Warning: Permanently added '2620:52:3:1:dead:beef:cafe:c191' (ED25519) to the list of known hosts. Running: /usr/bin/copr-rpmbuild --verbose --drop-resultdir --build-id 5017097 --chroot fedora-rawhide-x86_64 --detached Version: 0.61 PID: 13551 Logging PID: 13552 Task: {'appstream': False, 'background': True, 'build_id': 5017097, 'buildroot_pkgs': [], 'chroot': 'fedora-rawhide-x86_64', 'enable_net': False, 'fedora_review': False, 'git_hash': '2cf7f8251544bb917cda7885e32bac70c1849181', 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/djdelorie/make-4.4/wise2', 'isolation': 'default', 'memory_reqs': 2048, 'package_name': 'wise2', 'package_version': '2.4.1-15', 'project_dirname': 'make-4.4', 'project_name': 'make-4.4', 'project_owner': 'djdelorie', 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/djdelorie/make-4.4/fedora-rawhide-x86_64/', 'id': 'copr_base', 'name': 'Copr repository'}], 'sandbox': 'djdelorie/make-4.4--djdelorie', 'source_json': {}, 'source_type': None, 'submitter': 'djdelorie', 'tags': [], 'task_id': '5017097-fedora-rawhide-x86_64', 'timeout': 108000, 'uses_devel_repo': False, 'with_opts': [], 'without_opts': []} Running: git clone https://copr-dist-git.fedorainfracloud.org/git/djdelorie/make-4.4/wise2 /var/lib/copr-rpmbuild/workspace/workdir-du5o0hbf/wise2 --depth 500 --no-single-branch --recursive cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/djdelorie/make-4.4/wise2', '/var/lib/copr-rpmbuild/workspace/workdir-du5o0hbf/wise2', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-du5o0hbf/wise2'... Running: git checkout 2cf7f8251544bb917cda7885e32bac70c1849181 cmd: ['git', 'checkout', '2cf7f8251544bb917cda7885e32bac70c1849181'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-du5o0hbf/wise2 rc: 0 stdout: stderr: Note: switching to '2cf7f8251544bb917cda7885e32bac70c1849181'. You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by switching back to a branch. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -c with the switch command. Example: git switch -c Or undo this operation with: git switch - Turn off this advice by setting config variable advice.detachedHead to false HEAD is now at 2cf7f82 automatic import of wise2 Running: copr-distgit-client sources /usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated cmd: ['copr-distgit-client', 'sources'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-du5o0hbf/wise2 rc: 0 stdout: stderr: INFO: Reading stdout from command: git rev-parse --abbrev-ref HEAD INFO: Reading stdout from command: git rev-parse HEAD INFO: Reading sources specification file: sources INFO: Downloading wise2.4.1.tar.gz INFO: Calling: curl -H Pragma: -o wise2.4.1.tar.gz --location --remote-time --show-error --fail https://copr-dist-git.fedorainfracloud.org/repo/pkgs/djdelorie/make-4.4/wise2/wise2.4.1.tar.gz/md5/d70c404c1dc40ceef7718757b11bdaa0/wise2.4.1.tar.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 3119k 100 3119k 0 0 15.2M 0 --:--:-- --:--:-- --:--:-- 15.3M INFO: Reading stdout from command: md5sum wise2.4.1.tar.gz Running (timeout=108000): unbuffer mock --buildsrpm --spec /var/lib/copr-rpmbuild/workspace/workdir-du5o0hbf/wise2/wise2.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-du5o0hbf/wise2 --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1668213019.291541 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 3.3 starting (python version = 3.10.4, NVR = mock-3.3-1.fc35)... 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-du5o0hbf/wise2/wise2.spec) Config(fedora-rawhide-x86_64) Start: clean chroot Finish: clean chroot Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1668213019.291541/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: enabled HW Info plugin Mock Version: 3.3 INFO: Mock Version: 3.3 Start(bootstrap): dnf install No matches found for the following disable plugin patterns: local, spacewalk, versionlock Updating Subscription Management repositories. Unable to read consumer identity This system is not registered with an entitlement server. You can use subscription-manager to register. Copr repository 64 MB/s | 31 MB 00:00 fedora 30 MB/s | 65 MB 00:02 Last metadata expiration check: 0:00:07 ago on Sat Nov 12 00:30:29 2022. Dependencies resolved. ================================================================================ Package Arch Version Repo Size ================================================================================ Installing: dnf noarch 4.14.0-1.fc38 fedora 480 k dnf-plugins-core noarch 4.3.1-1.fc38 fedora 34 k Installing dependencies: alternatives x86_64 1.21-1.fc38 copr_base 38 k audit-libs x86_64 3.0.9-1.fc38 fedora 116 k basesystem noarch 11-14.fc37 fedora 7.0 k bash x86_64 5.2.2-2.fc38 copr_base 1.8 M bzip2-libs x86_64 1.0.8-12.fc38 copr_base 42 k ca-certificates noarch 2022.2.54-5.fc37 fedora 829 k coreutils x86_64 9.1-8.fc38 copr_base 1.1 M coreutils-common x86_64 9.1-8.fc38 copr_base 2.0 M crypto-policies noarch 20221110-1.git87a75f4.fc38 fedora 90 k curl x86_64 7.86.0-2.fc38 fedora 334 k cyrus-sasl-lib x86_64 2.1.28-8.fc38 fedora 792 k dbus-libs x86_64 1:1.14.4-1.fc38 copr_base 156 k dnf-data noarch 4.14.0-1.fc38 fedora 43 k elfutils-default-yama-scope noarch 0.188-3.fc38 fedora 15 k elfutils-libelf x86_64 0.188-3.fc38 fedora 196 k elfutils-libs x86_64 0.188-3.fc38 fedora 257 k expat x86_64 2.4.8-2.fc38 copr_base 110 k fedora-gpg-keys noarch 38-0.3 fedora 125 k fedora-release noarch 38-0.4 fedora 11 k fedora-release-common noarch 38-0.4 fedora 22 k fedora-release-identity-basic noarch 38-0.4 fedora 12 k fedora-repos noarch 38-0.3 fedora 10 k fedora-repos-rawhide noarch 38-0.3 fedora 9.7 k file-libs x86_64 5.42-4.fc38 copr_base 676 k filesystem x86_64 3.18-2.fc37 fedora 1.1 M findutils x86_64 1:4.9.0-2.fc38 copr_base 483 k gawk x86_64 5.1.1-4.fc38 copr_base 1.0 M gdbm-libs x86_64 1:1.23-2.fc38 copr_base 56 k glib2 x86_64 2.74.1-2.fc38 fedora 2.7 M glibc x86_64 2.36.9000-13.fc38 fedora 2.1 M glibc-common x86_64 2.36.9000-13.fc38 fedora 304 k glibc-minimal-langpack x86_64 2.36.9000-13.fc38 fedora 25 k gmp x86_64 1:6.2.1-3.fc38 copr_base 316 k gnupg2 x86_64 2.3.8-1.fc38 copr_base 2.5 M gnutls x86_64 3.7.8-9.fc38 fedora 1.1 M gpgme x86_64 1.17.0-4.fc37 fedora 210 k grep x86_64 3.8-1.fc38 copr_base 282 k ima-evm-utils x86_64 1.4-6.fc37 fedora 63 k json-c x86_64 0.16-3.fc38 fedora 41 k keyutils-libs x86_64 1.6.1-5.fc38 copr_base 32 k krb5-libs x86_64 1.19.2-11.fc38.1 copr_base 724 k libacl x86_64 2.3.1-4.fc38 copr_base 24 k libarchive x86_64 3.6.1-2.fc37 fedora 397 k libassuan x86_64 2.5.5-5.fc38 copr_base 67 k libattr x86_64 2.5.1-5.fc38 copr_base 18 k libb2 x86_64 0.98.1-7.fc38 copr_base 25 k libblkid x86_64 2.38.1-2.fc38 copr_base 107 k libbrotli x86_64 1.0.9-9.fc37 fedora 315 k libcap x86_64 2.48-5.fc38 copr_base 67 k libcap-ng x86_64 0.8.3-3.fc37 fedora 33 k libcom_err x86_64 1.46.5-3.fc38 copr_base 26 k libcomps x86_64 0.1.18-4.fc38 copr_base 77 k libcurl x86_64 7.86.0-2.fc38 fedora 305 k libdnf x86_64 0.68.0-1.fc38 fedora 673 k libevent x86_64 2.1.12-7.fc38 copr_base 259 k libffi x86_64 3.4.4-1.fc38 fedora 38 k libfsverity x86_64 1.4-8.fc38 copr_base 20 k libgcc x86_64 12.2.1-3.fc38 fedora 108 k libgcrypt x86_64 1.10.1-5.fc38 fedora 513 k libgomp x86_64 12.2.1-3.fc38 fedora 295 k libgpg-error x86_64 1.46-1.fc38 copr_base 222 k libidn2 x86_64 2.3.4-1.fc38 copr_base 154 k libksba x86_64 1.6.2-1.fc38 copr_base 158 k libmodulemd x86_64 2.14.0-4.fc37 fedora 234 k libmount x86_64 2.38.1-2.fc38 copr_base 136 k libnghttp2 x86_64 1.50.0-1.fc38 copr_base 75 k libnsl2 x86_64 2.0.0-4.fc38 copr_base 31 k libpsl x86_64 0.21.1-6.fc38 copr_base 64 k librepo x86_64 1.14.4-1.fc38 fedora 94 k libreport-filesystem noarch 2.17.6-1.fc38 fedora 14 k libselinux x86_64 3.4-5.fc37 fedora 86 k libsemanage x86_64 3.4-5.fc37 fedora 120 k libsepol x86_64 3.4-3.fc38 copr_base 322 k libsigsegv x86_64 2.14-3.fc38 copr_base 27 k libsmartcols x86_64 2.38.1-2.fc38 copr_base 65 k libsolv x86_64 0.7.22-3.fc37 fedora 405 k libssh x86_64 0.10.4-2.fc38 fedora 209 k libssh-config noarch 0.10.4-2.fc38 fedora 8.8 k libstdc++ x86_64 12.2.1-3.fc38 fedora 799 k libtasn1 x86_64 4.18.0-3.fc38 copr_base 75 k libtirpc x86_64 1.3.3-0.fc38 copr_base 94 k libunistring x86_64 1.0-2.fc38 copr_base 549 k libuuid x86_64 2.38.1-2.fc38 copr_base 28 k libverto x86_64 0.3.2-4.fc38 copr_base 21 k libxcrypt x86_64 4.4.30-3.fc38 fedora 118 k libxml2 x86_64 2.10.3-2.fc38 fedora 705 k libyaml x86_64 0.2.5-8.fc38 copr_base 60 k libzstd x86_64 1.5.2-3.fc37 fedora 294 k lua-libs x86_64 5.4.4-6.fc38 copr_base 132 k lz4-libs x86_64 1.9.3-5.fc38 copr_base 71 k mpdecimal x86_64 2.5.1-4.fc38 copr_base 102 k mpfr x86_64 4.1.0-10.fc38 copr_base 331 k ncurses-base noarch 6.3-3.20220501.fc38 copr_base 62 k ncurses-libs x86_64 6.3-3.20220501.fc38 copr_base 329 k nettle x86_64 3.8-2.fc38 copr_base 414 k npth x86_64 1.6-10.fc38 copr_base 25 k openldap x86_64 2.6.3-1.fc38 fedora 254 k openssl-libs x86_64 1:3.0.5-6.fc38 fedora 2.1 M p11-kit x86_64 0.24.1-3.fc37 fedora 376 k p11-kit-trust x86_64 0.24.1-3.fc37 fedora 138 k pcre2 x86_64 10.40-1.fc38.1 copr_base 237 k pcre2-syntax noarch 10.40-1.fc38.1 copr_base 143 k popt x86_64 1.19-1.fc38 copr_base 59 k publicsuffix-list-dafsa noarch 20210518-5.fc37 fedora 58 k python-pip-wheel noarch 22.2.2-2.fc38 fedora 1.4 M python-setuptools-wheel noarch 65.5.1-1.fc38 fedora 715 k python3 x86_64 3.11.0-1.fc38 fedora 27 k python3-dateutil noarch 1:2.8.2-4.fc38 copr_base 350 k python3-dbus x86_64 1.3.2-1.fc38 copr_base 147 k python3-distro noarch 1.8.0-1.fc38 fedora 49 k python3-dnf noarch 4.14.0-1.fc38 fedora 607 k python3-dnf-plugins-core noarch 4.3.1-1.fc38 fedora 277 k python3-gpg x86_64 1.17.0-4.fc37 fedora 298 k python3-hawkey x86_64 0.68.0-1.fc38 fedora 108 k python3-libcomps x86_64 0.1.18-4.fc38 copr_base 48 k python3-libdnf x86_64 0.68.0-1.fc38 fedora 818 k python3-libs x86_64 3.11.0-1.fc38 fedora 9.6 M python3-rpm x86_64 4.18.0-6.fc38 fedora 94 k python3-six noarch 1.16.0-8.fc37 fedora 42 k readline x86_64 8.2-2.fc38 copr_base 211 k rpm x86_64 4.18.0-6.fc38 fedora 572 k rpm-build-libs x86_64 4.18.0-6.fc38 fedora 94 k rpm-libs x86_64 4.18.0-6.fc38 fedora 320 k rpm-sign-libs x86_64 4.18.0-6.fc38 fedora 27 k sed x86_64 4.8-11.fc38 copr_base 297 k setup noarch 2.14.2-1.fc38 copr_base 145 k shadow-utils x86_64 2:4.13-1.fc38 fedora 1.3 M sqlite-libs x86_64 3.39.4-1.fc38 copr_base 659 k systemd-libs x86_64 252.1-588.fc38 fedora 631 k tpm2-tss x86_64 3.2.0-3.fc38 copr_base 596 k tzdata noarch 2022f-1.fc38 copr_base 431 k xz-libs x86_64 5.2.7-1.fc38 copr_base 93 k zchunk-libs x86_64 1.2.3-1.fc38 fedora 51 k zlib x86_64 1.2.12-5.fc38 copr_base 94 k Transaction Summary ================================================================================ Install 136 Packages Total download size: 55 M Installed size: 196 M Downloading Packages: (1/136): bzip2-libs-1.0.8-12.fc38.x86_64.rpm 882 kB/s | 42 kB 00:00 (2/136): alternatives-1.21-1.fc38.x86_64.rpm 748 kB/s | 38 kB 00:00 (3/136): bash-5.2.2-2.fc38.x86_64.rpm 21 MB/s | 1.8 MB 00:00 (4/136): coreutils-common-9.1-8.fc38.x86_64.rpm 32 MB/s | 2.0 MB 00:00 (5/136): coreutils-9.1-8.fc38.x86_64.rpm 15 MB/s | 1.1 MB 00:00 (6/136): dbus-libs-1.14.4-1.fc38.x86_64.rpm 2.8 MB/s | 156 kB 00:00 (7/136): expat-2.4.8-2.fc38.x86_64.rpm 4.6 MB/s | 110 kB 00:00 (8/136): file-libs-5.42-4.fc38.x86_64.rpm 35 MB/s | 676 kB 00:00 (9/136): gdbm-libs-1.23-2.fc38.x86_64.rpm 4.5 MB/s | 56 kB 00:00 (10/136): gmp-6.2.1-3.fc38.x86_64.rpm 15 MB/s | 316 kB 00:00 (11/136): gawk-5.1.1-4.fc38.x86_64.rpm 18 MB/s | 1.0 MB 00:00 (12/136): grep-3.8-1.fc38.x86_64.rpm 16 MB/s | 282 kB 00:00 (13/136): keyutils-libs-1.6.1-5.fc38.x86_64.rpm 1.8 MB/s | 32 kB 00:00 (14/136): findutils-4.9.0-2.fc38.x86_64.rpm 4.9 MB/s | 483 kB 00:00 (15/136): libacl-2.3.1-4.fc38.x86_64.rpm 780 kB/s | 24 kB 00:00 (16/136): krb5-libs-1.19.2-11.fc38.1.x86_64.rpm 17 MB/s | 724 kB 00:00 (17/136): gnupg2-2.3.8-1.fc38.x86_64.rpm 21 MB/s | 2.5 MB 00:00 (18/136): libattr-2.5.1-5.fc38.x86_64.rpm 874 kB/s | 18 kB 00:00 (19/136): libassuan-2.5.5-5.fc38.x86_64.rpm 2.1 MB/s | 67 kB 00:00 (20/136): libb2-0.98.1-7.fc38.x86_64.rpm 2.5 MB/s | 25 kB 00:00 (21/136): libblkid-2.38.1-2.fc38.x86_64.rpm 9.1 MB/s | 107 kB 00:00 (22/136): libcap-2.48-5.fc38.x86_64.rpm 5.6 MB/s | 67 kB 00:00 (23/136): libcom_err-1.46.5-3.fc38.x86_64.rpm 2.7 MB/s | 26 kB 00:00 (24/136): libcomps-0.1.18-4.fc38.x86_64.rpm 6.1 MB/s | 77 kB 00:00 (25/136): libfsverity-1.4-8.fc38.x86_64.rpm 1.7 MB/s | 20 kB 00:00 (26/136): libevent-2.1.12-7.fc38.x86_64.rpm 13 MB/s | 259 kB 00:00 (27/136): libidn2-2.3.4-1.fc38.x86_64.rpm 11 MB/s | 154 kB 00:00 (28/136): libgpg-error-1.46-1.fc38.x86_64.rpm 8.9 MB/s | 222 kB 00:00 (29/136): libksba-1.6.2-1.fc38.x86_64.rpm 7.9 MB/s | 158 kB 00:00 (30/136): libmount-2.38.1-2.fc38.x86_64.rpm 8.4 MB/s | 136 kB 00:00 (31/136): libnghttp2-1.50.0-1.fc38.x86_64.rpm 5.6 MB/s | 75 kB 00:00 (32/136): libnsl2-2.0.0-4.fc38.x86_64.rpm 2.3 MB/s | 31 kB 00:00 (33/136): libpsl-0.21.1-6.fc38.x86_64.rpm 6.8 MB/s | 64 kB 00:00 (34/136): libsigsegv-2.14-3.fc38.x86_64.rpm 3.2 MB/s | 27 kB 00:00 (35/136): libsepol-3.4-3.fc38.x86_64.rpm 16 MB/s | 322 kB 00:00 (36/136): libtasn1-4.18.0-3.fc38.x86_64.rpm 7.0 MB/s | 75 kB 00:00 (37/136): libtirpc-1.3.3-0.fc38.x86_64.rpm 8.3 MB/s | 94 kB 00:00 (38/136): libsmartcols-2.38.1-2.fc38.x86_64.rpm 2.5 MB/s | 65 kB 00:00 (39/136): libunistring-1.0-2.fc38.x86_64.rpm 24 MB/s | 549 kB 00:00 (40/136): libuuid-2.38.1-2.fc38.x86_64.rpm 2.0 MB/s | 28 kB 00:00 (41/136): libverto-0.3.2-4.fc38.x86_64.rpm 1.8 MB/s | 21 kB 00:00 (42/136): libyaml-0.2.5-8.fc38.x86_64.rpm 5.1 MB/s | 60 kB 00:00 (43/136): lz4-libs-1.9.3-5.fc38.x86_64.rpm 5.7 MB/s | 71 kB 00:00 (44/136): lua-libs-5.4.4-6.fc38.x86_64.rpm 8.8 MB/s | 132 kB 00:00 (45/136): mpdecimal-2.5.1-4.fc38.x86_64.rpm 8.8 MB/s | 102 kB 00:00 (46/136): ncurses-base-6.3-3.20220501.fc38.noar 5.2 MB/s | 62 kB 00:00 (47/136): mpfr-4.1.0-10.fc38.x86_64.rpm 16 MB/s | 331 kB 00:00 (48/136): npth-1.6-10.fc38.x86_64.rpm 2.1 MB/s | 25 kB 00:00 (49/136): ncurses-libs-6.3-3.20220501.fc38.x86_ 14 MB/s | 329 kB 00:00 (50/136): pcre2-10.40-1.fc38.1.x86_64.rpm 22 MB/s | 237 kB 00:00 (51/136): nettle-3.8-2.fc38.x86_64.rpm 12 MB/s | 414 kB 00:00 (52/136): pcre2-syntax-10.40-1.fc38.1.noarch.rp 7.2 MB/s | 143 kB 00:00 (53/136): popt-1.19-1.fc38.x86_64.rpm 4.8 MB/s | 59 kB 00:00 (54/136): python3-libcomps-0.1.18-4.fc38.x86_64 4.6 MB/s | 48 kB 00:00 (55/136): python3-dbus-1.3.2-1.fc38.x86_64.rpm 10 MB/s | 147 kB 00:00 (56/136): python3-dateutil-2.8.2-4.fc38.noarch. 13 MB/s | 350 kB 00:00 (57/136): readline-8.2-2.fc38.x86_64.rpm 11 MB/s | 211 kB 00:00 (58/136): setup-2.14.2-1.fc38.noarch.rpm 10 MB/s | 145 kB 00:00 (59/136): sed-4.8-11.fc38.x86_64.rpm 13 MB/s | 297 kB 00:00 (60/136): tzdata-2022f-1.fc38.noarch.rpm 28 MB/s | 431 kB 00:00 (61/136): tpm2-tss-3.2.0-3.fc38.x86_64.rpm 23 MB/s | 596 kB 00:00 (62/136): xz-libs-5.2.7-1.fc38.x86_64.rpm 7.3 MB/s | 93 kB 00:00 (63/136): sqlite-libs-3.39.4-1.fc38.x86_64.rpm 16 MB/s | 659 kB 00:00 (64/136): zlib-1.2.12-5.fc38.x86_64.rpm 8.7 MB/s | 94 kB 00:00 (65/136): audit-libs-3.0.9-1.fc38.x86_64.rpm 3.7 MB/s | 116 kB 00:00 (66/136): crypto-policies-20221110-1.git87a75f4 57 MB/s | 90 kB 00:00 (67/136): curl-7.86.0-2.fc38.x86_64.rpm 58 MB/s | 334 kB 00:00 (68/136): basesystem-11-14.fc37.noarch.rpm 213 kB/s | 7.0 kB 00:00 (69/136): cyrus-sasl-lib-2.1.28-8.fc38.x86_64.r 33 MB/s | 792 kB 00:00 (70/136): dnf-4.14.0-1.fc38.noarch.rpm 20 MB/s | 480 kB 00:00 (71/136): dnf-data-4.14.0-1.fc38.noarch.rpm 19 MB/s | 43 kB 00:00 (72/136): dnf-plugins-core-4.3.1-1.fc38.noarch. 19 MB/s | 34 kB 00:00 (73/136): elfutils-default-yama-scope-0.188-3.f 12 MB/s | 15 kB 00:00 (74/136): elfutils-libelf-0.188-3.fc38.x86_64.r 31 MB/s | 196 kB 00:00 (75/136): elfutils-libs-0.188-3.fc38.x86_64.rpm 38 MB/s | 257 kB 00:00 (76/136): fedora-gpg-keys-38-0.3.noarch.rpm 44 MB/s | 125 kB 00:00 (77/136): fedora-release-38-0.4.noarch.rpm 5.4 MB/s | 11 kB 00:00 (78/136): ca-certificates-2022.2.54-5.fc37.noar 12 MB/s | 829 kB 00:00 (79/136): fedora-release-identity-basic-38-0.4. 8.9 MB/s | 12 kB 00:00 (80/136): fedora-release-common-38-0.4.noarch.r 10 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libstdc++-12.2.1-3.fc38.x86_64.rpm 39 MB/s | 799 kB 00:00 (111/136): libzstd-1.5.2-3.fc37.x86_64.rpm 21 MB/s | 294 kB 00:00 (112/136): libxml2-2.10.3-2.fc38.x86_64.rpm 29 MB/s | 705 kB 00:00 (113/136): openldap-2.6.3-1.fc38.x86_64.rpm 40 MB/s | 254 kB 00:00 (114/136): p11-kit-trust-0.24.1-3.fc37.x86_64.r 27 MB/s | 138 kB 00:00 (115/136): publicsuffix-list-dafsa-20210518-5.f 12 MB/s | 58 kB 00:00 (116/136): p11-kit-0.24.1-3.fc37.x86_64.rpm 32 MB/s | 376 kB 00:00 (117/136): python-setuptools-wheel-65.5.1-1.fc3 22 MB/s | 715 kB 00:00 (118/136): python-pip-wheel-22.2.2-2.fc38.noarc 38 MB/s | 1.4 MB 00:00 (119/136): python3-3.11.0-1.fc38.x86_64.rpm 5.6 MB/s | 27 kB 00:00 (120/136): openssl-libs-3.0.5-6.fc38.x86_64.rpm 37 MB/s | 2.1 MB 00:00 (121/136): python3-distro-1.8.0-1.fc38.noarch.r 9.9 MB/s | 49 kB 00:00 (122/136): python3-dnf-plugins-core-4.3.1-1.fc3 25 MB/s | 277 kB 00:00 (123/136): python3-gpg-1.17.0-4.fc37.x86_64.rpm 26 MB/s | 298 kB 00:00 (124/136): python3-dnf-4.14.0-1.fc38.noarch.rpm 35 MB/s | 607 kB 00:00 (125/136): python3-hawkey-0.68.0-1.fc38.x86_64. 43 MB/s | 108 kB 00:00 (126/136): python3-rpm-4.18.0-6.fc38.x86_64.rpm 14 MB/s | 94 kB 00:00 (127/136): python3-six-1.16.0-8.fc37.noarch.rpm 7.5 MB/s | 42 kB 00:00 (128/136): python3-libdnf-0.68.0-1.fc38.x86_64. 49 MB/s | 818 kB 00:00 (129/136): rpm-build-libs-4.18.0-6.fc38.x86_64. 13 MB/s | 94 kB 00:00 (130/136): rpm-4.18.0-6.fc38.x86_64.rpm 29 MB/s | 572 kB 00:00 (131/136): rpm-libs-4.18.0-6.fc38.x86_64.rpm 27 MB/s | 320 kB 00:00 (132/136): rpm-sign-libs-4.18.0-6.fc38.x86_64.r 6.4 MB/s | 27 kB 00:00 (133/136): systemd-libs-252.1-588.fc38.x86_64.r 23 MB/s | 631 kB 00:00 (134/136): shadow-utils-4.13-1.fc38.x86_64.rpm 36 MB/s | 1.3 MB 00:00 (135/136): zchunk-libs-1.2.3-1.fc38.x86_64.rpm 7.5 MB/s | 51 kB 00:00 (136/136): python3-libs-3.11.0-1.fc38.x86_64.rp 62 MB/s | 9.6 MB 00:00 -------------------------------------------------------------------------------- Total 53 MB/s | 55 MB 00:01 fedora 1.6 MB/s | 1.6 kB 00:00 Importing GPG key 0xEB10B464: Userid : "Fedora (38) " Fingerprint: 6A51 BBAB BA3D 5467 B617 1221 809A 8D7C EB10 B464 From : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-38-primary Key imported successfully fedora 1.6 MB/s | 1.6 kB 00:00 GPG key at file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-38-primary (0xEB10B464) is already installed fedora 1.6 MB/s | 1.6 kB 00:00 Importing GPG key 0x5323552A: Userid : "Fedora (37) " Fingerprint: ACB5 EE4E 831C 74BB 7C16 8D27 F55A D3FB 5323 552A From : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-37-primary Key imported successfully Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Running scriptlet: filesystem-3.18-2.fc37.x86_64 1/1 Preparing : 1/1 Installing : libgcc-12.2.1-3.fc38.x86_64 1/136 Running scriptlet: libgcc-12.2.1-3.fc38.x86_64 1/136 Installing : crypto-policies-20221110-1.git87a75f4.fc38.noarc 2/136 Running scriptlet: crypto-policies-20221110-1.git87a75f4.fc38.noarc 2/136 Installing : tzdata-2022f-1.fc38.noarch 3/136 Installing : fedora-release-identity-basic-38-0.4.noarch 4/136 Installing : python-setuptools-wheel-65.5.1-1.fc38.noarch 5/136 Installing : publicsuffix-list-dafsa-20210518-5.fc37.noarch 6/136 Installing : libssh-config-0.10.4-2.fc38.noarch 7/136 Installing : libreport-filesystem-2.17.6-1.fc38.noarch 8/136 Installing : dnf-data-4.14.0-1.fc38.noarch 9/136 warning: /etc/dnf/dnf.conf created as /etc/dnf/dnf.conf.rpmnew Installing : fedora-gpg-keys-38-0.3.noarch 10/136 Installing : fedora-release-38-0.4.noarch 11/136 Installing : fedora-release-common-38-0.4.noarch 12/136 Installing : fedora-repos-rawhide-38-0.3.noarch 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Installing : gpgme-1.17.0-4.fc37.x86_64 120/136 Installing : librepo-1.14.4-1.fc38.x86_64 121/136 Installing : libdnf-0.68.0-1.fc38.x86_64 122/136 Installing : python3-libdnf-0.68.0-1.fc38.x86_64 123/136 Installing : python3-hawkey-0.68.0-1.fc38.x86_64 124/136 Installing : python3-gpg-1.17.0-4.fc37.x86_64 125/136 Running scriptlet: tpm2-tss-3.2.0-3.fc38.x86_64 126/136 useradd: Warning: missing or non-executable shell '/usr/sbin/nologin' Installing : tpm2-tss-3.2.0-3.fc38.x86_64 126/136 Installing : ima-evm-utils-1.4-6.fc37.x86_64 127/136 Installing : rpm-sign-libs-4.18.0-6.fc38.x86_64 128/136 Installing : python3-rpm-4.18.0-6.fc38.x86_64 129/136 Installing : python3-dnf-4.14.0-1.fc38.noarch 130/136 Installing : python3-dnf-plugins-core-4.3.1-1.fc38.noarch 131/136 Installing : curl-7.86.0-2.fc38.x86_64 132/136 Installing : libarchive-3.6.1-2.fc37.x86_64 133/136 Running scriptlet: rpm-4.18.0-6.fc38.x86_64 134/136 Installing : rpm-4.18.0-6.fc38.x86_64 134/136 Installing : dnf-plugins-core-4.3.1-1.fc38.noarch 135/136 Installing : dnf-4.14.0-1.fc38.noarch 136/136 Running scriptlet: dnf-4.14.0-1.fc38.noarch 136/136 Running scriptlet: filesystem-3.18-2.fc37.x86_64 136/136 Running scriptlet: ca-certificates-2022.2.54-5.fc37.noarch 136/136 Running scriptlet: rpm-4.18.0-6.fc38.x86_64 136/136 Running scriptlet: dnf-4.14.0-1.fc38.noarch 136/136 Verifying : alternatives-1.21-1.fc38.x86_64 1/136 Verifying : bash-5.2.2-2.fc38.x86_64 2/136 Verifying : bzip2-libs-1.0.8-12.fc38.x86_64 3/136 Verifying : coreutils-9.1-8.fc38.x86_64 4/136 Verifying : coreutils-common-9.1-8.fc38.x86_64 5/136 Verifying : dbus-libs-1:1.14.4-1.fc38.x86_64 6/136 Verifying : expat-2.4.8-2.fc38.x86_64 7/136 Verifying : file-libs-5.42-4.fc38.x86_64 8/136 Verifying : findutils-1:4.9.0-2.fc38.x86_64 9/136 Verifying : gawk-5.1.1-4.fc38.x86_64 10/136 Verifying : gdbm-libs-1:1.23-2.fc38.x86_64 11/136 Verifying : gmp-1:6.2.1-3.fc38.x86_64 12/136 Verifying : gnupg2-2.3.8-1.fc38.x86_64 13/136 Verifying : grep-3.8-1.fc38.x86_64 14/136 Verifying : keyutils-libs-1.6.1-5.fc38.x86_64 15/136 Verifying : krb5-libs-1.19.2-11.fc38.1.x86_64 16/136 Verifying : libacl-2.3.1-4.fc38.x86_64 17/136 Verifying : libassuan-2.5.5-5.fc38.x86_64 18/136 Verifying : libattr-2.5.1-5.fc38.x86_64 19/136 Verifying : libb2-0.98.1-7.fc38.x86_64 20/136 Verifying : libblkid-2.38.1-2.fc38.x86_64 21/136 Verifying : libcap-2.48-5.fc38.x86_64 22/136 Verifying : libcom_err-1.46.5-3.fc38.x86_64 23/136 Verifying : libcomps-0.1.18-4.fc38.x86_64 24/136 Verifying : libevent-2.1.12-7.fc38.x86_64 25/136 Verifying : libfsverity-1.4-8.fc38.x86_64 26/136 Verifying : libgpg-error-1.46-1.fc38.x86_64 27/136 Verifying : libidn2-2.3.4-1.fc38.x86_64 28/136 Verifying : libksba-1.6.2-1.fc38.x86_64 29/136 Verifying : libmount-2.38.1-2.fc38.x86_64 30/136 Verifying : libnghttp2-1.50.0-1.fc38.x86_64 31/136 Verifying : libnsl2-2.0.0-4.fc38.x86_64 32/136 Verifying : libpsl-0.21.1-6.fc38.x86_64 33/136 Verifying : libsepol-3.4-3.fc38.x86_64 34/136 Verifying : libsigsegv-2.14-3.fc38.x86_64 35/136 Verifying : libsmartcols-2.38.1-2.fc38.x86_64 36/136 Verifying : libtasn1-4.18.0-3.fc38.x86_64 37/136 Verifying : libtirpc-1.3.3-0.fc38.x86_64 38/136 Verifying : libunistring-1.0-2.fc38.x86_64 39/136 Verifying : libuuid-2.38.1-2.fc38.x86_64 40/136 Verifying : libverto-0.3.2-4.fc38.x86_64 41/136 Verifying : libyaml-0.2.5-8.fc38.x86_64 42/136 Verifying : lua-libs-5.4.4-6.fc38.x86_64 43/136 Verifying : lz4-libs-1.9.3-5.fc38.x86_64 44/136 Verifying : mpdecimal-2.5.1-4.fc38.x86_64 45/136 Verifying : mpfr-4.1.0-10.fc38.x86_64 46/136 Verifying : ncurses-base-6.3-3.20220501.fc38.noarch 47/136 Verifying : ncurses-libs-6.3-3.20220501.fc38.x86_64 48/136 Verifying : nettle-3.8-2.fc38.x86_64 49/136 Verifying : npth-1.6-10.fc38.x86_64 50/136 Verifying : pcre2-10.40-1.fc38.1.x86_64 51/136 Verifying : pcre2-syntax-10.40-1.fc38.1.noarch 52/136 Verifying : popt-1.19-1.fc38.x86_64 53/136 Verifying : python3-dateutil-1:2.8.2-4.fc38.noarch 54/136 Verifying : python3-dbus-1.3.2-1.fc38.x86_64 55/136 Verifying : python3-libcomps-0.1.18-4.fc38.x86_64 56/136 Verifying : readline-8.2-2.fc38.x86_64 57/136 Verifying : sed-4.8-11.fc38.x86_64 58/136 Verifying : setup-2.14.2-1.fc38.noarch 59/136 Verifying : sqlite-libs-3.39.4-1.fc38.x86_64 60/136 Verifying : tpm2-tss-3.2.0-3.fc38.x86_64 61/136 Verifying : tzdata-2022f-1.fc38.noarch 62/136 Verifying : xz-libs-5.2.7-1.fc38.x86_64 63/136 Verifying : zlib-1.2.12-5.fc38.x86_64 64/136 Verifying : audit-libs-3.0.9-1.fc38.x86_64 65/136 Verifying : basesystem-11-14.fc37.noarch 66/136 Verifying : ca-certificates-2022.2.54-5.fc37.noarch 67/136 Verifying : crypto-policies-20221110-1.git87a75f4.fc38.noarc 68/136 Verifying : curl-7.86.0-2.fc38.x86_64 69/136 Verifying : cyrus-sasl-lib-2.1.28-8.fc38.x86_64 70/136 Verifying : dnf-4.14.0-1.fc38.noarch 71/136 Verifying : dnf-data-4.14.0-1.fc38.noarch 72/136 Verifying : dnf-plugins-core-4.3.1-1.fc38.noarch 73/136 Verifying : elfutils-default-yama-scope-0.188-3.fc38.noarch 74/136 Verifying : elfutils-libelf-0.188-3.fc38.x86_64 75/136 Verifying : elfutils-libs-0.188-3.fc38.x86_64 76/136 Verifying : fedora-gpg-keys-38-0.3.noarch 77/136 Verifying : fedora-release-38-0.4.noarch 78/136 Verifying : fedora-release-common-38-0.4.noarch 79/136 Verifying : fedora-release-identity-basic-38-0.4.noarch 80/136 Verifying : fedora-repos-38-0.3.noarch 81/136 Verifying : fedora-repos-rawhide-38-0.3.noarch 82/136 Verifying : filesystem-3.18-2.fc37.x86_64 83/136 Verifying : glib2-2.74.1-2.fc38.x86_64 84/136 Verifying : glibc-2.36.9000-13.fc38.x86_64 85/136 Verifying : glibc-common-2.36.9000-13.fc38.x86_64 86/136 Verifying : glibc-minimal-langpack-2.36.9000-13.fc38.x86_64 87/136 Verifying : gnutls-3.7.8-9.fc38.x86_64 88/136 Verifying : gpgme-1.17.0-4.fc37.x86_64 89/136 Verifying : ima-evm-utils-1.4-6.fc37.x86_64 90/136 Verifying : json-c-0.16-3.fc38.x86_64 91/136 Verifying : libarchive-3.6.1-2.fc37.x86_64 92/136 Verifying : libbrotli-1.0.9-9.fc37.x86_64 93/136 Verifying : libcap-ng-0.8.3-3.fc37.x86_64 94/136 Verifying : libcurl-7.86.0-2.fc38.x86_64 95/136 Verifying : libdnf-0.68.0-1.fc38.x86_64 96/136 Verifying : libffi-3.4.4-1.fc38.x86_64 97/136 Verifying : libgcc-12.2.1-3.fc38.x86_64 98/136 Verifying : libgcrypt-1.10.1-5.fc38.x86_64 99/136 Verifying : libgomp-12.2.1-3.fc38.x86_64 100/136 Verifying : libmodulemd-2.14.0-4.fc37.x86_64 101/136 Verifying : librepo-1.14.4-1.fc38.x86_64 102/136 Verifying : libreport-filesystem-2.17.6-1.fc38.noarch 103/136 Verifying : libselinux-3.4-5.fc37.x86_64 104/136 Verifying : libsemanage-3.4-5.fc37.x86_64 105/136 Verifying : libsolv-0.7.22-3.fc37.x86_64 106/136 Verifying : libssh-0.10.4-2.fc38.x86_64 107/136 Verifying : libssh-config-0.10.4-2.fc38.noarch 108/136 Verifying : libstdc++-12.2.1-3.fc38.x86_64 109/136 Verifying : libxcrypt-4.4.30-3.fc38.x86_64 110/136 Verifying : libxml2-2.10.3-2.fc38.x86_64 111/136 Verifying : libzstd-1.5.2-3.fc37.x86_64 112/136 Verifying : openldap-2.6.3-1.fc38.x86_64 113/136 Verifying : openssl-libs-1:3.0.5-6.fc38.x86_64 114/136 Verifying : p11-kit-0.24.1-3.fc37.x86_64 115/136 Verifying : p11-kit-trust-0.24.1-3.fc37.x86_64 116/136 Verifying : publicsuffix-list-dafsa-20210518-5.fc37.noarch 117/136 Verifying : python-pip-wheel-22.2.2-2.fc38.noarch 118/136 Verifying : python-setuptools-wheel-65.5.1-1.fc38.noarch 119/136 Verifying : python3-3.11.0-1.fc38.x86_64 120/136 Verifying : python3-distro-1.8.0-1.fc38.noarch 121/136 Verifying : python3-dnf-4.14.0-1.fc38.noarch 122/136 Verifying : python3-dnf-plugins-core-4.3.1-1.fc38.noarch 123/136 Verifying : python3-gpg-1.17.0-4.fc37.x86_64 124/136 Verifying : python3-hawkey-0.68.0-1.fc38.x86_64 125/136 Verifying : python3-libdnf-0.68.0-1.fc38.x86_64 126/136 Verifying : python3-libs-3.11.0-1.fc38.x86_64 127/136 Verifying : python3-rpm-4.18.0-6.fc38.x86_64 128/136 Verifying : python3-six-1.16.0-8.fc37.noarch 129/136 Verifying : rpm-4.18.0-6.fc38.x86_64 130/136 Verifying : rpm-build-libs-4.18.0-6.fc38.x86_64 131/136 Verifying : rpm-libs-4.18.0-6.fc38.x86_64 132/136 Verifying : rpm-sign-libs-4.18.0-6.fc38.x86_64 133/136 Verifying : shadow-utils-2:4.13-1.fc38.x86_64 134/136 Verifying : systemd-libs-252.1-588.fc38.x86_64 135/136 Verifying : zchunk-libs-1.2.3-1.fc38.x86_64 136/136 Installed products updated. Installed: alternatives-1.21-1.fc38.x86_64 audit-libs-3.0.9-1.fc38.x86_64 basesystem-11-14.fc37.noarch bash-5.2.2-2.fc38.x86_64 bzip2-libs-1.0.8-12.fc38.x86_64 ca-certificates-2022.2.54-5.fc37.noarch coreutils-9.1-8.fc38.x86_64 coreutils-common-9.1-8.fc38.x86_64 crypto-policies-20221110-1.git87a75f4.fc38.noarch curl-7.86.0-2.fc38.x86_64 cyrus-sasl-lib-2.1.28-8.fc38.x86_64 dbus-libs-1:1.14.4-1.fc38.x86_64 dnf-4.14.0-1.fc38.noarch dnf-data-4.14.0-1.fc38.noarch dnf-plugins-core-4.3.1-1.fc38.noarch elfutils-default-yama-scope-0.188-3.fc38.noarch elfutils-libelf-0.188-3.fc38.x86_64 elfutils-libs-0.188-3.fc38.x86_64 expat-2.4.8-2.fc38.x86_64 fedora-gpg-keys-38-0.3.noarch fedora-release-38-0.4.noarch fedora-release-common-38-0.4.noarch fedora-release-identity-basic-38-0.4.noarch fedora-repos-38-0.3.noarch fedora-repos-rawhide-38-0.3.noarch file-libs-5.42-4.fc38.x86_64 filesystem-3.18-2.fc37.x86_64 findutils-1:4.9.0-2.fc38.x86_64 gawk-5.1.1-4.fc38.x86_64 gdbm-libs-1:1.23-2.fc38.x86_64 glib2-2.74.1-2.fc38.x86_64 glibc-2.36.9000-13.fc38.x86_64 glibc-common-2.36.9000-13.fc38.x86_64 glibc-minimal-langpack-2.36.9000-13.fc38.x86_64 gmp-1:6.2.1-3.fc38.x86_64 gnupg2-2.3.8-1.fc38.x86_64 gnutls-3.7.8-9.fc38.x86_64 gpgme-1.17.0-4.fc37.x86_64 grep-3.8-1.fc38.x86_64 ima-evm-utils-1.4-6.fc37.x86_64 json-c-0.16-3.fc38.x86_64 keyutils-libs-1.6.1-5.fc38.x86_64 krb5-libs-1.19.2-11.fc38.1.x86_64 libacl-2.3.1-4.fc38.x86_64 libarchive-3.6.1-2.fc37.x86_64 libassuan-2.5.5-5.fc38.x86_64 libattr-2.5.1-5.fc38.x86_64 libb2-0.98.1-7.fc38.x86_64 libblkid-2.38.1-2.fc38.x86_64 libbrotli-1.0.9-9.fc37.x86_64 libcap-2.48-5.fc38.x86_64 libcap-ng-0.8.3-3.fc37.x86_64 libcom_err-1.46.5-3.fc38.x86_64 libcomps-0.1.18-4.fc38.x86_64 libcurl-7.86.0-2.fc38.x86_64 libdnf-0.68.0-1.fc38.x86_64 libevent-2.1.12-7.fc38.x86_64 libffi-3.4.4-1.fc38.x86_64 libfsverity-1.4-8.fc38.x86_64 libgcc-12.2.1-3.fc38.x86_64 libgcrypt-1.10.1-5.fc38.x86_64 libgomp-12.2.1-3.fc38.x86_64 libgpg-error-1.46-1.fc38.x86_64 libidn2-2.3.4-1.fc38.x86_64 libksba-1.6.2-1.fc38.x86_64 libmodulemd-2.14.0-4.fc37.x86_64 libmount-2.38.1-2.fc38.x86_64 libnghttp2-1.50.0-1.fc38.x86_64 libnsl2-2.0.0-4.fc38.x86_64 libpsl-0.21.1-6.fc38.x86_64 librepo-1.14.4-1.fc38.x86_64 libreport-filesystem-2.17.6-1.fc38.noarch libselinux-3.4-5.fc37.x86_64 libsemanage-3.4-5.fc37.x86_64 libsepol-3.4-3.fc38.x86_64 libsigsegv-2.14-3.fc38.x86_64 libsmartcols-2.38.1-2.fc38.x86_64 libsolv-0.7.22-3.fc37.x86_64 libssh-0.10.4-2.fc38.x86_64 libssh-config-0.10.4-2.fc38.noarch libstdc++-12.2.1-3.fc38.x86_64 libtasn1-4.18.0-3.fc38.x86_64 libtirpc-1.3.3-0.fc38.x86_64 libunistring-1.0-2.fc38.x86_64 libuuid-2.38.1-2.fc38.x86_64 libverto-0.3.2-4.fc38.x86_64 libxcrypt-4.4.30-3.fc38.x86_64 libxml2-2.10.3-2.fc38.x86_64 libyaml-0.2.5-8.fc38.x86_64 libzstd-1.5.2-3.fc37.x86_64 lua-libs-5.4.4-6.fc38.x86_64 lz4-libs-1.9.3-5.fc38.x86_64 mpdecimal-2.5.1-4.fc38.x86_64 mpfr-4.1.0-10.fc38.x86_64 ncurses-base-6.3-3.20220501.fc38.noarch ncurses-libs-6.3-3.20220501.fc38.x86_64 nettle-3.8-2.fc38.x86_64 npth-1.6-10.fc38.x86_64 openldap-2.6.3-1.fc38.x86_64 openssl-libs-1:3.0.5-6.fc38.x86_64 p11-kit-0.24.1-3.fc37.x86_64 p11-kit-trust-0.24.1-3.fc37.x86_64 pcre2-10.40-1.fc38.1.x86_64 pcre2-syntax-10.40-1.fc38.1.noarch popt-1.19-1.fc38.x86_64 publicsuffix-list-dafsa-20210518-5.fc37.noarch python-pip-wheel-22.2.2-2.fc38.noarch python-setuptools-wheel-65.5.1-1.fc38.noarch python3-3.11.0-1.fc38.x86_64 python3-dateutil-1:2.8.2-4.fc38.noarch python3-dbus-1.3.2-1.fc38.x86_64 python3-distro-1.8.0-1.fc38.noarch python3-dnf-4.14.0-1.fc38.noarch python3-dnf-plugins-core-4.3.1-1.fc38.noarch python3-gpg-1.17.0-4.fc37.x86_64 python3-hawkey-0.68.0-1.fc38.x86_64 python3-libcomps-0.1.18-4.fc38.x86_64 python3-libdnf-0.68.0-1.fc38.x86_64 python3-libs-3.11.0-1.fc38.x86_64 python3-rpm-4.18.0-6.fc38.x86_64 python3-six-1.16.0-8.fc37.noarch readline-8.2-2.fc38.x86_64 rpm-4.18.0-6.fc38.x86_64 rpm-build-libs-4.18.0-6.fc38.x86_64 rpm-libs-4.18.0-6.fc38.x86_64 rpm-sign-libs-4.18.0-6.fc38.x86_64 sed-4.8-11.fc38.x86_64 setup-2.14.2-1.fc38.noarch shadow-utils-2:4.13-1.fc38.x86_64 sqlite-libs-3.39.4-1.fc38.x86_64 systemd-libs-252.1-588.fc38.x86_64 tpm2-tss-3.2.0-3.fc38.x86_64 tzdata-2022f-1.fc38.noarch xz-libs-5.2.7-1.fc38.x86_64 zchunk-libs-1.2.3-1.fc38.x86_64 zlib-1.2.12-5.fc38.x86_64 Complete! Finish(bootstrap): dnf install Start(bootstrap): creating root cache Finish(bootstrap): creating root cache Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-1668213019.291541/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 Mock Version: 3.3 INFO: Mock Version: 3.3 Start: dnf install No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 43 kB/s | 3.0 kB 00:00 Copr repository 57 MB/s | 31 MB 00:00 fedora 127 kB/s | 5.7 kB 00:00 Dependencies resolved. ================================================================================ Package Arch Version Repo Size ================================================================================ Installing group/module packages: bash x86_64 5.2.2-2.fc38 copr_base 1.8 M bzip2 x86_64 1.0.8-12.fc38 copr_base 53 k coreutils x86_64 9.1-8.fc38 copr_base 1.1 M cpio x86_64 2.13-13.fc38 copr_base 270 k diffutils x86_64 3.8-3.fc37 fedora 378 k fedora-release-common noarch 38-0.4 fedora 22 k findutils x86_64 1:4.9.0-2.fc38 copr_base 483 k gawk x86_64 5.1.1-4.fc38 copr_base 1.0 M glibc-minimal-langpack x86_64 2.36.9000-13.fc38 fedora 25 k grep x86_64 3.8-1.fc38 copr_base 282 k gzip x86_64 1.12-2.fc38 copr_base 159 k info x86_64 6.8-4.fc38 copr_base 225 k patch x86_64 2.7.6-17.fc38 copr_base 124 k redhat-rpm-config noarch 233-1.fc38 fedora 81 k rpm-build x86_64 4.18.0-6.fc38 fedora 77 k sed x86_64 4.8-11.fc38 copr_base 297 k shadow-utils x86_64 2:4.13-1.fc38 fedora 1.3 M tar x86_64 2:1.34-5.fc38 fedora 885 k unzip x86_64 6.0-58.fc38 copr_base 183 k util-linux x86_64 2.38.1-2.fc38 copr_base 2.3 M which x86_64 2.21-36.fc38 fedora 41 k xz x86_64 5.2.7-1.fc38 copr_base 294 k Installing dependencies: alternatives x86_64 1.21-1.fc38 copr_base 38 k ansible-srpm-macros noarch 1-8.1.fc38 fedora 8.6 k audit-libs x86_64 3.0.9-1.fc38 fedora 116 k authselect x86_64 1.4.0-3.fc37 fedora 144 k authselect-libs x86_64 1.4.0-3.fc37 fedora 248 k basesystem noarch 11-14.fc37 fedora 7.0 k binutils x86_64 2.39-5.fc38 fedora 5.4 M binutils-gold x86_64 2.39-5.fc38 fedora 777 k bzip2-libs x86_64 1.0.8-12.fc38 copr_base 42 k ca-certificates noarch 2022.2.54-5.fc37 fedora 829 k coreutils-common x86_64 9.1-8.fc38 copr_base 2.0 M cracklib x86_64 2.9.7-30.fc38 copr_base 81 k crypto-policies noarch 20221110-1.git87a75f4.fc38 fedora 90 k curl x86_64 7.86.0-2.fc38 fedora 334 k cyrus-sasl-lib x86_64 2.1.28-8.fc38 fedora 792 k debugedit x86_64 5.0-5.fc38 copr_base 77 k dwz x86_64 0.15-1.fc38 fedora 136 k ed x86_64 1.18-2.fc38 copr_base 79 k efi-srpm-macros noarch 5-6.fc38 copr_base 23 k elfutils x86_64 0.188-3.fc38 fedora 529 k elfutils-debuginfod-client x86_64 0.188-3.fc38 fedora 40 k elfutils-default-yama-scope noarch 0.188-3.fc38 fedora 15 k elfutils-libelf x86_64 0.188-3.fc38 fedora 196 k elfutils-libs x86_64 0.188-3.fc38 fedora 257 k fedora-gpg-keys noarch 38-0.3 fedora 125 k fedora-release noarch 38-0.4 fedora 11 k fedora-release-identity-basic noarch 38-0.4 fedora 12 k fedora-repos noarch 38-0.3 fedora 10 k fedora-repos-rawhide noarch 38-0.3 fedora 9.7 k file x86_64 5.42-4.fc38 copr_base 49 k file-libs x86_64 5.42-4.fc38 copr_base 676 k filesystem x86_64 3.18-2.fc37 fedora 1.1 M fonts-srpm-macros noarch 1:2.0.5-9.fc38 fedora 26 k fpc-srpm-macros noarch 1.3-6.fc37 fedora 7.7 k gdb-minimal x86_64 12.1-9.fc38 fedora 3.7 M gdbm-libs x86_64 1:1.23-2.fc38 copr_base 56 k ghc-srpm-macros noarch 1.5.0-7.fc37 fedora 7.8 k glibc x86_64 2.36.9000-13.fc38 fedora 2.1 M glibc-common x86_64 2.36.9000-13.fc38 fedora 304 k glibc-gconv-extra x86_64 2.36.9000-13.fc38 fedora 1.6 M gmp x86_64 1:6.2.1-3.fc38 copr_base 316 k gnat-srpm-macros noarch 4-16.fc37 fedora 8.3 k go-srpm-macros noarch 3.2.0-1.fc38 fedora 27 k jansson x86_64 2.13.1-5.fc38 copr_base 45 k kernel-srpm-macros noarch 1.0-15.fc37 fedora 9.4 k keyutils-libs x86_64 1.6.1-5.fc38 copr_base 32 k krb5-libs x86_64 1.19.2-11.fc38.1 copr_base 724 k libacl x86_64 2.3.1-4.fc38 copr_base 24 k libarchive x86_64 3.6.1-2.fc37 fedora 397 k libattr x86_64 2.5.1-5.fc38 copr_base 18 k libblkid x86_64 2.38.1-2.fc38 copr_base 107 k libbrotli x86_64 1.0.9-9.fc37 fedora 315 k libcap x86_64 2.48-5.fc38 copr_base 67 k libcap-ng x86_64 0.8.3-3.fc37 fedora 33 k libcom_err x86_64 1.46.5-3.fc38 copr_base 26 k libcurl x86_64 7.86.0-2.fc38 fedora 305 k libdb x86_64 5.3.28-53.fc37 fedora 760 k libeconf x86_64 0.4.0-4.fc38 copr_base 28 k libevent x86_64 2.1.12-7.fc38 copr_base 259 k libfdisk x86_64 2.38.1-2.fc38 copr_base 161 k libffi x86_64 3.4.4-1.fc38 fedora 38 k libgcc x86_64 12.2.1-3.fc38 fedora 108 k libgomp x86_64 12.2.1-3.fc38 fedora 295 k libidn2 x86_64 2.3.4-1.fc38 copr_base 154 k libmount x86_64 2.38.1-2.fc38 copr_base 136 k libnghttp2 x86_64 1.50.0-1.fc38 copr_base 75 k libnsl2 x86_64 2.0.0-4.fc38 copr_base 31 k libpkgconf x86_64 1.8.0-3.fc38 copr_base 36 k libpsl x86_64 0.21.1-6.fc38 copr_base 64 k libpwquality x86_64 1.4.4-11.fc38 copr_base 105 k libselinux x86_64 3.4-5.fc37 fedora 86 k libsemanage x86_64 3.4-5.fc37 fedora 120 k libsepol x86_64 3.4-3.fc38 copr_base 322 k libsigsegv x86_64 2.14-3.fc38 copr_base 27 k libsmartcols x86_64 2.38.1-2.fc38 copr_base 65 k libssh x86_64 0.10.4-2.fc38 fedora 209 k libssh-config noarch 0.10.4-2.fc38 fedora 8.8 k libstdc++ x86_64 12.2.1-3.fc38 fedora 799 k libtasn1 x86_64 4.18.0-3.fc38 copr_base 75 k libtirpc x86_64 1.3.3-0.fc38 copr_base 94 k libunistring x86_64 1.0-2.fc38 copr_base 549 k libutempter x86_64 1.2.1-7.fc38 copr_base 26 k libuuid x86_64 2.38.1-2.fc38 copr_base 28 k libverto x86_64 0.3.2-4.fc38 copr_base 21 k libxcrypt x86_64 4.4.30-3.fc38 fedora 118 k libxml2 x86_64 2.10.3-2.fc38 fedora 705 k libzstd x86_64 1.5.2-3.fc37 fedora 294 k lua-libs x86_64 5.4.4-6.fc38 copr_base 132 k lua-srpm-macros noarch 1-7.fc37 fedora 8.8 k lz4-libs x86_64 1.9.3-5.fc38 copr_base 71 k mpfr x86_64 4.1.0-10.fc38 copr_base 331 k ncurses-base noarch 6.3-3.20220501.fc38 copr_base 62 k ncurses-libs x86_64 6.3-3.20220501.fc38 copr_base 329 k nim-srpm-macros noarch 3-7.fc37 fedora 8.4 k ocaml-srpm-macros noarch 7-2.fc37 fedora 13 k openblas-srpm-macros noarch 2-12.fc37 fedora 7.5 k openldap x86_64 2.6.3-1.fc38 fedora 254 k openssl-libs x86_64 1:3.0.5-6.fc38 fedora 2.1 M p11-kit x86_64 0.24.1-3.fc37 fedora 376 k p11-kit-trust x86_64 0.24.1-3.fc37 fedora 138 k package-notes-srpm-macros noarch 0.5-6.fc38 fedora 11 k pam x86_64 1.5.2-14.fc37 fedora 560 k pam-libs x86_64 1.5.2-14.fc37 fedora 58 k pcre2 x86_64 10.40-1.fc38.1 copr_base 237 k pcre2-syntax noarch 10.40-1.fc38.1 copr_base 143 k perl-srpm-macros noarch 1-46.fc37 fedora 8.3 k pkgconf x86_64 1.8.0-3.fc38 copr_base 42 k pkgconf-m4 noarch 1.8.0-3.fc38 copr_base 15 k pkgconf-pkg-config x86_64 1.8.0-3.fc38 copr_base 11 k popt x86_64 1.19-1.fc38 copr_base 59 k publicsuffix-list-dafsa noarch 20210518-5.fc37 fedora 58 k python-srpm-macros noarch 3.11-5.fc38 fedora 24 k qt5-srpm-macros noarch 5.15.7-1.fc38 fedora 7.9 k readline x86_64 8.2-2.fc38 copr_base 211 k rpm x86_64 4.18.0-6.fc38 fedora 572 k rpm-build-libs x86_64 4.18.0-6.fc38 fedora 94 k rpm-libs x86_64 4.18.0-6.fc38 fedora 320 k rpmautospec-rpm-macros noarch 0.3.0-1.fc37 fedora 8.8 k rust-srpm-macros noarch 23-1.fc38 fedora 9.4 k setup noarch 2.14.2-1.fc38 copr_base 145 k sqlite-libs x86_64 3.39.4-1.fc38 copr_base 659 k systemd-libs x86_64 252.1-588.fc38 fedora 631 k tzdata noarch 2022f-1.fc38 copr_base 431 k util-linux-core x86_64 2.38.1-2.fc38 copr_base 455 k xxhash-libs x86_64 0.8.1-3.fc38 copr_base 41 k xz-libs x86_64 5.2.7-1.fc38 copr_base 93 k zip x86_64 3.0-33.fc38 copr_base 260 k zlib x86_64 1.2.12-5.fc38 copr_base 94 k zstd x86_64 1.5.2-3.fc37 fedora 447 k Installing Groups: Buildsystem building group Transaction Summary ================================================================================ Install 151 Packages Total size: 51 M Installed size: 177 M Downloading Packages: [SKIPPED] alternatives-1.21-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] bash-5.2.2-2.fc38.x86_64.rpm: Already downloaded [SKIPPED] bzip2-1.0.8-12.fc38.x86_64.rpm: Already downloaded [SKIPPED] bzip2-libs-1.0.8-12.fc38.x86_64.rpm: Already downloaded [SKIPPED] coreutils-9.1-8.fc38.x86_64.rpm: Already downloaded [SKIPPED] coreutils-common-9.1-8.fc38.x86_64.rpm: Already downloaded [SKIPPED] cpio-2.13-13.fc38.x86_64.rpm: Already downloaded [SKIPPED] cracklib-2.9.7-30.fc38.x86_64.rpm: Already downloaded [SKIPPED] debugedit-5.0-5.fc38.x86_64.rpm: Already downloaded [SKIPPED] ed-1.18-2.fc38.x86_64.rpm: Already downloaded [SKIPPED] efi-srpm-macros-5-6.fc38.noarch.rpm: Already downloaded [SKIPPED] file-5.42-4.fc38.x86_64.rpm: Already downloaded [SKIPPED] file-libs-5.42-4.fc38.x86_64.rpm: Already downloaded [SKIPPED] findutils-4.9.0-2.fc38.x86_64.rpm: Already downloaded [SKIPPED] gawk-5.1.1-4.fc38.x86_64.rpm: Already downloaded [SKIPPED] gdbm-libs-1.23-2.fc38.x86_64.rpm: Already downloaded [SKIPPED] gmp-6.2.1-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] grep-3.8-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] gzip-1.12-2.fc38.x86_64.rpm: Already downloaded [SKIPPED] info-6.8-4.fc38.x86_64.rpm: Already downloaded [SKIPPED] jansson-2.13.1-5.fc38.x86_64.rpm: Already downloaded [SKIPPED] keyutils-libs-1.6.1-5.fc38.x86_64.rpm: Already downloaded [SKIPPED] krb5-libs-1.19.2-11.fc38.1.x86_64.rpm: Already downloaded [SKIPPED] libacl-2.3.1-4.fc38.x86_64.rpm: Already downloaded [SKIPPED] libattr-2.5.1-5.fc38.x86_64.rpm: Already downloaded [SKIPPED] libblkid-2.38.1-2.fc38.x86_64.rpm: Already downloaded [SKIPPED] libcap-2.48-5.fc38.x86_64.rpm: Already downloaded [SKIPPED] libcom_err-1.46.5-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] libeconf-0.4.0-4.fc38.x86_64.rpm: Already downloaded [SKIPPED] libevent-2.1.12-7.fc38.x86_64.rpm: Already downloaded [SKIPPED] libfdisk-2.38.1-2.fc38.x86_64.rpm: Already downloaded [SKIPPED] libidn2-2.3.4-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] libmount-2.38.1-2.fc38.x86_64.rpm: Already downloaded [SKIPPED] libnghttp2-1.50.0-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] libnsl2-2.0.0-4.fc38.x86_64.rpm: Already downloaded [SKIPPED] libpkgconf-1.8.0-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] libpsl-0.21.1-6.fc38.x86_64.rpm: Already downloaded [SKIPPED] libpwquality-1.4.4-11.fc38.x86_64.rpm: Already downloaded [SKIPPED] libsepol-3.4-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] libsigsegv-2.14-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] libsmartcols-2.38.1-2.fc38.x86_64.rpm: Already downloaded [SKIPPED] libtasn1-4.18.0-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] libtirpc-1.3.3-0.fc38.x86_64.rpm: Already downloaded [SKIPPED] libunistring-1.0-2.fc38.x86_64.rpm: Already downloaded [SKIPPED] libutempter-1.2.1-7.fc38.x86_64.rpm: Already downloaded [SKIPPED] libuuid-2.38.1-2.fc38.x86_64.rpm: Already downloaded [SKIPPED] libverto-0.3.2-4.fc38.x86_64.rpm: Already downloaded [SKIPPED] lua-libs-5.4.4-6.fc38.x86_64.rpm: Already downloaded [SKIPPED] lz4-libs-1.9.3-5.fc38.x86_64.rpm: Already downloaded [SKIPPED] mpfr-4.1.0-10.fc38.x86_64.rpm: Already downloaded [SKIPPED] ncurses-base-6.3-3.20220501.fc38.noarch.rpm: Already downloaded [SKIPPED] ncurses-libs-6.3-3.20220501.fc38.x86_64.rpm: Already downloaded [SKIPPED] patch-2.7.6-17.fc38.x86_64.rpm: Already downloaded [SKIPPED] pcre2-10.40-1.fc38.1.x86_64.rpm: Already downloaded [SKIPPED] pcre2-syntax-10.40-1.fc38.1.noarch.rpm: Already downloaded [SKIPPED] pkgconf-1.8.0-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] pkgconf-m4-1.8.0-3.fc38.noarch.rpm: Already downloaded [SKIPPED] pkgconf-pkg-config-1.8.0-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] popt-1.19-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] readline-8.2-2.fc38.x86_64.rpm: Already downloaded [SKIPPED] sed-4.8-11.fc38.x86_64.rpm: Already downloaded [SKIPPED] setup-2.14.2-1.fc38.noarch.rpm: Already downloaded [SKIPPED] sqlite-libs-3.39.4-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] tzdata-2022f-1.fc38.noarch.rpm: Already downloaded [SKIPPED] unzip-6.0-58.fc38.x86_64.rpm: Already downloaded [SKIPPED] util-linux-2.38.1-2.fc38.x86_64.rpm: Already downloaded [SKIPPED] util-linux-core-2.38.1-2.fc38.x86_64.rpm: Already downloaded [SKIPPED] xxhash-libs-0.8.1-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] xz-5.2.7-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] xz-libs-5.2.7-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] zip-3.0-33.fc38.x86_64.rpm: Already downloaded [SKIPPED] zlib-1.2.12-5.fc38.x86_64.rpm: Already downloaded [SKIPPED] ansible-srpm-macros-1-8.1.fc38.noarch.rpm: Already downloaded [SKIPPED] audit-libs-3.0.9-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] authselect-1.4.0-3.fc37.x86_64.rpm: Already downloaded [SKIPPED] authselect-libs-1.4.0-3.fc37.x86_64.rpm: Already downloaded [SKIPPED] basesystem-11-14.fc37.noarch.rpm: Already downloaded [SKIPPED] binutils-2.39-5.fc38.x86_64.rpm: Already downloaded [SKIPPED] binutils-gold-2.39-5.fc38.x86_64.rpm: Already downloaded [SKIPPED] ca-certificates-2022.2.54-5.fc37.noarch.rpm: Already downloaded [SKIPPED] crypto-policies-20221110-1.git87a75f4.fc38.noarch.rpm: Already downloaded [SKIPPED] curl-7.86.0-2.fc38.x86_64.rpm: Already downloaded [SKIPPED] cyrus-sasl-lib-2.1.28-8.fc38.x86_64.rpm: Already downloaded [SKIPPED] diffutils-3.8-3.fc37.x86_64.rpm: Already downloaded [SKIPPED] dwz-0.15-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] elfutils-0.188-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] elfutils-debuginfod-client-0.188-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] elfutils-default-yama-scope-0.188-3.fc38.noarch.rpm: Already downloaded [SKIPPED] elfutils-libelf-0.188-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] elfutils-libs-0.188-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] fedora-gpg-keys-38-0.3.noarch.rpm: Already downloaded [SKIPPED] fedora-release-38-0.4.noarch.rpm: Already downloaded [SKIPPED] fedora-release-common-38-0.4.noarch.rpm: Already downloaded [SKIPPED] fedora-release-identity-basic-38-0.4.noarch.rpm: Already downloaded [SKIPPED] fedora-repos-38-0.3.noarch.rpm: Already downloaded [SKIPPED] fedora-repos-rawhide-38-0.3.noarch.rpm: Already downloaded [SKIPPED] filesystem-3.18-2.fc37.x86_64.rpm: Already downloaded [SKIPPED] fonts-srpm-macros-2.0.5-9.fc38.noarch.rpm: Already downloaded [SKIPPED] fpc-srpm-macros-1.3-6.fc37.noarch.rpm: Already downloaded [SKIPPED] gdb-minimal-12.1-9.fc38.x86_64.rpm: Already downloaded [SKIPPED] ghc-srpm-macros-1.5.0-7.fc37.noarch.rpm: Already downloaded [SKIPPED] glibc-2.36.9000-13.fc38.x86_64.rpm: Already downloaded [SKIPPED] glibc-common-2.36.9000-13.fc38.x86_64.rpm: Already downloaded [SKIPPED] glibc-gconv-extra-2.36.9000-13.fc38.x86_64.rpm: Already downloaded [SKIPPED] glibc-minimal-langpack-2.36.9000-13.fc38.x86_64.rpm: Already downloaded [SKIPPED] gnat-srpm-macros-4-16.fc37.noarch.rpm: Already downloaded [SKIPPED] go-srpm-macros-3.2.0-1.fc38.noarch.rpm: Already downloaded [SKIPPED] kernel-srpm-macros-1.0-15.fc37.noarch.rpm: Already downloaded [SKIPPED] libarchive-3.6.1-2.fc37.x86_64.rpm: Already downloaded [SKIPPED] libbrotli-1.0.9-9.fc37.x86_64.rpm: Already downloaded [SKIPPED] libcap-ng-0.8.3-3.fc37.x86_64.rpm: Already downloaded [SKIPPED] libcurl-7.86.0-2.fc38.x86_64.rpm: Already downloaded [SKIPPED] libdb-5.3.28-53.fc37.x86_64.rpm: Already downloaded [SKIPPED] libffi-3.4.4-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] libgcc-12.2.1-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] libgomp-12.2.1-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] libselinux-3.4-5.fc37.x86_64.rpm: Already downloaded [SKIPPED] libsemanage-3.4-5.fc37.x86_64.rpm: Already downloaded [SKIPPED] libssh-0.10.4-2.fc38.x86_64.rpm: Already downloaded [SKIPPED] libssh-config-0.10.4-2.fc38.noarch.rpm: Already downloaded [SKIPPED] libstdc++-12.2.1-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] libxcrypt-4.4.30-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] libxml2-2.10.3-2.fc38.x86_64.rpm: Already downloaded [SKIPPED] libzstd-1.5.2-3.fc37.x86_64.rpm: Already downloaded [SKIPPED] lua-srpm-macros-1-7.fc37.noarch.rpm: Already downloaded [SKIPPED] nim-srpm-macros-3-7.fc37.noarch.rpm: Already downloaded [SKIPPED] ocaml-srpm-macros-7-2.fc37.noarch.rpm: Already downloaded [SKIPPED] openblas-srpm-macros-2-12.fc37.noarch.rpm: Already downloaded [SKIPPED] openldap-2.6.3-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] openssl-libs-3.0.5-6.fc38.x86_64.rpm: Already downloaded [SKIPPED] p11-kit-0.24.1-3.fc37.x86_64.rpm: Already downloaded [SKIPPED] p11-kit-trust-0.24.1-3.fc37.x86_64.rpm: Already downloaded [SKIPPED] package-notes-srpm-macros-0.5-6.fc38.noarch.rpm: Already downloaded [SKIPPED] pam-1.5.2-14.fc37.x86_64.rpm: Already downloaded [SKIPPED] pam-libs-1.5.2-14.fc37.x86_64.rpm: Already downloaded [SKIPPED] perl-srpm-macros-1-46.fc37.noarch.rpm: Already downloaded [SKIPPED] publicsuffix-list-dafsa-20210518-5.fc37.noarch.rpm: Already downloaded [SKIPPED] python-srpm-macros-3.11-5.fc38.noarch.rpm: Already downloaded [SKIPPED] qt5-srpm-macros-5.15.7-1.fc38.noarch.rpm: Already downloaded [SKIPPED] redhat-rpm-config-233-1.fc38.noarch.rpm: Already downloaded [SKIPPED] rpm-4.18.0-6.fc38.x86_64.rpm: Already downloaded [SKIPPED] rpm-build-4.18.0-6.fc38.x86_64.rpm: Already downloaded [SKIPPED] rpm-build-libs-4.18.0-6.fc38.x86_64.rpm: Already downloaded [SKIPPED] rpm-libs-4.18.0-6.fc38.x86_64.rpm: Already downloaded [SKIPPED] rpmautospec-rpm-macros-0.3.0-1.fc37.noarch.rpm: Already downloaded [SKIPPED] rust-srpm-macros-23-1.fc38.noarch.rpm: Already downloaded [SKIPPED] shadow-utils-4.13-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] systemd-libs-252.1-588.fc38.x86_64.rpm: Already downloaded [SKIPPED] tar-1.34-5.fc38.x86_64.rpm: Already downloaded [SKIPPED] which-2.21-36.fc38.x86_64.rpm: Already downloaded [SKIPPED] zstd-1.5.2-3.fc37.x86_64.rpm: Already downloaded fedora 1.6 MB/s | 1.6 kB 00:00 Importing GPG key 0xEB10B464: Userid : "Fedora (38) " Fingerprint: 6A51 BBAB BA3D 5467 B617 1221 809A 8D7C EB10 B464 From : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-38-primary Key imported successfully fedora 1.6 MB/s | 1.6 kB 00:00 GPG key at file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-38-primary (0xEB10B464) is already installed fedora 1.6 MB/s | 1.6 kB 00:00 Importing GPG key 0x5323552A: Userid : "Fedora (37) " Fingerprint: ACB5 EE4E 831C 74BB 7C16 8D27 F55A D3FB 5323 552A From : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-37-primary Key imported successfully Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. 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filesystem-3.18-2.fc37.x86_64 97/151 Verifying : fonts-srpm-macros-1:2.0.5-9.fc38.noarch 98/151 Verifying : fpc-srpm-macros-1.3-6.fc37.noarch 99/151 Verifying : gdb-minimal-12.1-9.fc38.x86_64 100/151 Verifying : ghc-srpm-macros-1.5.0-7.fc37.noarch 101/151 Verifying : glibc-2.36.9000-13.fc38.x86_64 102/151 Verifying : glibc-common-2.36.9000-13.fc38.x86_64 103/151 Verifying : glibc-gconv-extra-2.36.9000-13.fc38.x86_64 104/151 Verifying : glibc-minimal-langpack-2.36.9000-13.fc38.x86_64 105/151 Verifying : gnat-srpm-macros-4-16.fc37.noarch 106/151 Verifying : go-srpm-macros-3.2.0-1.fc38.noarch 107/151 Verifying : kernel-srpm-macros-1.0-15.fc37.noarch 108/151 Verifying : libarchive-3.6.1-2.fc37.x86_64 109/151 Verifying : libbrotli-1.0.9-9.fc37.x86_64 110/151 Verifying : libcap-ng-0.8.3-3.fc37.x86_64 111/151 Verifying : libcurl-7.86.0-2.fc38.x86_64 112/151 Verifying : libdb-5.3.28-53.fc37.x86_64 113/151 Verifying : libffi-3.4.4-1.fc38.x86_64 114/151 Verifying : libgcc-12.2.1-3.fc38.x86_64 115/151 Verifying : libgomp-12.2.1-3.fc38.x86_64 116/151 Verifying : libselinux-3.4-5.fc37.x86_64 117/151 Verifying : libsemanage-3.4-5.fc37.x86_64 118/151 Verifying : libssh-0.10.4-2.fc38.x86_64 119/151 Verifying : libssh-config-0.10.4-2.fc38.noarch 120/151 Verifying : libstdc++-12.2.1-3.fc38.x86_64 121/151 Verifying : libxcrypt-4.4.30-3.fc38.x86_64 122/151 Verifying : libxml2-2.10.3-2.fc38.x86_64 123/151 Verifying : libzstd-1.5.2-3.fc37.x86_64 124/151 Verifying : lua-srpm-macros-1-7.fc37.noarch 125/151 Verifying : nim-srpm-macros-3-7.fc37.noarch 126/151 Verifying : ocaml-srpm-macros-7-2.fc37.noarch 127/151 Verifying : openblas-srpm-macros-2-12.fc37.noarch 128/151 Verifying : openldap-2.6.3-1.fc38.x86_64 129/151 Verifying : openssl-libs-1:3.0.5-6.fc38.x86_64 130/151 Verifying : p11-kit-0.24.1-3.fc37.x86_64 131/151 Verifying : p11-kit-trust-0.24.1-3.fc37.x86_64 132/151 Verifying : package-notes-srpm-macros-0.5-6.fc38.noarch 133/151 Verifying : pam-1.5.2-14.fc37.x86_64 134/151 Verifying : pam-libs-1.5.2-14.fc37.x86_64 135/151 Verifying : perl-srpm-macros-1-46.fc37.noarch 136/151 Verifying : publicsuffix-list-dafsa-20210518-5.fc37.noarch 137/151 Verifying : python-srpm-macros-3.11-5.fc38.noarch 138/151 Verifying : qt5-srpm-macros-5.15.7-1.fc38.noarch 139/151 Verifying : redhat-rpm-config-233-1.fc38.noarch 140/151 Verifying : rpm-4.18.0-6.fc38.x86_64 141/151 Verifying : rpm-build-4.18.0-6.fc38.x86_64 142/151 Verifying : rpm-build-libs-4.18.0-6.fc38.x86_64 143/151 Verifying : rpm-libs-4.18.0-6.fc38.x86_64 144/151 Verifying : rpmautospec-rpm-macros-0.3.0-1.fc37.noarch 145/151 Verifying : rust-srpm-macros-23-1.fc38.noarch 146/151 Verifying : shadow-utils-2:4.13-1.fc38.x86_64 147/151 Verifying : systemd-libs-252.1-588.fc38.x86_64 148/151 Verifying : tar-2:1.34-5.fc38.x86_64 149/151 Verifying : which-2.21-36.fc38.x86_64 150/151 Verifying : zstd-1.5.2-3.fc37.x86_64 151/151 Installed: alternatives-1.21-1.fc38.x86_64 ansible-srpm-macros-1-8.1.fc38.noarch audit-libs-3.0.9-1.fc38.x86_64 authselect-1.4.0-3.fc37.x86_64 authselect-libs-1.4.0-3.fc37.x86_64 basesystem-11-14.fc37.noarch bash-5.2.2-2.fc38.x86_64 binutils-2.39-5.fc38.x86_64 binutils-gold-2.39-5.fc38.x86_64 bzip2-1.0.8-12.fc38.x86_64 bzip2-libs-1.0.8-12.fc38.x86_64 ca-certificates-2022.2.54-5.fc37.noarch coreutils-9.1-8.fc38.x86_64 coreutils-common-9.1-8.fc38.x86_64 cpio-2.13-13.fc38.x86_64 cracklib-2.9.7-30.fc38.x86_64 crypto-policies-20221110-1.git87a75f4.fc38.noarch curl-7.86.0-2.fc38.x86_64 cyrus-sasl-lib-2.1.28-8.fc38.x86_64 debugedit-5.0-5.fc38.x86_64 diffutils-3.8-3.fc37.x86_64 dwz-0.15-1.fc38.x86_64 ed-1.18-2.fc38.x86_64 efi-srpm-macros-5-6.fc38.noarch elfutils-0.188-3.fc38.x86_64 elfutils-debuginfod-client-0.188-3.fc38.x86_64 elfutils-default-yama-scope-0.188-3.fc38.noarch elfutils-libelf-0.188-3.fc38.x86_64 elfutils-libs-0.188-3.fc38.x86_64 fedora-gpg-keys-38-0.3.noarch fedora-release-38-0.4.noarch fedora-release-common-38-0.4.noarch fedora-release-identity-basic-38-0.4.noarch fedora-repos-38-0.3.noarch fedora-repos-rawhide-38-0.3.noarch file-5.42-4.fc38.x86_64 file-libs-5.42-4.fc38.x86_64 filesystem-3.18-2.fc37.x86_64 findutils-1:4.9.0-2.fc38.x86_64 fonts-srpm-macros-1:2.0.5-9.fc38.noarch fpc-srpm-macros-1.3-6.fc37.noarch gawk-5.1.1-4.fc38.x86_64 gdb-minimal-12.1-9.fc38.x86_64 gdbm-libs-1:1.23-2.fc38.x86_64 ghc-srpm-macros-1.5.0-7.fc37.noarch glibc-2.36.9000-13.fc38.x86_64 glibc-common-2.36.9000-13.fc38.x86_64 glibc-gconv-extra-2.36.9000-13.fc38.x86_64 glibc-minimal-langpack-2.36.9000-13.fc38.x86_64 gmp-1:6.2.1-3.fc38.x86_64 gnat-srpm-macros-4-16.fc37.noarch go-srpm-macros-3.2.0-1.fc38.noarch grep-3.8-1.fc38.x86_64 gzip-1.12-2.fc38.x86_64 info-6.8-4.fc38.x86_64 jansson-2.13.1-5.fc38.x86_64 kernel-srpm-macros-1.0-15.fc37.noarch keyutils-libs-1.6.1-5.fc38.x86_64 krb5-libs-1.19.2-11.fc38.1.x86_64 libacl-2.3.1-4.fc38.x86_64 libarchive-3.6.1-2.fc37.x86_64 libattr-2.5.1-5.fc38.x86_64 libblkid-2.38.1-2.fc38.x86_64 libbrotli-1.0.9-9.fc37.x86_64 libcap-2.48-5.fc38.x86_64 libcap-ng-0.8.3-3.fc37.x86_64 libcom_err-1.46.5-3.fc38.x86_64 libcurl-7.86.0-2.fc38.x86_64 libdb-5.3.28-53.fc37.x86_64 libeconf-0.4.0-4.fc38.x86_64 libevent-2.1.12-7.fc38.x86_64 libfdisk-2.38.1-2.fc38.x86_64 libffi-3.4.4-1.fc38.x86_64 libgcc-12.2.1-3.fc38.x86_64 libgomp-12.2.1-3.fc38.x86_64 libidn2-2.3.4-1.fc38.x86_64 libmount-2.38.1-2.fc38.x86_64 libnghttp2-1.50.0-1.fc38.x86_64 libnsl2-2.0.0-4.fc38.x86_64 libpkgconf-1.8.0-3.fc38.x86_64 libpsl-0.21.1-6.fc38.x86_64 libpwquality-1.4.4-11.fc38.x86_64 libselinux-3.4-5.fc37.x86_64 libsemanage-3.4-5.fc37.x86_64 libsepol-3.4-3.fc38.x86_64 libsigsegv-2.14-3.fc38.x86_64 libsmartcols-2.38.1-2.fc38.x86_64 libssh-0.10.4-2.fc38.x86_64 libssh-config-0.10.4-2.fc38.noarch libstdc++-12.2.1-3.fc38.x86_64 libtasn1-4.18.0-3.fc38.x86_64 libtirpc-1.3.3-0.fc38.x86_64 libunistring-1.0-2.fc38.x86_64 libutempter-1.2.1-7.fc38.x86_64 libuuid-2.38.1-2.fc38.x86_64 libverto-0.3.2-4.fc38.x86_64 libxcrypt-4.4.30-3.fc38.x86_64 libxml2-2.10.3-2.fc38.x86_64 libzstd-1.5.2-3.fc37.x86_64 lua-libs-5.4.4-6.fc38.x86_64 lua-srpm-macros-1-7.fc37.noarch lz4-libs-1.9.3-5.fc38.x86_64 mpfr-4.1.0-10.fc38.x86_64 ncurses-base-6.3-3.20220501.fc38.noarch ncurses-libs-6.3-3.20220501.fc38.x86_64 nim-srpm-macros-3-7.fc37.noarch ocaml-srpm-macros-7-2.fc37.noarch openblas-srpm-macros-2-12.fc37.noarch openldap-2.6.3-1.fc38.x86_64 openssl-libs-1:3.0.5-6.fc38.x86_64 p11-kit-0.24.1-3.fc37.x86_64 p11-kit-trust-0.24.1-3.fc37.x86_64 package-notes-srpm-macros-0.5-6.fc38.noarch pam-1.5.2-14.fc37.x86_64 pam-libs-1.5.2-14.fc37.x86_64 patch-2.7.6-17.fc38.x86_64 pcre2-10.40-1.fc38.1.x86_64 pcre2-syntax-10.40-1.fc38.1.noarch perl-srpm-macros-1-46.fc37.noarch pkgconf-1.8.0-3.fc38.x86_64 pkgconf-m4-1.8.0-3.fc38.noarch pkgconf-pkg-config-1.8.0-3.fc38.x86_64 popt-1.19-1.fc38.x86_64 publicsuffix-list-dafsa-20210518-5.fc37.noarch python-srpm-macros-3.11-5.fc38.noarch qt5-srpm-macros-5.15.7-1.fc38.noarch readline-8.2-2.fc38.x86_64 redhat-rpm-config-233-1.fc38.noarch rpm-4.18.0-6.fc38.x86_64 rpm-build-4.18.0-6.fc38.x86_64 rpm-build-libs-4.18.0-6.fc38.x86_64 rpm-libs-4.18.0-6.fc38.x86_64 rpmautospec-rpm-macros-0.3.0-1.fc37.noarch rust-srpm-macros-23-1.fc38.noarch sed-4.8-11.fc38.x86_64 setup-2.14.2-1.fc38.noarch shadow-utils-2:4.13-1.fc38.x86_64 sqlite-libs-3.39.4-1.fc38.x86_64 systemd-libs-252.1-588.fc38.x86_64 tar-2:1.34-5.fc38.x86_64 tzdata-2022f-1.fc38.noarch unzip-6.0-58.fc38.x86_64 util-linux-2.38.1-2.fc38.x86_64 util-linux-core-2.38.1-2.fc38.x86_64 which-2.21-36.fc38.x86_64 xxhash-libs-0.8.1-3.fc38.x86_64 xz-5.2.7-1.fc38.x86_64 xz-libs-5.2.7-1.fc38.x86_64 zip-3.0-33.fc38.x86_64 zlib-1.2.12-5.fc38.x86_64 zstd-1.5.2-3.fc37.x86_64 Complete! Finish: dnf install Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: publicsuffix-list-dafsa-20210518-5.fc37.noarch efi-srpm-macros-5-6.fc38.noarch libmount-2.38.1-2.fc38.x86_64 libutempter-1.2.1-7.fc38.x86_64 xz-5.2.7-1.fc38.x86_64 file-libs-5.42-4.fc38.x86_64 pcre2-syntax-10.40-1.fc38.1.noarch gawk-5.1.1-4.fc38.x86_64 p11-kit-trust-0.24.1-3.fc37.x86_64 zlib-1.2.12-5.fc38.x86_64 libevent-2.1.12-7.fc38.x86_64 libunistring-1.0-2.fc38.x86_64 ghc-srpm-macros-1.5.0-7.fc37.noarch lz4-libs-1.9.3-5.fc38.x86_64 coreutils-9.1-8.fc38.x86_64 libacl-2.3.1-4.fc38.x86_64 binutils-gold-2.39-5.fc38.x86_64 p11-kit-0.24.1-3.fc37.x86_64 libbrotli-1.0.9-9.fc37.x86_64 lua-libs-5.4.4-6.fc38.x86_64 libcap-ng-0.8.3-3.fc37.x86_64 glibc-common-2.36.9000-13.fc38.x86_64 ed-1.18-2.fc38.x86_64 glibc-gconv-extra-2.36.9000-13.fc38.x86_64 kernel-srpm-macros-1.0-15.fc37.noarch libffi-3.4.4-1.fc38.x86_64 ansible-srpm-macros-1-8.1.fc38.noarch rpm-libs-4.18.0-6.fc38.x86_64 qt5-srpm-macros-5.15.7-1.fc38.noarch libstdc++-12.2.1-3.fc38.x86_64 gdbm-libs-1.23-2.fc38.x86_64 dwz-0.15-1.fc38.x86_64 glibc-minimal-langpack-2.36.9000-13.fc38.x86_64 libcurl-7.86.0-2.fc38.x86_64 gnat-srpm-macros-4-16.fc37.noarch basesystem-11-14.fc37.noarch openblas-srpm-macros-2-12.fc37.noarch bzip2-libs-1.0.8-12.fc38.x86_64 fedora-release-38-0.4.noarch util-linux-2.38.1-2.fc38.x86_64 which-2.21-36.fc38.x86_64 libsepol-3.4-3.fc38.x86_64 bzip2-1.0.8-12.fc38.x86_64 libxcrypt-4.4.30-3.fc38.x86_64 zip-3.0-33.fc38.x86_64 libpkgconf-1.8.0-3.fc38.x86_64 redhat-rpm-config-233-1.fc38.noarch gzip-1.12-2.fc38.x86_64 rpmautospec-rpm-macros-0.3.0-1.fc37.noarch fedora-gpg-keys-38-0.3.noarch rust-srpm-macros-23-1.fc38.noarch libpsl-0.21.1-6.fc38.x86_64 setup-2.14.2-1.fc38.noarch libpwquality-1.4.4-11.fc38.x86_64 systemd-libs-252.1-588.fc38.x86_64 coreutils-common-9.1-8.fc38.x86_64 libtasn1-4.18.0-3.fc38.x86_64 elfutils-0.188-3.fc38.x86_64 libsemanage-3.4-5.fc37.x86_64 libverto-0.3.2-4.fc38.x86_64 libssh-0.10.4-2.fc38.x86_64 rpm-build-4.18.0-6.fc38.x86_64 crypto-policies-20221110-1.git87a75f4.fc38.noarch tzdata-2022f-1.fc38.noarch util-linux-core-2.38.1-2.fc38.x86_64 libcom_err-1.46.5-3.fc38.x86_64 gdb-minimal-12.1-9.fc38.x86_64 elfutils-default-yama-scope-0.188-3.fc38.noarch cpio-2.13-13.fc38.x86_64 fpc-srpm-macros-1.3-6.fc37.noarch xxhash-libs-0.8.1-3.fc38.x86_64 mpfr-4.1.0-10.fc38.x86_64 file-5.42-4.fc38.x86_64 sqlite-libs-3.39.4-1.fc38.x86_64 ocaml-srpm-macros-7-2.fc37.noarch krb5-libs-1.19.2-11.fc38.1.x86_64 libnsl2-2.0.0-4.fc38.x86_64 findutils-4.9.0-2.fc38.x86_64 glibc-2.36.9000-13.fc38.x86_64 audit-libs-3.0.9-1.fc38.x86_64 pam-1.5.2-14.fc37.x86_64 fedora-repos-38-0.3.noarch gpg-pubkey-eb10b464-6202d9c6 rpm-4.18.0-6.fc38.x86_64 authselect-libs-1.4.0-3.fc37.x86_64 filesystem-3.18-2.fc37.x86_64 info-6.8-4.fc38.x86_64 libxml2-2.10.3-2.fc38.x86_64 fedora-release-common-38-0.4.noarch libfdisk-2.38.1-2.fc38.x86_64 pcre2-10.40-1.fc38.1.x86_64 libgcc-12.2.1-3.fc38.x86_64 fedora-repos-rawhide-38-0.3.noarch fedora-release-identity-basic-38-0.4.noarch libattr-2.5.1-5.fc38.x86_64 patch-2.7.6-17.fc38.x86_64 pkgconf-1.8.0-3.fc38.x86_64 libblkid-2.38.1-2.fc38.x86_64 python-srpm-macros-3.11-5.fc38.noarch libdb-5.3.28-53.fc37.x86_64 ncurses-libs-6.3-3.20220501.fc38.x86_64 curl-7.86.0-2.fc38.x86_64 libselinux-3.4-5.fc37.x86_64 package-notes-srpm-macros-0.5-6.fc38.noarch ncurses-base-6.3-3.20220501.fc38.noarch nim-srpm-macros-3-7.fc37.noarch pkgconf-m4-1.8.0-3.fc38.noarch popt-1.19-1.fc38.x86_64 keyutils-libs-1.6.1-5.fc38.x86_64 libeconf-0.4.0-4.fc38.x86_64 rpm-build-libs-4.18.0-6.fc38.x86_64 libnghttp2-1.50.0-1.fc38.x86_64 xz-libs-5.2.7-1.fc38.x86_64 libsigsegv-2.14-3.fc38.x86_64 libtirpc-1.3.3-0.fc38.x86_64 elfutils-libelf-0.188-3.fc38.x86_64 fonts-srpm-macros-2.0.5-9.fc38.noarch libidn2-2.3.4-1.fc38.x86_64 gmp-6.2.1-3.fc38.x86_64 libuuid-2.38.1-2.fc38.x86_64 jansson-2.13.1-5.fc38.x86_64 libcap-2.48-5.fc38.x86_64 pkgconf-pkg-config-1.8.0-3.fc38.x86_64 cracklib-2.9.7-30.fc38.x86_64 elfutils-debuginfod-client-0.188-3.fc38.x86_64 alternatives-1.21-1.fc38.x86_64 authselect-1.4.0-3.fc37.x86_64 cyrus-sasl-lib-2.1.28-8.fc38.x86_64 libgomp-12.2.1-3.fc38.x86_64 ca-certificates-2022.2.54-5.fc37.noarch elfutils-libs-0.188-3.fc38.x86_64 zstd-1.5.2-3.fc37.x86_64 openssl-libs-3.0.5-6.fc38.x86_64 libssh-config-0.10.4-2.fc38.noarch unzip-6.0-58.fc38.x86_64 tar-1.34-5.fc38.x86_64 grep-3.8-1.fc38.x86_64 libarchive-3.6.1-2.fc37.x86_64 sed-4.8-11.fc38.x86_64 gpg-pubkey-5323552a-6112bcdc go-srpm-macros-3.2.0-1.fc38.noarch bash-5.2.2-2.fc38.x86_64 libzstd-1.5.2-3.fc37.x86_64 pam-libs-1.5.2-14.fc37.x86_64 diffutils-3.8-3.fc37.x86_64 binutils-2.39-5.fc38.x86_64 perl-srpm-macros-1-46.fc37.noarch lua-srpm-macros-1-7.fc37.noarch libsmartcols-2.38.1-2.fc38.x86_64 openldap-2.6.3-1.fc38.x86_64 readline-8.2-2.fc38.x86_64 shadow-utils-4.13-1.fc38.x86_64 debugedit-5.0-5.fc38.x86_64 Start: buildsrpm Start: rpmbuild -bs Package glib-2.0 was not found in the pkg-config search path. Perhaps you should add the directory containing `glib-2.0.pc' to the PKG_CONFIG_PATH environment variable Package 'glib-2.0', required by 'virtual:world', not found Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1658534400 Wrote: /builddir/build/SRPMS/wise2-2.4.1-15.fc38.src.rpm Finish: rpmbuild -bs INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-x86_64-1668213019.291541/root/var/log/dnf.rpm.log /var/lib/mock/fedora-rawhide-x86_64-1668213019.291541/root/var/log/dnf.librepo.log /var/lib/mock/fedora-rawhide-x86_64-1668213019.291541/root/var/log/dnf.log Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-du5o0hbf/wise2/wise2.spec) Config(child) 1 minutes 1 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot Finish: run Running (timeout=108000): unbuffer mock --rebuild /var/lib/copr-rpmbuild/results/wise2-2.4.1-15.fc38.src.rpm --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1668213019.291541 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 3.3 starting (python version = 3.10.4, NVR = mock-3.3-1.fc35)... 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/results/wise2-2.4.1-15.fc38.src.rpm) Config(fedora-rawhide-x86_64) Start: clean chroot Finish: clean chroot Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1668213019.291541/root. INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1668213019.291541/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: enabled HW Info plugin Mock Version: 3.3 INFO: Mock Version: 3.3 Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-1668213019.291541/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 Mock Version: 3.3 INFO: Mock Version: 3.3 Start: dnf update No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 34 kB/s | 3.0 kB 00:00 Copr repository 59 MB/s | 31 MB 00:00 fedora 104 kB/s | 5.7 kB 00:00 Dependencies resolved. Nothing to do. Complete! Finish: dnf update Finish: chroot init Start: build phase for wise2-2.4.1-15.fc38.src.rpm Start: build setup for wise2-2.4.1-15.fc38.src.rpm Package glib-2.0 was not found in the pkg-config search path. Perhaps you should add the directory containing `glib-2.0.pc' to the PKG_CONFIG_PATH environment variable Package 'glib-2.0', required by 'virtual:world', not found Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1658534400 Wrote: /builddir/build/SRPMS/wise2-2.4.1-15.fc38.src.rpm No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 36 kB/s | 3.0 kB 00:00 fedora 100 kB/s | 5.7 kB 00:00 Package pkgconf-pkg-config-1.8.0-3.fc38.x86_64 is already installed. Dependencies resolved. ======================================================================================== Package Arch Version Repo Size ======================================================================================== Installing: gcc x86_64 12.2.1-3.fc38 fedora 33 M glib2-devel x86_64 2.74.1-2.fc38 fedora 574 k make x86_64 1:4.4-1.fc38 copr_base 571 k perl x86_64 4:5.36.0-492.fc38 copr_base 16 k strace x86_64 6.0-1.fc38 copr_base 1.4 M Installing dependencies: annobin-docs noarch 10.92-1.fc38 fedora 92 k annobin-plugin-gcc x86_64 10.92-1.fc38 fedora 888 k cpp x86_64 12.2.1-3.fc38 fedora 11 M expat x86_64 2.4.8-2.fc38 copr_base 110 k gc x86_64 8.2.2-1.fc38 copr_base 110 k gcc-c++ x86_64 12.2.1-3.fc38 fedora 13 M gcc-plugin-annobin x86_64 12.2.1-3.fc38 fedora 53 k glib2 x86_64 2.74.1-2.fc38 fedora 2.7 M glibc-devel x86_64 2.36.9000-13.fc38 fedora 42 k glibc-headers-x86 noarch 2.36.9000-13.fc38 fedora 520 k gnupg2 x86_64 2.3.8-1.fc38 copr_base 2.5 M gnutls x86_64 3.7.8-9.fc38 fedora 1.1 M groff-base x86_64 1.22.4-10.fc38 copr_base 1.0 M guile22 x86_64 2.2.7-6.fc38 copr_base 6.4 M kernel-headers x86_64 6.1.0-0.rc4.git0.1.fc38 fedora 1.5 M libassuan x86_64 2.5.5-5.fc38 copr_base 67 k libb2 x86_64 0.98.1-7.fc38 copr_base 25 k libblkid-devel x86_64 2.38.1-2.fc38 copr_base 17 k libffi-devel x86_64 3.4.4-1.fc38 fedora 28 k libgcrypt x86_64 1.10.1-5.fc38 fedora 513 k libgpg-error x86_64 1.46-1.fc38 copr_base 222 k libksba x86_64 1.6.2-1.fc38 copr_base 158 k libmount-devel x86_64 2.38.1-2.fc38 copr_base 19 k libmpc x86_64 1.2.1-5.fc38 copr_base 61 k libselinux-devel x86_64 3.4-5.fc37 fedora 148 k libsepol-devel x86_64 3.4-3.fc38 copr_base 41 k libstdc++-devel x86_64 12.2.1-3.fc38 fedora 2.5 M libtool-ltdl x86_64 2.4.7-2.fc37 fedora 37 k libxcrypt-devel x86_64 4.4.30-3.fc38 fedora 29 k mpdecimal x86_64 2.5.1-4.fc38 copr_base 102 k ncurses x86_64 6.3-3.20220501.fc38 copr_base 404 k nettle x86_64 3.8-2.fc38 copr_base 414 k npth x86_64 1.6-10.fc38 copr_base 25 k pcre2-devel x86_64 10.40-1.fc38.1 copr_base 474 k pcre2-utf16 x86_64 10.40-1.fc38.1 copr_base 216 k pcre2-utf32 x86_64 10.40-1.fc38.1 copr_base 203 k perl-Algorithm-Diff noarch 1.2010-7.fc38 copr_base 48 k perl-Archive-Tar noarch 2.40-490.fc38 copr_base 72 k perl-Archive-Zip noarch 1.68-9.fc38 copr_base 106 k perl-Attribute-Handlers noarch 1.02-492.fc38 copr_base 31 k perl-AutoLoader noarch 5.74-492.fc38 copr_base 25 k perl-AutoSplit noarch 5.74-492.fc38 copr_base 25 k perl-B x86_64 1.83-492.fc38 copr_base 185 k perl-Benchmark noarch 1.23-492.fc38 copr_base 30 k perl-CPAN noarch 2.34-4.fc38 copr_base 558 k perl-CPAN-Meta noarch 2.150010-489.fc38 copr_base 176 k perl-CPAN-Meta-Requirements noarch 2.140-490.fc38 copr_base 32 k perl-CPAN-Meta-YAML noarch 0.018-490.fc38 copr_base 27 k perl-Carp noarch 1.52-489.fc38 copr_base 29 k perl-Class-Struct noarch 0.66-492.fc38 copr_base 26 k perl-Compress-Bzip2 x86_64 2.28-10.fc38 copr_base 68 k perl-Compress-Raw-Bzip2 x86_64 2.201-2.fc38 copr_base 35 k perl-Compress-Raw-Lzma x86_64 2.201-4.fc38 copr_base 49 k perl-Compress-Raw-Zlib x86_64 2.202-3.fc38 copr_base 64 k perl-Config-Extensions noarch 0.03-492.fc38 copr_base 16 k perl-Config-Perl-V noarch 0.34-1.fc38 copr_base 22 k perl-DBM_Filter noarch 0.06-492.fc38 copr_base 35 k perl-DB_File x86_64 1.858-4.fc38 copr_base 82 k perl-Data-Dumper x86_64 2.184-490.fc38 copr_base 57 k perl-Data-OptList noarch 0.112-5.fc38 copr_base 27 k perl-Data-Section noarch 0.200007-17.fc38 copr_base 25 k perl-Devel-PPPort x86_64 3.68-490.fc38 copr_base 219 k perl-Devel-Peek x86_64 1.32-492.fc38 copr_base 36 k perl-Devel-SelfStubber noarch 1.06-492.fc38 copr_base 18 k perl-Devel-Size x86_64 0.83-13.fc38 copr_base 31 k perl-Digest noarch 1.20-489.fc38 copr_base 26 k perl-Digest-MD5 x86_64 2.58-489.fc38 copr_base 36 k perl-Digest-SHA x86_64 1:6.03-1.fc38 copr_base 63 k perl-Digest-SHA1 x86_64 2.13-37.fc38 copr_base 53 k perl-DirHandle noarch 1.05-492.fc38 copr_base 16 k perl-Dumpvalue noarch 2.27-492.fc38 copr_base 22 k perl-DynaLoader x86_64 1.52-492.fc38 copr_base 29 k perl-Encode x86_64 4:3.19-492.fc38 copr_base 1.7 M perl-Encode-devel x86_64 4:3.19-492.fc38 copr_base 42 k perl-English noarch 1.11-492.fc38 copr_base 17 k perl-Env noarch 1.05-489.fc38 copr_base 20 k perl-Errno x86_64 1.36-492.fc38 copr_base 18 k perl-Exporter noarch 5.77-489.fc38 copr_base 32 k perl-ExtUtils-CBuilder noarch 1:0.280236-489.fc38 copr_base 47 k perl-ExtUtils-Command noarch 2:7.64-490.fc38 copr_base 15 k perl-ExtUtils-Constant noarch 0.25-492.fc38 copr_base 50 k perl-ExtUtils-Embed noarch 1.35-492.fc38 copr_base 21 k perl-ExtUtils-Install noarch 2.20-489.fc38 copr_base 45 k perl-ExtUtils-MM-Utils noarch 2:7.64-490.fc38 copr_base 12 k perl-ExtUtils-MakeMaker noarch 2:7.64-490.fc38 copr_base 290 k perl-ExtUtils-Manifest noarch 1:1.73-489.fc38 copr_base 35 k perl-ExtUtils-Miniperl noarch 1.11-492.fc38 copr_base 18 k perl-ExtUtils-ParseXS noarch 1:3.45-489.fc38 copr_base 183 k perl-Fcntl x86_64 1.15-492.fc38 copr_base 24 k perl-File-Basename noarch 2.85-492.fc38 copr_base 21 k perl-File-Compare noarch 1.100.700-492.fc38 copr_base 17 k perl-File-Copy noarch 2.39-492.fc38 copr_base 23 k perl-File-DosGlob x86_64 1.12-492.fc38 copr_base 23 k perl-File-Fetch noarch 1.04-489.fc38 copr_base 31 k perl-File-Find noarch 1.40-492.fc38 copr_base 29 k perl-File-HomeDir noarch 1.006-7.fc38 copr_base 58 k perl-File-Path noarch 2.18-489.fc38 copr_base 36 k perl-File-Temp noarch 1:0.231.100-489.fc38 copr_base 60 k perl-File-Which noarch 1.27-6.fc38 copr_base 22 k perl-File-stat noarch 1.12-492.fc38 copr_base 21 k perl-FileCache noarch 1.10-492.fc38 copr_base 18 k perl-FileHandle noarch 2.03-492.fc38 copr_base 19 k perl-Filter x86_64 2:1.64-1.fc38 copr_base 82 k perl-Filter-Simple noarch 0.96-489.fc38 copr_base 27 k perl-FindBin noarch 1.53-492.fc38 copr_base 17 k perl-GDBM_File x86_64 1:1.23-492.fc38 copr_base 46 k perl-Getopt-Long noarch 1:2.52-489.fc38 copr_base 60 k perl-Getopt-Std noarch 1.13-492.fc38 copr_base 19 k perl-HTTP-Tiny noarch 0.082-1.fc38 copr_base 56 k perl-Hash-Util x86_64 0.28-492.fc38 copr_base 37 k perl-Hash-Util-FieldHash x86_64 1.26-492.fc38 copr_base 42 k perl-I18N-Collate noarch 1.02-492.fc38 copr_base 18 k perl-I18N-LangTags noarch 0.45-492.fc38 copr_base 58 k perl-I18N-Langinfo x86_64 0.21-492.fc38 copr_base 26 k perl-IO x86_64 1.50-492.fc38 copr_base 90 k perl-IO-Compress noarch 2.201-3.fc38 copr_base 263 k perl-IO-Compress-Lzma noarch 2.201-2.fc38 copr_base 74 k perl-IO-Socket-IP noarch 0.41-490.fc38 copr_base 42 k perl-IO-Zlib noarch 1:1.11-489.fc38 copr_base 20 k perl-IPC-Cmd noarch 2:1.04-490.fc38 copr_base 40 k perl-IPC-Open3 noarch 1.22-492.fc38 copr_base 26 k perl-IPC-SysV x86_64 2.09-490.fc38 copr_base 42 k perl-IPC-System-Simple noarch 1.30-9.fc38 copr_base 39 k perl-Importer noarch 0.026-7.fc38 copr_base 40 k perl-JSON-PP noarch 1:4.12-1.fc38 copr_base 68 k perl-Locale-Maketext noarch 1.32-1.fc38 copr_base 95 k perl-Locale-Maketext-Simple noarch 1:0.21-492.fc38 copr_base 21 k perl-MIME-Base64 x86_64 3.16-489.fc38 copr_base 31 k perl-MRO-Compat noarch 0.15-4.fc38 copr_base 26 k perl-Math-BigInt noarch 1:1.9998.37-2.fc38 copr_base 202 k perl-Math-BigInt-FastCalc x86_64 0.501.300-3.fc38 copr_base 28 k perl-Math-BigRat noarch 0.2624-2.fc38 copr_base 42 k perl-Math-Complex noarch 1.59-492.fc38 copr_base 50 k perl-Memoize noarch 1.03-492.fc38 copr_base 60 k perl-Module-Build noarch 2:0.42.31-15.fc37 fedora 264 k perl-Module-CoreList noarch 1:5.20221020-1.fc38 copr_base 85 k perl-Module-CoreList-tools noarch 1:5.20221020-1.fc38 copr_base 19 k perl-Module-Load noarch 1:0.36-489.fc38 copr_base 18 k perl-Module-Load-Conditional noarch 0.74-489.fc38 copr_base 23 k perl-Module-Loaded noarch 1:0.08-492.fc38 copr_base 17 k perl-Module-Metadata noarch 1.000037-489.fc38 copr_base 36 k perl-Module-Signature noarch 0.88-4.fc38 copr_base 84 k perl-NDBM_File x86_64 1.15-492.fc38 copr_base 26 k perl-NEXT noarch 0.69-492.fc38 copr_base 24 k perl-Net noarch 1.03-492.fc38 copr_base 29 k perl-Net-Ping noarch 2.75-2.fc38 fedora 50 k perl-ODBM_File x86_64 1.17-492.fc38 copr_base 26 k perl-Object-HashBase noarch 0.009-10.fc38 copr_base 26 k perl-Opcode x86_64 1.57-492.fc38 copr_base 40 k perl-POSIX x86_64 2.03-492.fc38 copr_base 101 k perl-Package-Generator noarch 1.106-26.fc38 copr_base 24 k perl-Params-Check noarch 1:0.38-489.fc38 copr_base 22 k perl-Params-Util x86_64 1.102-8.fc38 copr_base 34 k perl-PathTools x86_64 3.84-489.fc38 copr_base 85 k perl-Perl-OSType noarch 1.010-490.fc38 copr_base 23 k perl-PerlIO-via-QuotedPrint noarch 0.10-3.fc38 copr_base 22 k perl-Pod-Checker noarch 4:1.75-3.fc38 copr_base 32 k perl-Pod-Escapes noarch 1:1.07-489.fc38 copr_base 20 k perl-Pod-Functions noarch 1.14-492.fc38 copr_base 17 k perl-Pod-Html noarch 1.33-492.fc38 copr_base 35 k perl-Pod-Perldoc noarch 3.28.01-490.fc38 copr_base 84 k perl-Pod-Simple noarch 1:3.43-490.fc38 copr_base 216 k perl-Pod-Usage noarch 4:2.03-3.fc38 copr_base 41 k perl-Safe noarch 2.43-492.fc38 copr_base 28 k perl-Scalar-List-Utils x86_64 5:1.63-489.fc38 copr_base 73 k perl-Search-Dict noarch 1.07-492.fc38 copr_base 16 k perl-SelectSaver noarch 1.02-492.fc38 copr_base 15 k perl-SelfLoader noarch 1.26-492.fc38 copr_base 25 k perl-Socket x86_64 4:2.036-1.fc38 copr_base 56 k perl-Software-License noarch 0.104002-2.fc38 copr_base 133 k perl-Storable x86_64 1:3.26-489.fc38 copr_base 97 k perl-Sub-Exporter noarch 0.988-5.fc38 copr_base 72 k perl-Sub-Install noarch 0.928-33.fc38 copr_base 23 k perl-Symbol noarch 1.09-492.fc38 copr_base 18 k perl-Sys-Hostname x86_64 1.24-492.fc38 copr_base 21 k perl-Sys-Syslog x86_64 0.36-490.fc38 copr_base 47 k perl-Term-ANSIColor noarch 5.01-490.fc38 copr_base 48 k perl-Term-Cap noarch 1.17-489.fc38 copr_base 22 k perl-Term-Complete noarch 1.403-492.fc38 copr_base 16 k perl-Term-ReadLine noarch 1.17-492.fc38 copr_base 22 k perl-Term-Table noarch 0.016-4.fc38 copr_base 35 k perl-Test noarch 1.31-492.fc38 copr_base 32 k perl-Test-Harness noarch 1:3.44-490.fc38 copr_base 269 k perl-Test-Simple noarch 3:1.302191-2.fc38 copr_base 525 k perl-Text-Abbrev noarch 1.02-492.fc38 copr_base 16 k perl-Text-Balanced noarch 2.06-2.fc38 copr_base 50 k perl-Text-Diff noarch 1.45-16.fc38 copr_base 41 k perl-Text-Glob noarch 0.11-18.fc38 copr_base 14 k perl-Text-ParseWords noarch 3.31-489.fc38 copr_base 17 k perl-Text-Tabs+Wrap noarch 2021.0814-489.fc38 copr_base 23 k perl-Text-Template noarch 1.61-1.fc38 copr_base 60 k perl-Thread noarch 3.05-492.fc38 copr_base 21 k perl-Thread-Queue noarch 3.14-489.fc38 copr_base 22 k perl-Thread-Semaphore noarch 2.13-492.fc38 copr_base 19 k perl-Tie noarch 4.6-492.fc38 copr_base 35 k perl-Tie-File noarch 1.06-492.fc38 copr_base 47 k perl-Tie-Memoize noarch 1.1-492.fc38 copr_base 18 k perl-Tie-RefHash noarch 1.40-489.fc38 copr_base 23 k perl-Time noarch 1.03-492.fc38 copr_base 22 k perl-Time-HiRes x86_64 4:1.9770-489.fc38 copr_base 58 k perl-Time-Local noarch 2:1.300-489.fc38 copr_base 34 k perl-Time-Piece x86_64 1.3401-492.fc38 copr_base 45 k perl-URI noarch 5.17-1.fc38 fedora 123 k perl-Unicode-Collate x86_64 1.31-489.fc38 copr_base 734 k perl-Unicode-Normalize x86_64 1.31-489.fc38 copr_base 95 k perl-Unicode-UCD noarch 0.78-492.fc38 copr_base 82 k perl-User-pwent noarch 1.03-492.fc38 copr_base 24 k perl-autodie noarch 2.34-490.fc38 copr_base 95 k perl-autouse noarch 1.11-492.fc38 copr_base 17 k perl-base noarch 2.27-492.fc38 copr_base 20 k perl-bignum noarch 0.66-5.fc38 copr_base 51 k perl-blib noarch 1.07-492.fc38 copr_base 16 k perl-constant noarch 1.33-490.fc38 copr_base 23 k perl-debugger noarch 1.60-492.fc38 copr_base 138 k perl-deprecate noarch 0.04-492.fc38 copr_base 18 k perl-devel x86_64 4:5.36.0-492.fc38 copr_base 699 k perl-diagnostics noarch 1.39-492.fc38 copr_base 214 k perl-doc noarch 5.36.0-492.fc38 copr_base 4.7 M perl-encoding x86_64 4:3.00-492.fc38 copr_base 64 k perl-encoding-warnings noarch 0.13-492.fc38 copr_base 20 k perl-experimental noarch 0.029-1.fc38 copr_base 23 k perl-fields noarch 2.27-492.fc38 copr_base 20 k perl-filetest noarch 1.03-492.fc38 copr_base 18 k perl-if noarch 0.61.000-492.fc38 copr_base 17 k perl-inc-latest noarch 2:0.500-23.fc38 copr_base 24 k perl-interpreter x86_64 4:5.36.0-492.fc38 copr_base 76 k perl-less noarch 0.03-492.fc38 copr_base 17 k perl-lib x86_64 0.65-492.fc38 copr_base 18 k perl-libnet noarch 3.14-490.fc38 copr_base 127 k perl-libnetcfg noarch 4:5.36.0-492.fc38 copr_base 20 k perl-libs x86_64 4:5.36.0-492.fc38 copr_base 2.1 M perl-local-lib noarch 2.000029-3.fc38 copr_base 68 k perl-locale noarch 1.10-492.fc38 copr_base 17 k perl-macros noarch 4:5.36.0-492.fc38 copr_base 15 k perl-meta-notation noarch 5.36.0-492.fc38 copr_base 13 k perl-mro x86_64 1.26-492.fc38 copr_base 32 k perl-open noarch 1.13-492.fc38 copr_base 20 k perl-overload noarch 1.35-492.fc38 copr_base 49 k perl-overloading noarch 0.02-492.fc38 copr_base 16 k perl-parent noarch 1:0.238-489.fc38 copr_base 14 k perl-perlfaq noarch 5.20210520-489.fc38 copr_base 374 k perl-ph x86_64 5.36.0-492.fc38 copr_base 45 k perl-podlators noarch 1:4.14-489.fc38 copr_base 112 k perl-sigtrap noarch 1.10-492.fc38 copr_base 19 k perl-sort noarch 2.05-492.fc38 copr_base 17 k perl-subs noarch 1.04-492.fc38 copr_base 15 k perl-threads x86_64 1:2.27-489.fc38 copr_base 58 k perl-threads-shared x86_64 1.64-489.fc38 copr_base 45 k perl-utils noarch 5.36.0-492.fc38 copr_base 59 k perl-vars noarch 1.05-492.fc38 copr_base 16 k perl-version x86_64 8:0.99.29-490.fc38 copr_base 63 k perl-vmsish noarch 1.04-492.fc38 copr_base 18 k python-pip-wheel noarch 22.2.2-2.fc38 fedora 1.4 M python-setuptools-wheel noarch 65.5.1-1.fc38 fedora 715 k python3 x86_64 3.11.0-1.fc38 fedora 27 k python3-libs x86_64 3.11.0-1.fc38 fedora 9.6 M python3-pyparsing noarch 3.0.9-2.fc37 fedora 262 k sysprof-capture-devel x86_64 3.46.0-1.fc38 fedora 58 k systemtap-sdt-devel x86_64 4.8~pre16650659g6a096a7d-1.fc38 fedora 73 k zlib-devel x86_64 1.2.12-5.fc38 copr_base 45 k Transaction Summary ======================================================================================== Install 265 Packages Total size: 115 M Total download size: 47 M Installed size: 383 M Downloading Packages: [SKIPPED] expat-2.4.8-2.fc38.x86_64.rpm: Already downloaded [SKIPPED] gc-8.2.2-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] guile22-2.2.7-6.fc38.x86_64.rpm: Already downloaded [SKIPPED] libb2-0.98.1-7.fc38.x86_64.rpm: Already downloaded [SKIPPED] libmpc-1.2.1-5.fc38.x86_64.rpm: Already downloaded [SKIPPED] make-4.4-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] mpdecimal-2.5.1-4.fc38.x86_64.rpm: Already downloaded [SKIPPED] nettle-3.8-2.fc38.x86_64.rpm: Already downloaded [SKIPPED] zlib-devel-1.2.12-5.fc38.x86_64.rpm: Already downloaded [SKIPPED] annobin-docs-10.92-1.fc38.noarch.rpm: Already downloaded [SKIPPED] annobin-plugin-gcc-10.92-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] cpp-12.2.1-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] gcc-12.2.1-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] gcc-plugin-annobin-12.2.1-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] glibc-devel-2.36.9000-13.fc38.x86_64.rpm: Already downloaded [SKIPPED] glibc-headers-x86-2.36.9000-13.fc38.noarch.rpm: Already downloaded [SKIPPED] gnutls-3.7.8-9.fc38.x86_64.rpm: Already downloaded [SKIPPED] kernel-headers-6.1.0-0.rc4.git0.1.fc38.x86_64.rpm: Already downloaded [SKIPPED] libtool-ltdl-2.4.7-2.fc37.x86_64.rpm: Already downloaded [SKIPPED] libxcrypt-devel-4.4.30-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] python-pip-wheel-22.2.2-2.fc38.noarch.rpm: Already downloaded [SKIPPED] python-setuptools-wheel-65.5.1-1.fc38.noarch.rpm: Already downloaded [SKIPPED] python3-3.11.0-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] python3-libs-3.11.0-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] python3-pyparsing-3.0.9-2.fc37.noarch.rpm: Already downloaded (26/265): libassuan-2.5.5-5.fc38.x86_64.rpm 512 kB/s | 67 kB 00:00 (27/265): groff-base-1.22.4-10.fc38.x86_64.rpm 5.2 MB/s | 1.0 MB 00:00 (28/265): libblkid-devel-2.38.1-2.fc38.x86_64.r 165 kB/s | 17 kB 00:00 (29/265): libgpg-error-1.46-1.fc38.x86_64.rpm 5.3 MB/s | 222 kB 00:00 (30/265): gnupg2-2.3.8-1.fc38.x86_64.rpm 10 MB/s | 2.5 MB 00:00 (31/265): libksba-1.6.2-1.fc38.x86_64.rpm 8.0 MB/s | 158 kB 00:00 (32/265): libmount-devel-2.38.1-2.fc38.x86_64.r 1.3 MB/s | 19 kB 00:00 (33/265): libsepol-devel-3.4-3.fc38.x86_64.rpm 2.4 MB/s | 41 kB 00:00 (34/265): npth-1.6-10.fc38.x86_64.rpm 1.4 MB/s | 25 kB 00:00 (35/265): ncurses-6.3-3.20220501.fc38.x86_64.rp 8.0 MB/s | 404 kB 00:00 (36/265): pcre2-devel-10.40-1.fc38.1.x86_64.rpm 12 MB/s | 474 kB 00:00 (37/265): pcre2-utf16-10.40-1.fc38.1.x86_64.rpm 5.8 MB/s | 216 kB 00:00 (38/265): pcre2-utf32-10.40-1.fc38.1.x86_64.rpm 12 MB/s | 203 kB 00:00 (39/265): perl-5.36.0-492.fc38.x86_64.rpm 878 kB/s | 16 kB 00:00 (40/265): perl-Algorithm-Diff-1.2010-7.fc38.noa 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perl-vmsish-1.04-492.fc38.noarch.rpm 1.7 MB/s | 18 kB 00:00 (252/265): perl-version-0.99.29-490.fc38.x86_64 3.4 MB/s | 63 kB 00:00 (253/265): strace-6.0-1.fc38.x86_64.rpm 18 MB/s | 1.4 MB 00:00 (254/265): glib2-devel-2.74.1-2.fc38.x86_64.rpm 1.9 MB/s | 574 kB 00:00 (255/265): glib2-2.74.1-2.fc38.x86_64.rpm 7.2 MB/s | 2.7 MB 00:00 (256/265): libffi-devel-3.4.4-1.fc38.x86_64.rpm 660 kB/s | 28 kB 00:00 (257/265): libgcrypt-1.10.1-5.fc38.x86_64.rpm 5.9 MB/s | 513 kB 00:00 (258/265): libselinux-devel-3.4-5.fc37.x86_64.r 2.3 MB/s | 148 kB 00:00 (259/265): gcc-c++-12.2.1-3.fc38.x86_64.rpm 25 MB/s | 13 MB 00:00 (260/265): perl-Module-Build-0.42.31-15.fc37.no 4.1 MB/s | 264 kB 00:00 (261/265): libstdc++-devel-12.2.1-3.fc38.x86_64 34 MB/s | 2.5 MB 00:00 (262/265): perl-Net-Ping-2.75-2.fc38.noarch.rpm 1.2 MB/s | 50 kB 00:00 (263/265): sysprof-capture-devel-3.46.0-1.fc38. 1.5 MB/s | 58 kB 00:00 (264/265): perl-URI-5.17-1.fc38.noarch.rpm 2.7 MB/s | 123 kB 00:00 (265/265): systemtap-sdt-devel-4.8~pre16650659g 1.6 MB/s | 73 kB 00:00 -------------------------------------------------------------------------------- Total 21 MB/s | 47 MB 00:02 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. 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perl-Tie-4.6-492.fc38.noarch 179/265 Verifying : perl-Tie-File-1.06-492.fc38.noarch 180/265 Verifying : perl-Tie-Memoize-1.1-492.fc38.noarch 181/265 Verifying : perl-Tie-RefHash-1.40-489.fc38.noarch 182/265 Verifying : perl-Time-1.03-492.fc38.noarch 183/265 Verifying : perl-Time-HiRes-4:1.9770-489.fc38.x86_64 184/265 Verifying : perl-Time-Local-2:1.300-489.fc38.noarch 185/265 Verifying : perl-Time-Piece-1.3401-492.fc38.x86_64 186/265 Verifying : perl-Unicode-Collate-1.31-489.fc38.x86_64 187/265 Verifying : perl-Unicode-Normalize-1.31-489.fc38.x86_64 188/265 Verifying : perl-Unicode-UCD-0.78-492.fc38.noarch 189/265 Verifying : perl-User-pwent-1.03-492.fc38.noarch 190/265 Verifying : perl-autodie-2.34-490.fc38.noarch 191/265 Verifying : perl-autouse-1.11-492.fc38.noarch 192/265 Verifying : perl-base-2.27-492.fc38.noarch 193/265 Verifying : perl-bignum-0.66-5.fc38.noarch 194/265 Verifying : perl-blib-1.07-492.fc38.noarch 195/265 Verifying : perl-constant-1.33-490.fc38.noarch 196/265 Verifying : perl-debugger-1.60-492.fc38.noarch 197/265 Verifying : perl-deprecate-0.04-492.fc38.noarch 198/265 Verifying : perl-devel-4:5.36.0-492.fc38.x86_64 199/265 Verifying : perl-diagnostics-1.39-492.fc38.noarch 200/265 Verifying : perl-doc-5.36.0-492.fc38.noarch 201/265 Verifying : perl-encoding-4:3.00-492.fc38.x86_64 202/265 Verifying : perl-encoding-warnings-0.13-492.fc38.noarch 203/265 Verifying : perl-experimental-0.029-1.fc38.noarch 204/265 Verifying : perl-fields-2.27-492.fc38.noarch 205/265 Verifying : perl-filetest-1.03-492.fc38.noarch 206/265 Verifying : perl-if-0.61.000-492.fc38.noarch 207/265 Verifying : perl-inc-latest-2:0.500-23.fc38.noarch 208/265 Verifying : perl-interpreter-4:5.36.0-492.fc38.x86_64 209/265 Verifying : perl-less-0.03-492.fc38.noarch 210/265 Verifying : perl-lib-0.65-492.fc38.x86_64 211/265 Verifying : perl-libnet-3.14-490.fc38.noarch 212/265 Verifying : perl-libnetcfg-4:5.36.0-492.fc38.noarch 213/265 Verifying : perl-libs-4:5.36.0-492.fc38.x86_64 214/265 Verifying : perl-local-lib-2.000029-3.fc38.noarch 215/265 Verifying : perl-locale-1.10-492.fc38.noarch 216/265 Verifying : perl-macros-4:5.36.0-492.fc38.noarch 217/265 Verifying : perl-meta-notation-5.36.0-492.fc38.noarch 218/265 Verifying : perl-mro-1.26-492.fc38.x86_64 219/265 Verifying : perl-open-1.13-492.fc38.noarch 220/265 Verifying : perl-overload-1.35-492.fc38.noarch 221/265 Verifying : perl-overloading-0.02-492.fc38.noarch 222/265 Verifying : perl-parent-1:0.238-489.fc38.noarch 223/265 Verifying : perl-perlfaq-5.20210520-489.fc38.noarch 224/265 Verifying : perl-ph-5.36.0-492.fc38.x86_64 225/265 Verifying : perl-podlators-1:4.14-489.fc38.noarch 226/265 Verifying : perl-sigtrap-1.10-492.fc38.noarch 227/265 Verifying : perl-sort-2.05-492.fc38.noarch 228/265 Verifying : perl-subs-1.04-492.fc38.noarch 229/265 Verifying : perl-threads-1:2.27-489.fc38.x86_64 230/265 Verifying : perl-threads-shared-1.64-489.fc38.x86_64 231/265 Verifying : perl-utils-5.36.0-492.fc38.noarch 232/265 Verifying : perl-vars-1.05-492.fc38.noarch 233/265 Verifying : perl-version-8:0.99.29-490.fc38.x86_64 234/265 Verifying : perl-vmsish-1.04-492.fc38.noarch 235/265 Verifying : strace-6.0-1.fc38.x86_64 236/265 Verifying : zlib-devel-1.2.12-5.fc38.x86_64 237/265 Verifying : annobin-docs-10.92-1.fc38.noarch 238/265 Verifying : annobin-plugin-gcc-10.92-1.fc38.x86_64 239/265 Verifying : cpp-12.2.1-3.fc38.x86_64 240/265 Verifying : gcc-12.2.1-3.fc38.x86_64 241/265 Verifying : gcc-c++-12.2.1-3.fc38.x86_64 242/265 Verifying : gcc-plugin-annobin-12.2.1-3.fc38.x86_64 243/265 Verifying : glib2-2.74.1-2.fc38.x86_64 244/265 Verifying : glib2-devel-2.74.1-2.fc38.x86_64 245/265 Verifying : glibc-devel-2.36.9000-13.fc38.x86_64 246/265 Verifying : glibc-headers-x86-2.36.9000-13.fc38.noarch 247/265 Verifying : gnutls-3.7.8-9.fc38.x86_64 248/265 Verifying : kernel-headers-6.1.0-0.rc4.git0.1.fc38.x86_64 249/265 Verifying : libffi-devel-3.4.4-1.fc38.x86_64 250/265 Verifying : libgcrypt-1.10.1-5.fc38.x86_64 251/265 Verifying : libselinux-devel-3.4-5.fc37.x86_64 252/265 Verifying : libstdc++-devel-12.2.1-3.fc38.x86_64 253/265 Verifying : libtool-ltdl-2.4.7-2.fc37.x86_64 254/265 Verifying : libxcrypt-devel-4.4.30-3.fc38.x86_64 255/265 Verifying : perl-Module-Build-2:0.42.31-15.fc37.noarch 256/265 Verifying : perl-Net-Ping-2.75-2.fc38.noarch 257/265 Verifying : perl-URI-5.17-1.fc38.noarch 258/265 Verifying : python-pip-wheel-22.2.2-2.fc38.noarch 259/265 Verifying : python-setuptools-wheel-65.5.1-1.fc38.noarch 260/265 Verifying : python3-3.11.0-1.fc38.x86_64 261/265 Verifying : python3-libs-3.11.0-1.fc38.x86_64 262/265 Verifying : python3-pyparsing-3.0.9-2.fc37.noarch 263/265 Verifying : sysprof-capture-devel-3.46.0-1.fc38.x86_64 264/265 Verifying : systemtap-sdt-devel-4.8~pre16650659g6a096a7d-1.f 265/265 Installed: annobin-docs-10.92-1.fc38.noarch annobin-plugin-gcc-10.92-1.fc38.x86_64 cpp-12.2.1-3.fc38.x86_64 expat-2.4.8-2.fc38.x86_64 gc-8.2.2-1.fc38.x86_64 gcc-12.2.1-3.fc38.x86_64 gcc-c++-12.2.1-3.fc38.x86_64 gcc-plugin-annobin-12.2.1-3.fc38.x86_64 glib2-2.74.1-2.fc38.x86_64 glib2-devel-2.74.1-2.fc38.x86_64 glibc-devel-2.36.9000-13.fc38.x86_64 glibc-headers-x86-2.36.9000-13.fc38.noarch gnupg2-2.3.8-1.fc38.x86_64 gnutls-3.7.8-9.fc38.x86_64 groff-base-1.22.4-10.fc38.x86_64 guile22-2.2.7-6.fc38.x86_64 kernel-headers-6.1.0-0.rc4.git0.1.fc38.x86_64 libassuan-2.5.5-5.fc38.x86_64 libb2-0.98.1-7.fc38.x86_64 libblkid-devel-2.38.1-2.fc38.x86_64 libffi-devel-3.4.4-1.fc38.x86_64 libgcrypt-1.10.1-5.fc38.x86_64 libgpg-error-1.46-1.fc38.x86_64 libksba-1.6.2-1.fc38.x86_64 libmount-devel-2.38.1-2.fc38.x86_64 libmpc-1.2.1-5.fc38.x86_64 libselinux-devel-3.4-5.fc37.x86_64 libsepol-devel-3.4-3.fc38.x86_64 libstdc++-devel-12.2.1-3.fc38.x86_64 libtool-ltdl-2.4.7-2.fc37.x86_64 libxcrypt-devel-4.4.30-3.fc38.x86_64 make-1:4.4-1.fc38.x86_64 mpdecimal-2.5.1-4.fc38.x86_64 ncurses-6.3-3.20220501.fc38.x86_64 nettle-3.8-2.fc38.x86_64 npth-1.6-10.fc38.x86_64 pcre2-devel-10.40-1.fc38.1.x86_64 pcre2-utf16-10.40-1.fc38.1.x86_64 pcre2-utf32-10.40-1.fc38.1.x86_64 perl-4:5.36.0-492.fc38.x86_64 perl-Algorithm-Diff-1.2010-7.fc38.noarch perl-Archive-Tar-2.40-490.fc38.noarch perl-Archive-Zip-1.68-9.fc38.noarch perl-Attribute-Handlers-1.02-492.fc38.noarch perl-AutoLoader-5.74-492.fc38.noarch perl-AutoSplit-5.74-492.fc38.noarch perl-B-1.83-492.fc38.x86_64 perl-Benchmark-1.23-492.fc38.noarch perl-CPAN-2.34-4.fc38.noarch perl-CPAN-Meta-2.150010-489.fc38.noarch perl-CPAN-Meta-Requirements-2.140-490.fc38.noarch perl-CPAN-Meta-YAML-0.018-490.fc38.noarch perl-Carp-1.52-489.fc38.noarch perl-Class-Struct-0.66-492.fc38.noarch perl-Compress-Bzip2-2.28-10.fc38.x86_64 perl-Compress-Raw-Bzip2-2.201-2.fc38.x86_64 perl-Compress-Raw-Lzma-2.201-4.fc38.x86_64 perl-Compress-Raw-Zlib-2.202-3.fc38.x86_64 perl-Config-Extensions-0.03-492.fc38.noarch perl-Config-Perl-V-0.34-1.fc38.noarch perl-DBM_Filter-0.06-492.fc38.noarch perl-DB_File-1.858-4.fc38.x86_64 perl-Data-Dumper-2.184-490.fc38.x86_64 perl-Data-OptList-0.112-5.fc38.noarch perl-Data-Section-0.200007-17.fc38.noarch perl-Devel-PPPort-3.68-490.fc38.x86_64 perl-Devel-Peek-1.32-492.fc38.x86_64 perl-Devel-SelfStubber-1.06-492.fc38.noarch perl-Devel-Size-0.83-13.fc38.x86_64 perl-Digest-1.20-489.fc38.noarch perl-Digest-MD5-2.58-489.fc38.x86_64 perl-Digest-SHA-1:6.03-1.fc38.x86_64 perl-Digest-SHA1-2.13-37.fc38.x86_64 perl-DirHandle-1.05-492.fc38.noarch perl-Dumpvalue-2.27-492.fc38.noarch perl-DynaLoader-1.52-492.fc38.x86_64 perl-Encode-4:3.19-492.fc38.x86_64 perl-Encode-devel-4:3.19-492.fc38.x86_64 perl-English-1.11-492.fc38.noarch perl-Env-1.05-489.fc38.noarch perl-Errno-1.36-492.fc38.x86_64 perl-Exporter-5.77-489.fc38.noarch perl-ExtUtils-CBuilder-1:0.280236-489.fc38.noarch perl-ExtUtils-Command-2:7.64-490.fc38.noarch perl-ExtUtils-Constant-0.25-492.fc38.noarch perl-ExtUtils-Embed-1.35-492.fc38.noarch perl-ExtUtils-Install-2.20-489.fc38.noarch perl-ExtUtils-MM-Utils-2:7.64-490.fc38.noarch perl-ExtUtils-MakeMaker-2:7.64-490.fc38.noarch perl-ExtUtils-Manifest-1:1.73-489.fc38.noarch perl-ExtUtils-Miniperl-1.11-492.fc38.noarch perl-ExtUtils-ParseXS-1:3.45-489.fc38.noarch perl-Fcntl-1.15-492.fc38.x86_64 perl-File-Basename-2.85-492.fc38.noarch perl-File-Compare-1.100.700-492.fc38.noarch perl-File-Copy-2.39-492.fc38.noarch perl-File-DosGlob-1.12-492.fc38.x86_64 perl-File-Fetch-1.04-489.fc38.noarch perl-File-Find-1.40-492.fc38.noarch perl-File-HomeDir-1.006-7.fc38.noarch perl-File-Path-2.18-489.fc38.noarch perl-File-Temp-1:0.231.100-489.fc38.noarch perl-File-Which-1.27-6.fc38.noarch perl-File-stat-1.12-492.fc38.noarch perl-FileCache-1.10-492.fc38.noarch perl-FileHandle-2.03-492.fc38.noarch perl-Filter-2:1.64-1.fc38.x86_64 perl-Filter-Simple-0.96-489.fc38.noarch perl-FindBin-1.53-492.fc38.noarch perl-GDBM_File-1:1.23-492.fc38.x86_64 perl-Getopt-Long-1:2.52-489.fc38.noarch perl-Getopt-Std-1.13-492.fc38.noarch perl-HTTP-Tiny-0.082-1.fc38.noarch perl-Hash-Util-0.28-492.fc38.x86_64 perl-Hash-Util-FieldHash-1.26-492.fc38.x86_64 perl-I18N-Collate-1.02-492.fc38.noarch perl-I18N-LangTags-0.45-492.fc38.noarch perl-I18N-Langinfo-0.21-492.fc38.x86_64 perl-IO-1.50-492.fc38.x86_64 perl-IO-Compress-2.201-3.fc38.noarch perl-IO-Compress-Lzma-2.201-2.fc38.noarch perl-IO-Socket-IP-0.41-490.fc38.noarch perl-IO-Zlib-1:1.11-489.fc38.noarch perl-IPC-Cmd-2:1.04-490.fc38.noarch perl-IPC-Open3-1.22-492.fc38.noarch perl-IPC-SysV-2.09-490.fc38.x86_64 perl-IPC-System-Simple-1.30-9.fc38.noarch perl-Importer-0.026-7.fc38.noarch perl-JSON-PP-1:4.12-1.fc38.noarch perl-Locale-Maketext-1.32-1.fc38.noarch perl-Locale-Maketext-Simple-1:0.21-492.fc38.noarch perl-MIME-Base64-3.16-489.fc38.x86_64 perl-MRO-Compat-0.15-4.fc38.noarch perl-Math-BigInt-1:1.9998.37-2.fc38.noarch perl-Math-BigInt-FastCalc-0.501.300-3.fc38.x86_64 perl-Math-BigRat-0.2624-2.fc38.noarch perl-Math-Complex-1.59-492.fc38.noarch perl-Memoize-1.03-492.fc38.noarch perl-Module-Build-2:0.42.31-15.fc37.noarch perl-Module-CoreList-1:5.20221020-1.fc38.noarch perl-Module-CoreList-tools-1:5.20221020-1.fc38.noarch perl-Module-Load-1:0.36-489.fc38.noarch perl-Module-Load-Conditional-0.74-489.fc38.noarch perl-Module-Loaded-1:0.08-492.fc38.noarch perl-Module-Metadata-1.000037-489.fc38.noarch perl-Module-Signature-0.88-4.fc38.noarch perl-NDBM_File-1.15-492.fc38.x86_64 perl-NEXT-0.69-492.fc38.noarch perl-Net-1.03-492.fc38.noarch perl-Net-Ping-2.75-2.fc38.noarch perl-ODBM_File-1.17-492.fc38.x86_64 perl-Object-HashBase-0.009-10.fc38.noarch perl-Opcode-1.57-492.fc38.x86_64 perl-POSIX-2.03-492.fc38.x86_64 perl-Package-Generator-1.106-26.fc38.noarch perl-Params-Check-1:0.38-489.fc38.noarch perl-Params-Util-1.102-8.fc38.x86_64 perl-PathTools-3.84-489.fc38.x86_64 perl-Perl-OSType-1.010-490.fc38.noarch perl-PerlIO-via-QuotedPrint-0.10-3.fc38.noarch perl-Pod-Checker-4:1.75-3.fc38.noarch perl-Pod-Escapes-1:1.07-489.fc38.noarch perl-Pod-Functions-1.14-492.fc38.noarch perl-Pod-Html-1.33-492.fc38.noarch perl-Pod-Perldoc-3.28.01-490.fc38.noarch perl-Pod-Simple-1:3.43-490.fc38.noarch perl-Pod-Usage-4:2.03-3.fc38.noarch perl-Safe-2.43-492.fc38.noarch perl-Scalar-List-Utils-5:1.63-489.fc38.x86_64 perl-Search-Dict-1.07-492.fc38.noarch perl-SelectSaver-1.02-492.fc38.noarch perl-SelfLoader-1.26-492.fc38.noarch perl-Socket-4:2.036-1.fc38.x86_64 perl-Software-License-0.104002-2.fc38.noarch perl-Storable-1:3.26-489.fc38.x86_64 perl-Sub-Exporter-0.988-5.fc38.noarch perl-Sub-Install-0.928-33.fc38.noarch perl-Symbol-1.09-492.fc38.noarch perl-Sys-Hostname-1.24-492.fc38.x86_64 perl-Sys-Syslog-0.36-490.fc38.x86_64 perl-Term-ANSIColor-5.01-490.fc38.noarch perl-Term-Cap-1.17-489.fc38.noarch perl-Term-Complete-1.403-492.fc38.noarch perl-Term-ReadLine-1.17-492.fc38.noarch perl-Term-Table-0.016-4.fc38.noarch perl-Test-1.31-492.fc38.noarch perl-Test-Harness-1:3.44-490.fc38.noarch perl-Test-Simple-3:1.302191-2.fc38.noarch perl-Text-Abbrev-1.02-492.fc38.noarch perl-Text-Balanced-2.06-2.fc38.noarch perl-Text-Diff-1.45-16.fc38.noarch perl-Text-Glob-0.11-18.fc38.noarch perl-Text-ParseWords-3.31-489.fc38.noarch perl-Text-Tabs+Wrap-2021.0814-489.fc38.noarch perl-Text-Template-1.61-1.fc38.noarch perl-Thread-3.05-492.fc38.noarch perl-Thread-Queue-3.14-489.fc38.noarch perl-Thread-Semaphore-2.13-492.fc38.noarch perl-Tie-4.6-492.fc38.noarch perl-Tie-File-1.06-492.fc38.noarch perl-Tie-Memoize-1.1-492.fc38.noarch perl-Tie-RefHash-1.40-489.fc38.noarch perl-Time-1.03-492.fc38.noarch perl-Time-HiRes-4:1.9770-489.fc38.x86_64 perl-Time-Local-2:1.300-489.fc38.noarch perl-Time-Piece-1.3401-492.fc38.x86_64 perl-URI-5.17-1.fc38.noarch perl-Unicode-Collate-1.31-489.fc38.x86_64 perl-Unicode-Normalize-1.31-489.fc38.x86_64 perl-Unicode-UCD-0.78-492.fc38.noarch perl-User-pwent-1.03-492.fc38.noarch perl-autodie-2.34-490.fc38.noarch perl-autouse-1.11-492.fc38.noarch perl-base-2.27-492.fc38.noarch perl-bignum-0.66-5.fc38.noarch perl-blib-1.07-492.fc38.noarch perl-constant-1.33-490.fc38.noarch perl-debugger-1.60-492.fc38.noarch perl-deprecate-0.04-492.fc38.noarch perl-devel-4:5.36.0-492.fc38.x86_64 perl-diagnostics-1.39-492.fc38.noarch perl-doc-5.36.0-492.fc38.noarch perl-encoding-4:3.00-492.fc38.x86_64 perl-encoding-warnings-0.13-492.fc38.noarch perl-experimental-0.029-1.fc38.noarch perl-fields-2.27-492.fc38.noarch perl-filetest-1.03-492.fc38.noarch perl-if-0.61.000-492.fc38.noarch perl-inc-latest-2:0.500-23.fc38.noarch perl-interpreter-4:5.36.0-492.fc38.x86_64 perl-less-0.03-492.fc38.noarch perl-lib-0.65-492.fc38.x86_64 perl-libnet-3.14-490.fc38.noarch perl-libnetcfg-4:5.36.0-492.fc38.noarch perl-libs-4:5.36.0-492.fc38.x86_64 perl-local-lib-2.000029-3.fc38.noarch perl-locale-1.10-492.fc38.noarch perl-macros-4:5.36.0-492.fc38.noarch perl-meta-notation-5.36.0-492.fc38.noarch perl-mro-1.26-492.fc38.x86_64 perl-open-1.13-492.fc38.noarch perl-overload-1.35-492.fc38.noarch perl-overloading-0.02-492.fc38.noarch perl-parent-1:0.238-489.fc38.noarch perl-perlfaq-5.20210520-489.fc38.noarch perl-ph-5.36.0-492.fc38.x86_64 perl-podlators-1:4.14-489.fc38.noarch perl-sigtrap-1.10-492.fc38.noarch perl-sort-2.05-492.fc38.noarch perl-subs-1.04-492.fc38.noarch perl-threads-1:2.27-489.fc38.x86_64 perl-threads-shared-1.64-489.fc38.x86_64 perl-utils-5.36.0-492.fc38.noarch perl-vars-1.05-492.fc38.noarch perl-version-8:0.99.29-490.fc38.x86_64 perl-vmsish-1.04-492.fc38.noarch python-pip-wheel-22.2.2-2.fc38.noarch python-setuptools-wheel-65.5.1-1.fc38.noarch python3-3.11.0-1.fc38.x86_64 python3-libs-3.11.0-1.fc38.x86_64 python3-pyparsing-3.0.9-2.fc37.noarch strace-6.0-1.fc38.x86_64 sysprof-capture-devel-3.46.0-1.fc38.x86_64 systemtap-sdt-devel-4.8~pre16650659g6a096a7d-1.fc38.x86_64 zlib-devel-1.2.12-5.fc38.x86_64 Complete! Finish: build setup for wise2-2.4.1-15.fc38.src.rpm Start: rpmbuild wise2-2.4.1-15.fc38.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1658534400 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.jAEYwz + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf wise2.4.1 + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/wise2.4.1.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + cd wise2.4.1 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + echo 'Patch #0 (wise2-build.patch):' Patch #0 (wise2-build.patch): + /usr/bin/patch --no-backup-if-mismatch -f -p1 --fuzz=0 patching file src/makefile patching file src/welcome.csh Patch #1 (wise2-isnumber.patch): + echo 'Patch #1 (wise2-isnumber.patch):' + /usr/bin/patch --no-backup-if-mismatch -f -p1 --fuzz=0 patching file src/models/phasemodel.c Patch #2 (wise2-glib2.patch): + echo 'Patch #2 (wise2-glib2.patch):' + /usr/bin/patch --no-backup-if-mismatch -f -p1 --fuzz=0 patching file src/makefile patching file src/snp/makefile patching file src/corba/makefile patching file src/models/makefile patching file src/dnaindex/makefile patching file src/dnaindex/assembly/makefile patching file src/dynlibsrc/makefile patching file src/network/makefile patching file src/other_programs/makefile patching file src/base/makefile patching file src/HMMer2/Makefile Patch #3 (wise2-getline.patch): + echo 'Patch #3 (wise2-getline.patch):' + /usr/bin/patch --no-backup-if-mismatch -f -p1 --fuzz=0 patching file src/HMMer2/sqio.c Patch #4 (wise2-ld--as-needed.patch): + echo 'Patch #4 (wise2-ld--as-needed.patch):' + /usr/bin/patch --no-backup-if-mismatch -f -p1 --fuzz=0 patching file src/models/makefile + chmod a-x src/external/mott/mott_api.c + chmod a-x src/external/mott/mott_api.h + chmod a-x src/external/mott/gaplib.c + chmod a-x src/external/mott/gapstat.h + sed -i s#/usr/local/bin/perl#/usr/bin/perl# docs/gettex.pl + chmod -x test_data/rrm.HMM + for i in base dynlibsrc dyc + cp src/base/LICENSE LICENSE.base + for i in base dynlibsrc dyc + cp src/dynlibsrc/LICENSE LICENSE.dynlibsrc + for i in base dynlibsrc dyc + cp src/dyc/LICENSE LICENSE.dyc + cp src/models/GNULICENSE LICENSE.GPL + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.anpHPb + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd wise2.4.1 + export 'LDFLAGS=-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes' + make -C src CC=gcc 'CFLAGS= -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L' all make: Entering directory '/builddir/build/BUILD/wise2.4.1/src' (cd base ; make CC="gcc" CFLAGS="-c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L" libwisebase.a ) make[1]: Entering directory '/builddir/build/BUILD/wise2.4.1/src/base' gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L wiseconfig.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L wisestring.c wisestring.dy: In function 'Wise2_breakstring_protect': wisestring.dy:632:21: warning: variable 'c' set but not used [-Wunused-but-set-variable] 632 | auto char c; | ^ wisestring.dy: In function 'Wise2_show_text': wisestring.dy:761:23: warning: 'pushpoi' may be used uninitialized [-Wmaybe-uninitialized] 761 | line=pushpoi+1; | ~~~~^~~~~~~~~~ wisestring.dy:741:9: note: 'pushpoi' was declared here 741 | char *pushpoi; | ^~~~~~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L wiseerror.c wiseerror.dy: In function 'Wise2_show_message_stack': wiseerror.dy:176:16: warning: unused variable 'count' [-Wunused-variable] 176 | register int count; | ^~~~~ wiseerror.dy:175:16: warning: unused variable 'j' [-Wunused-variable] 175 | register int j; | ^ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L wisememman.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L wisefile.c wisefile.dy: In function 'Wise2_myfclose': wisefile.dy:72:18: warning: format '%d' expects argument of type 'int', but argument 3 has type 'FILE *' [-Wformat=] 72 | fprintf(stderr,"Closing %d\n",ofp); | ^~~~~~~~~~~~~~ ~~~ | | | FILE * wisefile.dy: In function 'Wise2_append_file_to_path': wisefile.dy:141:10: warning: variable 'runner' set but not used [-Wunused-but-set-variable] 141 | char * runner; | ^~~~~~ wisefile.dy: In function 'Wise2_openfile': wisefile.dy:212:3: warning: 'strncpy' specified bound 12 equals destination size [-Wstringop-truncation] 212 | strncpy(prot,passedprot,12); | ^ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L wiserandom.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L wisetime.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L wiseoverlay.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L wisestreaminterface.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L commandline.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L linesubs.c ar ru libwisebase.a wiseconfig.o wisestring.o wiseerror.o wisememman.o wisefile.o wiserandom.o wisetime.o wiseoverlay.o wisestreaminterface.o commandline.o linesubs.o ar: creating libwisebase.a if test -x /bin/ranlib; then /bin/ranlib libwisebase.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libwisebase.a; else exit 0; fi make[1]: Leaving directory '/builddir/build/BUILD/wise2.4.1/src/base' (cd HMMer2 ; make CC="gcc" CFLAGS="-c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L" libhmmer.a ) make[1]: Entering directory '/builddir/build/BUILD/wise2.4.1/src/HMMer2' gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c alphabet.c alphabet.c: In function 'DigitizeAlignment': alphabet.c:237:9: warning: suggest parentheses around operand of '!' or change '&' to '&&' or '!' to '~' [-Wparentheses] 237 | if (! ainfo->sqinfo[idx].flags & SQINFO_LEN) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ alphabet.c: In function 'P7CountSymbol': alphabet.c:264:13: warning: array subscript has type 'char' [-Wchar-subscripts] 264 | counters[symidx] += wt; | ^ alphabet.c: In function 'SetAlphabet': alphabet.c:108:5: warning: 'strncpy' output truncated before terminating nul copying 17 bytes from a string of the same length [-Wstringop-truncation] 108 | strncpy(Alphabet, "ACGTUNRYMKSWHBVDX", 17); | ^ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c core_algorithms.c core_algorithms.c: In function 'P7ViterbiTrace': core_algorithms.c:453:20: warning: 'k' may be used uninitialized [-Wmaybe-uninitialized] 453 | sc = mmx[i+1][k+1] - hmm->msc[(int) dsq[i+1]][k+1]; | ^ core_algorithms.c:420:7: note: 'k' was declared here 420 | int k; /* position in model (1..M) */ | ^ core_algorithms.c: In function 'P7ParsingViterbi': core_algorithms.c:958:11: warning: 'cur' may be used uninitialized [-Wmaybe-uninitialized] 958 | sc = xmx[cur][XMC] + hmm->xsc[XTC][MOVE]; | ^ core_algorithms.c:846:10: note: 'cur' was declared here 846 | int cur, prv; /* indices for rolling dp matrix */ | ^~~ core_algorithms.c: In function 'P7WeeViterbi': core_algorithms.c:1094:10: warning: 't2' may be used uninitialized [-Wmaybe-uninitialized] 1094 | if (t2 != STC && (s3 - s2 > 1 || (s3 - s2 == 1 && t3 == STT))) | ^ core_algorithms.c:1433:16: note: 't2' was declared here 1433 | enum p7stype t2; | ^~ core_algorithms.c:1081:19: warning: 'k2' may be used uninitialized [-Wmaybe-uninitialized] 1081 | kassign[s2] = k2; | ~~~~~~~~~~~~^~~~ core_algorithms.c:1432:16: note: 'k2' was declared here 1432 | int k2; | ^~ core_algorithms.c:1240:10: warning: 'ret_sc' may be used uninitialized [-Wmaybe-uninitialized] 1240 | return ret_sc; | ^~~~~~ core_algorithms.c:1047:16: note: 'ret_sc' was declared here 1047 | float ret_sc; /* optimal score over complete seq */ | ^~~~~~ core_algorithms.c: In function 'Plan7ESTViterbi': core_algorithms.c:1312:31: warning: 'codon' may be used uninitialized [-Wmaybe-uninitialized] 1312 | mmx[i][k] += hmm->dnam[codon][k]; | ^ core_algorithms.c:1260:9: note: 'codon' was declared here 1260 | int codon; | ^~~~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c debug.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c emit.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c emulation.c In file included from emulation.c:26: version.h:21:14: warning: 'copyright' defined but not used [-Wunused-variable] 21 | static char *copyright = "\ | ^~~~~~~~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c histogram.c histogram.c: In function 'PrintASCIIHistogram': histogram.c:274:15: warning: 'highbound' may be used uninitialized [-Wmaybe-uninitialized] 274 | else if (i == highbound && i != h->highscore) | ^ histogram.c:201:8: note: 'highbound' was declared here 201 | int highbound, highcount; /* cutoffs on the high side */ | ^~~~~~~~~ histogram.c:263:15: warning: 'lowbound' may be used uninitialized [-Wmaybe-uninitialized] 263 | else if (i == lowbound && i != h->lowscore) | ^ histogram.c:200:8: note: 'lowbound' was declared here 200 | int lowbound, lowcount; /* cutoffs on the low side */ | ^~~~~~~~ histogram.c: In function 'EVDMaxLikelyFit': histogram.c:1251:14: warning: 'total' may be used uninitialized [-Wmaybe-uninitialized] 1251 | mu = -1. * log(esum / total) / lambda; | ^~~~~~~~~~~~~~~~~ histogram.c:1171:10: note: 'total' was declared here 1171 | double total; | ^~~~~ histogram.c: In function 'ExtremeValueFitHistogram': histogram.c:659:42: warning: 'z' may be used uninitialized [-Wmaybe-uninitialized] 659 | (mu - (log (-1. * log((double) (n+z-1) / (double)(n+z))) / lambda)); | ~^~ histogram.c:576:10: note: 'z' was declared here 576 | int z; /* number of censored samples */ | ^ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c hmmio.c hmmio.c: In function 'read_asc19hmm': hmmio.c:847:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 847 | if ((s = Getword(fp, sqdARG_INT)) == NULL) goto FAILURE; M = atoi(s); /* model length */ | ^~ hmmio.c:847:64: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 847 | if ((s = Getword(fp, sqdARG_INT)) == NULL) goto FAILURE; M = atoi(s); /* model length */ | ^ hmmio.c:849:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 849 | if ((s = Getword(fp, sqdARG_STRING)) == NULL) goto FAILURE; Plan7SetName(hmm, s); /* name */ | ^~ hmmio.c:849:64: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 849 | if ((s = Getword(fp, sqdARG_STRING)) == NULL) goto FAILURE; Plan7SetName(hmm, s); /* name */ | ^~~~~~~~~~~~ hmmio.c:850:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 850 | if ((s = Getword(fp, sqdARG_STRING)) == NULL) goto FAILURE; s2upper(s); /* alphabet type */ | ^~ hmmio.c:850:64: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 850 | if ((s = Getword(fp, sqdARG_STRING)) == NULL) goto FAILURE; s2upper(s); /* alphabet type */ | ^~~~~~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c mathsupport.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c masks.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c misc.c In file included from misc.c:25: version.h:21:14: warning: 'copyright' defined but not used [-Wunused-variable] 21 | static char *copyright = "\ | ^~~~~~~~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c modelmakers.c modelmakers.c: In function 'P7Maxmodelmaker': modelmakers.c:238:11: warning: variable 't_me' set but not used [-Wunused-but-set-variable] 238 | float t_me; /* estimate for an internal M->E transition */ | ^~~~ modelmakers.c: At top level: modelmakers.c:850:1: warning: 'print_matassign' defined but not used [-Wunused-function] 850 | print_matassign(int *matassign, int alen) | ^~~~~~~~~~~~~~~ modelmakers.c: In function 'P7Maxmodelmaker': modelmakers.c:378:14: warning: 'first' may be used uninitialized [-Wmaybe-uninitialized] 378 | matassign[i] &= ~ASSIGN_INSERT; | ~~~~~~~~~^~~ modelmakers.c:235:11: note: 'first' was declared here 235 | int first, last; /* positions of first and last cols [1..alen] */ | ^~~~~ modelmakers.c:362:27: warning: 'j' may be used uninitialized [-Wmaybe-uninitialized] 362 | if (isgap(aseqs[idx][j-1])) | ^ modelmakers.c:224:14: note: 'j' was declared here 224 | int i, j; /* positions in alignment */ | ^ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c plan7.c plan7.c: In function 'Plan7ESTConfig': plan7.c:816:27: warning: 'tripnull' may be used uninitialized [-Wmaybe-uninitialized] 816 | hmm->dnam[x][k] = Prob2Score(p, tripnull[x]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ plan7.c:793:10: note: 'tripnull' was declared here 793 | float *tripnull; /* UNFINISHED!!! */ | ^~~~~~~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c plan9.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c prior.c prior.c: In function 'P7ReadPrior': prior.c:102:12: warning: implicit declaration of function 'strcmp' [-Wimplicit-function-declaration] 102 | if (strcmp(sptr, "DIRICHLET") == 0) pri->strategy = PRI_DCHLET; | ^~~~~~ prior.c:10:1: note: include '' or provide a declaration of 'strcmp' 9 | #include "funcs.h" +++ |+#include 10 | #include "squid.h" gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c tophits.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c trace.c In file included from trace.c:26: version.h:21:14: warning: 'copyright' defined but not used [-Wunused-variable] 21 | static char *copyright = "\ | ^~~~~~~~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c aligneval.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c alignio.c alignio.c: In function 'ReadAlignedFASTA': alignio.c:143:16: warning: 'aseq' may be used uninitialized [-Wmaybe-uninitialized] 143 | *ret_aseq = aseq; | ~~~~~~~~~~~~~^~~~~~ alignio.c:109:11: note: 'aseq' was declared here 109 | char **aseq; /* aligned sequences */ | ^~~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c cluster.c cluster.c: In function 'Cluster': cluster.c:210:31: warning: 'j' may be used uninitialized [-Wmaybe-uninitialized] 210 | tree[Np-2].right = coord[j]; | ^ cluster.c:152:17: note: 'j' was declared here 152 | int i, j; /* coords of minimum difference */ | ^ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c dayhoff.c dayhoff.c: In function 'ParsePAMFile': dayhoff.c:164:32: warning: 'scale' may be used uninitialized [-Wmaybe-uninitialized] 164 | if (gotscale) *ret_scale = scale; | ~~~~~~~~~~~^~~~~~~ dayhoff.c:74:12: note: 'scale' was declared here 74 | float scale; | ^~~~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c file.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c getopt.c getopt.c: In function 'Getopt': getopt.c:118:25: warning: 'opti' may be used uninitialized [-Wmaybe-uninitialized] 118 | *ret_optname = opt[opti].name; | ^ getopt.c:62:7: note: 'opti' was declared here 62 | int opti; | ^~~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c gnuregex.c gnuregex.c:35: warning: "_GNU_SOURCE" redefined 35 | #define _GNU_SOURCE | : note: this is the location of the previous definition gnuregex.c: In function 'regex_compile': gnuregex.c:1613:18: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] 1613 | if (COMPILE_STACK_EMPTY) | ^ gnuregex.c:1633:18: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] 1633 | if (COMPILE_STACK_EMPTY) | ^ gnuregex.c: In function 're_match_2': gnuregex.c:3752:31: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 3752 | if ((int) old_regend[r] >= (int) regstart[r]) | ^ gnuregex.c:3752:54: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 3752 | if ((int) old_regend[r] >= (int) regstart[r]) | ^ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2394:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' 2394 | PUSH_FAILURE_ITEM (lowest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:3758:19: note: in expansion of macro 'PUSH_FAILURE_POINT' 3758 | PUSH_FAILURE_POINT (p1 + mcnt, d, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2397:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' 2397 | PUSH_FAILURE_ITEM (highest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:3758:19: note: in expansion of macro 'PUSH_FAILURE_POINT' 3758 | PUSH_FAILURE_POINT (p1 + mcnt, d, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2341:11: warning: unused variable 'destination' [-Wunused-variable] 2341 | char *destination; \ | ^~~~~~~~~~~ gnuregex.c:3758:19: note: in expansion of macro 'PUSH_FAILURE_POINT' 3758 | PUSH_FAILURE_POINT (p1 + mcnt, d, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2394:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' 2394 | PUSH_FAILURE_ITEM (lowest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:3905:11: note: in expansion of macro 'PUSH_FAILURE_POINT' 3905 | PUSH_FAILURE_POINT (p + mcnt, NULL, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2397:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' 2397 | PUSH_FAILURE_ITEM (highest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:3905:11: note: in expansion of macro 'PUSH_FAILURE_POINT' 3905 | PUSH_FAILURE_POINT (p + mcnt, NULL, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2341:11: warning: unused variable 'destination' [-Wunused-variable] 2341 | char *destination; \ | ^~~~~~~~~~~ gnuregex.c:3905:11: note: in expansion of macro 'PUSH_FAILURE_POINT' 3905 | PUSH_FAILURE_POINT (p + mcnt, NULL, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2394:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' 2394 | PUSH_FAILURE_ITEM (lowest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:3958:11: note: in expansion of macro 'PUSH_FAILURE_POINT' 3958 | PUSH_FAILURE_POINT (p + mcnt, d, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2397:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' 2397 | PUSH_FAILURE_ITEM (highest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:3958:11: note: in expansion of macro 'PUSH_FAILURE_POINT' 3958 | PUSH_FAILURE_POINT (p + mcnt, d, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2341:11: warning: unused variable 'destination' [-Wunused-variable] 2341 | char *destination; \ | ^~~~~~~~~~~ gnuregex.c:3958:11: note: in expansion of macro 'PUSH_FAILURE_POINT' 3958 | PUSH_FAILURE_POINT (p + mcnt, d, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2482:14: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 2482 | high_reg = (unsigned) POP_FAILURE_ITEM (); \ | ^ gnuregex.c:4064:13: note: in expansion of macro 'POP_FAILURE_POINT' 4064 | POP_FAILURE_POINT (sdummy, pdummy, | ^~~~~~~~~~~~~~~~~ gnuregex.c:2485:13: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 2485 | low_reg = (unsigned) POP_FAILURE_ITEM (); \ | ^ gnuregex.c:4064:13: note: in expansion of macro 'POP_FAILURE_POINT' 4064 | POP_FAILURE_POINT (sdummy, pdummy, | ^~~~~~~~~~~~~~~~~ gnuregex.c:4061:19: warning: variable 'sdummy' set but not used [-Wunused-but-set-variable] 4061 | char *sdummy; | ^~~~~~ gnuregex.c:4060:28: warning: variable 'pdummy' set but not used [-Wunused-but-set-variable] 4060 | unsigned char *pdummy; | ^~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2394:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' 2394 | PUSH_FAILURE_ITEM (lowest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:4097:11: note: in expansion of macro 'PUSH_FAILURE_POINT' 4097 | PUSH_FAILURE_POINT (0, 0, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2397:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' 2397 | PUSH_FAILURE_ITEM (highest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:4097:11: note: in expansion of macro 'PUSH_FAILURE_POINT' 4097 | PUSH_FAILURE_POINT (0, 0, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2341:11: warning: unused variable 'destination' [-Wunused-variable] 2341 | char *destination; \ | ^~~~~~~~~~~ gnuregex.c:4097:11: note: in expansion of macro 'PUSH_FAILURE_POINT' 4097 | PUSH_FAILURE_POINT (0, 0, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2394:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' 2394 | PUSH_FAILURE_ITEM (lowest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:4110:11: note: in expansion of macro 'PUSH_FAILURE_POINT' 4110 | PUSH_FAILURE_POINT (0, 0, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2397:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' 2397 | PUSH_FAILURE_ITEM (highest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:4110:11: note: in expansion of macro 'PUSH_FAILURE_POINT' 4110 | PUSH_FAILURE_POINT (0, 0, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2341:11: warning: unused variable 'destination' [-Wunused-variable] 2341 | char *destination; \ | ^~~~~~~~~~~ gnuregex.c:4110:11: note: in expansion of macro 'PUSH_FAILURE_POINT' 4110 | PUSH_FAILURE_POINT (0, 0, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2482:14: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 2482 | high_reg = (unsigned) POP_FAILURE_ITEM (); \ | ^ gnuregex.c:4278:11: note: in expansion of macro 'POP_FAILURE_POINT' 4278 | POP_FAILURE_POINT (d, p, | ^~~~~~~~~~~~~~~~~ gnuregex.c:2485:13: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 2485 | low_reg = (unsigned) POP_FAILURE_ITEM (); \ | ^ gnuregex.c:4278:11: note: in expansion of macro 'POP_FAILURE_POINT' 4278 | POP_FAILURE_POINT (d, p, | ^~~~~~~~~~~~~~~~~ gnuregex.c: In function 'regex_compile': gnuregex.c:947:34: warning: pointer may be used after 'realloc' [-Wuse-after-free] 947 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:949:42: warning: pointer may be used after 'realloc' [-Wuse-after-free] 949 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:870:14: warning: pointer may be used after 'realloc' [-Wuse-after-free] 870 | while (b - bufp->buffer + (n) > bufp->allocated) \ | ~~^~~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:945:44: warning: pointer may be used after 'realloc' [-Wuse-after-free] 945 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:943:26: warning: pointer may be used after 'realloc' [-Wuse-after-free] 943 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:947:34: warning: pointer may be used after 'realloc' [-Wuse-after-free] 947 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:949:42: warning: pointer may be used after 'realloc' [-Wuse-after-free] 949 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:870:14: warning: pointer may be used after 'realloc' [-Wuse-after-free] 870 | while (b - bufp->buffer + (n) > bufp->allocated) \ | ~~^~~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:945:44: warning: pointer may be used after 'realloc' [-Wuse-after-free] 945 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:943:26: warning: pointer may be used after 'realloc' [-Wuse-after-free] 943 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:947:34: warning: pointer may be used after 'realloc' [-Wuse-after-free] 947 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:949:42: warning: pointer may be used after 'realloc' [-Wuse-after-free] 949 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:870:14: warning: pointer may be used after 'realloc' [-Wuse-after-free] 870 | while (b - bufp->buffer + (n) > bufp->allocated) \ | ~~^~~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:945:44: warning: pointer may be used after 'realloc' [-Wuse-after-free] 945 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:943:26: warning: pointer may be used after 'realloc' [-Wuse-after-free] 943 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:947:34: warning: pointer may be used after 'realloc' [-Wuse-after-free] 947 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:949:42: warning: pointer may be used after 'realloc' [-Wuse-after-free] 949 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:870:14: warning: pointer may be used after 'realloc' [-Wuse-after-free] 870 | while (b - bufp->buffer + (n) > bufp->allocated) \ | ~~^~~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:945:44: warning: pointer may be used after 'realloc' [-Wuse-after-free] 945 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:943:26: warning: pointer may be used after 'realloc' [-Wuse-after-free] 943 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:947:34: warning: pointer may be used after 'realloc' [-Wuse-after-free] 947 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:870:14: warning: pointer may be used after 'realloc' [-Wuse-after-free] 870 | while (b - bufp->buffer + (n) > bufp->allocated) \ | ~~^~~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:945:44: warning: pointer may be used after 'realloc' [-Wuse-after-free] 945 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:943:26: warning: pointer may be used after 'realloc' [-Wuse-after-free] 943 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:947:34: warning: pointer may be used after 'realloc' [-Wuse-after-free] 947 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:949:42: warning: pointer may be used after 'realloc' [-Wuse-after-free] 949 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:870:14: warning: pointer may be used after 'realloc' [-Wuse-after-free] 870 | while (b - bufp->buffer + (n) > bufp->allocated) \ | ~~^~~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:945:44: warning: pointer may be used after 'realloc' [-Wuse-after-free] 945 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:943:26: warning: pointer may be used after 'realloc' [-Wuse-after-free] 943 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:949:42: warning: pointer may be used after 'realloc' [-Wuse-after-free] 949 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:870:14: warning: pointer may be used after 'realloc' [-Wuse-after-free] 870 | while (b - bufp->buffer + (n) > bufp->allocated) \ | ~~^~~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:945:44: warning: pointer may be used after 'realloc' [-Wuse-after-free] 945 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:943:26: warning: pointer may be used after 'realloc' [-Wuse-after-free] 943 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:947:34: warning: pointer may be used after 'realloc' [-Wuse-after-free] 947 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:949:42: warning: pointer may be used after 'realloc' [-Wuse-after-free] 949 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:870:14: warning: pointer may be used after 'realloc' [-Wuse-after-free] 870 | while (b - bufp->buffer + (n) > bufp->allocated) \ | ~~^~~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:945:44: warning: pointer may be used after 'realloc' [-Wuse-after-free] 945 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:943:26: warning: pointer may be used after 'realloc' [-Wuse-after-free] 943 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:947:34: warning: pointer may be used after 'realloc' [-Wuse-after-free] 947 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:949:42: warning: pointer may be used after 'realloc' [-Wuse-after-free] 949 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:870:14: warning: pointer may be used after 'realloc' [-Wuse-after-free] 870 | while (b - bufp->buffer + (n) > bufp->allocated) \ | ~~^~~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:945:44: warning: pointer may be used after 'realloc' [-Wuse-after-free] 945 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:943:26: warning: pointer may be used after 'realloc' [-Wuse-after-free] 943 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:870:14: warning: pointer may be used after 'realloc' [-Wuse-after-free] 870 | while (b - bufp->buffer + (n) > bufp->allocated) \ | ~~^~~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:949:42: warning: pointer may be used after 'realloc' [-Wuse-after-free] 949 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:947:34: warning: pointer may be used after 'realloc' [-Wuse-after-free] 947 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:949:42: warning: pointer may be used after 'realloc' [-Wuse-after-free] 949 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:870:14: warning: pointer may be used after 'realloc' [-Wuse-after-free] 870 | while (b - bufp->buffer + (n) > bufp->allocated) \ | ~~^~~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:945:44: warning: pointer may be used after 'realloc' [-Wuse-after-free] 945 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:943:26: warning: pointer may be used after 'realloc' [-Wuse-after-free] 943 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:947:34: warning: pointer may be used after 'realloc' [-Wuse-after-free] 947 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:870:14: warning: pointer may be used after 'realloc' [-Wuse-after-free] 870 | while (b - bufp->buffer + (n) > bufp->allocated) \ | ~~^~~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:945:44: warning: pointer may be used after 'realloc' [-Wuse-after-free] 945 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:943:26: warning: pointer may be used after 'realloc' [-Wuse-after-free] 943 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:947:34: warning: pointer may be used after 'realloc' [-Wuse-after-free] 947 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:949:42: warning: pointer may be used after 'realloc' [-Wuse-after-free] 949 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:870:14: warning: pointer may be used after 'realloc' [-Wuse-after-free] 870 | while (b - bufp->buffer + (n) > bufp->allocated) \ | ~~^~~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:945:44: warning: pointer may be used after 'realloc' [-Wuse-after-free] 945 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:943:26: warning: pointer may be used after 'realloc' [-Wuse-after-free] 943 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:947:34: warning: pointer may be used after 'realloc' [-Wuse-after-free] 947 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:870:14: warning: pointer may be used after 'realloc' [-Wuse-after-free] 870 | while (b - bufp->buffer + (n) > bufp->allocated) \ | ~~^~~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:945:44: warning: pointer may be used after 'realloc' [-Wuse-after-free] 945 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:947:34: warning: pointer may be used after 'realloc' [-Wuse-after-free] 947 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:949:42: warning: pointer may be used after 'realloc' [-Wuse-after-free] 949 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:870:14: warning: pointer may be used after 'realloc' [-Wuse-after-free] 870 | while (b - bufp->buffer + (n) > bufp->allocated) \ | ~~^~~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:945:44: warning: pointer may be used after 'realloc' [-Wuse-after-free] 945 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:943:26: warning: pointer may be used after 'realloc' [-Wuse-after-free] 943 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:947:34: warning: pointer may be used after 'realloc' [-Wuse-after-free] 947 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:949:42: warning: pointer may be used after 'realloc' [-Wuse-after-free] 949 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:870:14: warning: pointer may be used after 'realloc' [-Wuse-after-free] 870 | while (b - bufp->buffer + (n) > bufp->allocated) \ | ~~^~~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:945:44: warning: pointer may be used after 'realloc' [-Wuse-after-free] 945 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:943:26: warning: pointer may be used after 'realloc' [-Wuse-after-free] 943 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:947:34: warning: pointer may be used after 'realloc' [-Wuse-after-free] 947 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:949:42: warning: pointer may be used after 'realloc' [-Wuse-after-free] 949 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:870:14: warning: pointer may be used after 'realloc' [-Wuse-after-free] 870 | while (b - bufp->buffer + (n) > bufp->allocated) \ | ~~^~~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:945:44: warning: pointer may be used after 'realloc' [-Wuse-after-free] 945 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:943:26: warning: pointer may be used after 'realloc' [-Wuse-after-free] 943 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:947:34: warning: pointer may be used after 'realloc' [-Wuse-after-free] 947 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:949:42: warning: pointer may be used after 'realloc' [-Wuse-after-free] 949 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:870:14: warning: pointer may be used after 'realloc' [-Wuse-after-free] 870 | while (b - bufp->buffer + (n) > bufp->allocated) \ | ~~^~~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:945:44: warning: pointer may be used after 'realloc' [-Wuse-after-free] 945 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:943:26: warning: pointer may be used after 'realloc' [-Wuse-after-free] 943 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:947:34: warning: pointer may be used after 'realloc' [-Wuse-after-free] 947 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:949:42: warning: pointer may be used after 'realloc' [-Wuse-after-free] 949 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:870:14: warning: pointer may be used after 'realloc' [-Wuse-after-free] 870 | while (b - bufp->buffer + (n) > bufp->allocated) \ | ~~^~~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:945:44: warning: pointer may be used after 'realloc' [-Wuse-after-free] 945 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:943:26: warning: pointer may be used after 'realloc' [-Wuse-after-free] 943 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:947:34: warning: pointer may be used after 'realloc' [-Wuse-after-free] 947 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:949:42: warning: pointer may be used after 'realloc' [-Wuse-after-free] 949 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:870:14: warning: pointer may be used after 'realloc' [-Wuse-after-free] 870 | while (b - bufp->buffer + (n) > bufp->allocated) \ | ~~^~~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:945:44: warning: pointer may be used after 'realloc' [-Wuse-after-free] 945 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:943:26: warning: pointer may be used after 'realloc' [-Wuse-after-free] 943 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:947:34: warning: pointer may be used after 'realloc' [-Wuse-after-free] 947 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:949:42: warning: pointer may be used after 'realloc' [-Wuse-after-free] 949 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:870:14: warning: pointer may be used after 'realloc' [-Wuse-after-free] 870 | while (b - bufp->buffer + (n) > bufp->allocated) \ | ~~^~~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:945:44: warning: pointer may be used after 'realloc' [-Wuse-after-free] 945 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:943:26: warning: pointer may be used after 'realloc' [-Wuse-after-free] 943 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:947:34: warning: pointer may be used after 'realloc' [-Wuse-after-free] 947 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:949:42: warning: pointer may be used after 'realloc' [-Wuse-after-free] 949 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:870:14: warning: pointer may be used after 'realloc' [-Wuse-after-free] 870 | while (b - bufp->buffer + (n) > bufp->allocated) \ | ~~^~~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:945:44: warning: pointer may be used after 'realloc' [-Wuse-after-free] 945 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:943:26: warning: pointer may be used after 'realloc' [-Wuse-after-free] 943 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:947:34: warning: pointer may be used after 'realloc' [-Wuse-after-free] 947 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:949:42: warning: pointer may be used after 'realloc' [-Wuse-after-free] 949 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:870:14: warning: pointer may be used after 'realloc' [-Wuse-after-free] 870 | while (b - bufp->buffer + (n) > bufp->allocated) \ | ~~^~~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:945:44: warning: pointer may be used after 'realloc' [-Wuse-after-free] 945 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:943:26: warning: pointer may be used after 'realloc' [-Wuse-after-free] 943 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:947:34: warning: pointer may be used after 'realloc' [-Wuse-after-free] 947 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:949:42: warning: pointer may be used after 'realloc' [-Wuse-after-free] 949 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:870:14: warning: pointer may be used after 'realloc' [-Wuse-after-free] 870 | while (b - bufp->buffer + (n) > bufp->allocated) \ | ~~^~~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:945:44: warning: pointer may be used after 'realloc' [-Wuse-after-free] 945 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:943:26: warning: pointer may be used after 'realloc' [-Wuse-after-free] 943 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:947:34: warning: pointer may be used after 'realloc' [-Wuse-after-free] 947 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:949:42: warning: pointer may be used after 'realloc' [-Wuse-after-free] 949 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:870:14: warning: pointer may be used after 'realloc' [-Wuse-after-free] 870 | while (b - bufp->buffer + (n) > bufp->allocated) \ | ~~^~~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:945:44: warning: pointer may be used after 'realloc' [-Wuse-after-free] 945 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:943:26: warning: pointer may be used after 'realloc' [-Wuse-after-free] 943 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:947:34: warning: pointer may be used after 'realloc' [-Wuse-after-free] 947 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:949:42: warning: pointer may be used after 'realloc' [-Wuse-after-free] 949 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:870:14: warning: pointer may be used after 'realloc' [-Wuse-after-free] 870 | while (b - bufp->buffer + (n) > bufp->allocated) \ | ~~^~~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:945:44: warning: pointer may be used after 'realloc' [-Wuse-after-free] 945 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:943:26: warning: pointer may be used after 'realloc' [-Wuse-after-free] 943 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:947:34: warning: pointer may be used after 'realloc' [-Wuse-after-free] 947 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:949:42: warning: pointer may be used after 'realloc' [-Wuse-after-free] 949 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:870:14: warning: pointer may be used after 'realloc' [-Wuse-after-free] 870 | while (b - bufp->buffer + (n) > bufp->allocated) \ | ~~^~~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:945:44: warning: pointer may be used after 'realloc' [-Wuse-after-free] 945 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:943:26: warning: pointer may be used after 'realloc' [-Wuse-after-free] 943 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ gnuregex.c:936:38: note: call to 'realloc' here 936 | bufp->buffer = (unsigned char *) realloc (bufp->buffer, bufp->allocated);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c interleaved.c interleaved.c: In function 'ReadInterleaved': interleaved.c:427:3: warning: 'blocks' may be used uninitialized [-Wmaybe-uninitialized] 427 | free(blocks); | ^~~~~~~~~~~~ interleaved.c:283:6: note: 'blocks' was declared here 283 | } *blocks; | ^~~~~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c iupac.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c msf.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c revcomp.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c selex.c selex.c: In function 'ReadSELEX': selex.c:445:3: warning: 'blocks' may be used uninitialized [-Wmaybe-uninitialized] 445 | free(blocks); | ^~~~~~~~~~~~ selex.c:74:6: note: 'blocks' was declared here 74 | } *blocks; | ^~~~~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c sqerror.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c sqio.c sqio.c: In function 'SeqfileFormat': sqio.c:1033:11: warning: the comparison will always evaluate as 'false' for the address of 'sp' will never be NULL [-Waddress] 1033 | if (sp==NULL || *sp=='\0') | ^~ sqio.c:1010:9: note: 'sp' declared here 1010 | char sp[LINEBUFLEN]; | ^~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c sre_ctype.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c sre_math.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c sre_string.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c stack.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c translate.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c types.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c weight.c weight.c: In function 'GSCWeights': weight.c:71:21: warning: 'rwt' may be used uninitialized [-Wmaybe-uninitialized] 71 | lwt[i] = rwt[i] = 0.0; | ~~~~~~~^~~~~ weight.c:43:17: note: 'rwt' was declared here 43 | float *lwt, *rwt; /* weight on left, right of this tree node */ | ^~~ weight.c: In function 'VoronoiWeights': weight.c:291:17: warning: 'best' may be used uninitialized [-Wmaybe-uninitialized] 291 | ainfo->wgt[best] += 1.0; | ~~~~~~~~~~^~~~~~ weight.c:163:11: note: 'best' was declared here 163 | int best; /* index of nearest real sequence */ | ^~~~ ar rcv libhmmer.a alphabet.o core_algorithms.o debug.o emit.o emulation.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o prior.o tophits.o trace.o aligneval.o alignio.o cluster.o dayhoff.o file.o getopt.o gnuregex.o interleaved.o iupac.o msf.o revcomp.o selex.o sqerror.o sqio.o sre_ctype.o sre_math.o sre_string.o stack.o translate.o types.o weight.o a - alphabet.o a - core_algorithms.o a - debug.o a - emit.o a - emulation.o a - histogram.o a - hmmio.o a - mathsupport.o a - masks.o a - misc.o a - modelmakers.o a - plan7.o a - plan9.o a - prior.o a - tophits.o a - trace.o a - aligneval.o a - alignio.o a - cluster.o a - dayhoff.o a - file.o a - getopt.o a - gnuregex.o a - interleaved.o a - iupac.o a - msf.o a - revcomp.o a - selex.o a - sqerror.o a - sqio.o a - sre_ctype.o a - sre_math.o a - sre_string.o a - stack.o a - translate.o a - types.o a - weight.o if test -x /bin/ranlib; then /bin/ranlib libhmmer.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libhmmer.a; else exit 0; fi if test -x ranlib; then ranlib libhmmer.a; else exit 0; fi chmod 644 libhmmer.a make[1]: Leaving directory '/builddir/build/BUILD/wise2.4.1/src/HMMer2' (cd dynlibsrc ; make CC="gcc" CFLAGS="-c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L" libdyna.a ) make[1]: Entering directory '/builddir/build/BUILD/wise2.4.1/src/dynlibsrc' gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ packaln.c packaln.dy: In function 'Wise2_read_simple_PackAln': packaln.dy:88:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 88 | fgets(buffer,MAXLINE,ifp); | ^~~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ aln.c aln.dy: In function 'Wise2_swallow_AlnColumn_multiple': aln.dy:580:16: warning: variable 'i' set but not used [-Wunused-but-set-variable] 580 | register int i; | ^ aln.dy: In function 'Wise2_mapped_ascii_AlnBlock': aln.dy:867:19: warning: too many arguments for format [-Wformat-extra-args] 867 | fprintf(ofp," {%3.2f} ",(double)(*score_to_double)(cuml),cuml); | ^~~~~~~~~~~~ aln.dy: In function 'Wise2_read_dumped_ascii_AlnColumn_line': aln.dy:918:11: warning: variable 'base' set but not used [-Wunused-but-set-variable] 918 | char ** base, **bstr; | ^~~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ dnamatrix.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ probability.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ alnrange.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ alnconvert.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ basematrix.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ shattermatrix.c shattermatrix.dy: In function 'Wise2_new_ShatterMatrixComponent': shattermatrix.dy:124:7: warning: unused variable 'j' [-Wunused-variable] 124 | int j; | ^ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ matrixdebug.c matrixdebug.dy: In function 'Wise2_show_PackAln_Debug': matrixdebug.dy:67:7: warning: unused variable 'cum' [-Wunused-variable] 67 | int cum; | ^~~ matrixdebug.dy:66:7: warning: unused variable 'j' [-Wunused-variable] 66 | int j,k; | ^ matrixdebug.dy: In function 'Wise2_user_DebugMatrix': matrixdebug.dy:208:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 208 | fgets(buffer,MAXLINE,in); | ^~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ dpenvelope.c dpenvelope.dy: In function 'Wise2_read_DPEnvelope': dpenvelope.dy:98:11: warning: variable 'base' set but not used [-Wunused-but-set-variable] 98 | char ** base; | ^~~~ dpenvelope.dy: In function 'Wise2_overlap_DPUnit': dpenvelope.dy:68:1: warning: control reaches end of non-void function [-Wreturn-type] 68 | } | ^ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ dbsearchimpl.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ dprunimpl.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ complexsequence.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ complexevalset.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ complexconsensi.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ sequence.c sequence.dy: In function 'Wise2_read_fasta_Sequence': sequence.dy:767:11: warning: unused variable 'seen_weight' [-Wunused-variable] 767 | boolean seen_weight = 0; | ^~~~~~~~~~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ sequencestream.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ seqalign.c seqalign.dy: In function 'Wise2_read_selex_SeqAlign': seqalign.dy:421:25: warning: 'pos' may be used uninitialized [-Wmaybe-uninitialized] 421 | for(seq = buffer+pos;*seq;seq++) { | ~~~~~~^~~~ seqalign.dy:350:7: note: 'pos' was declared here 350 | int pos; | ^~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ hitlist.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ hsp.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ hspstream.c hspstream.dy: In function 'Wise2_typed_LinearHSPmanager_from_Stream': hspstream.dy:109:7: warning: unused variable 'i' [-Wunused-variable] 109 | int i; | ^ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ codon.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ compmat.c compmat.dy: In function 'Wise2_write_Blast_CompMat_alphabet.part.0': compmat.dy:307:3: warning: 'minnumbers' may be used uninitialized [-Wmaybe-uninitialized] 307 | fprintf(ofp,"% d",minnumbers[0]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compmat.dy:268:7: note: 'minnumbers' declared here 268 | int minnumbers[26]; | ^~~~~~~~~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ codonmatrix.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ codonmapper.c codonmapper.dy: In function 'Wise2_new_CodonMapper': codonmapper.dy:379:10: warning: variable 'total_freq' set but not used [-Wunused-but-set-variable] 379 | double total_freq; | ^~~~~~~~~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ sequencedb.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ hscore.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ seqlookup.c seqlookup.dy: In function 'Wise2_load_SequenceDB_SeqLookupLoadPara': seqlookup.dy:143:7: warning: variable 'base' set but not used [-Wunused-but-set-variable] 143 | int base[5]; | ^~~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ arrayseqlookup.c arrayseqlookup.dy: In function 'Wise2_add_ArraySeqHead': arrayseqlookup.dy:294:24: warning: variable 'temp' set but not used [-Wunused-but-set-variable] 294 | ArraySeqLookupUnit * temp; | ^~~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ genericindexresult.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ linkedlist_lookpos.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ singlenumberspace.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ histogram.c histogram.dy: In function 'Wise2_PrintASCIIHistogram': histogram.dy:350:15: warning: 'highbound' may be used uninitialized [-Wmaybe-uninitialized] 350 | else if (i == highbound && i != h->highscore) | ^ histogram.dy:277:8: note: 'highbound' was declared here 277 | int highbound, highcount; /* cutoffs on the high side */ | ^~~~~~~~~ histogram.dy:339:15: warning: 'lowbound' may be used uninitialized [-Wmaybe-uninitialized] 339 | else if (i == lowbound && i != h->lowscore) | ^ histogram.dy:276:8: note: 'lowbound' was declared here 276 | int lowbound, lowcount; /* cutoffs on the low side */ | ^~~~~~~~ histogram.dy: In function 'Wise2_EVDMaxLikelyFit': histogram.dy:1325:14: warning: 'total' may be used uninitialized [-Wmaybe-uninitialized] 1325 | mu = -1. * log(esum / total) / lambda; | ^~~~~~~~~~~~~~~~~ histogram.dy:1245:10: note: 'total' was declared here 1245 | double total; | ^~~~~ histogram.dy: In function 'Wise2_ExtremeValueFitHistogram': histogram.dy:647:42: warning: 'z' may be used uninitialized [-Wmaybe-uninitialized] 647 | (mu - (log (-1. * log((double) (n+z-1) / (double)(n+z))) / lambda)); | ~^~ histogram.dy:545:10: note: 'z' was declared here 545 | int z; /* number of censored samples */ | ^ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ searchstatinterface.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ searchstatlookup.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ proteindb.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ protein.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ pairbase.c pairbase.dy: In function 'Wise2_diagonal_tweak_PairBaseCodonModel': pairbase.dy:48:7: warning: unused variable 'codon_b' [-Wunused-variable] 48 | int codon_b; | ^~~~~~~ pairbase.dy:47:7: warning: unused variable 'codon_a' [-Wunused-variable] 47 | int codon_a; | ^~~~~~~ pairbase.dy: In function 'Wise2_flatten_diagonal_PairBaseCodonModel': pairbase.dy:106:25: warning: 'p' may be used uninitialized [-Wmaybe-uninitialized] 106 | m->codon[p] = 0.0; | ~~~~~~~~~~~~^~~~~ pairbase.dy:96:7: note: 'p' was declared here 96 | int p; | ^ pairbase.dy: In function 'Wise2_flatten_diagonal_PairBaseCodonModelScore': pairbase.dy:148:25: warning: 'p' may be used uninitialized [-Wmaybe-uninitialized] 148 | m->codon[p] = NEGI; pairbase.dy:138:7: note: 'p' was declared here 138 | int p; | ^ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ pairbaseseq.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ genomicdb.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ randommodel.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ randomdb.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ genomic.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ cdna.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ cdnadb.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ dna.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ embl.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ genomicregion.c genomicregion.dy: In function 'Wise2_read_EMBL_FT_into_GenomicRegion': genomicregion.dy:756:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 756 | fgets(buffer,maxlen,ifp); | ^~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ gene.c gene.dy: In function 'Wise2_write_Embl_FT_Gene': gene.dy:404:11: warning: 'tr' may be used uninitialized [-Wmaybe-uninitialized] 404 | if( tr->ex_len > 1 ) { | ~~^~~~~~~~ gene.dy:364:16: note: 'tr' was declared here 364 | Transcript * tr; | ^~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ transcript.c transcript.dy: In function 'Wise2_show_Transcript': transcript.dy:170:23: warning: unused variable 'sf' [-Wunused-variable] 170 | SupportingFeature * sf; | ^~ transcript.dy:169:7: warning: unused variable 'k' [-Wunused-variable] 169 | int k; | ^ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ translation.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ btcanvas.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ asciibtcanvas.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ dynlibcross.c ar ru libdyna.a packaln.o aln.o dnamatrix.o probability.o alnrange.o alnconvert.o basematrix.o shattermatrix.o matrixdebug.o dpenvelope.o dbsearchimpl.o dprunimpl.o complexsequence.o complexevalset.o complexconsensi.o sequence.o sequencestream.o seqalign.o hitlist.o hsp.o hspstream.o codon.o compmat.o codonmatrix.o codonmapper.o sequencedb.o hscore.o seqlookup.o arrayseqlookup.o genericindexresult.o linkedlist_lookpos.o singlenumberspace.o histogram.o searchstatinterface.o searchstatlookup.o proteindb.o protein.o pairbase.o pairbaseseq.o genomicdb.o randommodel.o randomdb.o genomic.o cdna.o cdnadb.o dna.o embl.o genomicregion.o gene.o transcript.o translation.o btcanvas.o asciibtcanvas.o dynlibcross.o ar: creating libdyna.a if test -x /bin/ranlib; then /bin/ranlib libdyna.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libdyna.a; else exit 0; fi make[1]: Leaving directory '/builddir/build/BUILD/wise2.4.1/src/dynlibsrc' (cd dynlibsrc ; make CC="gcc" CFLAGS="-c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L" libdyna_glib.a ) make[1]: Entering directory '/builddir/build/BUILD/wise2.4.1/src/dynlibsrc' gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ subseqhash.c subseqhash.dy: In function 'Wise2_is_populated_subseqhash_ghash': subseqhash.dy:111:29: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 111 | if( g_hash_table_lookup(h,(gconstpointer)seq_number) == NULL ) { | ^ subseqhash.dy: In function 'Wise2_lookup_subseqhash_ghash': subseqhash.dy:128:85: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 128 | return new_linkedl_SeqLookupResultInterface((SeqLookupPos *)g_hash_table_lookup(h,(gconstpointer)seq_number)); | ^ subseqhash.dy: In function 'Wise2_add_seq_subseqhash_ghash': subseqhash.dy:160:54: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 160 | if((ret = (SeqLookupPos *) g_hash_table_lookup(h,(gconstpointer)seq_number)) == NULL ) { | ^ subseqhash.dy:161:29: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 161 | g_hash_table_insert(h,(gpointer)seq_number,p); | ^ subseqhash.dy: In function 'Wise2_add_direct_number_subseqhash_ghash': subseqhash.dy:188:52: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 188 | if((ret = (SeqLookupPos *) g_hash_table_lookup(h,(gconstpointer)seq_number)) == NULL ) { | ^ subseqhash.dy:189:27: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 189 | g_hash_table_insert(h,(gpointer)seq_number,p); | ^ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ intallocator.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ proteinstreamedindex.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ shadowseq.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ shadowseqindex.c shadowseqindex.dy: In function 'Wise2_dump_stats_ShadowSequenceIndex': shadowseqindex.dy:285:15: warning: format '%f' expects argument of type 'double', but argument 4 has type 'long unsigned int' [-Wformat=] 285 | fprintf(ofp,"Head memory %d [%.2f Mbytes]\n",total_head,(total_head*sizeof(ShadowArraySeqHead))/100000); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long unsigned int gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ hsphandler.c hsphandler.dy: In function 'Wise2_truncated_LinearHSPmanager': hsphandler.dy:278:13: warning: variable 'worst' set but not used [-Wunused-but-set-variable] 278 | HSPset ** worst; | ^~~~~ hsphandler.dy: In function 'Wise2_new_consistent_HSPset': hsphandler.dy:342:7: warning: variable 'eaten' set but not used [-Wunused-but-set-variable] 342 | int eaten; | ^~~~~ hsphandler.dy: In function 'Wise2_new_LinearHSPmanager_simple_heuristic': hsphandler.dy:387:7: warning: unused variable 'j' [-Wunused-variable] 387 | int j; | ^ hsphandler.dy:386:7: warning: unused variable 'i' [-Wunused-variable] 386 | int i; | ^ hsphandler.dy: In function 'Wise2_new_HSP_QuerySeqHSP': hsphandler.dy:786:15: warning: variable 'pause_j' set but not used [-Wunused-but-set-variable] 786 | int pause_i,pause_j; | ^~~~~~~ hsphandler.dy:786:7: warning: variable 'pause_i' set but not used [-Wunused-but-set-variable] 786 | int pause_i,pause_j; | ^~~~~~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ hspscaninterface.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ hsp2hitscan.c hsp2hitscan.dy: In function 'Wise2_one_off_two_hit_HSPscan_query_direct': hsp2hitscan.dy:209:18: warning: format '%d' expects argument of type 'int', but argument 3 has type '__time_t' {aka 'long int'} [-Wformat=] 209 | fprintf(stderr,"START %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 210 | use.ru_utime.tv_sec, | ~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:209:18: warning: format '%d' expects argument of type 'int', but argument 4 has type '__time_t' {aka 'long int'} [-Wformat=] 209 | fprintf(stderr,"START %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 210 | use.ru_utime.tv_sec, 211 | use.ru_utime.tv_sec/1000, | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:209:18: warning: format '%d' expects argument of type 'int', but argument 5 has type '__time_t' {aka 'long int'} [-Wformat=] 209 | fprintf(stderr,"START %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 212 | use.ru_stime.tv_sec, | ~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:209:18: warning: format '%d' expects argument of type 'int', but argument 6 has type '__time_t' {aka 'long int'} [-Wformat=] 209 | fprintf(stderr,"START %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 213 | use.ru_stime.tv_sec/1000 | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:273:18: warning: format '%d' expects argument of type 'int', but argument 3 has type '__time_t' {aka 'long int'} [-Wformat=] 273 | fprintf(stderr,"END OF SEED %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 274 | use.ru_utime.tv_sec, | ~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:273:18: warning: format '%d' expects argument of type 'int', but argument 4 has type '__time_t' {aka 'long int'} [-Wformat=] 273 | fprintf(stderr,"END OF SEED %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 274 | use.ru_utime.tv_sec, 275 | use.ru_utime.tv_sec/1000, | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:273:18: warning: format '%d' expects argument of type 'int', but argument 5 has type '__time_t' {aka 'long int'} [-Wformat=] 273 | fprintf(stderr,"END OF SEED %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 276 | use.ru_stime.tv_sec, | ~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:273:18: warning: format '%d' expects argument of type 'int', but argument 6 has type '__time_t' {aka 'long int'} [-Wformat=] 273 | fprintf(stderr,"END OF SEED %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 277 | use.ru_stime.tv_sec/1000 | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:286:18: warning: format '%d' expects argument of type 'int', but argument 3 has type '__time_t' {aka 'long int'} [-Wformat=] 286 | fprintf(stderr,"POPULATION %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 287 | use.ru_utime.tv_sec, | ~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:286:18: warning: format '%d' expects argument of type 'int', but argument 4 has type '__time_t' {aka 'long int'} [-Wformat=] 286 | fprintf(stderr,"POPULATION %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 287 | use.ru_utime.tv_sec, 288 | use.ru_utime.tv_sec/1000, | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:286:18: warning: format '%d' expects argument of type 'int', but argument 5 has type '__time_t' {aka 'long int'} [-Wformat=] 286 | fprintf(stderr,"POPULATION %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 289 | use.ru_stime.tv_sec, | ~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:286:18: warning: format '%d' expects argument of type 'int', but argument 6 has type '__time_t' {aka 'long int'} [-Wformat=] 286 | fprintf(stderr,"POPULATION %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 290 | use.ru_stime.tv_sec/1000 | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:302:18: warning: format '%d' expects argument of type 'int', but argument 3 has type '__time_t' {aka 'long int'} [-Wformat=] 302 | fprintf(stdout,"LINEARISED %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 303 | use.ru_utime.tv_sec, | ~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:302:18: warning: format '%d' expects argument of type 'int', but argument 4 has type '__time_t' {aka 'long int'} [-Wformat=] 302 | fprintf(stdout,"LINEARISED %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 303 | use.ru_utime.tv_sec, 304 | use.ru_utime.tv_sec/1000, | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:302:18: warning: format '%d' expects argument of type 'int', but argument 5 has type '__time_t' {aka 'long int'} [-Wformat=] 302 | fprintf(stdout,"LINEARISED %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 305 | use.ru_stime.tv_sec, | ~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:302:18: warning: format '%d' expects argument of type 'int', but argument 6 has type '__time_t' {aka 'long int'} [-Wformat=] 302 | fprintf(stdout,"LINEARISED %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 306 | use.ru_stime.tv_sec/1000 | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:192:9: warning: unused variable 'k' [-Wunused-variable] 192 | int i,k,j; | ^ hsp2hitscan.dy:185:7: warning: variable 'score' set but not used [-Wunused-but-set-variable] 185 | int score; | ^~~~~ hsp2hitscan.dy:183:7: warning: variable 'no' set but not used [-Wunused-but-set-variable] 183 | int no; | ^~ hsp2hitscan.dy:182:18: warning: unused variable 'head' [-Wunused-variable] 182 | ArraySeqHead * head; | ^~~~ hsp2hitscan.dy:181:7: warning: unused variable 'start_base' [-Wunused-variable] 181 | int start_base; | ^~~~~~~~~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ hsplookupscan.c hsplookupscan.dy: In function 'Wise2_one_off_HSPscan_scan_query_direct': hsplookupscan.dy:144:8: warning: variable 'newseq' set but not used [-Wunused-but-set-variable] 144 | char newseq[5]; | ^~~~~~ hsplookupscan.dy:143:7: warning: variable 'score' set but not used [-Wunused-but-set-variable] 143 | int score; | ^~~~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ hsplookupthreaded.c hsplookupthreaded.dy: In function 'Wise2_one_off_ordered_HSPscan_scan_query_direct': hsplookupthreaded.dy:263:18: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 263 | fprintf(stderr,"retrieved array with %d elements\n",current_oph); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~ | | | long int hsplookupthreaded.dy:136:7: warning: variable 'score' set but not used [-Wunused-but-set-variable] 136 | int score; | ^~~~~ hsplookupthreaded.dy:116:22: warning: unused variable 'hsp_para' [-Wunused-variable] 116 | LineariseHSPPara * hsp_para; | ^~~~~~~~ hsplookupthreaded.dy: In function 'Wise2_hsp_thread_worker': hsplookupthreaded.dy:659:27: warning: variable 'asl' set but not used [-Wunused-but-set-variable] 659 | auto ArraySeqLookup * asl; | ^~~ hsplookupthreaded.dy:627:8: warning: variable 'newseq' set but not used [-Wunused-but-set-variable] 627 | char newseq[5]; | ^~~~~~ hsplookupthreaded.dy:621:7: warning: variable 'score' set but not used [-Wunused-but-set-variable] 621 | int score; | ^~~~~ hsplookupthreaded.dy: In function 'Wise2_merge_HSPmanager': hsplookupthreaded.dy:567:1: warning: control reaches end of non-void function [-Wreturn-type] 567 | } | ^ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ hspthreadeddb.c hspthreadeddb.dy: In function 'Wise2_threadeddb_scan_worker': hspthreadeddb.dy:154:77: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 154 | fprintf(stderr,"For segment %d, finished query with %d (%d) linear\n",seg,(int)seg->lm,seg->lm->len); | ^ hspthreadeddb.dy:154:18: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Wise2_HSPDatabaseSegment *' [-Wformat=] 154 | fprintf(stderr,"For segment %d, finished query with %d (%d) linear\n",seg,(int)seg->lm,seg->lm->len); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~ | | | Wise2_HSPDatabaseSegment * gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ hspscanruntime.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ hsptwohitscan.c hsptwohitscan.dy: In function 'Wise2_twohit_one_off_HSPscan_scan_query_direct': hsptwohitscan.dy:113:7: warning: variable 'has_seen' set but not used [-Wunused-but-set-variable] 113 | int has_seen; | ^~~~~~~~ hsptwohitscan.dy:105:8: warning: variable 'newseq' set but not used [-Wunused-but-set-variable] 105 | char newseq[5]; | ^~~~~~ hsptwohitscan.dy:104:7: warning: variable 'score' set but not used [-Wunused-but-set-variable] 104 | int score; | ^~~~~ hsptwohitscan.dy: In function 'Wise2_add_to_TwoHitBuffer': hsptwohitscan.dy:354:7: warning: unused variable 'j' [-Wunused-variable] 354 | int j; | ^ hsptwohitscan.dy:353:7: warning: unused variable 'i' [-Wunused-variable] 353 | int i; | ^ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ proteinindexcons.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ dnaindexcons.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ staticseq.c ar ru libdyna_glib.a subseqhash.o intallocator.o proteinstreamedindex.o shadowseq.o shadowseqindex.o hsphandler.o hspscaninterface.o hsp2hitscan.o hsplookupscan.o hsplookupthreaded.o hspthreadeddb.o hspscanruntime.o hsptwohitscan.o proteinindexcons.o dnaindexcons.o staticseq.o ar: creating libdyna_glib.a if test -x /bin/ranlib; then /bin/ranlib libdyna_glib.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libdyna_glib.a; else exit 0; fi make[1]: Leaving directory '/builddir/build/BUILD/wise2.4.1/src/dynlibsrc' (cd external ; make CC="gcc" CFLAGS="-c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L" all ) make[1]: Entering directory '/builddir/build/BUILD/wise2.4.1/src/external' (cd mott; make CC="gcc" CFLAGS="-c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L" all) make[2]: Entering directory '/builddir/build/BUILD/wise2.4.1/src/external/mott' gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c -o mott_api.o mott_api.c mott_api.c: In function 'InitPvaluesMott': mott_api.c:64:3: warning: implicit declaration of function 'free' [-Wimplicit-function-declaration] 64 | free(freq0); | ^~~~ mott_api.c:5:1: note: include '' or provide a declaration of 'free' 4 | #include"gapstat.h" +++ |+#include 5 | mott_api.c:64:3: warning: incompatible implicit declaration of built-in function 'free' [-Wbuiltin-declaration-mismatch] 64 | free(freq0); | ^~~~ mott_api.c:64:3: note: include '' or provide a declaration of 'free' mott_api.c: In function 'SW_PValueMott': mott_api.c:104:7: warning: incompatible implicit declaration of built-in function 'free' [-Wbuiltin-declaration-mismatch] 104 | free(freqA); | ^~~~ mott_api.c:104:7: note: include '' or provide a declaration of 'free' mott_api.c: In function 'KarlinAltschulStatistics2': mott_api.c:144:5: warning: incompatible implicit declaration of built-in function 'free' [-Wbuiltin-declaration-mismatch] 144 | free(h+hmin); | ^~~~ mott_api.c:144:5: note: include '' or provide a declaration of 'free' mott_api.c:155:5: warning: incompatible implicit declaration of built-in function 'free' [-Wbuiltin-declaration-mismatch] 155 | free(h+hmin); | ^~~~ mott_api.c:155:5: note: include '' or provide a declaration of 'free' mott_api.c:150:9: warning: unused variable 'n' [-Wunused-variable] 150 | int n; | ^ mott_api.c: In function 'GetHistogram': mott_api.c:179:16: warning: implicit declaration of function 'calloc' [-Wimplicit-function-declaration] 179 | h = (double*)calloc(*hmax-*hmin+1,sizeof(double))-*hmin; | ^~~~~~ mott_api.c:179:16: note: include '' or provide a declaration of 'calloc' mott_api.c:179:16: warning: incompatible implicit declaration of built-in function 'calloc' [-Wbuiltin-declaration-mismatch] mott_api.c:179:16: note: include '' or provide a declaration of 'calloc' mott_api.c: In function 'PseudoResidueFrequencies2': mott_api.c:207:12: warning: implicit declaration of function 'toupper' [-Wimplicit-function-declaration] 207 | freq[toupper(seq[n])]++; | ^~~~~~~ mott_api.c:5:1: note: include '' or provide a declaration of 'toupper' 4 | #include"gapstat.h" +++ |+#include 5 | mott_api.c: In function 'RobinsonResidueFrequencies2': mott_api.c:230:27: warning: incompatible implicit declaration of built-in function 'calloc' [-Wbuiltin-declaration-mismatch] 230 | double *freq = (double*)calloc(256, sizeof(double)); | ^~~~~~ mott_api.c:230:27: note: include '' or provide a declaration of 'calloc' gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c -o gaplib.o gaplib.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../../dynlibsrc -I../../base wise2_mott_bridge.c ar ru libmott.a mott_api.o gaplib.o wise2_mott_bridge.o ar: creating libmott.a if test -x /bin/ranlib; then /bin/ranlib libmott.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libmott.a; else exit 0; fi make[2]: Leaving directory '/builddir/build/BUILD/wise2.4.1/src/external/mott' make[1]: Leaving directory '/builddir/build/BUILD/wise2.4.1/src/external' (cd socket ; make CC="gcc" CFLAGS="-c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L" libwisesocket.a ) make[1]: Entering directory '/builddir/build/BUILD/wise2.4.1/src/socket' gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ functionserver.c functionserver.dy: In function 'Wise2_main_loop_forking_FunctionServer': functionserver.dy:55:10: warning: unused variable 'ofp' [-Wunused-variable] 55 | FILE * ofp; | ^~~ functionserver.dy: In function 'Wise2_new_FunctionServer': functionserver.dy:216:21: warning: unused variable 'name' [-Wunused-variable] 216 | struct sockaddr * name; | ^~~~ functionserver.dy: In function 'Wise2_main_loop_forking_FunctionServer': functionserver.dy:129:11: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 129 | write(new_socket,buf,9); | ^~~~~~~~~~~~~~~~~~~~~~~ functionserver.dy:141:9: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 141 | write(new_socket,buf,6); | ^~~~~~~~~~~~~~~~~~~~~~~ functionserver.dy:183:9: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 183 | write(new_socket,buf,5); | ^~~~~~~~~~~~~~~~~~~~~~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ functionclient.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ anonobj.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ transferinterface.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ directsocketwrite.c ar ru libwisesocket.a functionserver.o functionclient.o anonobj.o transferinterface.o directsocketwrite.o ar: creating libwisesocket.a if test -x /bin/ranlib; then /bin/ranlib libwisesocket.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libwisesocket.a; else exit 0; fi make[1]: Leaving directory '/builddir/build/BUILD/wise2.4.1/src/socket' (cd dnaindex ; make CC="gcc" CFLAGS="-c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L" all ) make[1]: Entering directory '/builddir/build/BUILD/wise2.4.1/src/dnaindex' gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models kmer_assembly.c kmer_assembly.dy: In function 'Wise2_show_KmerAssemblyNode': kmer_assembly.dy:296:15: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'kmer_t' {aka 'long long int'} [-Wformat=] 296 | fprintf(ofp,"Node %ld of sequence %s \n",node->number,buffer); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly.dy:302:17: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'kmer_t' {aka 'long long int'} [-Wformat=] 302 | fprintf(ofp," ... prev ... %c, %d to %ld\n",node->prev[i]->base,node->prev[i]->sequence_label_len,node->prev[i]->prev->number); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly.dy:309:17: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'kmer_t' {aka 'long long int'} [-Wformat=] 309 | fprintf(ofp," ... next ... %c, %d to %ld\n",node->next[i]->base,node->next[i]->sequence_label_len,node->next[i]->next->number); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly.dy: In function 'Wise2_remove_sequence_label_KmerAssemblyLink': kmer_assembly.dy:365:18: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'KmerAssemblyLink *' [-Wformat=] 365 | fprintf(stderr," ...unable to remove label %ld from link %ld (%d labels)\n",label,kal,kal->sequence_label_len); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~ | | | KmerAssemblyLink * kmer_assembly.dy:367:20: warning: format '%d' expects a matching 'int' argument [-Wformat=] 367 | fprintf(stderr," [%ld] is %d label\n",kal->sequence_label[i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models kmer_index_interface.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models kmer_direct.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models kmer_hash.c kmer_hash.dy: In function 'Wise2_insert_by_kmer_KmerHashIndex': kmer_hash.dy:252:7: warning: unused variable 'i' [-Wunused-variable] 252 | int i; | ^ kmer_hash.dy: In function 'Wise2_free_KmerHashIndex': kmer_hash.dy:318:19: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'kmer_t' {aka 'long long int'} [-Wformat=] 318 | fprintf(stderr, "min_kmer: %016lx\n", khi->min_kmer); | ^~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_hash.dy:319:19: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'kmer_t' {aka 'long long int'} [-Wformat=] 319 | fprintf(stderr, "max_kmer: %016lx\n", khi->max_kmer); | ^~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | kmer_t {aka long long int} gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models kmer_count.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models kmer_glib_index.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models singleseqspace.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models dnamapping.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models largeseqreader.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_untangler.c kmer_assembly_untangler.dy: In function 'Wise2_show_KmerAssemblyPath': kmer_assembly_untangler.dy:52:65: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 52 | fprintf(ofp,"%3d memory %d, from [%s] to [%s], base %c\n",i,(int)kap->stack[i],back,forw,kap->stack[i]->base); | ^ kmer_assembly_untangler.dy: In function 'Wise2_untangle_KmerAssembly': kmer_assembly_untangler.dy:120:22: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'kmer_t' {aka 'long long int'} [-Wformat=] 120 | fprintf(stderr,"TANGLE: Node %ld, %s has forward %d and back %d links\n",node->number,buffer,node->next_len,node->prev_len); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_untangler.dy:141:22: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'kmer_t' {aka 'long long int'} [-Wformat=] 141 | fprintf(stderr,"Will attempt untangle starting at %ld to %ld\n",node->prev[i]->prev->number,node->number); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_untangler.dy:141:22: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'kmer_t' {aka 'long long int'} [-Wformat=] 141 | fprintf(stderr,"Will attempt untangle starting at %ld to %ld\n",node->prev[i]->prev->number,node->number); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_untangler.dy:157:22: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'kmer_t' {aka 'long long int'} [-Wformat=] 157 | fprintf(stderr,"RESOLVED: Node %ld [%s] Fully untangled now...\n",node->number,buffer); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_untangler.dy:159:22: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'kmer_t' {aka 'long long int'} [-Wformat=] 159 | fprintf(stderr,"UNRESOLVED: Node %ld [%s] still tangled...\n",node->number,buffer); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_untangler.dy:101:22: warning: variable 'link_set' set but not used [-Wunused-but-set-variable] 101 | KmerAssemblyLink * link_set[1024]; | ^~~~~~~~ kmer_assembly_untangler.dy: In function 'Wise2_old_attempt_forward_untangle_KmerAssembly': kmer_assembly_untangler.dy:444:20: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'kmer_t' {aka 'long long int'} [-Wformat=] 444 | fprintf(stderr,"looking at node %ld with path length %d, next length %d depth %d\n",current->next->number,pathlen,current->next->next_len,current->sequence_label_len); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_untangler.dy:568:82: warning: passing argument 4 of 'Wise2_lift_backward_tangled_tail' from incompatible pointer type [-Wincompatible-pointer-types] 568 | lift_backward_tangled_tail(kai,newpath->stack[newpath->stack_len-1],path,transferred_label,transferred_pos,transferred_len); | ^~~~~~~~~~~~~~~~~ | | | long int * In file included from kmer_assembly_untangler.c:4: kmer_assembly_untangler.h:174:116: note: expected 'int *' but argument is of type 'long int *' 174 | void Wise2_lift_backward_tangled_tail(KmerAssemblyIndex * kai,KmerAssemblyLink * new,KmerAssemblyPath * tail,int * start_label,SinglePosSequence ** positions,int label_len); | ~~~~~~^~~~~~~~~~~ kmer_assembly_untangler.dy: In function 'Wise2_lift_forward_tangled_KmerAssemblyPath': kmer_assembly_untangler.dy:746:20: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'kmer_t' {aka 'long long int'} [-Wformat=] 746 | fprintf(stderr,"Moving stack position %d, depth %d, transfer %d, between %ld [%s] and %ld [%s]\n",i,kap->stack[i]->sequence_label_len,label_len,kap->stack[i]->prev->number,back,kap->stack[i]->next->number,forw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_untangler.dy:746:20: warning: format '%ld' expects argument of type 'long int', but argument 8 has type 'kmer_t' {aka 'long long int'} [-Wformat=] 746 | fprintf(stderr,"Moving stack position %d, depth %d, transfer %d, between %ld [%s] and %ld [%s]\n",i,kap->stack[i]->sequence_label_len,label_len,kap->stack[i]->prev->number,back,kap->stack[i]->next->number,forw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_untangler.h: In function 'Wise2_attempt_forward_untangle_KmerAssembly': kmer_assembly_untangler.h:102:31: warning: 'newpath' may be used uninitialized [-Wmaybe-uninitialized] 102 | #define free_KmerAssemblyPath Wise2_free_KmerAssemblyPath | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ kmer_assembly_untangler.dy:363:22: note: 'newpath' was declared here 363 | KmerAssemblyPath * newpath; | ^~~~~~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_contig.c kmer_assembly_contig.dy: In function 'Wise2_KmerAssemblyContigSet_from_KmerAssemblyIndex': kmer_assembly_contig.dy:66:27: warning: unused variable 'final' [-Wunused-variable] 66 | KmerAssemblyContigSet * final; | ^~~~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_error.c kmer_assembly_error.dy: In function 'Wise2_mark_tangles_KmerAssembly': kmer_assembly_error.dy:93:22: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'kmer_t' {aka 'long long int'} [-Wformat=] 93 | fprintf(stderr,"Marking node (%ld) [%s] as next tangled\n",node->number,buffer); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_error.dy:105:22: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'kmer_t' {aka 'long long int'} [-Wformat=] 105 | fprintf(stderr,"Marking node (%ld) [%s] as prev tangled\n",node->number,buffer); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_error.dy: In function 'Wise2_attempt_resolve_forward_error_KmerAssembly': kmer_assembly_error.dy:208:8: warning: unused variable 'next' [-Wunused-variable] 208 | char next[256]; | ^~~~ kmer_assembly_error.dy: In function 'Wise2_extend_indel_path_KmerAssembly': kmer_assembly_error.dy:351:24: warning: format '%d' expects argument of type 'int', but argument 4 has type 'int *' [-Wformat=] 351 | fprintf(stderr,"in considering indel (%d, path %d), real (%c) and error (%c) do not agree at position %d,%d\n",delete_length,current_path,real->base,error->base,real_pos,error_pos); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ | | | int * gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models assembly.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models assembly_stream_interface.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models assembly_stream_fasta.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models assembly_sanger_project.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models assembly_stream_cons.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -I../models compressed_protein_index.c compressed_protein_index.dy: In function 'Wise2_add_direct_number_CompressedProteinIndex': compressed_protein_index.dy:223:10: warning: returning 'void *' from a function with return type 'boolean' {aka 'int'} makes integer from pointer without a cast [-Wint-conversion] 223 | return NULL; | ^~~~ make[1]: Leaving directory '/builddir/build/BUILD/wise2.4.1/src/dnaindex' (cd network ; make CC="gcc" CFLAGS="-c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L" all ) make[1]: Entering directory '/builddir/build/BUILD/wise2.4.1/src/network' gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../socket -I../dynlibsrc -I../dnaindex wise_proteinindex_server.c wise_proteinindex_server.c: In function 'main': wise_proteinindex_server.c:93:10: warning: unused variable 'temp' [-Wunused-variable] 93 | char * temp; | ^~~~ wise_proteinindex_server.c:91:10: warning: unused variable 'ior_file' [-Wunused-variable] 91 | char * ior_file; | ^~~~~~~~ wise_proteinindex_server.c:84:7: warning: unused variable 'count' [-Wunused-variable] 84 | int count = 0; | ^~~~~ wise_proteinindex_server.c:76:7: warning: unused variable 'ret' [-Wunused-variable] 76 | int ret; | ^~~ wise_proteinindex_server.c:75:14: warning: unused variable 'seq' [-Wunused-variable] 75 | Sequence * seq; | ^~~ wise_proteinindex_server.c:70:7: warning: unused variable 'i' [-Wunused-variable] 70 | int i; | ^ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../socket -I../dynlibsrc -I../dnaindex net_hspscan.c gcc -g -o scanwise_server wise_proteinindex_server.o net_hspscan.o ../dnaindex/compressed_protein_index.o ../dnaindex/kmer_index_interface.o ../dnaindex/singleseqspace.o ../dnaindex/kmer_direct.o -ldyna_glib -ldyna -lwisesocket -lwisebase -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `pkg-config --libs glib-2.0` -lpthread gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../socket -I../dynlibsrc -I../dnaindex client_multihspscan.c client_multihspscan.dy: In function 'Wise2_new_multiclient_HSPScanInterface': client_multihspscan.dy:128:1: warning: control reaches end of non-void function [-Wreturn-type] 128 | } | ^ make[1]: Leaving directory '/builddir/build/BUILD/wise2.4.1/src/network' (cd models ; make CC="gcc" CFLAGS="-c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L" EXTRALIBS="-lm" HMMER_DEFINE="HMMER_INTERNAL" HMMER_INCLUDE="../HMMer2/" HMMER_LIBS="../HMMer2/" all ) make[1]: Entering directory '/builddir/build/BUILD/wise2.4.1/src/models' gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ dnal.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ dnaalign.c dnaalign.c: In function 'Wise2_calculate_shatter_DnaAlign': dnaalign.c:336:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] 336 | int j; | ^~ dnaalign.c:335:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] 335 | int i; | ^~ dnaalign.c:333:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] 333 | boolean calculate_shatter_DnaAlign(DnaAlign * mat,DPEnvelope * dpenv) | ^~~~ dnaalign.c: In function 'Wise2_serial_search_DnaAlign': dnaalign.c:621:9: warning: unused variable 'db_status' [-Wunused-variable] 621 | * | ^ dnaalign.c: In function 'Wise2_PackAln_bestmemory_DnaAlign': dnaalign.c:900:19: warning: unused variable 'de' [-Wunused-variable] 900 | */ | ^ dnaalign.c: In function 'Wise2_max_special_strip_DnaAlign': dnaalign.c:1799:9: warning: variable 'cscore' set but not used [-Wunused-but-set-variable] 1799 | * Return [UNKN ] Undocumented return value [int] | ^~~~~~ dnaalign.c:1798:9: warning: unused variable 'temp' [-Wunused-variable] 1798 | * | ^ dnaalign.c: In function 'Wise2_PackAln_bestmemory_DnaAlign': dnaalign.c:961:12: warning: 'out' may be used uninitialized [-Wmaybe-uninitialized] 961 | } | ^ dnaalign.c:899:15: note: 'out' was declared here 899 | * | ^ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ seqaligndisplay.c gcc -o dnal dnal.o dnaalign.o seqaligndisplay.o -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ psw.c In file included from /usr/include/stdio.h:906, from ../base/wisebase.h:6, from ../dynlibsrc/packaln.h:7, from ../dynlibsrc/dyna.h:12, from proteinsw.h:6, from sw_wrap.h:6, from psw.c:8: In function 'fprintf', inlined from 'main' at psw.c:241:5: /usr/include/bits/stdio2.h:79:10: warning: 'tend' may be used uninitialized [-Wmaybe-uninitialized] 79 | return __fprintf_chk (__stream, __USE_FORTIFY_LEVEL - 1, __fmt, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ psw.c: In function 'main': psw.c:62:7: note: 'tend' was declared here 62 | int tend; | ^~~~ In function 'fprintf', inlined from 'main' at psw.c:241:5: /usr/include/bits/stdio2.h:79:10: warning: 'qend' may be used uninitialized [-Wmaybe-uninitialized] 79 | return __fprintf_chk (__stream, __USE_FORTIFY_LEVEL - 1, __fmt, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ psw.c: In function 'main': psw.c:60:7: note: 'qend' was declared here 60 | int qend; | ^~~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ proteinsw.c proteinsw.c: In function 'Wise2_calculate_shatter_ProteinSW': proteinsw.c:124:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] 124 | int lenj; | ^~~ proteinsw.c:123:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] 123 | int leni; | ^~~ proteinsw.c:121:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] 121 | int k; | ^~ proteinsw.c: In function 'Wise2_PackAln_bestmemory_ProteinSW': proteinsw.c:824:19: warning: unused variable 'de' [-Wunused-variable] 824 | ProteinSW * mat; | ^~ proteinsw.c: In function 'Wise2_max_special_strip_ProteinSW': proteinsw.c:1678:9: warning: variable 'cscore' set but not used [-Wunused-but-set-variable] 1678 | { | ^ proteinsw.c:1677:9: warning: unused variable 'temp' [-Wunused-variable] 1677 | int max_special_strip_ProteinSW(ProteinSW * mat,int i,int j,int state,boolean isspecial,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore) | ^~~~ proteinsw.c: In function 'Wise2_PackAln_bestmemory_ProteinSW': proteinsw.c:885:12: warning: 'out' may be used uninitialized [-Wmaybe-uninitialized] 885 | | ^ proteinsw.c:823:15: note: 'out' was declared here 823 | long long total; | ^~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ sw_wrap.c sw_wrap.dy: In function 'Wise2_Hscore_from_ProteinSW': sw_wrap.dy:355:23: warning: variable 'ret' set but not used [-Wunused-but-set-variable] 355 | Search_Return_Type ret; | ^~~ sw_wrap.dy: In function 'Wise2_Hscore_from_ProteinABC': sw_wrap.dy:407:23: warning: variable 'ret' set but not used [-Wunused-but-set-variable] 407 | Search_Return_Type ret; | ^~~ sw_wrap.dy: In function 'Wise2_Hscore_from_ProteinBA': sw_wrap.dy:460:23: warning: variable 'ret' set but not used [-Wunused-but-set-variable] 460 | Search_Return_Type ret; | ^~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ abc.c abc.c: In function 'Wise2_calculate_shatter_abc': abc.c:123:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] 123 | int lenj; | ^~~ abc.c:122:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] 122 | int leni; | ^~~ abc.c:120:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] 120 | int k; | ^~ abc.c: In function 'Wise2_PackAln_bestmemory_abc': abc.c:822:19: warning: unused variable 'de' [-Wunused-variable] 822 | abc * mat; | ^ abc.c: In function 'Wise2_max_special_strip_abc': abc.c:1687:9: warning: variable 'cscore' set but not used [-Wunused-but-set-variable] 1687 | { | ^ abc.c:1686:9: warning: unused variable 'temp' [-Wunused-variable] 1686 | int max_special_strip_abc(abc * mat,int i,int j,int state,boolean isspecial,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore) | ^~~~ abc.c: In function 'Wise2_PackAln_bestmemory_abc': abc.c:883:12: warning: 'out' may be used uninitialized [-Wmaybe-uninitialized] 883 | | ^ abc.c:821:15: note: 'out' was declared here 821 | long long total; | ^~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ pba.c pba.c: In function 'Wise2_calculate_shatter_ProteinBlockAligner': pba.c:126:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] 126 | int lenj; | ^~~ pba.c:125:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] 125 | int leni; | ^~~ pba.c:123:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] 123 | int k; | ^~ pba.c: In function 'Wise2_PackAln_bestmemory_ProteinBlockAligner': pba.c:929:19: warning: unused variable 'de' [-Wunused-variable] 929 | ProteinBlockAligner * mat; | ^~ pba.c: In function 'Wise2_max_special_strip_ProteinBlockAligner': pba.c:1884:9: warning: variable 'cscore' set but not used [-Wunused-but-set-variable] 1884 | { | ^ pba.c:1883:9: warning: unused variable 'temp' [-Wunused-variable] 1883 | int max_special_strip_ProteinBlockAligner(ProteinBlockAligner * mat,int i,int j,int state,boolean isspecial,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore) | ^~~~ pba.c: In function 'Wise2_PackAln_bestmemory_ProteinBlockAligner': pba.c:990:12: warning: 'out' may be used uninitialized [-Wmaybe-uninitialized] 990 | | ^ pba.c:928:15: note: 'out' was declared here 928 | long long total; | ^~~ gcc -o psw psw.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ pswdb.c gcc -o pswdb pswdb.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ dbac.c dbac.c: In function 'make_SeqAlign_from_align': dbac.c:413:32: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 413 | fprintf(stderr,"Got %d with %d vs %d\n",i,strlen(seq),one->len); | ~^ ~~~~~~~~~~~ | | | | int size_t {aka long unsigned int} | %ld dbac.c: In function 'main': dbac.c:463:7: warning: unused variable 'score' [-Wunused-variable] 463 | int score; | ^~~~~ dbac.c:460:19: warning: unused variable 'dmat' [-Wunused-variable] 460 | DnaMatchBlock * dmat; | ^~~~ dbac.c: In function 'showPFF': dbac.c:250:43: warning: 'currMatch' may be used uninitialized [-Wmaybe-uninitialized] 250 | *(currMatch/0.25)))/log(2); | ~~~~~~~~~~^~~~~~ dbac.c:169:10: note: 'currMatch' was declared here 169 | double currMatch; | ^~~~~~~~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ dba.c dba.c: In function 'Wise2_calculate_shatter_DnaMatchBlock': dba.c:127:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] 127 | int lenj; | ^~~ dba.c:126:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] 126 | int leni; | ^~~ dba.c:124:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] 124 | int k; | ^~ dba.c: In function 'Wise2_serial_search_DnaMatchBlock': dba.c:467:9: warning: unused variable 'db_status' [-Wunused-variable] 467 | Search_Return_Type serial_search_DnaMatchBlock(Hscore * out,ComplexSequence* query,ComplexSequence* target ,DnaMatrix* comp65,DnaMatrix* comp75,DnaMatrix* comp85,DnaMatrix* comp95,Score g,Score u,Score v,Score s,Score b) | ^~~~~~~~~ dba.c: In function 'Wise2_PackAln_bestmemory_DnaMatchBlock': dba.c:801:19: warning: unused variable 'de' [-Wunused-variable] 801 | DnaMatchBlock * mat; | ^~ dba.c: In function 'Wise2_max_special_strip_DnaMatchBlock': dba.c:1943:9: warning: variable 'cscore' set but not used [-Wunused-but-set-variable] 1943 | { | ^ dba.c:1942:9: warning: unused variable 'temp' [-Wunused-variable] 1942 | int max_special_strip_DnaMatchBlock(DnaMatchBlock * mat,int i,int j,int state,boolean isspecial,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore) | ^~~~ dba.c: In function 'Wise2_PackAln_bestmemory_DnaMatchBlock': dba.c:862:12: warning: 'out' may be used uninitialized [-Wmaybe-uninitialized] 862 | | ^ dba.c:800:15: note: 'out' was declared here 800 | long long total; | ^~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ slimdba.c slimdba.c: In function 'Wise2_calculate_shatter_SlimDnaMatchBlock': slimdba.c:124:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] 124 | int lenj; | ^~~ slimdba.c:123:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] 123 | int leni; | ^~~ slimdba.c:121:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] 121 | int k; | ^~ slimdba.c: In function 'Wise2_serial_search_SlimDnaMatchBlock': slimdba.c:359:9: warning: unused variable 'db_status' [-Wunused-variable] 359 | Search_Return_Type serial_search_SlimDnaMatchBlock(Hscore * out,ComplexSequence* query,ComplexSequence* target ,DnaMatrix* comp65,Score g,Score u,Score v,Score s,Score b) | ^~~~~~~~~ slimdba.c: In function 'Wise2_PackAln_bestmemory_SlimDnaMatchBlock': slimdba.c:588:19: warning: unused variable 'de' [-Wunused-variable] 588 | SlimDnaMatchBlock * mat; | ^~ slimdba.c: In function 'Wise2_max_special_strip_SlimDnaMatchBlock': slimdba.c:1469:9: warning: variable 'cscore' set but not used [-Wunused-but-set-variable] 1469 | { | ^ slimdba.c:1468:9: warning: unused variable 'temp' [-Wunused-variable] 1468 | int max_special_strip_SlimDnaMatchBlock(SlimDnaMatchBlock * mat,int i,int j,int state,boolean isspecial,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore) | ^~~~ slimdba.c: In function 'Wise2_PackAln_bestmemory_SlimDnaMatchBlock': slimdba.c:649:12: warning: 'out' may be used uninitialized [-Wmaybe-uninitialized] 649 | | ^ slimdba.c:587:15: note: 'out' was declared here 587 | long long total; | ^~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ bigdba.c bigdba.c: In function 'Wise2_calculate_shatter_BigDnaMatchBlock': bigdba.c:128:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] 128 | int lenj; | ^~~ bigdba.c:127:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] 127 | int leni; | ^~~ bigdba.c:125:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] 125 | int k; | ^~ bigdba.c: In function 'Wise2_serial_search_BigDnaMatchBlock': bigdba.c:507:9: warning: unused variable 'db_status' [-Wunused-variable] 507 | Search_Return_Type serial_search_BigDnaMatchBlock(Hscore * out,ComplexSequence* query,ComplexSequence* target ,DnaMatrix* comp55,DnaMatrix* comp65,DnaMatrix* comp75,DnaMatrix* comp85,DnaMatrix* comp95,Score g,Score g65,Score g55,Score u,Score v,Score s,Score b) | ^~~~~~~~~ bigdba.c: In function 'Wise2_PackAln_bestmemory_BigDnaMatchBlock': bigdba.c:880:19: warning: unused variable 'de' [-Wunused-variable] 880 | BigDnaMatchBlock * mat; | ^~ bigdba.c: In function 'Wise2_max_special_strip_BigDnaMatchBlock': bigdba.c:2117:9: warning: variable 'cscore' set but not used [-Wunused-but-set-variable] 2117 | { | ^ bigdba.c:2116:9: warning: unused variable 'temp' [-Wunused-variable] 2116 | int max_special_strip_BigDnaMatchBlock(BigDnaMatchBlock * mat,int i,int j,int state,boolean isspecial,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore) | ^~~~ bigdba.c: In function 'Wise2_PackAln_bestmemory_BigDnaMatchBlock': bigdba.c:941:12: warning: 'out' may be used uninitialized [-Wmaybe-uninitialized] 941 | | ^ bigdba.c:879:15: note: 'out' was declared here 879 | long long total; | ^~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ dbadisplay.c dbadisplay.dy: In function 'Wise2_show_pretty_dba_align_btcanvas': dbadisplay.dy:71:11: warning: variable 'is_reversed' set but not used [-Wunused-but-set-variable] 71 | boolean is_reversed; | ^~~~~~~~~~~ dbadisplay.dy:283:36: warning: 'end_alc' may be used uninitialized [-Wmaybe-uninitialized] 283 | sprintf(buffer,"%d",end_alc->alu[1]->start+1); | ~~~~~~~^~~~~ dbadisplay.dy:64:15: note: 'end_alc' was declared here 64 | AlnColumn * end_alc; | ^~~~~~~ gcc -o dba dbac.o dba.o slimdba.o bigdba.o dbadisplay.o -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L estwise.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I. gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ geneparser21.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ geneparameter.c geneparameter.dy: In function 'Wise2_GeneParameter21_from_GeneModel': geneparameter.dy:132:25: warning: unused variable 'cse' [-Wunused-variable] 132 | ComplexSequenceEval * cse; | ^~~ geneparameter.dy:131:25: warning: unused variable 'rmds' [-Wunused-variable] 131 | RandomModelDNAScore * rmds; | ^~~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ genestats.c genestats.dy: In function 'Wise2_get_genestat_emission': genestats.dy:753:10: warning: unused variable 'd' [-Wunused-variable] 753 | double d; | ^ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ genewisehsp.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ geneutil.c geneutil.dy: In function 'Wise2_add_Genes_to_GenomicRegion_new': geneutil.dy:92:15: warning: unused variable 'intron_start' [-Wunused-variable] 92 | AlnColumn * intron_start; | ^~~~~~~~~~~~ geneutil.dy:82:7: warning: unused variable 'count' [-Wunused-variable] 82 | int count = 0; | ^~~~~ geneutil.dy: In function 'Wise2_Gene_from_AlnColumn_new': geneutil.dy:446:20: warning: 'prev' may be used uninitialized [-Wmaybe-uninitialized] 446 | exon_end = prev->alu[1]->end +1 - out->start; | ~~~~^~~~~ geneutil.dy:381:15: note: 'prev' was declared here 381 | AlnColumn * prev; | ^~~~ geneutil.dy:504:16: warning: 'ex' may be used uninitialized [-Wmaybe-uninitialized] 504 | out->end = ex->end + out->start; | ~~^~~~~ geneutil.dy:367:10: note: 'ex' was declared here 367 | Exon * ex; | ^~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ geneoutput.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ threestatemodel.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ genefrequency.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ splicesitemodeler.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ genewise4.c genewise4.c: In function 'Wise2_calculate_shatter_GeneWise4': genewise4.c:126:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] 126 | int lenj; | ^~~ genewise4.c:125:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] 125 | int leni; | ^~~ genewise4.c:123:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] 123 | int k; | ^~ genewise4.c: In function 'Wise2_PackAln_bestmemory_GeneWise4': genewise4.c:1068:19: warning: unused variable 'de' [-Wunused-variable] 1068 | GeneWise4 * mat; | ^~ genewise4.c: In function 'Wise2_max_special_strip_GeneWise4': genewise4.c:2217:9: warning: variable 'cscore' set but not used [-Wunused-but-set-variable] 2217 | { | ^ genewise4.c:2216:9: warning: unused variable 'temp' [-Wunused-variable] 2216 | int max_special_strip_GeneWise4(GeneWise4 * mat,int i,int j,int state,boolean isspecial,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore) | ^~~~ genewise4.c: In function 'Wise2_PackAln_bestmemory_GeneWise4': genewise4.c:1129:12: warning: 'out' may be used uninitialized [-Wmaybe-uninitialized] 1129 | | ^ genewise4.c:1067:15: note: 'out' was declared here 1067 | long long total; | ^~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ genewise6.c genewise6.c: In function 'Wise2_calculate_shatter_GeneWise6': genewise6.c:128:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] 128 | int lenj; | ^~~ genewise6.c:127:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] 127 | int leni; | ^~~ genewise6.c:125:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] 125 | int k; | ^~ genewise6.c: In function 'Wise2_PackAln_bestmemory_GeneWise6': genewise6.c:1180:19: warning: unused variable 'de' [-Wunused-variable] 1180 | GeneWise6 * mat; | ^~ genewise6.c: In function 'Wise2_max_special_strip_GeneWise6': genewise6.c:2417:9: warning: variable 'cscore' set but not used [-Wunused-but-set-variable] 2417 | { | ^ genewise6.c:2416:9: warning: unused variable 'temp' [-Wunused-variable] 2416 | int max_special_strip_GeneWise6(GeneWise6 * mat,int i,int j,int state,boolean isspecial,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore) | ^~~~ genewise6.c: In function 'Wise2_PackAln_bestmemory_GeneWise6': genewise6.c:1241:12: warning: 'out' may be used uninitialized [-Wmaybe-uninitialized] 1241 | | ^ genewise6.c:1179:15: note: 'out' was declared here 1179 | long long total; | ^~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ genestretch6.c genestretch6.c: In function 'Wise2_calculate_shatter_GeneStretch6': genestretch6.c:130:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] 130 | int lenj; | ^~~ genestretch6.c:129:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] 129 | int leni; | ^~~ genestretch6.c:127:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] 127 | int k; | ^~ genestretch6.c: In function 'Wise2_PackAln_bestmemory_GeneStretch6': genestretch6.c:1339:19: warning: unused variable 'de' [-Wunused-variable] 1339 | GeneStretch6 * mat; | ^~ genestretch6.c: In function 'Wise2_PackAln_calculate_Small_GeneStretch6': genestretch6.c:1839:19: warning: unused variable 'pau' [-Wunused-variable] 1839 | int score; | ^ genestretch6.c: In function 'Wise2_PackAln_bestmemory_GeneStretch6': genestretch6.c:1400:12: warning: 'out' may be used uninitialized [-Wmaybe-uninitialized] 1400 | | ^ genestretch6.c:1338:15: note: 'out' was declared here 1338 | long long total; | ^~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ genewise21.c genewise21.c: In function 'Wise2_calculate_shatter_GeneWise21': genewise21.c:154:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] 154 | int lenj; | ^~~ genewise21.c:153:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] 153 | int leni; | ^~~ genewise21.c:151:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] 151 | int k; | ^~ genewise21.c: In function 'Wise2_PackAln_bestmemory_GeneWise21': genewise21.c:2606:19: warning: unused variable 'de' [-Wunused-variable] 2606 | GeneWise21 * mat; | ^~ genewise21.c: In function 'Wise2_PackAln_calculate_Small_GeneWise21': genewise21.c:3507:19: warning: unused variable 'pau' [-Wunused-variable] 3507 | int score; | ^ genewise21.c: In function 'Wise2_PackAln_bestmemory_GeneWise21': genewise21.c:2667:12: warning: 'out' may be used uninitialized [-Wmaybe-uninitialized] 2667 | | ^ genewise21.c:2605:15: note: 'out' was declared here 2605 | long long total; | ^~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ geneloop21.c geneloop21.c: In function 'Wise2_calculate_shatter_GeneLoop21': geneloop21.c:147:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] 147 | int lenj; | ^~~ geneloop21.c:146:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] 146 | int leni; | ^~~ geneloop21.c:144:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] 144 | int k; | ^~ geneloop21.c: In function 'Wise2_PackAln_bestmemory_GeneLoop21': geneloop21.c:2280:19: warning: unused variable 'de' [-Wunused-variable] 2280 | GeneLoop21 * mat; | ^~ geneloop21.c: In function 'Wise2_PackAln_calculate_Small_GeneLoop21': geneloop21.c:3093:19: warning: unused variable 'pau' [-Wunused-variable] 3093 | int score; | ^ geneloop21.c: In function 'Wise2_PackAln_bestmemory_GeneLoop21': geneloop21.c:2341:12: warning: 'out' may be used uninitialized [-Wmaybe-uninitialized] 2341 | | ^ geneloop21.c:2279:15: note: 'out' was declared here 2279 | long long total; | ^~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ geneloop6.c geneloop6.c: In function 'Wise2_calculate_shatter_GeneLoop6': geneloop6.c:129:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] 129 | int lenj; | ^~~ geneloop6.c:128:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] 128 | int leni; | ^~~ geneloop6.c:126:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] 126 | int k; | ^~ geneloop6.c: In function 'Wise2_PackAln_bestmemory_GeneLoop6': geneloop6.c:1268:19: warning: unused variable 'de' [-Wunused-variable] 1268 | GeneLoop6 * mat; | ^~ geneloop6.c: In function 'Wise2_PackAln_calculate_Small_GeneLoop6': geneloop6.c:1742:19: warning: unused variable 'pau' [-Wunused-variable] 1742 | int score; | ^ geneloop6.c: In function 'Wise2_PackAln_bestmemory_GeneLoop6': geneloop6.c:1329:12: warning: 'out' may be used uninitialized [-Wmaybe-uninitialized] 1329 | | ^ geneloop6.c:1267:15: note: 'out' was declared here 1267 | long long total; | ^~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ genephase6.c genephase6.c: In function 'Wise2_calculate_shatter_GenePhase6': genephase6.c:215:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] 215 | int lenj; | ^~~ genephase6.c:214:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] 214 | int leni; | ^~~ genephase6.c:212:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] 212 | int k; | ^~ genephase6.c: In function 'Wise2_PackAln_bestmemory_GenePhase6': genephase6.c:1492:19: warning: unused variable 'de' [-Wunused-variable] 1492 | GenePhase6 * mat; | ^~ genephase6.c: In function 'Wise2_PackAln_calculate_Small_GenePhase6': genephase6.c:2052:19: warning: unused variable 'pau' [-Wunused-variable] 2052 | int score; | ^ genephase6.c: In function 'Wise2_thread_loop_GenePhase6': genephase6.c:873:1: warning: control reaches end of non-void function [-Wreturn-type] 873 | { | ^ genephase6.c: In function 'Wise2_PackAln_bestmemory_GenePhase6': genephase6.c:1553:12: warning: 'out' may be used uninitialized [-Wmaybe-uninitialized] 1553 | | ^ genephase6.c:1491:15: note: 'out' was declared here 1491 | long long total; | ^~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ gwlite.c gwlite.c: In function 'Wise2_calculate_shatter_GeneLiteModel': gwlite.c:127:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] 127 | int lenj; | ^~~ gwlite.c:126:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] 126 | int leni; | ^~~ gwlite.c:124:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] 124 | int k; | ^~ gwlite.c: In function 'Wise2_PackAln_bestmemory_GeneLiteModel': gwlite.c:1117:19: warning: unused variable 'de' [-Wunused-variable] 1117 | GeneLiteModel * mat; | ^~ gwlite.c: In function 'Wise2_max_special_strip_GeneLiteModel': gwlite.c:2294:9: warning: variable 'cscore' set but not used [-Wunused-but-set-variable] 2294 | { | ^ gwlite.c:2293:9: warning: unused variable 'temp' [-Wunused-variable] 2293 | int max_special_strip_GeneLiteModel(GeneLiteModel * mat,int i,int j,int state,boolean isspecial,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore) | ^~~~ gwlite.c: In function 'Wise2_PackAln_bestmemory_GeneLiteModel': gwlite.c:1178:12: warning: 'out' may be used uninitialized [-Wmaybe-uninitialized] 1178 | | ^ gwlite.c:1116:15: note: 'out' was declared here 1116 | long long total; | ^~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ gwlitemodel.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ gwrap.c gwrap.dy: In function 'Wise2_Hscore_from_TSM_genewise': gwrap.dy:527:25: warning: unused variable 'tempcse' [-Wunused-variable] 527 | ComplexSequenceEval * tempcse; | ^~~~~~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ matchsum.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ estwrap.c estwrap.dy: In function 'Wise2_Hscore_from_TSM_estwise': estwrap.dy:269:22: warning: variable 'ret' set but not used [-Wunused-but-set-variable] 269 | Search_Return_Type ret; | ^~~ estwrap.dy: In function 'Wise2_AlnBlock_from_TSM_estwise_wrap': estwrap.dy:138:14: warning: 'out' may be used uninitialized [-Wmaybe-uninitialized] 138 | AlnBlock * out; | ^~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ genewisemodel.c genewisemodel.dy: In function 'Wise2_pack_GeneWiseScore': genewisemodel.dy:114:10: warning: 'out' is used uninitialized [-Wuninitialized] 114 | return out; | ^~~ genewisemodel.dy:112:10: note: 'out' was declared here 112 | char * out; | ^~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ phasemodel.c phasemodel.dy: In function 'Wise2_read_ProteinIntronList': phasemodel.dy:65:10: warning: unused variable 'run2' [-Wunused-variable] 65 | char * run2; | ^~~~ phasemodel.dy:64:10: warning: unused variable 'run1' [-Wunused-variable] 64 | char * run1; | ^~~~ phasemodel.dy: In function 'Wise2_read_fasta_PhasedProtein': phasemodel.dy:233:7: warning: unused variable 'j' [-Wunused-variable] 233 | int j; | ^ phasemodel.dy:231:14: warning: unused variable 'input' [-Wunused-variable] 231 | Sequence * input; | ^~~~~ phasemodel.dy:241:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fgets(name,10000,ifp); | ^~~~~~~~~~~~~~~~~~~~~ phasemodel.dy:241:3: warning: 'fgets' writing 10000 bytes into a region of size 2000 overflows the destination [-Wstringop-overflow=] 241 | fgets(name,10000,ifp); | ^~~~~~~~~~~~~~~~~~~~~ phasemodel.dy:235:8: note: destination object 'name' of size 2000 235 | char name[2000]; | ^~~~ In file included from /usr/include/stdio.h:906, from ../base/wisebase.h:6, from ../dynlibsrc/probability.h:7, from geneparser21.h:6, from genewisemodel.h:6, from phasemodel.h:6, from phasemodel.c:4: /usr/include/bits/stdio2.h:209:1: note: in a call to function 'fgets' declared with attribute 'access (write_only, 1, 2)' 209 | fgets (char *__restrict __s, int __n, FILE *__restrict __stream) | ^~~~~ In function 'fgets', inlined from 'Wise2_read_fasta_PhasedProtein' at phasemodel.dy:241:3: /usr/include/bits/stdio2.h:215:12: warning: call to '*__fgets_chk' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 215 | return __fgets_chk_warn (__s, sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ cdparser.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ genedisplay.c genedisplay.dy: In function 'Wise2_write_intron_desc': genedisplay.dy:493:20: warning: too many arguments for format [-Wformat-extra-args] 493 | sprintf(buffer," Intron ??? ",in_number); | ^~~~~~~~~~~~~~~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ estwise3.c estwise3.c: In function 'Wise2_calculate_shatter_EstWise3': estwise3.c:124:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] 124 | int lenj; | ^~~ estwise3.c:123:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] 123 | int leni; | ^~~ estwise3.c:121:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] 121 | int k; | ^~ estwise3.c: In function 'Wise2_PackAln_bestmemory_EstWise3': estwise3.c:1144:19: warning: unused variable 'de' [-Wunused-variable] 1144 | EstWise3 * mat; | ^ estwise3.c: In function 'Wise2_max_special_strip_EstWise3': estwise3.c:2402:9: warning: variable 'cscore' set but not used [-Wunused-but-set-variable] 2402 | { | ^ estwise3.c:2401:9: warning: unused variable 'temp' [-Wunused-variable] 2401 | int max_special_strip_EstWise3(EstWise3 * mat,int i,int j,int state,boolean isspecial,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore) | ^~~~ estwise3.c: In function 'Wise2_PackAln_bestmemory_EstWise3': estwise3.c:1205:12: warning: 'out' may be used uninitialized [-Wmaybe-uninitialized] 1205 | | ^ estwise3.c:1143:15: note: 'out' was declared here 1143 | long long total; | ^~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ estslim3.c estslim3.c: In function 'Wise2_calculate_shatter_EstSlim3': estslim3.c:124:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] 124 | int lenj; | ^~~ estslim3.c:123:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] 123 | int leni; | ^~~ estslim3.c:121:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] 121 | int k; | ^~ estslim3.c: In function 'Wise2_PackAln_bestmemory_EstSlim3': estslim3.c:936:19: warning: unused variable 'de' [-Wunused-variable] 936 | EstSlim3 * mat; | ^ estslim3.c: In function 'Wise2_max_special_strip_EstSlim3': estslim3.c:1894:9: warning: variable 'cscore' set but not used [-Wunused-but-set-variable] 1894 | { | ^ estslim3.c:1893:9: warning: unused variable 'temp' [-Wunused-variable] 1893 | int max_special_strip_EstSlim3(EstSlim3 * mat,int i,int j,int state,boolean isspecial,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore) | ^~~~ estslim3.c: In function 'Wise2_PackAln_bestmemory_EstSlim3': estslim3.c:997:12: warning: 'out' may be used uninitialized [-Wmaybe-uninitialized] 997 | | ^ estslim3.c:935:15: note: 'out' was declared here 935 | long long total; | ^~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ estloop3.c estloop3.c: In function 'Wise2_calculate_shatter_EstLoop3': estloop3.c:125:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] 125 | int lenj; | ^~~ estloop3.c:124:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] 124 | int leni; | ^~~ estloop3.c:122:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] 122 | int k; | ^~ estloop3.c: In function 'Wise2_PackAln_bestmemory_EstLoop3': estloop3.c:1312:19: warning: unused variable 'de' [-Wunused-variable] 1312 | EstLoop3 * mat; | ^ estloop3.c: In function 'Wise2_PackAln_calculate_Small_EstLoop3': estloop3.c:1809:19: warning: unused variable 'pau' [-Wunused-variable] 1809 | int score; | ^ estloop3.c: In function 'Wise2_PackAln_bestmemory_EstLoop3': estloop3.c:1373:12: warning: 'out' may be used uninitialized [-Wmaybe-uninitialized] 1373 | | ^ estloop3.c:1311:15: note: 'out' was declared here 1311 | long long total; | ^~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ estfrag3.c estfrag3.c: In function 'Wise2_calculate_shatter_EstFrag3': estfrag3.c:124:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] 124 | int lenj; | ^~~ estfrag3.c:123:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] 123 | int leni; | ^~~ estfrag3.c:121:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] 121 | int k; | ^~ estfrag3.c: In function 'Wise2_PackAln_bestmemory_EstFrag3': estfrag3.c:965:19: warning: unused variable 'de' [-Wunused-variable] 965 | EstFrag3 * mat; | ^ estfrag3.c: In function 'Wise2_max_special_strip_EstFrag3': estfrag3.c:2242:9: warning: variable 'cscore' set but not used [-Wunused-but-set-variable] 2242 | { | ^ estfrag3.c:2241:9: warning: unused variable 'temp' [-Wunused-variable] 2241 | int max_special_strip_EstFrag3(EstFrag3 * mat,int i,int j,int state,boolean isspecial,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore) | ^~~~ estfrag3.c: In function 'Wise2_PackAln_bestmemory_EstFrag3': estfrag3.c:1026:12: warning: 'out' may be used uninitialized [-Wmaybe-uninitialized] 1026 | | ^ estfrag3.c:964:15: note: 'out' was declared here 964 | long long total; | ^~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ estslimloop.c estslimloop.c: In function 'Wise2_calculate_shatter_EstSlimLoop3': estslimloop.c:125:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] 125 | int lenj; | ^~~ estslimloop.c:124:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] 124 | int leni; | ^~~ estslimloop.c:122:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] 122 | int k; | ^~ estslimloop.c: In function 'Wise2_PackAln_bestmemory_EstSlimLoop3': estslimloop.c:1114:19: warning: unused variable 'de' [-Wunused-variable] 1114 | EstSlimLoop3 * mat; | ^~ estslimloop.c: In function 'Wise2_PackAln_calculate_Small_EstSlimLoop3': estslimloop.c:1535:19: warning: unused variable 'pau' [-Wunused-variable] 1535 | int score; | ^ estslimloop.c: In function 'Wise2_PackAln_bestmemory_EstSlimLoop3': estslimloop.c:1175:12: warning: 'out' may be used uninitialized [-Wmaybe-uninitialized] 1175 | | ^ estslimloop.c:1113:15: note: 'out' was declared here 1113 | long long total; | ^~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ gwquickdb.c gwquickdb.dy: In function 'Wise2_init_GeneWiseQuickDB': gwquickdb.dy:46:1: warning: control reaches end of non-void function [-Wreturn-type] 46 | } | ^ gwquickdb.dy: In function 'Wise2_reload_GeneWiseQuickDB': gwquickdb.dy:65:1: warning: control reaches end of non-void function [-Wreturn-type] 65 | } | ^ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ threestatedb.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ pfamhmmer1db.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ pwmdna.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../HMMer2/ -DHMMER_INTERNAL -I../base/ -I../dynlibsrc/ wise2xhmmer2.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ genewisemodeldb.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ seqhit.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ standardout.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ geneparser4.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ estquick3.c estquick3.c: In function 'Wise2_calculate_shatter_EstQuick3': estquick3.c:124:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] 124 | int lenj; | ^~~ estquick3.c:123:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] 123 | int leni; | ^~~ estquick3.c:121:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] 121 | int k; | ^~ estquick3.c: In function 'Wise2_PackAln_bestmemory_EstQuick3': estquick3.c:860:19: warning: unused variable 'de' [-Wunused-variable] 860 | EstQuick3 * mat; | ^~ estquick3.c: In function 'Wise2_max_special_strip_EstQuick3': estquick3.c:1766:9: warning: variable 'cscore' set but not used [-Wunused-but-set-variable] 1766 | { | ^ estquick3.c:1765:9: warning: unused variable 'temp' [-Wunused-variable] 1765 | int max_special_strip_EstQuick3(EstQuick3 * mat,int i,int j,int state,boolean isspecial,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore) | ^~~~ estquick3.c: In function 'Wise2_PackAln_bestmemory_EstQuick3': estquick3.c:921:12: warning: 'out' may be used uninitialized [-Wmaybe-uninitialized] 921 | | ^ estquick3.c:859:15: note: 'out' was declared here 859 | long long total; | ^~~ gcc -g -o estwise estwise.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna -lwisebase -lm -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L genewise.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I. genewise.c: In function 'build_objects': genewise.c:446:10: warning: unused variable 'ifp' [-Wunused-variable] 446 | FILE * ifp; | ^~~ gcc -o genewise genewise.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase -lm -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` In function 'Wise2_GeneWiseCodonModel_from_GeneFrequencies', inlined from 'Wise2_GeneParameter21_from_GeneFrequency21' at geneparameter.dy:205:15: geneparameter.dy:115:34: warning: iteration 2 invokes undefined behavior [-Waggressive-loop-optimizations] 115 | out->in_acceptor[perm] = acceptor->gsc[l]->number / 64.0; | ^ geneparameter.dy:108:14: note: within this loop 108 | for(i=0;i<4;i++) | ^ geneparameter.dy:97:24: warning: iteration 2 invokes undefined behavior [-Waggressive-loop-optimizations] 97 | out->in_donor[perm] += donor->gsc[l]->number / 64.0; | ^ geneparameter.dy:90:14: note: within this loop 90 | for(i=0;i<4;i++) | ^ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L genewisedb.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ In file included from ../dynlibsrc/dyna.h:53, from threestatemodel.h:7, from wise2xhmmer2.h:24, from genewisedb.c:4: ../dynlibsrc/genomicregion.h: In function 'show_output': ../dynlibsrc/genomicregion.h:453:35: warning: 'cgr' may be used uninitialized [-Wmaybe-uninitialized] 453 | #define add_Gene_to_GenomicRegion Wise2_add_Gene_to_GenomicRegion | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genewisedb.c:216:19: note: 'cgr' was declared here 216 | GenomicRegion * cgr; | ^~~ gcc -g -o genewisedb genewisedb.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna -lwisebase -lm -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` In function 'Wise2_GeneWiseCodonModel_from_GeneFrequencies', inlined from 'Wise2_GeneParameter21_from_GeneFrequency21' at geneparameter.dy:205:15, inlined from 'Wise2_GeneParameter21_wrap' at gwrap.dy:76:9, inlined from 'build_db_objects' at genewisedb.c:554:11: geneparameter.dy:115:34: warning: iteration 2 invokes undefined behavior [-Waggressive-loop-optimizations] 115 | out->in_acceptor[perm] = acceptor->gsc[l]->number / 64.0; | ^ geneparameter.dy:108:14: note: within this loop 108 | for(i=0;i<4;i++) | ^ geneparameter.dy:97:24: warning: iteration 2 invokes undefined behavior [-Waggressive-loop-optimizations] 97 | out->in_donor[perm] += donor->gsc[l]->number / 64.0; | ^ geneparameter.dy:90:14: note: within this loop 90 | for(i=0;i<4;i++) | ^ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L estwisedb.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ In file included from ../dynlibsrc/seqalign.h:6, from wise2xhmmer2.h:23, from estwisedb.c:4: ../dynlibsrc/sequence.h: In function 'show_output': ../dynlibsrc/sequence.h:665:25: warning: 'set' may be used uninitialized [-Wmaybe-uninitialized] 665 | #define add_SequenceSet Wise2_add_SequenceSet | ^~~~~~~~~~~~~~~~~~~~~ estwisedb.c:183:17: note: 'set' was declared here 183 | SequenceSet * set; | ^~~ In file included from estwisedb.c:16: estwrap.h:166:36: warning: 'anchored' may be used uninitialized [-Wmaybe-uninitialized] 166 | #define write_mul_estwise_AlnBlock Wise2_write_mul_estwise_AlnBlock | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ estwisedb.c:182:14: note: 'anchored' was declared here 182 | AlnBlock * anchored; | ^~~~~~~~ gcc -g -o estwisedb estwisedb.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna -lwisebase -lm -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ genomewise.c genomewise.c: In function 'main': genomewise.c:95:10: warning: unused variable 'divide_string' [-Wunused-variable] 95 | char * divide_string = "//"; | ^~~~~~~~~~~~~ genomewise.c:81:7: warning: unused variable 'kbyte' [-Wunused-variable] 81 | int kbyte = 10000; | ^~~~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ genomewise9.c genomewise9.c: In function 'Wise2_calculate_shatter_GenomeWise9': genomewise9.c:137:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] 137 | int lenj; | ^~~ genomewise9.c:136:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] 136 | int leni; | ^~~ genomewise9.c:134:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] 134 | int k; | ^~ genomewise9.c: In function 'Wise2_PackAln_bestmemory_GenomeWise9': genomewise9.c:1331:19: warning: unused variable 'de' [-Wunused-variable] 1331 | GenomeWise9 * mat; | ^~ genomewise9.c: In function 'Wise2_PackAln_calculate_Small_GenomeWise9': genomewise9.c:1895:19: warning: unused variable 'pau' [-Wunused-variable] 1895 | int score; | ^ genomewise9.c: In function 'Wise2_thread_loop_GenomeWise9': genomewise9.c:745:1: warning: control reaches end of non-void function [-Wreturn-type] 745 | { | ^ genomewise9.c: In function 'Wise2_PackAln_bestmemory_GenomeWise9': genomewise9.c:1392:12: warning: 'out' may be used uninitialized [-Wmaybe-uninitialized] 1392 | | ^ genomewise9.c:1330:15: note: 'out' was declared here 1330 | long long total; | ^~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ genome_evidence.c genome_evidence.dy: In function 'Wise2_free_GenomeEvidenceUnit': genome_evidence.dy:61:1: warning: control reaches end of non-void function [-Wreturn-type] 61 | } | ^ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ est_evidence.c est_evidence.dy: In function 'Wise2_new_est_GenomeEvidenceUnit': est_evidence.dy:142:16: warning: assignment to 'int (*)(void *)' from incompatible pointer type 'Wise2_EstEvidence * (*)(Wise2_EstEvidence *)' [-Wincompatible-pointer-types] 142 | in->geu_free = free_EstEvidence; | ^ est_evidence.dy: In function 'Wise2_est_start_pot': est_evidence.dy:183:7: warning: unused variable 'i' [-Wunused-variable] 183 | int i; | ^ est_evidence.dy: In function 'Wise2_est_stop_pot': est_evidence.dy:203:7: warning: unused variable 'i' [-Wunused-variable] 203 | int i; | ^ gcc -g -o genomewise genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneoutput.o geneutil.o -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ sywise.c sywise.c: In function 'make_PairBaseCodonModelScore': sywise.c:64:10: warning: unused variable 'ifp' [-Wunused-variable] 64 | FILE * ifp; | ^~~ sywise.c: In function 'show_score_sequence': sywise.c:117:37: warning: array subscript has type 'char' [-Wchar-subscripts] 117 | match_score = m->base[pbs->seq[alc->alu[1]->start+1]]; | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ sywise.c:118:38: warning: array subscript has type 'char' [-Wchar-subscripts] 118 | match_score += m->base[pbs->seq[alc->alu[1]->start+2]]; | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ sywise.c:119:38: warning: array subscript has type 'char' [-Wchar-subscripts] 119 | match_score += m->base[pbs->seq[alc->alu[1]->start+3]]; | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ sywise.c: In function 'main': sywise.c:212:11: warning: unused variable 'show_gene_raw' [-Wunused-variable] 212 | boolean show_gene_raw = 0; | ^~~~~~~~~~~~~ sywise.c:211:11: warning: unused variable 'show_trans' [-Wunused-variable] 211 | boolean show_trans = 1; | ^~~~~~~~~~ sywise.c:204:27: warning: variable 'std_opt' set but not used [-Wunused-but-set-variable] 204 | StandardOutputOptions * std_opt; | ^~~~~~~ sywise.c:202:13: warning: unused variable 'trans' [-Wunused-variable] 202 | Protein * trans; | ^~~~~ sywise.c:201:19: warning: variable 'gr2' set but not used [-Wunused-but-set-variable] 201 | GenomicRegion * gr2; | ^~~ sywise.c:183:13: warning: unused variable 'score_mat' [-Wunused-variable] 183 | CompMat * score_mat; | ^~~~~~~~~ sywise.c:168:7: warning: unused variable 'i' [-Wunused-variable] 168 | int i; | ^ In file included from sywise.c:1: sywise20.h:328:46: warning: 'pal' may be used uninitialized [-Wmaybe-uninitialized] 328 | #define convert_PackAln_to_AlnBlock_SyWise20 Wise2_convert_PackAln_to_AlnBlock_SyWise20 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sywise.c:196:13: note: 'pal' was declared here 196 | PackAln * pal; | ^~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ sywise20.c sywise20.c: In function 'Wise2_calculate_shatter_SyWise20': sywise20.c:137:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] 137 | int lenj; | ^~~ sywise20.c:136:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] 136 | int leni; | ^~~ sywise20.c:134:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] 134 | int k; | ^~ sywise20.c: In function 'Wise2_serial_search_SyWise20': sywise20.c:789:9: warning: unused variable 'db_status' [-Wunused-variable] 789 | Search_Return_Type serial_search_SyWise20(Hscore * out,SyExonScore* exonmodel,ComplexSequence* seq ,PairBaseCodonModelScore* codon,PairBaseModelScore* nonc,PairBaseCodonModelScore* start,PairBaseCodonModelScore* stop,Score intron_open,Score gene_open,Score nonc_cost) | ^~~~~~~~~ sywise20.c: In function 'Wise2_PackAln_bestmemory_SyWise20': sywise20.c:1355:19: warning: unused variable 'de' [-Wunused-variable] 1355 | SyWise20 * mat; | ^ sywise20.c: In function 'Wise2_PackAln_calculate_Small_SyWise20': sywise20.c:1943:19: warning: unused variable 'pau' [-Wunused-variable] 1943 | int score; | ^ sywise20.c: In function 'Wise2_thread_loop_SyWise20': sywise20.c:764:1: warning: control reaches end of non-void function [-Wreturn-type] 764 | { | ^ sywise20.c: In function 'Wise2_PackAln_bestmemory_SyWise20': sywise20.c:1416:12: warning: 'out' may be used uninitialized [-Wmaybe-uninitialized] 1416 | | ^ sywise20.c:1354:15: note: 'out' was declared here 1354 | long long total; | ^~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ syexonmodel.c gcc -g -o sywise sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o standardout.o geneutil.o -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ pseudowise.c pseudowise.c: In function 'pseudo_gene_assessment': pseudowise.c:99:39: warning: array subscript has type 'char' [-Wchar-subscripts] 99 | if( protein->comp[aa][pep->seq[pep_pos]] < 0 ) { | ~~~~~~~~^~~~~~~~~ pseudowise.c:57:9: warning: unused variable 'j' [-Wunused-variable] 57 | int i,j; | ^ pseudowise.c:57:7: warning: unused variable 'i' [-Wunused-variable] 57 | int i,j; | ^ pseudowise.c: In function 'main': pseudowise.c:180:7: warning: variable 'offset' set but not used [-Wunused-but-set-variable] 180 | int offset; | ^~~~~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ pseudowise7.c pseudowise7.c: In function 'Wise2_calculate_shatter_PseudoWise7': pseudowise7.c:128:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] 128 | int lenj; | ^~~ pseudowise7.c:127:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] 127 | int leni; | ^~~ pseudowise7.c:125:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] 125 | int k; | ^~ pseudowise7.c: In function 'Wise2_PackAln_bestmemory_PseudoWise7': pseudowise7.c:1207:19: warning: unused variable 'de' [-Wunused-variable] 1207 | PseudoWise7 * mat; | ^~ pseudowise7.c: In function 'Wise2_max_special_strip_PseudoWise7': pseudowise7.c:2471:9: warning: variable 'cscore' set but not used [-Wunused-but-set-variable] 2471 | { | ^ pseudowise7.c:2470:9: warning: unused variable 'temp' [-Wunused-variable] 2470 | int max_special_strip_PseudoWise7(PseudoWise7 * mat,int i,int j,int state,boolean isspecial,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore) | ^~~~ pseudowise7.c: In function 'Wise2_PackAln_bestmemory_PseudoWise7': pseudowise7.c:1268:12: warning: 'out' may be used uninitialized [-Wmaybe-uninitialized] 1268 | | ^ pseudowise7.c:1206:15: note: 'out' was declared here 1206 | long long total; | ^~~ gcc -g -o pseudowise pseudowise.o pseudowise7.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna -lwisebase -lm -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` promoterwise.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ localdba.c localdba.c: In function 'Wise2_calculate_shatter_LocalDnaMatchBlock': localdba.c:127:9: warning: variable 'num' set but not used [-Wunused-but-set-variable] 127 | int lenj; | ^~~ localdba.c:126:9: warning: variable 'tot' set but not used [-Wunused-but-set-variable] 126 | int leni; | ^~~ localdba.c:124:9: warning: variable 'leni' set but not used [-Wunused-but-set-variable] 124 | int k; | ^~ localdba.c: In function 'Wise2_serial_search_LocalDnaMatchBlock': localdba.c:487:9: warning: unused variable 'db_status' [-Wunused-variable] 487 | Search_Return_Type serial_search_LocalDnaMatchBlock(Hscore * out,ComplexSequence* query,ComplexSequence* target ,LocalCisHitScore* lchs) | ^~~~~~~~~ localdba.c: In function 'Wise2_PackAln_bestmemory_LocalDnaMatchBlock': localdba.c:841:19: warning: unused variable 'de' [-Wunused-variable] 841 | LocalDnaMatchBlock * mat; | ^~ localdba.c: In function 'Wise2_max_special_strip_LocalDnaMatchBlock': localdba.c:1984:9: warning: variable 'cscore' set but not used [-Wunused-but-set-variable] 1984 | { | ^ localdba.c:1983:9: warning: unused variable 'temp' [-Wunused-variable] 1983 | int max_special_strip_LocalDnaMatchBlock(LocalDnaMatchBlock * mat,int i,int j,int state,boolean isspecial,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore) | ^~~~ localdba.c: In function 'Wise2_PackAln_bestmemory_LocalDnaMatchBlock': localdba.c:902:12: warning: 'out' may be used uninitialized [-Wmaybe-uninitialized] 902 | | ^ localdba.c:840:15: note: 'out' was declared here 840 | long long total; | ^~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` localcishit.c localcishit.dy: In function 'Wise2_expand_to_subhits_LocalCisHitSet': localcishit.dy:91:7: warning: variable 'score' set but not used [-Wunused-but-set-variable] 91 | int score; | ^~~~~ localcishit.dy:90:7: warning: unused variable 'score_start' [-Wunused-variable] 90 | int score_start; | ^~~~~~~~~~~ localcishit.dy:89:7: warning: unused variable 'tend' [-Wunused-variable] 89 | int tend; | ^~~~ localcishit.dy:88:7: warning: unused variable 'qend' [-Wunused-variable] 88 | int qend; | ^~~~ localcishit.dy:87:7: warning: variable 'tstart' set but not used [-Wunused-but-set-variable] 87 | int tstart; | ^~~~~~ localcishit.dy:86:7: warning: variable 'qstart' set but not used [-Wunused-but-set-variable] 86 | int qstart; | ^~~~~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ localcispara.c gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ motifmatrix.c motifmatrix.c: In function 'Wise2_MotifConsMatrix_alloc_matrix': motifmatrix.c:408:24: warning: assignment to 'char' from 'void *' makes integer from pointer without a cast [-Wint-conversion] 408 | for(i=0;iseed = temp; | ~~~~~~~~~~^~~~~~ transfactor.dy:838:14: note: 'temp' was declared here 838 | SeqAlign * temp; | ^~~~ transfactor.dy: In function 'Wise2_read_ben_IUPAC_TransFactorSet': transfactor.dy:680:21: warning: '%s' directive writing up to 511 bytes into a region of size between 495 and 504 [-Wformat-overflow=] 680 | sprintf(sbuffer,"motif_%d_%s",motif_no,buffer); | ^~~~~~~~~~~~~ ~~~~~~ In file included from /usr/include/stdio.h:906, from ../base/wisebase.h:6, from pwmdna.h:6, from transfactor.h:6, from transfactor.c:4: In function 'sprintf', inlined from 'Wise2_read_ben_IUPAC_TransFactorSet' at transfactor.dy:680:5: /usr/include/bits/stdio2.h:30:10: note: '__sprintf_chk' output between 9 and 529 bytes into a destination of size 512 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ transfactor.dy: In function 'Wise2_calculate_TransFactorMatchSet': transfactor.dy:437:9: warning: 'cutoff' may be used uninitialized [-Wmaybe-uninitialized] 437 | if( rev_prob > cutoff ) { | ^ transfactor.dy:366:10: note: 'cutoff' was declared here 366 | double cutoff; | ^~~~~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ pairwiseshortdna.c pairwiseshortdna.dy: In function 'Wise2_query_to_reverse_target': pairwiseshortdna.dy:56:11: warning: variable 'reverse_tree' set but not used [-Wunused-but-set-variable] 56 | GTree * reverse_tree; | ^~~~~~~~~~~~ pairwiseshortdna.dy:55:11: warning: variable 'forward_tree' set but not used [-Wunused-but-set-variable] 55 | GTree * forward_tree; | ^~~~~~~~~~~~ gcc -g -o promoterwise promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm `pkg-config --libs glib-2.0` -lpthread gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c scanwisep.c: In function 'new_HSPScanInterface_from_ScanWiseHSPImpl': scanwisep.c:73:7: warning: unused variable 'c' [-Wunused-variable] 73 | int c; | ^ scanwisep.c:72:7: warning: unused variable 'ret' [-Wunused-variable] 72 | int ret; | ^~~ scanwisep.c:70:14: warning: unused variable 'seq' [-Wunused-variable] 70 | Sequence * seq; | ^~~ scanwisep.c: In function 'HitPair_from_HSPset_sw': scanwisep.c:305:7: warning: unused variable 'i' [-Wunused-variable] 305 | int i; | ^ scanwisep.c: In function 'HitList_from_LinearHSPmanager_sw': scanwisep.c:326:30: warning: unused variable 'conv' [-Wunused-variable] 326 | struct convert_data_fulldp conv; | ^~~~ scanwisep.c: In function 'main': scanwisep.c:476:25: warning: variable 'ssl' set but not used [-Wunused-but-set-variable] 476 | SearchStatInterface * ssl; | ^~~ scanwisep.c: In function 'new_HSPScanInterface_from_ScanWiseHSPImpl': scanwisep.c:144:10: warning: 'out' may be used uninitialized [-Wmaybe-uninitialized] 144 | return out; | ^~~ scanwisep.c:67:22: note: 'out' was declared here 67 | HSPScanInterface * out; | ^~~ gcc -c -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` hsp2aln_sw.c hsp2aln_sw.dy: In function 'Wise2_worker_thread_LM2HitList': hsp2aln_sw.dy:119:71: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 119 | if( tm->current_pos >= tm->input->len || tm->para->no_hitalns > 0 && tm->current_pos > tm->para->no_hitalns || | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -o scanwise scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../network/net_hspscan.o ../network/client_multihspscan.o -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase -lm -lpthread -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` ar ru libmodel.a geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o ar: creating libmodel.a make[1]: Leaving directory '/builddir/build/BUILD/wise2.4.1/src/models' make bin make[1]: Entering directory '/builddir/build/BUILD/wise2.4.1/src' mkdir bin cp models/pswdb models/psw models/genewisedb models/estwisedb models/estwise models/genewise models/dba models/dnal models/promoterwise network/scanwise_server models/scanwise ./bin ./welcome.csh Welcome to Wise2.4 The executable programs are in the ./bin directory You must set your WISECONFIGDIR to the config directory before using the programs ie, type setenv WISECONFIGDIR /builddir/build/BUILD/wise2.4.1/src/../wisecfg/ to try an example, try cd example and then ../bin/genewise road.pep human.genomic to build perl, type make perl and follow the instructions to test the package, type make test make[1]: Leaving directory '/builddir/build/BUILD/wise2.4.1/src' make: Leaving directory '/builddir/build/BUILD/wise2.4.1/src' + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.7Vbgip + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/wise2-2.4.1-15.fc38.x86_64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/wise2-2.4.1-15.fc38.x86_64 ++ dirname /builddir/build/BUILDROOT/wise2-2.4.1-15.fc38.x86_64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/wise2-2.4.1-15.fc38.x86_64 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CFLAGS ~/build/BUILD/wise2.4.1/src/bin ~/build/BUILD/wise2.4.1 + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd wise2.4.1 + pushd src/bin + mkdir -p /builddir/build/BUILDROOT/wise2-2.4.1-15.fc38.x86_64/usr/bin + for i in dba dnal estwise estwisedb genewise genewisedb promoterwise scanwise scanwise_server psw pswdb + install -pm 755 dba /builddir/build/BUILDROOT/wise2-2.4.1-15.fc38.x86_64/usr/bin + for i in dba dnal estwise estwisedb genewise genewisedb promoterwise scanwise scanwise_server psw pswdb + install -pm 755 dnal /builddir/build/BUILDROOT/wise2-2.4.1-15.fc38.x86_64/usr/bin + for i in dba dnal estwise estwisedb genewise genewisedb promoterwise scanwise scanwise_server psw pswdb + install -pm 755 estwise /builddir/build/BUILDROOT/wise2-2.4.1-15.fc38.x86_64/usr/bin + for i in dba dnal estwise estwisedb genewise genewisedb promoterwise scanwise scanwise_server psw pswdb + install -pm 755 estwisedb /builddir/build/BUILDROOT/wise2-2.4.1-15.fc38.x86_64/usr/bin + for i in dba dnal estwise estwisedb genewise genewisedb promoterwise scanwise scanwise_server psw pswdb + install -pm 755 genewise /builddir/build/BUILDROOT/wise2-2.4.1-15.fc38.x86_64/usr/bin + for i in dba dnal estwise estwisedb genewise genewisedb promoterwise scanwise scanwise_server psw pswdb + install -pm 755 genewisedb /builddir/build/BUILDROOT/wise2-2.4.1-15.fc38.x86_64/usr/bin + for i in dba dnal estwise estwisedb genewise genewisedb promoterwise scanwise scanwise_server psw pswdb + install -pm 755 promoterwise /builddir/build/BUILDROOT/wise2-2.4.1-15.fc38.x86_64/usr/bin + for i in dba dnal estwise estwisedb genewise genewisedb promoterwise scanwise scanwise_server psw pswdb + install -pm 755 scanwise /builddir/build/BUILDROOT/wise2-2.4.1-15.fc38.x86_64/usr/bin + for i in dba dnal estwise estwisedb genewise genewisedb promoterwise scanwise scanwise_server psw pswdb + install -pm 755 scanwise_server /builddir/build/BUILDROOT/wise2-2.4.1-15.fc38.x86_64/usr/bin + for i in dba dnal estwise estwisedb genewise genewisedb promoterwise scanwise scanwise_server psw pswdb + install -pm 755 psw /builddir/build/BUILDROOT/wise2-2.4.1-15.fc38.x86_64/usr/bin + for i in dba dnal estwise estwisedb genewise genewisedb promoterwise scanwise scanwise_server psw pswdb + install -pm 755 pswdb /builddir/build/BUILDROOT/wise2-2.4.1-15.fc38.x86_64/usr/bin + popd ~/build/BUILD/wise2.4.1 + mkdir -p /builddir/build/BUILDROOT/wise2-2.4.1-15.fc38.x86_64/usr/share/wise2 + pushd wisecfg ~/build/BUILD/wise2.4.1/wisecfg ~/build/BUILD/wise2.4.1 + install -pm 644 BLOSUM30.bla BLOSUM45.bla BLOSUM62.bla BLOSUM80.bla aa.rnd cb.tmf codon.martian codon.table gene.stat gon120.bla gon160.bla gon200.bla gon250.bla gon350.bla human.gf human.gp human.stats idenity.bla methods pb.gf pombe.gf tm.pri wag55 wag65 wag75 wag85 wise.2 wise.per worm.gf /builddir/build/BUILDROOT/wise2-2.4.1-15.fc38.x86_64/usr/share/wise2 + popd ~/build/BUILD/wise2.4.1 + mkdir -p /builddir/build/BUILDROOT/wise2-2.4.1-15.fc38.x86_64/usr/share/wise2/examples + pushd test_data ~/build/BUILD/wise2.4.1/test_data ~/build/BUILD/wise2.4.1 + install -pm 644 HOX.HMM Q8NAN2.dna Q8NAN2.pep README alignwise.gen db.hmm dummy_hox.dna epo.genomic epo.pep fugu.gen fugu_human.pep hn_est.fa human.genomic jason.dna jason.pep keratin_intron.human keratin_intron.mouse pep.fa phased_roa1.pep road.pep rpo_fugu.gen rpo_h_f.anchor rpo_h_m.anchor rpo_h_r.anchor rpo_human.gen rpo_human.intron rpo_human.pep rpo_mouse.gen rpo_rat.gen rrm.HMM rua1.pep vav.dna vav_promoter.human vav_promoter.mouse xeno.cdna xeno.pep /builddir/build/BUILDROOT/wise2-2.4.1-15.fc38.x86_64/usr/share/wise2/examples + popd ~/build/BUILD/wise2.4.1 + mkdir -p /builddir/build/BUILDROOT/wise2-2.4.1-15.fc38.x86_64/etc/profile.d + echo 'export WISECONFIGDIR=/usr/share/wise2/' + echo 'setenv WISECONFIGDIR /usr/share/wise2/' + /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 2.4.1-15.fc38 --unique-debug-suffix -2.4.1-15.fc38.x86_64 --unique-debug-src-base wise2-2.4.1-15.fc38.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/wise2.4.1 extracting debug info from /builddir/build/BUILDROOT/wise2-2.4.1-15.fc38.x86_64/usr/bin/dba extracting debug info from /builddir/build/BUILDROOT/wise2-2.4.1-15.fc38.x86_64/usr/bin/dnal extracting debug info from /builddir/build/BUILDROOT/wise2-2.4.1-15.fc38.x86_64/usr/bin/estwise extracting debug info from /builddir/build/BUILDROOT/wise2-2.4.1-15.fc38.x86_64/usr/bin/estwisedb extracting debug info from /builddir/build/BUILDROOT/wise2-2.4.1-15.fc38.x86_64/usr/bin/genewise extracting debug info from /builddir/build/BUILDROOT/wise2-2.4.1-15.fc38.x86_64/usr/bin/genewisedb extracting debug info from /builddir/build/BUILDROOT/wise2-2.4.1-15.fc38.x86_64/usr/bin/promoterwise extracting debug info from /builddir/build/BUILDROOT/wise2-2.4.1-15.fc38.x86_64/usr/bin/psw extracting debug info from /builddir/build/BUILDROOT/wise2-2.4.1-15.fc38.x86_64/usr/bin/pswdb extracting debug info from /builddir/build/BUILDROOT/wise2-2.4.1-15.fc38.x86_64/usr/bin/scanwise extracting debug info from /builddir/build/BUILDROOT/wise2-2.4.1-15.fc38.x86_64/usr/bin/scanwise_server original debug info size: 15232kB, size after compression: 11764kB /usr/bin/sepdebugcrcfix: Updated 11 CRC32s, 0 CRC32s did match. 23175 blocks + /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 *** WARNING: ./usr/src/debug/wise2-2.4.1-15.fc38.x86_64/src/base/wisetime.dy is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/wise2-2.4.1-15.fc38.x86_64/src/base/wiseoverlay.dy is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/wise2-2.4.1-15.fc38.x86_64/src/base/wisememman.dy is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/wise2-2.4.1-15.fc38.x86_64/src/base/wisefile.dy is executable but has no shebang, removing executable bit + /usr/lib/rpm/brp-remove-la-files + /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 + /usr/lib/rpm/redhat/brp-python-hardlink Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.HKLAiz + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd wise2.4.1 + export WISECONFIGDIR=/builddir/build/BUILD/wise2.4.1/wisecfg + WISECONFIGDIR=/builddir/build/BUILD/wise2.4.1/wisecfg + make -C src test make: Entering directory '/builddir/build/BUILD/wise2.4.1/src' cd test ; perl testman.pl -cf ../wisecfg < short.test >>> Doing promoterwise promoterwise standard test >>> Calling [../bin/promoterwise -silent pw.human pw.mouse > TEMP-PW] >>> promoterwise ... Passed >>> Doing basic-cdna cdna test case (protein v cdna), all outputs >>> Calling [../bin/estwise short.pep short.dna -indel 1e-5 -subs 1e-5 -pretty -para -sum -alb -pal -silent -alg 333 > TEMP] >>> basic-cdna ... Passed >>> Doing basic-genomic genomic test case (protein v genomic), all outputs >>> Calling [../bin/genewise short.pep short.dna -pretty -para -genes -sum -cdna -trans -ace -gener -alb -pal -quiet -dymem linear > TEMP] >>> basic-genomic ... Passed >>> Doing hmm-binary-cdna cdna test case (protein v cdna), all outputs >>> Calling [../bin/estwise HMM.binary -indel 1e-5 -subs 1e-5 -hmmer short.dna -pretty -para -sum -alb -pal -quiet -alg 333L > TEMP] FATAL: No support for non-protein, non-nucleic acid alphabets. >>> Bad exit status - 256 (system - ) >>> hmm-binary-cdna ... Failed >>> Doing hmm-wrong-dna HMMs vs DNA sequence when there is no match >>> Calling [../bin/genewise wrong.hmm -hmmer short.dna -alg 623 -pal > TEMP] Information In making HSHNCPA1 a genomic sequence, converted 2 bases (0.5%) to N's from non ATGCN GeneWise6 Matrix calculation: [ 0] Cells 0%[ 1000] Cells 3%[ 2000] Cells 6%[ 3000] Cells 9%[ 4000] Cells 12%[ 5000] Cells 15%[ 6000] Cells 18%[ 7000] Cells 21%[ 8000] Cells 24%[ 9000] Cells 27%[ 10000] Cells 30%[ 11000] Cells 33%[ 12000] Cells 36%[ 13000] Cells 39%[ 14000] Cells 42%[ 15000] Cells 45%[ 16000] Cells 48%[ 17000] Cells 51%[ 18000] Cells 54%[ 19000] Cells 57%[ 20000] Cells 61%[ 21000] Cells 64%[ 22000] Cells 67%[ 23000] Cells 70%[ 24000] Cells 73%[ 25000] Cells 76%[ 26000] Cells 79%[ 27000] Cells 82%[ 28000] Cells 85%[ 29000] Cells 88%[ 30000] Cells 91%[ 31000] Cells 94%[ 32000] Cells 97% >>> hmm-wrong-dna ... Passed >>> Doing hmm-wrong-dna-est HMMs vs DNA sequence when there is no match >>> Calling [../bin/estwise wrong.hmm -hmmer short.dna -alg 333 -pal > TEMP] Information In making HSHNCPA1 a cdna sequence, converted 2 bases (0.5%) to N's from non ATGCN EstWise3 Matrix calculation: [ 0] Cells 0%[ 1000] Cells 3%[ 2000] Cells 6%[ 3000] Cells 9%[ 4000] Cells 12%[ 5000] Cells 15%[ 6000] Cells 18%[ 7000] Cells 21%[ 8000] Cells 24%[ 9000] Cells 27%[ 10000] Cells 30%[ 11000] Cells 33%[ 12000] Cells 36%[ 13000] Cells 39%[ 14000] Cells 42%[ 15000] Cells 45%[ 16000] Cells 48%[ 17000] Cells 51%[ 18000] Cells 54%[ 19000] Cells 57%[ 20000] Cells 61%[ 21000] Cells 64%[ 22000] Cells 67%[ 23000] Cells 70%[ 24000] Cells 73%[ 25000] Cells 76%[ 26000] Cells 79%[ 27000] Cells 82%[ 28000] Cells 85%[ 29000] Cells 88%[ 30000] Cells 91%[ 31000] Cells 94%[ 32000] Cells 97% EstWise3 Matrix calculation: [ 0] Cells 0%[ 1000] Cells 3%[ 2000] Cells 6%[ 3000] Cells 9%[ 4000] Cells 12%[ 5000] Cells 15%[ 6000] Cells 18%[ 7000] Cells 21%[ 8000] Cells 24%[ 9000] Cells 27%[ 10000] Cells 30%[ 11000] Cells 33%[ 12000] Cells 36%[ 13000] Cells 39%[ 14000] Cells 42%[ 15000] Cells 45%[ 16000] Cells 48%[ 17000] Cells 51%[ 18000] Cells 54%[ 19000] Cells 57%[ 20000] Cells 61%[ 21000] Cells 64%[ 22000] Cells 67%[ 23000] Cells 70%[ 24000] Cells 73%[ 25000] Cells 76%[ 26000] Cells 79%[ 27000] Cells 82%[ 28000] Cells 85%[ 29000] Cells 88%[ 30000] Cells 91%[ 31000] Cells 94%[ 32000] Cells 97% >>> hmm-wrong-dna-est ... Passed >>> Doing hmm-ascii-genomic cdna test case (protein v cdna), all outputs >>> Calling [../bin/genewise -init local HMM.ascii -hmmer short.dna -pretty -para -genes -sum -cdna -trans -ace -gener -alb -pal -quiet > TEMP] FATAL: No support for non-protein, non-nucleic acid alphabets. >>> Bad exit status - 256 (system - ) >>> hmm-ascii-genomic ... Failed >>> Doing genewise-db genewisedb hmm vs DNA sequences. Could take a while >>> Calling [../bin/genewisedb rrm.HMM -hmmer dna.db -pretty -para -gener -genes -cdna -trans -ace -quiet -init global > TEMP] >>> genewise-db ... Passed >>> Doing genewise-db-lite genewisedb hmm vs DNA sequences, using GWLITE. Could take a while >>> Calling [../bin/genewisedb rrm.HMM -hmmer dna.db -pretty -para -gener -genes -cdna -trans -ace -quiet -init global -alg 6LITE > TEMP] >>> genewise-db-lite ... Passed >>> Doing estwise-db estwisedb hmm vs DNA sequences. Could take a while >>> Calling [../bin/estwisedb -init local rrm.HMM -hmmer dna.db -pretty -para -alb -quiet -alg 333 -aalg 333 > TEMP] >>> estwise-db ... Passed >>> Doing pswdb Protein smith waterman db search >>> Calling [../bin/pswdb road.pep pep.fa -quiet > TEMP ] >>> pswdb ... Passed >>> Doing genewisedb-pfam-mode genewisedb designed for Pfam searching >>> Calling [../bin/genewisedb -pfam rrm.HMM -dnas short.dna -pretty -para -alb -quiet -alg 623 -aalg 623L > TEMP] >>> genewisedb-pfam-mode ... Passed Tests failed PLEASE: email ewan birney (birney@sanger.ac.uk) with the test.results file make: Leaving directory '/builddir/build/BUILD/wise2.4.1/src' + RPM_EC=0 ++ jobs -p + exit 0 Processing files: wise2-2.4.1-15.fc38.x86_64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.FAclFs + umask 022 + cd /builddir/build/BUILD + cd wise2.4.1 + DOCDIR=/builddir/build/BUILDROOT/wise2-2.4.1-15.fc38.x86_64/usr/share/doc/wise2 + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/wise2-2.4.1-15.fc38.x86_64/usr/share/doc/wise2 + cp -pr README /builddir/build/BUILDROOT/wise2-2.4.1-15.fc38.x86_64/usr/share/doc/wise2 + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.SJTBtN + umask 022 + cd /builddir/build/BUILD + cd wise2.4.1 + LICENSEDIR=/builddir/build/BUILDROOT/wise2-2.4.1-15.fc38.x86_64/usr/share/licenses/wise2 + export LC_ALL=C + LC_ALL=C + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/wise2-2.4.1-15.fc38.x86_64/usr/share/licenses/wise2 + cp -pr LICENSE /builddir/build/BUILDROOT/wise2-2.4.1-15.fc38.x86_64/usr/share/licenses/wise2 + cp -pr LICENSE.base /builddir/build/BUILDROOT/wise2-2.4.1-15.fc38.x86_64/usr/share/licenses/wise2 + cp -pr LICENSE.dynlibsrc /builddir/build/BUILDROOT/wise2-2.4.1-15.fc38.x86_64/usr/share/licenses/wise2 + cp -pr LICENSE.dyc /builddir/build/BUILDROOT/wise2-2.4.1-15.fc38.x86_64/usr/share/licenses/wise2 + cp -pr LICENSE.GPL /builddir/build/BUILDROOT/wise2-2.4.1-15.fc38.x86_64/usr/share/licenses/wise2 + RPM_EC=0 ++ jobs -p + exit 0 Provides: config(wise2) = 2.4.1-15.fc38 wise2 = 2.4.1-15.fc38 wise2(x86-64) = 2.4.1-15.fc38 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: 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_2.34)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.7)(64bit) libglib-2.0.so.0()(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.29)(64bit) rtld(GNU_HASH) Processing files: wise2-doc-2.4.1-15.fc38.noarch Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.z7jCMj + umask 022 + cd /builddir/build/BUILD + cd wise2.4.1 + DOCDIR=/builddir/build/BUILDROOT/wise2-2.4.1-15.fc38.x86_64/usr/share/doc/wise2-doc + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/wise2-2.4.1-15.fc38.x86_64/usr/share/doc/wise2-doc + cp -pr docs /builddir/build/BUILDROOT/wise2-2.4.1-15.fc38.x86_64/usr/share/doc/wise2-doc + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.LDuhU4 + umask 022 + cd /builddir/build/BUILD + cd wise2.4.1 + LICENSEDIR=/builddir/build/BUILDROOT/wise2-2.4.1-15.fc38.x86_64/usr/share/licenses/wise2-doc + export LC_ALL=C + LC_ALL=C + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/wise2-2.4.1-15.fc38.x86_64/usr/share/licenses/wise2-doc + cp -pr LICENSE /builddir/build/BUILDROOT/wise2-2.4.1-15.fc38.x86_64/usr/share/licenses/wise2-doc + RPM_EC=0 ++ jobs -p + exit 0 Provides: wise2-doc = 2.4.1-15.fc38 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: wise2-examples-2.4.1-15.fc38.x86_64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.F4nc9d + umask 022 + cd /builddir/build/BUILD + cd wise2.4.1 + DOCDIR=/builddir/build/BUILDROOT/wise2-2.4.1-15.fc38.x86_64/usr/share/doc/wise2-examples + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/wise2-2.4.1-15.fc38.x86_64/usr/share/doc/wise2-examples + cp -pr test_data/README /builddir/build/BUILDROOT/wise2-2.4.1-15.fc38.x86_64/usr/share/doc/wise2-examples + RPM_EC=0 ++ jobs -p + exit 0 Provides: wise2-examples = 2.4.1-15.fc38 wise2-examples(x86-64) = 2.4.1-15.fc38 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: wise2-debugsource-2.4.1-15.fc38.x86_64 Provides: wise2-debugsource = 2.4.1-15.fc38 wise2-debugsource(x86-64) = 2.4.1-15.fc38 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: wise2-debuginfo-2.4.1-15.fc38.x86_64 Provides: debuginfo(build-id) = 0d3ac8dee84d50042d9a26295d9ce9bc62e6fb0b debuginfo(build-id) = 0fc9d361e12004ac993ada2ddd568f76d0f58768 debuginfo(build-id) = 2df0ae445146e6588d23485c06be7bae1fd0c04f debuginfo(build-id) = 3029c0d6a5e439e9d01800889916c64640cc6740 debuginfo(build-id) = 4426456a4285d4e1ed4756509bf50f76091774b5 debuginfo(build-id) = 58e0aea280f8116919ccc7a0a468fa2f8703155e debuginfo(build-id) = 5a85a76aeca33bd553d0ae03badd0f6e3b914639 debuginfo(build-id) = a8fac5c549f5f4b0d04745d7bc6b2ce1d2d80ed5 debuginfo(build-id) = dbb22854c6b3c7a083f49a120f89326b72fbcfb2 debuginfo(build-id) = e47c196e396c62b02131d5f9fdb55808f6e77ed6 debuginfo(build-id) = f1908ec1a2af2bc3d75de05c7d15a09bd3347087 wise2-debuginfo = 2.4.1-15.fc38 wise2-debuginfo(x86-64) = 2.4.1-15.fc38 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: wise2-debugsource(x86-64) = 2.4.1-15.fc38 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/wise2-2.4.1-15.fc38.x86_64 Wrote: /builddir/build/RPMS/wise2-debuginfo-2.4.1-15.fc38.x86_64.rpm Wrote: /builddir/build/RPMS/wise2-2.4.1-15.fc38.x86_64.rpm Wrote: /builddir/build/RPMS/wise2-examples-2.4.1-15.fc38.x86_64.rpm Wrote: /builddir/build/RPMS/wise2-doc-2.4.1-15.fc38.noarch.rpm Wrote: /builddir/build/RPMS/wise2-debugsource-2.4.1-15.fc38.x86_64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.gEeOUK + umask 022 + cd /builddir/build/BUILD + cd wise2.4.1 + /usr/bin/rm -rf /builddir/build/BUILDROOT/wise2-2.4.1-15.fc38.x86_64 + RPM_EC=0 ++ jobs -p + exit 0 Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.p88bhb + umask 022 + cd /builddir/build/BUILD + rm -rf wise2.4.1 wise2.4.1.gemspec + RPM_EC=0 ++ jobs -p + exit 0 Finish: rpmbuild wise2-2.4.1-15.fc38.src.rpm Finish: build phase for wise2-2.4.1-15.fc38.src.rpm INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-x86_64-1668213019.291541/root/var/log/dnf.rpm.log /var/lib/mock/fedora-rawhide-x86_64-1668213019.291541/root/var/log/dnf.librepo.log /var/lib/mock/fedora-rawhide-x86_64-1668213019.291541/root/var/log/dnf.log INFO: Done(/var/lib/copr-rpmbuild/results/wise2-2.4.1-15.fc38.src.rpm) Config(child) 2 minutes 47 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