file, "numContigs = %*d\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/contigorder.c:57:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 57 | fscanf (file, "seqLen = %*d\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/contigorder.c:63:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 63 | fscanf (file, "%d", &((*score)[i][j])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/contigorder.c: In function ‘solveOrder’: utils/contigorder.c:247:44: warning: ‘bestState’ may be used uninitialized [-Wmaybe-uninitialized] 247 | for (i = 0; k && i < numCols; i++) if (bestState & (1 << i)){ | ^~~~~~~~~ utils/contigorder.c:177:22: note: ‘bestState’ was declared here 177 | int bestScore = 0, bestState, bestRange, newBest, addedScore; | ^~~~~~~~~ utils/contigorder.c:249:63: warning: ‘bestRange’ may be used uninitialized [-Wmaybe-uninitialized] 249 | for (j = 0; k && j < numRanges; j++) if (last[j] < first[bestRange]){ | ^ utils/contigorder.c:177:33: note: ‘bestRange’ was declared here 177 | int bestScore = 0, bestState, bestRange, newBest, addedScore; | ^~~~~~~~~ gcc -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 -o ../utils/getbounds utils/getbounds.c utils/getbounds.c: In function ‘main’: utils/getbounds.c:32:27: warning: unused variable ‘ext’ [-Wunused-variable] 32 | int S1B, S1E, S2B, S2E, ext, len1, len2; | ^~~ utils/getbounds.c: In function ‘getLength’: utils/getbounds.c:18:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 18 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -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 -o ../utils/getlength utils/getlength.c utils/getlength.c: In function ‘main’: utils/getlength.c:20:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 20 | fgets (buffer, BUF_SIZE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -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 -o ../utils/getoverlap utils/getoverlap.c gcc -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 -o ../utils/rc utils/rc.c utils/rc.c: In function ‘main’: utils/rc.c:39:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | fgets(temp, 255, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~ gcc -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 -o ../utils/seqmerge utils/seqmerge.c utils/seqmerge.c: In function ‘main’: utils/seqmerge.c:33:15: warning: suggest parentheses around comparison in operand of ‘^’ [-Wparentheses] 33 | if (written ^ 60 != 0) printf ("\n"); | ^ utils/seqmerge.c:19:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 19 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -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 -o ../utils/scorealign utils/scorealign.c -lm utils/scorealign.c: In function ‘getSequence’: utils/scorealign.c:262:8: warning: variable ‘prevch’ set but not used [-Wunused-but-set-variable] 262 | char prevch = '~'; | ^~~~~~ utils/scorealign.c: In function ‘getSequences’: utils/scorealign.c:322:10: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 322 | while (newseq = getSequence (file, &si, &ss, &se, &sd, &sc)){ | ^~~~~~ utils/scorealign.c:310:7: warning: unused variable ‘i’ [-Wunused-variable] 310 | int i, si, ss, se; | ^ utils/scorealign.c: In function ‘processSequences’: utils/scorealign.c:353:10: warning: unused variable ‘j’ [-Wunused-variable] 353 | int i, j; | ^ utils/scorealign.c: In function ‘getSequence’: utils/scorealign.c:266:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 266 | fgets (line, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ utils/scorealign.c: In function ‘readScoreMatrix’: utils/scorealign.c:411:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 411 | fgets (line, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ utils/scorealign.c:419:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 419 | fscanf (file, "%1s", &(line[0])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/scorealign.c:421:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 421 | fscanf (file, "%d", &k); | ^~~~~~~~~~~~~~~~~~~~~~~ gcc -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 -o ../utils/scorecontigs utils/scorecontigs.c -lm utils/scorealign.c:426:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 426 | fscanf (file, "%d%d", &gapopen, &gapcont); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/scorecontigs.c: In function ‘analyze’: utils/scorecontigs.c:345:13: warning: unused variable ‘k’ [-Wunused-variable] 345 | int i, j, k; | ^ utils/scorecontigs.c: In function ‘main’: utils/scorecontigs.c:385:38: warning: format ‘%s’ expects argument of type ‘char *’, but argument 6 has type ‘char (*)[1024]’ [-Wformat=] 385 | if (fscanf (filelist, "%d %d %d %s\n", &(num[numseqs]), &(offs1[numseqs]), &(offs2[numseqs]), &(contignames[numseqs])) == 4){ | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | char * char (*)[1024] utils/scorecontigs.c: In function ‘cntlets’: utils/scorecontigs.c:56:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 56 | fgets(temp, 1024, input); | ^~~~~~~~~~~~~~~~~~~~~~~~ utils/scorecontigs.c: In function ‘readseq’: utils/scorecontigs.c:82:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 82 | fgets (temp, 1024, input); | ^~~~~~~~~~~~~~~~~~~~~~~~~ gcc -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 -o ../utils/getcontigpos utils/getcontigpos.c gcc -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 -o ../utils/fa2xfa utils/fa2xfa.c utils/getcontigpos.c: In function ‘print’: utils/getcontigpos.c:66:46: warning: unused variable ‘j’ [-Wunused-variable] 66 | int i = 0, pos = 0, pos2 = 0, written = 0, j = 0; | ^ utils/getcontigpos.c:66:33: warning: unused variable ‘written’ [-Wunused-variable] 66 | int i = 0, pos = 0, pos2 = 0, written = 0, j = 0; | ^~~~~~~ utils/getcontigpos.c: In function ‘getLength’: utils/getcontigpos.c:16:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ utils/getcontigpos.c: In function ‘readfile’: utils/getcontigpos.c:41:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 41 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ utils/fa2xfa.c: In function ‘print’: utils/fa2xfa.c:81:36: warning: unused variable ‘j’ [-Wunused-variable] 81 | int i = 0, pos = 0, written = 0, j = 0; | ^ utils/fa2xfa.c:81:14: warning: unused variable ‘pos’ [-Wunused-variable] 81 | int i = 0, pos = 0, written = 0, j = 0; | ^~~ utils/fa2xfa.c: In function ‘getLength’: utils/fa2xfa.c:30:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 30 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ utils/fa2xfa.c: In function ‘readfile’: utils/fa2xfa.c:55:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 55 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ utils/getcontigpos.c:59:8: warning: ‘ch’ may be used uninitialized [-Wmaybe-uninitialized] 59 | if (ch == '>') ungetc (ch, file); | ^ utils/getcontigpos.c:29:22: note: ‘ch’ was declared here 29 | char buffer[1024], ch; | ^~ utils/fa2xfa.c:74:8: warning: ‘ch’ may be used uninitialized [-Wmaybe-uninitialized] 74 | if (ch == '>') ungetc (ch, file); | ^ utils/fa2xfa.c:43:22: note: ‘ch’ was declared here 43 | char buffer[1024], ch; | ^~ g++ -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 -o ../utils/Glue utils/Glue.cpp g++ -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 -o ../utils/dotplot utils/dotplot.cpp utils/dotplot.cpp: In function ‘int main(int, char**)’: utils/dotplot.cpp:6:27: warning: variable ‘pa’ set but not used [-Wunused-but-set-variable] 6 | int s1b, s1e, s2b, s2e, pa, pb, maxa = 0, maxb = 0; | ^~ utils/dotplot.cpp:6:31: warning: variable ‘pb’ set but not used [-Wunused-but-set-variable] 6 | int s1b, s1e, s2b, s2e, pa, pb, maxa = 0, maxb = 0; | ^~ utils/dotplot.cpp:37:11: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | fgets (buffer, 105, file); | ~~~~~~^~~~~~~~~~~~~~~~~~~ utils/dotplot.cpp:74:11: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 74 | fgets (buffer, 105, file); | ~~~~~~^~~~~~~~~~~~~~~~~~~ utils/dotplot.cpp:97:11: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 97 | fgets (buffer, 105, file); | ~~~~~~^~~~~~~~~~~~~~~~~~~ gcc -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 -o ../utils/overlay utils/overlay.c utils/overlay.c: In function ‘read_align’: utils/overlay.c:102:30: warning: unused variable ‘tt’ [-Wunused-variable] 102 | char currchar, checkchar, *tt; | ^~ utils/overlay.c: In function ‘read_sequences’: utils/overlay.c:177:19: warning: unused variable ‘breaker’ [-Wunused-variable] 177 | int i, j, kmer, breaker; | ^~~~~~~ utils/overlay.c:177:13: warning: unused variable ‘kmer’ [-Wunused-variable] 177 | int i, j, kmer, breaker; | ^~~~ utils/overlay.c:177:10: warning: unused variable ‘j’ [-Wunused-variable] 177 | int i, j, kmer, breaker; | ^ utils/overlay.c: In function ‘main’: utils/overlay.c:233:16: warning: unused variable ‘test’ [-Wunused-variable] 233 | float ttree, test; | ^~~~ utils/overlay.c:233:9: warning: unused variable ‘ttree’ [-Wunused-variable] 233 | float ttree, test; | ^~~~~ utils/overlay.c:232:7: warning: unused variable ‘moved’ [-Wunused-variable] 232 | int moved, i; | ^~~~~ utils/overlay.c:231:8: warning: unused variable ‘string_tree’ [-Wunused-variable] 231 | char string_tree[16537]; //noone will ever need more :))) | ^~~~~~~~~~~ utils/overlay.c: In function ‘read_align’: utils/overlay.c:110:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 110 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ utils/overlay.c:135:5: warning: ‘__strncpy_chk’ specified bound depends on the length of the source argument [-Wstringop-truncation] 135 | strncpy(allseqs[target]->seqname, temp, strlen(temp)+1); | ^ utils/overlay.c:135:45: note: length computed here 135 | strncpy(allseqs[target]->seqname, temp, strlen(temp)+1); | ^~~~~~~~~~~~ utils/Glue.cpp: In function ‘void readScoreMatrix(char*)’: utils/Glue.cpp:33:15: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 33 | lagan_dir = "/usr/lib64/lagan"; | ^~~~~~~~~~~~~~~~~~ utils/Glue.cpp: In function ‘void calculateScoreMatrix(int)’: utils/Glue.cpp:60:17: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 60 | char *alpha = "ATCG"; | ^~~~~~ utils/Glue.cpp:11:32: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 11 | #define NUCLEOTIDE_MATRIX_FILE "nucmatrix.txt" | ^~~~~~~~~~~~~~~ utils/Glue.cpp:68:22: note: in expansion of macro ‘NUCLEOTIDE_MATRIX_FILE’ 68 | readScoreMatrix (NUCLEOTIDE_MATRIX_FILE); | ^~~~~~~~~~~~~~~~~~~~~~ utils/Glue.cpp: In function ‘int countLets(SafeVector&)’: utils/Glue.cpp:228:24: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 228 | if (data[i] >= 'A' && data[i] <= 'Z' || data[i] >= 'a' && data[i] <= 'z') utils/Glue.cpp: In function ‘int main(int, char**)’: utils/Glue.cpp:372:19: warning: variable ‘end1’ set but not used [-Wunused-but-set-variable] 372 | int begin1 = 1, end1 = 1; | ^~~~ utils/Glue.cpp: In function ‘void readScoreMatrix(char*)’: utils/Glue.cpp:40:9: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 40 | fgets (line, 1024, file); | ~~~~~~^~~~~~~~~~~~~~~~~~ utils/Glue.cpp:48:12: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 48 | fscanf (file, "%1s", &(line[0])); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ utils/Glue.cpp:50:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 50 | fscanf (file, "%d", &k); | ~~~~~~~^~~~~~~~~~~~~~~~ utils/Glue.cpp:55:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 55 | fscanf (file, "%d%d", &gapopen, &gapcont); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ (cd glocal; make) make[2]: Entering directory '/builddir/build/BUILD/lagan-2.0-build/lagan20/src/glocal' g++ -Wno-deprecated -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 -I./ -c glocal.cpp g++ -Wno-deprecated -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 -I./ -c io.cpp In file included from ./score.h:4, from glocal.cpp:1: glocal.cpp: In function ‘int main(int, char**)’: ./structs.h:31:50: warning: suggest parentheses around ‘+’ inside ‘<<’ [-Wparentheses] 31 | #define TOTALSHIFT UPSTRANDBITS + DOWNSTRANDBITS + RELPOSBITS | ^ glocal.cpp:64:23: note: in expansion of macro ‘TOTALSHIFT’ 64 | for (i=0;i<1<>’ [-Wparentheses] 30 | #define RELPOSSHIFT UPSTRANDBITS + DOWNSTRANDBITS | ^ leftinfluence.cpp:135:29: note: in expansion of macro ‘RELPOSSHIFT’ 135 | if (((scoreIndex >> RELPOSSHIFT) & 1) == LEFT) { | ^~~~~~~~~~~ In file included from ./rightinfluence.h:4, from rightinfluence.cpp:1: rightinfluence.cpp: In function ‘void initRI(RI*, long long int)’: ./structs.h:30:34: warning: suggest parentheses around ‘+’ inside ‘>>’ [-Wparentheses] 30 | #define RELPOSSHIFT UPSTRANDBITS + DOWNSTRANDBITS | ^ rightinfluence.cpp:9:29: note: in expansion of macro ‘RELPOSSHIFT’ 9 | if (((scoreIndex >> RELPOSSHIFT) & 1) == LEFT) { | ^~~~~~~~~~~ rightinfluence.cpp: In function ‘long long int RICommitEndPoint(RI*, Fragment*)’: ./structs.h:30:34: warning: suggest parentheses around ‘+’ inside ‘<<’ [-Wparentheses] 30 | #define RELPOSSHIFT UPSTRANDBITS + DOWNSTRANDBITS | ^ rightinfluence.cpp:119:85: note: in expansion of macro ‘RELPOSSHIFT’ 119 | int possibleCase = NEGATIVE << DOWNSTRANDSHIFT | NEGATIVE <>’ [-Wparentheses] 30 | #define RELPOSSHIFT UPSTRANDBITS + DOWNSTRANDBITS | ^ score.cpp:143:33: note: in expansion of macro ‘RELPOSSHIFT’ 143 | if (ret_case >> RELPOSSHIFT != UNRELATED) { | ^~~~~~~~~~~ score.cpp: In function ‘float fragmentSetScore(Fragment*, Fragment*, LI*, RI*, long long int)’: ./structs.h:30:34: warning: suggest parentheses around ‘+’ inside ‘<<’ [-Wparentheses] 30 | #define RELPOSSHIFT UPSTRANDBITS + DOWNSTRANDBITS | ^ score.cpp:185:134: note: in expansion of macro ‘RELPOSSHIFT’ 185 | tempScore = scoreAll(owner,current, current->strand << DOWNSTRANDSHIFT | owner->strand <= 5.5.0 perl(Cwd) perl(File::Basename) perl(File::Copy) perl(File::Path) perl(Getopt::Long) perl(IO::Handle) perl(IPC::Open2) perl(constant) perl(strict) perl(warnings) rtld(GNU_HASH) Processing files: lagan-debugsource-2.0-42.fc42.x86_64 Provides: lagan-debugsource = 2.0-42.fc42 lagan-debugsource(x86-64) = 2.0-42.fc42 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: lagan-debuginfo-2.0-42.fc42.x86_64 Provides: debuginfo(build-id) = 00791e30f9f51cbbfa0380f01beeb38800195aa2 debuginfo(build-id) = 0665b0c81479780bb86de74620256f9d74dfcb8e debuginfo(build-id) = 1f77b5d0e439484c69d145f10ecabcdf62045808 debuginfo(build-id) = 26bdea13102b51f21c31f5f85274ec5c567cdbe6 debuginfo(build-id) = 2e8f26dacb0eadba071ba030968d0ce265edbba1 debuginfo(build-id) = 37dc44b4a93092397cb3eca2da052a391f5b46b4 debuginfo(build-id) = 40b07bf479457ae8e324bd0502fba5acc8ebbd3a debuginfo(build-id) = 4baa965168471fe8d6472e5af10d52bcac22239a debuginfo(build-id) = 5c6565a1e9e30eea17e0f20d18a5b1ee826e5fc8 debuginfo(build-id) = 6bd0efcf824498a42538d2bfd732803ad2cecfcb debuginfo(build-id) = 76f1b6dc52915412b7453608d21c189e6b8c29ea debuginfo(build-id) = 8012a600d9ca73733cdd08f4c02209187889beb1 debuginfo(build-id) = 8c8992d679b36f5545288c3b7acd108cb425d48e debuginfo(build-id) = 91b436222b47ce022a92602644cf77162e8dd946 debuginfo(build-id) = 92846a99a667fd0ba4abeb0146dcf8ec3ead3cc8 debuginfo(build-id) = b578e84433956bb398544427da1df53004246e5d debuginfo(build-id) = c0fc880128383e861ee280688390d39f8ea8ae45 debuginfo(build-id) = cadb9a04e1aef13ad757c925961fe6d71365b1ce debuginfo(build-id) = dd12930cb0cce2dfbaa01074065f125b5714385c debuginfo(build-id) = e585ae909765e2f1a978d7c6e71aa98ba2ff614a debuginfo(build-id) = eaae01276bf8aeff5403817d99a2263e9716a396 debuginfo(build-id) = ef8e8960537705f8af3071fdced12848c11253b5 debuginfo(build-id) = fb4489828b1b9bf6e9bb10252cac090ec18710a4 lagan-debuginfo = 2.0-42.fc42 lagan-debuginfo(x86-64) = 2.0-42.fc42 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: lagan-debugsource(x86-64) = 2.0-42.fc42 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILD/lagan-2.0-build/BUILDROOT Wrote: /builddir/build/RPMS/lagan-2.0-42.fc42.x86_64.rpm Wrote: /builddir/build/RPMS/lagan-debugsource-2.0-42.fc42.x86_64.rpm Wrote: /builddir/build/RPMS/lagan-debuginfo-2.0-42.fc42.x86_64.rpm Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.ARh2CL + umask 022 + cd /builddir/build/BUILD/lagan-2.0-build + test -d /builddir/build/BUILD/lagan-2.0-build + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w /builddir/build/BUILD/lagan-2.0-build + rm -rf /builddir/build/BUILD/lagan-2.0-build + RPM_EC=0 ++ jobs -p + exit 0 Finish: rpmbuild lagan-2.0-42.fc42.src.rpm Finish: build phase for lagan-2.0-42.fc42.src.rpm INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-x86_64-1734698755.945548/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/lagan-2.0-42.fc42.src.rpm) Config(child) 0 minutes 28 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": "lagan-debugsource", "epoch": null, "version": "2.0", "release": "42.fc42", "arch": "x86_64" }, { "name": "lagan", "epoch": null, "version": "2.0", "release": "42.fc42", "arch": "src" }, { "name": "lagan-debuginfo", "epoch": null, "version": "2.0", "release": "42.fc42", "arch": "x86_64" }, { "name": "lagan", "epoch": null, "version": "2.0", "release": "42.fc42", "arch": "x86_64" } ] } RPMResults finished