Warning: Permanently added '54.221.33.239' (ED25519) to the list of known hosts. Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-_4un3wja/python-pyhmmer/python-pyhmmer.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-_4un3wja/python-pyhmmer --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1728412359.829131 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 5.9 starting (python version = 3.12.1, NVR = mock-5.9-1.fc39), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-_4un3wja/python-pyhmmer/python-pyhmmer.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-_4un3wja/python-pyhmmer --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1728412359.829131 -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-_4un3wja/python-pyhmmer/python-pyhmmer.spec) Config(fedora-41-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-41-x86_64-bootstrap-1728412359.829131/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:41 INFO: Pulling image: registry.fedoraproject.org/fedora:41 INFO: Copy content of container registry.fedoraproject.org/fedora:41 to /var/lib/mock/fedora-41-x86_64-bootstrap-1728412359.829131/root INFO: Checking that registry.fedoraproject.org/fedora:41 image matches host's architecture INFO: mounting registry.fedoraproject.org/fedora:41 with podman image mount INFO: image registry.fedoraproject.org/fedora:41 as /var/lib/containers/storage/overlay/235841db8784fe7d0447b027207a6784cc2861ee578f6fda51c59150d70ed3df/merged INFO: umounting image registry.fedoraproject.org/fedora:41 (/var/lib/containers/storage/overlay/235841db8784fe7d0447b027207a6784cc2861ee578f6fda51c59150d70ed3df/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-41-x86_64-1728412359.829131/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin INFO: Package manager dnf5 detected and used (direct choice) INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-4.19.94-1.fc41.x86_64 rpm-sequoia-1.7.0-2.fc41.x86_64 dnf5-5.2.6.2-1.fc41.x86_64 dnf5-plugins-5.2.6.2-1.fc41.x86_64 Start: installing minimal buildroot with dnf5 Updating and loading repositories: updates 100% | 104.1 KiB/s | 28.6 KiB | 00m00s fedora 100% | 95.0 KiB/s | 25.9 KiB | 00m00s Copr repository 100% | 102.7 KiB/s | 1.5 KiB | 00m00s Copr repository 100% | 150.1 MiB/s | 41.9 MiB | 00m00s Repositories loaded. Package Arch Version Repository Size Installing group/module packages: bash x86_64 5.2.32-1.fc41 fedora 8.2 MiB bzip2 x86_64 1.0.8-19.fc41 fedora 95.7 KiB coreutils x86_64 9.5-10.fc41 fedora 5.6 MiB cpio x86_64 2.15-2.fc41 fedora 1.1 MiB diffutils x86_64 3.10-8.fc41 fedora 1.6 MiB fedora-release-common noarch 41-0.21 fedora 19.4 KiB findutils x86_64 1:4.10.0-4.fc41 fedora 1.8 MiB gawk x86_64 5.3.0-4.fc41 fedora 1.7 MiB glibc-minimal-langpack x86_64 2.40-3.fc41 fedora 0.0 B grep x86_64 3.11-9.fc41 fedora 1.0 MiB gzip x86_64 1.13-2.fc41 fedora 389.0 KiB info x86_64 7.1-3.fc41 fedora 361.8 KiB patch x86_64 2.7.6-25.fc41 fedora 266.7 KiB redhat-rpm-config noarch 293-1.fc41 fedora 183.5 KiB rpm-build x86_64 4.19.94-1.fc41 fedora 194.3 KiB sed x86_64 4.9-3.fc41 fedora 861.5 KiB shadow-utils x86_64 2:4.15.1-11.fc41 fedora 4.1 MiB tar x86_64 2:1.35-4.fc41 fedora 2.9 MiB unzip x86_64 6.0-64.fc41 fedora 386.8 KiB util-linux x86_64 2.40.2-4.fc41 fedora 3.7 MiB which x86_64 2.21-42.fc41 fedora 80.2 KiB xz x86_64 1:5.6.2-2.fc41 fedora 1.2 MiB Installing dependencies: add-determinism x86_64 0.3.6-1.fc41 fedora 2.2 MiB alternatives x86_64 1.30-1.fc41 fedora 66.3 KiB ansible-srpm-macros noarch 1-16.fc41 fedora 35.7 KiB audit-libs x86_64 4.0.2-1.fc41 fedora 331.3 KiB authselect x86_64 1.5.0-7.fc41 fedora 153.5 KiB authselect-libs x86_64 1.5.0-7.fc41 fedora 818.3 KiB basesystem noarch 11-21.fc41 fedora 0.0 B binutils x86_64 2.43.1-2.fc41 fedora 27.5 MiB build-reproducibility-srpm-macros noarch 0.3.6-1.fc41 fedora 735.0 B bzip2-libs x86_64 1.0.8-19.fc41 fedora 80.7 KiB ca-certificates noarch 2024.2.69_v8.0.401-1.0.fc41 fedora 2.4 MiB coreutils-common x86_64 9.5-10.fc41 fedora 11.2 MiB cracklib x86_64 2.9.11-6.fc41 fedora 238.9 KiB crypto-policies noarch 20240826-1.gite824389.fc41 fedora 136.9 KiB curl x86_64 8.9.1-2.fc41 fedora 796.2 KiB cyrus-sasl-lib x86_64 2.1.28-27.fc41 fedora 2.3 MiB debugedit x86_64 5.0-17.fc41 fedora 199.3 KiB dwz x86_64 0.15-7.fc41 fedora 290.9 KiB ed x86_64 1.20.2-2.fc41 fedora 146.9 KiB efi-srpm-macros noarch 5-12.fc41 fedora 40.1 KiB elfutils x86_64 0.191-8.fc41 fedora 2.6 MiB elfutils-debuginfod-client x86_64 0.191-8.fc41 fedora 64.9 KiB elfutils-default-yama-scope noarch 0.191-8.fc41 fedora 1.8 KiB elfutils-libelf x86_64 0.191-8.fc41 fedora 1.2 MiB elfutils-libs x86_64 0.191-8.fc41 fedora 646.2 KiB fedora-gpg-keys noarch 41-0.5 fedora 126.4 KiB fedora-release noarch 41-0.21 fedora 0.0 B fedora-release-identity-basic noarch 41-0.21 fedora 684.0 B fedora-repos noarch 41-0.5 fedora 4.9 KiB file x86_64 5.45-7.fc41 fedora 103.5 KiB file-libs x86_64 5.45-7.fc41 fedora 9.9 MiB filesystem x86_64 3.18-23.fc41 fedora 106.0 B fonts-srpm-macros noarch 1:2.0.5-17.fc41 fedora 55.8 KiB forge-srpm-macros noarch 0.3.2-1.fc41 fedora 39.0 KiB fpc-srpm-macros noarch 1.3-13.fc41 fedora 144.0 B gdb-minimal x86_64 15.1-1.fc41 fedora 13.0 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 1.9.1-2.fc41 fedora 747.0 B glibc x86_64 2.40-3.fc41 fedora 6.7 MiB glibc-common x86_64 2.40-3.fc41 fedora 1.0 MiB glibc-gconv-extra x86_64 2.40-3.fc41 fedora 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 3.6.0-3.fc41 fedora 60.8 KiB jansson x86_64 2.13.1-10.fc41 fedora 88.3 KiB kernel-srpm-macros noarch 1.0-24.fc41 fedora 1.9 KiB keyutils-libs x86_64 1.6.3-4.fc41 fedora 54.4 KiB krb5-libs x86_64 1.21.3-2.fc41 fedora 2.3 MiB libacl x86_64 2.3.2-2.fc41 fedora 40.0 KiB libarchive x86_64 3.7.4-3.fc41 fedora 922.6 KiB libattr x86_64 2.5.2-4.fc41 fedora 28.5 KiB libblkid x86_64 2.40.2-4.fc41 fedora 258.5 KiB libbrotli x86_64 1.1.0-5.fc41 fedora 837.6 KiB libcap x86_64 2.70-4.fc41 fedora 220.2 KiB libcap-ng x86_64 0.8.5-3.fc41 fedora 69.2 KiB libcom_err x86_64 1.47.1-3.fc41 fedora 67.2 KiB libcurl x86_64 8.9.1-2.fc41 fedora 818.1 KiB libeconf x86_64 0.6.2-3.fc41 fedora 58.0 KiB libevent x86_64 2.1.12-14.fc41 fedora 895.7 KiB libfdisk x86_64 2.40.2-4.fc41 fedora 362.9 KiB libffi x86_64 3.4.6-3.fc41 fedora 86.4 KiB libgcc x86_64 14.2.1-3.fc41 fedora 274.6 KiB libgomp x86_64 14.2.1-3.fc41 fedora 523.5 KiB libidn2 x86_64 2.3.7-2.fc41 fedora 329.1 KiB libmount x86_64 2.40.2-4.fc41 fedora 351.8 KiB libnghttp2 x86_64 1.62.1-2.fc41 fedora 166.1 KiB libnsl2 x86_64 2.0.1-2.fc41 fedora 57.9 KiB libpkgconf x86_64 2.3.0-1.fc41 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 3.7-5.fc41 fedora 181.0 KiB libsemanage x86_64 3.7-2.fc41 fedora 293.5 KiB libsepol x86_64 3.7-2.fc41 fedora 817.8 KiB libsmartcols x86_64 2.40.2-4.fc41 fedora 180.4 KiB libssh x86_64 0.10.6-8.fc41 fedora 513.3 KiB libssh-config noarch 0.10.6-8.fc41 fedora 277.0 B libstdc++ x86_64 14.2.1-3.fc41 fedora 2.8 MiB libtasn1 x86_64 4.19.0-9.fc41 fedora 175.7 KiB libtirpc x86_64 1.3.5-0.fc41 fedora 202.7 KiB libtool-ltdl x86_64 2.4.7-12.fc41 fedora 66.2 KiB libunistring x86_64 1.1-8.fc41 fedora 1.7 MiB libutempter x86_64 1.2.1-15.fc41 fedora 57.7 KiB libuuid x86_64 2.40.2-4.fc41 fedora 37.5 KiB libverto x86_64 0.3.2-9.fc41 fedora 29.5 KiB libxcrypt x86_64 4.4.36-7.fc41 fedora 266.8 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 5.4.6-6.fc41 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 2.6.8-5.fc41 fedora 644.2 KiB openssl-libs x86_64 1:3.2.2-9.fc41 fedora 7.8 MiB p11-kit x86_64 0.25.5-3.fc41 fedora 2.2 MiB p11-kit-trust x86_64 0.25.5-3.fc41 fedora 391.4 KiB package-notes-srpm-macros noarch 0.5-12.fc41 fedora 1.6 KiB pam x86_64 1.6.1-5.fc41 fedora 1.8 MiB pam-libs x86_64 1.6.1-5.fc41 fedora 139.0 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.fc41 fedora 88.6 KiB pkgconf-m4 noarch 2.3.0-1.fc41 fedora 14.4 KiB pkgconf-pkg-config x86_64 2.3.0-1.fc41 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 1.15.0-1.fc41 fedora 1.9 KiB python-srpm-macros noarch 3.13-3.fc41 fedora 51.0 KiB qt5-srpm-macros noarch 5.15.15-1.fc41 fedora 500.0 B qt6-srpm-macros noarch 6.7.2-3.fc41 fedora 456.0 B readline x86_64 8.2-10.fc41 fedora 493.2 KiB rpm x86_64 4.19.94-1.fc41 fedora 3.1 MiB rpm-build-libs x86_64 4.19.94-1.fc41 fedora 206.7 KiB rpm-libs x86_64 4.19.94-1.fc41 fedora 721.9 KiB rpm-sequoia x86_64 1.7.0-2.fc41 fedora 2.4 MiB rust-srpm-macros noarch 26.3-3.fc41 fedora 4.8 KiB setup noarch 2.15.0-5.fc41 fedora 720.7 KiB sqlite-libs x86_64 3.46.1-1.fc41 fedora 1.4 MiB systemd-libs x86_64 256.6-1.fc41 fedora 2.0 MiB util-linux-core x86_64 2.40.2-4.fc41 fedora 1.5 MiB xxhash-libs x86_64 0.8.2-3.fc41 fedora 88.5 KiB xz-libs x86_64 1:5.6.2-2.fc41 fedora 214.4 KiB zig-srpm-macros noarch 1-3.fc41 fedora 1.1 KiB zip x86_64 3.0-41.fc41 fedora 703.2 KiB zlib-ng-compat x86_64 2.1.7-3.fc41 fedora 134.0 KiB zstd x86_64 1.5.6-2.fc41 fedora 1.7 MiB Installing groups: Buildsystem building group Transaction Summary: Installing: 153 packages Total size of inbound packages is 53 MiB. Need to download 0 B. After this operation, 180 MiB extra will be used (install 180 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] bzip2-0:1.0.8-19.fc41.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] redhat-rpm-config-0:293-1.fc41.no 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] rpm-build-0:4.19.94-1.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] unzip-0:6.0-64.fc41.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded 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Already downloaded -------------------------------------------------------------------------------- [153/153] Total 100% | 0.0 B/s | 0.0 B | 00m00s Running transaction Importing PGP 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. [ 1/155] Verify package files 100% | 921.0 B/s | 153.0 B | 00m00s [ 2/155] Prepare transaction 100% | 4.4 KiB/s | 153.0 B | 00m00s [ 3/155] Installing libgcc-0:14.2.1-3. 100% | 269.8 MiB/s | 276.3 KiB | 00m00s [ 4/155] Installing libssh-config-0:0. 100% | 0.0 B/s | 816.0 B | 00m00s [ 5/155] Installing publicsuffix-list- 100% | 0.0 B/s | 68.3 KiB | 00m00s [ 6/155] Installing fedora-release-ide 100% | 0.0 B/s | 940.0 B | 00m00s [ 7/155] Installing fedora-gpg-keys-0: 100% | 56.1 MiB/s | 172.2 KiB | 00m00s [ 8/155] Installing fedora-repos-0:41- 100% | 0.0 B/s | 5.7 KiB | 00m00s [ 9/155] Installing fedora-release-com 100% | 23.1 MiB/s | 23.7 KiB | 00m00s [ 10/155] Installing fedora-release-0:4 100% | 0.0 B/s | 124.0 B | 00m00s [ 11/155] Installing setup-0:2.15.0-5.f 100% | 59.1 MiB/s | 726.1 KiB | 00m00s [ 12/155] Installing filesystem-0:3.18- 100% | 3.6 MiB/s | 212.5 KiB | 00m00s [ 13/155] Installing basesystem-0:11-21 100% | 0.0 B/s | 124.0 B | 00m00s [ 14/155] Installing pkgconf-m4-0:2.3.0 100% | 0.0 B/s | 14.8 KiB | 00m00s [ 15/155] Installing pcre2-syntax-0:10. 100% | 248.1 MiB/s | 254.1 KiB | 00m00s [ 16/155] Installing ncurses-base-0:6.5 100% | 85.9 MiB/s | 351.7 KiB | 00m00s [ 17/155] Installing glibc-minimal-lang 100% | 0.0 B/s | 124.0 B | 00m00s [ 18/155] Installing ncurses-libs-0:6.5 100% | 239.7 MiB/s | 981.8 KiB | 00m00s warning: posix.fork(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead warning: posix.wait(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead warning: posix.exec(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead warning: posix.fork(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead warning: posix.wait(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead warning: posix.exec(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead [ 19/155] Installing glibc-0:2.40-3.fc4 100% | 202.3 MiB/s | 6.7 MiB | 00m00s [ 20/155] Installing bash-0:5.2.32-1.fc 100% | 408.5 MiB/s | 8.2 MiB | 00m00s [ 21/155] Installing glibc-common-0:2.4 100% | 209.4 MiB/s | 1.0 MiB | 00m00s warning: posix.fork(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead warning: posix.wait(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead warning: posix.exec(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead [ 22/155] Installing glibc-gconv-extra- 100% | 245.4 MiB/s | 8.1 MiB | 00m00s [ 23/155] Installing zlib-ng-compat-0:2 100% | 131.6 MiB/s | 134.8 KiB | 00m00s [ 24/155] Installing bzip2-libs-0:1.0.8 100% | 0.0 B/s | 81.8 KiB | 00m00s [ 25/155] 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13.0 MiB | 00m00s [127/155] Installing debugedit-0:5.0-17 100% | 197.3 MiB/s | 202.0 KiB | 00m00s [128/155] Installing curl-0:8.9.1-2.fc4 100% | 60.0 MiB/s | 798.6 KiB | 00m00s [129/155] Installing rpm-0:4.19.94-1.fc 100% | 192.5 MiB/s | 2.5 MiB | 00m00s [130/155] Installing efi-srpm-macros-0: 100% | 40.2 MiB/s | 41.2 KiB | 00m00s [131/155] Installing lua-srpm-macros-0: 100% | 0.0 B/s | 1.9 KiB | 00m00s [132/155] Installing zig-srpm-macros-0: 100% | 0.0 B/s | 1.7 KiB | 00m00s [133/155] Installing rust-srpm-macros-0 100% | 0.0 B/s | 5.6 KiB | 00m00s [134/155] Installing qt6-srpm-macros-0: 100% | 0.0 B/s | 732.0 B | 00m00s [135/155] Installing qt5-srpm-macros-0: 100% | 0.0 B/s | 776.0 B | 00m00s [136/155] Installing perl-srpm-macros-0 100% | 0.0 B/s | 1.1 KiB | 00m00s [137/155] Installing package-notes-srpm 100% | 0.0 B/s | 2.0 KiB | 00m00s [138/155] Installing openblas-srpm-macr 100% | 0.0 B/s | 392.0 B | 00m00s [139/155] Installing ocaml-srpm-macros- 100% | 0.0 B/s | 2.2 KiB | 00m00s [140/155] Installing kernel-srpm-macros 100% | 0.0 B/s | 2.3 KiB | 00m00s [141/155] Installing gnat-srpm-macros-0 100% | 0.0 B/s | 1.3 KiB | 00m00s [142/155] Installing ghc-srpm-macros-0: 100% | 0.0 B/s | 1.0 KiB | 00m00s [143/155] Installing fpc-srpm-macros-0: 100% | 0.0 B/s | 420.0 B | 00m00s [144/155] Installing ansible-srpm-macro 100% | 0.0 B/s | 36.2 KiB | 00m00s [145/155] Installing fonts-srpm-macros- 100% | 0.0 B/s | 57.0 KiB | 00m00s [146/155] Installing forge-srpm-macros- 100% | 0.0 B/s | 40.4 KiB | 00m00s [147/155] Installing go-srpm-macros-0:3 100% | 0.0 B/s | 62.0 KiB | 00m00s [148/155] Installing python-srpm-macros 100% | 0.0 B/s | 52.2 KiB | 00m00s [149/155] Installing redhat-rpm-config- 100% | 185.6 MiB/s | 190.1 KiB | 00m00s [150/155] Installing rpm-build-0:4.19.9 100% | 99.0 MiB/s | 202.8 KiB | 00m00s [151/155] Installing pyproject-srpm-mac 100% | 2.4 MiB/s | 2.5 KiB | 00m00s [152/155] Installing util-linux-0:2.40. 100% | 163.0 MiB/s | 3.7 MiB | 00m00s [153/155] Installing authselect-0:1.5.0 100% | 77.1 MiB/s | 157.9 KiB | 00m00s [154/155] Installing which-0:2.21-42.fc 100% | 80.5 MiB/s | 82.4 KiB | 00m00s warning: posix.fork(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead warning: posix.wait(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead warning: posix.exec(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead [155/155] Installing info-0:7.1-3.fc41. 100% | 457.9 KiB/s | 362.2 KiB | 00m01s Complete! Finish: installing minimal buildroot with dnf5 Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: add-determinism-0.3.6-1.fc41.x86_64 alternatives-1.30-1.fc41.x86_64 ansible-srpm-macros-1-16.fc41.noarch audit-libs-4.0.2-1.fc41.x86_64 authselect-1.5.0-7.fc41.x86_64 authselect-libs-1.5.0-7.fc41.x86_64 basesystem-11-21.fc41.noarch bash-5.2.32-1.fc41.x86_64 binutils-2.43.1-2.fc41.x86_64 build-reproducibility-srpm-macros-0.3.6-1.fc41.noarch bzip2-1.0.8-19.fc41.x86_64 bzip2-libs-1.0.8-19.fc41.x86_64 ca-certificates-2024.2.69_v8.0.401-1.0.fc41.noarch coreutils-9.5-10.fc41.x86_64 coreutils-common-9.5-10.fc41.x86_64 cpio-2.15-2.fc41.x86_64 cracklib-2.9.11-6.fc41.x86_64 crypto-policies-20240826-1.gite824389.fc41.noarch curl-8.9.1-2.fc41.x86_64 cyrus-sasl-lib-2.1.28-27.fc41.x86_64 debugedit-5.0-17.fc41.x86_64 diffutils-3.10-8.fc41.x86_64 dwz-0.15-7.fc41.x86_64 ed-1.20.2-2.fc41.x86_64 efi-srpm-macros-5-12.fc41.noarch elfutils-0.191-8.fc41.x86_64 elfutils-debuginfod-client-0.191-8.fc41.x86_64 elfutils-default-yama-scope-0.191-8.fc41.noarch elfutils-libelf-0.191-8.fc41.x86_64 elfutils-libs-0.191-8.fc41.x86_64 fedora-gpg-keys-41-0.5.noarch fedora-release-41-0.21.noarch fedora-release-common-41-0.21.noarch fedora-release-identity-basic-41-0.21.noarch fedora-repos-41-0.5.noarch file-5.45-7.fc41.x86_64 file-libs-5.45-7.fc41.x86_64 filesystem-3.18-23.fc41.x86_64 findutils-4.10.0-4.fc41.x86_64 fonts-srpm-macros-2.0.5-17.fc41.noarch forge-srpm-macros-0.3.2-1.fc41.noarch fpc-srpm-macros-1.3-13.fc41.noarch gawk-5.3.0-4.fc41.x86_64 gdb-minimal-15.1-1.fc41.x86_64 gdbm-1.23-7.fc41.x86_64 gdbm-libs-1.23-7.fc41.x86_64 ghc-srpm-macros-1.9.1-2.fc41.noarch glibc-2.40-3.fc41.x86_64 glibc-common-2.40-3.fc41.x86_64 glibc-gconv-extra-2.40-3.fc41.x86_64 glibc-minimal-langpack-2.40-3.fc41.x86_64 gmp-6.3.0-2.fc41.x86_64 gnat-srpm-macros-6-6.fc41.noarch go-srpm-macros-3.6.0-3.fc41.noarch gpg-pubkey-e99d6ad1-64d2612c grep-3.11-9.fc41.x86_64 gzip-1.13-2.fc41.x86_64 info-7.1-3.fc41.x86_64 jansson-2.13.1-10.fc41.x86_64 kernel-srpm-macros-1.0-24.fc41.noarch keyutils-libs-1.6.3-4.fc41.x86_64 krb5-libs-1.21.3-2.fc41.x86_64 libacl-2.3.2-2.fc41.x86_64 libarchive-3.7.4-3.fc41.x86_64 libattr-2.5.2-4.fc41.x86_64 libblkid-2.40.2-4.fc41.x86_64 libbrotli-1.1.0-5.fc41.x86_64 libcap-2.70-4.fc41.x86_64 libcap-ng-0.8.5-3.fc41.x86_64 libcom_err-1.47.1-3.fc41.x86_64 libcurl-8.9.1-2.fc41.x86_64 libeconf-0.6.2-3.fc41.x86_64 libevent-2.1.12-14.fc41.x86_64 libfdisk-2.40.2-4.fc41.x86_64 libffi-3.4.6-3.fc41.x86_64 libgcc-14.2.1-3.fc41.x86_64 libgomp-14.2.1-3.fc41.x86_64 libidn2-2.3.7-2.fc41.x86_64 libmount-2.40.2-4.fc41.x86_64 libnghttp2-1.62.1-2.fc41.x86_64 libnsl2-2.0.1-2.fc41.x86_64 libpkgconf-2.3.0-1.fc41.x86_64 libpsl-0.21.5-4.fc41.x86_64 libpwquality-1.4.5-11.fc41.x86_64 libselinux-3.7-5.fc41.x86_64 libsemanage-3.7-2.fc41.x86_64 libsepol-3.7-2.fc41.x86_64 libsmartcols-2.40.2-4.fc41.x86_64 libssh-0.10.6-8.fc41.x86_64 libssh-config-0.10.6-8.fc41.noarch libstdc++-14.2.1-3.fc41.x86_64 libtasn1-4.19.0-9.fc41.x86_64 libtirpc-1.3.5-0.fc41.x86_64 libtool-ltdl-2.4.7-12.fc41.x86_64 libunistring-1.1-8.fc41.x86_64 libutempter-1.2.1-15.fc41.x86_64 libuuid-2.40.2-4.fc41.x86_64 libverto-0.3.2-9.fc41.x86_64 libxcrypt-4.4.36-7.fc41.x86_64 libxml2-2.12.8-2.fc41.x86_64 libzstd-1.5.6-2.fc41.x86_64 lua-libs-5.4.6-6.fc41.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-2.6.8-5.fc41.x86_64 openssl-libs-3.2.2-9.fc41.x86_64 p11-kit-0.25.5-3.fc41.x86_64 p11-kit-trust-0.25.5-3.fc41.x86_64 package-notes-srpm-macros-0.5-12.fc41.noarch pam-1.6.1-5.fc41.x86_64 pam-libs-1.6.1-5.fc41.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.fc41.x86_64 pkgconf-m4-2.3.0-1.fc41.noarch pkgconf-pkg-config-2.3.0-1.fc41.x86_64 popt-1.19-7.fc41.x86_64 publicsuffix-list-dafsa-20240107-4.fc41.noarch pyproject-srpm-macros-1.15.0-1.fc41.noarch python-srpm-macros-3.13-3.fc41.noarch qt5-srpm-macros-5.15.15-1.fc41.noarch qt6-srpm-macros-6.7.2-3.fc41.noarch readline-8.2-10.fc41.x86_64 redhat-rpm-config-293-1.fc41.noarch rpm-4.19.94-1.fc41.x86_64 rpm-build-4.19.94-1.fc41.x86_64 rpm-build-libs-4.19.94-1.fc41.x86_64 rpm-libs-4.19.94-1.fc41.x86_64 rpm-sequoia-1.7.0-2.fc41.x86_64 rust-srpm-macros-26.3-3.fc41.noarch sed-4.9-3.fc41.x86_64 setup-2.15.0-5.fc41.noarch shadow-utils-4.15.1-11.fc41.x86_64 sqlite-libs-3.46.1-1.fc41.x86_64 systemd-libs-256.6-1.fc41.x86_64 tar-1.35-4.fc41.x86_64 unzip-6.0-64.fc41.x86_64 util-linux-2.40.2-4.fc41.x86_64 util-linux-core-2.40.2-4.fc41.x86_64 which-2.21-42.fc41.x86_64 xxhash-libs-0.8.2-3.fc41.x86_64 xz-5.6.2-2.fc41.x86_64 xz-libs-5.6.2-2.fc41.x86_64 zig-srpm-macros-1-3.fc41.noarch zip-3.0-41.fc41.x86_64 zlib-ng-compat-2.1.7-3.fc41.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=1728345600 Wrote: /builddir/build/SRPMS/python-pyhmmer-0.10.15-1.fc41.src.rpm Finish: rpmbuild -bs INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-41-x86_64-1728412359.829131/root/var/log/dnf5.log Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-_4un3wja/python-pyhmmer/python-pyhmmer.spec) Config(child) 0 minutes 16 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/python-pyhmmer-0.10.15-1.fc41.src.rpm) Config(fedora-41-x86_64) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-41-x86_64-bootstrap-1728412359.829131/root. INFO: reusing tmpfs at /var/lib/mock/fedora-41-x86_64-bootstrap-1728412359.829131/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-41-x86_64-1728412359.829131/root. INFO: calling preinit hooks INFO: enabled root cache Start: unpacking root cache Finish: unpacking root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-4.19.94-1.fc41.x86_64 rpm-sequoia-1.7.0-2.fc41.x86_64 dnf5-5.2.6.2-1.fc41.x86_64 dnf5-plugins-5.2.6.2-1.fc41.x86_64 Finish: chroot init Start: build phase for python-pyhmmer-0.10.15-1.fc41.src.rpm Start: build setup for python-pyhmmer-0.10.15-1.fc41.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1728345600 Wrote: /builddir/build/SRPMS/python-pyhmmer-0.10.15-1.fc41.src.rpm Updating and loading repositories: updates 100% | 107.6 KiB/s | 28.6 KiB | 00m00s fedora 100% | 178.8 KiB/s | 25.9 KiB | 00m00s Copr repository 100% | 102.7 KiB/s | 1.5 KiB | 00m00s Repositories loaded. Package Arch Version Repository Size Installing: gcc x86_64 14.2.1-3.fc41 fedora 104.3 MiB python3-devel x86_64 3.13.0~rc2-3.fc41 fedora 1.8 MiB Installing dependencies: annobin-docs noarch 12.69-1.fc41 fedora 97.7 KiB annobin-plugin-gcc x86_64 12.69-1.fc41 fedora 985.0 KiB cpp x86_64 14.2.1-3.fc41 fedora 35.0 MiB expat x86_64 2.6.3-1.fc41 fedora 291.5 KiB gcc-plugin-annobin x86_64 14.2.1-3.fc41 fedora 61.1 KiB glibc-devel x86_64 2.40-3.fc41 fedora 35.0 KiB glibc-headers-x86 noarch 2.40-3.fc41 fedora 2.2 MiB kernel-headers x86_64 6.11.0-63.fc41 fedora 6.4 MiB libb2 x86_64 0.98.1-12.fc41 fedora 42.2 KiB libmpc x86_64 1.3.1-6.fc41 fedora 164.7 KiB libxcrypt-devel x86_64 4.4.36-7.fc41 fedora 30.3 KiB make x86_64 1:4.4.1-8.fc41 fedora 1.8 MiB mpdecimal x86_64 2.5.1-16.fc41 fedora 204.9 KiB pyproject-rpm-macros noarch 1.15.0-1.fc41 fedora 109.0 KiB python-pip-wheel noarch 24.2-1.fc41 fedora 1.2 MiB python-rpm-macros noarch 3.13-3.fc41 fedora 22.1 KiB python3 x86_64 3.13.0~rc2-3.fc41 fedora 31.8 KiB python3-libs x86_64 3.13.0~rc2-3.fc41 fedora 40.3 MiB python3-packaging noarch 24.1-2.fc41 fedora 422.3 KiB python3-rpm-generators noarch 14-11.fc41 fedora 81.7 KiB python3-rpm-macros noarch 3.13-3.fc41 fedora 6.4 KiB tzdata noarch 2024a-9.fc41 fedora 1.7 MiB Transaction Summary: Installing: 24 packages Total size of inbound packages is 65 MiB. Need to download 53 MiB. After this operation, 197 MiB extra will be used (install 197 MiB, remove 0 B). [1/2] python3-devel-0:3.13.0~rc2-3.fc41 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [2/6] python3-libs-0:3.13.0~rc2-3.fc41. 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [3/7] expat-0:2.6.3-1.fc41.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [4/8] libb2-0:0.98.1-12.fc41.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [5/9] mpdecimal-0:2.5.1-16.fc41.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 6/10] python-pip-wheel-0:24.2-1.fc41. 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 7/11] tzdata-0:2024a-9.fc41.noarch 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 8/12] python3-0:3.13.0~rc2-3.fc41.x86 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 9/20] pyproject-rpm-macros-0:1.15.0-1 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [10/21] python-rpm-macros-0:3.13-3.fc41 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [11/22] python3-rpm-generators-0:14-11. 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [12/23] python3-rpm-macros-0:3.13-3.fc4 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [13/24] python3-packaging-0:24.1-2.fc41 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [14/24] libmpc-0:1.3.1-6.fc41.x86_64 100% | 5.0 MiB/s | 71.1 KiB | 00m00s [15/24] make-1:4.4.1-8.fc41.x86_64 100% | 81.8 MiB/s | 586.1 KiB | 00m00s [16/24] glibc-devel-0:2.40-3.fc41.x86_6 100% | 32.5 MiB/s | 133.3 KiB | 00m00s [17/24] glibc-headers-x86-0:2.40-3.fc41 100% | 123.2 MiB/s | 630.8 KiB | 00m00s [18/24] libxcrypt-devel-0:4.4.36-7.fc41 100% | 9.4 MiB/s | 28.9 KiB | 00m00s [19/24] kernel-headers-0:6.11.0-63.fc41 100% | 162.5 MiB/s | 1.6 MiB | 00m00s [20/24] annobin-plugin-gcc-0:12.69-1.fc 100% | 135.5 MiB/s | 971.0 KiB | 00m00s [21/24] cpp-0:14.2.1-3.fc41.x86_64 100% | 178.3 MiB/s | 11.9 MiB | 00m00s [22/24] gcc-plugin-annobin-0:14.2.1-3.f 100% | 4.1 MiB/s | 55.1 KiB | 00m00s [23/24] annobin-docs-0:12.69-1.fc41.noa 100% | 44.8 MiB/s | 91.8 KiB | 00m00s [24/24] gcc-0:14.2.1-3.fc41.x86_64 100% | 256.6 MiB/s | 36.9 MiB | 00m00s -------------------------------------------------------------------------------- [24/24] Total 100% | 227.6 MiB/s | 53.0 MiB | 00m00s Running transaction [ 1/26] Verify package files 100% | 134.0 B/s | 24.0 B | 00m00s [ 2/26] Prepare transaction 100% | 800.0 B/s | 24.0 B | 00m00s [ 3/26] Installing python-rpm-macros-0: 100% | 0.0 B/s | 22.8 KiB | 00m00s [ 4/26] Installing python3-rpm-macros-0 100% | 0.0 B/s | 6.7 KiB | 00m00s [ 5/26] Installing libmpc-0:1.3.1-6.fc4 100% | 162.3 MiB/s | 166.2 KiB | 00m00s [ 6/26] Installing cpp-0:14.2.1-3.fc41. 100% | 393.3 MiB/s | 35.0 MiB | 00m00s [ 7/26] Installing pyproject-rpm-macros 100% | 108.4 MiB/s | 111.0 KiB | 00m00s [ 8/26] Installing annobin-docs-0:12.69 100% | 48.2 MiB/s | 98.8 KiB | 00m00s [ 9/26] Installing kernel-headers-0:6.1 100% | 225.6 MiB/s | 6.5 MiB | 00m00s [10/26] Installing glibc-headers-x86-0: 100% | 207.8 MiB/s | 2.3 MiB | 00m00s [11/26] Installing libxcrypt-devel-0:4. 100% | 31.8 MiB/s | 32.6 KiB | 00m00s [12/26] Installing glibc-devel-0:2.40-3 100% | 9.4 MiB/s | 38.4 KiB | 00m00s [13/26] Installing tzdata-0:2024a-9.fc4 100% | 71.9 MiB/s | 1.9 MiB | 00m00s [14/26] Installing python-pip-wheel-0:2 100% | 620.8 MiB/s | 1.2 MiB | 00m00s [15/26] Installing mpdecimal-0:2.5.1-16 100% | 201.2 MiB/s | 206.0 KiB | 00m00s [16/26] Installing libb2-0:0.98.1-12.fc 100% | 0.0 B/s | 43.3 KiB | 00m00s [17/26] Installing expat-0:2.6.3-1.fc41 100% | 57.3 MiB/s | 293.6 KiB | 00m00s [18/26] Installing python3-libs-0:3.13. 100% | 354.0 MiB/s | 40.7 MiB | 00m00s [19/26] Installing python3-0:3.13.0~rc2 100% | 32.8 MiB/s | 33.6 KiB | 00m00s [20/26] Installing python3-packaging-0: 100% | 211.5 MiB/s | 433.2 KiB | 00m00s [21/26] Installing python3-rpm-generato 100% | 81.0 MiB/s | 82.9 KiB | 00m00s [22/26] Installing make-1:4.4.1-8.fc41. 100% | 300.0 MiB/s | 1.8 MiB | 00m00s [23/26] Installing gcc-0:14.2.1-3.fc41. 100% | 442.3 MiB/s | 104.4 MiB | 00m00s [24/26] Installing annobin-plugin-gcc-0 100% | 74.1 MiB/s | 986.7 KiB | 00m00s [25/26] Installing gcc-plugin-annobin-0 100% | 4.7 MiB/s | 62.6 KiB | 00m00s warning: posix.fork(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead warning: posix.wait(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead warning: posix.exec(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead [26/26] Installing python3-devel-0:3.13 100% | 15.5 MiB/s | 1.8 MiB | 00m00s Complete! Finish: build setup for python-pyhmmer-0.10.15-1.fc41.src.rpm Start: rpmbuild python-pyhmmer-0.10.15-1.fc41.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1728345600 Executing(%mkbuilddir): /bin/sh -e /var/tmp/rpm-tmp.xH7Ipr + umask 022 + cd /builddir/build/BUILD/python-pyhmmer-0.10.15-build + test -d /builddir/build/BUILD/python-pyhmmer-0.10.15-build + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w /builddir/build/BUILD/python-pyhmmer-0.10.15-build + /usr/bin/rm -rf /builddir/build/BUILD/python-pyhmmer-0.10.15-build + /usr/bin/mkdir -p /builddir/build/BUILD/python-pyhmmer-0.10.15-build + /usr/bin/mkdir -p /builddir/build/BUILD/python-pyhmmer-0.10.15-build/SPECPARTS + RPM_EC=0 ++ jobs -p + exit 0 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.cha6Ol + umask 022 + cd /builddir/build/BUILD/python-pyhmmer-0.10.15-build + cd /builddir/build/BUILD/python-pyhmmer-0.10.15-build + rm -rf pyhmmer-0.10.15 + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/pyhmmer-0.10.15.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + cd pyhmmer-0.10.15 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + RPM_EC=0 ++ jobs -p + exit 0 Executing(%generate_buildrequires): /bin/sh -e /var/tmp/rpm-tmp.Z0Owr4 + umask 022 + cd /builddir/build/BUILD/python-pyhmmer-0.10.15-build + cd pyhmmer-0.10.15 + echo pyproject-rpm-macros + echo python3-devel + echo 'python3dist(packaging)' + echo 'python3dist(pip) >= 19' + '[' -f pyproject.toml ']' + echo '(python3dist(tomli) if python3-devel < 3.11)' + rm -rfv '*.dist-info/' + '[' -f /usr/bin/python3 ']' + mkdir -p /builddir/build/BUILD/python-pyhmmer-0.10.15-build/pyhmmer-0.10.15/.pyproject-builddir + echo -n + 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 ' + 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 ' + 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 ' + 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 ' + VALAFLAGS=-g + 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' + 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 ' + LT_SYS_LIBRARY_PATH=/usr/lib64: + CC=gcc + CXX=g++ + TMPDIR=/builddir/build/BUILD/python-pyhmmer-0.10.15-build/pyhmmer-0.10.15/.pyproject-builddir + RPM_TOXENV=py313 + HOSTNAME=rpmbuild + /usr/bin/python3 -Bs /usr/lib/rpm/redhat/pyproject_buildrequires.py --generate-extras --python3_pkgversion 3 --wheeldir /builddir/build/BUILD/python-pyhmmer-0.10.15-build/pyhmmer-0.10.15/pyproject-wheeldir --output /builddir/build/BUILD/python-pyhmmer-0.10.15-build/python-pyhmmer-0.10.15-1.fc41.x86_64-pyproject-buildrequires Handling setuptools >=46.4 from build-system.requires Requirement not satisfied: setuptools >=46.4 Handling cython ~=3.0 from build-system.requires Requirement not satisfied: cython ~=3.0 Exiting dependency generation pass: build backend + cat /builddir/build/BUILD/python-pyhmmer-0.10.15-build/python-pyhmmer-0.10.15-1.fc41.x86_64-pyproject-buildrequires + rm -rfv '*.dist-info/' + RPM_EC=0 ++ jobs -p + exit 0 Wrote: /builddir/build/SRPMS/python-pyhmmer-0.10.15-1.fc41.buildreqs.nosrc.rpm INFO: Going to install missing dynamic buildrequires Updating and loading repositories: updates 100% | 155.6 KiB/s | 28.6 KiB | 00m00s fedora 100% | 174.0 KiB/s | 25.9 KiB | 00m00s Copr repository 100% | 128.3 KiB/s | 1.5 KiB | 00m00s Repositories loaded. Package "gcc-14.2.1-3.fc41.x86_64" is already installed. Package "pyproject-rpm-macros-1.15.0-1.fc41.noarch" is already installed. Package "python3-devel-3.13.0~rc2-3.fc41.x86_64" is already installed. Package "python3-packaging-24.1-2.fc41.noarch" is already installed. Package Arch Version Repository Size Installing: python3-cython x86_64 3.0.11-1.fc41 copr_base 17.7 MiB python3-pip noarch 24.2-1.fc41 fedora 11.4 MiB python3-setuptools noarch 69.2.0-8.fc41 fedora 7.2 MiB Transaction Summary: Installing: 3 packages Total size of inbound packages is 8 MiB. Need to download 4 MiB. After this operation, 36 MiB extra will be used (install 36 MiB, remove 0 B). [1/2] python3-pip-0:24.2-1.fc41.noarch 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [2/3] python3-setuptools-0:69.2.0-8.fc4 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [3/3] python3-cython-0:3.0.11-1.fc41.x8 100% | 37.0 MiB/s | 3.7 MiB | 00m00s -------------------------------------------------------------------------------- [3/3] Total 100% | 35.6 MiB/s | 3.7 MiB | 00m00s Running transaction [1/5] Verify package files 100% | 125.0 B/s | 3.0 B | 00m00s [2/5] Prepare transaction 100% | 107.0 B/s | 3.0 B | 00m00s [3/5] Installing python3-setuptools-0:6 100% | 236.5 MiB/s | 7.3 MiB | 00m00s [4/5] Installing python3-pip-0:24.2-1.f 100% | 228.8 MiB/s | 11.7 MiB | 00m00s warning: posix.fork(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead warning: posix.wait(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead warning: posix.exec(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead [5/5] Installing python3-cython-0:3.0.1 100% | 278.4 MiB/s | 17.8 MiB | 00m00s Warning: skipped PGP checks for 1 package from repository: copr_base Complete! Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1728345600 Executing(%generate_buildrequires): /bin/sh -e /var/tmp/rpm-tmp.SURrnO + umask 022 + cd /builddir/build/BUILD/python-pyhmmer-0.10.15-build + cd pyhmmer-0.10.15 + echo pyproject-rpm-macros + echo python3-devel + echo 'python3dist(packaging)' + echo 'python3dist(pip) >= 19' + '[' -f pyproject.toml ']' + echo '(python3dist(tomli) if python3-devel < 3.11)' + rm -rfv '*.dist-info/' + '[' -f /usr/bin/python3 ']' + mkdir -p /builddir/build/BUILD/python-pyhmmer-0.10.15-build/pyhmmer-0.10.15/.pyproject-builddir + echo -n + 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 ' + 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 ' + 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 ' + 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 ' + VALAFLAGS=-g + 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' + 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 ' + LT_SYS_LIBRARY_PATH=/usr/lib64: + CC=gcc + CXX=g++ + TMPDIR=/builddir/build/BUILD/python-pyhmmer-0.10.15-build/pyhmmer-0.10.15/.pyproject-builddir + RPM_TOXENV=py313 + HOSTNAME=rpmbuild + /usr/bin/python3 -Bs /usr/lib/rpm/redhat/pyproject_buildrequires.py --generate-extras --python3_pkgversion 3 --wheeldir /builddir/build/BUILD/python-pyhmmer-0.10.15-build/pyhmmer-0.10.15/pyproject-wheeldir --output /builddir/build/BUILD/python-pyhmmer-0.10.15-build/python-pyhmmer-0.10.15-1.fc41.x86_64-pyproject-buildrequires Handling setuptools >=46.4 from build-system.requires Requirement satisfied: setuptools >=46.4 (installed: setuptools 69.2.0) Handling cython ~=3.0 from build-system.requires Requirement satisfied: cython ~=3.0 (installed: cython 3.0.11) Handling wheel from get_requires_for_build_wheel Requirement not satisfied: wheel Handling setuptools >=46.4 from get_requires_for_build_wheel Requirement satisfied: setuptools >=46.4 (installed: setuptools 69.2.0) Handling cython ~=3.0 from get_requires_for_build_wheel Requirement satisfied: cython ~=3.0 (installed: cython 3.0.11) Exiting dependency generation pass: get_requires_for_build_wheel + cat /builddir/build/BUILD/python-pyhmmer-0.10.15-build/python-pyhmmer-0.10.15-1.fc41.x86_64-pyproject-buildrequires + rm -rfv '*.dist-info/' + RPM_EC=0 ++ jobs -p + exit 0 Wrote: /builddir/build/SRPMS/python-pyhmmer-0.10.15-1.fc41.buildreqs.nosrc.rpm INFO: Going to install missing dynamic buildrequires Updating and loading repositories: updates 100% | 272.7 KiB/s | 28.6 KiB | 00m00s fedora 100% | 98.6 KiB/s | 25.9 KiB | 00m00s Copr repository 100% | 140.0 KiB/s | 1.5 KiB | 00m00s Repositories loaded. Package "gcc-14.2.1-3.fc41.x86_64" is already installed. Package "pyproject-rpm-macros-1.15.0-1.fc41.noarch" is already installed. Package "python3-devel-3.13.0~rc2-3.fc41.x86_64" is already installed. Package "python3-packaging-24.1-2.fc41.noarch" is already installed. Package "python3-pip-24.2-1.fc41.noarch" is already installed. Package "python3-setuptools-69.2.0-8.fc41.noarch" is already installed. Package Arch Version Repository Size Installing: python3-wheel noarch 1:0.43.0-4.fc41 fedora 516.1 KiB Transaction Summary: Installing: 1 package Total size of inbound packages is 166 KiB. Need to download 0 B. After this operation, 516 KiB extra will be used (install 516 KiB, remove 0 B). [1/1] python3-wheel-1:0.43.0-4.fc41.noa 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [1/1] Total 100% | 0.0 B/s | 0.0 B | 00m00s Running transaction [1/3] Verify package files 100% | 0.0 B/s | 1.0 B | 00m00s [2/3] Prepare transaction 100% | 250.0 B/s | 1.0 B | 00m00s warning: posix.fork(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead warning: posix.wait(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead warning: posix.exec(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead [3/3] Installing python3-wheel-1:0.43.0 100% | 34.8 MiB/s | 535.1 KiB | 00m00s Complete! Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1728345600 Executing(%generate_buildrequires): /bin/sh -e /var/tmp/rpm-tmp.SOXJ4s + umask 022 + cd /builddir/build/BUILD/python-pyhmmer-0.10.15-build + cd pyhmmer-0.10.15 + echo pyproject-rpm-macros + echo python3-devel + echo 'python3dist(packaging)' + echo 'python3dist(pip) >= 19' + '[' -f pyproject.toml ']' + echo '(python3dist(tomli) if python3-devel < 3.11)' + rm -rfv '*.dist-info/' + '[' -f /usr/bin/python3 ']' + mkdir -p /builddir/build/BUILD/python-pyhmmer-0.10.15-build/pyhmmer-0.10.15/.pyproject-builddir + echo -n + 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 ' + 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 ' + 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 ' + 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 ' + VALAFLAGS=-g + 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' + 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 ' + LT_SYS_LIBRARY_PATH=/usr/lib64: + CC=gcc + CXX=g++ + TMPDIR=/builddir/build/BUILD/python-pyhmmer-0.10.15-build/pyhmmer-0.10.15/.pyproject-builddir + RPM_TOXENV=py313 + HOSTNAME=rpmbuild + /usr/bin/python3 -Bs /usr/lib/rpm/redhat/pyproject_buildrequires.py --generate-extras --python3_pkgversion 3 --wheeldir /builddir/build/BUILD/python-pyhmmer-0.10.15-build/pyhmmer-0.10.15/pyproject-wheeldir --output /builddir/build/BUILD/python-pyhmmer-0.10.15-build/python-pyhmmer-0.10.15-1.fc41.x86_64-pyproject-buildrequires Handling setuptools >=46.4 from build-system.requires Requirement satisfied: setuptools >=46.4 (installed: setuptools 69.2.0) Handling cython ~=3.0 from build-system.requires Requirement satisfied: cython ~=3.0 (installed: cython 3.0.11) Handling wheel from get_requires_for_build_wheel Requirement satisfied: wheel (installed: wheel 0.43.0) Handling setuptools >=46.4 from get_requires_for_build_wheel Requirement satisfied: setuptools >=46.4 (installed: setuptools 69.2.0) Handling cython ~=3.0 from get_requires_for_build_wheel Requirement satisfied: cython ~=3.0 (installed: cython 3.0.11) running dist_info writing pyhmmer.egg-info/PKG-INFO writing dependency_links to pyhmmer.egg-info/dependency_links.txt writing requirements to pyhmmer.egg-info/requires.txt writing top-level names to pyhmmer.egg-info/top_level.txt reading manifest file 'pyhmmer.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files matching '*.ai' found under directory 'vendor/hmmer' warning: no previously-included files matching '*.pl' found under directory 'vendor' no previously-included directories found matching 'vendor/easel/demotic' no previously-included directories found matching 'vendor/easel/documentation' no previously-included directories found matching 'vendor/easel/esl_msa_testfiles' no previously-included directories found matching 'vendor/easel/miniapps' no previously-included directories found matching 'vendor/easel/testsuite' no previously-included directories found matching 'vendor/hmmer/autobuild' no previously-included directories found matching 'vendor/hmmer/documentation' no previously-included directories found matching 'vendor/hmmer/contrib' no previously-included directories found matching 'vendor/hmmer/profmark' no previously-included directories found matching 'vendor/hmmer/testsuite' no previously-included directories found matching 'vendor/hmmer/test-speed' no previously-included directories found matching 'vendor/hmmer/tutorial' adding license file 'COPYING' writing manifest file 'pyhmmer.egg-info/SOURCES.txt' creating '/builddir/build/BUILD/python-pyhmmer-0.10.15-build/pyhmmer-0.10.15/pyhmmer-0.10.15.dist-info' Handling psutil ~=5.8 from hook generated metadata: Requires-Dist (pyhmmer) Requirement not satisfied: psutil ~=5.8 + cat /builddir/build/BUILD/python-pyhmmer-0.10.15-build/python-pyhmmer-0.10.15-1.fc41.x86_64-pyproject-buildrequires + rm -rfv pyhmmer-0.10.15.dist-info/ removed 'pyhmmer-0.10.15.dist-info/COPYING' removed 'pyhmmer-0.10.15.dist-info/METADATA' removed 'pyhmmer-0.10.15.dist-info/top_level.txt' removed directory 'pyhmmer-0.10.15.dist-info/' + RPM_EC=0 ++ jobs -p + exit 0 Wrote: /builddir/build/SRPMS/python-pyhmmer-0.10.15-1.fc41.buildreqs.nosrc.rpm INFO: Going to install missing dynamic buildrequires Updating and loading repositories: updates 100% | 1.1 MiB/s | 28.6 KiB | 00m00s fedora 100% | 425.0 KiB/s | 25.9 KiB | 00m00s Copr repository 100% | 102.7 KiB/s | 1.5 KiB | 00m00s Repositories loaded. Package "gcc-14.2.1-3.fc41.x86_64" is already installed. Package "pyproject-rpm-macros-1.15.0-1.fc41.noarch" is already installed. Package "python3-devel-3.13.0~rc2-3.fc41.x86_64" is already installed. Package "python3-packaging-24.1-2.fc41.noarch" is already installed. Package "python3-pip-24.2-1.fc41.noarch" is already installed. Package "python3-setuptools-69.2.0-8.fc41.noarch" is already installed. Package "python3-wheel-1:0.43.0-4.fc41.noarch" is already installed. Total size of inbound packages is 272 KiB. Need to download 272 KiB. After this operation, 1 MiB extra will be used (install 1 MiB, remove 0 B). Package Arch Version Repository Size Installing: python3-psutil x86_64 5.9.8-4.fc41 fedora 1.4 MiB Transaction Summary: Installing: 1 package [1/1] python3-psutil-0:5.9.8-4.fc41.x86 100% | 20.4 MiB/s | 271.9 KiB | 00m00s -------------------------------------------------------------------------------- [1/1] Total 100% | 1.0 MiB/s | 271.9 KiB | 00m00s Running transaction [1/3] Verify package files 100% | 0.0 B/s | 1.0 B | 00m00s [2/3] Prepare transaction 100% | 66.0 B/s | 1.0 B | 00m00s warning: posix.fork(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead warning: posix.wait(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead warning: posix.exec(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead [3/3] Installing python3-psutil-0:5.9.8 100% | 84.9 MiB/s | 1.4 MiB | 00m00s Complete! Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1728345600 Executing(%generate_buildrequires): /bin/sh -e /var/tmp/rpm-tmp.qcRIBb + umask 022 + cd /builddir/build/BUILD/python-pyhmmer-0.10.15-build + cd pyhmmer-0.10.15 + echo pyproject-rpm-macros + echo python3-devel + echo 'python3dist(packaging)' + echo 'python3dist(pip) >= 19' + '[' -f pyproject.toml ']' + echo '(python3dist(tomli) if python3-devel < 3.11)' + rm -rfv '*.dist-info/' + '[' -f /usr/bin/python3 ']' + mkdir -p /builddir/build/BUILD/python-pyhmmer-0.10.15-build/pyhmmer-0.10.15/.pyproject-builddir + echo -n + 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 ' + 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 ' + 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 ' + 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 ' + VALAFLAGS=-g + 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' + 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 ' + LT_SYS_LIBRARY_PATH=/usr/lib64: + CC=gcc + CXX=g++ + TMPDIR=/builddir/build/BUILD/python-pyhmmer-0.10.15-build/pyhmmer-0.10.15/.pyproject-builddir + RPM_TOXENV=py313 + HOSTNAME=rpmbuild + /usr/bin/python3 -Bs /usr/lib/rpm/redhat/pyproject_buildrequires.py --generate-extras --python3_pkgversion 3 --wheeldir /builddir/build/BUILD/python-pyhmmer-0.10.15-build/pyhmmer-0.10.15/pyproject-wheeldir --output /builddir/build/BUILD/python-pyhmmer-0.10.15-build/python-pyhmmer-0.10.15-1.fc41.x86_64-pyproject-buildrequires Handling setuptools >=46.4 from build-system.requires Requirement satisfied: setuptools >=46.4 (installed: setuptools 69.2.0) Handling cython ~=3.0 from build-system.requires Requirement satisfied: cython ~=3.0 (installed: cython 3.0.11) Handling wheel from get_requires_for_build_wheel Requirement satisfied: wheel (installed: wheel 0.43.0) Handling setuptools >=46.4 from get_requires_for_build_wheel Requirement satisfied: setuptools >=46.4 (installed: setuptools 69.2.0) Handling cython ~=3.0 from get_requires_for_build_wheel Requirement satisfied: cython ~=3.0 (installed: cython 3.0.11) running dist_info writing pyhmmer.egg-info/PKG-INFO writing dependency_links to pyhmmer.egg-info/dependency_links.txt writing requirements to pyhmmer.egg-info/requires.txt writing top-level names to pyhmmer.egg-info/top_level.txt reading manifest file 'pyhmmer.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files matching '*.ai' found under directory 'vendor/hmmer' warning: no previously-included files matching '*.pl' found under directory 'vendor' no previously-included directories found matching 'vendor/easel/demotic' no previously-included directories found matching 'vendor/easel/documentation' no previously-included directories found matching 'vendor/easel/esl_msa_testfiles' no previously-included directories found matching 'vendor/easel/miniapps' no previously-included directories found matching 'vendor/easel/testsuite' no previously-included directories found matching 'vendor/hmmer/autobuild' no previously-included directories found matching 'vendor/hmmer/documentation' no previously-included directories found matching 'vendor/hmmer/contrib' no previously-included directories found matching 'vendor/hmmer/profmark' no previously-included directories found matching 'vendor/hmmer/testsuite' no previously-included directories found matching 'vendor/hmmer/test-speed' no previously-included directories found matching 'vendor/hmmer/tutorial' adding license file 'COPYING' writing manifest file 'pyhmmer.egg-info/SOURCES.txt' creating '/builddir/build/BUILD/python-pyhmmer-0.10.15-build/pyhmmer-0.10.15/pyhmmer-0.10.15.dist-info' Handling psutil ~=5.8 from hook generated metadata: Requires-Dist (pyhmmer) Requirement satisfied: psutil ~=5.8 (installed: psutil 5.9.8) + cat /builddir/build/BUILD/python-pyhmmer-0.10.15-build/python-pyhmmer-0.10.15-1.fc41.x86_64-pyproject-buildrequires + rm -rfv pyhmmer-0.10.15.dist-info/ removed 'pyhmmer-0.10.15.dist-info/COPYING' removed 'pyhmmer-0.10.15.dist-info/METADATA' removed 'pyhmmer-0.10.15.dist-info/top_level.txt' removed directory 'pyhmmer-0.10.15.dist-info/' + RPM_EC=0 ++ jobs -p + exit 0 Wrote: /builddir/build/SRPMS/python-pyhmmer-0.10.15-1.fc41.buildreqs.nosrc.rpm INFO: Going to install missing dynamic buildrequires Updating and loading repositories: updates 100% | 275.3 KiB/s | 28.6 KiB | 00m00s fedora 100% | 93.9 KiB/s | 25.9 KiB | 00m00s Copr repository 100% | 96.3 KiB/s | 1.5 KiB | 00m00s Repositories loaded. Package "gcc-14.2.1-3.fc41.x86_64" is already installed. Package "pyproject-rpm-macros-1.15.0-1.fc41.noarch" is already installed. Package "python3-devel-3.13.0~rc2-3.fc41.x86_64" is already installed. Package "python3-packaging-24.1-2.fc41.noarch" is already installed. Package "python3-pip-24.2-1.fc41.noarch" is already installed. Package "python3-setuptools-69.2.0-8.fc41.noarch" is already installed. Package "python3-wheel-1:0.43.0-4.fc41.noarch" is already installed. Nothing to do. Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1728345600 Executing(%generate_buildrequires): /bin/sh -e /var/tmp/rpm-tmp.VzGBI3 + umask 022 + cd /builddir/build/BUILD/python-pyhmmer-0.10.15-build + cd pyhmmer-0.10.15 + echo pyproject-rpm-macros + echo python3-devel + echo 'python3dist(packaging)' + echo 'python3dist(pip) >= 19' + '[' -f pyproject.toml ']' + echo '(python3dist(tomli) if python3-devel < 3.11)' + rm -rfv '*.dist-info/' + '[' -f /usr/bin/python3 ']' + mkdir -p /builddir/build/BUILD/python-pyhmmer-0.10.15-build/pyhmmer-0.10.15/.pyproject-builddir + echo -n + 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 ' + 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 ' + 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 ' + 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 ' + VALAFLAGS=-g + 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' + 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 ' + LT_SYS_LIBRARY_PATH=/usr/lib64: + CC=gcc + CXX=g++ + TMPDIR=/builddir/build/BUILD/python-pyhmmer-0.10.15-build/pyhmmer-0.10.15/.pyproject-builddir + RPM_TOXENV=py313 + HOSTNAME=rpmbuild + /usr/bin/python3 -Bs /usr/lib/rpm/redhat/pyproject_buildrequires.py --generate-extras --python3_pkgversion 3 --wheeldir /builddir/build/BUILD/python-pyhmmer-0.10.15-build/pyhmmer-0.10.15/pyproject-wheeldir --output /builddir/build/BUILD/python-pyhmmer-0.10.15-build/python-pyhmmer-0.10.15-1.fc41.x86_64-pyproject-buildrequires Handling setuptools >=46.4 from build-system.requires Requirement satisfied: setuptools >=46.4 (installed: setuptools 69.2.0) Handling cython ~=3.0 from build-system.requires Requirement satisfied: cython ~=3.0 (installed: cython 3.0.11) Handling wheel from get_requires_for_build_wheel Requirement satisfied: wheel (installed: wheel 0.43.0) Handling setuptools >=46.4 from get_requires_for_build_wheel Requirement satisfied: setuptools >=46.4 (installed: setuptools 69.2.0) Handling cython ~=3.0 from get_requires_for_build_wheel Requirement satisfied: cython ~=3.0 (installed: cython 3.0.11) running dist_info writing pyhmmer.egg-info/PKG-INFO writing dependency_links to pyhmmer.egg-info/dependency_links.txt writing requirements to pyhmmer.egg-info/requires.txt writing top-level names to pyhmmer.egg-info/top_level.txt reading manifest file 'pyhmmer.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files matching '*.ai' found under directory 'vendor/hmmer' warning: no previously-included files matching '*.pl' found under directory 'vendor' no previously-included directories found matching 'vendor/easel/demotic' no previously-included directories found matching 'vendor/easel/documentation' no previously-included directories found matching 'vendor/easel/esl_msa_testfiles' no previously-included directories found matching 'vendor/easel/miniapps' no previously-included directories found matching 'vendor/easel/testsuite' no previously-included directories found matching 'vendor/hmmer/autobuild' no previously-included directories found matching 'vendor/hmmer/documentation' no previously-included directories found matching 'vendor/hmmer/contrib' no previously-included directories found matching 'vendor/hmmer/profmark' no previously-included directories found matching 'vendor/hmmer/testsuite' no previously-included directories found matching 'vendor/hmmer/test-speed' no previously-included directories found matching 'vendor/hmmer/tutorial' adding license file 'COPYING' writing manifest file 'pyhmmer.egg-info/SOURCES.txt' creating '/builddir/build/BUILD/python-pyhmmer-0.10.15-build/pyhmmer-0.10.15/pyhmmer-0.10.15.dist-info' Handling psutil ~=5.8 from hook generated metadata: Requires-Dist (pyhmmer) Requirement satisfied: psutil ~=5.8 (installed: psutil 5.9.8) + cat /builddir/build/BUILD/python-pyhmmer-0.10.15-build/python-pyhmmer-0.10.15-1.fc41.x86_64-pyproject-buildrequires + rm -rfv pyhmmer-0.10.15.dist-info/ removed 'pyhmmer-0.10.15.dist-info/COPYING' removed 'pyhmmer-0.10.15.dist-info/METADATA' removed 'pyhmmer-0.10.15.dist-info/top_level.txt' removed directory 'pyhmmer-0.10.15.dist-info/' + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.BXk8yG + umask 022 + cd /builddir/build/BUILD/python-pyhmmer-0.10.15-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 pyhmmer-0.10.15 + mkdir -p /builddir/build/BUILD/python-pyhmmer-0.10.15-build/pyhmmer-0.10.15/.pyproject-builddir + 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 ' + 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 ' + 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 ' + 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 ' + VALAFLAGS=-g + 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' + 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 ' + LT_SYS_LIBRARY_PATH=/usr/lib64: + CC=gcc + CXX=g++ + TMPDIR=/builddir/build/BUILD/python-pyhmmer-0.10.15-build/pyhmmer-0.10.15/.pyproject-builddir + /usr/bin/python3 -Bs /usr/lib/rpm/redhat/pyproject_wheel.py /builddir/build/BUILD/python-pyhmmer-0.10.15-build/pyhmmer-0.10.15/pyproject-wheeldir Processing /builddir/build/BUILD/python-pyhmmer-0.10.15-build/pyhmmer-0.10.15 Preparing metadata (pyproject.toml): started Running command Preparing metadata (pyproject.toml) running dist_info creating /builddir/build/BUILD/python-pyhmmer-0.10.15-build/pyhmmer-0.10.15/.pyproject-builddir/pip-modern-metadata-hirn2axx/pyhmmer.egg-info writing /builddir/build/BUILD/python-pyhmmer-0.10.15-build/pyhmmer-0.10.15/.pyproject-builddir/pip-modern-metadata-hirn2axx/pyhmmer.egg-info/PKG-INFO writing dependency_links to /builddir/build/BUILD/python-pyhmmer-0.10.15-build/pyhmmer-0.10.15/.pyproject-builddir/pip-modern-metadata-hirn2axx/pyhmmer.egg-info/dependency_links.txt writing requirements to /builddir/build/BUILD/python-pyhmmer-0.10.15-build/pyhmmer-0.10.15/.pyproject-builddir/pip-modern-metadata-hirn2axx/pyhmmer.egg-info/requires.txt writing top-level names to /builddir/build/BUILD/python-pyhmmer-0.10.15-build/pyhmmer-0.10.15/.pyproject-builddir/pip-modern-metadata-hirn2axx/pyhmmer.egg-info/top_level.txt writing manifest file '/builddir/build/BUILD/python-pyhmmer-0.10.15-build/pyhmmer-0.10.15/.pyproject-builddir/pip-modern-metadata-hirn2axx/pyhmmer.egg-info/SOURCES.txt' reading manifest file '/builddir/build/BUILD/python-pyhmmer-0.10.15-build/pyhmmer-0.10.15/.pyproject-builddir/pip-modern-metadata-hirn2axx/pyhmmer.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files matching '*.ai' found under directory 'vendor/hmmer' warning: no previously-included files matching '*.pl' found under directory 'vendor' no previously-included directories found matching 'vendor/easel/demotic' no previously-included directories found matching 'vendor/easel/documentation' no previously-included directories found matching 'vendor/easel/esl_msa_testfiles' no previously-included directories found matching 'vendor/easel/miniapps' no previously-included directories found matching 'vendor/easel/testsuite' no previously-included directories found matching 'vendor/hmmer/autobuild' no previously-included directories found matching 'vendor/hmmer/documentation' no previously-included directories found matching 'vendor/hmmer/contrib' no previously-included directories found matching 'vendor/hmmer/profmark' no previously-included directories found matching 'vendor/hmmer/testsuite' no previously-included directories found matching 'vendor/hmmer/test-speed' no previously-included directories found matching 'vendor/hmmer/tutorial' adding license file 'COPYING' writing manifest file '/builddir/build/BUILD/python-pyhmmer-0.10.15-build/pyhmmer-0.10.15/.pyproject-builddir/pip-modern-metadata-hirn2axx/pyhmmer.egg-info/SOURCES.txt' creating '/builddir/build/BUILD/python-pyhmmer-0.10.15-build/pyhmmer-0.10.15/.pyproject-builddir/pip-modern-metadata-hirn2axx/pyhmmer-0.10.15.dist-info' Preparing metadata (pyproject.toml): finished with status 'done' Building wheels for collected packages: pyhmmer Building wheel for pyhmmer (pyproject.toml): started Running command Building wheel for pyhmmer (pyproject.toml) running bdist_wheel running build running build_py creating build creating build/lib.linux-x86_64-cpython-313 creating build/lib.linux-x86_64-cpython-313/pyhmmer copying pyhmmer/utils.py -> build/lib.linux-x86_64-cpython-313/pyhmmer copying pyhmmer/hmmer.py -> build/lib.linux-x86_64-cpython-313/pyhmmer copying pyhmmer/__init__.py -> build/lib.linux-x86_64-cpython-313/pyhmmer creating build/lib.linux-x86_64-cpython-313/pyhmmer/tests copying pyhmmer/tests/utils.py -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests copying pyhmmer/tests/test_hmmer.py -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests copying pyhmmer/tests/test_errors.py -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests copying pyhmmer/tests/test_doctest.py -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests copying pyhmmer/tests/__init__.py -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests creating build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_plan7 copying pyhmmer/tests/test_plan7/test_traces.py -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_plan7 copying pyhmmer/tests/test_plan7/test_tracealigner.py -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_plan7 copying pyhmmer/tests/test_plan7/test_tophits.py -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_plan7 copying pyhmmer/tests/test_plan7/test_profile.py -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_plan7 copying pyhmmer/tests/test_plan7/test_pipeline.py -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_plan7 copying pyhmmer/tests/test_plan7/test_optimizedprofile.py -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_plan7 copying pyhmmer/tests/test_plan7/test_hmmfile.py -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_plan7 copying pyhmmer/tests/test_plan7/test_hmm.py -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_plan7 copying pyhmmer/tests/test_plan7/test_hit.py -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_plan7 copying pyhmmer/tests/test_plan7/test_builder.py -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_plan7 copying pyhmmer/tests/test_plan7/test_block.py -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_plan7 copying pyhmmer/tests/test_plan7/test_background.py -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_plan7 copying pyhmmer/tests/test_plan7/test_alignment.py -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_plan7 copying pyhmmer/tests/test_plan7/__init__.py -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_plan7 creating build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_easel copying pyhmmer/tests/test_easel/test_vector.py -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_easel copying pyhmmer/tests/test_easel/test_ssi.py -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_easel copying pyhmmer/tests/test_easel/test_sequencefile.py -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_easel copying pyhmmer/tests/test_easel/test_sequence.py -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_easel copying pyhmmer/tests/test_easel/test_randomness.py -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_easel copying pyhmmer/tests/test_easel/test_msafile.py -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_easel copying pyhmmer/tests/test_easel/test_msa.py -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_easel copying pyhmmer/tests/test_easel/test_matrix.py -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_easel copying pyhmmer/tests/test_easel/test_keyhash.py -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_easel copying pyhmmer/tests/test_easel/test_gencode.py -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_easel copying pyhmmer/tests/test_easel/test_block.py -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_easel copying pyhmmer/tests/test_easel/test_bitfield.py -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_easel copying pyhmmer/tests/test_easel/test_alphabet.py -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_easel copying pyhmmer/tests/test_easel/__init__.py -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_easel running egg_info writing pyhmmer.egg-info/PKG-INFO writing dependency_links to pyhmmer.egg-info/dependency_links.txt writing requirements to pyhmmer.egg-info/requires.txt writing top-level names to pyhmmer.egg-info/top_level.txt reading manifest file 'pyhmmer.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files matching '*.ai' found under directory 'vendor/hmmer' warning: no previously-included files matching '*.pl' found under directory 'vendor' no previously-included directories found matching 'vendor/easel/demotic' no previously-included directories found matching 'vendor/easel/documentation' no previously-included directories found matching 'vendor/easel/esl_msa_testfiles' no previously-included directories found matching 'vendor/easel/miniapps' no previously-included directories found matching 'vendor/easel/testsuite' no previously-included directories found matching 'vendor/hmmer/autobuild' no previously-included directories found matching 'vendor/hmmer/documentation' no previously-included directories found matching 'vendor/hmmer/contrib' no previously-included directories found matching 'vendor/hmmer/profmark' no previously-included directories found matching 'vendor/hmmer/testsuite' no previously-included directories found matching 'vendor/hmmer/test-speed' no previously-included directories found matching 'vendor/hmmer/tutorial' adding license file 'COPYING' writing manifest file 'pyhmmer.egg-info/SOURCES.txt' /usr/lib/python3.13/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'pyhmmer.fileobj' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pyhmmer.fileobj' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pyhmmer.fileobj' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pyhmmer.fileobj' to be distributed and are already explicitly excluding 'pyhmmer.fileobj' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3.13/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'pyhmmer.reexports' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pyhmmer.reexports' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pyhmmer.reexports' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pyhmmer.reexports' to be distributed and are already explicitly excluding 'pyhmmer.reexports' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3.13/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'pyhmmer.tests.data' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pyhmmer.tests.data' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pyhmmer.tests.data' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pyhmmer.tests.data' to be distributed and are already explicitly excluding 'pyhmmer.tests.data' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3.13/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'pyhmmer.tests.data.hmms' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pyhmmer.tests.data.hmms' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pyhmmer.tests.data.hmms' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pyhmmer.tests.data.hmms' to be distributed and are already explicitly excluding 'pyhmmer.tests.data.hmms' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3.13/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'pyhmmer.tests.data.hmms.bin' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pyhmmer.tests.data.hmms.bin' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pyhmmer.tests.data.hmms.bin' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pyhmmer.tests.data.hmms.bin' to be distributed and are already explicitly excluding 'pyhmmer.tests.data.hmms.bin' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3.13/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'pyhmmer.tests.data.hmms.db' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pyhmmer.tests.data.hmms.db' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pyhmmer.tests.data.hmms.db' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pyhmmer.tests.data.hmms.db' to be distributed and are already explicitly excluding 'pyhmmer.tests.data.hmms.db' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3.13/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'pyhmmer.tests.data.hmms.txt' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pyhmmer.tests.data.hmms.txt' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pyhmmer.tests.data.hmms.txt' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pyhmmer.tests.data.hmms.txt' to be distributed and are already explicitly excluding 'pyhmmer.tests.data.hmms.txt' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3.13/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'pyhmmer.tests.data.hmms.txt2' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pyhmmer.tests.data.hmms.txt2' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pyhmmer.tests.data.hmms.txt2' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pyhmmer.tests.data.hmms.txt2' to be distributed and are already explicitly excluding 'pyhmmer.tests.data.hmms.txt2' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3.13/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'pyhmmer.tests.data.jackhmmer' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pyhmmer.tests.data.jackhmmer' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pyhmmer.tests.data.jackhmmer' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pyhmmer.tests.data.jackhmmer' to be distributed and are already explicitly excluding 'pyhmmer.tests.data.jackhmmer' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3.13/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'pyhmmer.tests.data.msa' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pyhmmer.tests.data.msa' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pyhmmer.tests.data.msa' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pyhmmer.tests.data.msa' to be distributed and are already explicitly excluding 'pyhmmer.tests.data.msa' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3.13/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'pyhmmer.tests.data.seqs' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pyhmmer.tests.data.seqs' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pyhmmer.tests.data.seqs' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pyhmmer.tests.data.seqs' to be distributed and are already explicitly excluding 'pyhmmer.tests.data.seqs' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3.13/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'pyhmmer.tests.data.tables' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pyhmmer.tests.data.tables' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pyhmmer.tests.data.tables' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pyhmmer.tests.data.tables' to be distributed and are already explicitly excluding 'pyhmmer.tests.data.tables' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) copying pyhmmer/_getid.pxi -> build/lib.linux-x86_64-cpython-313/pyhmmer copying pyhmmer/daemon.pxd -> build/lib.linux-x86_64-cpython-313/pyhmmer copying pyhmmer/daemon.pyi -> build/lib.linux-x86_64-cpython-313/pyhmmer copying pyhmmer/daemon.pyx -> build/lib.linux-x86_64-cpython-313/pyhmmer copying pyhmmer/easel.pxd -> build/lib.linux-x86_64-cpython-313/pyhmmer copying pyhmmer/easel.pyi -> build/lib.linux-x86_64-cpython-313/pyhmmer copying pyhmmer/easel.pyx -> build/lib.linux-x86_64-cpython-313/pyhmmer copying pyhmmer/errors.pyi -> build/lib.linux-x86_64-cpython-313/pyhmmer copying pyhmmer/errors.pyx -> build/lib.linux-x86_64-cpython-313/pyhmmer copying pyhmmer/exceptions.pxi -> build/lib.linux-x86_64-cpython-313/pyhmmer copying pyhmmer/plan7.pxd -> build/lib.linux-x86_64-cpython-313/pyhmmer copying pyhmmer/plan7.pyi -> build/lib.linux-x86_64-cpython-313/pyhmmer copying pyhmmer/plan7.pyx -> build/lib.linux-x86_64-cpython-313/pyhmmer copying pyhmmer/py.typed -> build/lib.linux-x86_64-cpython-313/pyhmmer creating build/lib.linux-x86_64-cpython-313/pyhmmer/fileobj copying pyhmmer/fileobj/__init__.pxd -> build/lib.linux-x86_64-cpython-313/pyhmmer/fileobj copying pyhmmer/fileobj/bsd.h -> build/lib.linux-x86_64-cpython-313/pyhmmer/fileobj copying pyhmmer/fileobj/bsd.pxd -> build/lib.linux-x86_64-cpython-313/pyhmmer/fileobj copying pyhmmer/fileobj/linux.h -> build/lib.linux-x86_64-cpython-313/pyhmmer/fileobj copying pyhmmer/fileobj/linux.pxd -> build/lib.linux-x86_64-cpython-313/pyhmmer/fileobj copying pyhmmer/fileobj/util.h -> build/lib.linux-x86_64-cpython-313/pyhmmer/fileobj creating build/lib.linux-x86_64-cpython-313/pyhmmer/reexports copying pyhmmer/reexports/__init__.pxd -> build/lib.linux-x86_64-cpython-313/pyhmmer/reexports copying pyhmmer/reexports/esl_sqio_ascii.h -> build/lib.linux-x86_64-cpython-313/pyhmmer/reexports copying pyhmmer/reexports/esl_sqio_ascii.pxd -> build/lib.linux-x86_64-cpython-313/pyhmmer/reexports copying pyhmmer/reexports/p7_hmmfile.h -> build/lib.linux-x86_64-cpython-313/pyhmmer/reexports copying pyhmmer/reexports/p7_hmmfile.pxd -> build/lib.linux-x86_64-cpython-313/pyhmmer/reexports copying pyhmmer/reexports/p7_tophits.h -> build/lib.linux-x86_64-cpython-313/pyhmmer/reexports copying pyhmmer/reexports/p7_tophits.pxd -> build/lib.linux-x86_64-cpython-313/pyhmmer/reexports copying pyhmmer/tests/requirements.txt -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests creating build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data copying pyhmmer/tests/data/README.md -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data creating build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms copying pyhmmer/tests/data/hmms/make.sh -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms creating build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/bin copying pyhmmer/tests/data/hmms/bin/PF02826.h3m -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/bin copying pyhmmer/tests/data/hmms/bin/PKSI-AT.h3m -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/bin copying pyhmmer/tests/data/hmms/bin/RF00001.h3m -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/bin copying pyhmmer/tests/data/hmms/bin/RREFam.h3m -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/bin copying pyhmmer/tests/data/hmms/bin/Thioesterase.h3m -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/bin creating build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/db copying pyhmmer/tests/data/hmms/db/PF02826.hmm -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/db copying pyhmmer/tests/data/hmms/db/PF02826.hmm.h3f -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/db copying pyhmmer/tests/data/hmms/db/PF02826.hmm.h3i -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/db copying pyhmmer/tests/data/hmms/db/PF02826.hmm.h3m -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/db copying pyhmmer/tests/data/hmms/db/PF02826.hmm.h3p -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/db copying pyhmmer/tests/data/hmms/db/PKSI-AT.hmm -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/db copying pyhmmer/tests/data/hmms/db/PKSI-AT.hmm.h3f -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/db copying pyhmmer/tests/data/hmms/db/PKSI-AT.hmm.h3i -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/db copying pyhmmer/tests/data/hmms/db/PKSI-AT.hmm.h3m -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/db copying pyhmmer/tests/data/hmms/db/PKSI-AT.hmm.h3p -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/db copying pyhmmer/tests/data/hmms/db/RREFam.hmm -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/db copying pyhmmer/tests/data/hmms/db/RREFam.hmm.h3f -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/db copying pyhmmer/tests/data/hmms/db/RREFam.hmm.h3i -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/db copying pyhmmer/tests/data/hmms/db/RREFam.hmm.h3m -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/db copying pyhmmer/tests/data/hmms/db/RREFam.hmm.h3p -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/db copying pyhmmer/tests/data/hmms/db/Thioesterase.hmm -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/db copying pyhmmer/tests/data/hmms/db/Thioesterase.hmm.h3f -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/db copying pyhmmer/tests/data/hmms/db/Thioesterase.hmm.h3i -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/db copying pyhmmer/tests/data/hmms/db/Thioesterase.hmm.h3m -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/db copying pyhmmer/tests/data/hmms/db/Thioesterase.hmm.h3p -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/db creating build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/txt copying pyhmmer/tests/data/hmms/txt/KR.hmm -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/txt copying pyhmmer/tests/data/hmms/txt/LuxC.hmm -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/txt copying pyhmmer/tests/data/hmms/txt/PF02826.hmm -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/txt copying pyhmmer/tests/data/hmms/txt/PKSI-AT.hmm -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/txt copying pyhmmer/tests/data/hmms/txt/RF00001.hmm -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/txt copying pyhmmer/tests/data/hmms/txt/RREFam.hmm -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/txt copying pyhmmer/tests/data/hmms/txt/Thioesterase.hmm -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/txt copying pyhmmer/tests/data/hmms/txt/bmyD.hmm -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/txt copying pyhmmer/tests/data/hmms/txt/laccase.hmm -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/txt creating build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/txt2 copying pyhmmer/tests/data/hmms/txt2/RREFam.hmm2 -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/txt2 copying pyhmmer/tests/data/hmms/txt2/Thioesterase.hmm2 -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/txt2 creating build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/jackhmmer copying pyhmmer/tests/data/jackhmmer/KR-1.sto -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/jackhmmer copying pyhmmer/tests/data/jackhmmer/KR-1_bkup.sto -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/jackhmmer copying pyhmmer/tests/data/jackhmmer/KR-2.sto -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/jackhmmer copying pyhmmer/tests/data/jackhmmer/KR-3.sto -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/jackhmmer copying pyhmmer/tests/data/jackhmmer/KR-4.sto -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/jackhmmer copying pyhmmer/tests/data/jackhmmer/KR-5.sto -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/jackhmmer copying pyhmmer/tests/data/jackhmmer/KR-6.sto -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/jackhmmer copying pyhmmer/tests/data/jackhmmer/p12748-1.sto -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/jackhmmer copying pyhmmer/tests/data/jackhmmer/p12748-2.sto -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/jackhmmer copying pyhmmer/tests/data/jackhmmer/p12748-3.sto -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/jackhmmer creating build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/msa copying pyhmmer/tests/data/msa/LuxC.faa -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/msa copying pyhmmer/tests/data/msa/LuxC.hmmalign.sto -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/msa copying pyhmmer/tests/data/msa/LuxC.sto -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/msa copying pyhmmer/tests/data/msa/laccase.clw -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/msa creating build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/seqs copying pyhmmer/tests/data/seqs/1390.SAMEA104415756.OFHT01000022.fna -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/seqs copying pyhmmer/tests/data/seqs/1390.SAMEA104415756.OFHT01000024.fna -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/seqs copying pyhmmer/tests/data/seqs/938293.PRJEB85.HG003687.faa -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/seqs copying pyhmmer/tests/data/seqs/BGC0001090.gbk -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/seqs copying pyhmmer/tests/data/seqs/CP040672.1.genes_100.fna -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/seqs copying pyhmmer/tests/data/seqs/LuxC.faa -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/seqs copying pyhmmer/tests/data/seqs/PKSI.faa -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/seqs copying pyhmmer/tests/data/seqs/bmyD.fna -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/seqs creating build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/tables copying pyhmmer/tests/data/tables/A0A089QRB9.domtbl -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/tables copying pyhmmer/tests/data/tables/PF02826.domtbl -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/tables copying pyhmmer/tests/data/tables/PF02826.tbl -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/tables copying pyhmmer/tests/data/tables/RREFam.domtbl -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/tables copying pyhmmer/tests/data/tables/RREFam.scan.tbl -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/tables copying pyhmmer/tests/data/tables/RREFam.tbl -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/tables copying pyhmmer/tests/data/tables/bmyD1.tbl -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/tables copying pyhmmer/tests/data/tables/bmyD2.tbl -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/tables copying pyhmmer/tests/data/tables/bmyD3.tbl -> build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/tables running build_clib creating build/temp.linux-x86_64-cpython-313 generating "divsufsort.h" for divsufsort library copying vendor/hmmer/libdivsufsort/divsufsort.h.in -> build/temp.linux-x86_64-cpython-313/divsufsort.h generating "esl_config.h" for easel library gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -c build/temp.linux-x86_64-cpython-313/have_SSE4.c -o build/temp.linux-x86_64-cpython-313/have_SSE4.o gcc -msse4.1 build/temp.linux-x86_64-cpython-313/have_SSE4.o -o build/temp.linux-x86_64-cpython-313/have_SSE4 checking whether compiler can build SSE4 code... yes, but cannot run code gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -c build/temp.linux-x86_64-cpython-313/have_stdio_h.c -o build/temp.linux-x86_64-cpython-313/have_stdio_h.o checking whether can be included... yes gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -c build/temp.linux-x86_64-cpython-313/have_stdlib_h.c -o build/temp.linux-x86_64-cpython-313/have_stdlib_h.o checking whether can be included... yes gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -c build/temp.linux-x86_64-cpython-313/have_string_h.c -o build/temp.linux-x86_64-cpython-313/have_string_h.o checking whether can be included... yes gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -c build/temp.linux-x86_64-cpython-313/have_inttypes_h.c -o build/temp.linux-x86_64-cpython-313/have_inttypes_h.o checking whether can be included... yes gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -c build/temp.linux-x86_64-cpython-313/have_stdint_h.c -o build/temp.linux-x86_64-cpython-313/have_stdint_h.o checking whether can be included... yes gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -c build/temp.linux-x86_64-cpython-313/have_strings_h.c -o build/temp.linux-x86_64-cpython-313/have_strings_h.o checking whether can be included... yes gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -c build/temp.linux-x86_64-cpython-313/have_sys_stat_h.c -o build/temp.linux-x86_64-cpython-313/have_sys_stat_h.o checking whether can be included... yes gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -c build/temp.linux-x86_64-cpython-313/have_sys_types_h.c -o build/temp.linux-x86_64-cpython-313/have_sys_types_h.o checking whether can be included... yes gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -c build/temp.linux-x86_64-cpython-313/have_unistd_h.c -o build/temp.linux-x86_64-cpython-313/have_unistd_h.o checking whether can be included... yes gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -c build/temp.linux-x86_64-cpython-313/have_endian_h.c -o build/temp.linux-x86_64-cpython-313/have_endian_h.o checking whether can be included... yes gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -c build/temp.linux-x86_64-cpython-313/have_netinet_in_h.c -o build/temp.linux-x86_64-cpython-313/have_netinet_in_h.o checking whether can be included... yes gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -c build/temp.linux-x86_64-cpython-313/have_sys_param_h.c -o build/temp.linux-x86_64-cpython-313/have_sys_param_h.o checking whether can be included... yes gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -c build/temp.linux-x86_64-cpython-313/have_sys_sysctl_h.c -o build/temp.linux-x86_64-cpython-313/have_sys_sysctl_h.o build/temp.linux-x86_64-cpython-313/have_sys_sysctl_h.c:1:10: fatal error: sys/sysctl.h: No such file or directory 1 | #include "sys/sysctl.h" | ^~~~~~~~~~~~~~ compilation terminated. checking whether can be included... no gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -c build/temp.linux-x86_64-cpython-313/have_aligned_alloc.c -o build/temp.linux-x86_64-cpython-313/have_aligned_alloc.o -Wno-all cc1: error: ‘-Wformat-security’ ignored without ‘-Wformat’ [-Werror=format-security] build/temp.linux-x86_64-cpython-313/have_aligned_alloc.c: warning: -Wno-implicit-int detected - is this intentional ? build/temp.linux-x86_64-cpython-313/have_aligned_alloc.c: warning: -Wno-implicit-function-declaration detected - is this intentional ? build/temp.linux-x86_64-cpython-313/have_aligned_alloc.c: In function ‘main’: build/temp.linux-x86_64-cpython-313/have_aligned_alloc.c:2:14: warning: ignoring return value of ‘aligned_alloc’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2 | int main() { aligned_alloc(0, 0); return 0; } | ^~~~~~~~~~~~~~~~~~~ cc1: some warnings being treated as errors checking whether function 'aligned_alloc' is available... no gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -c build/temp.linux-x86_64-cpython-313/have_erfc.c -o build/temp.linux-x86_64-cpython-313/have_erfc.o -Wno-all cc1: error: ‘-Wformat-security’ ignored without ‘-Wformat’ [-Werror=format-security] build/temp.linux-x86_64-cpython-313/have_erfc.c: warning: -Wno-implicit-int detected - is this intentional ? build/temp.linux-x86_64-cpython-313/have_erfc.c: warning: -Wno-implicit-function-declaration detected - is this intentional ? cc1: some warnings being treated as errors checking whether function 'erfc' is available... no gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -c build/temp.linux-x86_64-cpython-313/have_getpid.c -o build/temp.linux-x86_64-cpython-313/have_getpid.o -Wno-all cc1: error: ‘-Wformat-security’ ignored without ‘-Wformat’ [-Werror=format-security] build/temp.linux-x86_64-cpython-313/have_getpid.c: warning: -Wno-implicit-int detected - is this intentional ? build/temp.linux-x86_64-cpython-313/have_getpid.c: warning: -Wno-implicit-function-declaration detected - is this intentional ? cc1: some warnings being treated as errors checking whether function 'getpid' is available... no gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -c build/temp.linux-x86_64-cpython-313/have__mm_malloc.c -o build/temp.linux-x86_64-cpython-313/have__mm_malloc.o -Wno-all cc1: error: ‘-Wformat-security’ ignored without ‘-Wformat’ [-Werror=format-security] build/temp.linux-x86_64-cpython-313/have__mm_malloc.c: warning: -Wno-implicit-int detected - is this intentional ? build/temp.linux-x86_64-cpython-313/have__mm_malloc.c: warning: -Wno-implicit-function-declaration detected - is this intentional ? cc1: some warnings being treated as errors checking whether function '_mm_malloc' is available... no gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -c build/temp.linux-x86_64-cpython-313/have_popen.c -o build/temp.linux-x86_64-cpython-313/have_popen.o -Wno-all cc1: error: ‘-Wformat-security’ ignored without ‘-Wformat’ [-Werror=format-security] build/temp.linux-x86_64-cpython-313/have_popen.c: warning: -Wno-implicit-int detected - is this intentional ? build/temp.linux-x86_64-cpython-313/have_popen.c: warning: -Wno-implicit-function-declaration detected - is this intentional ? build/temp.linux-x86_64-cpython-313/have_popen.c: In function ‘main’: build/temp.linux-x86_64-cpython-313/have_popen.c:2:14: warning: ignoring return value of ‘popen’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2 | int main() { popen(NULL, NULL); return 0; } | ^~~~~~~~~~~~~~~~~ cc1: some warnings being treated as errors checking whether function 'popen' is available... no gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -c build/temp.linux-x86_64-cpython-313/have_posix_memalign.c -o build/temp.linux-x86_64-cpython-313/have_posix_memalign.o -Wno-all cc1: error: ‘-Wformat-security’ ignored without ‘-Wformat’ [-Werror=format-security] build/temp.linux-x86_64-cpython-313/have_posix_memalign.c: warning: -Wno-implicit-int detected - is this intentional ? build/temp.linux-x86_64-cpython-313/have_posix_memalign.c: warning: -Wno-implicit-function-declaration detected - is this intentional ? build/temp.linux-x86_64-cpython-313/have_posix_memalign.c: In function ‘main’: build/temp.linux-x86_64-cpython-313/have_posix_memalign.c:2:14: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2 | int main() { posix_memalign(NULL, 0, 0); return 0; } | ^~~~~~~~~~~~~~~~~~~~~~~~~~ cc1: some warnings being treated as errors checking whether function 'posix_memalign' is available... no gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -c build/temp.linux-x86_64-cpython-313/have_strcasecmp.c -o build/temp.linux-x86_64-cpython-313/have_strcasecmp.o -Wno-all cc1: error: ‘-Wformat-security’ ignored without ‘-Wformat’ [-Werror=format-security] build/temp.linux-x86_64-cpython-313/have_strcasecmp.c: warning: -Wno-implicit-int detected - is this intentional ? build/temp.linux-x86_64-cpython-313/have_strcasecmp.c: warning: -Wno-implicit-function-declaration detected - is this intentional ? cc1: some warnings being treated as errors checking whether function 'strcasecmp' is available... no gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -c build/temp.linux-x86_64-cpython-313/have_strsep.c -o build/temp.linux-x86_64-cpython-313/have_strsep.o -Wno-all cc1: error: ‘-Wformat-security’ ignored without ‘-Wformat’ [-Werror=format-security] build/temp.linux-x86_64-cpython-313/have_strsep.c: warning: -Wno-implicit-int detected - is this intentional ? build/temp.linux-x86_64-cpython-313/have_strsep.c: warning: -Wno-implicit-function-declaration detected - is this intentional ? cc1: some warnings being treated as errors checking whether function 'strsep' is available... no gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -c build/temp.linux-x86_64-cpython-313/have_sysconf.c -o build/temp.linux-x86_64-cpython-313/have_sysconf.o -Wno-all cc1: error: ‘-Wformat-security’ ignored without ‘-Wformat’ [-Werror=format-security] build/temp.linux-x86_64-cpython-313/have_sysconf.c: warning: -Wno-implicit-int detected - is this intentional ? build/temp.linux-x86_64-cpython-313/have_sysconf.c: warning: -Wno-implicit-function-declaration detected - is this intentional ? cc1: some warnings being treated as errors checking whether function 'sysconf' is available... no gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -c build/temp.linux-x86_64-cpython-313/have_sysctl.c -o build/temp.linux-x86_64-cpython-313/have_sysctl.o -Wno-all cc1: error: ‘-Wformat-security’ ignored without ‘-Wformat’ [-Werror=format-security] build/temp.linux-x86_64-cpython-313/have_sysctl.c: warning: -Wno-implicit-int detected - is this intentional ? build/temp.linux-x86_64-cpython-313/have_sysctl.c: warning: -Wno-implicit-function-declaration detected - is this intentional ? build/temp.linux-x86_64-cpython-313/have_sysctl.c:2:10: fatal error: sys/sysctl.h: No such file or directory 2 | #include | ^~~~~~~~~~~~~~ compilation terminated. cc1: some warnings being treated as errors checking whether function 'sysctl' is available... no gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -c build/temp.linux-x86_64-cpython-313/have_times.c -o build/temp.linux-x86_64-cpython-313/have_times.o -Wno-all cc1: error: ‘-Wformat-security’ ignored without ‘-Wformat’ [-Werror=format-security] build/temp.linux-x86_64-cpython-313/have_times.c: warning: -Wno-implicit-int detected - is this intentional ? build/temp.linux-x86_64-cpython-313/have_times.c: warning: -Wno-implicit-function-declaration detected - is this intentional ? cc1: some warnings being treated as errors checking whether function 'times' is available... no gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -c build/temp.linux-x86_64-cpython-313/have_fseeko.c -o build/temp.linux-x86_64-cpython-313/have_fseeko.o -Wno-all cc1: error: ‘-Wformat-security’ ignored without ‘-Wformat’ [-Werror=format-security] build/temp.linux-x86_64-cpython-313/have_fseeko.c: warning: -Wno-implicit-int detected - is this intentional ? build/temp.linux-x86_64-cpython-313/have_fseeko.c: warning: -Wno-implicit-function-declaration detected - is this intentional ? cc1: some warnings being treated as errors checking whether function 'fseeko' is available... no generating "p7_config.h" for hmmer library gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -c build/temp.linux-x86_64-cpython-313/have_SSE4.c -o build/temp.linux-x86_64-cpython-313/have_SSE4.o gcc -msse4.1 build/temp.linux-x86_64-cpython-313/have_SSE4.o -o build/temp.linux-x86_64-cpython-313/have_SSE4 checking whether compiler can build SSE4 code... yes, but cannot run code gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -c build/temp.linux-x86_64-cpython-313/have_endian_h.c -o build/temp.linux-x86_64-cpython-313/have_endian_h.o checking whether can be included... yes gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -c build/temp.linux-x86_64-cpython-313/have_inttypes_h.c -o build/temp.linux-x86_64-cpython-313/have_inttypes_h.o checking whether can be included... yes gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -c build/temp.linux-x86_64-cpython-313/have_stdint_h.c -o build/temp.linux-x86_64-cpython-313/have_stdint_h.o checking whether can be included... yes gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -c build/temp.linux-x86_64-cpython-313/have_unistd_h.c -o build/temp.linux-x86_64-cpython-313/have_unistd_h.o checking whether can be included... yes gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -c build/temp.linux-x86_64-cpython-313/have_sys_types_h.c -o build/temp.linux-x86_64-cpython-313/have_sys_types_h.o checking whether can be included... yes gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -c build/temp.linux-x86_64-cpython-313/have_netinet_in_h.c -o build/temp.linux-x86_64-cpython-313/have_netinet_in_h.o checking whether can be included... yes gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -c build/temp.linux-x86_64-cpython-313/have_sys_param_h.c -o build/temp.linux-x86_64-cpython-313/have_sys_param_h.o checking whether can be included... yes gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -c build/temp.linux-x86_64-cpython-313/have_sys_sysctl_h.c -o build/temp.linux-x86_64-cpython-313/have_sys_sysctl_h.o build/temp.linux-x86_64-cpython-313/have_sys_sysctl_h.c:1:10: fatal error: sys/sysctl.h: No such file or directory 1 | #include "sys/sysctl.h" | ^~~~~~~~~~~~~~ compilation terminated. checking whether can be included... no gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -c build/temp.linux-x86_64-cpython-313/have_mkstemp.c -o build/temp.linux-x86_64-cpython-313/have_mkstemp.o -Wno-all cc1: error: ‘-Wformat-security’ ignored without ‘-Wformat’ [-Werror=format-security] build/temp.linux-x86_64-cpython-313/have_mkstemp.c: warning: -Wno-implicit-int detected - is this intentional ? build/temp.linux-x86_64-cpython-313/have_mkstemp.c: warning: -Wno-implicit-function-declaration detected - is this intentional ? build/temp.linux-x86_64-cpython-313/have_mkstemp.c: In function ‘main’: build/temp.linux-x86_64-cpython-313/have_mkstemp.c:2:14: warning: ignoring return value of ‘mkstemp’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2 | int main() { mkstemp(NULL); return 0; } | ^~~~~~~~~~~~~ cc1: some warnings being treated as errors checking whether function 'mkstemp' is available... no gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -c build/temp.linux-x86_64-cpython-313/have_popen.c -o build/temp.linux-x86_64-cpython-313/have_popen.o -Wno-all cc1: error: ‘-Wformat-security’ ignored without ‘-Wformat’ [-Werror=format-security] build/temp.linux-x86_64-cpython-313/have_popen.c: warning: -Wno-implicit-int detected - is this intentional ? build/temp.linux-x86_64-cpython-313/have_popen.c: warning: -Wno-implicit-function-declaration detected - is this intentional ? build/temp.linux-x86_64-cpython-313/have_popen.c: In function ‘main’: build/temp.linux-x86_64-cpython-313/have_popen.c:2:14: warning: ignoring return value of ‘popen’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2 | int main() { popen(NULL, NULL); return 0; } | ^~~~~~~~~~~~~~~~~ cc1: some warnings being treated as errors checking whether function 'popen' is available... no gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -c build/temp.linux-x86_64-cpython-313/have_putenv.c -o build/temp.linux-x86_64-cpython-313/have_putenv.o -Wno-all cc1: error: ‘-Wformat-security’ ignored without ‘-Wformat’ [-Werror=format-security] build/temp.linux-x86_64-cpython-313/have_putenv.c: warning: -Wno-implicit-int detected - is this intentional ? build/temp.linux-x86_64-cpython-313/have_putenv.c: warning: -Wno-implicit-function-declaration detected - is this intentional ? cc1: some warnings being treated as errors checking whether function 'putenv' is available... no gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -c build/temp.linux-x86_64-cpython-313/have_strcasecmp.c -o build/temp.linux-x86_64-cpython-313/have_strcasecmp.o -Wno-all cc1: error: ‘-Wformat-security’ ignored without ‘-Wformat’ [-Werror=format-security] build/temp.linux-x86_64-cpython-313/have_strcasecmp.c: warning: -Wno-implicit-int detected - is this intentional ? build/temp.linux-x86_64-cpython-313/have_strcasecmp.c: warning: -Wno-implicit-function-declaration detected - is this intentional ? cc1: some warnings being treated as errors checking whether function 'strcasecmp' is available... no gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -c build/temp.linux-x86_64-cpython-313/have_strsep.c -o build/temp.linux-x86_64-cpython-313/have_strsep.o -Wno-all cc1: error: ‘-Wformat-security’ ignored without ‘-Wformat’ [-Werror=format-security] build/temp.linux-x86_64-cpython-313/have_strsep.c: warning: -Wno-implicit-int detected - is this intentional ? build/temp.linux-x86_64-cpython-313/have_strsep.c: warning: -Wno-implicit-function-declaration detected - is this intentional ? cc1: some warnings being treated as errors checking whether function 'strsep' is available... no gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -c build/temp.linux-x86_64-cpython-313/have_times.c -o build/temp.linux-x86_64-cpython-313/have_times.o -Wno-all cc1: error: ‘-Wformat-security’ ignored without ‘-Wformat’ [-Werror=format-security] build/temp.linux-x86_64-cpython-313/have_times.c: warning: -Wno-implicit-int detected - is this intentional ? build/temp.linux-x86_64-cpython-313/have_times.c: warning: -Wno-implicit-function-declaration detected - is this intentional ? cc1: some warnings being treated as errors checking whether function 'times' is available... no gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -c build/temp.linux-x86_64-cpython-313/have_getpid.c -o build/temp.linux-x86_64-cpython-313/have_getpid.o -Wno-all cc1: error: ‘-Wformat-security’ ignored without ‘-Wformat’ [-Werror=format-security] build/temp.linux-x86_64-cpython-313/have_getpid.c: warning: -Wno-implicit-int detected - is this intentional ? build/temp.linux-x86_64-cpython-313/have_getpid.c: warning: -Wno-implicit-function-declaration detected - is this intentional ? cc1: some warnings being treated as errors checking whether function 'getpid' is available... no gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -c build/temp.linux-x86_64-cpython-313/have_sysctl.c -o build/temp.linux-x86_64-cpython-313/have_sysctl.o -Wno-all cc1: error: ‘-Wformat-security’ ignored without ‘-Wformat’ [-Werror=format-security] build/temp.linux-x86_64-cpython-313/have_sysctl.c: warning: -Wno-implicit-int detected - is this intentional ? build/temp.linux-x86_64-cpython-313/have_sysctl.c: warning: -Wno-implicit-function-declaration detected - is this intentional ? build/temp.linux-x86_64-cpython-313/have_sysctl.c:2:10: fatal error: sys/sysctl.h: No such file or directory 2 | #include | ^~~~~~~~~~~~~~ compilation terminated. cc1: some warnings being treated as errors checking whether function 'sysctl' is available... no gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -c build/temp.linux-x86_64-cpython-313/have_sysconf.c -o build/temp.linux-x86_64-cpython-313/have_sysconf.o -Wno-all cc1: error: ‘-Wformat-security’ ignored without ‘-Wformat’ [-Werror=format-security] build/temp.linux-x86_64-cpython-313/have_sysconf.c: warning: -Wno-implicit-int detected - is this intentional ? build/temp.linux-x86_64-cpython-313/have_sysconf.c: warning: -Wno-implicit-function-declaration detected - is this intentional ? cc1: some warnings being treated as errors checking whether function 'sysconf' is available... no gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -c build/temp.linux-x86_64-cpython-313/have_getcwd.c -o build/temp.linux-x86_64-cpython-313/have_getcwd.o -Wno-all cc1: error: ‘-Wformat-security’ ignored without ‘-Wformat’ [-Werror=format-security] build/temp.linux-x86_64-cpython-313/have_getcwd.c: warning: -Wno-implicit-int detected - is this intentional ? build/temp.linux-x86_64-cpython-313/have_getcwd.c: warning: -Wno-implicit-function-declaration detected - is this intentional ? build/temp.linux-x86_64-cpython-313/have_getcwd.c: In function ‘main’: build/temp.linux-x86_64-cpython-313/have_getcwd.c:2:14: warning: ignoring return value of ‘getcwd’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2 | int main() { getcwd(NULL, 0); return 0; } | ^~~~~~~~~~~~~~~ cc1: some warnings being treated as errors checking whether function 'getcwd' is available... no gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -c build/temp.linux-x86_64-cpython-313/have_chmod.c -o build/temp.linux-x86_64-cpython-313/have_chmod.o -Wno-all cc1: error: ‘-Wformat-security’ ignored without ‘-Wformat’ [-Werror=format-security] build/temp.linux-x86_64-cpython-313/have_chmod.c: warning: -Wno-implicit-int detected - is this intentional ? build/temp.linux-x86_64-cpython-313/have_chmod.c: warning: -Wno-implicit-function-declaration detected - is this intentional ? cc1: some warnings being treated as errors checking whether function 'chmod' is available... no gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -c build/temp.linux-x86_64-cpython-313/have_stat.c -o build/temp.linux-x86_64-cpython-313/have_stat.o -Wno-all cc1: error: ‘-Wformat-security’ ignored without ‘-Wformat’ [-Werror=format-security] build/temp.linux-x86_64-cpython-313/have_stat.c: warning: -Wno-implicit-int detected - is this intentional ? build/temp.linux-x86_64-cpython-313/have_stat.c: warning: -Wno-implicit-function-declaration detected - is this intentional ? cc1: some warnings being treated as errors checking whether function 'stat' is available... no gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -c build/temp.linux-x86_64-cpython-313/have_fstat.c -o build/temp.linux-x86_64-cpython-313/have_fstat.o -Wno-all cc1: error: ‘-Wformat-security’ ignored without ‘-Wformat’ [-Werror=format-security] build/temp.linux-x86_64-cpython-313/have_fstat.c: warning: -Wno-implicit-int detected - is this intentional ? build/temp.linux-x86_64-cpython-313/have_fstat.c: warning: -Wno-implicit-function-declaration detected - is this intentional ? cc1: some warnings being treated as errors checking whether function 'fstat' is available... no gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -c build/temp.linux-x86_64-cpython-313/have_erfc.c -o build/temp.linux-x86_64-cpython-313/have_erfc.o -Wno-all cc1: error: ‘-Wformat-security’ ignored without ‘-Wformat’ [-Werror=format-security] build/temp.linux-x86_64-cpython-313/have_erfc.c: warning: -Wno-implicit-int detected - is this intentional ? build/temp.linux-x86_64-cpython-313/have_erfc.c: warning: -Wno-implicit-function-declaration detected - is this intentional ? cc1: some warnings being treated as errors checking whether function 'erfc' is available... no generating build/temp.linux-x86_64-cpython-313/libdivsufsort.a from vendor/hmmer/libdivsufsort/divsufsort.c generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/libdivsufsort/divsufsort.o from vendor/hmmer/libdivsufsort/divsufsort.c creating build/temp.linux-x86_64-cpython-313/vendor creating build/temp.linux-x86_64-cpython-313/vendor/hmmer creating build/temp.linux-x86_64-cpython-313/vendor/hmmer/libdivsufsort gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/libdivsufsort/divsufsort.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/libdivsufsort/divsufsort.o ar rcs build/temp.linux-x86_64-cpython-313/libdivsufsort.a build/temp.linux-x86_64-cpython-313/vendor/hmmer/libdivsufsort/divsufsort.o generating build/temp.linux-x86_64-cpython-313/libeasel.a from vendor/easel/interface_lapack.c, vendor/easel/interface_gsl.c, vendor/easel/esl_wuss.c, vendor/easel/esl_workqueue.c, vendor/easel/esl_weibull.c, vendor/easel/esl_vmx.c, vendor/easel/esl_vectorops.c, vendor/easel/esl_varint.c, vendor/easel/esl_tree.c, vendor/easel/esl_threads.c, vendor/easel/esl_swat.c, vendor/easel/esl_subcmd.c, vendor/easel/esl_stretchexp.c, vendor/easel/esl_stopwatch.c, vendor/easel/esl_stats.c, vendor/easel/esl_stack.c, vendor/easel/esl_ssi.c, vendor/easel/esl_sse.c, vendor/easel/esl_sqio_ncbi.c, vendor/easel/esl_sqio_ascii.c, vendor/easel/esl_sqio.c, vendor/easel/esl_sq.c, vendor/easel/esl_scorematrix.c, vendor/easel/esl_rootfinder.c, vendor/easel/esl_regexp.c, vendor/easel/esl_red_black.c, vendor/easel/esl_recorder.c, vendor/easel/esl_ratematrix.c, vendor/easel/esl_randomseq.c, vendor/easel/esl_random.c, vendor/easel/esl_rand64.c, vendor/easel/esl_quicksort.c, vendor/easel/esl_paml.c, vendor/easel/esl_normal.c, vendor/easel/esl_neon.c, vendor/easel/esl_msaweight.c, vendor/easel/esl_msashuffle.c, vendor/easel/esl_msafile_stockholm.c, vendor/easel/esl_msafile_selex.c, vendor/easel/esl_msafile_psiblast.c, vendor/easel/esl_msafile_phylip.c, vendor/easel/esl_msafile_clustal.c, vendor/easel/esl_msafile_afa.c, vendor/easel/esl_msafile_a2m.c, vendor/easel/esl_msafile2.c, vendor/easel/esl_msafile.c, vendor/easel/esl_msacluster.c, vendor/easel/esl_msa.c, vendor/easel/esl_mpi.c, vendor/easel/esl_mixgev.c, vendor/easel/esl_mixdchlet.c, vendor/easel/esl_minimizer.c, vendor/easel/esl_mem.c, vendor/easel/esl_matrixops.c, vendor/easel/esl_lognormal.c, vendor/easel/esl_keyhash.c, vendor/easel/esl_json.c, vendor/easel/esl_iset.c, vendor/easel/esl_hyperexp.c, vendor/easel/esl_huffman.c, vendor/easel/esl_hmm.c, vendor/easel/esl_histogram.c, vendor/easel/esl_heap.c, vendor/easel/esl_gumbel.c, vendor/easel/esl_graph.c, vendor/easel/esl_gev.c, vendor/easel/esl_getopts.c, vendor/easel/esl_gencode.c, vendor/easel/esl_gamma.c, vendor/easel/esl_fileparser.c, vendor/easel/esl_exponential.c, vendor/easel/esl_dsqdata.c, vendor/easel/esl_dmatrix.c, vendor/easel/esl_distance.c, vendor/easel/esl_dirichlet.c, vendor/easel/esl_cpu.c, vendor/easel/esl_composition.c, vendor/easel/esl_cluster.c, vendor/easel/esl_buffer.c, vendor/easel/esl_bitfield.c, vendor/easel/esl_avx512.c, vendor/easel/esl_avx.c, vendor/easel/esl_arr3.c, vendor/easel/esl_arr2.c, vendor/easel/esl_alphabet.c, vendor/easel/esl_alloc.c, vendor/easel/easel.c generating build/temp.linux-x86_64-cpython-313/esl_sqio_ascii.c from vendor/easel/esl_sqio_ascii.c generating build/temp.linux-x86_64-cpython-313/vendor/easel/interface_lapack.o from vendor/easel/interface_lapack.c generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_sqio_ncbi.o from vendor/easel/esl_sqio_ncbi.c creating build/temp.linux-x86_64-cpython-313/vendor/easel generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_stretchexp.o from vendor/easel/esl_stretchexp.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_stretchexp.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_stretchexp.o creating build/temp.linux-x86_64-cpython-313/vendor/easel gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/interface_lapack.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/interface_lapack.o gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_sqio_ncbi.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_sqio_ncbi.o generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_vectorops.o from vendor/easel/esl_vectorops.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_vectorops.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_vectorops.o generating build/temp.linux-x86_64-cpython-313/vendor/easel/interface_gsl.o from vendor/easel/interface_gsl.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/interface_gsl.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/interface_gsl.o generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_wuss.o from vendor/easel/esl_wuss.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_wuss.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_wuss.o vendor/easel/esl_sqio_ncbi.c: In function ‘sqncbi_ParseIndexFile’: vendor/easel/esl_sqio_ncbi.c:216:24: warning: comparison of integer expressions of different signedness: ‘__uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 216 | if (htobe32(info[1]) != dbtype) status = eslEUNIMPLEMENTED; | ^~ vendor/easel/esl_sqio_ncbi.c:226:58: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 226 | if (fread(ncbi->title, sizeof(char), len, ncbi->fppin) != len) { status = eslFAIL; goto ERROR; } | ^~ vendor/easel/esl_sqio_ncbi.c:233:62: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 233 | if (fread(ncbi->timestamp, sizeof(char), len, ncbi->fppin) != len) { status = eslFAIL; goto ERROR; } | ^~ vendor/easel/esl_sqio_ncbi.c: In function ‘sqncbi_Read’: vendor/easel/esl_sqio_ncbi.c:758:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 758 | if (ncbi->index >= ncbi->num_seq) return eslEOF; | ^~ vendor/easel/esl_sqio_ncbi.c: In function ‘sqncbi_ReadInfo’: vendor/easel/esl_sqio_ncbi.c:809:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 809 | if (ncbi->index >= ncbi->num_seq) return eslEOF; | ^~ vendor/easel/esl_sqio_ncbi.c: In function ‘sqncbi_ReadSequence’: vendor/easel/esl_sqio_ncbi.c:860:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 860 | if (ncbi->index >= ncbi->num_seq) return eslEOF; | ^~ vendor/easel/esl_sqio_ncbi.c: In function ‘sqncbi_ReadWindow’: vendor/easel/esl_sqio_ncbi.c:1036:33: warning: comparison of integer expressions of different signedness: ‘uint64_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1036 | if (status != eslOK || nres != W) { | ^~ vendor/easel/esl_sqio_ncbi.c:1059:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 1059 | if (ncbi->index >= ncbi->num_seq) return eslEOF; | ^~ vendor/easel/esl_sqio_ncbi.c: In function ‘volume_open’: vendor/easel/esl_sqio_ncbi.c:1421:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 1421 | if (volume < 0 || volume > ncbi->volumes) return eslEINVAL; | ^ vendor/easel/esl_sqio_ncbi.c:1458:24: warning: comparison of integer expressions of different signedness: ‘__uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 1458 | if (htobe32(info[1]) != dbtype) status = eslEFORMAT; | ^~ vendor/easel/esl_sqio_ncbi.c: In function ‘pos_sequence’: vendor/easel/esl_sqio_ncbi.c:1513:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 1513 | if (inx < 0 || inx > ncbi->num_seq) return eslEINVAL; | ^ vendor/easel/esl_sqio_ncbi.c:1519:25: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 1519 | if (ncbi->index_start == -1 || inx < start || inx > end) { | ^~ vendor/easel/esl_sqio_ncbi.c:1519:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 1519 | if (ncbi->index_start == -1 || inx < start || inx > end) { | ^ vendor/easel/esl_sqio_ncbi.c:1519:53: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 1519 | if (ncbi->index_start == -1 || inx < start || inx > end) { | ^ vendor/easel/esl_sqio_ncbi.c:1524:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 1524 | if (inx < volume->start_seq || inx > volume->end_seq) { | ^ vendor/easel/esl_sqio_ncbi.c:1524:42: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 1524 | if (inx < volume->start_seq || inx > volume->end_seq) { | ^ vendor/easel/esl_sqio_ncbi.c:1526:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 1526 | for (cnt = 0; cnt < ncbi->volumes; ++cnt) { | ^ vendor/easel/esl_sqio_ncbi.c:1527:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 1527 | if (inx < volume->end_seq) break; | ^ vendor/easel/esl_sqio_ncbi.c:1532:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 1532 | if (cnt >= ncbi->volumes) return eslFAIL; | ^~ vendor/easel/esl_sqio_ncbi.c:1539:27: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 1539 | if (ncbi->index_start == -1 || inx > end) { | ^~ vendor/easel/esl_sqio_ncbi.c:1539:40: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 1539 | if (ncbi->index_start == -1 || inx > end) { | ^ vendor/easel/esl_sqio_ncbi.c:1564:70: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1564 | if (fread(ncbi->hdr_indexes, sizeof(uint32_t), cnt, ncbi->fppin) != cnt) { | ^~ vendor/easel/esl_sqio_ncbi.c:1572:70: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1572 | if (fread(ncbi->seq_indexes, sizeof(uint32_t), cnt, ncbi->fppin) != cnt) { | ^~ vendor/easel/esl_sqio_ncbi.c:1581:72: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1581 | if (fread(ncbi->amb_indexes, sizeof(uint32_t), cnt, ncbi->fppin) != cnt) { | ^~ vendor/easel/esl_sqio_ncbi.c: In function ‘read_amino’: vendor/easel/esl_sqio_ncbi.c:1623:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 1623 | if (ncbi->index >= ncbi->num_seq) return eslEOF; | ^~ vendor/easel/esl_sqio_ncbi.c:1633:53: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1633 | if (fread(ptr, sizeof(char), size, ncbi->fppsq) != size) return eslEFORMAT; | ^~ vendor/easel/esl_sqio_ncbi.c:1641:53: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1641 | if (fread(ptr, sizeof(char), size, ncbi->fppsq) != size) return eslEFORMAT; | ^~ vendor/easel/esl_sqio_ncbi.c: In function ‘read_dna’: vendor/easel/esl_sqio_ncbi.c:1690:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 1690 | if (ncbi->index >= ncbi->num_seq) return eslEOF; | ^~ vendor/easel/esl_sqio_ncbi.c:1701:61: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1701 | if (fread(ncbi->hdr_buf, sizeof(char), size, ncbi->fppsq) != size) return eslEFORMAT; | ^~ vendor/easel/esl_sqio_ncbi.c: In function ‘read_nres_amino’: vendor/easel/esl_sqio_ncbi.c:1831:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 1831 | if (ncbi->index >= ncbi->num_seq) return eslEOF; | ^~ vendor/easel/esl_sqio_ncbi.c:1856:51: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1856 | if (fread(ptr, sizeof(char), size, ncbi->fppsq) != size) return eslEFORMAT; | ^~ vendor/easel/esl_sqio_ncbi.c: In function ‘correct_ambiguity’: vendor/easel/esl_sqio_ncbi.c:1924:65: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int64_t’ {aka ‘long int’} [-Wsign-compare] 1924 | if (fread(ncbi->hdr_buf, sizeof(char), size, ncbi->fppsq) != size) return eslEFORMAT; | ^~ vendor/easel/esl_sqio_ncbi.c: In function ‘read_nres_dna’: vendor/easel/esl_sqio_ncbi.c:2005:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2005 | if (ncbi->index >= ncbi->num_seq) return eslEOF; | ^~ vendor/easel/esl_wuss.c: In function ‘esl_wuss2ct’: vendor/easel/esl_sqio_ncbi.c:2047:62: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 2047 | if (fread(ncbi->hdr_buf, sizeof(char), ssize, ncbi->fppsq) != ssize) return eslEFORMAT; | ^~ vendor/easel/esl_wuss.c:136:10: warning: ‘status’ may be used uninitialized [-Wmaybe-uninitialized] 136 | return status; | ^~~~~~ vendor/easel/esl_wuss.c:56:14: note: ‘status’ was declared here 56 | int status; /* success or failure return status */ | ^~~~~~ vendor/easel/esl_sqio_ncbi.c: In function ‘inmap_ncbi_dna’: vendor/easel/esl_sqio_ncbi.c:2178:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2178 | for (x = 0; x < strlen(ncbisym); ++x) { | ^ vendor/easel/esl_sqio_ncbi.c:2179:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2179 | for (y = 0; y < strlen(abc->sym); ++y) { | ^ vendor/easel/esl_sqio_ncbi.c:2187:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2187 | if (y >= strlen(abc->sym)) return eslEFORMAT; | ^~ vendor/easel/esl_sqio_ncbi.c: In function ‘inmap_ncbi_amino’: vendor/easel/esl_sqio_ncbi.c:2226:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2226 | for (x = 0; x < strlen(ncbisym); ++x) { | ^ vendor/easel/esl_sqio_ncbi.c:2227:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2227 | for (y = 0; y < strlen(abc->sym); ++y) { | ^ vendor/easel/esl_sqio_ncbi.c:2235:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2235 | if (y >= strlen(abc->sym)) return eslEFORMAT; | ^~ vendor/easel/esl_sqio_ncbi.c: In function ‘parse_header’: vendor/easel/esl_sqio_ncbi.c:2463:61: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 2463 | if (fread(ncbi->hdr_buf, sizeof(char), size, ncbi->fpphr) != size) return eslEFORMAT; | ^~ generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_stopwatch.o from vendor/easel/esl_stopwatch.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_stopwatch.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_stopwatch.o vendor/easel/esl_stopwatch.c:15:15: warning: ‘stopwatch_getRealTime’ declared ‘static’ but never defined [-Wunused-function] 15 | static double stopwatch_getRealTime(void); | ^~~~~~~~~~~~~~~~~~~~~ generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_stats.o from vendor/easel/esl_stats.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_stats.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_stats.o generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_workqueue.o from vendor/easel/esl_workqueue.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_workqueue.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_workqueue.o generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_weibull.o from vendor/easel/esl_weibull.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_weibull.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_weibull.o generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_vmx.o from vendor/easel/esl_vmx.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_vmx.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_vmx.o generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_stack.o from vendor/easel/esl_stack.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_stack.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_stack.o generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_red_black.o from vendor/easel/esl_red_black.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_red_black.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_red_black.o generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_recorder.o from vendor/easel/esl_recorder.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_recorder.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_recorder.o generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_ssi.o from vendor/easel/esl_ssi.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_ssi.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_ssi.o vendor/easel/esl_ssi.c: In function ‘esl_ssi_FindNumber’: vendor/easel/esl_ssi.c:261:12: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 261 | if (nkey >= ssi->nprimary) { status = eslENOTFOUND; goto ERROR; } | ^~ vendor/easel/esl_ssi.c: In function ‘esl_newssi_AddFile’: vendor/easel/esl_ssi.c:728:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 728 | if ((n+1) > ns->flen) ns->flen = n+1; | ^ vendor/easel/esl_ssi.c: In function ‘esl_newssi_AddKey’: vendor/easel/esl_ssi.c:862:9: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 862 | if (n > ns->plen) ns->plen = n; | ^ vendor/easel/esl_ssi.c:893:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 893 | for (i = ns->nprimary; i < ns->nprimary + eslSSI_KCHUNK; i++) | ^ vendor/easel/esl_ssi.c: In function ‘esl_newssi_AddAlias’: vendor/easel/esl_ssi.c:941:9: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 941 | if (n > ns->slen) ns->slen = n; | ^ vendor/easel/esl_ssi.c:957:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 957 | for (i = ns->nsecondary; i < ns->nsecondary+eslSSI_KCHUNK; i++) { | ^ vendor/easel/esl_ssi.c: In function ‘esl_newssi_Write’: vendor/easel/esl_ssi.c:1143:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1143 | for (i = 0; i < ns->nprimary; i++) | ^ vendor/easel/esl_ssi.c:1161:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1161 | for (i = 0; i < ns->nprimary; i++) | ^ vendor/easel/esl_ssi.c:1181:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1181 | for (i = 0; i < ns->nsecondary; i++) | ^ vendor/easel/esl_ssi.c:1198:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1198 | for (i = 0; i < ns->nsecondary; i++) | ^ vendor/easel/esl_ssi.c: In function ‘esl_newssi_Close’: vendor/easel/esl_ssi.c:1247:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1247 | for (i = 0; i < ns->nprimary; i++) | ^ vendor/easel/esl_ssi.c:1253:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1253 | for (i = 0; i < ns->nsecondary; i++) | ^ vendor/easel/esl_ssi.c: In function ‘activate_external_sort’: vendor/easel/esl_ssi.c:1345:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1345 | for (i = 0; i < ns->nprimary; i++) { | ^ vendor/easel/esl_ssi.c:1364:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1364 | for (i = 0; i < ns->nsecondary; i++) | ^ vendor/easel/esl_ssi.c:1370:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1370 | for (i = 0; i < ns->nprimary; i++) free(ns->pkeys[i].key); | ^ vendor/easel/esl_ssi.c:1371:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1371 | for (i = 0; i < ns->nsecondary; i++) free(ns->skeys[i].key); | ^ vendor/easel/esl_ssi.c:1372:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1372 | for (i = 0; i < ns->nsecondary; i++) free(ns->skeys[i].pkey); | ^ generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_varint.o from vendor/easel/esl_varint.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_varint.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_varint.o generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_ratematrix.o from vendor/easel/esl_ratematrix.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_ratematrix.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_ratematrix.o vendor/easel/esl_varint.c: In function ‘esl_varint_google_decode’: vendor/easel/esl_varint.c:471:11: warning: ‘grp’ may be used uninitialized [-Wmaybe-uninitialized] 471 | if (grp & cmask) { status = eslEOD; goto ERROR; } | ~~~~^~~~~~~ vendor/easel/esl_varint.c:461:12: note: ‘grp’ was declared here 461 | uint64_t grp; // current k-bit code group | ^~~ generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_tree.o from vendor/easel/esl_tree.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_tree.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_tree.o generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_randomseq.o from vendor/easel/esl_randomseq.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_randomseq.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_randomseq.o generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_sse.o from vendor/easel/esl_sse.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_sse.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_sse.o generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_sqio.o from vendor/easel/esl_sqio.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_sqio.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_sqio.o generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_random.o from vendor/easel/esl_random.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_random.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_random.o generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_sq.o from vendor/easel/esl_sq.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_sq.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_sq.o vendor/easel/esl_random.c: In function ‘esl_rnd_Roll’: vendor/easel/esl_random.c:319:54: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 319 | do { u = esl_random_uint32(r) / factor; } while (u >= n); | ^~ vendor/easel/esl_random.c: In function ‘gamma_integer’: vendor/easel/esl_random.c:655:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 655 | for (i = 0; i < a; i++) | ^ vendor/easel/esl_sq.c: In function ‘esl_sq_CreateFrom’: vendor/easel/esl_sq.c:104:22: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int64_t’ {aka ‘long int’} [-Wsign-compare] 104 | if (strlen(ss) != n) ESL_XEXCEPTION(eslEINVAL, "ss, seq lengths mismatch"); | ^~ vendor/easel/esl_sq.c: In function ‘esl_sq_CreateDigitalFrom’: vendor/easel/esl_sq.c:787:22: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int64_t’ {aka ‘long int’} [-Wsign-compare] 787 | if (strlen(ss) != sq->n) ESL_XEXCEPTION(eslEINVAL, "ss, seq lengths mismatch"); | ^~ vendor/easel/esl_sq.c: In function ‘esl_sq_Checksum’: vendor/easel/esl_sq.c:1638:25: warning: comparison of integer expressions of different signedness: ‘uint64_t’ {aka ‘long unsigned int’} and ‘int64_t’ {aka ‘long int’} [-Wsign-compare] 1638 | for (pos = 0; pos < sq->n; pos++) | ^ vendor/easel/esl_sq.c:1647:25: warning: comparison of integer expressions of different signedness: ‘uint64_t’ {aka ‘long unsigned int’} and ‘int64_t’ {aka ‘long int’} [-Wsign-compare] 1647 | for (pos = 1; pos <= sq->n; pos++) | ^~ vendor/easel/esl_sq.c: In function ‘esl_sq_Validate’: vendor/easel/esl_sq.c:2023:35: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int64_t’ {aka ‘long int’} [-Wsign-compare] 2023 | if (strlen(sq->ss+1) != sq->n) ESL_FAIL(eslFAIL, errmsg, "ss annotation length (for digital seq) doesn't agree with sq->n"); | ^~ vendor/easel/esl_sq.c:2030:36: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int64_t’ {aka ‘long int’} [-Wsign-compare] 2030 | if (strlen(sq->seq) != sq->n) ESL_FAIL(eslFAIL, errmsg, "text seq length doesn't agree with sq->n"); | ^~ vendor/easel/esl_sq.c:2031:36: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int64_t’ {aka ‘long int’} [-Wsign-compare] 2031 | if (sq->ss && strlen(sq->ss) != sq->n) ESL_FAIL(eslFAIL, errmsg, "ss annotation length (for text seq) doesn't agree with sq->n"); | ^~ generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_threads.o from vendor/easel/esl_threads.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_threads.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_threads.o generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_swat.o from vendor/easel/esl_swat.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_swat.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_swat.o generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_quicksort.o from vendor/easel/esl_quicksort.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_quicksort.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_quicksort.o generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_subcmd.o from vendor/easel/esl_subcmd.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_subcmd.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_subcmd.o generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_rand64.o from vendor/easel/esl_rand64.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_rand64.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_rand64.o generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_paml.o from vendor/easel/esl_paml.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_paml.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_paml.o generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_msafile_stockholm.o from vendor/easel/esl_msafile_stockholm.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_msafile_stockholm.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_msafile_stockholm.o generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_normal.o from vendor/easel/esl_normal.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_normal.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_normal.o generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_neon.o from vendor/easel/esl_neon.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_neon.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_neon.o generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_msaweight.o from vendor/easel/esl_msaweight.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_msaweight.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_msaweight.o generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_msafile_a2m.o from vendor/easel/esl_msafile_a2m.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_msafile_a2m.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_msafile_a2m.o generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_scorematrix.o from vendor/easel/esl_scorematrix.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_scorematrix.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_scorematrix.o generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_msafile2.o from vendor/easel/esl_msafile2.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_msafile2.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_msafile2.o vendor/easel/esl_msaweight.c: In function ‘esl_msaweight_IDFilter_adv’: vendor/easel/esl_msaweight.c:1035:9: warning: ‘conscols_104’ may be used uninitialized [-Wmaybe-uninitialized] 1035 | collect_counts(cfg, msa, conscols, ncons, ct, NULL); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ vendor/easel/esl_msaweight.c:435:1: note: by argument 3 of type ‘const int *’ to ‘collect_counts.isra.0’ declared here 435 | collect_counts(const ESL_MSAWEIGHT_CFG *cfg, const ESL_MSA *msa, const int *conscols, int ncons, int **ct, ESL_MSAWEIGHT_DAT *dat) | ^~~~~~~~~~~~~~ vendor/easel/esl_msafile2.c: In function ‘msafile2_open’: vendor/easel/esl_msafile2.c:173:17: warning: unused variable ‘nc’ [-Wunused-variable] 173 | int nc; | ^~ In file included from vendor/easel/esl_msafile2.c:26: vendor/easel/esl_msafile2.c: In function ‘esl_msafile2_ReadInfoPfam’: vendor/easel/easel.h:432:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 432 | #define ESL_MAX(a,b) (((a)>(b))?(a):(b)) | ^ vendor/easel/esl_msafile2.c:632:43: note: in expansion of macro ‘ESL_MAX’ 632 | for(i = 0; i < msa->ngc; i++) maxgc = ESL_MAX(maxgc, strlen(msa->gc_tag[i])); | ^~~~~~~ vendor/easel/easel.h:432:42: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘size_t’ {aka ‘long unsigned int’} due to unsignedness of other operand [-Wsign-compare] 432 | #define ESL_MAX(a,b) (((a)>(b))?(a):(b)) | ^~~ vendor/easel/esl_msafile2.c:632:43: note: in expansion of macro ‘ESL_MAX’ 632 | for(i = 0; i < msa->ngc; i++) maxgc = ESL_MAX(maxgc, strlen(msa->gc_tag[i])); | ^~~~~~~ vendor/easel/easel.h:432:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 432 | #define ESL_MAX(a,b) (((a)>(b))?(a):(b)) | ^ vendor/easel/esl_msafile2.c:641:43: note: in expansion of macro ‘ESL_MAX’ 641 | for(i = 0; i < msa->ngf; i++) maxgf = ESL_MAX(maxgf, strlen(msa->gf_tag[i])); | ^~~~~~~ vendor/easel/easel.h:432:42: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘size_t’ {aka ‘long unsigned int’} due to unsignedness of other operand [-Wsign-compare] 432 | #define ESL_MAX(a,b) (((a)>(b))?(a):(b)) | ^~~ vendor/easel/esl_msafile2.c:641:43: note: in expansion of macro ‘ESL_MAX’ 641 | for(i = 0; i < msa->ngf; i++) maxgf = ESL_MAX(maxgf, strlen(msa->gf_tag[i])); | ^~~~~~~ generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_msashuffle.o from vendor/easel/esl_msashuffle.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_msashuffle.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_msashuffle.o vendor/easel/esl_msashuffle.c: In function ‘esl_msashuffle_CQRNA’: vendor/easel/esl_msashuffle.c:449:17: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 449 | if (strlen(y) != L) ESL_XEXCEPTION(eslEINVAL, "sequences of different lengths in qrna shuffle"); | ^~ generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_msafile_selex.o from vendor/easel/esl_msafile_selex.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_msafile_selex.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_msafile_selex.o generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_mixgev.o from vendor/easel/esl_mixgev.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_mixgev.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_mixgev.o generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_rootfinder.o from vendor/easel/esl_rootfinder.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_rootfinder.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_rootfinder.o generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_mixdchlet.o from vendor/easel/esl_mixdchlet.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_mixdchlet.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_mixdchlet.o generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_regexp.o from vendor/easel/esl_regexp.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_regexp.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_regexp.o generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_msafile.o from vendor/easel/esl_msafile.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_msafile.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_msafile.o generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_msafile_psiblast.o from vendor/easel/esl_msafile_psiblast.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_msafile_psiblast.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_msafile_psiblast.o generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_minimizer.o from vendor/easel/esl_minimizer.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_minimizer.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_minimizer.o vendor/easel/esl_minimizer.c: In function ‘esl_min_ConjugateGradientDescent’: vendor/easel/esl_minimizer.c:243:23: warning: ‘fx’ may be used uninitialized [-Wmaybe-uninitialized] 243 | if (opt_fx) *opt_fx = fx; | ~~~~~~~~^~~~ vendor/easel/esl_minimizer.c:119:10: note: ‘fx’ was declared here 119 | double fx; | ^~ In function ‘brent’, inlined from ‘esl_min_ConjugateGradientDescent’ at vendor/easel/esl_minimizer.c:192:7: vendor/easel/esl_minimizer.c:720:21: warning: ‘ax’ may be used uninitialized [-Wmaybe-uninitialized] 720 | m = 0.5 * (a+b); | ~~^~~ vendor/easel/esl_minimizer.c: In function ‘esl_min_ConjugateGradientDescent’: vendor/easel/esl_minimizer.c:118:10: note: ‘ax’ was declared here 118 | double ax,bx,cx; | ^~ In function ‘brent’, inlined from ‘esl_min_ConjugateGradientDescent’ at vendor/easel/esl_minimizer.c:192:7: vendor/easel/esl_minimizer.c:720:21: warning: ‘cx’ may be used uninitialized [-Wmaybe-uninitialized] 720 | m = 0.5 * (a+b); | ~~^~~ vendor/easel/esl_minimizer.c: In function ‘esl_min_ConjugateGradientDescent’: vendor/easel/esl_minimizer.c:118:16: note: ‘cx’ was declared here 118 | double ax,bx,cx; | ^~ generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_msafile_phylip.o from vendor/easel/esl_msafile_phylip.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_msafile_phylip.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_msafile_phylip.o generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_msacluster.o from vendor/easel/esl_msacluster.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_msacluster.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_msacluster.o generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_msa.o from vendor/easel/esl_msa.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_msa.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_msa.o generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_keyhash.o from vendor/easel/esl_keyhash.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_keyhash.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_keyhash.o generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_mem.o from vendor/easel/esl_mem.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_mem.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_mem.o vendor/easel/esl_msa.c: In function ‘esl_msa_AddGS’: vendor/easel/esl_msa.c:1697:42: warning: operand of ‘?:’ changes signedness from ‘esl_pos_t’ {aka ‘long int’} to ‘size_t’ {aka ‘long unsigned int’} due to unsignedness of other operand [-Wsign-compare] 1697 | n2 = (vlen == -1 ? strlen(value) : vlen); | ^~~~ vendor/easel/esl_keyhash.c: In function ‘esl_keyhash_Clone’: vendor/easel/esl_keyhash.c:94:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 94 | for (h = 0; h < kh->hashsize; h++) | ^ vendor/easel/esl_keyhash.c: In function ‘esl_keyhash_Reuse’: vendor/easel/esl_keyhash.c:171:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 171 | for (i = 0; i < kh->hashsize; i++) kh->hashtable[i] = -1; | ^ vendor/easel/esl_keyhash.c: In function ‘esl_keyhash_Dump’: vendor/easel/esl_keyhash.c:215:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 215 | for (h = 0; h < kh->hashsize; h++) | ^ vendor/easel/esl_keyhash.c: In function ‘esl_keyhash_Store’: vendor/easel/esl_keyhash.c:310:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 310 | if (kh->nkeys > 3*kh->hashsize) | ^ vendor/easel/esl_keyhash.c: In function ‘keyhash_create’: vendor/easel/esl_keyhash.c:401:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 401 | for (i = 0; i < kh->hashsize; i++) kh->hashtable[i] = -1; | ^ vendor/easel/esl_keyhash.c: In function ‘key_upsize’: vendor/easel/esl_keyhash.c:491:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 491 | for (i = 0; i < kh->hashsize; i++) kh->hashtable[i] = -1; | ^ vendor/easel/esl_msa.c: In function ‘esl_msa_Validate’: vendor/easel/esl_msa.c:3168:38: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int64_t’ {aka ‘long int’} [-Wsign-compare] 3168 | if (strlen(msa->aseq[idx]) != msa->alen) ESL_FAIL(eslFAIL, errmsg, "seq %d: wrong length", idx); | ^~ vendor/easel/esl_msa.c:3175:61: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int64_t’ {aka ‘long int’} [-Wsign-compare] 3175 | if (msa->ss && msa->ss[idx] && strlen(msa->ss[idx]) != msa->alen) ESL_FAIL(eslFAIL, errmsg, "seq %d: SS wrong length", idx); | ^~ vendor/easel/esl_msa.c:3176:61: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int64_t’ {aka ‘long int’} [-Wsign-compare] 3176 | if (msa->sa && msa->sa[idx] && strlen(msa->sa[idx]) != msa->alen) ESL_FAIL(eslFAIL, errmsg, "seq %d: SA wrong length", idx); | ^~ vendor/easel/esl_msa.c:3177:61: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int64_t’ {aka ‘long int’} [-Wsign-compare] 3177 | if (msa->pp && msa->pp[idx] && strlen(msa->pp[idx]) != msa->alen) ESL_FAIL(eslFAIL, errmsg, "seq %d: PP wrong length", idx); | ^~ vendor/easel/esl_msa.c:3181:44: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int64_t’ {aka ‘long int’} [-Wsign-compare] 3181 | if (msa->ss_cons && strlen(msa->ss_cons) != msa->alen) ESL_FAIL(eslFAIL, errmsg, "SS_cons wrong length"); | ^~ vendor/easel/esl_msa.c:3182:44: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int64_t’ {aka ‘long int’} [-Wsign-compare] 3182 | if (msa->sa_cons && strlen(msa->sa_cons) != msa->alen) ESL_FAIL(eslFAIL, errmsg, "SA_cons wrong length"); | ^~ vendor/easel/esl_msa.c:3183:44: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int64_t’ {aka ‘long int’} [-Wsign-compare] 3183 | if (msa->pp_cons && strlen(msa->pp_cons) != msa->alen) ESL_FAIL(eslFAIL, errmsg, "PP_cons wrong length"); | ^~ vendor/easel/esl_msa.c:3184:44: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int64_t’ {aka ‘long int’} [-Wsign-compare] 3184 | if (msa->rf && strlen(msa->rf) != msa->alen) ESL_FAIL(eslFAIL, errmsg, "RF wrong length"); | ^~ vendor/easel/esl_msa.c:3185:44: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int64_t’ {aka ‘long int’} [-Wsign-compare] 3185 | if (msa->mm && strlen(msa->mm ) != msa->alen) ESL_FAIL(eslFAIL, errmsg, "MM wrong length"); | ^~ In function ‘phylip_interleaved_Read’, inlined from ‘esl_msafile_phylip_Read’ at vendor/easel/esl_msafile_phylip.c:284:56: vendor/easel/esl_msafile_phylip.c:452:15: warning: ‘block_alen’ may be used uninitialized [-Wmaybe-uninitialized] 452 | else if (cur_alen - alen != block_alen) ESL_XFAIL(eslEFORMAT, afp->errmsg, "number of residues on line differs from previous seqs in alignment block"); | ^ vendor/easel/esl_msafile_phylip.c: In function ‘esl_msafile_phylip_Read’: vendor/easel/esl_msafile_phylip.c:422:13: note: ‘block_alen’ was declared here 422 | int64_t block_alen; /* # of residues being added by current block */ | ^~~~~~~~~~ generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_json.o from vendor/easel/esl_json.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_json.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_json.o In function ‘phylip_check_interleaved’, inlined from ‘esl_msafile_phylip_CheckFileFormat’ at vendor/easel/esl_msafile_phylip.c:389:13: vendor/easel/esl_msafile_phylip.c:739:16: warning: ‘nres1’ may be used uninitialized [-Wmaybe-uninitialized] 739 | if (nres1+nres2 == alen) break; | ~~~~~^~~~~~ vendor/easel/esl_msafile_phylip.c: In function ‘esl_msafile_phylip_CheckFileFormat’: vendor/easel/esl_msafile_phylip.c:687:13: note: ‘nres1’ was declared here 687 | int nres1; | ^~~~~ In function ‘phylip_deduce_namewidth’, inlined from ‘phylip_check_interleaved’ at vendor/easel/esl_msafile_phylip.c:747:22, inlined from ‘esl_msafile_phylip_CheckFileFormat’ at vendor/easel/esl_msafile_phylip.c:389:13: vendor/easel/esl_msafile_phylip.c:1048:10: warning: ‘ncols0’ may be used uninitialized [-Wmaybe-uninitialized] 1048 | for (c = ncols0-1; nres1 && c >= 0; c--) | ~~^~~~~~~~~~ vendor/easel/esl_msafile_phylip.c: In function ‘esl_msafile_phylip_CheckFileFormat’: vendor/easel/esl_msafile_phylip.c:683:20: note: ‘ncols0’ was declared here 683 | int ncols, ncols0; | ^~~~~~ generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_matrixops.o from vendor/easel/esl_matrixops.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_matrixops.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_matrixops.o generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_msafile_clustal.o from vendor/easel/esl_msafile_clustal.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_msafile_clustal.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_msafile_clustal.o generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_lognormal.o from vendor/easel/esl_lognormal.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_lognormal.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_lognormal.o generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_histogram.o from vendor/easel/esl_histogram.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_histogram.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_histogram.o generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_iset.o from vendor/easel/esl_iset.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_iset.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_iset.o vendor/easel/esl_histogram.c: In function ‘esl_histogram_GetRank’: vendor/easel/esl_histogram.c:541:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 541 | if (rank > h->n) | ^ generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_msafile_afa.o from vendor/easel/esl_msafile_afa.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_msafile_afa.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_msafile_afa.o vendor/easel/esl_iset.c: In function ‘esl_iset_monoCobalt’: vendor/easel/esl_iset.c:127:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 127 | for (v = 0; v < n; v++) a[v] = n-v-1; // initialize by putting all vertices into array a | ^ vendor/easel/esl_iset.c:131:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 131 | for (j = 0; j < n; j++) | ^ vendor/easel/esl_iset.c:135:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 135 | for (i = n; i < n+nb; i++) | ^ vendor/easel/esl_iset.c: In function ‘esl_iset_biCobalt’: vendor/easel/esl_iset.c:209:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 209 | for (v = 0; v < n; v++) a[v] = n-v-1; // initialize by putting all vertices into an array | ^ vendor/easel/esl_iset.c:213:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 213 | for (j = 0; j validR = ESL_MIN(mx->ncells / mx->allocM, mx->allocR); | ^~~~~~~ vendor/easel/easel.h:431:46: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint64_t’ {aka ‘long unsigned int’} due to unsignedness of other operand [-Wsign-compare] 431 | #define ESL_MIN(a,b) (((a)<(b))?(a):(b)) | ^~~ vendor/easel/esl_hmm.c:265:20: note: in expansion of macro ‘ESL_MIN’ 265 | mx->validR = ESL_MIN(mx->ncells / mx->allocM, mx->allocR); | ^~~~~~~ gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_getopts.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_getopts.o vendor/easel/esl_dsqdata.c: In function ‘esl_dsqdata_Open’: vendor/easel/esl_dsqdata.c:255:21: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 255 | if (alphatype != dd->abc_r->type) | ^~ vendor/easel/esl_dsqdata.c: In function ‘esl_dsqdata_Write’: vendor/easel/esl_dsqdata.c:617:17: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 617 | if (sq->n > max_seqlen) max_seqlen = sq->n; | ^ vendor/easel/esl_dsqdata.c:618:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 618 | n = strlen(sq->name); if (n > max_namelen) max_namelen = n; | ^ vendor/easel/esl_dsqdata.c:619:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 619 | n = strlen(sq->acc); if (n > max_acclen) max_acclen = n; | ^ vendor/easel/esl_dsqdata.c:620:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 620 | n = strlen(sq->desc); if (n > max_desclen) max_desclen = n; | ^ vendor/easel/esl_dsqdata.c:677:53: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 677 | if ( fwrite(psq, sizeof(uint32_t), plen, sfp) != plen) | ^~ vendor/easel/esl_dsqdata.c:683:53: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 683 | if ( fwrite(sq->name, sizeof(char), n+1, mfp) != n+1) | ^~ vendor/easel/esl_dsqdata.c:688:53: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 688 | if ( fwrite(sq->acc, sizeof(char), n+1, mfp) != n+1) | ^~ vendor/easel/esl_dsqdata.c:693:53: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 693 | if ( fwrite(sq->desc, sizeof(char), n+1, mfp) != n+1) | ^~ vendor/easel/esl_dsqdata.c: In function ‘dsqdata_unpacker_thread’: vendor/easel/esl_dsqdata.c:1130:1: warning: control reaches end of non-void function [-Wreturn-type] 1130 | } | ^ vendor/easel/esl_dsqdata.c: In function ‘dsqdata_loader_thread’: vendor/easel/esl_dsqdata.c:1053:1: warning: control reaches end of non-void function [-Wreturn-type] 1053 | } | ^ generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_dirichlet.o from vendor/easel/esl_dirichlet.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_dirichlet.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_dirichlet.o vendor/easel/esl_getopts.c: In function ‘get_optidx_abbrev’: vendor/easel/esl_getopts.c:1391:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1391 | if (n == strlen(g->opt[i].name)) { nexact++; break; } /* an exact match; can stop now (xref bug #e4) */ | ^~ generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_cpu.o from vendor/easel/esl_cpu.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_cpu.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_cpu.o generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_composition.o from vendor/easel/esl_composition.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_composition.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_composition.o generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_cluster.o from vendor/easel/esl_cluster.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_cluster.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_cluster.o generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_bitfield.o from vendor/easel/esl_bitfield.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_bitfield.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_bitfield.o vendor/easel/esl_cluster.c: In function ‘esl_cluster_SingleLinkage’: vendor/easel/esl_cluster.c:151:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 151 | for (v = 0; v < n; v++) a[v] = n-v-1; /* initialize by pushing all vertices onto available list (backwards) */ | ^ generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_buffer.o from vendor/easel/esl_buffer.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_buffer.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_buffer.o generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_avx512.o from vendor/easel/esl_avx512.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_avx512.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_avx512.o generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_avx.o from vendor/easel/esl_avx.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_avx.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_avx.o vendor/easel/esl_buffer.c: In function ‘esl_buffer_OpenMem’: vendor/easel/esl_buffer.c:433:41: warning: operand of ‘?:’ changes signedness from ‘esl_pos_t’ {aka ‘long int’} to ‘size_t’ {aka ‘long unsigned int’} due to unsignedness of other operand [-Wsign-compare] 433 | bf->n = (n == -1) ? strlen(p) : n; | ^ generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_arr3.o from vendor/easel/esl_arr3.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_arr3.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_arr3.o vendor/easel/esl_buffer.c: In function ‘esl_buffer_Read’: vendor/easel/esl_buffer.c:1494:23: warning: comparison of integer expressions of different signedness: ‘esl_pos_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1494 | if (bf->n - bf->pos < nbytes) | ^ vendor/easel/esl_buffer.c:1499:31: warning: comparison of integer expressions of different signedness: ‘esl_pos_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1499 | else if (bf->n-bf->pos < nbytes) return eslEOF; | ^ generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_arr2.o from vendor/easel/esl_arr2.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_arr2.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_arr2.o generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_alphabet.o from vendor/easel/esl_alphabet.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_alphabet.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_alphabet.o generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_dmatrix.o from vendor/easel/esl_dmatrix.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_dmatrix.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_dmatrix.o vendor/easel/esl_alphabet.c: In function ‘esl_alphabet_CreateCustom’: vendor/easel/esl_alphabet.c:107:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 107 | if (strlen(alphabet) != Kp) ESL_XEXCEPTION(eslEINVAL, "alphabet length != Kp"); | ^~ generating build/temp.linux-x86_64-cpython-313/vendor/easel/esl_alloc.o from vendor/easel/esl_alloc.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/esl_alloc.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_alloc.o generating build/temp.linux-x86_64-cpython-313/vendor/easel/easel.o from vendor/easel/easel.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/easel/easel.c -o build/temp.linux-x86_64-cpython-313/vendor/easel/easel.o vendor/easel/easel.c: In function ‘esl_FileNewSuffix’: vendor/easel/easel.c:1942:46: warning: operand of ‘?:’ changes signedness from ‘long int’ to ‘size_t’ {aka ‘long unsigned int’} due to unsignedness of other operand [-Wsign-compare] 1942 | nf = (lastdot == NULL)? strlen(filename) : lastdot-filename; | ^~~~~~~~~~~~~~~~ generating build/temp.linux-x86_64-cpython-313/build/temp.linux-x86_64-cpython-313/esl_sqio_ascii.o from build/temp.linux-x86_64-cpython-313/esl_sqio_ascii.c creating build/temp.linux-x86_64-cpython-313/build creating build/temp.linux-x86_64-cpython-313/build/temp.linux-x86_64-cpython-313 gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c build/temp.linux-x86_64-cpython-313/esl_sqio_ascii.c -o build/temp.linux-x86_64-cpython-313/build/temp.linux-x86_64-cpython-313/esl_sqio_ascii.o build/temp.linux-x86_64-cpython-313/esl_sqio_ascii.c: In function ‘esl_sqascii_Open’: build/temp.linux-x86_64-cpython-313/esl_sqio_ascii.c:141:15: warning: unused variable ‘nc’ [-Wunused-variable] 141 | int nc; | ^~ build/temp.linux-x86_64-cpython-313/esl_sqio_ascii.c:140:15: warning: unused variable ‘n’ [-Wunused-variable] 140 | int n; | ^ build/temp.linux-x86_64-cpython-313/esl_sqio_ascii.c: In function ‘sqascii_Echo’: build/temp.linux-x86_64-cpython-313/esl_sqio_ascii.c:1671:60: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1671 | if (fwrite(ascii->buf, sizeof(char), ascii->nc, ofp) != ascii->nc) ESL_EXCEPTION(eslESYS, "fwrite() failed"); | ^~ ar rcs build/temp.linux-x86_64-cpython-313/libeasel.a build/temp.linux-x86_64-cpython-313/vendor/easel/interface_lapack.o build/temp.linux-x86_64-cpython-313/vendor/easel/interface_gsl.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_wuss.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_workqueue.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_weibull.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_vmx.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_vectorops.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_varint.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_tree.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_threads.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_swat.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_subcmd.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_stretchexp.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_stopwatch.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_stats.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_stack.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_ssi.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_sse.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_sqio_ncbi.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_sqio.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_sq.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_scorematrix.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_rootfinder.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_regexp.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_red_black.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_recorder.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_ratematrix.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_randomseq.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_random.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_rand64.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_quicksort.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_paml.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_normal.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_neon.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_msaweight.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_msashuffle.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_msafile_stockholm.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_msafile_selex.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_msafile_psiblast.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_msafile_phylip.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_msafile_clustal.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_msafile_afa.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_msafile_a2m.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_msafile2.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_msafile.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_msacluster.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_msa.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_mpi.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_mixgev.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_mixdchlet.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_minimizer.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_mem.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_matrixops.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_lognormal.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_keyhash.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_json.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_iset.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_hyperexp.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_huffman.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_hmm.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_histogram.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_heap.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_gumbel.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_graph.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_gev.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_getopts.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_gencode.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_gamma.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_fileparser.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_exponential.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_dsqdata.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_dmatrix.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_distance.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_dirichlet.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_cpu.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_composition.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_cluster.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_buffer.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_bitfield.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_avx512.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_avx.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_arr3.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_arr2.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_alphabet.o build/temp.linux-x86_64-cpython-313/vendor/easel/esl_alloc.o build/temp.linux-x86_64-cpython-313/vendor/easel/easel.o build/temp.linux-x86_64-cpython-313/build/temp.linux-x86_64-cpython-313/esl_sqio_ascii.o generating build/temp.linux-x86_64-cpython-313/libhmmer.a from vendor/hmmer/src/build.c, vendor/hmmer/src/cachedb.c, vendor/hmmer/src/cachedb_shard.c, vendor/hmmer/src/emit.c, vendor/hmmer/src/errors.c, vendor/hmmer/src/evalues.c, vendor/hmmer/src/eweight.c, vendor/hmmer/src/generic_decoding.c, vendor/hmmer/src/generic_fwdback.c, vendor/hmmer/src/generic_fwdback_chk.c, vendor/hmmer/src/generic_fwdback_banded.c, vendor/hmmer/src/generic_null2.c, vendor/hmmer/src/generic_msv.c, vendor/hmmer/src/generic_optacc.c, vendor/hmmer/src/generic_stotrace.c, vendor/hmmer/src/generic_viterbi.c, vendor/hmmer/src/generic_vtrace.c, vendor/hmmer/src/h2_io.c, vendor/hmmer/src/heatmap.c, vendor/hmmer/src/hmmlogo.c, vendor/hmmer/src/hmmdmstr.c, vendor/hmmer/src/hmmdmstr_shard.c, vendor/hmmer/src/hmmd_search_status.c, vendor/hmmer/src/hmmdwrkr.c, vendor/hmmer/src/hmmdwrkr_shard.c, vendor/hmmer/src/hmmdutils.c, vendor/hmmer/src/hmmer.c, vendor/hmmer/src/logsum.c, vendor/hmmer/src/modelconfig.c, vendor/hmmer/src/modelstats.c, vendor/hmmer/src/mpisupport.c, vendor/hmmer/src/seqmodel.c, vendor/hmmer/src/tracealign.c, vendor/hmmer/src/p7_alidisplay.c, vendor/hmmer/src/p7_bg.c, vendor/hmmer/src/p7_builder.c, vendor/hmmer/src/p7_domain.c, vendor/hmmer/src/p7_domaindef.c, vendor/hmmer/src/p7_gbands.c, vendor/hmmer/src/p7_gmx.c, vendor/hmmer/src/p7_gmxb.c, vendor/hmmer/src/p7_gmxchk.c, vendor/hmmer/src/p7_hit.c, vendor/hmmer/src/p7_hmm.c, vendor/hmmer/src/p7_hmmcache.c, vendor/hmmer/src/p7_hmmd_search_stats.c, vendor/hmmer/src/p7_hmmfile.c, vendor/hmmer/src/p7_hmmwindow.c, vendor/hmmer/src/p7_pipeline.c, vendor/hmmer/src/p7_prior.c, vendor/hmmer/src/p7_profile.c, vendor/hmmer/src/p7_spensemble.c, vendor/hmmer/src/p7_tophits.c, vendor/hmmer/src/p7_trace.c, vendor/hmmer/src/p7_scoredata.c, vendor/hmmer/src/hmmpgmd2msa.c, vendor/hmmer/src/fm_alphabet.c, vendor/hmmer/src/fm_general.c, vendor/hmmer/src/fm_sse.c, vendor/hmmer/src/fm_ssv.c generating build/temp.linux-x86_64-cpython-313/p7_hmmfile.c from vendor/hmmer/src/p7_hmmfile.c generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/evalues.o from vendor/hmmer/src/evalues.c creating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/generic_viterbi.o from vendor/hmmer/src/generic_viterbi.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/evalues.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/evalues.o generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/generic_fwdback_banded.o from vendor/hmmer/src/generic_fwdback_banded.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/generic_fwdback_banded.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/generic_fwdback_banded.o generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/build.o from vendor/hmmer/src/build.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/build.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/build.o gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/generic_viterbi.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/generic_viterbi.o generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/generic_null2.o from vendor/hmmer/src/generic_null2.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/generic_null2.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/generic_null2.o generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/eweight.o from vendor/hmmer/src/eweight.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/eweight.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/eweight.o generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/generic_vtrace.o from vendor/hmmer/src/generic_vtrace.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/generic_vtrace.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/generic_vtrace.o generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/cachedb.o from vendor/hmmer/src/cachedb.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/cachedb.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/cachedb.o generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/generic_msv.o from vendor/hmmer/src/generic_msv.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/generic_msv.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/generic_msv.o vendor/hmmer/src/cachedb.c: In function ‘p7_seqcache_Open’: vendor/hmmer/src/cachedb.c:95:14: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘long unsigned int’ [-Wsign-compare] 95 | if (db_cnt > (sizeof(db_inx)/sizeof(db_inx[0]))) return eslEFORMAT; | ^ vendor/hmmer/src/cachedb.c:157:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 157 | if (inx >= seq_cnt) { printf("inx: %d\n", inx); return eslEFORMAT; } | ^~ vendor/hmmer/src/cachedb.c:158:19: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 158 | if (sq->n + 1 > res_size) { printf("inx: %d size %d %d\n", inx, (int)sq->n + 1, (int)res_size); return eslEFORMAT; } | ^ vendor/hmmer/src/cachedb.c:179:16: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 179 | if (db_key >= (1 << (db_cnt + 1))) { printf("inx: %d db %d %s\n", inx, db_key, sq->desc); return eslEFORMAT; } | ^~ vendor/hmmer/src/cachedb.c:212:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 212 | if (inx != seq_cnt) { printf("inx:: %d %" PRIu64 "\n", inx, seq_cnt); return eslEFORMAT; } | ^~ vendor/hmmer/src/cachedb.c:222:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 222 | for (i = 0 ; i < seq_cnt; ++i) { | ^ vendor/hmmer/src/cachedb.c:230:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 230 | for (i = 0 ; i < seq_cnt; ++i) { | ^ vendor/hmmer/src/cachedb.c:236:25: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 236 | if (db_inx[inx] >= db->count) { printf("sort:: %d %d\n", db_inx[inx], db->count); return eslEFORMAT; } | ^~ vendor/hmmer/src/cachedb.c:246:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 246 | for (i = 0; i < cache->db_cnt; ++i) { | ^ vendor/hmmer/src/cachedb.c: In function ‘p7_seqcache_Close’: vendor/hmmer/src/cachedb.c:284:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 284 | for (i = 0; i < cache->db_cnt; ++i) { | ^ generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/generic_decoding.o from vendor/hmmer/src/generic_decoding.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/generic_decoding.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/generic_decoding.o generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/h2_io.o from vendor/hmmer/src/h2_io.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/h2_io.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/h2_io.o vendor/hmmer/src/h2_io.c: In function ‘h2_multiline’: vendor/hmmer/src/h2_io.c:213:47: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 213 | if (fwrite(sptr, sizeof(char), n, fp) != n) ESL_EXCEPTION_SYS(eslEWRITE, "h2 profile write failed"); /* using fwrite lets us write fixed # of chars */ | ^~ generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/cachedb_shard.o from vendor/hmmer/src/cachedb_shard.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/cachedb_shard.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/cachedb_shard.o generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/generic_fwdback.o from vendor/hmmer/src/generic_fwdback.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/generic_fwdback.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/generic_fwdback.o generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/generic_optacc.o from vendor/hmmer/src/generic_optacc.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/generic_optacc.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/generic_optacc.o vendor/hmmer/src/cachedb_shard.c: In function ‘p7_seqcache_Open_master’: vendor/hmmer/src/cachedb_shard.c:117:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 117 | for (i = 0; i < db_cnt; ++i) { | ^ vendor/hmmer/src/cachedb_shard.c:159:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 159 | for (i = 0; i < db_cnt; ++i) db_inx[i] = 0; | ^ vendor/hmmer/src/cachedb_shard.c:167:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 167 | if (inx >= seq_cnt) { printf("inx: %d\n", inx); return eslEFORMAT; } | ^~ vendor/hmmer/src/cachedb_shard.c:191:16: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 191 | if (db_key >= (1 << (db_cnt + 1))) { printf("inx: %d db_cnt %d db %d %s\n", inx, db_cnt, db_key, sq->desc); return eslEFORMAT; } | ^~ vendor/hmmer/src/cachedb_shard.c:225:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 225 | if (inx != seq_cnt) { printf("inx:: %d %" PRIu64 "\n", inx, seq_cnt); return eslEFORMAT; } | ^~ vendor/hmmer/src/cachedb_shard.c:235:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 235 | for (i = 0 ; i < seq_cnt; ++i) { | ^ vendor/hmmer/src/cachedb_shard.c:243:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 243 | for (i = 0 ; i < seq_cnt; ++i) { | ^ vendor/hmmer/src/cachedb_shard.c:259:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 259 | for (i = 0; i < cache->db_cnt; ++i) { | ^ vendor/hmmer/src/cachedb_shard.c:282:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 282 | for (i = 0; i < db_cnt; ++i) { | ^ vendor/hmmer/src/cachedb_shard.c: In function ‘p7_seqcache_Close_master’: vendor/hmmer/src/cachedb_shard.c:297:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 297 | for (i = 0; i < cache->db_cnt; ++i) { | ^ vendor/hmmer/src/cachedb_shard.c: In function ‘p7_seqcache_Open_shard’: vendor/hmmer/src/cachedb_shard.c:388:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 388 | for (i = 0; i < db_cnt; ++i) { | ^ vendor/hmmer/src/cachedb_shard.c:398:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 398 | for (i = 0; i < db_cnt; i++){ | ^ vendor/hmmer/src/cachedb_shard.c:434:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 434 | for (i = 0; i < db_cnt; ++i) db_inx[i] = 0; | ^ vendor/hmmer/src/cachedb_shard.c:445:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 445 | if (inx >= seq_cnt) { printf("inx: %d\n", inx); return eslEFORMAT; } | ^~ vendor/hmmer/src/cachedb_shard.c:446:19: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 446 | if (sq->n + 1 > res_size) { printf("inx: %d size %d %d\n", inx, (int)sq->n + 1, (int)res_size); return eslEFORMAT; } | ^ vendor/hmmer/src/cachedb_shard.c:463:41: warning: comparison of integer expressions of different signedness: ‘uint64_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 463 | if(db_seq_count[i] % num_shards == my_shard){ //this sequence is part of database i and belongs to this node's shard | ^~ vendor/hmmer/src/cachedb_shard.c:475:16: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 475 | if (db_key >= (1 << (db_cnt + 1))) { printf("inx: %d db %d %s\n", inx, db_key, sq->desc); return eslEFORMAT; } | ^~ vendor/hmmer/src/cachedb_shard.c:544:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 544 | for(i = 0; i < db_cnt; i++){ | ^ vendor/hmmer/src/cachedb_shard.c:560:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 560 | for (i = 0 ; i < seq_cnt; ++i) { | ^ vendor/hmmer/src/cachedb_shard.c:568:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 568 | for (i = 0 ; i < seq_cnt; ++i) { | ^ vendor/hmmer/src/cachedb_shard.c:585:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 585 | for (i = 0; i < cache->db_cnt; ++i) { | ^ vendor/hmmer/src/cachedb_shard.c:615:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 615 | for (i = 0; i < db_cnt; ++i) { | ^ generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/heatmap.o from vendor/hmmer/src/heatmap.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/heatmap.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/heatmap.o generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/hmmlogo.o from vendor/hmmer/src/hmmlogo.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/hmmlogo.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/hmmlogo.o generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/generic_fwdback_chk.o from vendor/hmmer/src/generic_fwdback_chk.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/generic_fwdback_chk.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/generic_fwdback_chk.o generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/generic_stotrace.o from vendor/hmmer/src/generic_stotrace.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/generic_stotrace.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/generic_stotrace.o generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/emit.o from vendor/hmmer/src/emit.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/emit.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/emit.o vendor/hmmer/src/generic_stotrace.c: In function ‘p7_GStochasticTrace’: vendor/hmmer/src/generic_stotrace.c:172:21: warning: ‘scur’ may be used uninitialized [-Wmaybe-uninitialized] 172 | if ((status = p7_trace_Append(tr, scur, k, i)) != eslOK) goto ERROR; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ vendor/hmmer/src/generic_stotrace.c:57:11: note: ‘scur’ was declared here 57 | int scur, sprv; | ^~~~ generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/hmmdmstr.o from vendor/hmmer/src/hmmdmstr.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/hmmdmstr.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/hmmdmstr.o generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/hmmdmstr_shard.o from vendor/hmmer/src/hmmdmstr_shard.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/hmmdmstr_shard.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/hmmdmstr_shard.o generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/hmmd_search_status.o from vendor/hmmer/src/hmmd_search_status.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/hmmd_search_status.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/hmmd_search_status.o generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/hmmdutils.o from vendor/hmmer/src/hmmdutils.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/hmmdutils.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/hmmdutils.o generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/hmmer.o from vendor/hmmer/src/hmmer.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/hmmer.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/hmmer.o generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/mpisupport.o from vendor/hmmer/src/mpisupport.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/mpisupport.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/mpisupport.o generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/seqmodel.o from vendor/hmmer/src/seqmodel.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/seqmodel.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/seqmodel.o generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/hmmdwrkr.o from vendor/hmmer/src/hmmdwrkr.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/hmmdwrkr.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/hmmdwrkr.o generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/hmmdwrkr_shard.o from vendor/hmmer/src/hmmdwrkr_shard.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/hmmdwrkr_shard.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/hmmdwrkr_shard.o generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/logsum.o from vendor/hmmer/src/logsum.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/logsum.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/logsum.o generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_builder.o from vendor/hmmer/src/p7_builder.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/p7_builder.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_builder.o generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/errors.o from vendor/hmmer/src/errors.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/errors.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/errors.o generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/tracealign.o from vendor/hmmer/src/tracealign.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/tracealign.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/tracealign.o generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/modelconfig.o from vendor/hmmer/src/modelconfig.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/modelconfig.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/modelconfig.o generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_gmxb.o from vendor/hmmer/src/p7_gmxb.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/p7_gmxb.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_gmxb.o generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/modelstats.o from vendor/hmmer/src/modelstats.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/modelstats.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/modelstats.o generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_gmxchk.o from vendor/hmmer/src/p7_gmxchk.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/p7_gmxchk.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_gmxchk.o generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_domain.o from vendor/hmmer/src/p7_domain.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/p7_domain.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_domain.o generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_hit.o from vendor/hmmer/src/p7_hit.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/p7_hit.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_hit.o generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_hmmd_search_stats.o from vendor/hmmer/src/p7_hmmd_search_stats.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/p7_hmmd_search_stats.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_hmmd_search_stats.o vendor/hmmer/src/p7_domain.c: In function ‘p7_domain_Serialize’: vendor/hmmer/src/p7_domain.c:228:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 228 | network_32bit = esl_hton32(*((uint32_t *) &(obj->envsc))); // ow, this hurts, but is probably the best way to get the | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~ vendor/hmmer/src/p7_domain.c:235:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 235 | network_32bit = esl_hton32(*((uint32_t *) &(obj->domcorrection))); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ vendor/hmmer/src/p7_domain.c:240:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 240 | network_32bit = esl_hton32(*((uint32_t *) &(obj->dombias))); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ vendor/hmmer/src/p7_domain.c:245:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 245 | network_32bit = esl_hton32(*((uint32_t *) &(obj->oasc))); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~ vendor/hmmer/src/p7_domain.c:250:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 250 | network_32bit = esl_hton32(*((uint32_t *) &(obj->bitscore))); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ vendor/hmmer/src/p7_domain.c:255:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 255 | network_64bit = esl_hton64(*((uint64_t *) &(obj->lnP))); | ~^~~~~~~~~~~~~~~~~~~~~~~~~ vendor/hmmer/src/p7_domain.c: In function ‘p7_domain_Deserialize’: vendor/hmmer/src/p7_domain.c:379:22: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 379 | ret_obj->envsc = *((float *) &host_32bit); | ~^~~~~~~~~~~~~~~~~~~~~~ vendor/hmmer/src/p7_domain.c:385:30: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 385 | ret_obj->domcorrection = *((float *) &host_32bit); | ~^~~~~~~~~~~~~~~~~~~~~~ vendor/hmmer/src/p7_domain.c:391:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 391 | ret_obj->dombias = *((float *) &host_32bit); | ~^~~~~~~~~~~~~~~~~~~~~~ vendor/hmmer/src/p7_domain.c:397:21: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 397 | ret_obj->oasc = *((float *) &host_32bit); | ~^~~~~~~~~~~~~~~~~~~~~~ vendor/hmmer/src/p7_domain.c:403:25: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 403 | ret_obj->bitscore = *((float *) &host_32bit); | ~^~~~~~~~~~~~~~~~~~~~~~ vendor/hmmer/src/p7_domain.c:409:20: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 409 | ret_obj->lnP = *((double *) &host_64bit); | ~^~~~~~~~~~~~~~~~~~~~~~~ vendor/hmmer/src/p7_domain.c:436:38: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 436 | ret_obj->scores_per_pos[i] = *((float *) &host_32bit); | ~^~~~~~~~~~~~~~~~~~~~~~ vendor/hmmer/src/p7_hit.c: In function ‘p7_hit_Serialize’: vendor/hmmer/src/p7_hit.c:287:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 287 | network_64bit = esl_hton64(*((uint64_t *) &(obj->sortkey))); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ vendor/hmmer/src/p7_hit.c:292:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 292 | network_32bit = esl_hton32(*((uint32_t *) &(obj->score))); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~ vendor/hmmer/src/p7_hit.c:297:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 297 | network_32bit = esl_hton32(*((uint32_t *) &(obj->pre_score))); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ vendor/hmmer/src/p7_hit.c:302:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 302 | network_32bit = esl_hton32(*((uint32_t *) &(obj->sum_score))); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ vendor/hmmer/src/p7_hit.c:307:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 307 | network_64bit = esl_hton64(*((uint64_t *) &(obj->lnP))); | ~^~~~~~~~~~~~~~~~~~~~~~~~~ vendor/hmmer/src/p7_hit.c:312:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 312 | network_64bit = esl_hton64(*((uint64_t *) &(obj->pre_lnP))); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ vendor/hmmer/src/p7_hit.c:317:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 317 | network_64bit = esl_hton64(*((uint64_t *) &(obj->sum_lnP))); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ vendor/hmmer/src/p7_hit.c:322:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 322 | network_32bit = esl_hton32(*((uint32_t *) &(obj->nexpected))); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ vendor/hmmer/src/p7_hit.c: In function ‘p7_hit_Deserialize’: vendor/hmmer/src/p7_hit.c:471:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 471 | ret_obj->sortkey = *((double *) &host_64bit); | ~^~~~~~~~~~~~~~~~~~~~~~~ vendor/hmmer/src/p7_hit.c:477:22: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 477 | ret_obj->score = *((float *) &host_32bit); | ~^~~~~~~~~~~~~~~~~~~~~~ vendor/hmmer/src/p7_hit.c:483:26: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 483 | ret_obj->pre_score = *((float *) &host_32bit); | ~^~~~~~~~~~~~~~~~~~~~~~ vendor/hmmer/src/p7_hmmd_search_stats.c: In function ‘p7_hmmd_search_stats_Serialize’: vendor/hmmer/src/p7_hmmd_search_stats.c:89:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 89 | network_64bit = esl_hton64(*((uint64_t *) &(obj->elapsed))); // ow, this hurts, but is probably the best way to get the | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ vendor/hmmer/src/p7_hmmd_search_stats.c:97:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 97 | network_64bit = esl_hton64(*((uint64_t *) &(obj->user))); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~ vendor/hmmer/src/p7_hmmd_search_stats.c:103:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 103 | network_64bit = esl_hton64(*((uint64_t *) &(obj->sys))); | ~^~~~~~~~~~~~~~~~~~~~~~~~~ vendor/hmmer/src/p7_hmmd_search_stats.c:109:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 109 | network_64bit = esl_hton64(*((uint64_t *) &(obj->Z))); | ~^~~~~~~~~~~~~~~~~~~~~~~ vendor/hmmer/src/p7_hmmd_search_stats.c:115:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 115 | network_64bit = esl_hton64(*((uint64_t *) &(obj->domZ))); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~ vendor/hmmer/src/p7_hmmd_search_stats.c:205:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 205 | for (i = 0; i < obj->nhits; i++) | ^ vendor/hmmer/src/p7_hmmd_search_stats.c: In function ‘p7_hmmd_search_stats_Deserialize’: vendor/hmmer/src/p7_hmmd_search_stats.c:258:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 258 | ret_obj->elapsed = *((double *) &host_64bit); | ~^~~~~~~~~~~~~~~~~~~~~~~ vendor/hmmer/src/p7_hmmd_search_stats.c:264:21: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 264 | ret_obj->user = *((double *) &host_64bit); | ~^~~~~~~~~~~~~~~~~~~~~~~ vendor/hmmer/src/p7_hmmd_search_stats.c:270:20: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 270 | ret_obj->sys = *((double *) &host_64bit); | ~^~~~~~~~~~~~~~~~~~~~~~~ vendor/hmmer/src/p7_hmmd_search_stats.c:276:18: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 276 | ret_obj->Z = *((double *) &host_64bit); | ~^~~~~~~~~~~~~~~~~~~~~~~ vendor/hmmer/src/p7_hmmd_search_stats.c:282:21: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 282 | ret_obj->domZ = *((double *) &host_64bit); | ~^~~~~~~~~~~~~~~~~~~~~~~ vendor/hmmer/src/p7_hmmd_search_stats.c:380:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 380 | for (i = 1; i < ret_obj->nhits; i++) | ^ vendor/hmmer/src/p7_hit.c:489:26: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 489 | ret_obj->sum_score = *((float *) &host_32bit); | ~^~~~~~~~~~~~~~~~~~~~~~ vendor/hmmer/src/p7_hit.c:495:20: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 495 | ret_obj->lnP = *((double *) &host_64bit); | ~^~~~~~~~~~~~~~~~~~~~~~~ vendor/hmmer/src/p7_hit.c:501:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 501 | ret_obj->pre_lnP = *((double *) &host_64bit); | ~^~~~~~~~~~~~~~~~~~~~~~~ vendor/hmmer/src/p7_hit.c:507:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 507 | ret_obj->sum_lnP = *((double *) &host_64bit); | ~^~~~~~~~~~~~~~~~~~~~~~~ vendor/hmmer/src/p7_hit.c:513:26: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 513 | ret_obj->nexpected = *((float *) &host_32bit); | ~^~~~~~~~~~~~~~~~~~~~~~ generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_alidisplay.o from vendor/hmmer/src/p7_alidisplay.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/p7_alidisplay.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_alidisplay.o generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_hmmwindow.o from vendor/hmmer/src/p7_hmmwindow.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/p7_hmmwindow.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_hmmwindow.o generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_domaindef.o from vendor/hmmer/src/p7_domaindef.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/p7_domaindef.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_domaindef.o vendor/hmmer/src/p7_alidisplay.c: In function ‘p7_alidisplay_Deserialize’: vendor/hmmer/src/p7_alidisplay.c:725:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 725 | if(ret_obj->memsize < (obj_size - SER_BASE_SIZE)){ // ret_obj doesn't have enough space for this P7_ALIDISPLAY | ^ vendor/hmmer/src/p7_alidisplay.c:885:29: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘long unsigned int’ [-Wsign-compare] 885 | if(mem_ptr - ret_obj->mem != (obj_size - SER_BASE_SIZE)){ | ^~ generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_pipeline.o from vendor/hmmer/src/p7_pipeline.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/p7_pipeline.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_pipeline.o generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_hmm.o from vendor/hmmer/src/p7_hmm.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/p7_hmm.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_hmm.o In file included from vendor/hmmer/src/p7_pipeline.c:15: vendor/hmmer/src/p7_pipeline.c: In function ‘p7_pli_postSSV_LongTarget’: vendor/easel/easel.h:431:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 431 | #define ESL_MIN(a,b) (((a)<(b))?(a):(b)) | ^ vendor/hmmer/src/p7_pipeline.c:1407:61: note: in expansion of macro ‘ESL_MIN’ 1407 | p7_hmmwindow_new(vit_windowlist, 0, new_n, 0, 0, ESL_MIN(max_window_len,new_len), 0.0, p7_NOCOMPLEMENT, new_len ); | ^~~~~~~ vendor/hmmer/src/p7_domaindef.c: In function ‘rescore_isolated_domain’: vendor/easel/easel.h:431:42: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 431 | #define ESL_MIN(a,b) (((a)<(b))?(a):(b)) | ^~~ vendor/hmmer/src/p7_pipeline.c:1407:61: note: in expansion of macro ‘ESL_MIN’ 1407 | p7_hmmwindow_new(vit_windowlist, 0, new_n, 0, 0, ESL_MIN(max_window_len,new_len), 0.0, p7_NOCOMPLEMENT, new_len ); | ^~~~~~~ vendor/hmmer/src/p7_pipeline.c:1408:27: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 1408 | } while (new_len > max_window_len); | ^ vendor/hmmer/src/p7_domaindef.c:932:5: warning: ‘orig_L’ may be used uninitialized [-Wmaybe-uninitialized] 932 | p7_oprofile_ReconfigRestLength(om, orig_L); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ vendor/hmmer/src/p7_pipeline.c: In function ‘p7_Pipeline_LongTarget’: vendor/hmmer/src/p7_pipeline.c:1655:46: warning: operand of ‘?:’ changes signedness from ‘int64_t’ {aka ‘long int’} to ‘uint64_t’ {aka ‘long unsigned int’} due to unsignedness of other operand [-Wsign-compare] 1655 | (fmf != NULL ? seq_start : sq->start), | ^~~~~~~~~ vendor/hmmer/src/p7_pipeline.c:1660:46: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 1660 | (fmf != NULL ? seq_data.length : -1), | ^~ vendor/hmmer/src/p7_domaindef.c:827:18: note: ‘orig_L’ was declared here 827 | int orig_L; | ^~~~~~ vendor/hmmer/src/p7_hmm.c: In function ‘p7_hmm_Validate’: vendor/hmmer/src/p7_hmm.c:1282:85: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1282 | if (hmm->flags & p7H_RF) { if (hmm->rf == NULL || strlen(hmm->rf) != hmm->M+1) ESL_XFAIL(eslFAIL, errbuf, "p7H_RF flag up, but rf string is invalid"); } | ^~ vendor/hmmer/src/p7_hmm.c:1285:86: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1285 | if (hmm->flags & p7H_MMASK) { if (hmm->mm == NULL || strlen(hmm->mm) != hmm->M+1) ESL_XFAIL(eslFAIL, errbuf, "p7H_MMASK flag up, but mm string is invalid"); } | ^~ vendor/hmmer/src/p7_hmm.c:1288:85: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1288 | if (hmm->flags & p7H_CONS) { if (hmm->consensus == NULL || strlen(hmm->consensus) != hmm->M+1) ESL_XFAIL(eslFAIL, errbuf, "p7H_CONS flag up, but consensus string is invalid"); } | ^~ vendor/hmmer/src/p7_hmm.c:1291:85: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1291 | if (hmm->flags & p7H_CS) { if (hmm->cs == NULL || strlen(hmm->cs) != hmm->M+1) ESL_XFAIL(eslFAIL, errbuf, "p7H_CS flag up, but cs string is invalid"); } | ^~ vendor/hmmer/src/p7_hmm.c:1294:85: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1294 | if (hmm->flags & p7H_CA) { if (hmm->ca == NULL || strlen(hmm->ca) != hmm->M+1) ESL_XFAIL(eslFAIL, errbuf, "p7H_CA flag up, but ca string is invalid"); } | ^~ generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_gbands.o from vendor/hmmer/src/p7_gbands.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/p7_gbands.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_gbands.o generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_gmx.o from vendor/hmmer/src/p7_gmx.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/p7_gmx.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_gmx.o In file included from vendor/hmmer/src/hmmer.h:42, from vendor/hmmer/src/p7_gmx.c:11: vendor/hmmer/src/p7_gmx.c: In function ‘p7_gmx_GrowTo’: vendor/easel/easel.h:431:36: warning: comparison of integer expressions of different signedness: ‘uint64_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 431 | #define ESL_MIN(a,b) (((a)<(b))?(a):(b)) | ^ vendor/hmmer/src/p7_gmx.c:144:20: note: in expansion of macro ‘ESL_MIN’ 144 | gx->validR = ESL_MIN(gx->ncells / gx->allocW, gx->allocR); | ^~~~~~~ vendor/easel/easel.h:431:46: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint64_t’ {aka ‘long unsigned int’} due to unsignedness of other operand [-Wsign-compare] 431 | #define ESL_MIN(a,b) (((a)<(b))?(a):(b)) | ^~~ vendor/hmmer/src/p7_gmx.c:144:20: note: in expansion of macro ‘ESL_MIN’ 144 | gx->validR = ESL_MIN(gx->ncells / gx->allocW, gx->allocR); | ^~~~~~~ generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_hmmcache.o from vendor/hmmer/src/p7_hmmcache.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/p7_hmmcache.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_hmmcache.o vendor/hmmer/src/p7_hmmcache.c: In function ‘p7_hmmcache_Sizeof’: vendor/hmmer/src/p7_hmmcache.c:111:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 111 | for (i = 0; i < cache->n; i++) | ^ vendor/hmmer/src/p7_hmmcache.c: In function ‘p7_hmmcache_SetNumericNames’: vendor/hmmer/src/p7_hmmcache.c:139:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 139 | for (i = 0; i < cache->n; i++) | ^ vendor/hmmer/src/p7_hmmcache.c: In function ‘p7_hmmcache_Close’: vendor/hmmer/src/p7_hmmcache.c:162:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 162 | for (i = 0; i < cache->n; i++) | ^ generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_spensemble.o from vendor/hmmer/src/p7_spensemble.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/p7_spensemble.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_spensemble.o generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_bg.o from vendor/hmmer/src/p7_bg.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/p7_bg.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_bg.o generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/fm_alphabet.o from vendor/hmmer/src/fm_alphabet.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/fm_alphabet.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/fm_alphabet.o generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_prior.o from vendor/hmmer/src/p7_prior.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/p7_prior.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_prior.o generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/fm_general.o from vendor/hmmer/src/fm_general.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/fm_general.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/fm_general.o In file included from vendor/hmmer/src/p7_spensemble.c:7: vendor/hmmer/src/p7_spensemble.c: In function ‘p7_spensemble_Cluster’: vendor/hmmer/src/p7_spensemble.c:344:43: warning: ‘imax’ may be used uninitialized [-Wmaybe-uninitialized] 344 | cwindow_width = ESL_MAX(ESL_MAX(imax-imin+1, jmax-jmin+1), | ~~~~^~~~~ vendor/hmmer/src/p7_spensemble.c:294:7: note: ‘imax’ was declared here 294 | int imax, jmax, kmax, mmax; | ^~~~ vendor/hmmer/src/p7_spensemble.c:344:56: warning: ‘jmin’ may be used uninitialized [-Wmaybe-uninitialized] 344 | cwindow_width = ESL_MAX(ESL_MAX(imax-imin+1, jmax-jmin+1), | ~~~~^~~~~ vendor/hmmer/src/p7_spensemble.c:293:13: note: ‘jmin’ was declared here 293 | int imin, jmin, kmin, mmin; | ^~~~ vendor/hmmer/src/p7_spensemble.c:345:43: warning: ‘kmin’ may be used uninitialized [-Wmaybe-uninitialized] 345 | ESL_MAX(kmax-kmin+1, mmax-mmin+1)); | ~~~~^~~~~ vendor/hmmer/src/p7_spensemble.c:293:19: note: ‘kmin’ was declared here 293 | int imin, jmin, kmin, mmin; | ^~~~ vendor/hmmer/src/p7_spensemble.c:345:56: warning: ‘mmin’ may be used uninitialized [-Wmaybe-uninitialized] 345 | ESL_MAX(kmax-kmin+1, mmax-mmin+1)); | ~~~~^~~~~ vendor/hmmer/src/p7_spensemble.c:293:25: note: ‘mmin’ was declared here 293 | int imin, jmin, kmin, mmin; | ^~~~ vendor/hmmer/src/p7_spensemble.c:344:56: warning: ‘jmax’ may be used uninitialized [-Wmaybe-uninitialized] 344 | cwindow_width = ESL_MAX(ESL_MAX(imax-imin+1, jmax-jmin+1), | ~~~~^~~~~ vendor/hmmer/src/p7_spensemble.c:294:13: note: ‘jmax’ was declared here 294 | int imax, jmax, kmax, mmax; | ^~~~ vendor/hmmer/src/p7_spensemble.c:345:43: warning: ‘kmax’ may be used uninitialized [-Wmaybe-uninitialized] 345 | ESL_MAX(kmax-kmin+1, mmax-mmin+1)); | ~~~~^~~~~ vendor/hmmer/src/p7_spensemble.c:294:19: note: ‘kmax’ was declared here 294 | int imax, jmax, kmax, mmax; | ^~~~ vendor/hmmer/src/p7_spensemble.c:345:56: warning: ‘mmax’ may be used uninitialized [-Wmaybe-uninitialized] 345 | ESL_MAX(kmax-kmin+1, mmax-mmin+1)); | ~~~~^~~~~ vendor/hmmer/src/p7_spensemble.c:294:25: note: ‘mmax’ was declared here 294 | int imax, jmax, kmax, mmax; | ^~~~ vendor/hmmer/src/fm_general.c: In function ‘fm_findOverlappingAmbiguityBlock’: vendor/hmmer/src/fm_general.c:292:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 292 | if (ranges[lo].lower > end) return -1; | ^ generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/impl_sse/vitfilter.o from vendor/hmmer/src/impl_sse/vitfilter.c creating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/impl_sse gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/impl_sse/vitfilter.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/impl_sse/vitfilter.o generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_profile.o from vendor/hmmer/src/p7_profile.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/p7_profile.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_profile.o vendor/hmmer/src/fm_general.c:293:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 293 | if (ranges[hi].upper < start) return -1; | ^ vendor/hmmer/src/fm_general.c:297:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 297 | if (ranges[mid].lower < start) lo = mid + 1; // too far left | ^ vendor/hmmer/src/fm_general.c:302:42: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 302 | if (lo>0 && ranges[lo-1].upper >= start && ranges[lo-1].lower <= end) return lo-1; | ^~ vendor/hmmer/src/fm_general.c:302:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 302 | if (lo>0 && ranges[lo-1].upper >= start && ranges[lo-1].lower <= end) return lo-1; | ^~ vendor/hmmer/src/fm_general.c:303:42: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 303 | else if ( ranges[lo].upper >= start && ranges[lo].lower <= end) return lo; | ^~ vendor/hmmer/src/fm_general.c:303:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 303 | else if ( ranges[lo].upper >= start && ranges[lo].lower <= end) return lo; | ^~ vendor/hmmer/src/fm_general.c: In function ‘fm_convertRange2DSQ’: vendor/hmmer/src/fm_general.c:350:20: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 350 | while (pos <= fm->ambig_offset + fm->ambig_cnt -1 && meta->ambig_list->ranges[pos].lower <= first+length-1) { | ^~ vendor/hmmer/src/fm_general.c:350:98: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 350 | while (pos <= fm->ambig_offset + fm->ambig_cnt -1 && meta->ambig_list->ranges[pos].lower <= first+length-1) { | ^~ In file included from vendor/hmmer/src/fm_general.c:12: vendor/easel/easel.h:432:36: warning: comparison of integer expressions of different signedness: ‘uint64_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 432 | #define ESL_MAX(a,b) (((a)>(b))?(a):(b)) | ^ vendor/hmmer/src/fm_general.c:351:23: note: in expansion of macro ‘ESL_MAX’ 351 | int start = ESL_MAX(first, meta->ambig_list->ranges[pos].lower); | ^~~~~~~ vendor/easel/easel.h:432:46: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint64_t’ {aka ‘long unsigned int’} due to unsignedness of other operand [-Wsign-compare] 432 | #define ESL_MAX(a,b) (((a)>(b))?(a):(b)) | ^~~ vendor/hmmer/src/fm_general.c:351:23: note: in expansion of macro ‘ESL_MAX’ 351 | int start = ESL_MAX(first, meta->ambig_list->ranges[pos].lower); | ^~~~~~~ vendor/easel/easel.h:431:36: warning: comparison of integer expressions of different signedness: ‘uint64_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 431 | #define ESL_MIN(a,b) (((a)<(b))?(a):(b)) | ^ vendor/hmmer/src/fm_general.c:352:23: note: in expansion of macro ‘ESL_MIN’ 352 | int end = ESL_MIN(first+length-1, meta->ambig_list->ranges[pos].upper); | ^~~~~~~ vendor/easel/easel.h:431:46: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint64_t’ {aka ‘long unsigned int’} due to unsignedness of other operand [-Wsign-compare] 431 | #define ESL_MIN(a,b) (((a)<(b))?(a):(b)) | ^~~ vendor/hmmer/src/fm_general.c:352:23: note: in expansion of macro ‘ESL_MIN’ 352 | int end = ESL_MIN(first+length-1, meta->ambig_list->ranges[pos].upper); | ^~~~~~~ vendor/hmmer/src/fm_general.c:353:27: warning: comparison of integer expressions of different signedness: ‘uint64_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 353 | for (j= start; j<=end; j++) | ^~ vendor/hmmer/src/fm_general.c: In function ‘fm_FM_read’: vendor/hmmer/src/fm_general.c:537:75: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare] 537 | (getAll && fread(fm->T, sizeof(uint8_t), compressed_bytes, meta->fp) != compressed_bytes) || | ^~ vendor/hmmer/src/fm_general.c:538:68: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare] 538 | (fread(fm->BWT, sizeof(uint8_t), compressed_bytes, meta->fp) != compressed_bytes) || | ^~ vendor/hmmer/src/fm_general.c: In function ‘fm_readFMmeta’: vendor/hmmer/src/fm_general.c:620:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 620 | for (i=0; iseq_count; i++) { | ^ vendor/hmmer/src/fm_general.c:638:101: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 638 | fread(meta->seq_data[i].name, sizeof(char), meta->seq_data[i].name_length+1 , meta->fp) != meta->seq_data[i].name_length+1 || | ^~ vendor/hmmer/src/fm_general.c:639:101: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 639 | fread(meta->seq_data[i].acc, sizeof(char), meta->seq_data[i].acc_length+1 , meta->fp) != meta->seq_data[i].acc_length+1 || | ^~ vendor/hmmer/src/fm_general.c:640:101: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 640 | fread(meta->seq_data[i].source, sizeof(char), meta->seq_data[i].source_length+1 , meta->fp) != meta->seq_data[i].source_length+1 || | ^~ vendor/hmmer/src/fm_general.c:641:101: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 641 | fread(meta->seq_data[i].desc, sizeof(char), meta->seq_data[i].desc_length+1 , meta->fp) != meta->seq_data[i].desc_length+1 | ^~ vendor/hmmer/src/fm_general.c:651:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 651 | for (i=0; iambig_list->count; i++) { | ^ vendor/hmmer/src/fm_general.c:663:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 663 | for (i=0; iseq_count; i++) | ^ vendor/hmmer/src/fm_general.c: In function ‘fm_metaDestroy’: vendor/hmmer/src/fm_general.c:727:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 727 | for (i=0; iseq_count; i++) { | ^ generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_tophits.o from vendor/hmmer/src/p7_tophits.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/p7_tophits.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_tophits.o vendor/hmmer/src/p7_tophits.c: In function ‘p7_tophits_Clone’: vendor/hmmer/src/p7_tophits.c:92:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 92 | for (i = 0; i < h2->N; i++) { | ^ vendor/hmmer/src/p7_tophits.c:100:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 100 | for (i = 0; i < h2->N; i++) { | ^ vendor/hmmer/src/p7_tophits.c: In function ‘p7_tophits_Grow’: vendor/hmmer/src/p7_tophits.c:143:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 143 | for (i = 0; i < h->N; i++) | ^ vendor/hmmer/src/p7_tophits.c: In function ‘p7_tophits_SortBySortkey’: vendor/hmmer/src/p7_tophits.c:398:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 398 | for (i = 0; i < h->N; i++) h->hit[i] = h->unsrt + i; | ^ vendor/hmmer/src/p7_tophits.c: In function ‘p7_tophits_SortBySeqidxAndAlipos’: vendor/hmmer/src/p7_tophits.c:431:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 431 | for (i = 0; i < h->N; i++) h->hit[i] = h->unsrt + i; | ^ vendor/hmmer/src/p7_tophits.c: In function ‘p7_tophits_SortByModelnameAndAlipos’: vendor/hmmer/src/p7_tophits.c:452:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 452 | for (i = 0; i < h->N; i++) h->hit[i] = h->unsrt + i; | ^ vendor/hmmer/src/p7_tophits.c: In function ‘p7_tophits_Merge’: vendor/hmmer/src/p7_tophits.c:496:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 496 | for (i = 0; i < h1->N; i++) | ^ vendor/hmmer/src/p7_tophits.c:504:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 504 | for (i=0,j=0,k=0; i < h1->N && j < h2->N ; k++) | ^ vendor/hmmer/src/p7_tophits.c:504:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 504 | for (i=0,j=0,k=0; i < h1->N && j < h2->N ; k++) | ^ vendor/hmmer/src/p7_tophits.c:506:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 506 | while (i < h1->N) new_hit[k++] = h1->hit[i++]; | ^ vendor/hmmer/src/p7_tophits.c:507:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 507 | while (j < h2->N) new_hit[k++] = new2 + (h2->hit[j++] - h2->unsrt); | ^ vendor/hmmer/src/p7_tophits.c:511:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 511 | for (i = 0; i < h2->N; i++) | ^ vendor/hmmer/src/p7_tophits.c: In function ‘p7_tophits_GetMaxPositionLength’: vendor/hmmer/src/p7_tophits.c:559:17: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 559 | for (i = 0; i < h->N; i++) { | ^ vendor/hmmer/src/p7_tophits.c: In function ‘p7_tophits_GetMaxNameLength’: vendor/hmmer/src/p7_tophits.c:589:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 589 | for (max = 0, i = 0; i < h->N; i++) | ^ vendor/hmmer/src/p7_tophits.c: In function ‘p7_tophits_GetMaxAccessionLength’: vendor/hmmer/src/p7_tophits.c:608:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 608 | for (max = 0, i = 0; i < h->N; i++) | ^ vendor/hmmer/src/p7_tophits.c: In function ‘p7_tophits_GetMaxShownLength’: vendor/hmmer/src/p7_tophits.c:630:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 630 | for (max = 0, i = 0; i < h->N; i++) | ^ vendor/hmmer/src/p7_tophits.c: In function ‘p7_tophits_Reuse’: vendor/hmmer/src/p7_tophits.c:663:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 663 | for (i = 0; i < h->N; i++) | ^ vendor/hmmer/src/p7_tophits.c: In function ‘p7_tophits_Destroy’: vendor/hmmer/src/p7_tophits.c:693:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 693 | for (i = 0; i < h->N; i++) | ^ vendor/hmmer/src/p7_tophits.c: In function ‘workaround_bug_h74’: vendor/hmmer/src/p7_tophits.c:762:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 762 | for (h = 0; h < th->N; h++) | ^ vendor/hmmer/src/p7_tophits.c: In function ‘p7_tophits_ComputeNhmmerEvalues’: vendor/hmmer/src/p7_tophits.c:800:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 800 | for (i = 0; i < th->N ; i++) | ^ vendor/hmmer/src/p7_tophits.c: In function ‘p7_tophits_RemoveDuplicates’: vendor/hmmer/src/p7_tophits.c:836:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 836 | for (i = 1; i < th->N; i++) | ^ vendor/hmmer/src/p7_tophits.c: In function ‘p7_tophits_Threshold’: vendor/hmmer/src/p7_tophits.c:935:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 935 | for (h = 0; h < th->N; h++) | ^ vendor/hmmer/src/p7_tophits.c:956:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 956 | for (h = 0; h < th->N; h++) | ^ vendor/hmmer/src/p7_tophits.c:974:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 974 | for (h = 0; h < th->N; h++) | ^ vendor/hmmer/src/p7_tophits.c:991:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 991 | for (h = 0; h < th->N; h++) { | ^ vendor/hmmer/src/p7_tophits.c: In function ‘p7_tophits_CompareRanking’: vendor/hmmer/src/p7_tophits.c:1069:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1069 | for (h = 0; h < th->N; h++) | ^ vendor/hmmer/src/p7_tophits.c:1085:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1085 | for (h = 0; h < th->N; h++) | ^ vendor/hmmer/src/p7_tophits.c: In function ‘p7_tophits_Targets’: vendor/hmmer/src/p7_tophits.c:1173:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1173 | for (h = 0; h < th->N; h++) | ^ vendor/hmmer/src/p7_tophits.c: In function ‘p7_tophits_Domains’: vendor/hmmer/src/p7_tophits.c:1289:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1289 | for (h = 0; h < th->N; h++) | ^ vendor/hmmer/src/p7_tophits.c: In function ‘p7_tophits_Alignment’: vendor/hmmer/src/p7_tophits.c:1528:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1528 | for (h = 0; h < th->N; h++) | ^ vendor/hmmer/src/p7_tophits.c:1554:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1554 | for (h = 0; h < th->N; h++) | ^ vendor/hmmer/src/p7_tophits.c: In function ‘p7_tophits_TabularTargets’: vendor/hmmer/src/p7_tophits.c:1643:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1643 | for (h = 0; h < th->N; h++) | ^ vendor/hmmer/src/p7_tophits.c: In function ‘p7_tophits_TabularDomains’: vendor/hmmer/src/p7_tophits.c:1736:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1736 | for (h = 0; h < th->N; h++) | ^ vendor/hmmer/src/p7_tophits.c: In function ‘p7_tophits_TabularXfam’: vendor/hmmer/src/p7_tophits.c:1838:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1838 | for (h = 0; h < th->N; h++) | ^ vendor/hmmer/src/p7_tophits.c:1872:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1872 | for (h = 0; h < th->N; h++) | ^ vendor/hmmer/src/p7_tophits.c:1893:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1893 | for (h = 0; h < th->N; h++) | ^ vendor/hmmer/src/p7_tophits.c:1927:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1927 | for (h = 0; h < domHitlist->N; h++) | ^ vendor/hmmer/src/p7_tophits.c: In function ‘p7_tophits_AliScores’: vendor/hmmer/src/p7_tophits.c:1980:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1980 | for (h = 0; h < th->N; h++) { | ^ generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/impl_sse/optacc.o from vendor/hmmer/src/impl_sse/optacc.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/impl_sse/optacc.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/impl_sse/optacc.o generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/fm_sse.o from vendor/hmmer/src/fm_sse.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/fm_sse.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/fm_sse.o vendor/hmmer/src/fm_sse.c: In function ‘fm_getOccCount’: vendor/hmmer/src/fm_sse.c:201:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 201 | if (landmark >= fm->N) { // special case: for a count in the final block, just count from the bottom | ^~ vendor/hmmer/src/fm_sse.c:218:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 218 | else if ( b_pos != sb_pos * (meta->freq_cnt_sb / meta->freq_cnt_b) ) | ^~ vendor/hmmer/src/fm_sse.c:221:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 221 | if ( landmark < fm->N || landmark == -1 ) { | ^ vendor/hmmer/src/fm_sse.c:342:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 342 | if (c==0 && pos >= fm->term_loc) { // I overcounted 'A' by one, because '$' was replaced with an 'A' | ^~ vendor/hmmer/src/fm_sse.c: In function ‘fm_getOccCountLT’: vendor/hmmer/src/fm_sse.c:389:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 389 | if (landmark >= fm->N) { // special case: for a count in the final block, just count from the bottom | ^~ vendor/hmmer/src/fm_sse.c:404:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 404 | } else if ( b_pos != sb_pos * (meta->freq_cnt_sb / meta->freq_cnt_b)) { | ^~ vendor/hmmer/src/fm_sse.c:413:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 413 | if ( landmark < fm->N - 1 || landmark == -1 ) { | ^ vendor/hmmer/src/fm_sse.c:610:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 610 | if ( pos >= fm->term_loc) { | ^~ In file included from /usr/include/stdio.h:970, from vendor/easel/easel.h:22, from vendor/hmmer/src/p7_tophits.c:16: In function ‘fprintf’, inlined from ‘p7_tophits_Targets’ at vendor/hmmer/src/p7_tophits.c:1200:12: /usr/include/bits/stdio2.h:111:10: warning: ‘posw’ may be used uninitialized [-Wmaybe-uninitialized] 111 | return __fprintf_chk (__stream, __USE_FORTIFY_LEVEL - 1, __fmt, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 112 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ vendor/hmmer/src/p7_tophits.c: In function ‘p7_tophits_Targets’: vendor/hmmer/src/p7_tophits.c:1126:10: note: ‘posw’ was declared here 1126 | int posw; | ^~~~ generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/impl_sse/stotrace.o from vendor/hmmer/src/impl_sse/stotrace.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/impl_sse/stotrace.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/impl_sse/stotrace.o generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/fm_ssv.o from vendor/hmmer/src/fm_ssv.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/fm_ssv.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/fm_ssv.o vendor/hmmer/src/fm_ssv.c: In function ‘FM_mergeSeeds’: vendor/hmmer/src/fm_ssv.c:70:33: warning: comparison of integer expressions of different signedness: ‘uint64_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 70 | && ( next.n - next.k) == curr_diagval //overlapping diagonals will share the same value of (n - k) | ^~ vendor/hmmer/src/fm_ssv.c:71:35: warning: comparison of integer expressions of different signedness: ‘uint64_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 71 | && next.n + next.length < curr_n + curr_len + ssv_length //overlapping, or close to it | ^ vendor/hmmer/src/fm_ssv.c: In function ‘FM_backtrackSeed’: vendor/hmmer/src/fm_ssv.c:134:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 134 | while ( j != fmf->term_loc && (j % fm_cfg->meta->freq_SA)) { //go until we hit a position in the full SA that was sampled during FM index construction | ^~ vendor/hmmer/src/fm_ssv.c:141:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 141 | return len + (j==fmf->term_loc ? 0 : fmf->SA[ j / fm_cfg->meta->freq_SA ]) ; // len is how many backward steps we had to take to find a sampled SA position | ^~ vendor/hmmer/src/fm_ssv.c: In function ‘FM_extendSeed’: vendor/hmmer/src/fm_ssv.c:664:18: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 664 | if (target_end > fm->N-2) { | ^ vendor/hmmer/src/fm_ssv.c:678:14: warning: comparison of integer expressions of different signedness: ‘uint64_t’ {aka ‘long unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare] 678 | for ( ; k <= model_end; k++, n++) { | ^~ In function ‘get_postprob’, inlined from ‘p7_OATrace’ at vendor/hmmer/src/impl_sse/optacc.c:254:18: vendor/hmmer/src/impl_sse/optacc.c:269:21: warning: ‘kmax’ may be used uninitialized [-Wmaybe-uninitialized] 269 | int q = (k-1) % Q; /* (q,r) is position of the current DP cell M(i,k) */ | ~~^~~ vendor/hmmer/src/impl_sse/optacc.c: In function ‘p7_OATrace’: vendor/hmmer/src/impl_sse/optacc.c:396:16: note: ‘kmax’ was declared here 396 | int smax, kmax; | ^~~~ In function ‘FM_extendSeed’, inlined from ‘p7_SSVFM_longlarget’ at vendor/hmmer/src/fm_ssv.c:808:5: vendor/hmmer/src/fm_ssv.c:695:32: warning: ‘max_hit_start’ may be used uninitialized [-Wmaybe-uninitialized] 695 | diag->k = model_start + max_hit_start - 1; | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~ vendor/hmmer/src/fm_ssv.c: In function ‘p7_SSVFM_longlarget’: vendor/hmmer/src/fm_ssv.c:647:22: note: ‘max_hit_start’ was declared here 647 | int64_t hit_start, max_hit_start, max_hit_end; | ^~~~~~~~~~~~~ In function ‘FM_extendSeed’, inlined from ‘p7_SSVFM_longlarget’ at vendor/hmmer/src/fm_ssv.c:808:5: vendor/hmmer/src/fm_ssv.c:696:31: warning: ‘max_hit_end’ may be used uninitialized [-Wmaybe-uninitialized] 696 | diag->length = max_hit_end - max_hit_start + 1; | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ vendor/hmmer/src/fm_ssv.c: In function ‘p7_SSVFM_longlarget’: vendor/hmmer/src/fm_ssv.c:647:37: note: ‘max_hit_end’ was declared here 647 | int64_t hit_start, max_hit_start, max_hit_end; | ^~~~~~~~~~~ generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/impl_sse/null2.o from vendor/hmmer/src/impl_sse/null2.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/impl_sse/null2.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/impl_sse/null2.o generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_trace.o from vendor/hmmer/src/p7_trace.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/p7_trace.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_trace.o generating build/temp.linux-x86_64-cpython-313/build/temp.linux-x86_64-cpython-313/p7_hmmfile.o from build/temp.linux-x86_64-cpython-313/p7_hmmfile.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c build/temp.linux-x86_64-cpython-313/p7_hmmfile.c -o build/temp.linux-x86_64-cpython-313/build/temp.linux-x86_64-cpython-313/p7_hmmfile.o build/temp.linux-x86_64-cpython-313/p7_hmmfile.c: In function ‘p7_hmmfile_WriteBinary’: build/temp.linux-x86_64-cpython-313/p7_hmmfile.c:1026:70: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1026 | if (fwrite((char *) hmm->mat[k], sizeof(float), hmm->abc->K, fp) != hmm->abc->K) ESL_EXCEPTION_SYS(eslEWRITE, "hmm binary write failed"); | ^~ build/temp.linux-x86_64-cpython-313/p7_hmmfile.c:1028:70: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1028 | if (fwrite((char *) hmm->ins[k], sizeof(float), hmm->abc->K, fp) != hmm->abc->K) ESL_EXCEPTION_SYS(eslEWRITE, "hmm binary write failed"); | ^~ build/temp.linux-x86_64-cpython-313/p7_hmmfile.c:1037:95: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1037 | if ((hmm->flags & p7H_RF) && (fwrite((char *) hmm->rf, sizeof(char), hmm->M+2, fp) != hmm->M+2)) ESL_EXCEPTION_SYS(eslEWRITE, "hmm binary write failed"); /* +2: 1..M and trailing \0 */ | ^~ build/temp.linux-x86_64-cpython-313/p7_hmmfile.c:1038:95: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1038 | if ((hmm->flags & p7H_MMASK)&& (fwrite((char *) hmm->mm, sizeof(char), hmm->M+2, fp) != hmm->M+2)) ESL_EXCEPTION_SYS(eslEWRITE, "hmm binary write failed"); /* +2: 1..M and trailing \0 */ | ^~ build/temp.linux-x86_64-cpython-313/p7_hmmfile.c:1039:95: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1039 | if ((hmm->flags & p7H_CONS) && (fwrite((char *) hmm->consensus, sizeof(char), hmm->M+2, fp) != hmm->M+2)) ESL_EXCEPTION_SYS(eslEWRITE, "hmm binary write failed"); /* don't need to test for >=3e format; p7H_CONS flag suffices (didn't exist pre-3e) */ | ^~ build/temp.linux-x86_64-cpython-313/p7_hmmfile.c:1040:95: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1040 | if ((hmm->flags & p7H_CS) && (fwrite((char *) hmm->cs, sizeof(char), hmm->M+2, fp) != hmm->M+2)) ESL_EXCEPTION_SYS(eslEWRITE, "hmm binary write failed"); | ^~ build/temp.linux-x86_64-cpython-313/p7_hmmfile.c:1041:95: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1041 | if ((hmm->flags & p7H_CA) && (fwrite((char *) hmm->ca, sizeof(char), hmm->M+2, fp) != hmm->M+2)) ESL_EXCEPTION_SYS(eslEWRITE, "hmm binary write failed"); | ^~ build/temp.linux-x86_64-cpython-313/p7_hmmfile.c:1047:95: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1047 | if ((hmm->flags & p7H_MAP) && (fwrite((char *) hmm->map, sizeof(int), hmm->M+1, fp) != hmm->M+1)) ESL_EXCEPTION_SYS(eslEWRITE, "hmm binary write failed"); | ^~ build/temp.linux-x86_64-cpython-313/p7_hmmfile.c:1064:96: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1064 | if ((hmm->flags & p7H_COMPO) && (fwrite((char *) hmm->compo, sizeof(float), hmm->abc->K, fp) != hmm->abc->K)) ESL_EXCEPTION_SYS(eslEWRITE, "hmm binary write failed"); | ^~ build/temp.linux-x86_64-cpython-313/p7_hmmfile.c: In function ‘multiline’: build/temp.linux-x86_64-cpython-313/p7_hmmfile.c:2022:44: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 2022 | if (fwrite(sptr, sizeof(char), n, fp) != n) ESL_EXCEPTION_SYS(eslEWRITE, "hmm write failed"); /* using fwrite lets us write fixed # of chars */ | ^~ build/temp.linux-x86_64-cpython-313/p7_hmmfile.c: In function ‘write_bin_string’: build/temp.linux-x86_64-cpython-313/p7_hmmfile.c:2145:56: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 2145 | if (fwrite((char *) s, sizeof(char), len, fp) != len) ESL_EXCEPTION_SYS(eslEWRITE, "hmm binary write failed"); | ^~ generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/impl_sse/ssvfilter.o from vendor/hmmer/src/impl_sse/ssvfilter.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/impl_sse/ssvfilter.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/impl_sse/ssvfilter.o generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/impl_sse/msvfilter.o from vendor/hmmer/src/impl_sse/msvfilter.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/impl_sse/msvfilter.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/impl_sse/msvfilter.o generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_scoredata.o from vendor/hmmer/src/p7_scoredata.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/p7_scoredata.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_scoredata.o generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/hmmpgmd2msa.o from vendor/hmmer/src/hmmpgmd2msa.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/hmmpgmd2msa.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/hmmpgmd2msa.o vendor/hmmer/src/hmmpgmd2msa.c: In function ‘hmmpgmd2msa’: vendor/hmmer/src/hmmpgmd2msa.c:131:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 131 | for (i = 0; i < stats->nhits; ++i) { | ^ vendor/hmmer/src/hmmpgmd2msa.c:144:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 144 | for (i=0; inhits; i++) { | ^ vendor/hmmer/src/hmmpgmd2msa.c:163:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 163 | for (i = 0; i < th->N; i++) { | ^ vendor/hmmer/src/hmmpgmd2msa.c:172:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 172 | for (i = 0; i < th->N; i++) { | ^ vendor/hmmer/src/hmmpgmd2msa.c: In function ‘hmmpgmd2stats_old’: vendor/hmmer/src/hmmpgmd2msa.c:311:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 311 | for (i=0; inhits; i++) { | ^ vendor/hmmer/src/hmmpgmd2msa.c:327:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 327 | for (i = 0; i < th.N; i++) | ^ vendor/hmmer/src/hmmpgmd2msa.c:450:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 450 | for (i = 0; i < th.N; i++) { | ^ vendor/hmmer/src/hmmpgmd2msa.c:473:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 473 | for (i = 0; i < th.N; i++) { | ^ generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/impl_sse/mpi.o from vendor/hmmer/src/impl_sse/mpi.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/impl_sse/mpi.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/impl_sse/mpi.o generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/impl_sse/io.o from vendor/hmmer/src/impl_sse/io.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/impl_sse/io.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/impl_sse/io.o generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/impl_sse/fwdback.o from vendor/hmmer/src/impl_sse/fwdback.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/impl_sse/fwdback.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/impl_sse/fwdback.o vendor/hmmer/src/impl_sse/io.c: In function ‘p7_oprofile_Write’: vendor/hmmer/src/impl_sse/io.c:101:77: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 101 | if (fwrite((char *) om->name, sizeof(char), n+1, ffp) != n+1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed"); | ^~ vendor/hmmer/src/impl_sse/io.c:111:77: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 111 | if (fwrite( (char *) om->sbv[x], sizeof(__m128i), Q16x, ffp) != Q16x) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed"); | ^~ vendor/hmmer/src/impl_sse/io.c:114:77: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 114 | if (fwrite( (char *) om->rbv[x], sizeof(__m128i), Q16, ffp) != Q16) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed"); | ^~ vendor/hmmer/src/impl_sse/io.c:126:77: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 126 | if (fwrite((char *) om->name, sizeof(char), n+1, pfp) != n+1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed"); | ^~ vendor/hmmer/src/impl_sse/io.c:134:77: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 134 | if (fwrite((char *) om->acc, sizeof(char), n+1, pfp) != n+1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed"); | ^~ vendor/hmmer/src/impl_sse/io.c:143:77: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 143 | if (fwrite((char *) om->desc, sizeof(char), n+1, pfp) != n+1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed"); | ^~ vendor/hmmer/src/impl_sse/io.c:146:77: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 146 | if (fwrite((char *) om->rf, sizeof(char), om->M+2, pfp) != om->M+2) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed"); | ^~ vendor/hmmer/src/impl_sse/io.c:147:77: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 147 | if (fwrite((char *) om->mm, sizeof(char), om->M+2, pfp) != om->M+2) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed"); | ^~ vendor/hmmer/src/impl_sse/io.c:148:77: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 148 | if (fwrite((char *) om->cs, sizeof(char), om->M+2, pfp) != om->M+2) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed"); | ^~ vendor/hmmer/src/impl_sse/io.c:149:77: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 149 | if (fwrite((char *) om->consensus, sizeof(char), om->M+2, pfp) != om->M+2) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed"); | ^~ vendor/hmmer/src/impl_sse/io.c:152:80: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 152 | if (fwrite((char *) om->twv, sizeof(__m128i), 8*Q8, pfp) != 8*Q8) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed"); | ^~ vendor/hmmer/src/impl_sse/io.c:154:80: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 154 | if (fwrite( (char *) om->rwv[x], sizeof(__m128i), Q8, pfp) != Q8) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed"); | ^~ vendor/hmmer/src/impl_sse/io.c:163:77: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 163 | if (fwrite((char *) om->tfv, sizeof(__m128), 8*Q4, pfp) != 8*Q4) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed"); | ^~ vendor/hmmer/src/impl_sse/io.c:165:77: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 165 | if (fwrite( (char *) om->rfv[x], sizeof(__m128), Q4, pfp) != Q4) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed"); | ^~ generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/impl_sse/decoding.o from vendor/hmmer/src/impl_sse/decoding.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/impl_sse/decoding.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/impl_sse/decoding.o generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/impl_sse/p7_oprofile.o from vendor/hmmer/src/impl_sse/p7_oprofile.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/impl_sse/p7_oprofile.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/impl_sse/p7_oprofile.o generating build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/impl_sse/p7_omx.o from vendor/hmmer/src/impl_sse/p7_omx.c gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -msse4.1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.linux-x86_64-cpython-313 -I/usr/include/python3.13 -c vendor/hmmer/src/impl_sse/p7_omx.c -o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/impl_sse/p7_omx.o ar rcs build/temp.linux-x86_64-cpython-313/libhmmer.a build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/build.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/cachedb.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/cachedb_shard.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/emit.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/errors.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/evalues.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/eweight.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/generic_decoding.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/generic_fwdback.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/generic_fwdback_chk.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/generic_fwdback_banded.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/generic_null2.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/generic_msv.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/generic_optacc.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/generic_stotrace.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/generic_viterbi.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/generic_vtrace.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/h2_io.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/heatmap.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/hmmlogo.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/hmmdmstr.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/hmmdmstr_shard.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/hmmd_search_status.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/hmmdwrkr.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/hmmdwrkr_shard.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/hmmdutils.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/hmmer.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/logsum.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/modelconfig.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/modelstats.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/mpisupport.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/seqmodel.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/tracealign.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_alidisplay.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_bg.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_builder.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_domain.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_domaindef.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_gbands.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_gmx.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_gmxb.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_gmxchk.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_hit.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_hmm.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_hmmcache.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_hmmd_search_stats.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_hmmwindow.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_pipeline.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_prior.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_profile.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_spensemble.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_tophits.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_trace.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/p7_scoredata.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/hmmpgmd2msa.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/fm_alphabet.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/fm_general.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/fm_sse.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/fm_ssv.o build/temp.linux-x86_64-cpython-313/build/temp.linux-x86_64-cpython-313/p7_hmmfile.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/impl_sse/vitfilter.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/impl_sse/stotrace.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/impl_sse/ssvfilter.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/impl_sse/p7_oprofile.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/impl_sse/p7_omx.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/impl_sse/optacc.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/impl_sse/null2.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/impl_sse/msvfilter.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/impl_sse/mpi.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/impl_sse/io.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/impl_sse/fwdback.o build/temp.linux-x86_64-cpython-313/vendor/hmmer/src/impl_sse/decoding.o running build_ext Building HMMER with SSE for CPU architecture: 'x86_64' performance hint: pyhmmer/exceptions.pxi:45:5: Exception check on '_py_handler' will always require the GIL to be acquired. Possible solutions: 1. Declare '_py_handler' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on '_py_handler' to allow an error code to be returned. performance hint: pyhmmer/exceptions.pxi:45:5: Exception check on '_py_handler' will always require the GIL to be acquired. Possible solutions: 1. Declare '_py_handler' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on '_py_handler' to allow an error code to be returned. Compiling pyhmmer/errors.pyx because it changed. Compiling pyhmmer/easel.pyx because it changed. Compiling pyhmmer/plan7.pyx because it changed. Compiling pyhmmer/daemon.pyx because it changed. [1/4] Cythonizing pyhmmer/daemon.pyx [2/4] Cythonizing pyhmmer/easel.pyx [3/4] Cythonizing pyhmmer/errors.pyx [4/4] Cythonizing pyhmmer/plan7.pyx checking whether `PyInterpreterState_GetID` is available creating builddir creating builddir/build creating builddir/build/BUILD creating builddir/build/BUILD/python-pyhmmer-0.10.15-build creating builddir/build/BUILD/python-pyhmmer-0.10.15-build/pyhmmer-0.10.15 creating builddir/build/BUILD/python-pyhmmer-0.10.15-build/pyhmmer-0.10.15/build creating builddir/build/BUILD/python-pyhmmer-0.10.15-build/pyhmmer-0.10.15/build/temp.linux-x86_64-cpython-313 gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -I/usr/include/python3.13 -c /builddir/build/BUILD/python-pyhmmer-0.10.15-build/pyhmmer-0.10.15/build/temp.linux-x86_64-cpython-313/have_getidc10tg29w.c -o builddir/build/BUILD/python-pyhmmer-0.10.15-build/pyhmmer-0.10.15/build/temp.linux-x86_64-cpython-313/have_getidc10tg29w.o -Werror=implicit-function-declaration yes building pyhmmer.errors for linux-x86_64 with unix compiler building 'pyhmmer.errors' extension creating build/temp.linux-x86_64-cpython-313/pyhmmer gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -DHAS_PYINTERPRETERSTATE_GETID=1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -DCYTHON_WITHOUT_ASSERTIONS=1 -Ibuild/temp.linux-x86_64-cpython-313 -Ivendor/easel -I/usr/include/python3.13 -c pyhmmer/errors.c -o build/temp.linux-x86_64-cpython-313/pyhmmer/errors.o -msse4.1 -Wno-unused-variable gcc -shared -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 -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 build/temp.linux-x86_64-cpython-313/pyhmmer/errors.o build/temp.linux-x86_64-cpython-313/libeasel.a -Lbuild/temp.linux-x86_64-cpython-313 -L/usr/lib64 -Lbuild/temp.linux-x86_64-cpython-313 -leasel -ldivsufsort -leasel -lhmmer -o build/lib.linux-x86_64-cpython-313/pyhmmer/errors.cpython-313-x86_64-linux-gnu.so -msse4.1 -g1 building pyhmmer.easel for linux-x86_64 with unix compiler building 'pyhmmer.easel' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -DHAS_PYINTERPRETERSTATE_GETID=1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -DCYTHON_WITHOUT_ASSERTIONS=1 -Ibuild/temp.linux-x86_64-cpython-313 -Ivendor/easel -I/usr/include/python3.13 -c pyhmmer/easel.c -o build/temp.linux-x86_64-cpython-313/pyhmmer/easel.o -msse4.1 -Wno-unused-variable In file included from pyhmmer/easel.c:1283: pyhmmer/fileobj/linux.h: In function ‘fileobj_linux_read’: pyhmmer/fileobj/linux.h:54:13: warning: comparison of integer expressions of different signedness: ‘Py_ssize_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 54 | if (len > size) { | ^ gcc -shared -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 -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 build/temp.linux-x86_64-cpython-313/pyhmmer/easel.o build/temp.linux-x86_64-cpython-313/libeasel.a -Lbuild/temp.linux-x86_64-cpython-313 -L/usr/lib64 -Lbuild/temp.linux-x86_64-cpython-313 -leasel -ldivsufsort -leasel -lhmmer -o build/lib.linux-x86_64-cpython-313/pyhmmer/easel.cpython-313-x86_64-linux-gnu.so -msse4.1 -g1 building pyhmmer.plan7 for linux-x86_64 with unix compiler building 'pyhmmer.plan7' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -DHAS_PYINTERPRETERSTATE_GETID=1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -DCYTHON_WITHOUT_ASSERTIONS=1 -Ibuild/temp.linux-x86_64-cpython-313 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ivendor/easel -I/usr/include/python3.13 -c pyhmmer/plan7.c -o build/temp.linux-x86_64-cpython-313/pyhmmer/plan7.o -msse4.1 -Wno-unused-variable In file included from pyhmmer/plan7.c:1281: pyhmmer/fileobj/linux.h: In function ‘fileobj_linux_read’: pyhmmer/fileobj/linux.h:54:13: warning: comparison of integer expressions of different signedness: ‘Py_ssize_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 54 | if (len > size) { | ^ pyhmmer/plan7.c: In function ‘__pyx_f_8libhmmer_6nhmmer_idlen_list_assign’: pyhmmer/plan7.c:20293:30: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 20293 | __pyx_t_5 = (__pyx_v_j < __pyx_v_l->count); | ^ pyhmmer/plan7.c:20309:28: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 20309 | __pyx_t_4 = (__pyx_v_j == __pyx_v_l->count); | ^~ pyhmmer/plan7.c: In function ‘__pyx_f_7pyhmmer_5plan7_21OptimizedProfileBlock__allocate’: pyhmmer/plan7.c:62601:66: warning: comparison of integer expressions of different signedness: ‘Py_ssize_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 62601 | for (__pyx_t_10 = __pyx_v_self->_block->listSize; __pyx_t_10 < __pyx_t_9; __pyx_t_10+=1) { | ^ pyhmmer/plan7.c: In function ‘__pyx_fuse_1__pyx_f_7pyhmmer_5plan7_8Pipeline_search_hmm’: pyhmmer/plan7.c:72285:27: warning: comparison of integer expressions of different signedness: ‘Py_ssize_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 72285 | __pyx_t_6 = (__pyx_t_10 > __pyx_v_7pyhmmer_5plan7_HMMER_TARGET_LIMIT); | ^ pyhmmer/plan7.c: In function ‘__pyx_f_7pyhmmer_5plan7_8Pipeline__search_loop_file’: pyhmmer/plan7.c:74125:36: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 74125 | __pyx_t_1 = (__pyx_v_dbsq->L > __pyx_v_7pyhmmer_5plan7_HMMER_TARGET_LIMIT); | ^ pyhmmer/plan7.c: In function ‘__pyx_fuse_0__pyx_f_7pyhmmer_5plan7_8Pipeline_scan_seq’: pyhmmer/plan7.c:75402:49: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 75402 | __pyx_t_7 = (__pyx_v_query->__pyx_base._sq->n > __pyx_v_7pyhmmer_5plan7_HMMER_TARGET_LIMIT); | ^ pyhmmer/plan7.c: In function ‘__pyx_fuse_1__pyx_f_7pyhmmer_5plan7_8Pipeline_scan_seq’: pyhmmer/plan7.c:75795:49: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 75795 | __pyx_t_6 = (__pyx_v_query->__pyx_base._sq->n > __pyx_v_7pyhmmer_5plan7_HMMER_TARGET_LIMIT); | ^ gcc -shared -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 -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 build/temp.linux-x86_64-cpython-313/pyhmmer/plan7.o build/temp.linux-x86_64-cpython-313/libhmmer.a build/temp.linux-x86_64-cpython-313/libeasel.a build/temp.linux-x86_64-cpython-313/libdivsufsort.a -Lbuild/temp.linux-x86_64-cpython-313 -L/usr/lib64 -Lbuild/temp.linux-x86_64-cpython-313 -lhmmer -leasel -ldivsufsort -ldivsufsort -leasel -lhmmer -o build/lib.linux-x86_64-cpython-313/pyhmmer/plan7.cpython-313-x86_64-linux-gnu.so -msse4.1 -g1 building pyhmmer.daemon for linux-x86_64 with unix compiler building 'pyhmmer.daemon' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -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 -fPIC -DHAS_PYINTERPRETERSTATE_GETID=1 -DeslENABLE_SSE=1 -DeslENABLE_SSE4=1 -DCYTHON_WITHOUT_ASSERTIONS=1 -Ibuild/temp.linux-x86_64-cpython-313 -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ivendor/easel -I/usr/include/python3.13 -c pyhmmer/daemon.c -o build/temp.linux-x86_64-cpython-313/pyhmmer/daemon.o -msse4.1 -Wno-unused-variable pyhmmer/daemon.c: In function ‘__pyx_f_8libhmmer_6nhmmer_idlen_list_assign’: pyhmmer/daemon.c:14158:30: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 14158 | __pyx_t_5 = (__pyx_v_j < __pyx_v_l->count); | ^ pyhmmer/daemon.c:14174:28: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 14174 | __pyx_t_4 = (__pyx_v_j == __pyx_v_l->count); | ^~ gcc -shared -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 -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 build/temp.linux-x86_64-cpython-313/pyhmmer/daemon.o build/temp.linux-x86_64-cpython-313/libhmmer.a build/temp.linux-x86_64-cpython-313/libeasel.a build/temp.linux-x86_64-cpython-313/libdivsufsort.a -Lbuild/temp.linux-x86_64-cpython-313 -L/usr/lib64 -Lbuild/temp.linux-x86_64-cpython-313 -lhmmer -leasel -ldivsufsort -ldivsufsort -leasel -lhmmer -o build/lib.linux-x86_64-cpython-313/pyhmmer/daemon.cpython-313-x86_64-linux-gnu.so -msse4.1 -g1 installing to build/bdist.linux-x86_64/wheel running install running install_lib creating build/bdist.linux-x86_64 creating build/bdist.linux-x86_64/wheel creating build/bdist.linux-x86_64/wheel/pyhmmer copying build/lib.linux-x86_64-cpython-313/pyhmmer/daemon.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/pyhmmer copying build/lib.linux-x86_64-cpython-313/pyhmmer/plan7.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/pyhmmer copying build/lib.linux-x86_64-cpython-313/pyhmmer/easel.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/pyhmmer copying build/lib.linux-x86_64-cpython-313/pyhmmer/errors.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/pyhmmer creating build/bdist.linux-x86_64/wheel/pyhmmer/reexports copying build/lib.linux-x86_64-cpython-313/pyhmmer/reexports/p7_tophits.pxd -> build/bdist.linux-x86_64/wheel/pyhmmer/reexports copying build/lib.linux-x86_64-cpython-313/pyhmmer/reexports/p7_tophits.h -> build/bdist.linux-x86_64/wheel/pyhmmer/reexports copying build/lib.linux-x86_64-cpython-313/pyhmmer/reexports/p7_hmmfile.pxd -> build/bdist.linux-x86_64/wheel/pyhmmer/reexports copying build/lib.linux-x86_64-cpython-313/pyhmmer/reexports/p7_hmmfile.h -> build/bdist.linux-x86_64/wheel/pyhmmer/reexports copying build/lib.linux-x86_64-cpython-313/pyhmmer/reexports/esl_sqio_ascii.pxd -> build/bdist.linux-x86_64/wheel/pyhmmer/reexports copying build/lib.linux-x86_64-cpython-313/pyhmmer/reexports/esl_sqio_ascii.h -> build/bdist.linux-x86_64/wheel/pyhmmer/reexports copying build/lib.linux-x86_64-cpython-313/pyhmmer/reexports/__init__.pxd -> build/bdist.linux-x86_64/wheel/pyhmmer/reexports creating build/bdist.linux-x86_64/wheel/pyhmmer/fileobj copying build/lib.linux-x86_64-cpython-313/pyhmmer/fileobj/util.h -> build/bdist.linux-x86_64/wheel/pyhmmer/fileobj copying build/lib.linux-x86_64-cpython-313/pyhmmer/fileobj/linux.pxd -> build/bdist.linux-x86_64/wheel/pyhmmer/fileobj copying build/lib.linux-x86_64-cpython-313/pyhmmer/fileobj/linux.h -> build/bdist.linux-x86_64/wheel/pyhmmer/fileobj copying build/lib.linux-x86_64-cpython-313/pyhmmer/fileobj/bsd.pxd -> build/bdist.linux-x86_64/wheel/pyhmmer/fileobj copying build/lib.linux-x86_64-cpython-313/pyhmmer/fileobj/bsd.h -> build/bdist.linux-x86_64/wheel/pyhmmer/fileobj copying build/lib.linux-x86_64-cpython-313/pyhmmer/fileobj/__init__.pxd -> build/bdist.linux-x86_64/wheel/pyhmmer/fileobj copying build/lib.linux-x86_64-cpython-313/pyhmmer/py.typed -> build/bdist.linux-x86_64/wheel/pyhmmer copying build/lib.linux-x86_64-cpython-313/pyhmmer/plan7.pyx -> build/bdist.linux-x86_64/wheel/pyhmmer copying build/lib.linux-x86_64-cpython-313/pyhmmer/plan7.pyi -> build/bdist.linux-x86_64/wheel/pyhmmer copying build/lib.linux-x86_64-cpython-313/pyhmmer/plan7.pxd -> build/bdist.linux-x86_64/wheel/pyhmmer copying build/lib.linux-x86_64-cpython-313/pyhmmer/exceptions.pxi -> build/bdist.linux-x86_64/wheel/pyhmmer copying build/lib.linux-x86_64-cpython-313/pyhmmer/errors.pyx -> build/bdist.linux-x86_64/wheel/pyhmmer copying build/lib.linux-x86_64-cpython-313/pyhmmer/errors.pyi -> build/bdist.linux-x86_64/wheel/pyhmmer copying build/lib.linux-x86_64-cpython-313/pyhmmer/easel.pyx -> build/bdist.linux-x86_64/wheel/pyhmmer copying build/lib.linux-x86_64-cpython-313/pyhmmer/easel.pyi -> build/bdist.linux-x86_64/wheel/pyhmmer copying build/lib.linux-x86_64-cpython-313/pyhmmer/easel.pxd -> build/bdist.linux-x86_64/wheel/pyhmmer copying build/lib.linux-x86_64-cpython-313/pyhmmer/daemon.pyx -> build/bdist.linux-x86_64/wheel/pyhmmer copying build/lib.linux-x86_64-cpython-313/pyhmmer/daemon.pyi -> build/bdist.linux-x86_64/wheel/pyhmmer copying build/lib.linux-x86_64-cpython-313/pyhmmer/daemon.pxd -> build/bdist.linux-x86_64/wheel/pyhmmer copying build/lib.linux-x86_64-cpython-313/pyhmmer/_getid.pxi -> build/bdist.linux-x86_64/wheel/pyhmmer creating build/bdist.linux-x86_64/wheel/pyhmmer/tests creating build/bdist.linux-x86_64/wheel/pyhmmer/tests/data creating build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/tables copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/tables/bmyD3.tbl -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/tables copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/tables/bmyD2.tbl -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/tables copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/tables/bmyD1.tbl -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/tables copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/tables/RREFam.tbl -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/tables copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/tables/RREFam.scan.tbl -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/tables copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/tables/RREFam.domtbl -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/tables copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/tables/PF02826.tbl -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/tables copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/tables/PF02826.domtbl -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/tables copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/tables/A0A089QRB9.domtbl -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/tables creating build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/seqs copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/seqs/bmyD.fna -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/seqs copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/seqs/PKSI.faa -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/seqs copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/seqs/LuxC.faa -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/seqs copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/seqs/CP040672.1.genes_100.fna -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/seqs copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/seqs/BGC0001090.gbk -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/seqs copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/seqs/938293.PRJEB85.HG003687.faa -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/seqs copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/seqs/1390.SAMEA104415756.OFHT01000024.fna -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/seqs copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/seqs/1390.SAMEA104415756.OFHT01000022.fna -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/seqs creating build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/msa copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/msa/laccase.clw -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/msa copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/msa/LuxC.sto -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/msa copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/msa/LuxC.hmmalign.sto -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/msa copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/msa/LuxC.faa -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/msa creating build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/jackhmmer copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/jackhmmer/p12748-3.sto -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/jackhmmer copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/jackhmmer/p12748-2.sto -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/jackhmmer copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/jackhmmer/p12748-1.sto -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/jackhmmer copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/jackhmmer/KR-6.sto -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/jackhmmer copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/jackhmmer/KR-5.sto -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/jackhmmer copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/jackhmmer/KR-4.sto -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/jackhmmer copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/jackhmmer/KR-3.sto -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/jackhmmer copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/jackhmmer/KR-2.sto -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/jackhmmer copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/jackhmmer/KR-1_bkup.sto -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/jackhmmer copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/jackhmmer/KR-1.sto -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/jackhmmer creating build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/hmms creating build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/hmms/txt2 copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/txt2/Thioesterase.hmm2 -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/hmms/txt2 copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/txt2/RREFam.hmm2 -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/hmms/txt2 creating build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/hmms/txt copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/txt/laccase.hmm -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/hmms/txt copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/txt/bmyD.hmm -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/hmms/txt copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/txt/Thioesterase.hmm -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/hmms/txt copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/txt/RREFam.hmm -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/hmms/txt copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/txt/RF00001.hmm -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/hmms/txt copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/txt/PKSI-AT.hmm -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/hmms/txt copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/txt/PF02826.hmm -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/hmms/txt copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/txt/LuxC.hmm -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/hmms/txt copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/txt/KR.hmm -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/hmms/txt creating build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/hmms/db copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/db/Thioesterase.hmm.h3p -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/hmms/db copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/db/Thioesterase.hmm.h3m -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/hmms/db copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/db/Thioesterase.hmm.h3i -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/hmms/db copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/db/Thioesterase.hmm.h3f -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/hmms/db copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/db/Thioesterase.hmm -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/hmms/db copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/db/RREFam.hmm.h3p -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/hmms/db copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/db/RREFam.hmm.h3m -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/hmms/db copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/db/RREFam.hmm.h3i -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/hmms/db copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/db/RREFam.hmm.h3f -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/hmms/db copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/db/RREFam.hmm -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/hmms/db copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/db/PKSI-AT.hmm.h3p -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/hmms/db copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/db/PKSI-AT.hmm.h3m -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/hmms/db copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/db/PKSI-AT.hmm.h3i -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/hmms/db copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/db/PKSI-AT.hmm.h3f -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/hmms/db copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/db/PKSI-AT.hmm -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/hmms/db copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/db/PF02826.hmm.h3p -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/hmms/db copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/db/PF02826.hmm.h3m -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/hmms/db copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/db/PF02826.hmm.h3i -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/hmms/db copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/db/PF02826.hmm.h3f -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/hmms/db copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/db/PF02826.hmm -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/hmms/db creating build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/hmms/bin copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/bin/Thioesterase.h3m -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/hmms/bin copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/bin/RREFam.h3m -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/hmms/bin copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/bin/RF00001.h3m -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/hmms/bin copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/bin/PKSI-AT.h3m -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/hmms/bin copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/bin/PF02826.h3m -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/hmms/bin copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/hmms/make.sh -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data/hmms copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/data/README.md -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/data copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/requirements.txt -> build/bdist.linux-x86_64/wheel/pyhmmer/tests creating build/bdist.linux-x86_64/wheel/pyhmmer/tests/test_easel copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_easel/__init__.py -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/test_easel copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_easel/test_alphabet.py -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/test_easel copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_easel/test_bitfield.py -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/test_easel copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_easel/test_block.py -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/test_easel copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_easel/test_gencode.py -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/test_easel copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_easel/test_keyhash.py -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/test_easel copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_easel/test_matrix.py -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/test_easel copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_easel/test_msa.py -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/test_easel copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_easel/test_msafile.py -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/test_easel copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_easel/test_randomness.py -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/test_easel copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_easel/test_sequence.py -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/test_easel copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_easel/test_sequencefile.py -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/test_easel copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_easel/test_ssi.py -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/test_easel copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_easel/test_vector.py -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/test_easel creating build/bdist.linux-x86_64/wheel/pyhmmer/tests/test_plan7 copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_plan7/__init__.py -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/test_plan7 copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_plan7/test_alignment.py -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/test_plan7 copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_plan7/test_background.py -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/test_plan7 copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_plan7/test_block.py -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/test_plan7 copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_plan7/test_builder.py -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/test_plan7 copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_plan7/test_hit.py -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/test_plan7 copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_plan7/test_hmm.py -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/test_plan7 copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_plan7/test_hmmfile.py -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/test_plan7 copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_plan7/test_optimizedprofile.py -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/test_plan7 copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_plan7/test_pipeline.py -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/test_plan7 copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_plan7/test_profile.py -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/test_plan7 copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_plan7/test_tophits.py -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/test_plan7 copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_plan7/test_tracealigner.py -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/test_plan7 copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_plan7/test_traces.py -> build/bdist.linux-x86_64/wheel/pyhmmer/tests/test_plan7 copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/__init__.py -> build/bdist.linux-x86_64/wheel/pyhmmer/tests copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_doctest.py -> build/bdist.linux-x86_64/wheel/pyhmmer/tests copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_errors.py -> build/bdist.linux-x86_64/wheel/pyhmmer/tests copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/test_hmmer.py -> build/bdist.linux-x86_64/wheel/pyhmmer/tests copying build/lib.linux-x86_64-cpython-313/pyhmmer/tests/utils.py -> build/bdist.linux-x86_64/wheel/pyhmmer/tests copying build/lib.linux-x86_64-cpython-313/pyhmmer/__init__.py -> build/bdist.linux-x86_64/wheel/pyhmmer copying build/lib.linux-x86_64-cpython-313/pyhmmer/hmmer.py -> build/bdist.linux-x86_64/wheel/pyhmmer copying build/lib.linux-x86_64-cpython-313/pyhmmer/utils.py -> build/bdist.linux-x86_64/wheel/pyhmmer running install_egg_info Copying pyhmmer.egg-info to build/bdist.linux-x86_64/wheel/pyhmmer-0.10.15-py3.13.egg-info running install_scripts creating build/bdist.linux-x86_64/wheel/pyhmmer-0.10.15.dist-info/WHEEL creating '/builddir/build/BUILD/python-pyhmmer-0.10.15-build/pyhmmer-0.10.15/.pyproject-builddir/pip-wheel-j7n009jh/.tmp-13zw09ug/pyhmmer-0.10.15-cp313-cp313-linux_x86_64.whl' and adding 'build/bdist.linux-x86_64/wheel' to it adding 'pyhmmer/__init__.py' adding 'pyhmmer/_getid.pxi' adding 'pyhmmer/daemon.cpython-313-x86_64-linux-gnu.so' adding 'pyhmmer/daemon.pxd' adding 'pyhmmer/daemon.pyi' adding 'pyhmmer/daemon.pyx' adding 'pyhmmer/easel.cpython-313-x86_64-linux-gnu.so' adding 'pyhmmer/easel.pxd' adding 'pyhmmer/easel.pyi' adding 'pyhmmer/easel.pyx' adding 'pyhmmer/errors.cpython-313-x86_64-linux-gnu.so' adding 'pyhmmer/errors.pyi' adding 'pyhmmer/errors.pyx' adding 'pyhmmer/exceptions.pxi' adding 'pyhmmer/hmmer.py' adding 'pyhmmer/plan7.cpython-313-x86_64-linux-gnu.so' adding 'pyhmmer/plan7.pxd' adding 'pyhmmer/plan7.pyi' adding 'pyhmmer/plan7.pyx' adding 'pyhmmer/py.typed' adding 'pyhmmer/utils.py' adding 'pyhmmer/fileobj/__init__.pxd' adding 'pyhmmer/fileobj/bsd.h' adding 'pyhmmer/fileobj/bsd.pxd' adding 'pyhmmer/fileobj/linux.h' adding 'pyhmmer/fileobj/linux.pxd' adding 'pyhmmer/fileobj/util.h' adding 'pyhmmer/reexports/__init__.pxd' adding 'pyhmmer/reexports/esl_sqio_ascii.h' adding 'pyhmmer/reexports/esl_sqio_ascii.pxd' adding 'pyhmmer/reexports/p7_hmmfile.h' adding 'pyhmmer/reexports/p7_hmmfile.pxd' adding 'pyhmmer/reexports/p7_tophits.h' adding 'pyhmmer/reexports/p7_tophits.pxd' adding 'pyhmmer/tests/__init__.py' adding 'pyhmmer/tests/requirements.txt' adding 'pyhmmer/tests/test_doctest.py' adding 'pyhmmer/tests/test_errors.py' adding 'pyhmmer/tests/test_hmmer.py' adding 'pyhmmer/tests/utils.py' adding 'pyhmmer/tests/data/README.md' adding 'pyhmmer/tests/data/hmms/make.sh' adding 'pyhmmer/tests/data/hmms/bin/PF02826.h3m' adding 'pyhmmer/tests/data/hmms/bin/PKSI-AT.h3m' adding 'pyhmmer/tests/data/hmms/bin/RF00001.h3m' adding 'pyhmmer/tests/data/hmms/bin/RREFam.h3m' adding 'pyhmmer/tests/data/hmms/bin/Thioesterase.h3m' adding 'pyhmmer/tests/data/hmms/db/PF02826.hmm' adding 'pyhmmer/tests/data/hmms/db/PF02826.hmm.h3f' adding 'pyhmmer/tests/data/hmms/db/PF02826.hmm.h3i' adding 'pyhmmer/tests/data/hmms/db/PF02826.hmm.h3m' adding 'pyhmmer/tests/data/hmms/db/PF02826.hmm.h3p' adding 'pyhmmer/tests/data/hmms/db/PKSI-AT.hmm' adding 'pyhmmer/tests/data/hmms/db/PKSI-AT.hmm.h3f' adding 'pyhmmer/tests/data/hmms/db/PKSI-AT.hmm.h3i' adding 'pyhmmer/tests/data/hmms/db/PKSI-AT.hmm.h3m' adding 'pyhmmer/tests/data/hmms/db/PKSI-AT.hmm.h3p' adding 'pyhmmer/tests/data/hmms/db/RREFam.hmm' adding 'pyhmmer/tests/data/hmms/db/RREFam.hmm.h3f' adding 'pyhmmer/tests/data/hmms/db/RREFam.hmm.h3i' adding 'pyhmmer/tests/data/hmms/db/RREFam.hmm.h3m' adding 'pyhmmer/tests/data/hmms/db/RREFam.hmm.h3p' adding 'pyhmmer/tests/data/hmms/db/Thioesterase.hmm' adding 'pyhmmer/tests/data/hmms/db/Thioesterase.hmm.h3f' adding 'pyhmmer/tests/data/hmms/db/Thioesterase.hmm.h3i' adding 'pyhmmer/tests/data/hmms/db/Thioesterase.hmm.h3m' adding 'pyhmmer/tests/data/hmms/db/Thioesterase.hmm.h3p' adding 'pyhmmer/tests/data/hmms/txt/KR.hmm' adding 'pyhmmer/tests/data/hmms/txt/LuxC.hmm' adding 'pyhmmer/tests/data/hmms/txt/PF02826.hmm' adding 'pyhmmer/tests/data/hmms/txt/PKSI-AT.hmm' adding 'pyhmmer/tests/data/hmms/txt/RF00001.hmm' adding 'pyhmmer/tests/data/hmms/txt/RREFam.hmm' adding 'pyhmmer/tests/data/hmms/txt/Thioesterase.hmm' adding 'pyhmmer/tests/data/hmms/txt/bmyD.hmm' adding 'pyhmmer/tests/data/hmms/txt/laccase.hmm' adding 'pyhmmer/tests/data/hmms/txt2/RREFam.hmm2' adding 'pyhmmer/tests/data/hmms/txt2/Thioesterase.hmm2' adding 'pyhmmer/tests/data/jackhmmer/KR-1.sto' adding 'pyhmmer/tests/data/jackhmmer/KR-1_bkup.sto' adding 'pyhmmer/tests/data/jackhmmer/KR-2.sto' adding 'pyhmmer/tests/data/jackhmmer/KR-3.sto' adding 'pyhmmer/tests/data/jackhmmer/KR-4.sto' adding 'pyhmmer/tests/data/jackhmmer/KR-5.sto' adding 'pyhmmer/tests/data/jackhmmer/KR-6.sto' adding 'pyhmmer/tests/data/jackhmmer/p12748-1.sto' adding 'pyhmmer/tests/data/jackhmmer/p12748-2.sto' adding 'pyhmmer/tests/data/jackhmmer/p12748-3.sto' adding 'pyhmmer/tests/data/msa/LuxC.faa' adding 'pyhmmer/tests/data/msa/LuxC.hmmalign.sto' adding 'pyhmmer/tests/data/msa/LuxC.sto' adding 'pyhmmer/tests/data/msa/laccase.clw' adding 'pyhmmer/tests/data/seqs/1390.SAMEA104415756.OFHT01000022.fna' adding 'pyhmmer/tests/data/seqs/1390.SAMEA104415756.OFHT01000024.fna' adding 'pyhmmer/tests/data/seqs/938293.PRJEB85.HG003687.faa' adding 'pyhmmer/tests/data/seqs/BGC0001090.gbk' adding 'pyhmmer/tests/data/seqs/CP040672.1.genes_100.fna' adding 'pyhmmer/tests/data/seqs/LuxC.faa' adding 'pyhmmer/tests/data/seqs/PKSI.faa' adding 'pyhmmer/tests/data/seqs/bmyD.fna' adding 'pyhmmer/tests/data/tables/A0A089QRB9.domtbl' adding 'pyhmmer/tests/data/tables/PF02826.domtbl' adding 'pyhmmer/tests/data/tables/PF02826.tbl' adding 'pyhmmer/tests/data/tables/RREFam.domtbl' adding 'pyhmmer/tests/data/tables/RREFam.scan.tbl' adding 'pyhmmer/tests/data/tables/RREFam.tbl' adding 'pyhmmer/tests/data/tables/bmyD1.tbl' adding 'pyhmmer/tests/data/tables/bmyD2.tbl' adding 'pyhmmer/tests/data/tables/bmyD3.tbl' adding 'pyhmmer/tests/test_easel/__init__.py' adding 'pyhmmer/tests/test_easel/test_alphabet.py' adding 'pyhmmer/tests/test_easel/test_bitfield.py' adding 'pyhmmer/tests/test_easel/test_block.py' adding 'pyhmmer/tests/test_easel/test_gencode.py' adding 'pyhmmer/tests/test_easel/test_keyhash.py' adding 'pyhmmer/tests/test_easel/test_matrix.py' adding 'pyhmmer/tests/test_easel/test_msa.py' adding 'pyhmmer/tests/test_easel/test_msafile.py' adding 'pyhmmer/tests/test_easel/test_randomness.py' adding 'pyhmmer/tests/test_easel/test_sequence.py' adding 'pyhmmer/tests/test_easel/test_sequencefile.py' adding 'pyhmmer/tests/test_easel/test_ssi.py' adding 'pyhmmer/tests/test_easel/test_vector.py' adding 'pyhmmer/tests/test_plan7/__init__.py' adding 'pyhmmer/tests/test_plan7/test_alignment.py' adding 'pyhmmer/tests/test_plan7/test_background.py' adding 'pyhmmer/tests/test_plan7/test_block.py' adding 'pyhmmer/tests/test_plan7/test_builder.py' adding 'pyhmmer/tests/test_plan7/test_hit.py' adding 'pyhmmer/tests/test_plan7/test_hmm.py' adding 'pyhmmer/tests/test_plan7/test_hmmfile.py' adding 'pyhmmer/tests/test_plan7/test_optimizedprofile.py' adding 'pyhmmer/tests/test_plan7/test_pipeline.py' adding 'pyhmmer/tests/test_plan7/test_profile.py' adding 'pyhmmer/tests/test_plan7/test_tophits.py' adding 'pyhmmer/tests/test_plan7/test_tracealigner.py' adding 'pyhmmer/tests/test_plan7/test_traces.py' adding 'pyhmmer-0.10.15.dist-info/COPYING' adding 'pyhmmer-0.10.15.dist-info/METADATA' adding 'pyhmmer-0.10.15.dist-info/WHEEL' adding 'pyhmmer-0.10.15.dist-info/top_level.txt' adding 'pyhmmer-0.10.15.dist-info/RECORD' removing build/bdist.linux-x86_64/wheel Building wheel for pyhmmer (pyproject.toml): finished with status 'done' Created wheel for pyhmmer: filename=pyhmmer-0.10.15-cp313-cp313-linux_x86_64.whl size=9140987 sha256=4ab298a5d44430ace02f357b0bc31d81c70b0b750768d88303c8dad0852aa504 Stored in directory: /builddir/.cache/pip/wheels/13/53/a1/771ef92db7421bb44d91a188db19e5285a333c10aa0c866c9a Successfully built pyhmmer + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.FZIf9K + umask 022 + cd /builddir/build/BUILD/python-pyhmmer-0.10.15-build + '[' /builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT '!=' / ']' + rm -rf /builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT ++ dirname /builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT + mkdir -p /builddir/build/BUILD/python-pyhmmer-0.10.15-build + mkdir /builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd pyhmmer-0.10.15 ++ ls /builddir/build/BUILD/python-pyhmmer-0.10.15-build/pyhmmer-0.10.15/pyproject-wheeldir/pyhmmer-0.10.15-cp313-cp313-linux_x86_64.whl ++ xargs basename --multiple ++ sed -E 's/([^-]+)-([^-]+)-.+\.whl/\1==\2/' + specifier=pyhmmer==0.10.15 + '[' -z pyhmmer==0.10.15 ']' + TMPDIR=/builddir/build/BUILD/python-pyhmmer-0.10.15-build/pyhmmer-0.10.15/.pyproject-builddir + /usr/bin/python3 -m pip install --root /builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT --prefix /usr --no-deps --disable-pip-version-check --progress-bar off --verbose --ignore-installed --no-warn-script-location --no-index --no-cache-dir --find-links /builddir/build/BUILD/python-pyhmmer-0.10.15-build/pyhmmer-0.10.15/pyproject-wheeldir pyhmmer==0.10.15 Using pip 24.2 from /usr/lib/python3.13/site-packages/pip (python 3.13) Looking in links: /builddir/build/BUILD/python-pyhmmer-0.10.15-build/pyhmmer-0.10.15/pyproject-wheeldir Processing ./pyproject-wheeldir/pyhmmer-0.10.15-cp313-cp313-linux_x86_64.whl Installing collected packages: pyhmmer Successfully installed pyhmmer-0.10.15 + '[' -d /builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT/usr/bin ']' + rm -f /builddir/build/BUILD/python-pyhmmer-0.10.15-build/python-pyhmmer-0.10.15-1.fc41.x86_64-pyproject-ghost-distinfo + site_dirs=() + '[' -d /builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT/usr/lib/python3.13/site-packages ']' + '[' /builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT/usr/lib64/python3.13/site-packages '!=' /builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT/usr/lib/python3.13/site-packages ']' + '[' -d /builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT/usr/lib64/python3.13/site-packages ']' + site_dirs+=("/usr/lib64/python3.13/site-packages") + for site_dir in ${site_dirs[@]} + for distinfo in /builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT$site_dir/*.dist-info + echo '%ghost /usr/lib64/python3.13/site-packages/pyhmmer-0.10.15.dist-info' + sed -i s/pip/rpm/ /builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT/usr/lib64/python3.13/site-packages/pyhmmer-0.10.15.dist-info/INSTALLER + PYTHONPATH=/usr/lib/rpm/redhat + /usr/bin/python3 -B /usr/lib/rpm/redhat/pyproject_preprocess_record.py --buildroot /builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT --record /builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT/usr/lib64/python3.13/site-packages/pyhmmer-0.10.15.dist-info/RECORD --output /builddir/build/BUILD/python-pyhmmer-0.10.15-build/python-pyhmmer-0.10.15-1.fc41.x86_64-pyproject-record + rm -fv /builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT/usr/lib64/python3.13/site-packages/pyhmmer-0.10.15.dist-info/RECORD removed '/builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT/usr/lib64/python3.13/site-packages/pyhmmer-0.10.15.dist-info/RECORD' + rm -fv /builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT/usr/lib64/python3.13/site-packages/pyhmmer-0.10.15.dist-info/REQUESTED removed '/builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT/usr/lib64/python3.13/site-packages/pyhmmer-0.10.15.dist-info/REQUESTED' ++ wc -l /builddir/build/BUILD/python-pyhmmer-0.10.15-build/python-pyhmmer-0.10.15-1.fc41.x86_64-pyproject-ghost-distinfo ++ cut -f1 '-d ' + lines=1 + '[' 1 -ne 1 ']' + RPM_FILES_ESCAPE=4.19 + /usr/bin/python3 /usr/lib/rpm/redhat/pyproject_save_files.py --output-files /builddir/build/BUILD/python-pyhmmer-0.10.15-build/python-pyhmmer-0.10.15-1.fc41.x86_64-pyproject-files --output-modules /builddir/build/BUILD/python-pyhmmer-0.10.15-build/python-pyhmmer-0.10.15-1.fc41.x86_64-pyproject-modules --buildroot /builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT --sitelib /usr/lib/python3.13/site-packages --sitearch /usr/lib64/python3.13/site-packages --python-version 3.13 --pyproject-record /builddir/build/BUILD/python-pyhmmer-0.10.15-build/python-pyhmmer-0.10.15-1.fc41.x86_64-pyproject-record --prefix /usr '*' +auto + /usr/bin/find-debuginfo -j4 --strict-build-id -m -i --build-id-seed 0.10.15-1.fc41 --unique-debug-suffix -0.10.15-1.fc41.x86_64 --unique-debug-src-base python-pyhmmer-0.10.15-1.fc41.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/python-pyhmmer-0.10.15-build/pyhmmer-0.10.15 find-debuginfo: starting Extracting debug info from 4 files DWARF-compressing 4 files sepdebugcrcfix: Updated 4 CRC32s, 0 CRC32s did match. Creating .debug symlinks for symlinks to ELF files Copying sources found by 'debugedit -l' to /usr/src/debug/python-pyhmmer-0.10.15-1.fc41.x86_64 34698 blocks find-debuginfo: done + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + /usr/lib/rpm/brp-compress + /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/check-rpaths + /usr/lib/rpm/redhat/brp-mangle-shebangs + /usr/lib/rpm/brp-remove-la-files + env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j4 Bytecompiling .py files below /builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT/usr/lib/debug/usr/lib64/python3.13 using python3.13 Bytecompiling .py files below /builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT/usr/lib64/python3.13 using python3.13 + /usr/lib/rpm/redhat/brp-python-hardlink + /usr/bin/add-determinism --brp -j4 /builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT /builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT/usr/lib64/python3.13/site-packages/pyhmmer/__pycache__/utils.cpython-313.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT/usr/lib64/python3.13/site-packages/pyhmmer/__pycache__/__init__.cpython-313.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT/usr/lib64/python3.13/site-packages/pyhmmer/tests/__pycache__/utils.cpython-313.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT/usr/lib64/python3.13/site-packages/pyhmmer/__pycache__/hmmer.cpython-313.opt-1.pyc: replacing with normalized version /builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT/usr/lib64/python3.13/site-packages/pyhmmer/tests/__pycache__/test_errors.cpython-313.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT/usr/lib64/python3.13/site-packages/pyhmmer/__pycache__/hmmer.cpython-313.pyc: replacing with normalized version /builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT/usr/lib64/python3.13/site-packages/pyhmmer/tests/__pycache__/test_doctest.cpython-313.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT/usr/lib64/python3.13/site-packages/pyhmmer/tests/__pycache__/__init__.cpython-313.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT/usr/lib64/python3.13/site-packages/pyhmmer/tests/test_plan7/__pycache__/test_background.cpython-313.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT/usr/lib64/python3.13/site-packages/pyhmmer/tests/test_plan7/__pycache__/test_alignment.cpython-313.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT/usr/lib64/python3.13/site-packages/pyhmmer/tests/test_plan7/__pycache__/__init__.cpython-313.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT/usr/lib64/python3.13/site-packages/pyhmmer/tests/__pycache__/test_hmmer.cpython-313.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT/usr/lib64/python3.13/site-packages/pyhmmer/tests/test_plan7/__pycache__/test_hmm.cpython-313.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT/usr/lib64/python3.13/site-packages/pyhmmer/tests/test_plan7/__pycache__/test_traces.cpython-313.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT/usr/lib64/python3.13/site-packages/pyhmmer/tests/test_plan7/__pycache__/test_tracealigner.cpython-313.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT/usr/lib64/python3.13/site-packages/pyhmmer/tests/test_plan7/__pycache__/test_profile.cpython-313.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT/usr/lib64/python3.13/site-packages/pyhmmer/tests/test_plan7/__pycache__/test_tophits.cpython-313.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT/usr/lib64/python3.13/site-packages/pyhmmer/tests/test_plan7/__pycache__/test_hit.cpython-313.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT/usr/lib64/python3.13/site-packages/pyhmmer/tests/test_plan7/__pycache__/test_pipeline.cpython-313.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT/usr/lib64/python3.13/site-packages/pyhmmer/tests/test_plan7/__pycache__/test_optimizedprofile.cpython-313.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT/usr/lib64/python3.13/site-packages/pyhmmer/tests/test_plan7/__pycache__/test_builder.cpython-313.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT/usr/lib64/python3.13/site-packages/pyhmmer/tests/test_plan7/__pycache__/test_block.cpython-313.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT/usr/lib64/python3.13/site-packages/pyhmmer/tests/test_plan7/__pycache__/test_hmmfile.cpython-313.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT/usr/lib64/python3.13/site-packages/pyhmmer/tests/test_easel/__pycache__/test_sequence.cpython-313.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT/usr/lib64/python3.13/site-packages/pyhmmer/tests/test_easel/__pycache__/test_vector.cpython-313.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT/usr/lib64/python3.13/site-packages/pyhmmer/tests/test_easel/__pycache__/test_ssi.cpython-313.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT/usr/lib64/python3.13/site-packages/pyhmmer/tests/test_easel/__pycache__/test_randomness.cpython-313.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT/usr/lib64/python3.13/site-packages/pyhmmer/tests/test_easel/__pycache__/test_matrix.cpython-313.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT/usr/lib64/python3.13/site-packages/pyhmmer/tests/test_easel/__pycache__/test_keyhash.cpython-313.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT/usr/lib64/python3.13/site-packages/pyhmmer/tests/test_easel/__pycache__/test_sequencefile.cpython-313.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT/usr/lib64/python3.13/site-packages/pyhmmer/tests/test_easel/__pycache__/test_msafile.cpython-313.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT/usr/lib64/python3.13/site-packages/pyhmmer/tests/test_easel/__pycache__/test_gencode.cpython-313.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT/usr/lib64/python3.13/site-packages/pyhmmer/tests/test_easel/__pycache__/test_bitfield.cpython-313.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT/usr/lib64/python3.13/site-packages/pyhmmer/tests/test_easel/__pycache__/test_msa.cpython-313.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT/usr/lib64/python3.13/site-packages/pyhmmer/tests/test_easel/__pycache__/test_block.cpython-313.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT/usr/lib64/python3.13/site-packages/pyhmmer/tests/test_easel/__pycache__/__init__.cpython-313.opt-1.pyc: rewriting with normalized contents /builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT/usr/lib64/python3.13/site-packages/pyhmmer/tests/test_easel/__pycache__/test_alphabet.cpython-313.opt-1.pyc: rewriting with normalized contents Scanned 47 directories and 387 files, processed 37 inodes, 37 modified (2 replaced + 35 rewritten), 0 unsupported format, 0 errors Reading /builddir/build/BUILD/python-pyhmmer-0.10.15-build/SPECPARTS/rpm-debuginfo.specpart Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.T3AteB + umask 022 + cd /builddir/build/BUILD/python-pyhmmer-0.10.15-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 pyhmmer-0.10.15 + '[' '!' -f /builddir/build/BUILD/python-pyhmmer-0.10.15-build/python-pyhmmer-0.10.15-1.fc41.x86_64-pyproject-modules ']' + PATH=/builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT/usr/lib/python3.13/site-packages + _PYTHONSITE=/builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + /usr/bin/python3 -sP /usr/lib/rpm/redhat/import_all_modules.py -f /builddir/build/BUILD/python-pyhmmer-0.10.15-build/python-pyhmmer-0.10.15-1.fc41.x86_64-pyproject-modules -t Check import: pyhmmer + RPM_EC=0 ++ jobs -p + exit 0 Processing files: python3-pyhmmer-0.10.15-1.fc41.x86_64 Provides: python-pyhmmer = 0.10.15-1.fc41 python3-pyhmmer = 0.10.15-1.fc41 python3-pyhmmer(x86-64) = 0.10.15-1.fc41 python3.13-pyhmmer = 0.10.15-1.fc41 python3.13dist(pyhmmer) = 0.10.15 python3dist(pyhmmer) = 0.10.15 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PartialHardlinkSets) <= 4.0.4-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: (python3.13dist(psutil) >= 5.8 with python3.13dist(psutil) < 6) libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.7)(64bit) libc.so.6(GLIBC_ABI_DT_RELR)(64bit) python(abi) = 3.13 rtld(GNU_HASH) Processing files: python-pyhmmer-debugsource-0.10.15-1.fc41.x86_64 Provides: python-pyhmmer-debugsource = 0.10.15-1.fc41 python-pyhmmer-debugsource(x86-64) = 0.10.15-1.fc41 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: python3-pyhmmer-debuginfo-0.10.15-1.fc41.x86_64 Provides: debuginfo(build-id) = 33776734a429693d7403c51287d3f69b82c694d9 debuginfo(build-id) = 9f7fa6d02b65c197cee1ce5cc818c1291a9b1626 debuginfo(build-id) = dc4e8138edd0c06b9138371db58cf3e9a0865caf debuginfo(build-id) = de0bedcb134a1898702813d4f6eea819aa8ebcd8 python-pyhmmer-debuginfo = 0.10.15-1.fc41 python3-pyhmmer-debuginfo = 0.10.15-1.fc41 python3-pyhmmer-debuginfo(x86-64) = 0.10.15-1.fc41 python3.13-pyhmmer-debuginfo = 0.10.15-1.fc41 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: python-pyhmmer-debugsource(x86-64) = 0.10.15-1.fc41 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILD/python-pyhmmer-0.10.15-build/BUILDROOT Wrote: /builddir/build/SRPMS/python-pyhmmer-0.10.15-1.fc41.src.rpm Wrote: /builddir/build/RPMS/python3-pyhmmer-debuginfo-0.10.15-1.fc41.x86_64.rpm Wrote: /builddir/build/RPMS/python3-pyhmmer-0.10.15-1.fc41.x86_64.rpm Wrote: /builddir/build/RPMS/python-pyhmmer-debugsource-0.10.15-1.fc41.x86_64.rpm Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.7C1NfG + umask 022 + cd /builddir/build/BUILD/python-pyhmmer-0.10.15-build + test -d /builddir/build/BUILD/python-pyhmmer-0.10.15-build + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w /builddir/build/BUILD/python-pyhmmer-0.10.15-build + rm -rf /builddir/build/BUILD/python-pyhmmer-0.10.15-build + RPM_EC=0 ++ jobs -p + exit 0 Finish: rpmbuild python-pyhmmer-0.10.15-1.fc41.src.rpm Finish: build phase for python-pyhmmer-0.10.15-1.fc41.src.rpm INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-41-x86_64-1728412359.829131/root/var/log/dnf5.log INFO: Done(/var/lib/copr-rpmbuild/results/python-pyhmmer-0.10.15-1.fc41.src.rpm) Config(child) 2 minutes 57 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": "python-pyhmmer", "epoch": null, "version": "0.10.15", "release": "1.fc41", "arch": "src" }, { "name": "python3-pyhmmer", "epoch": null, "version": "0.10.15", "release": "1.fc41", "arch": "x86_64" }, { "name": "python3-pyhmmer-debuginfo", "epoch": null, "version": "0.10.15", "release": "1.fc41", "arch": "x86_64" }, { "name": "python-pyhmmer-debugsource", "epoch": null, "version": "0.10.15", "release": "1.fc41", "arch": "x86_64" } ] } RPMResults finished