Warning: Permanently added '2620:52:3:1:dead:beef:cafe:c14c' (ED25519) to the list of known hosts. Running: /usr/bin/copr-rpmbuild --verbose --drop-resultdir --build-id 5187320 --chroot fedora-rawhide-i386 --detached Version: 0.62 PID: 4879 Logging PID: 4880 Task: {'appstream': False, 'background': True, 'build_id': 5187320, 'buildroot_pkgs': [], 'chroot': 'fedora-rawhide-i386', 'enable_net': False, 'fedora_review': False, 'git_hash': '8fbc1d633396b5384af19025a2f015cdd5774096', 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/jakub/gcc-13-test/wise2', 'isolation': 'default', 'memory_reqs': 2048, 'package_name': 'wise2', 'package_version': '2.4.1-16', 'project_dirname': 'gcc-13-test', 'project_name': 'gcc-13-test', 'project_owner': 'jakub', 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/jakub/gcc-13-test/fedora-rawhide-i386/', 'id': 'copr_base', 'name': 'Copr repository'}, {'baseurl': 'https://jakub.fedorapeople.org/fedora-gcc13-$arch/', 'id': 'https_jakub_fedorapeople_org_fedora_gcc13_arch', 'name': 'Additional repo https_jakub_fedorapeople_org_fedora_gcc13_arch'}], 'sandbox': 'jakub/gcc-13-test--jakub', 'source_json': {}, 'source_type': None, 'submitter': 'jakub', 'tags': [], 'task_id': '5187320-fedora-rawhide-i386', 'timeout': 115200, 'uses_devel_repo': False, 'with_opts': [], 'without_opts': []} Running: git clone https://copr-dist-git.fedorainfracloud.org/git/jakub/gcc-13-test/wise2 /var/lib/copr-rpmbuild/workspace/workdir-cc4xf4pg/wise2 --depth 500 --no-single-branch --recursive cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/jakub/gcc-13-test/wise2', '/var/lib/copr-rpmbuild/workspace/workdir-cc4xf4pg/wise2', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-cc4xf4pg/wise2'... Running: git checkout 8fbc1d633396b5384af19025a2f015cdd5774096 cmd: ['git', 'checkout', '8fbc1d633396b5384af19025a2f015cdd5774096'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-cc4xf4pg/wise2 rc: 0 stdout: stderr: Note: switching to '8fbc1d633396b5384af19025a2f015cdd5774096'. 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 8fbc1d6 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-cc4xf4pg/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/jakub/gcc-13-test/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 20.0M 0 --:--:-- --:--:-- --:--:-- 20.1M INFO: Reading stdout from command: md5sum wise2.4.1.tar.gz Running (timeout=115200): unbuffer mock --buildsrpm --spec /var/lib/copr-rpmbuild/workspace/workdir-cc4xf4pg/wise2/wise2.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-cc4xf4pg/wise2 --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1672387198.750766 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 3.5 starting (python version = 3.11.0, NVR = mock-3.5-1.fc37)... 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-cc4xf4pg/wise2/wise2.spec) Config(fedora-rawhide-i686) Start: clean chroot Finish: clean chroot Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-i686-bootstrap-1672387198.750766/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: 3.5 INFO: Mock Version: 3.5 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 51 MB/s | 40 MB 00:00 Additional repo https_jakub_fedorapeople_org_fe 342 kB/s | 86 kB 00:00 local 73 MB/s | 60 MB 00:00 Last metadata expiration check: 0:00:01 ago on Fri Dec 30 08:00:10 2022. Dependencies resolved. ========================================================================================================================= Package Arch Version Repository Size ========================================================================================================================= Installing: dnf noarch 4.14.0-1.fc38 local 469 k dnf-plugins-core noarch 4.3.1-1.fc38 local 34 k Installing dependencies: alternatives i686 1.21-1.fc38 copr_base 39 k audit-libs i686 3.0.9-2.fc38 local 122 k basesystem noarch 11-14.fc37 local 7.0 k bash i686 5.2.9-3.fc38 copr_base 1.8 M bzip2-libs i686 1.0.8-12.fc38 copr_base 42 k ca-certificates noarch 2022.2.54-5.fc37 local 829 k coreutils i686 9.1-8.fc38 copr_base 1.1 M coreutils-common i686 9.1-8.fc38 copr_base 2.0 M crypto-policies noarch 20221215-1.gita4c31a3.fc38 local 63 k curl i686 7.87.0-1.fc38 copr_base 347 k cyrus-sasl-lib i686 2.1.28-8.fc38 copr_base 858 k dbus-libs i686 1:1.14.4-1.fc38 copr_base 167 k dnf-data noarch 4.14.0-1.fc38 local 43 k elfutils-default-yama-scope noarch 0.188-3.fc38 copr_base 16 k elfutils-libelf i686 0.188-3.fc38 copr_base 204 k elfutils-libs i686 0.188-3.fc38 copr_base 287 k expat i686 2.5.0-1.fc38 copr_base 115 k fedora-gpg-keys noarch 38-0.3 local 115 k fedora-release noarch 38-0.6 local 11 k fedora-release-common noarch 38-0.6 local 21 k fedora-release-identity-basic noarch 38-0.6 local 11 k fedora-repos noarch 38-0.3 local 10 k fedora-repos-rawhide noarch 38-0.3 local 9.7 k file-libs i686 5.42-4.fc38 copr_base 684 k filesystem i686 3.18-2.fc37 local 1.1 M findutils i686 1:4.9.0-2.fc38 copr_base 494 k gawk i686 5.1.1-4.fc38 copr_base 1.0 M gdbm-libs i686 1:1.23-2.fc38 copr_base 60 k glib2 i686 2.74.1-2.fc38 copr_base 2.8 M glibc i686 2.36.9000-19.fc38 local 1.9 M glibc-common i686 2.36.9000-19.fc38 local 315 k glibc-minimal-langpack i686 2.36.9000-19.fc38 local 30 k gmp i686 1:6.2.1-3.fc38 copr_base 306 k gnupg2 i686 2.3.8-1.fc38 copr_base 2.6 M gnutls i686 3.7.8-9.fc38 copr_base 1.1 M gpgme i686 1.17.1-3.fc38 copr_base 219 k grep i686 3.8-1.fc38 copr_base 289 k ima-evm-utils i686 1.4-6.fc38 copr_base 63 k json-c i686 0.16-3.fc38 copr_base 44 k keyutils-libs i686 1.6.1-5.fc38 copr_base 32 k krb5-libs i686 1.20.1-3.fc38 copr_base 764 k libacl i686 2.3.1-4.fc38 copr_base 25 k libarchive i686 3.6.1-3.fc38 copr_base 442 k libassuan i686 2.5.5-5.fc38 copr_base 69 k libattr i686 2.5.1-5.fc38 copr_base 19 k libb2 i686 0.98.1-7.fc38 copr_base 29 k libblkid i686 2.38.1-3.fc38 copr_base 117 k libbrotli i686 1.0.9-9.fc38 copr_base 318 k libcap i686 2.48-5.fc38 copr_base 69 k libcap-ng i686 0.8.3-4.fc38 copr_base 33 k libcom_err i686 1.46.5-3.fc37 local 26 k libcomps i686 0.1.18-4.fc38 copr_base 84 k libcurl i686 7.87.0-1.fc38 copr_base 327 k libdnf i686 0.68.0-1.fc38 copr_base 713 k libevent i686 2.1.12-7.fc38 copr_base 277 k libffi i686 3.4.4-1.fc38 copr_base 36 k libfsverity i686 1.4-8.fc38 copr_base 21 k libgcc i686 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 101 k libgcrypt i686 1.10.1-6.fc38 copr_base 479 k libgomp i686 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 304 k libgpg-error i686 1.46-1.fc38 copr_base 226 k libidn2 i686 2.3.4-1.fc38 copr_base 155 k libksba i686 1.6.3-1.fc38 copr_base 161 k libmodulemd i686 2.14.0-4.fc38 copr_base 242 k libmount i686 2.38.1-3.fc38 copr_base 141 k libnghttp2 i686 1.51.0-1.fc38 copr_base 81 k libnsl2 i686 2.0.0-4.fc38 copr_base 32 k libpsl i686 0.21.2-1.fc38 local 66 k librepo i686 1.15.1-1.fc38 copr_base 102 k libreport-filesystem noarch 2.17.6-1.fc38 copr_base 14 k libselinux i686 3.5-0.rc1.1.fc38 local 91 k libsemanage i686 3.5-0.rc1.1.fc38 local 128 k libsepol i686 3.5-0.rc1.1.fc38 local 336 k libsigsegv i686 2.14-3.fc38 copr_base 28 k libsmartcols i686 2.38.1-3.fc38 copr_base 66 k libsolv i686 0.7.22-3.fc38 copr_base 426 k libssh i686 0.10.4-2.fc38 copr_base 223 k libssh-config noarch 0.10.4-2.fc38 copr_base 9.3 k libstdc++ i686 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 857 k libtasn1 i686 4.19.0-1.fc38 copr_base 77 k libtirpc i686 1.3.3-0.fc38 copr_base 101 k libunistring i686 1.0-2.fc38 copr_base 549 k libuuid i686 2.38.1-3.fc38 copr_base 29 k libverto i686 0.3.2-4.fc38 copr_base 22 k libxcrypt i686 4.4.33-5.fc38 copr_base 124 k libxml2 i686 2.10.3-2.fc38 copr_base 744 k libyaml i686 0.2.5-8.fc38 copr_base 62 k libzstd i686 1.5.2-3.fc37 local 274 k lua-libs i686 5.4.4-6.fc38 copr_base 149 k lz4-libs i686 1.9.3-5.fc38 copr_base 72 k mpdecimal i686 2.5.1-4.fc38 copr_base 107 k mpfr i686 4.1.1-2.fc38 copr_base 637 k ncurses-base noarch 6.3-5.20221126.fc38 copr_base 62 k ncurses-libs i686 6.3-5.20221126.fc38 copr_base 351 k nettle i686 3.8-2.fc38 copr_base 426 k npth i686 1.6-10.fc38 copr_base 25 k openldap i686 2.6.3-1.fc38 copr_base 274 k openssl-libs i686 1:3.0.5-6.fc38 copr_base 2.1 M p11-kit i686 0.24.1-5.fc38 copr_base 335 k p11-kit-trust i686 0.24.1-5.fc38 copr_base 136 k pcre2 i686 10.40-1.fc38.1 copr_base 235 k pcre2-syntax noarch 10.40-1.fc38.1 copr_base 143 k popt i686 1.19-1.fc38 copr_base 62 k publicsuffix-list-dafsa noarch 20221208-1.fc38 local 59 k python-pip-wheel noarch 22.3.1-1.fc38 local 1.4 M python-setuptools-wheel noarch 65.5.1-1.fc38 local 715 k python3 i686 3.11.1-1.fc38 copr_base 28 k python3-dateutil noarch 1:2.8.2-4.fc37 local 350 k python3-dbus i686 1.3.2-1.fc38 copr_base 151 k python3-distro noarch 1.8.0-1.fc38 local 45 k python3-dnf noarch 4.14.0-1.fc38 local 567 k python3-dnf-plugins-core noarch 4.3.1-1.fc38 local 263 k python3-gpg i686 1.17.1-3.fc38 copr_base 277 k python3-hawkey i686 0.68.0-1.fc38 copr_base 113 k python3-libcomps i686 0.1.18-4.fc38 copr_base 52 k python3-libdnf i686 0.68.0-1.fc38 copr_base 838 k python3-libs i686 3.11.1-1.fc38 copr_base 9.3 M python3-rpm i686 4.18.0-8.fc38 copr_base 96 k python3-six noarch 1.16.0-8.fc37 local 42 k readline i686 8.2-2.fc38 copr_base 219 k rpm i686 4.18.0-8.fc38 copr_base 541 k rpm-build-libs i686 4.18.0-8.fc38 copr_base 102 k rpm-libs i686 4.18.0-8.fc38 copr_base 342 k rpm-sequoia i686 1.2.0-1.fc38 copr_base 914 k rpm-sign-libs i686 4.18.0-8.fc38 copr_base 28 k sed i686 4.8-11.fc38 copr_base 301 k setup noarch 2.14.3-1.fc38 local 146 k shadow-utils i686 2:4.13-3.fc38 copr_base 1.2 M sqlite-libs i686 3.40.0-1.fc38 copr_base 706 k systemd-libs i686 252.4-598.fc38 local 662 k tpm2-tss i686 4.0.0-0.1.rc2.fc38 copr_base 603 k tzdata noarch 2022g-1.fc38 local 432 k xz-libs i686 5.2.9-1.fc38 local 101 k zchunk-libs i686 1.2.3-1.fc38 local 54 k zlib i686 1.2.13-1.fc38 local 92 k Transaction Summary ========================================================================================================================= Install 137 Packages Total download size: 57 M Installed size: 198 M Downloading Packages: (1/137): bzip2-libs-1.0.8-12.fc38.i686.rpm 384 kB/s | 42 kB 00:00 (2/137): alternatives-1.21-1.fc38.i686.rpm 316 kB/s | 39 kB 00:00 (3/137): coreutils-9.1-8.fc38.i686.rpm 8.9 MB/s | 1.1 MB 00:00 (4/137): curl-7.87.0-1.fc38.i686.rpm 3.6 MB/s | 347 kB 00:00 (5/137): bash-5.2.9-3.fc38.i686.rpm 5.2 MB/s | 1.8 MB 00:00 (6/137): coreutils-common-9.1-8.fc38.i686.rpm 8.3 MB/s | 2.0 MB 00:00 (7/137): dbus-libs-1.14.4-1.fc38.i686.rpm 3.6 MB/s | 167 kB 00:00 (8/137): cyrus-sasl-lib-2.1.28-8.fc38.i686.rpm 13 MB/s | 858 kB 00:00 (9/137): elfutils-default-yama-scope-0.188-3.fc 512 kB/s | 16 kB 00:00 (10/137): elfutils-libelf-0.188-3.fc38.i686.rpm 17 MB/s | 204 kB 00:00 (11/137): elfutils-libs-0.188-3.fc38.i686.rpm 19 MB/s | 287 kB 00:00 (12/137): expat-2.5.0-1.fc38.i686.rpm 6.4 MB/s | 115 kB 00:00 (13/137): file-libs-5.42-4.fc38.i686.rpm 23 MB/s | 684 kB 00:00 (14/137): findutils-4.9.0-2.fc38.i686.rpm 13 MB/s | 494 kB 00:00 (15/137): gawk-5.1.1-4.fc38.i686.rpm 15 MB/s | 1.0 MB 00:00 (16/137): gdbm-libs-1.23-2.fc38.i686.rpm 1.3 MB/s | 60 kB 00:00 (17/137): gmp-6.2.1-3.fc38.i686.rpm 5.3 MB/s | 306 kB 00:00 (18/137): glib2-2.74.1-2.fc38.i686.rpm 22 MB/s | 2.8 MB 00:00 (19/137): gnutls-3.7.8-9.fc38.i686.rpm 15 MB/s | 1.1 MB 00:00 (20/137): gnupg2-2.3.8-1.fc38.i686.rpm 18 MB/s | 2.6 MB 00:00 (21/137): gpgme-1.17.1-3.fc38.i686.rpm 3.8 MB/s | 219 kB 00:00 (22/137): grep-3.8-1.fc38.i686.rpm 9.7 MB/s | 289 kB 00:00 (23/137): ima-evm-utils-1.4-6.fc38.i686.rpm 4.3 MB/s | 63 kB 00:00 (24/137): json-c-0.16-3.fc38.i686.rpm 3.2 MB/s | 44 kB 00:00 (25/137): keyutils-libs-1.6.1-5.fc38.i686.rpm 2.7 MB/s | 32 kB 00:00 (26/137): krb5-libs-1.20.1-3.fc38.i686.rpm 30 MB/s | 764 kB 00:00 (27/137): libacl-2.3.1-4.fc38.i686.rpm 1.0 MB/s | 25 kB 00:00 (28/137): libarchive-3.6.1-3.fc38.i686.rpm 11 MB/s | 442 kB 00:00 (29/137): libattr-2.5.1-5.fc38.i686.rpm 1.0 MB/s | 19 kB 00:00 (30/137): libassuan-2.5.5-5.fc38.i686.rpm 3.5 MB/s | 69 kB 00:00 (31/137): libbrotli-1.0.9-9.fc38.i686.rpm 19 MB/s | 318 kB 00:00 (32/137): libb2-0.98.1-7.fc38.i686.rpm 1.6 MB/s | 29 kB 00:00 (33/137): libblkid-2.38.1-3.fc38.i686.rpm 5.7 MB/s | 117 kB 00:00 (34/137): libcap-2.48-5.fc38.i686.rpm 7.4 MB/s | 69 kB 00:00 (35/137): libcap-ng-0.8.3-4.fc38.i686.rpm 3.4 MB/s | 33 kB 00:00 (36/137): libcomps-0.1.18-4.fc38.i686.rpm 7.9 MB/s | 84 kB 00:00 (37/137): libcurl-7.87.0-1.fc38.i686.rpm 23 MB/s | 327 kB 00:00 (38/137): libdnf-0.68.0-1.fc38.i686.rpm 26 MB/s | 713 kB 00:00 (39/137): libevent-2.1.12-7.fc38.i686.rpm 8.8 MB/s | 277 kB 00:00 (40/137): libffi-3.4.4-1.fc38.i686.rpm 1.7 MB/s | 36 kB 00:00 (41/137): libfsverity-1.4-8.fc38.i686.rpm 2.0 MB/s | 21 kB 00:00 (42/137): libgcrypt-1.10.1-6.fc38.i686.rpm 24 MB/s | 479 kB 00:00 (43/137): libgpg-error-1.46-1.fc38.i686.rpm 9.7 MB/s | 226 kB 00:00 (44/137): libidn2-2.3.4-1.fc38.i686.rpm 6.7 MB/s | 155 kB 00:00 (45/137): libksba-1.6.3-1.fc38.i686.rpm 12 MB/s | 161 kB 00:00 (46/137): libmodulemd-2.14.0-4.fc38.i686.rpm 16 MB/s | 242 kB 00:00 (47/137): libmount-2.38.1-3.fc38.i686.rpm 9.2 MB/s | 141 kB 00:00 (48/137): libnghttp2-1.51.0-1.fc38.i686.rpm 6.7 MB/s | 81 kB 00:00 (49/137): 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11 MB/s | 662 kB 00:00 -------------------------------------------------------------------------------- Total 28 MB/s | 57 MB 00:02 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Running scriptlet: filesystem-3.18-2.fc37.i686 1/1 Preparing : 1/1 Installing : crypto-policies-20221215-1.gita4c31a3.fc38.noarc 1/137 Running scriptlet: crypto-policies-20221215-1.gita4c31a3.fc38.noarc 1/137 Installing : tzdata-2022g-1.fc38.noarch 2/137 Installing : fedora-release-identity-basic-38-0.6.noarch 3/137 Installing : python-setuptools-wheel-65.5.1-1.fc38.noarch 4/137 Installing : publicsuffix-list-dafsa-20221208-1.fc38.noarch 5/137 Installing : fedora-gpg-keys-38-0.3.noarch 6/137 Installing : fedora-release-38-0.6.noarch 7/137 Installing : fedora-release-common-38-0.6.noarch 8/137 Installing : fedora-repos-rawhide-38-0.3.noarch 9/137 Installing : fedora-repos-38-0.3.noarch 10/137 Installing : setup-2.14.3-1.fc38.noarch 11/137 Running scriptlet: setup-2.14.3-1.fc38.noarch 11/137 Installing : filesystem-3.18-2.fc37.i686 12/137 Installing : basesystem-11-14.fc37.noarch 13/137 Installing : pcre2-syntax-10.40-1.fc38.1.noarch 14/137 Installing : 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scriptlet: ca-certificates-2022.2.54-5.fc37.noarch 137/137 Running scriptlet: rpm-4.18.0-8.fc38.i686 137/137 Verifying : alternatives-1.21-1.fc38.i686 1/137 Verifying : bash-5.2.9-3.fc38.i686 2/137 Verifying : bzip2-libs-1.0.8-12.fc38.i686 3/137 Verifying : coreutils-9.1-8.fc38.i686 4/137 Verifying : coreutils-common-9.1-8.fc38.i686 5/137 Verifying : curl-7.87.0-1.fc38.i686 6/137 Verifying : cyrus-sasl-lib-2.1.28-8.fc38.i686 7/137 Verifying : dbus-libs-1:1.14.4-1.fc38.i686 8/137 Verifying : elfutils-default-yama-scope-0.188-3.fc38.noarch 9/137 Verifying : elfutils-libelf-0.188-3.fc38.i686 10/137 Verifying : elfutils-libs-0.188-3.fc38.i686 11/137 Verifying : expat-2.5.0-1.fc38.i686 12/137 Verifying : file-libs-5.42-4.fc38.i686 13/137 Verifying : findutils-1:4.9.0-2.fc38.i686 14/137 Verifying : gawk-5.1.1-4.fc38.i686 15/137 Verifying : gdbm-libs-1:1.23-2.fc38.i686 16/137 Verifying : glib2-2.74.1-2.fc38.i686 17/137 Verifying : gmp-1:6.2.1-3.fc38.i686 18/137 Verifying : 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Verifying : libfsverity-1.4-8.fc38.i686 41/137 Verifying : libgcrypt-1.10.1-6.fc38.i686 42/137 Verifying : libgpg-error-1.46-1.fc38.i686 43/137 Verifying : libidn2-2.3.4-1.fc38.i686 44/137 Verifying : libksba-1.6.3-1.fc38.i686 45/137 Verifying : libmodulemd-2.14.0-4.fc38.i686 46/137 Verifying : libmount-2.38.1-3.fc38.i686 47/137 Verifying : libnghttp2-1.51.0-1.fc38.i686 48/137 Verifying : libnsl2-2.0.0-4.fc38.i686 49/137 Verifying : librepo-1.15.1-1.fc38.i686 50/137 Verifying : libreport-filesystem-2.17.6-1.fc38.noarch 51/137 Verifying : libsigsegv-2.14-3.fc38.i686 52/137 Verifying : libsmartcols-2.38.1-3.fc38.i686 53/137 Verifying : libsolv-0.7.22-3.fc38.i686 54/137 Verifying : libssh-0.10.4-2.fc38.i686 55/137 Verifying : libssh-config-0.10.4-2.fc38.noarch 56/137 Verifying : libtasn1-4.19.0-1.fc38.i686 57/137 Verifying : libtirpc-1.3.3-0.fc38.i686 58/137 Verifying : libunistring-1.0-2.fc38.i686 59/137 Verifying : libuuid-2.38.1-3.fc38.i686 60/137 Verifying : libverto-0.3.2-4.fc38.i686 61/137 Verifying : libxcrypt-4.4.33-5.fc38.i686 62/137 Verifying : libxml2-2.10.3-2.fc38.i686 63/137 Verifying : libyaml-0.2.5-8.fc38.i686 64/137 Verifying : lua-libs-5.4.4-6.fc38.i686 65/137 Verifying : lz4-libs-1.9.3-5.fc38.i686 66/137 Verifying : mpdecimal-2.5.1-4.fc38.i686 67/137 Verifying : mpfr-4.1.1-2.fc38.i686 68/137 Verifying : ncurses-base-6.3-5.20221126.fc38.noarch 69/137 Verifying : ncurses-libs-6.3-5.20221126.fc38.i686 70/137 Verifying : nettle-3.8-2.fc38.i686 71/137 Verifying : npth-1.6-10.fc38.i686 72/137 Verifying : openldap-2.6.3-1.fc38.i686 73/137 Verifying : openssl-libs-1:3.0.5-6.fc38.i686 74/137 Verifying : p11-kit-0.24.1-5.fc38.i686 75/137 Verifying : p11-kit-trust-0.24.1-5.fc38.i686 76/137 Verifying : pcre2-10.40-1.fc38.1.i686 77/137 Verifying : pcre2-syntax-10.40-1.fc38.1.noarch 78/137 Verifying : popt-1.19-1.fc38.i686 79/137 Verifying : python3-3.11.1-1.fc38.i686 80/137 Verifying : python3-dbus-1.3.2-1.fc38.i686 81/137 Verifying : python3-gpg-1.17.1-3.fc38.i686 82/137 Verifying : python3-hawkey-0.68.0-1.fc38.i686 83/137 Verifying : python3-libcomps-0.1.18-4.fc38.i686 84/137 Verifying : python3-libdnf-0.68.0-1.fc38.i686 85/137 Verifying : python3-libs-3.11.1-1.fc38.i686 86/137 Verifying : python3-rpm-4.18.0-8.fc38.i686 87/137 Verifying : readline-8.2-2.fc38.i686 88/137 Verifying : rpm-4.18.0-8.fc38.i686 89/137 Verifying : rpm-build-libs-4.18.0-8.fc38.i686 90/137 Verifying : rpm-libs-4.18.0-8.fc38.i686 91/137 Verifying : rpm-sequoia-1.2.0-1.fc38.i686 92/137 Verifying : rpm-sign-libs-4.18.0-8.fc38.i686 93/137 Verifying : sed-4.8-11.fc38.i686 94/137 Verifying : shadow-utils-2:4.13-3.fc38.i686 95/137 Verifying : sqlite-libs-3.40.0-1.fc38.i686 96/137 Verifying : tpm2-tss-4.0.0-0.1.rc2.fc38.i686 97/137 Verifying : libgcc-13.0.0-0.4.fc38.i686 98/137 Verifying : libgomp-13.0.0-0.4.fc38.i686 99/137 Verifying : libstdc++-13.0.0-0.4.fc38.i686 100/137 Verifying : audit-libs-3.0.9-2.fc38.i686 101/137 Verifying : basesystem-11-14.fc37.noarch 102/137 Verifying : ca-certificates-2022.2.54-5.fc37.noarch 103/137 Verifying : crypto-policies-20221215-1.gita4c31a3.fc38.noarc 104/137 Verifying : dnf-4.14.0-1.fc38.noarch 105/137 Verifying : dnf-data-4.14.0-1.fc38.noarch 106/137 Verifying : dnf-plugins-core-4.3.1-1.fc38.noarch 107/137 Verifying : fedora-gpg-keys-38-0.3.noarch 108/137 Verifying : fedora-release-38-0.6.noarch 109/137 Verifying : fedora-release-common-38-0.6.noarch 110/137 Verifying : fedora-release-identity-basic-38-0.6.noarch 111/137 Verifying : fedora-repos-38-0.3.noarch 112/137 Verifying : fedora-repos-rawhide-38-0.3.noarch 113/137 Verifying : filesystem-3.18-2.fc37.i686 114/137 Verifying : glibc-2.36.9000-19.fc38.i686 115/137 Verifying : glibc-common-2.36.9000-19.fc38.i686 116/137 Verifying : glibc-minimal-langpack-2.36.9000-19.fc38.i686 117/137 Verifying : libcom_err-1.46.5-3.fc37.i686 118/137 Verifying : libpsl-0.21.2-1.fc38.i686 119/137 Verifying : libselinux-3.5-0.rc1.1.fc38.i686 120/137 Verifying : libsemanage-3.5-0.rc1.1.fc38.i686 121/137 Verifying : libsepol-3.5-0.rc1.1.fc38.i686 122/137 Verifying : libzstd-1.5.2-3.fc37.i686 123/137 Verifying : publicsuffix-list-dafsa-20221208-1.fc38.noarch 124/137 Verifying : python-pip-wheel-22.3.1-1.fc38.noarch 125/137 Verifying : python-setuptools-wheel-65.5.1-1.fc38.noarch 126/137 Verifying : python3-dateutil-1:2.8.2-4.fc37.noarch 127/137 Verifying : python3-distro-1.8.0-1.fc38.noarch 128/137 Verifying : python3-dnf-4.14.0-1.fc38.noarch 129/137 Verifying : python3-dnf-plugins-core-4.3.1-1.fc38.noarch 130/137 Verifying : python3-six-1.16.0-8.fc37.noarch 131/137 Verifying : setup-2.14.3-1.fc38.noarch 132/137 Verifying : systemd-libs-252.4-598.fc38.i686 133/137 Verifying : tzdata-2022g-1.fc38.noarch 134/137 Verifying : xz-libs-5.2.9-1.fc38.i686 135/137 Verifying : zchunk-libs-1.2.3-1.fc38.i686 136/137 Verifying : zlib-1.2.13-1.fc38.i686 137/137 Installed products updated. Installed: alternatives-1.21-1.fc38.i686 audit-libs-3.0.9-2.fc38.i686 basesystem-11-14.fc37.noarch bash-5.2.9-3.fc38.i686 bzip2-libs-1.0.8-12.fc38.i686 ca-certificates-2022.2.54-5.fc37.noarch coreutils-9.1-8.fc38.i686 coreutils-common-9.1-8.fc38.i686 crypto-policies-20221215-1.gita4c31a3.fc38.noarch curl-7.87.0-1.fc38.i686 cyrus-sasl-lib-2.1.28-8.fc38.i686 dbus-libs-1:1.14.4-1.fc38.i686 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.i686 elfutils-libs-0.188-3.fc38.i686 expat-2.5.0-1.fc38.i686 fedora-gpg-keys-38-0.3.noarch fedora-release-38-0.6.noarch fedora-release-common-38-0.6.noarch fedora-release-identity-basic-38-0.6.noarch fedora-repos-38-0.3.noarch fedora-repos-rawhide-38-0.3.noarch file-libs-5.42-4.fc38.i686 filesystem-3.18-2.fc37.i686 findutils-1:4.9.0-2.fc38.i686 gawk-5.1.1-4.fc38.i686 gdbm-libs-1:1.23-2.fc38.i686 glib2-2.74.1-2.fc38.i686 glibc-2.36.9000-19.fc38.i686 glibc-common-2.36.9000-19.fc38.i686 glibc-minimal-langpack-2.36.9000-19.fc38.i686 gmp-1:6.2.1-3.fc38.i686 gnupg2-2.3.8-1.fc38.i686 gnutls-3.7.8-9.fc38.i686 gpgme-1.17.1-3.fc38.i686 grep-3.8-1.fc38.i686 ima-evm-utils-1.4-6.fc38.i686 json-c-0.16-3.fc38.i686 keyutils-libs-1.6.1-5.fc38.i686 krb5-libs-1.20.1-3.fc38.i686 libacl-2.3.1-4.fc38.i686 libarchive-3.6.1-3.fc38.i686 libassuan-2.5.5-5.fc38.i686 libattr-2.5.1-5.fc38.i686 libb2-0.98.1-7.fc38.i686 libblkid-2.38.1-3.fc38.i686 libbrotli-1.0.9-9.fc38.i686 libcap-2.48-5.fc38.i686 libcap-ng-0.8.3-4.fc38.i686 libcom_err-1.46.5-3.fc37.i686 libcomps-0.1.18-4.fc38.i686 libcurl-7.87.0-1.fc38.i686 libdnf-0.68.0-1.fc38.i686 libevent-2.1.12-7.fc38.i686 libffi-3.4.4-1.fc38.i686 libfsverity-1.4-8.fc38.i686 libgcc-13.0.0-0.4.fc38.i686 libgcrypt-1.10.1-6.fc38.i686 libgomp-13.0.0-0.4.fc38.i686 libgpg-error-1.46-1.fc38.i686 libidn2-2.3.4-1.fc38.i686 libksba-1.6.3-1.fc38.i686 libmodulemd-2.14.0-4.fc38.i686 libmount-2.38.1-3.fc38.i686 libnghttp2-1.51.0-1.fc38.i686 libnsl2-2.0.0-4.fc38.i686 libpsl-0.21.2-1.fc38.i686 librepo-1.15.1-1.fc38.i686 libreport-filesystem-2.17.6-1.fc38.noarch libselinux-3.5-0.rc1.1.fc38.i686 libsemanage-3.5-0.rc1.1.fc38.i686 libsepol-3.5-0.rc1.1.fc38.i686 libsigsegv-2.14-3.fc38.i686 libsmartcols-2.38.1-3.fc38.i686 libsolv-0.7.22-3.fc38.i686 libssh-0.10.4-2.fc38.i686 libssh-config-0.10.4-2.fc38.noarch libstdc++-13.0.0-0.4.fc38.i686 libtasn1-4.19.0-1.fc38.i686 libtirpc-1.3.3-0.fc38.i686 libunistring-1.0-2.fc38.i686 libuuid-2.38.1-3.fc38.i686 libverto-0.3.2-4.fc38.i686 libxcrypt-4.4.33-5.fc38.i686 libxml2-2.10.3-2.fc38.i686 libyaml-0.2.5-8.fc38.i686 libzstd-1.5.2-3.fc37.i686 lua-libs-5.4.4-6.fc38.i686 lz4-libs-1.9.3-5.fc38.i686 mpdecimal-2.5.1-4.fc38.i686 mpfr-4.1.1-2.fc38.i686 ncurses-base-6.3-5.20221126.fc38.noarch ncurses-libs-6.3-5.20221126.fc38.i686 nettle-3.8-2.fc38.i686 npth-1.6-10.fc38.i686 openldap-2.6.3-1.fc38.i686 openssl-libs-1:3.0.5-6.fc38.i686 p11-kit-0.24.1-5.fc38.i686 p11-kit-trust-0.24.1-5.fc38.i686 pcre2-10.40-1.fc38.1.i686 pcre2-syntax-10.40-1.fc38.1.noarch popt-1.19-1.fc38.i686 publicsuffix-list-dafsa-20221208-1.fc38.noarch python-pip-wheel-22.3.1-1.fc38.noarch python-setuptools-wheel-65.5.1-1.fc38.noarch python3-3.11.1-1.fc38.i686 python3-dateutil-1:2.8.2-4.fc37.noarch python3-dbus-1.3.2-1.fc38.i686 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-1.17.1-3.fc38.i686 python3-hawkey-0.68.0-1.fc38.i686 python3-libcomps-0.1.18-4.fc38.i686 python3-libdnf-0.68.0-1.fc38.i686 python3-libs-3.11.1-1.fc38.i686 python3-rpm-4.18.0-8.fc38.i686 python3-six-1.16.0-8.fc37.noarch readline-8.2-2.fc38.i686 rpm-4.18.0-8.fc38.i686 rpm-build-libs-4.18.0-8.fc38.i686 rpm-libs-4.18.0-8.fc38.i686 rpm-sequoia-1.2.0-1.fc38.i686 rpm-sign-libs-4.18.0-8.fc38.i686 sed-4.8-11.fc38.i686 setup-2.14.3-1.fc38.noarch shadow-utils-2:4.13-3.fc38.i686 sqlite-libs-3.40.0-1.fc38.i686 systemd-libs-252.4-598.fc38.i686 tpm2-tss-4.0.0-0.1.rc2.fc38.i686 tzdata-2022g-1.fc38.noarch xz-libs-5.2.9-1.fc38.i686 zchunk-libs-1.2.3-1.fc38.i686 zlib-1.2.13-1.fc38.i686 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-i686-1672387198.750766/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: 3.5 INFO: Mock Version: 3.5 Start: dnf install No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 35 MB/s | 40 MB 00:01 Additional repo https_jakub_fedorapeople_org_fe 134 kB/s | 86 kB 00:00 local 16 MB/s | 60 MB 00:03 Dependencies resolved. ========================================================================================================================= Package Arch Version Repository Size ========================================================================================================================= Installing group/module packages: bash i686 5.2.9-3.fc38 copr_base 1.8 M bzip2 i686 1.0.8-12.fc38 copr_base 53 k coreutils i686 9.1-8.fc38 copr_base 1.1 M cpio i686 2.13-13.fc38 copr_base 274 k diffutils i686 3.8-3.fc38 copr_base 375 k fedora-release noarch 38-0.6 local 11 k findutils i686 1:4.9.0-2.fc38 copr_base 494 k gawk i686 5.1.1-4.fc38 copr_base 1.0 M glibc-minimal-langpack i686 2.36.9000-19.fc38 local 30 k grep i686 3.8-1.fc38 copr_base 289 k gzip i686 1.12-2.fc38 copr_base 158 k info i686 7.0.1-1.fc38 copr_base 184 k patch i686 2.7.6-17.fc38 copr_base 138 k redhat-rpm-config noarch 236-1.fc38 local 74 k rpm-build i686 4.18.0-8.fc38 copr_base 70 k sed i686 4.8-11.fc38 copr_base 301 k shadow-utils i686 2:4.13-3.fc38 copr_base 1.2 M tar i686 2:1.34-5.fc38 copr_base 894 k unzip i686 6.0-58.fc38 copr_base 179 k util-linux i686 2.38.1-3.fc38 copr_base 2.3 M which i686 2.21-36.fc38 copr_base 42 k xz i686 5.2.9-1.fc38 local 300 k Installing dependencies: alternatives i686 1.21-1.fc38 copr_base 39 k ansible-srpm-macros noarch 1-8.1.fc38 local 8.6 k audit-libs i686 3.0.9-2.fc38 local 122 k authselect i686 1.4.2-1.fc38 copr_base 141 k authselect-libs i686 1.4.2-1.fc38 copr_base 239 k basesystem noarch 11-14.fc37 local 7.0 k binutils i686 2.39-6.fc38 copr_base 5.6 M binutils-gold i686 2.39-6.fc38 copr_base 853 k bzip2-libs i686 1.0.8-12.fc38 copr_base 42 k ca-certificates noarch 2022.2.54-5.fc37 local 829 k coreutils-common i686 9.1-8.fc38 copr_base 2.0 M cracklib i686 2.9.7-30.fc38 copr_base 82 k crypto-policies noarch 20221215-1.gita4c31a3.fc38 local 63 k curl i686 7.87.0-1.fc38 copr_base 347 k cyrus-sasl-lib i686 2.1.28-8.fc38 copr_base 858 k debugedit i686 5.0-5.fc37 local 78 k dwz i686 0.15-1.fc38 copr_base 144 k ed i686 1.18-2.fc38 copr_base 78 k efi-srpm-macros noarch 5-6.fc37 local 22 k elfutils i686 0.188-3.fc38 copr_base 543 k elfutils-debuginfod-client i686 0.188-3.fc38 copr_base 41 k elfutils-default-yama-scope noarch 0.188-3.fc38 copr_base 16 k elfutils-libelf i686 0.188-3.fc38 copr_base 204 k elfutils-libs i686 0.188-3.fc38 copr_base 287 k fedora-gpg-keys noarch 38-0.3 local 115 k fedora-release-common noarch 38-0.6 local 21 k fedora-release-identity-basic noarch 38-0.6 local 11 k fedora-repos noarch 38-0.3 local 10 k fedora-repos-rawhide noarch 38-0.3 local 9.7 k file i686 5.42-4.fc38 copr_base 49 k file-libs i686 5.42-4.fc38 copr_base 684 k filesystem i686 3.18-2.fc37 local 1.1 M fonts-srpm-macros noarch 1:2.0.5-10.fc38 local 26 k fpc-srpm-macros noarch 1.3-6.fc37 local 7.7 k gdb-minimal i686 12.1-10.fc38 local 3.9 M gdbm-libs i686 1:1.23-2.fc38 copr_base 60 k ghc-srpm-macros noarch 1.5.0-7.fc37 local 7.8 k glibc i686 2.36.9000-19.fc38 local 1.9 M glibc-common i686 2.36.9000-19.fc38 local 315 k glibc-gconv-extra i686 2.36.9000-19.fc38 local 1.6 M gmp i686 1:6.2.1-3.fc38 copr_base 306 k gnat-srpm-macros noarch 4-16.fc37 local 8.3 k go-srpm-macros noarch 3.2.0-1.fc38 local 27 k jansson i686 2.13.1-5.fc38 copr_base 47 k kernel-srpm-macros noarch 1.0-15.fc37 local 9.4 k keyutils-libs i686 1.6.1-5.fc38 copr_base 32 k krb5-libs i686 1.20.1-3.fc38 copr_base 764 k libacl i686 2.3.1-4.fc38 copr_base 25 k libarchive i686 3.6.1-3.fc38 copr_base 442 k libattr i686 2.5.1-5.fc38 copr_base 19 k libblkid i686 2.38.1-3.fc38 copr_base 117 k libbrotli i686 1.0.9-9.fc38 copr_base 318 k libcap i686 2.48-5.fc38 copr_base 69 k libcap-ng i686 0.8.3-4.fc38 copr_base 33 k libcom_err i686 1.46.5-3.fc37 local 26 k libcurl i686 7.87.0-1.fc38 copr_base 327 k libdb i686 5.3.28-54.fc38 copr_base 823 k libeconf i686 0.4.0-4.fc38 copr_base 29 k libevent i686 2.1.12-7.fc38 copr_base 277 k libfdisk i686 2.38.1-3.fc38 copr_base 174 k libffi i686 3.4.4-1.fc38 copr_base 36 k libgcc i686 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 101 k libgomp i686 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 304 k libidn2 i686 2.3.4-1.fc38 copr_base 155 k libmount i686 2.38.1-3.fc38 copr_base 141 k libnghttp2 i686 1.51.0-1.fc38 copr_base 81 k libnsl2 i686 2.0.0-4.fc38 copr_base 32 k libpkgconf i686 1.8.0-3.fc38 copr_base 39 k libpsl i686 0.21.2-1.fc38 local 66 k libpwquality i686 1.4.5-1.fc38 local 108 k libselinux i686 3.5-0.rc1.1.fc38 local 91 k libsemanage i686 3.5-0.rc1.1.fc38 local 128 k libsepol i686 3.5-0.rc1.1.fc38 local 336 k libsigsegv i686 2.14-3.fc38 copr_base 28 k libsmartcols i686 2.38.1-3.fc38 copr_base 66 k libssh i686 0.10.4-2.fc38 copr_base 223 k libssh-config noarch 0.10.4-2.fc38 copr_base 9.3 k libstdc++ i686 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 857 k libtasn1 i686 4.19.0-1.fc38 copr_base 77 k libtirpc i686 1.3.3-0.fc38 copr_base 101 k libunistring i686 1.0-2.fc38 copr_base 549 k libutempter i686 1.2.1-7.fc38 copr_base 27 k libuuid i686 2.38.1-3.fc38 copr_base 29 k libverto i686 0.3.2-4.fc38 copr_base 22 k libxcrypt i686 4.4.33-5.fc38 copr_base 124 k libxml2 i686 2.10.3-2.fc38 copr_base 744 k libzstd i686 1.5.2-3.fc37 local 274 k lua-libs i686 5.4.4-6.fc38 copr_base 149 k lua-srpm-macros noarch 1-7.fc37 local 8.8 k lz4-libs i686 1.9.3-5.fc38 copr_base 72 k mpfr i686 4.1.1-2.fc38 copr_base 637 k ncurses-base noarch 6.3-5.20221126.fc38 copr_base 62 k ncurses-libs i686 6.3-5.20221126.fc38 copr_base 351 k nettle i686 3.8-2.fc38 copr_base 426 k nim-srpm-macros noarch 3-7.fc37 local 8.4 k ocaml-srpm-macros noarch 7-2.fc37 local 13 k openblas-srpm-macros noarch 2-12.fc37 local 7.5 k openldap i686 2.6.3-1.fc38 copr_base 274 k openssl-libs i686 1:3.0.5-6.fc38 copr_base 2.1 M p11-kit i686 0.24.1-5.fc38 copr_base 335 k p11-kit-trust i686 0.24.1-5.fc38 copr_base 136 k package-notes-srpm-macros noarch 0.5-6.fc38 local 11 k pam i686 1.5.2-15.fc38 copr_base 536 k pam-libs i686 1.5.2-15.fc38 copr_base 60 k pcre2 i686 10.40-1.fc38.1 copr_base 235 k pcre2-syntax noarch 10.40-1.fc38.1 copr_base 143 k perl-srpm-macros noarch 1-47.fc38 local 8.2 k pkgconf i686 1.8.0-3.fc38 copr_base 42 k pkgconf-m4 noarch 1.8.0-3.fc38 copr_base 15 k pkgconf-pkg-config i686 1.8.0-3.fc38 copr_base 11 k popt i686 1.19-1.fc38 copr_base 62 k publicsuffix-list-dafsa noarch 20221208-1.fc38 local 59 k python-srpm-macros noarch 3.11-6.fc38 local 25 k qt5-srpm-macros noarch 5.15.7-1.fc38 copr_base 8.5 k readline i686 8.2-2.fc38 copr_base 219 k rpm i686 4.18.0-8.fc38 copr_base 541 k rpm-build-libs i686 4.18.0-8.fc38 copr_base 102 k rpm-libs i686 4.18.0-8.fc38 copr_base 342 k rpm-sequoia i686 1.2.0-1.fc38 copr_base 914 k rpmautospec-rpm-macros noarch 0.3.1-1.fc38 copr_base 9.4 k rust-srpm-macros noarch 23-1.fc38 local 9.4 k setup noarch 2.14.3-1.fc38 local 146 k sqlite-libs i686 3.40.0-1.fc38 copr_base 706 k systemd-libs i686 252.4-598.fc38 local 662 k tzdata noarch 2022g-1.fc38 local 432 k util-linux-core i686 2.38.1-3.fc38 copr_base 470 k xxhash-libs i686 0.8.1-3.fc37 local 59 k xz-libs i686 5.2.9-1.fc38 local 101 k zip i686 3.0-35.fc38 local 263 k zlib i686 1.2.13-1.fc38 local 92 k zstd i686 1.5.2-3.fc37 local 418 k Installing Groups: build Transaction Summary ========================================================================================================================= Install 153 Packages Total download size: 53 M Installed size: 179 M Downloading Packages: (1/153): alternatives-1.21-1.fc38.i686.rpm 482 kB/s | 39 kB 00:00 (2/153): authselect-1.4.2-1.fc38.i686.rpm 1.4 MB/s | 141 kB 00:00 (3/153): authselect-libs-1.4.2-1.fc38.i686.rpm 2.3 MB/s | 239 kB 00:00 (4/153): bash-5.2.9-3.fc38.i686.rpm 17 MB/s | 1.8 MB 00:00 (5/153): binutils-gold-2.39-6.fc38.i686.rpm 8.7 MB/s | 853 kB 00:00 (6/153): bzip2-1.0.8-12.fc38.i686.rpm 1.6 MB/s | 53 kB 00:00 (7/153): bzip2-libs-1.0.8-12.fc38.i686.rpm 1.2 MB/s | 42 kB 00:00 (8/153): coreutils-9.1-8.fc38.i686.rpm 17 MB/s | 1.1 MB 00:00 (9/153): binutils-2.39-6.fc38.i686.rpm 27 MB/s | 5.6 MB 00:00 (10/153): coreutils-common-9.1-8.fc38.i686.rpm 22 MB/s | 2.0 MB 00:00 (11/153): cpio-2.13-13.fc38.i686.rpm 7.5 MB/s | 274 kB 00:00 (12/153): cracklib-2.9.7-30.fc38.i686.rpm 6.9 MB/s | 82 kB 00:00 (13/153): curl-7.87.0-1.fc38.i686.rpm 25 MB/s | 347 kB 00:00 (14/153): diffutils-3.8-3.fc38.i686.rpm 17 MB/s | 375 kB 00:00 (15/153): cyrus-sasl-lib-2.1.28-8.fc38.i686.rpm 34 MB/s | 858 kB 00:00 (16/153): dwz-0.15-1.fc38.i686.rpm 11 MB/s | 144 kB 00:00 (17/153): ed-1.18-2.fc38.i686.rpm 7.5 MB/s | 78 kB 00:00 (18/153): elfutils-0.188-3.fc38.i686.rpm 37 MB/s | 543 kB 00:00 (19/153): elfutils-debuginfod-client-0.188-3.fc 2.8 MB/s | 41 kB 00:00 (20/153): elfutils-default-yama-scope-0.188-3.f 1.8 MB/s | 16 kB 00:00 (21/153): elfutils-libelf-0.188-3.fc38.i686.rpm 18 MB/s | 204 kB 00:00 (22/153): elfutils-libs-0.188-3.fc38.i686.rpm 22 MB/s | 287 kB 00:00 (23/153): file-5.42-4.fc38.i686.rpm 4.3 MB/s | 49 kB 00:00 (24/153): file-libs-5.42-4.fc38.i686.rpm 41 MB/s | 684 kB 00:00 (25/153): findutils-4.9.0-2.fc38.i686.rpm 26 MB/s | 494 kB 00:00 (26/153): gawk-5.1.1-4.fc38.i686.rpm 36 MB/s | 1.0 MB 00:00 (27/153): gdbm-libs-1.23-2.fc38.i686.rpm 4.1 MB/s | 60 kB 00:00 (28/153): gmp-6.2.1-3.fc38.i686.rpm 24 MB/s | 306 kB 00:00 (29/153): grep-3.8-1.fc38.i686.rpm 21 MB/s | 289 kB 00:00 (30/153): gzip-1.12-2.fc38.i686.rpm 11 MB/s | 158 kB 00:00 (31/153): info-7.0.1-1.fc38.i686.rpm 14 MB/s | 184 kB 00:00 (32/153): keyutils-libs-1.6.1-5.fc38.i686.rpm 3.4 MB/s | 32 kB 00:00 (33/153): jansson-2.13.1-5.fc38.i686.rpm 4.1 MB/s | 47 kB 00:00 (34/153): krb5-libs-1.20.1-3.fc38.i686.rpm 43 MB/s | 764 kB 00:00 (35/153): libacl-2.3.1-4.fc38.i686.rpm 2.5 MB/s | 25 kB 00:00 (36/153): libarchive-3.6.1-3.fc38.i686.rpm 32 MB/s | 442 kB 00:00 (37/153): libattr-2.5.1-5.fc38.i686.rpm 2.1 MB/s | 19 kB 00:00 (38/153): libblkid-2.38.1-3.fc38.i686.rpm 12 MB/s | 117 kB 00:00 (39/153): libbrotli-1.0.9-9.fc38.i686.rpm 26 MB/s | 318 kB 00:00 (40/153): libcap-2.48-5.fc38.i686.rpm 6.9 MB/s | 69 kB 00:00 (41/153): libcap-ng-0.8.3-4.fc38.i686.rpm 3.7 MB/s | 33 kB 00:00 (42/153): libcurl-7.87.0-1.fc38.i686.rpm 25 MB/s | 327 kB 00:00 (43/153): libdb-5.3.28-54.fc38.i686.rpm 43 MB/s | 823 kB 00:00 (44/153): libeconf-0.4.0-4.fc38.i686.rpm 1.6 MB/s | 29 kB 00:00 (45/153): libevent-2.1.12-7.fc38.i686.rpm 23 MB/s | 277 kB 00:00 (46/153): libfdisk-2.38.1-3.fc38.i686.rpm 15 MB/s | 174 kB 00:00 (47/153): libffi-3.4.4-1.fc38.i686.rpm 3.2 MB/s | 36 kB 00:00 (48/153): libidn2-2.3.4-1.fc38.i686.rpm 14 MB/s | 155 kB 00:00 (49/153): libmount-2.38.1-3.fc38.i686.rpm 13 MB/s | 141 kB 00:00 (50/153): libnghttp2-1.51.0-1.fc38.i686.rpm 6.9 MB/s | 81 kB 00:00 (51/153): libnsl2-2.0.0-4.fc38.i686.rpm 3.3 MB/s | 32 kB 00:00 (52/153): libpkgconf-1.8.0-3.fc38.i686.rpm 4.3 MB/s | 39 kB 00:00 (53/153): libsigsegv-2.14-3.fc38.i686.rpm 2.7 MB/s | 28 kB 00:00 (54/153): libsmartcols-2.38.1-3.fc38.i686.rpm 6.9 MB/s | 66 kB 00:00 (55/153): libssh-0.10.4-2.fc38.i686.rpm 20 MB/s | 223 kB 00:00 (56/153): libssh-config-0.10.4-2.fc38.noarch.rp 998 kB/s | 9.3 kB 00:00 (57/153): libtasn1-4.19.0-1.fc38.i686.rpm 7.8 MB/s | 77 kB 00:00 (58/153): libutempter-1.2.1-7.fc38.i686.rpm 3.0 MB/s | 27 kB 00:00 (59/153): libtirpc-1.3.3-0.fc38.i686.rpm 9.6 MB/s | 101 kB 00:00 (60/153): libunistring-1.0-2.fc38.i686.rpm 35 MB/s | 549 kB 00:00 (61/153): libuuid-2.38.1-3.fc38.i686.rpm 3.0 MB/s | 29 kB 00:00 (62/153): libverto-0.3.2-4.fc38.i686.rpm 2.0 MB/s | 22 kB 00:00 (63/153): libxcrypt-4.4.33-5.fc38.i686.rpm 12 MB/s | 124 kB 00:00 (64/153): libxml2-2.10.3-2.fc38.i686.rpm 42 MB/s | 744 kB 00:00 (65/153): lua-libs-5.4.4-6.fc38.i686.rpm 8.9 MB/s | 149 kB 00:00 (66/153): lz4-libs-1.9.3-5.fc38.i686.rpm 5.7 MB/s | 72 kB 00:00 (67/153): mpfr-4.1.1-2.fc38.i686.rpm 40 MB/s | 637 kB 00:00 (68/153): ncurses-base-6.3-5.20221126.fc38.noar 3.8 MB/s | 62 kB 00:00 (69/153): ncurses-libs-6.3-5.20221126.fc38.i686 19 MB/s | 351 kB 00:00 (70/153): nettle-3.8-2.fc38.i686.rpm 31 MB/s | 426 kB 00:00 (71/153): openldap-2.6.3-1.fc38.i686.rpm 18 MB/s | 274 kB 00:00 (72/153): openssl-libs-3.0.5-6.fc38.i686.rpm 62 MB/s | 2.1 MB 00:00 (73/153): p11-kit-0.24.1-5.fc38.i686.rpm 13 MB/s | 335 kB 00:00 (74/153): p11-kit-trust-0.24.1-5.fc38.i686.rpm 5.8 MB/s | 136 kB 00:00 (75/153): pam-libs-1.5.2-15.fc38.i686.rpm 5.6 MB/s | 60 kB 00:00 (76/153): pam-1.5.2-15.fc38.i686.rpm 31 MB/s | 536 kB 00:00 (77/153): patch-2.7.6-17.fc38.i686.rpm 8.4 MB/s | 138 kB 00:00 (78/153): pcre2-10.40-1.fc38.1.i686.rpm 21 MB/s | 235 kB 00:00 (79/153): pcre2-syntax-10.40-1.fc38.1.noarch.rp 14 MB/s | 143 kB 00:00 (80/153): pkgconf-1.8.0-3.fc38.i686.rpm 4.1 MB/s | 42 kB 00:00 (81/153): pkgconf-m4-1.8.0-3.fc38.noarch.rpm 1.6 MB/s | 15 kB 00:00 (82/153): pkgconf-pkg-config-1.8.0-3.fc38.i686. 1.2 MB/s | 11 kB 00:00 (83/153): popt-1.19-1.fc38.i686.rpm 6.3 MB/s | 62 kB 00:00 (84/153): qt5-srpm-macros-5.15.7-1.fc38.noarch. 827 kB/s | 8.5 kB 00:00 (85/153): readline-8.2-2.fc38.i686.rpm 20 MB/s | 219 kB 00:00 (86/153): rpm-4.18.0-8.fc38.i686.rpm 37 MB/s | 541 kB 00:00 (87/153): rpm-build-4.18.0-8.fc38.i686.rpm 6.8 MB/s | 70 kB 00:00 (88/153): rpm-build-libs-4.18.0-8.fc38.i686.rpm 11 MB/s | 102 kB 00:00 (89/153): rpm-libs-4.18.0-8.fc38.i686.rpm 27 MB/s | 342 kB 00:00 (90/153): rpm-sequoia-1.2.0-1.fc38.i686.rpm 44 MB/s | 914 kB 00:00 (91/153): rpmautospec-rpm-macros-0.3.1-1.fc38.n 569 kB/s | 9.4 kB 00:00 (92/153): sed-4.8-11.fc38.i686.rpm 25 MB/s | 301 kB 00:00 (93/153): sqlite-libs-3.40.0-1.fc38.i686.rpm 30 MB/s | 706 kB 00:00 (94/153): shadow-utils-4.13-3.fc38.i686.rpm 43 MB/s | 1.2 MB 00:00 (95/153): tar-1.34-5.fc38.i686.rpm 27 MB/s | 894 kB 00:00 (96/153): unzip-6.0-58.fc38.i686.rpm 14 MB/s | 179 kB 00:00 (97/153): util-linux-2.38.1-3.fc38.i686.rpm 72 MB/s | 2.3 MB 00:00 (98/153): util-linux-core-2.38.1-3.fc38.i686.rp 17 MB/s | 470 kB 00:00 (99/153): which-2.21-36.fc38.i686.rpm 1.5 MB/s | 42 kB 00:00 (100/153): libgcc-13.0.0-0.4.fc38.i686.rpm 334 kB/s | 101 kB 00:00 (101/153): libgomp-13.0.0-0.4.fc38.i686.rpm 950 kB/s | 304 kB 00:00 (102/153): ansible-srpm-macros-1-8.1.fc38.noarc 157 kB/s | 8.6 kB 00:00 (103/153): basesystem-11-14.fc37.noarch.rpm 473 kB/s | 7.0 kB 00:00 (104/153): libstdc++-13.0.0-0.4.fc38.i686.rpm 2.2 MB/s | 857 kB 00:00 (105/153): audit-libs-3.0.9-2.fc38.i686.rpm 1.6 MB/s | 122 kB 00:00 (106/153): debugedit-5.0-5.fc37.i686.rpm 6.4 MB/s | 78 kB 00:00 (107/153): efi-srpm-macros-5-6.fc37.noarch.rpm 2.0 MB/s | 22 kB 00:00 (108/153): fedora-gpg-keys-38-0.3.noarch.rpm 5.4 MB/s | 115 kB 00:00 (109/153): ca-certificates-2022.2.54-5.fc37.noa 11 MB/s | 829 kB 00:00 (110/153): crypto-policies-20221215-1.gita4c31a 952 kB/s | 63 kB 00:00 (111/153): fedora-release-38-0.6.noarch.rpm 751 kB/s | 11 kB 00:00 (112/153): fedora-release-common-38-0.6.noarch. 1.5 MB/s | 21 kB 00:00 (113/153): fedora-release-identity-basic-38-0.6 917 kB/s | 11 kB 00:00 (114/153): fedora-repos-38-0.3.noarch.rpm 667 kB/s | 10 kB 00:00 (115/153): fedora-repos-rawhide-38-0.3.noarch.r 699 kB/s | 9.7 kB 00:00 (116/153): fonts-srpm-macros-2.0.5-10.fc38.noar 1.8 MB/s | 26 kB 00:00 (117/153): fpc-srpm-macros-1.3-6.fc37.noarch.rp 569 kB/s | 7.7 kB 00:00 (118/153): ghc-srpm-macros-1.5.0-7.fc37.noarch. 719 kB/s | 7.8 kB 00:00 (119/153): filesystem-3.18-2.fc37.i686.rpm 20 MB/s | 1.1 MB 00:00 (120/153): glibc-common-2.36.9000-19.fc38.i686. 12 MB/s | 315 kB 00:00 (121/153): glibc-2.36.9000-19.fc38.i686.rpm 27 MB/s | 1.9 MB 00:00 (122/153): gdb-minimal-12.1-10.fc38.i686.rpm 39 MB/s | 3.9 MB 00:00 (123/153): glibc-gconv-extra-2.36.9000-19.fc38. 37 MB/s | 1.6 MB 00:00 (124/153): glibc-minimal-langpack-2.36.9000-19. 2.2 MB/s | 30 kB 00:00 (125/153): gnat-srpm-macros-4-16.fc37.noarch.rp 745 kB/s | 8.3 kB 00:00 (126/153): kernel-srpm-macros-1.0-15.fc37.noarc 842 kB/s | 9.4 kB 00:00 (127/153): go-srpm-macros-3.2.0-1.fc38.noarch.r 1.3 MB/s | 27 kB 00:00 (128/153): libcom_err-1.46.5-3.fc37.i686.rpm 1.2 MB/s | 26 kB 00:00 (129/153): libpsl-0.21.2-1.fc38.i686.rpm 3.0 MB/s | 66 kB 00:00 (130/153): libpwquality-1.4.5-1.fc38.i686.rpm 8.3 MB/s | 108 kB 00:00 (131/153): libselinux-3.5-0.rc1.1.fc38.i686.rpm 4.0 MB/s | 91 kB 00:00 (132/153): libsepol-3.5-0.rc1.1.fc38.i686.rpm 16 MB/s | 336 kB 00:00 (133/153): libsemanage-3.5-0.rc1.1.fc38.i686.rp 4.2 MB/s | 128 kB 00:00 (134/153): libzstd-1.5.2-3.fc37.i686.rpm 15 MB/s | 274 kB 00:00 (135/153): lua-srpm-macros-1-7.fc37.noarch.rpm 499 kB/s | 8.8 kB 00:00 (136/153): nim-srpm-macros-3-7.fc37.noarch.rpm 638 kB/s | 8.4 kB 00:00 (137/153): ocaml-srpm-macros-7-2.fc37.noarch.rp 857 kB/s | 13 kB 00:00 (138/153): package-notes-srpm-macros-0.5-6.fc38 969 kB/s | 11 kB 00:00 (139/153): openblas-srpm-macros-2-12.fc37.noarc 447 kB/s | 7.5 kB 00:00 (140/153): perl-srpm-macros-1-47.fc38.noarch.rp 695 kB/s | 8.2 kB 00:00 (141/153): python-srpm-macros-3.11-6.fc38.noarc 2.1 MB/s | 25 kB 00:00 (142/153): publicsuffix-list-dafsa-20221208-1.f 3.8 MB/s | 59 kB 00:00 (143/153): rust-srpm-macros-23-1.fc38.noarch.rp 889 kB/s | 9.4 kB 00:00 (144/153): redhat-rpm-config-236-1.fc38.noarch. 5.2 MB/s | 74 kB 00:00 (145/153): setup-2.14.3-1.fc38.noarch.rpm 7.2 MB/s | 146 kB 00:00 (146/153): xxhash-libs-0.8.1-3.fc37.i686.rpm 4.3 MB/s | 59 kB 00:00 (147/153): tzdata-2022g-1.fc38.noarch.rpm 15 MB/s | 432 kB 00:00 (148/153): systemd-libs-252.4-598.fc38.i686.rpm 18 MB/s | 662 kB 00:00 (149/153): xz-5.2.9-1.fc38.i686.rpm 15 MB/s | 300 kB 00:00 (150/153): xz-libs-5.2.9-1.fc38.i686.rpm 5.1 MB/s | 101 kB 00:00 (151/153): zip-3.0-35.fc38.i686.rpm 9.9 MB/s | 263 kB 00:00 (152/153): zstd-1.5.2-3.fc37.i686.rpm 25 MB/s | 418 kB 00:00 (153/153): zlib-1.2.13-1.fc38.i686.rpm 3.5 MB/s | 92 kB 00:00 -------------------------------------------------------------------------------- Total 34 MB/s | 53 MB 00:01 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Running scriptlet: filesystem-3.18-2.fc37.i686 1/1 Preparing : 1/1 Installing : crypto-policies-20221215-1.gita4c31a3.fc38.noarc 1/153 Running scriptlet: crypto-policies-20221215-1.gita4c31a3.fc38.noarc 1/153 Installing : fedora-release-identity-basic-38-0.6.noarch 2/153 Installing : tzdata-2022g-1.fc38.noarch 3/153 Installing : rust-srpm-macros-23-1.fc38.noarch 4/153 Installing : publicsuffix-list-dafsa-20221208-1.fc38.noarch 5/153 Installing : perl-srpm-macros-1-47.fc38.noarch 6/153 Installing : package-notes-srpm-macros-0.5-6.fc38.noarch 7/153 Installing : openblas-srpm-macros-2-12.fc37.noarch 8/153 Installing : ocaml-srpm-macros-7-2.fc37.noarch 9/153 Installing : nim-srpm-macros-3-7.fc37.noarch 10/153 Installing : kernel-srpm-macros-1.0-15.fc37.noarch 11/153 Installing : gnat-srpm-macros-4-16.fc37.noarch 12/153 Installing : ghc-srpm-macros-1.5.0-7.fc37.noarch 13/153 Installing : fpc-srpm-macros-1.3-6.fc37.noarch 14/153 Installing : fedora-gpg-keys-38-0.3.noarch 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libpkgconf-1.8.0-3.fc38.i686 106/153 Installing : pkgconf-1.8.0-3.fc38.i686 107/153 Installing : pkgconf-pkg-config-1.8.0-3.fc38.i686 108/153 Installing : libsigsegv-2.14-3.fc38.i686 109/153 Installing : gawk-5.1.1-4.fc38.i686 110/153 Installing : libtasn1-4.19.0-1.fc38.i686 111/153 Installing : p11-kit-trust-0.24.1-5.fc38.i686 112/153 Running scriptlet: p11-kit-trust-0.24.1-5.fc38.i686 112/153 Installing : openssl-libs-1:3.0.5-6.fc38.i686 113/153 Installing : coreutils-9.1-8.fc38.i686 114/153 Running scriptlet: ca-certificates-2022.2.54-5.fc37.noarch 115/153 Installing : ca-certificates-2022.2.54-5.fc37.noarch 115/153 Running scriptlet: ca-certificates-2022.2.54-5.fc37.noarch 115/153 Running scriptlet: authselect-libs-1.4.2-1.fc38.i686 116/153 Installing : authselect-libs-1.4.2-1.fc38.i686 116/153 Installing : gzip-1.12-2.fc38.i686 117/153 Installing : cracklib-2.9.7-30.fc38.i686 118/153 Installing : libpwquality-1.4.5-1.fc38.i686 119/153 Installing : authselect-1.4.2-1.fc38.i686 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rpm-4.18.0-8.fc38.i686 153/153 Running scriptlet: info-7.0.1-1.fc38.i686 153/153 Verifying : alternatives-1.21-1.fc38.i686 1/153 Verifying : authselect-1.4.2-1.fc38.i686 2/153 Verifying : authselect-libs-1.4.2-1.fc38.i686 3/153 Verifying : bash-5.2.9-3.fc38.i686 4/153 Verifying : binutils-2.39-6.fc38.i686 5/153 Verifying : binutils-gold-2.39-6.fc38.i686 6/153 Verifying : bzip2-1.0.8-12.fc38.i686 7/153 Verifying : bzip2-libs-1.0.8-12.fc38.i686 8/153 Verifying : coreutils-9.1-8.fc38.i686 9/153 Verifying : coreutils-common-9.1-8.fc38.i686 10/153 Verifying : cpio-2.13-13.fc38.i686 11/153 Verifying : cracklib-2.9.7-30.fc38.i686 12/153 Verifying : curl-7.87.0-1.fc38.i686 13/153 Verifying : cyrus-sasl-lib-2.1.28-8.fc38.i686 14/153 Verifying : diffutils-3.8-3.fc38.i686 15/153 Verifying : dwz-0.15-1.fc38.i686 16/153 Verifying : ed-1.18-2.fc38.i686 17/153 Verifying : elfutils-0.188-3.fc38.i686 18/153 Verifying : elfutils-debuginfod-client-0.188-3.fc38.i686 19/153 Verifying : elfutils-default-yama-scope-0.188-3.fc38.noarch 20/153 Verifying : elfutils-libelf-0.188-3.fc38.i686 21/153 Verifying : elfutils-libs-0.188-3.fc38.i686 22/153 Verifying : file-5.42-4.fc38.i686 23/153 Verifying : file-libs-5.42-4.fc38.i686 24/153 Verifying : findutils-1:4.9.0-2.fc38.i686 25/153 Verifying : gawk-5.1.1-4.fc38.i686 26/153 Verifying : gdbm-libs-1:1.23-2.fc38.i686 27/153 Verifying : gmp-1:6.2.1-3.fc38.i686 28/153 Verifying : grep-3.8-1.fc38.i686 29/153 Verifying : gzip-1.12-2.fc38.i686 30/153 Verifying : info-7.0.1-1.fc38.i686 31/153 Verifying : jansson-2.13.1-5.fc38.i686 32/153 Verifying : keyutils-libs-1.6.1-5.fc38.i686 33/153 Verifying : krb5-libs-1.20.1-3.fc38.i686 34/153 Verifying : libacl-2.3.1-4.fc38.i686 35/153 Verifying : libarchive-3.6.1-3.fc38.i686 36/153 Verifying : libattr-2.5.1-5.fc38.i686 37/153 Verifying : libblkid-2.38.1-3.fc38.i686 38/153 Verifying : libbrotli-1.0.9-9.fc38.i686 39/153 Verifying : libcap-2.48-5.fc38.i686 40/153 Verifying : libcap-ng-0.8.3-4.fc38.i686 41/153 Verifying : libcurl-7.87.0-1.fc38.i686 42/153 Verifying : libdb-5.3.28-54.fc38.i686 43/153 Verifying : libeconf-0.4.0-4.fc38.i686 44/153 Verifying : libevent-2.1.12-7.fc38.i686 45/153 Verifying : libfdisk-2.38.1-3.fc38.i686 46/153 Verifying : libffi-3.4.4-1.fc38.i686 47/153 Verifying : libidn2-2.3.4-1.fc38.i686 48/153 Verifying : libmount-2.38.1-3.fc38.i686 49/153 Verifying : libnghttp2-1.51.0-1.fc38.i686 50/153 Verifying : libnsl2-2.0.0-4.fc38.i686 51/153 Verifying : libpkgconf-1.8.0-3.fc38.i686 52/153 Verifying : libsigsegv-2.14-3.fc38.i686 53/153 Verifying : libsmartcols-2.38.1-3.fc38.i686 54/153 Verifying : libssh-0.10.4-2.fc38.i686 55/153 Verifying : libssh-config-0.10.4-2.fc38.noarch 56/153 Verifying : libtasn1-4.19.0-1.fc38.i686 57/153 Verifying : libtirpc-1.3.3-0.fc38.i686 58/153 Verifying : libunistring-1.0-2.fc38.i686 59/153 Verifying : libutempter-1.2.1-7.fc38.i686 60/153 Verifying : libuuid-2.38.1-3.fc38.i686 61/153 Verifying : libverto-0.3.2-4.fc38.i686 62/153 Verifying : libxcrypt-4.4.33-5.fc38.i686 63/153 Verifying : libxml2-2.10.3-2.fc38.i686 64/153 Verifying : lua-libs-5.4.4-6.fc38.i686 65/153 Verifying : lz4-libs-1.9.3-5.fc38.i686 66/153 Verifying : mpfr-4.1.1-2.fc38.i686 67/153 Verifying : ncurses-base-6.3-5.20221126.fc38.noarch 68/153 Verifying : ncurses-libs-6.3-5.20221126.fc38.i686 69/153 Verifying : nettle-3.8-2.fc38.i686 70/153 Verifying : openldap-2.6.3-1.fc38.i686 71/153 Verifying : openssl-libs-1:3.0.5-6.fc38.i686 72/153 Verifying : p11-kit-0.24.1-5.fc38.i686 73/153 Verifying : p11-kit-trust-0.24.1-5.fc38.i686 74/153 Verifying : pam-1.5.2-15.fc38.i686 75/153 Verifying : pam-libs-1.5.2-15.fc38.i686 76/153 Verifying : patch-2.7.6-17.fc38.i686 77/153 Verifying : pcre2-10.40-1.fc38.1.i686 78/153 Verifying : pcre2-syntax-10.40-1.fc38.1.noarch 79/153 Verifying : pkgconf-1.8.0-3.fc38.i686 80/153 Verifying : pkgconf-m4-1.8.0-3.fc38.noarch 81/153 Verifying : pkgconf-pkg-config-1.8.0-3.fc38.i686 82/153 Verifying : popt-1.19-1.fc38.i686 83/153 Verifying : qt5-srpm-macros-5.15.7-1.fc38.noarch 84/153 Verifying : readline-8.2-2.fc38.i686 85/153 Verifying : rpm-4.18.0-8.fc38.i686 86/153 Verifying : rpm-build-4.18.0-8.fc38.i686 87/153 Verifying : rpm-build-libs-4.18.0-8.fc38.i686 88/153 Verifying : rpm-libs-4.18.0-8.fc38.i686 89/153 Verifying : rpm-sequoia-1.2.0-1.fc38.i686 90/153 Verifying : rpmautospec-rpm-macros-0.3.1-1.fc38.noarch 91/153 Verifying : sed-4.8-11.fc38.i686 92/153 Verifying : shadow-utils-2:4.13-3.fc38.i686 93/153 Verifying : sqlite-libs-3.40.0-1.fc38.i686 94/153 Verifying : tar-2:1.34-5.fc38.i686 95/153 Verifying : unzip-6.0-58.fc38.i686 96/153 Verifying : util-linux-2.38.1-3.fc38.i686 97/153 Verifying : util-linux-core-2.38.1-3.fc38.i686 98/153 Verifying : which-2.21-36.fc38.i686 99/153 Verifying : libgcc-13.0.0-0.4.fc38.i686 100/153 Verifying : libgomp-13.0.0-0.4.fc38.i686 101/153 Verifying : libstdc++-13.0.0-0.4.fc38.i686 102/153 Verifying : ansible-srpm-macros-1-8.1.fc38.noarch 103/153 Verifying : audit-libs-3.0.9-2.fc38.i686 104/153 Verifying : basesystem-11-14.fc37.noarch 105/153 Verifying : ca-certificates-2022.2.54-5.fc37.noarch 106/153 Verifying : crypto-policies-20221215-1.gita4c31a3.fc38.noarc 107/153 Verifying : debugedit-5.0-5.fc37.i686 108/153 Verifying : efi-srpm-macros-5-6.fc37.noarch 109/153 Verifying : fedora-gpg-keys-38-0.3.noarch 110/153 Verifying : fedora-release-38-0.6.noarch 111/153 Verifying : fedora-release-common-38-0.6.noarch 112/153 Verifying : fedora-release-identity-basic-38-0.6.noarch 113/153 Verifying : fedora-repos-38-0.3.noarch 114/153 Verifying : fedora-repos-rawhide-38-0.3.noarch 115/153 Verifying : filesystem-3.18-2.fc37.i686 116/153 Verifying : fonts-srpm-macros-1:2.0.5-10.fc38.noarch 117/153 Verifying : fpc-srpm-macros-1.3-6.fc37.noarch 118/153 Verifying : gdb-minimal-12.1-10.fc38.i686 119/153 Verifying : ghc-srpm-macros-1.5.0-7.fc37.noarch 120/153 Verifying : glibc-2.36.9000-19.fc38.i686 121/153 Verifying : glibc-common-2.36.9000-19.fc38.i686 122/153 Verifying : glibc-gconv-extra-2.36.9000-19.fc38.i686 123/153 Verifying : glibc-minimal-langpack-2.36.9000-19.fc38.i686 124/153 Verifying : gnat-srpm-macros-4-16.fc37.noarch 125/153 Verifying : go-srpm-macros-3.2.0-1.fc38.noarch 126/153 Verifying : kernel-srpm-macros-1.0-15.fc37.noarch 127/153 Verifying : libcom_err-1.46.5-3.fc37.i686 128/153 Verifying : libpsl-0.21.2-1.fc38.i686 129/153 Verifying : libpwquality-1.4.5-1.fc38.i686 130/153 Verifying : libselinux-3.5-0.rc1.1.fc38.i686 131/153 Verifying : libsemanage-3.5-0.rc1.1.fc38.i686 132/153 Verifying : libsepol-3.5-0.rc1.1.fc38.i686 133/153 Verifying : libzstd-1.5.2-3.fc37.i686 134/153 Verifying : lua-srpm-macros-1-7.fc37.noarch 135/153 Verifying : nim-srpm-macros-3-7.fc37.noarch 136/153 Verifying : ocaml-srpm-macros-7-2.fc37.noarch 137/153 Verifying : openblas-srpm-macros-2-12.fc37.noarch 138/153 Verifying : package-notes-srpm-macros-0.5-6.fc38.noarch 139/153 Verifying : perl-srpm-macros-1-47.fc38.noarch 140/153 Verifying : publicsuffix-list-dafsa-20221208-1.fc38.noarch 141/153 Verifying : python-srpm-macros-3.11-6.fc38.noarch 142/153 Verifying : redhat-rpm-config-236-1.fc38.noarch 143/153 Verifying : rust-srpm-macros-23-1.fc38.noarch 144/153 Verifying : setup-2.14.3-1.fc38.noarch 145/153 Verifying : systemd-libs-252.4-598.fc38.i686 146/153 Verifying : tzdata-2022g-1.fc38.noarch 147/153 Verifying : xxhash-libs-0.8.1-3.fc37.i686 148/153 Verifying : xz-5.2.9-1.fc38.i686 149/153 Verifying : xz-libs-5.2.9-1.fc38.i686 150/153 Verifying : zip-3.0-35.fc38.i686 151/153 Verifying : zlib-1.2.13-1.fc38.i686 152/153 Verifying : zstd-1.5.2-3.fc37.i686 153/153 Installed: alternatives-1.21-1.fc38.i686 ansible-srpm-macros-1-8.1.fc38.noarch audit-libs-3.0.9-2.fc38.i686 authselect-1.4.2-1.fc38.i686 authselect-libs-1.4.2-1.fc38.i686 basesystem-11-14.fc37.noarch bash-5.2.9-3.fc38.i686 binutils-2.39-6.fc38.i686 binutils-gold-2.39-6.fc38.i686 bzip2-1.0.8-12.fc38.i686 bzip2-libs-1.0.8-12.fc38.i686 ca-certificates-2022.2.54-5.fc37.noarch coreutils-9.1-8.fc38.i686 coreutils-common-9.1-8.fc38.i686 cpio-2.13-13.fc38.i686 cracklib-2.9.7-30.fc38.i686 crypto-policies-20221215-1.gita4c31a3.fc38.noarch curl-7.87.0-1.fc38.i686 cyrus-sasl-lib-2.1.28-8.fc38.i686 debugedit-5.0-5.fc37.i686 diffutils-3.8-3.fc38.i686 dwz-0.15-1.fc38.i686 ed-1.18-2.fc38.i686 efi-srpm-macros-5-6.fc37.noarch elfutils-0.188-3.fc38.i686 elfutils-debuginfod-client-0.188-3.fc38.i686 elfutils-default-yama-scope-0.188-3.fc38.noarch elfutils-libelf-0.188-3.fc38.i686 elfutils-libs-0.188-3.fc38.i686 fedora-gpg-keys-38-0.3.noarch fedora-release-38-0.6.noarch fedora-release-common-38-0.6.noarch fedora-release-identity-basic-38-0.6.noarch fedora-repos-38-0.3.noarch fedora-repos-rawhide-38-0.3.noarch file-5.42-4.fc38.i686 file-libs-5.42-4.fc38.i686 filesystem-3.18-2.fc37.i686 findutils-1:4.9.0-2.fc38.i686 fonts-srpm-macros-1:2.0.5-10.fc38.noarch fpc-srpm-macros-1.3-6.fc37.noarch gawk-5.1.1-4.fc38.i686 gdb-minimal-12.1-10.fc38.i686 gdbm-libs-1:1.23-2.fc38.i686 ghc-srpm-macros-1.5.0-7.fc37.noarch glibc-2.36.9000-19.fc38.i686 glibc-common-2.36.9000-19.fc38.i686 glibc-gconv-extra-2.36.9000-19.fc38.i686 glibc-minimal-langpack-2.36.9000-19.fc38.i686 gmp-1:6.2.1-3.fc38.i686 gnat-srpm-macros-4-16.fc37.noarch go-srpm-macros-3.2.0-1.fc38.noarch grep-3.8-1.fc38.i686 gzip-1.12-2.fc38.i686 info-7.0.1-1.fc38.i686 jansson-2.13.1-5.fc38.i686 kernel-srpm-macros-1.0-15.fc37.noarch keyutils-libs-1.6.1-5.fc38.i686 krb5-libs-1.20.1-3.fc38.i686 libacl-2.3.1-4.fc38.i686 libarchive-3.6.1-3.fc38.i686 libattr-2.5.1-5.fc38.i686 libblkid-2.38.1-3.fc38.i686 libbrotli-1.0.9-9.fc38.i686 libcap-2.48-5.fc38.i686 libcap-ng-0.8.3-4.fc38.i686 libcom_err-1.46.5-3.fc37.i686 libcurl-7.87.0-1.fc38.i686 libdb-5.3.28-54.fc38.i686 libeconf-0.4.0-4.fc38.i686 libevent-2.1.12-7.fc38.i686 libfdisk-2.38.1-3.fc38.i686 libffi-3.4.4-1.fc38.i686 libgcc-13.0.0-0.4.fc38.i686 libgomp-13.0.0-0.4.fc38.i686 libidn2-2.3.4-1.fc38.i686 libmount-2.38.1-3.fc38.i686 libnghttp2-1.51.0-1.fc38.i686 libnsl2-2.0.0-4.fc38.i686 libpkgconf-1.8.0-3.fc38.i686 libpsl-0.21.2-1.fc38.i686 libpwquality-1.4.5-1.fc38.i686 libselinux-3.5-0.rc1.1.fc38.i686 libsemanage-3.5-0.rc1.1.fc38.i686 libsepol-3.5-0.rc1.1.fc38.i686 libsigsegv-2.14-3.fc38.i686 libsmartcols-2.38.1-3.fc38.i686 libssh-0.10.4-2.fc38.i686 libssh-config-0.10.4-2.fc38.noarch libstdc++-13.0.0-0.4.fc38.i686 libtasn1-4.19.0-1.fc38.i686 libtirpc-1.3.3-0.fc38.i686 libunistring-1.0-2.fc38.i686 libutempter-1.2.1-7.fc38.i686 libuuid-2.38.1-3.fc38.i686 libverto-0.3.2-4.fc38.i686 libxcrypt-4.4.33-5.fc38.i686 libxml2-2.10.3-2.fc38.i686 libzstd-1.5.2-3.fc37.i686 lua-libs-5.4.4-6.fc38.i686 lua-srpm-macros-1-7.fc37.noarch lz4-libs-1.9.3-5.fc38.i686 mpfr-4.1.1-2.fc38.i686 ncurses-base-6.3-5.20221126.fc38.noarch ncurses-libs-6.3-5.20221126.fc38.i686 nettle-3.8-2.fc38.i686 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.i686 openssl-libs-1:3.0.5-6.fc38.i686 p11-kit-0.24.1-5.fc38.i686 p11-kit-trust-0.24.1-5.fc38.i686 package-notes-srpm-macros-0.5-6.fc38.noarch pam-1.5.2-15.fc38.i686 pam-libs-1.5.2-15.fc38.i686 patch-2.7.6-17.fc38.i686 pcre2-10.40-1.fc38.1.i686 pcre2-syntax-10.40-1.fc38.1.noarch perl-srpm-macros-1-47.fc38.noarch pkgconf-1.8.0-3.fc38.i686 pkgconf-m4-1.8.0-3.fc38.noarch pkgconf-pkg-config-1.8.0-3.fc38.i686 popt-1.19-1.fc38.i686 publicsuffix-list-dafsa-20221208-1.fc38.noarch python-srpm-macros-3.11-6.fc38.noarch qt5-srpm-macros-5.15.7-1.fc38.noarch readline-8.2-2.fc38.i686 redhat-rpm-config-236-1.fc38.noarch rpm-4.18.0-8.fc38.i686 rpm-build-4.18.0-8.fc38.i686 rpm-build-libs-4.18.0-8.fc38.i686 rpm-libs-4.18.0-8.fc38.i686 rpm-sequoia-1.2.0-1.fc38.i686 rpmautospec-rpm-macros-0.3.1-1.fc38.noarch rust-srpm-macros-23-1.fc38.noarch sed-4.8-11.fc38.i686 setup-2.14.3-1.fc38.noarch shadow-utils-2:4.13-3.fc38.i686 sqlite-libs-3.40.0-1.fc38.i686 systemd-libs-252.4-598.fc38.i686 tar-2:1.34-5.fc38.i686 tzdata-2022g-1.fc38.noarch unzip-6.0-58.fc38.i686 util-linux-2.38.1-3.fc38.i686 util-linux-core-2.38.1-3.fc38.i686 which-2.21-36.fc38.i686 xxhash-libs-0.8.1-3.fc37.i686 xz-5.2.9-1.fc38.i686 xz-libs-5.2.9-1.fc38.i686 zip-3.0-35.fc38.i686 zlib-1.2.13-1.fc38.i686 zstd-1.5.2-3.fc37.i686 Complete! Finish: dnf install Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: rpm-4.18.0-8.fc38.i686 libcap-ng-0.8.3-4.fc38.i686 sqlite-libs-3.40.0-1.fc38.i686 libgomp-13.0.0-0.4.fc38.i686 authselect-libs-1.4.2-1.fc38.i686 libutempter-1.2.1-7.fc38.i686 rust-srpm-macros-23-1.fc38.noarch ncurses-libs-6.3-5.20221126.fc38.i686 filesystem-3.18-2.fc37.i686 kernel-srpm-macros-1.0-15.fc37.noarch libbrotli-1.0.9-9.fc38.i686 binutils-gold-2.39-6.fc38.i686 grep-3.8-1.fc38.i686 package-notes-srpm-macros-0.5-6.fc38.noarch ncurses-base-6.3-5.20221126.fc38.noarch pcre2-10.40-1.fc38.1.i686 jansson-2.13.1-5.fc38.i686 openssl-libs-3.0.5-6.fc38.i686 patch-2.7.6-17.fc38.i686 xz-libs-5.2.9-1.fc38.i686 libpwquality-1.4.5-1.fc38.i686 bzip2-libs-1.0.8-12.fc38.i686 fedora-gpg-keys-38-0.3.noarch keyutils-libs-1.6.1-5.fc38.i686 bash-5.2.9-3.fc38.i686 which-2.21-36.fc38.i686 libacl-2.3.1-4.fc38.i686 pkgconf-1.8.0-3.fc38.i686 gzip-1.12-2.fc38.i686 basesystem-11-14.fc37.noarch authselect-1.4.2-1.fc38.i686 gdb-minimal-12.1-10.fc38.i686 go-srpm-macros-3.2.0-1.fc38.noarch binutils-2.39-6.fc38.i686 sed-4.8-11.fc38.i686 lua-srpm-macros-1-7.fc37.noarch glibc-gconv-extra-2.36.9000-19.fc38.i686 p11-kit-trust-0.24.1-5.fc38.i686 setup-2.14.3-1.fc38.noarch glibc-2.36.9000-19.fc38.i686 readline-8.2-2.fc38.i686 libidn2-2.3.4-1.fc38.i686 coreutils-common-9.1-8.fc38.i686 gmp-6.2.1-3.fc38.i686 redhat-rpm-config-236-1.fc38.noarch gdbm-libs-1.23-2.fc38.i686 elfutils-libs-0.188-3.fc38.i686 zip-3.0-35.fc38.i686 libmount-2.38.1-3.fc38.i686 libssh-0.10.4-2.fc38.i686 rpm-build-4.18.0-8.fc38.i686 efi-srpm-macros-5-6.fc37.noarch gawk-5.1.1-4.fc38.i686 coreutils-9.1-8.fc38.i686 tar-1.34-5.fc38.i686 nim-srpm-macros-3-7.fc37.noarch ghc-srpm-macros-1.5.0-7.fc37.noarch libffi-3.4.4-1.fc38.i686 libstdc++-13.0.0-0.4.fc38.i686 systemd-libs-252.4-598.fc38.i686 libcap-2.48-5.fc38.i686 libarchive-3.6.1-3.fc38.i686 zstd-1.5.2-3.fc37.i686 p11-kit-0.24.1-5.fc38.i686 libgcc-13.0.0-0.4.fc38.i686 debugedit-5.0-5.fc37.i686 pkgconf-m4-1.8.0-3.fc38.noarch elfutils-debuginfod-client-0.188-3.fc38.i686 libcurl-7.87.0-1.fc38.i686 fonts-srpm-macros-2.0.5-10.fc38.noarch nettle-3.8-2.fc38.i686 libssh-config-0.10.4-2.fc38.noarch diffutils-3.8-3.fc38.i686 rpmautospec-rpm-macros-0.3.1-1.fc38.noarch libzstd-1.5.2-3.fc37.i686 fedora-release-38-0.6.noarch libevent-2.1.12-7.fc38.i686 libnghttp2-1.51.0-1.fc38.i686 rpm-build-libs-4.18.0-8.fc38.i686 ed-1.18-2.fc38.i686 rpm-sequoia-1.2.0-1.fc38.i686 libattr-2.5.1-5.fc38.i686 fpc-srpm-macros-1.3-6.fc37.noarch util-linux-2.38.1-3.fc38.i686 libselinux-3.5-0.rc1.1.fc38.i686 libsigsegv-2.14-3.fc38.i686 alternatives-1.21-1.fc38.i686 qt5-srpm-macros-5.15.7-1.fc38.noarch rpm-libs-4.18.0-8.fc38.i686 krb5-libs-1.20.1-3.fc38.i686 libtirpc-1.3.3-0.fc38.i686 dwz-0.15-1.fc38.i686 file-libs-5.42-4.fc38.i686 libnsl2-2.0.0-4.fc38.i686 lua-libs-5.4.4-6.fc38.i686 pam-1.5.2-15.fc38.i686 ca-certificates-2022.2.54-5.fc37.noarch zlib-1.2.13-1.fc38.i686 findutils-4.9.0-2.fc38.i686 libblkid-2.38.1-3.fc38.i686 libsepol-3.5-0.rc1.1.fc38.i686 libsemanage-3.5-0.rc1.1.fc38.i686 util-linux-core-2.38.1-3.fc38.i686 libpsl-0.21.2-1.fc38.i686 fedora-repos-rawhide-38-0.3.noarch libeconf-0.4.0-4.fc38.i686 libpkgconf-1.8.0-3.fc38.i686 cracklib-2.9.7-30.fc38.i686 libverto-0.3.2-4.fc38.i686 glibc-minimal-langpack-2.36.9000-19.fc38.i686 xz-5.2.9-1.fc38.i686 libxcrypt-4.4.33-5.fc38.i686 libxml2-2.10.3-2.fc38.i686 ansible-srpm-macros-1-8.1.fc38.noarch python-srpm-macros-3.11-6.fc38.noarch lz4-libs-1.9.3-5.fc38.i686 libuuid-2.38.1-3.fc38.i686 elfutils-default-yama-scope-0.188-3.fc38.noarch shadow-utils-4.13-3.fc38.i686 libsmartcols-2.38.1-3.fc38.i686 cyrus-sasl-lib-2.1.28-8.fc38.i686 fedora-release-identity-basic-38-0.6.noarch audit-libs-3.0.9-2.fc38.i686 libunistring-1.0-2.fc38.i686 mpfr-4.1.1-2.fc38.i686 pam-libs-1.5.2-15.fc38.i686 bzip2-1.0.8-12.fc38.i686 tzdata-2022g-1.fc38.noarch pcre2-syntax-10.40-1.fc38.1.noarch libfdisk-2.38.1-3.fc38.i686 libdb-5.3.28-54.fc38.i686 elfutils-libelf-0.188-3.fc38.i686 openldap-2.6.3-1.fc38.i686 libtasn1-4.19.0-1.fc38.i686 unzip-6.0-58.fc38.i686 elfutils-0.188-3.fc38.i686 openblas-srpm-macros-2-12.fc37.noarch xxhash-libs-0.8.1-3.fc37.i686 perl-srpm-macros-1-47.fc38.noarch curl-7.87.0-1.fc38.i686 gnat-srpm-macros-4-16.fc37.noarch fedora-release-common-38-0.6.noarch glibc-common-2.36.9000-19.fc38.i686 publicsuffix-list-dafsa-20221208-1.fc38.noarch file-5.42-4.fc38.i686 libcom_err-1.46.5-3.fc37.i686 pkgconf-pkg-config-1.8.0-3.fc38.i686 crypto-policies-20221215-1.gita4c31a3.fc38.noarch cpio-2.13-13.fc38.i686 popt-1.19-1.fc38.i686 ocaml-srpm-macros-7-2.fc37.noarch fedora-repos-38-0.3.noarch info-7.0.1-1.fc38.i686 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: i686 Building for target i686 setting SOURCE_DATE_EPOCH=1671753600 Wrote: /builddir/build/SRPMS/wise2-2.4.1-16.fc38.src.rpm Finish: rpmbuild -bs cp: ‘var/lib/mock/fedora-rawhide-i686-1672387198.750766/root/var/log’: No such file or directory INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-i686-1672387198.750766/root/var/log/dnf.rpm.log /var/lib/mock/fedora-rawhide-i686-1672387198.750766/root/var/log/dnf.librepo.log /var/lib/mock/fedora-rawhide-i686-1672387198.750766/root/var/log/dnf.log Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-cc4xf4pg/wise2/wise2.spec) Config(child) 1 minutes 34 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=115200): unbuffer mock --rebuild /var/lib/copr-rpmbuild/results/wise2-2.4.1-16.fc38.src.rpm --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1672387198.750766 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 3.5 starting (python version = 3.11.0, NVR = mock-3.5-1.fc37)... 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/wise2-2.4.1-16.fc38.src.rpm) Config(fedora-rawhide-i686) Start: clean chroot Finish: clean chroot Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-i686-bootstrap-1672387198.750766/root. INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-i686-bootstrap-1672387198.750766/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: 3.5 INFO: Mock Version: 3.5 Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-i686-1672387198.750766/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: 3.5 INFO: Mock Version: 3.5 Start: dnf update No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 12 kB/s | 3.0 kB 00:00 Copr repository 33 MB/s | 40 MB 00:01 Additional repo https_jakub_fedorapeople_org_fe 9.9 kB/s | 3.0 kB 00:00 local 14 kB/s | 3.8 kB 00:00 Dependencies resolved. Nothing to do. Complete! Finish: dnf update Finish: chroot init Start: build phase for wise2-2.4.1-16.fc38.src.rpm Start: build setup for wise2-2.4.1-16.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: i686 Building for target i686 setting SOURCE_DATE_EPOCH=1671753600 Wrote: /builddir/build/SRPMS/wise2-2.4.1-16.fc38.src.rpm No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 12 kB/s | 3.0 kB 00:00 Additional repo https_jakub_fedorapeople_org_fe 2.4 kB/s | 3.0 kB 00:01 local 14 kB/s | 3.8 kB 00:00 Package pkgconf-pkg-config-1.8.0-3.fc38.i686 is already installed. Dependencies resolved. ============================================================================================================================= Package Arch Version Repository Size ============================================================================================================================= Installing: gcc i686 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 34 M glib2-devel i686 2.74.1-2.fc38 copr_base 519 k make i686 1:4.3-11.fc38 copr_base 542 k perl i686 4:5.36.0-492.fc38 copr_base 16 k strace i686 6.1-1.fc38 copr_base 1.3 M Installing dependencies: annobin-docs noarch 10.99-1.0.1.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 93 k annobin-plugin-gcc i686 10.99-1.0.1.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 889 k cpp i686 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 11 M expat i686 2.5.0-1.fc38 copr_base 115 k gc i686 8.2.2-1.fc38 copr_base 113 k gcc-c++ i686 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 13 M gcc-plugin-annobin i686 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 30 k glib2 i686 2.74.1-2.fc38 copr_base 2.8 M glibc-devel i686 2.36.9000-19.fc38 local 43 k glibc-headers-x86 noarch 2.36.9000-19.fc38 local 450 k gnupg2 i686 2.3.8-1.fc38 copr_base 2.6 M gnutls i686 3.7.8-9.fc38 copr_base 1.1 M groff-base i686 1.22.4-10.fc38 copr_base 1.0 M guile22 i686 2.2.7-6.fc38 copr_base 6.5 M kernel-headers i686 6.1.0-1.fc38 local 1.4 M libasan i686 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 491 k libassuan i686 2.5.5-5.fc38 copr_base 69 k libatomic i686 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 17 k libb2 i686 0.98.1-7.fc38 copr_base 29 k libblkid-devel i686 2.38.1-3.fc38 copr_base 17 k libffi-devel i686 3.4.4-1.fc38 copr_base 29 k libgcrypt i686 1.10.1-6.fc38 copr_base 479 k libgpg-error i686 1.46-1.fc38 copr_base 226 k libksba i686 1.6.3-1.fc38 copr_base 161 k libmount-devel i686 2.38.1-3.fc38 copr_base 18 k libmpc i686 1.2.1-5.fc38 copr_base 66 k libselinux-devel i686 3.5-0.rc1.1.fc38 local 114 k libsepol-devel i686 3.5-0.rc1.1.fc38 local 40 k libstdc++-devel i686 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 2.4 M libtool-ltdl i686 2.4.7-3.0.1.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 39 k libubsan i686 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 219 k libxcrypt-devel i686 4.4.33-5.fc38 copr_base 31 k mpdecimal i686 2.5.1-4.fc38 copr_base 107 k ncurses i686 6.3-5.20221126.fc38 copr_base 409 k npth i686 1.6-10.fc38 copr_base 25 k pcre2-devel i686 10.40-1.fc38.1 copr_base 474 k pcre2-utf16 i686 10.40-1.fc38.1 copr_base 217 k pcre2-utf32 i686 10.40-1.fc38.1 copr_base 204 k perl-Algorithm-Diff noarch 1.2010-7.fc37 local 47 k perl-Archive-Tar noarch 2.40-490.fc37 local 71 k perl-Archive-Zip noarch 1.68-9.fc37 local 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 i686 1.83-492.fc38 copr_base 189 k perl-Benchmark noarch 1.23-492.fc38 copr_base 30 k perl-CPAN noarch 2.34-4.fc37 local 557 k perl-CPAN-Meta noarch 2.150010-489.fc37 local 176 k perl-CPAN-Meta-Requirements noarch 2.140-490.fc37 local 31 k perl-CPAN-Meta-YAML noarch 0.018-490.fc37 local 26 k perl-Carp noarch 1.52-489.fc37 local 29 k perl-Class-Struct noarch 0.66-492.fc38 copr_base 26 k perl-Compress-Bzip2 i686 2.28-11.fc38 copr_base 69 k perl-Compress-Raw-Bzip2 i686 2.201-2.fc38 copr_base 35 k perl-Compress-Raw-Lzma i686 2.201-5.fc38 copr_base 51 k perl-Compress-Raw-Zlib i686 2.202-4.fc38 copr_base 65 k perl-Config-Extensions noarch 0.03-492.fc38 copr_base 16 k perl-Config-Perl-V noarch 0.34-1.fc38 local 21 k perl-DBM_Filter noarch 0.06-492.fc38 copr_base 35 k perl-DB_File i686 1.858-4.fc38 copr_base 82 k perl-Data-Dumper i686 2.184-490.fc38 copr_base 59 k perl-Data-OptList noarch 0.112-5.fc37 local 27 k perl-Data-Section noarch 0.200007-17.fc37 local 25 k perl-Devel-PPPort i686 3.68-490.fc38 copr_base 227 k perl-Devel-Peek i686 1.32-492.fc38 copr_base 36 k perl-Devel-SelfStubber noarch 1.06-492.fc38 copr_base 18 k perl-Devel-Size i686 0.83-13.fc38 copr_base 31 k perl-Digest noarch 1.20-489.fc37 local 26 k perl-Digest-MD5 i686 2.58-489.fc38 copr_base 37 k perl-Digest-SHA i686 1:6.03-1.fc38 copr_base 62 k perl-Digest-SHA1 i686 2.13-37.fc38 copr_base 54 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 i686 1.52-492.fc38 copr_base 30 k perl-Encode i686 4:3.19-492.fc38 copr_base 1.2 M perl-Encode-devel i686 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.fc37 local 20 k perl-Errno i686 1.36-492.fc38 copr_base 18 k perl-Exporter noarch 5.77-489.fc37 local 31 k perl-ExtUtils-CBuilder noarch 1:0.280236-490.fc38 copr_base 46 k perl-ExtUtils-Command noarch 2:7.64-490.fc37 local 14 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.fc37 local 44 k perl-ExtUtils-MM-Utils noarch 2:7.64-490.fc37 local 12 k perl-ExtUtils-MakeMaker noarch 2:7.64-490.fc37 local 290 k perl-ExtUtils-Manifest noarch 1:1.73-489.fc37 local 34 k perl-ExtUtils-Miniperl noarch 1.11-492.fc38 copr_base 18 k perl-ExtUtils-ParseXS noarch 1:3.45-489.fc37 local 182 k perl-Fcntl i686 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 24 k perl-File-DosGlob i686 1.12-492.fc38 copr_base 23 k perl-File-Fetch noarch 1.04-489.fc37 local 31 k perl-File-Find noarch 1.40-492.fc38 copr_base 29 k perl-File-HomeDir noarch 1.006-7.fc37 local 57 k perl-File-Path noarch 2.18-489.fc37 local 35 k perl-File-Temp noarch 1:0.231.100-489.fc37 local 59 k perl-File-Which noarch 1.27-6.fc37 local 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 i686 2:1.64-1.fc38 copr_base 80 k perl-Filter-Simple noarch 0.96-489.fc37 local 27 k perl-FindBin noarch 1.53-492.fc38 copr_base 18 k perl-GDBM_File i686 1:1.23-492.fc38 copr_base 48 k perl-Getopt-Long noarch 1:2.54-1.fc38 local 60 k perl-Getopt-Std noarch 1.13-492.fc38 copr_base 19 k perl-HTTP-Tiny noarch 0.082-1.fc37 local 55 k perl-Hash-Util i686 0.28-492.fc38 copr_base 39 k perl-Hash-Util-FieldHash i686 1.26-492.fc38 copr_base 43 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 i686 0.21-492.fc38 copr_base 26 k perl-IO i686 1.50-492.fc38 copr_base 92 k perl-IO-Compress noarch 2.201-3.fc37 local 262 k perl-IO-Compress-Lzma noarch 2.201-2.fc37 local 74 k perl-IO-Socket-IP noarch 0.41-490.fc37 local 42 k perl-IO-Zlib noarch 1:1.11-489.fc37 local 19 k perl-IPC-Cmd noarch 2:1.04-490.fc37 local 40 k perl-IPC-Open3 noarch 1.22-492.fc38 copr_base 26 k perl-IPC-SysV i686 2.09-490.fc38 copr_base 42 k perl-IPC-System-Simple noarch 1.30-9.fc37 local 39 k perl-Importer noarch 0.026-8.fc38 local 39 k perl-JSON-PP noarch 1:4.15-1.fc38 local 67 k perl-Locale-Maketext noarch 1.32-1.fc38 local 95 k perl-Locale-Maketext-Simple noarch 1:0.21-492.fc38 copr_base 21 k perl-MIME-Base64 i686 3.16-489.fc38 copr_base 31 k perl-MRO-Compat noarch 0.15-4.fc37 local 26 k perl-Math-BigInt noarch 1:1.9998.37-2.fc37 local 201 k perl-Math-BigInt-FastCalc i686 0.501.300-3.fc38 copr_base 29 k perl-Math-BigRat noarch 0.2624-2.fc37 local 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 2:0.42.32-1.fc38 local 236 k perl-Module-CoreList noarch 1:5.20221220-1.fc38 local 84 k perl-Module-CoreList-tools noarch 1:5.20221220-1.fc38 local 18 k perl-Module-Load noarch 1:0.36-489.fc37 local 17 k perl-Module-Load-Conditional noarch 0.74-489.fc37 local 22 k perl-Module-Loaded noarch 1:0.08-492.fc38 copr_base 17 k perl-Module-Metadata noarch 1.000037-489.fc37 local 35 k perl-Module-Signature noarch 0.88-4.fc37 local 83 k perl-NDBM_File i686 1.15-492.fc38 copr_base 27 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 local 50 k perl-ODBM_File i686 1.17-492.fc38 copr_base 27 k perl-Object-HashBase noarch 0.009-11.fc38 local 25 k perl-Opcode i686 1.57-492.fc38 copr_base 41 k perl-POSIX i686 2.03-492.fc38 copr_base 105 k perl-Package-Generator noarch 1.106-26.fc37 local 23 k perl-Params-Check noarch 1:0.38-489.fc37 local 22 k perl-Params-Util i686 1.102-9.fc38 copr_base 33 k perl-PathTools i686 3.84-489.fc38 copr_base 83 k perl-Perl-OSType noarch 1.010-490.fc38 copr_base 23 k perl-PerlIO-via-QuotedPrint noarch 0.10-3.fc37 local 22 k perl-Pod-Checker noarch 4:1.75-3.fc37 local 32 k perl-Pod-Escapes noarch 1:1.07-489.fc37 local 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.fc37 local 84 k perl-Pod-Simple noarch 1:3.43-490.fc37 local 215 k perl-Pod-Usage noarch 4:2.03-3.fc37 local 40 k perl-Safe noarch 2.43-492.fc38 copr_base 29 k perl-Scalar-List-Utils i686 5:1.63-489.fc38 copr_base 75 k perl-Search-Dict noarch 1.07-492.fc38 copr_base 17 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 i686 4:2.036-1.fc38 copr_base 56 k perl-Software-License noarch 0.104002-2.fc37 local 133 k perl-Storable i686 1:3.26-489.fc38 copr_base 99 k perl-Sub-Exporter noarch 0.988-5.fc37 local 72 k perl-Sub-Install noarch 0.928-33.fc37 local 22 k perl-Symbol noarch 1.09-492.fc38 copr_base 18 k perl-Sys-Hostname i686 1.24-492.fc38 copr_base 21 k perl-Sys-Syslog i686 0.36-490.fc38 copr_base 47 k perl-Term-ANSIColor noarch 5.01-490.fc37 local 48 k perl-Term-Cap noarch 1.17-489.fc37 local 22 k perl-Term-Complete noarch 1.403-492.fc38 copr_base 17 k perl-Term-ReadLine noarch 1.17-492.fc38 copr_base 23 k perl-Term-Table noarch 0.016-5.fc38 local 34 k perl-Test noarch 1.31-492.fc38 copr_base 32 k perl-Test-Harness noarch 1:3.44-490.fc37 local 268 k perl-Test-Simple noarch 3:1.302191-2.fc37 local 525 k perl-Text-Abbrev noarch 1.02-492.fc38 copr_base 16 k perl-Text-Balanced noarch 2.06-2.fc37 local 49 k perl-Text-Diff noarch 1.45-16.fc37 local 41 k perl-Text-Glob noarch 0.11-19.fc38 local 13 k perl-Text-ParseWords noarch 3.31-489.fc37 local 16 k perl-Text-Tabs+Wrap noarch 2021.0814-489.fc37 local 22 k perl-Text-Template noarch 1.61-1.fc38 local 60 k perl-Thread noarch 3.05-492.fc38 copr_base 22 k perl-Thread-Queue noarch 3.14-489.fc37 local 21 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.fc37 local 23 k perl-Time noarch 1.03-492.fc38 copr_base 22 k perl-Time-HiRes i686 4:1.9770-489.fc38 copr_base 59 k perl-Time-Local noarch 2:1.300-489.fc37 local 33 k perl-Time-Piece i686 1.3401-492.fc38 copr_base 45 k perl-URI noarch 5.17-1.fc38 local 111 k perl-Unicode-Collate i686 1.31-489.fc38 copr_base 666 k perl-Unicode-Normalize i686 1.31-489.fc38 copr_base 85 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.fc37 local 94 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.fc37 local 50 k perl-blib noarch 1.07-492.fc38 copr_base 16 k perl-constant noarch 1.33-490.fc37 local 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 i686 4:5.36.0-492.fc38 copr_base 700 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 i686 4:3.00-492.fc38 copr_base 64 k perl-encoding-warnings noarch 0.13-492.fc38 copr_base 20 k perl-experimental noarch 0.030-1.fc38 local 22 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 18 k perl-inc-latest noarch 2:0.500-23.fc37 local 24 k perl-interpreter i686 4:5.36.0-492.fc38 copr_base 76 k perl-less noarch 0.03-492.fc38 copr_base 17 k perl-lib i686 0.65-492.fc38 copr_base 18 k perl-libnet noarch 3.14-490.fc37 local 126 k perl-libnetcfg noarch 4:5.36.0-492.fc38 copr_base 20 k perl-libs i686 4:5.36.0-492.fc38 copr_base 2.2 M perl-local-lib noarch 2.000029-3.fc37 local 67 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 i686 1.26-492.fc38 copr_base 33 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 1:0.239-1.fc38 local 14 k perl-perlfaq noarch 5.20210520-489.fc37 local 374 k perl-ph i686 5.36.0-492.fc38 copr_base 45 k perl-podlators noarch 1:5.00-1.fc38 local 122 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 i686 1:2.27-489.fc37 local 59 k perl-threads-shared i686 1.64-489.fc37 local 45 k perl-utils noarch 5.36.0-492.fc38 copr_base 59 k perl-vars noarch 1.05-492.fc38 copr_base 17 k perl-version i686 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 22.3.1-1.fc38 local 1.4 M python-setuptools-wheel noarch 65.5.1-1.fc38 local 715 k python3 i686 3.11.1-1.fc38 copr_base 28 k python3-libs i686 3.11.1-1.fc38 copr_base 9.3 M python3-pyparsing noarch 3.0.9-2.fc37 local 255 k sysprof-capture-devel i686 3.46.0-1.fc38 copr_base 64 k systemtap-sdt-devel i686 4.8~pre16650659g6a096a7d-1.fc38 copr_base 73 k zlib-devel i686 1.2.13-1.fc38 local 45 k Transaction Summary ============================================================================================================================= Install 267 Packages Total download size: 116 M Installed size: 375 M Downloading Packages: (1/267): expat-2.5.0-1.fc38.i686.rpm 413 kB/s | 115 kB 00:00 (2/267): gc-8.2.2-1.fc38.i686.rpm 399 kB/s | 113 kB 00:00 (3/267): glib2-devel-2.74.1-2.fc38.i686.rpm 5.8 MB/s | 519 kB 00:00 (4/267): glib2-2.74.1-2.fc38.i686.rpm 4.7 MB/s | 2.8 MB 00:00 (5/267): gnutls-3.7.8-9.fc38.i686.rpm 4.5 MB/s | 1.1 MB 00:00 (6/267): gnupg2-2.3.8-1.fc38.i686.rpm 7.9 MB/s | 2.6 MB 00:00 (7/267): groff-base-1.22.4-10.fc38.i686.rpm 17 MB/s | 1.0 MB 00:00 (8/267): libassuan-2.5.5-5.fc38.i686.rpm 1.2 MB/s | 69 kB 00:00 (9/267): libb2-0.98.1-7.fc38.i686.rpm 631 kB/s | 29 kB 00:00 (10/267): libblkid-devel-2.38.1-3.fc38.i686.rpm 341 kB/s | 17 kB 00:00 (11/267): libffi-devel-3.4.4-1.fc38.i686.rpm 593 kB/s | 29 kB 00:00 (12/267): libgcrypt-1.10.1-6.fc38.i686.rpm 6.7 MB/s | 479 kB 00:00 (13/267): libgpg-error-1.46-1.fc38.i686.rpm 3.6 MB/s | 226 kB 00:00 (14/267): libksba-1.6.3-1.fc38.i686.rpm 3.5 MB/s | 161 kB 00:00 (15/267): libmount-devel-2.38.1-3.fc38.i686.rpm 339 kB/s | 18 kB 00:00 (16/267): libmpc-1.2.1-5.fc38.i686.rpm 1.3 MB/s | 66 kB 00:00 (17/267): libxcrypt-devel-4.4.33-5.fc38.i686.rp 682 kB/s | 31 kB 00:00 (18/267): make-4.3-11.fc38.i686.rpm 6.2 MB/s | 542 kB 00:00 (19/267): mpdecimal-2.5.1-4.fc38.i686.rpm 1.7 MB/s | 107 kB 00:00 (20/267): guile22-2.2.7-6.fc38.i686.rpm 16 MB/s | 6.5 MB 00:00 (21/267): ncurses-6.3-5.20221126.fc38.i686.rpm 8.1 MB/s | 409 kB 00:00 (22/267): npth-1.6-10.fc38.i686.rpm 527 kB/s | 25 kB 00:00 (23/267): pcre2-devel-10.40-1.fc38.1.i686.rpm 14 MB/s | 474 kB 00:00 (24/267): pcre2-utf16-10.40-1.fc38.1.i686.rpm 7.5 MB/s | 217 kB 00:00 (25/267): pcre2-utf32-10.40-1.fc38.1.i686.rpm 5.9 MB/s | 204 kB 00:00 (26/267): perl-5.36.0-492.fc38.i686.rpm 985 kB/s | 16 kB 00:00 (27/267): perl-Attribute-Handlers-1.02-492.fc38 3.0 MB/s | 31 kB 00:00 (28/267): perl-AutoLoader-5.74-492.fc38.noarch. 2.7 MB/s | 25 kB 00:00 (29/267): perl-AutoSplit-5.74-492.fc38.noarch.r 2.5 MB/s | 25 kB 00:00 (30/267): perl-B-1.83-492.fc38.i686.rpm 12 MB/s | 189 kB 00:00 (31/267): perl-Benchmark-1.23-492.fc38.noarch.r 2.6 MB/s | 30 kB 00:00 (32/267): perl-Class-Struct-0.66-492.fc38.noarc 2.4 MB/s | 26 kB 00:00 (33/267): perl-Compress-Raw-Bzip2-2.201-2.fc38. 3.5 MB/s | 35 kB 00:00 (34/267): perl-Compress-Bzip2-2.28-11.fc38.i686 4.0 MB/s | 69 kB 00:00 (35/267): perl-Compress-Raw-Zlib-2.202-4.fc38.i 5.9 MB/s | 65 kB 00:00 (36/267): perl-Compress-Raw-Lzma-2.201-5.fc38.i 2.3 MB/s | 51 kB 00:00 (37/267): perl-Config-Extensions-0.03-492.fc38. 1.6 MB/s | 16 kB 00:00 (38/267): 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perl-Exporter-5.77-489.fc37.noarch 190/267 Verifying : perl-ExtUtils-Command-2:7.64-490.fc37.noarch 191/267 Verifying : perl-ExtUtils-Install-2.20-489.fc37.noarch 192/267 Verifying : perl-ExtUtils-MM-Utils-2:7.64-490.fc37.noarch 193/267 Verifying : perl-ExtUtils-MakeMaker-2:7.64-490.fc37.noarch 194/267 Verifying : perl-ExtUtils-Manifest-1:1.73-489.fc37.noarch 195/267 Verifying : perl-ExtUtils-ParseXS-1:3.45-489.fc37.noarch 196/267 Verifying : perl-File-Fetch-1.04-489.fc37.noarch 197/267 Verifying : perl-File-HomeDir-1.006-7.fc37.noarch 198/267 Verifying : perl-File-Path-2.18-489.fc37.noarch 199/267 Verifying : perl-File-Temp-1:0.231.100-489.fc37.noarch 200/267 Verifying : perl-File-Which-1.27-6.fc37.noarch 201/267 Verifying : perl-Filter-Simple-0.96-489.fc37.noarch 202/267 Verifying : perl-Getopt-Long-1:2.54-1.fc38.noarch 203/267 Verifying : perl-HTTP-Tiny-0.082-1.fc37.noarch 204/267 Verifying : perl-IO-Compress-2.201-3.fc37.noarch 205/267 Verifying : perl-IO-Compress-Lzma-2.201-2.fc37.noarch 206/267 Verifying : perl-IO-Socket-IP-0.41-490.fc37.noarch 207/267 Verifying : perl-IO-Zlib-1:1.11-489.fc37.noarch 208/267 Verifying : perl-IPC-Cmd-2:1.04-490.fc37.noarch 209/267 Verifying : perl-IPC-System-Simple-1.30-9.fc37.noarch 210/267 Verifying : perl-Importer-0.026-8.fc38.noarch 211/267 Verifying : perl-JSON-PP-1:4.15-1.fc38.noarch 212/267 Verifying : perl-Locale-Maketext-1.32-1.fc38.noarch 213/267 Verifying : perl-MRO-Compat-0.15-4.fc37.noarch 214/267 Verifying : perl-Math-BigInt-1:1.9998.37-2.fc37.noarch 215/267 Verifying : perl-Math-BigRat-0.2624-2.fc37.noarch 216/267 Verifying : perl-Module-Build-2:0.42.32-1.fc38.noarch 217/267 Verifying : perl-Module-CoreList-1:5.20221220-1.fc38.noarch 218/267 Verifying : perl-Module-CoreList-tools-1:5.20221220-1.fc38.n 219/267 Verifying : perl-Module-Load-1:0.36-489.fc37.noarch 220/267 Verifying : perl-Module-Load-Conditional-0.74-489.fc37.noarc 221/267 Verifying : perl-Module-Metadata-1.000037-489.fc37.noarch 222/267 Verifying : perl-Module-Signature-0.88-4.fc37.noarch 223/267 Verifying : perl-Net-Ping-2.75-2.fc38.noarch 224/267 Verifying : perl-Object-HashBase-0.009-11.fc38.noarch 225/267 Verifying : perl-Package-Generator-1.106-26.fc37.noarch 226/267 Verifying : perl-Params-Check-1:0.38-489.fc37.noarch 227/267 Verifying : perl-PerlIO-via-QuotedPrint-0.10-3.fc37.noarch 228/267 Verifying : perl-Pod-Checker-4:1.75-3.fc37.noarch 229/267 Verifying : perl-Pod-Escapes-1:1.07-489.fc37.noarch 230/267 Verifying : perl-Pod-Perldoc-3.28.01-490.fc37.noarch 231/267 Verifying : perl-Pod-Simple-1:3.43-490.fc37.noarch 232/267 Verifying : perl-Pod-Usage-4:2.03-3.fc37.noarch 233/267 Verifying : perl-Software-License-0.104002-2.fc37.noarch 234/267 Verifying : perl-Sub-Exporter-0.988-5.fc37.noarch 235/267 Verifying : perl-Sub-Install-0.928-33.fc37.noarch 236/267 Verifying : perl-Term-ANSIColor-5.01-490.fc37.noarch 237/267 Verifying : perl-Term-Cap-1.17-489.fc37.noarch 238/267 Verifying : perl-Term-Table-0.016-5.fc38.noarch 239/267 Verifying : perl-Test-Harness-1:3.44-490.fc37.noarch 240/267 Verifying : perl-Test-Simple-3:1.302191-2.fc37.noarch 241/267 Verifying : perl-Text-Balanced-2.06-2.fc37.noarch 242/267 Verifying : perl-Text-Diff-1.45-16.fc37.noarch 243/267 Verifying : perl-Text-Glob-0.11-19.fc38.noarch 244/267 Verifying : perl-Text-ParseWords-3.31-489.fc37.noarch 245/267 Verifying : perl-Text-Tabs+Wrap-2021.0814-489.fc37.noarch 246/267 Verifying : perl-Text-Template-1.61-1.fc38.noarch 247/267 Verifying : perl-Thread-Queue-3.14-489.fc37.noarch 248/267 Verifying : perl-Tie-RefHash-1.40-489.fc37.noarch 249/267 Verifying : perl-Time-Local-2:1.300-489.fc37.noarch 250/267 Verifying : perl-URI-5.17-1.fc38.noarch 251/267 Verifying : perl-autodie-2.34-490.fc37.noarch 252/267 Verifying : perl-bignum-0.66-5.fc37.noarch 253/267 Verifying : perl-constant-1.33-490.fc37.noarch 254/267 Verifying : perl-experimental-0.030-1.fc38.noarch 255/267 Verifying : perl-inc-latest-2:0.500-23.fc37.noarch 256/267 Verifying : perl-libnet-3.14-490.fc37.noarch 257/267 Verifying : perl-local-lib-2.000029-3.fc37.noarch 258/267 Verifying : perl-parent-1:0.239-1.fc38.noarch 259/267 Verifying : perl-perlfaq-5.20210520-489.fc37.noarch 260/267 Verifying : perl-podlators-1:5.00-1.fc38.noarch 261/267 Verifying : perl-threads-1:2.27-489.fc37.i686 262/267 Verifying : perl-threads-shared-1.64-489.fc37.i686 263/267 Verifying : python-pip-wheel-22.3.1-1.fc38.noarch 264/267 Verifying : python-setuptools-wheel-65.5.1-1.fc38.noarch 265/267 Verifying : python3-pyparsing-3.0.9-2.fc37.noarch 266/267 Verifying : zlib-devel-1.2.13-1.fc38.i686 267/267 Installed: annobin-docs-10.99-1.0.1.fc38.noarch annobin-plugin-gcc-10.99-1.0.1.fc38.i686 cpp-13.0.0-0.4.fc38.i686 expat-2.5.0-1.fc38.i686 gc-8.2.2-1.fc38.i686 gcc-13.0.0-0.4.fc38.i686 gcc-c++-13.0.0-0.4.fc38.i686 gcc-plugin-annobin-13.0.0-0.4.fc38.i686 glib2-2.74.1-2.fc38.i686 glib2-devel-2.74.1-2.fc38.i686 glibc-devel-2.36.9000-19.fc38.i686 glibc-headers-x86-2.36.9000-19.fc38.noarch gnupg2-2.3.8-1.fc38.i686 gnutls-3.7.8-9.fc38.i686 groff-base-1.22.4-10.fc38.i686 guile22-2.2.7-6.fc38.i686 kernel-headers-6.1.0-1.fc38.i686 libasan-13.0.0-0.4.fc38.i686 libassuan-2.5.5-5.fc38.i686 libatomic-13.0.0-0.4.fc38.i686 libb2-0.98.1-7.fc38.i686 libblkid-devel-2.38.1-3.fc38.i686 libffi-devel-3.4.4-1.fc38.i686 libgcrypt-1.10.1-6.fc38.i686 libgpg-error-1.46-1.fc38.i686 libksba-1.6.3-1.fc38.i686 libmount-devel-2.38.1-3.fc38.i686 libmpc-1.2.1-5.fc38.i686 libselinux-devel-3.5-0.rc1.1.fc38.i686 libsepol-devel-3.5-0.rc1.1.fc38.i686 libstdc++-devel-13.0.0-0.4.fc38.i686 libtool-ltdl-2.4.7-3.0.1.fc38.i686 libubsan-13.0.0-0.4.fc38.i686 libxcrypt-devel-4.4.33-5.fc38.i686 make-1:4.3-11.fc38.i686 mpdecimal-2.5.1-4.fc38.i686 ncurses-6.3-5.20221126.fc38.i686 npth-1.6-10.fc38.i686 pcre2-devel-10.40-1.fc38.1.i686 pcre2-utf16-10.40-1.fc38.1.i686 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perl-Data-Section-0.200007-17.fc37.noarch perl-Devel-PPPort-3.68-490.fc38.i686 perl-Devel-Peek-1.32-492.fc38.i686 perl-Devel-SelfStubber-1.06-492.fc38.noarch perl-Devel-Size-0.83-13.fc38.i686 perl-Digest-1.20-489.fc37.noarch perl-Digest-MD5-2.58-489.fc38.i686 perl-Digest-SHA-1:6.03-1.fc38.i686 perl-Digest-SHA1-2.13-37.fc38.i686 perl-DirHandle-1.05-492.fc38.noarch perl-Dumpvalue-2.27-492.fc38.noarch perl-DynaLoader-1.52-492.fc38.i686 perl-Encode-4:3.19-492.fc38.i686 perl-Encode-devel-4:3.19-492.fc38.i686 perl-English-1.11-492.fc38.noarch perl-Env-1.05-489.fc37.noarch perl-Errno-1.36-492.fc38.i686 perl-Exporter-5.77-489.fc37.noarch perl-ExtUtils-CBuilder-1:0.280236-490.fc38.noarch perl-ExtUtils-Command-2:7.64-490.fc37.noarch perl-ExtUtils-Constant-0.25-492.fc38.noarch perl-ExtUtils-Embed-1.35-492.fc38.noarch perl-ExtUtils-Install-2.20-489.fc37.noarch perl-ExtUtils-MM-Utils-2:7.64-490.fc37.noarch perl-ExtUtils-MakeMaker-2:7.64-490.fc37.noarch perl-ExtUtils-Manifest-1:1.73-489.fc37.noarch perl-ExtUtils-Miniperl-1.11-492.fc38.noarch perl-ExtUtils-ParseXS-1:3.45-489.fc37.noarch perl-Fcntl-1.15-492.fc38.i686 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.i686 perl-File-Fetch-1.04-489.fc37.noarch perl-File-Find-1.40-492.fc38.noarch perl-File-HomeDir-1.006-7.fc37.noarch perl-File-Path-2.18-489.fc37.noarch perl-File-Temp-1:0.231.100-489.fc37.noarch perl-File-Which-1.27-6.fc37.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.i686 perl-Filter-Simple-0.96-489.fc37.noarch perl-FindBin-1.53-492.fc38.noarch perl-GDBM_File-1:1.23-492.fc38.i686 perl-Getopt-Long-1:2.54-1.fc38.noarch perl-Getopt-Std-1.13-492.fc38.noarch perl-HTTP-Tiny-0.082-1.fc37.noarch perl-Hash-Util-0.28-492.fc38.i686 perl-Hash-Util-FieldHash-1.26-492.fc38.i686 perl-I18N-Collate-1.02-492.fc38.noarch perl-I18N-LangTags-0.45-492.fc38.noarch perl-I18N-Langinfo-0.21-492.fc38.i686 perl-IO-1.50-492.fc38.i686 perl-IO-Compress-2.201-3.fc37.noarch perl-IO-Compress-Lzma-2.201-2.fc37.noarch perl-IO-Socket-IP-0.41-490.fc37.noarch perl-IO-Zlib-1:1.11-489.fc37.noarch perl-IPC-Cmd-2:1.04-490.fc37.noarch perl-IPC-Open3-1.22-492.fc38.noarch perl-IPC-SysV-2.09-490.fc38.i686 perl-IPC-System-Simple-1.30-9.fc37.noarch perl-Importer-0.026-8.fc38.noarch perl-JSON-PP-1:4.15-1.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.i686 perl-MRO-Compat-0.15-4.fc37.noarch perl-Math-BigInt-1:1.9998.37-2.fc37.noarch perl-Math-BigInt-FastCalc-0.501.300-3.fc38.i686 perl-Math-BigRat-0.2624-2.fc37.noarch perl-Math-Complex-1.59-492.fc38.noarch perl-Memoize-1.03-492.fc38.noarch perl-Module-Build-2:0.42.32-1.fc38.noarch perl-Module-CoreList-1:5.20221220-1.fc38.noarch perl-Module-CoreList-tools-1:5.20221220-1.fc38.noarch perl-Module-Load-1:0.36-489.fc37.noarch perl-Module-Load-Conditional-0.74-489.fc37.noarch perl-Module-Loaded-1:0.08-492.fc38.noarch perl-Module-Metadata-1.000037-489.fc37.noarch perl-Module-Signature-0.88-4.fc37.noarch perl-NDBM_File-1.15-492.fc38.i686 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.i686 perl-Object-HashBase-0.009-11.fc38.noarch perl-Opcode-1.57-492.fc38.i686 perl-POSIX-2.03-492.fc38.i686 perl-Package-Generator-1.106-26.fc37.noarch perl-Params-Check-1:0.38-489.fc37.noarch perl-Params-Util-1.102-9.fc38.i686 perl-PathTools-3.84-489.fc38.i686 perl-Perl-OSType-1.010-490.fc38.noarch perl-PerlIO-via-QuotedPrint-0.10-3.fc37.noarch perl-Pod-Checker-4:1.75-3.fc37.noarch perl-Pod-Escapes-1:1.07-489.fc37.noarch perl-Pod-Functions-1.14-492.fc38.noarch perl-Pod-Html-1.33-492.fc38.noarch perl-Pod-Perldoc-3.28.01-490.fc37.noarch perl-Pod-Simple-1:3.43-490.fc37.noarch perl-Pod-Usage-4:2.03-3.fc37.noarch perl-Safe-2.43-492.fc38.noarch perl-Scalar-List-Utils-5:1.63-489.fc38.i686 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.i686 perl-Software-License-0.104002-2.fc37.noarch perl-Storable-1:3.26-489.fc38.i686 perl-Sub-Exporter-0.988-5.fc37.noarch perl-Sub-Install-0.928-33.fc37.noarch perl-Symbol-1.09-492.fc38.noarch perl-Sys-Hostname-1.24-492.fc38.i686 perl-Sys-Syslog-0.36-490.fc38.i686 perl-Term-ANSIColor-5.01-490.fc37.noarch perl-Term-Cap-1.17-489.fc37.noarch perl-Term-Complete-1.403-492.fc38.noarch perl-Term-ReadLine-1.17-492.fc38.noarch perl-Term-Table-0.016-5.fc38.noarch perl-Test-1.31-492.fc38.noarch perl-Test-Harness-1:3.44-490.fc37.noarch perl-Test-Simple-3:1.302191-2.fc37.noarch perl-Text-Abbrev-1.02-492.fc38.noarch perl-Text-Balanced-2.06-2.fc37.noarch perl-Text-Diff-1.45-16.fc37.noarch perl-Text-Glob-0.11-19.fc38.noarch perl-Text-ParseWords-3.31-489.fc37.noarch perl-Text-Tabs+Wrap-2021.0814-489.fc37.noarch perl-Text-Template-1.61-1.fc38.noarch perl-Thread-3.05-492.fc38.noarch perl-Thread-Queue-3.14-489.fc37.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.fc37.noarch perl-Time-1.03-492.fc38.noarch perl-Time-HiRes-4:1.9770-489.fc38.i686 perl-Time-Local-2:1.300-489.fc37.noarch perl-Time-Piece-1.3401-492.fc38.i686 perl-URI-5.17-1.fc38.noarch perl-Unicode-Collate-1.31-489.fc38.i686 perl-Unicode-Normalize-1.31-489.fc38.i686 perl-Unicode-UCD-0.78-492.fc38.noarch perl-User-pwent-1.03-492.fc38.noarch perl-autodie-2.34-490.fc37.noarch perl-autouse-1.11-492.fc38.noarch perl-base-2.27-492.fc38.noarch perl-bignum-0.66-5.fc37.noarch perl-blib-1.07-492.fc38.noarch perl-constant-1.33-490.fc37.noarch perl-debugger-1.60-492.fc38.noarch perl-deprecate-0.04-492.fc38.noarch perl-devel-4:5.36.0-492.fc38.i686 perl-diagnostics-1.39-492.fc38.noarch perl-doc-5.36.0-492.fc38.noarch perl-encoding-4:3.00-492.fc38.i686 perl-encoding-warnings-0.13-492.fc38.noarch perl-experimental-0.030-1.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.fc37.noarch perl-interpreter-4:5.36.0-492.fc38.i686 perl-less-0.03-492.fc38.noarch perl-lib-0.65-492.fc38.i686 perl-libnet-3.14-490.fc37.noarch perl-libnetcfg-4:5.36.0-492.fc38.noarch perl-libs-4:5.36.0-492.fc38.i686 perl-local-lib-2.000029-3.fc37.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.i686 perl-open-1.13-492.fc38.noarch perl-overload-1.35-492.fc38.noarch perl-overloading-0.02-492.fc38.noarch perl-parent-1:0.239-1.fc38.noarch perl-perlfaq-5.20210520-489.fc37.noarch perl-ph-5.36.0-492.fc38.i686 perl-podlators-1:5.00-1.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.fc37.i686 perl-threads-shared-1.64-489.fc37.i686 perl-utils-5.36.0-492.fc38.noarch perl-vars-1.05-492.fc38.noarch perl-version-8:0.99.29-490.fc38.i686 perl-vmsish-1.04-492.fc38.noarch python-pip-wheel-22.3.1-1.fc38.noarch python-setuptools-wheel-65.5.1-1.fc38.noarch python3-3.11.1-1.fc38.i686 python3-libs-3.11.1-1.fc38.i686 python3-pyparsing-3.0.9-2.fc37.noarch strace-6.1-1.fc38.i686 sysprof-capture-devel-3.46.0-1.fc38.i686 systemtap-sdt-devel-4.8~pre16650659g6a096a7d-1.fc38.i686 zlib-devel-1.2.13-1.fc38.i686 Complete! Finish: build setup for wise2-2.4.1-16.fc38.src.rpm Start: rpmbuild wise2-2.4.1-16.fc38.src.rpm Building target platforms: i686 Building for target i686 setting SOURCE_DATE_EPOCH=1671753600 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.sGSSw9 + 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 . Patch #0 (wise2-build.patch): + echo '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 Patch #6 (wise2-c99.patch): + echo 'Patch #6 (wise2-c99.patch):' + /usr/bin/patch --no-backup-if-mismatch -f -p1 --fuzz=0 patching file src/HMMer2/prior.c patching file src/external/mott/mott_api.c + 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.aW6gMT + 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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/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/lib: + 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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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:771:23: warning: 'pushpoi' may be used uninitialized [-Wmaybe-uninitialized] 771 | 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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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:513:20: warning: 'k' may be used uninitialized [-Wmaybe-uninitialized] 513 | sc = imx[i+1][k] - hmm->isc[(int) dsq[i+1]][k]; | ^ 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: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:1082:19: warning: 't2' may be used uninitialized [-Wmaybe-uninitialized] 1082 | tassign[s2] = t2; | ~~~~~~~~~~~~^~~~ core_algorithms.c:1433:16: note: 't2' was declared here 1433 | enum p7stype t2; | ^~ 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 */ | ^~~~~~ 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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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:223:26: warning: 'lowbound' may be used uninitialized [-Wmaybe-uninitialized] 223 | for (num = 0; lowbound > h->lowscore; lowbound--) | ~~~~~~~~~^~~~~~~~~~~~~ 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:1249:13: warning: 'total' may be used uninitialized [-Wmaybe-uninitialized] 1249 | total += mult; | ~~~~~~^~~~~~~ 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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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) | ^~~~~~~~~~~~~~~ In file included from structs.h:22, from modelmakers.c:29: modelmakers.c: In function 'P7Maxmodelmaker': 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 */ | ^ 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] */ | ^~~~~ 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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c prior.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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c dayhoff.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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -c file.c file.c: In function 'EnvFileOpen': file.c:159:26: warning: '%s' directive writing up to 1022 bytes into a region of size between 1 and 1023 [-Wformat-overflow=] 159 | sprintf(full, "%s%c%s", s, DIRSLASH, fname); | ^~ In file included from /usr/include/stdio.h:906, from file.c:12: In function 'sprintf', inlined from 'EnvFileOpen' at file.c:159:7: /usr/include/bits/stdio2.h:30:10: note: '__sprintf_chk' output between 2 and 2046 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ 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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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: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: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: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: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: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: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: 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: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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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:215:25: warning: 'num' may be used uninitialized [-Wmaybe-uninitialized] 215 | aseqs = (char **) MallocOrDie (num * sizeof(char *)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ selex.c:68:12: note: 'num' was declared here 68 | int num; /* number of seqs read */ | ^~~ selex.c:354:21: warning: 'blocks' may be used uninitialized [-Wmaybe-uninitialized] 354 | if (! copy_alignment_line(aseqs[seqidx], currlen, strlen(nptr)-1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 355 | buffer, blocks[currblock].lcol, blocks[currblock].rcol, (char) '.')) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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:79:3: warning: 'rwt' may be used uninitialized [-Wmaybe-uninitialized] 79 | downweight(tree, ainfo->nseq, lwt, rwt, fwt, ainfo->nseq); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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:299:26: warning: 'lowbound' may be used uninitialized [-Wmaybe-uninitialized] 299 | for (num = 0; lowbound > h->lowscore; lowbound--) | ~~~~~~~~~^~~~~~~~~~~~~ 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:1323:13: warning: 'total' may be used uninitialized [-Wmaybe-uninitialized] 1323 | total += mult; | ~~~~~~^~~~~~~ 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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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; | ^~~~~~~ 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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ subseqhash.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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/sysprof-4 -pthread -D_POSIX_C_SOURCE=200112L -I../base/ intallocator.c intallocator.dy: In function 'Wise2_show_allocator_status_IntAllocator': intallocator.dy:216:15: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'unsigned int' [-Wformat=] 216 | fprintf(ofp,"%d blocks allocated, using %ld bytes\n",ia->current_allocated_block,ia->current_allocated_block * (sizeof(IntAllocatorHeader)+(sizeof(int)*ia->size)) * IntAllocator_BLOCKSIZE); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 'unsigned int' [-Wformat=] 285 | fprintf(ofp,"Head memory %d [%.2f Mbytes]\n",total_head,(total_head*sizeof(ShadowArraySeqHead))/100000); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | 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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 '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, | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | 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 'long int' [-Wformat=] 209 | fprintf(stderr,"START %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 213 | use.ru_stime.tv_sec/1000 | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | 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 '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, | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | 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 'long int' [-Wformat=] 273 | fprintf(stderr,"END OF SEED %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 277 | use.ru_stime.tv_sec/1000 | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | 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 '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, | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | 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 'long int' [-Wformat=] 286 | fprintf(stderr,"POPULATION %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 290 | use.ru_stime.tv_sec/1000 | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | 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 '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, | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | 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 'long int' [-Wformat=] 302 | fprintf(stdout,"LINEARISED %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 306 | use.ru_stime.tv_sec/1000 | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | 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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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:154:18: 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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 'KarlinAltschulStatistics2': mott_api.c:152:9: warning: unused variable 'n' [-Wunused-variable] 152 | int n; | ^ 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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 kmer_glib_index.dy: In function 'Wise2_retrieve_by_kmer_KmerGlibIndex': kmer_glib_index.dy:77:48: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 77 | return (void*) g_hash_table_lookup(kgi->hash,(gconstpointer)kmer); | ^ kmer_glib_index.dy: In function 'Wise2_insert_by_kmer_KmerGlibIndex': kmer_glib_index.dy:84:33: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 84 | g_hash_table_insert(kgi->hash,(gpointer)kmer,poi); | ^ kmer_glib_index.dy: In function 'Wise2_retrieve_active_kmer_KmerGlibIndex': kmer_glib_index.dy:124:40: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 124 | kgi->active_index[kgi->kmer_pos++] = (kmer_t) key; | ^ 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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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_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.dy: 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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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: '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; | ^~~~ 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; | ^~~~ 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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 '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:259:38: warning: 'currMatch' may be used uninitialized [-Wmaybe-uninitialized] 259 | *( ((1-currMatch)/3)/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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:278:34: warning: 'end_alc' may be used uninitialized [-Wmaybe-uninitialized] 278 | sprintf(buffer,"%d",end_alc->alu[0]->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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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: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; | ^~ 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; | ^~~~ 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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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:244:10: warning: 'out' may be used uninitialized [-Wmaybe-uninitialized] 244 | return out; | ^~~ estwrap.dy:138:14: note: 'out' was declared here 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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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, inlined from 'Wise2_GeneParameter21_wrap' at gwrap.dy:76:9: 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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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: genewisedb.c: 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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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/dyna.h:29, from threestatemodel.h:7, from wise2xhmmer2.h:24, from estwisedb.c:4: estwisedb.c: In function 'show_output': ../dynlibsrc/aln.h:222:34: warning: 'anchored' may be used uninitialized [-Wmaybe-uninitialized] 222 | #define add_to_anchored_AlnBlock Wise2_add_to_anchored_AlnBlock estwisedb.c:182:14: note: 'anchored' was declared here 182 | AlnBlock * anchored; | ^~~~~~~~ In file included from ../dynlibsrc/seqalign.h:6, from wise2xhmmer2.h:23: ../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; | ^~~ 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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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:427:9: warning: 'cutoff' may be used uninitialized [-Wmaybe-uninitialized] 427 | if( 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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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; | ^~~ 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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread -D_GNU_SOURCE -I/usr/include/glib-2.0 -I/usr/lib/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.GSzVNa + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/wise2-2.4.1-16.fc38.i386 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/wise2-2.4.1-16.fc38.i386 ++ dirname /builddir/build/BUILDROOT/wise2-2.4.1-16.fc38.i386 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/wise2-2.4.1-16.fc38.i386 + 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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/gfortran/modules' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS ~/build/BUILD/wise2.4.1/src/bin ~/build/BUILD/wise2.4.1 + 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/lib: + 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/wise2-2.4.1-16.fc38.i386/usr/bin + for i in dba dnal estwise estwisedb genewise genewisedb promoterwise scanwise scanwise_server psw pswdb + install -pm 755 dba /builddir/build/BUILDROOT/wise2-2.4.1-16.fc38.i386/usr/bin + for i in dba dnal estwise estwisedb genewise genewisedb promoterwise scanwise scanwise_server psw pswdb + install -pm 755 dnal /builddir/build/BUILDROOT/wise2-2.4.1-16.fc38.i386/usr/bin + for i in dba dnal estwise estwisedb genewise genewisedb promoterwise scanwise scanwise_server psw pswdb + install -pm 755 estwise /builddir/build/BUILDROOT/wise2-2.4.1-16.fc38.i386/usr/bin + for i in dba dnal estwise estwisedb genewise genewisedb promoterwise scanwise scanwise_server psw pswdb + install -pm 755 estwisedb /builddir/build/BUILDROOT/wise2-2.4.1-16.fc38.i386/usr/bin + for i in dba dnal estwise estwisedb genewise genewisedb promoterwise scanwise scanwise_server psw pswdb + install -pm 755 genewise /builddir/build/BUILDROOT/wise2-2.4.1-16.fc38.i386/usr/bin + for i in dba dnal estwise estwisedb genewise genewisedb promoterwise scanwise scanwise_server psw pswdb + install -pm 755 genewisedb /builddir/build/BUILDROOT/wise2-2.4.1-16.fc38.i386/usr/bin + for i in dba dnal estwise estwisedb genewise genewisedb promoterwise scanwise scanwise_server psw pswdb + install -pm 755 promoterwise /builddir/build/BUILDROOT/wise2-2.4.1-16.fc38.i386/usr/bin + for i in dba dnal estwise estwisedb genewise genewisedb promoterwise scanwise scanwise_server psw pswdb + install -pm 755 scanwise /builddir/build/BUILDROOT/wise2-2.4.1-16.fc38.i386/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/wise2-2.4.1-16.fc38.i386/usr/bin + for i in dba dnal estwise estwisedb genewise genewisedb promoterwise scanwise scanwise_server psw pswdb + install -pm 755 psw /builddir/build/BUILDROOT/wise2-2.4.1-16.fc38.i386/usr/bin + for i in dba dnal estwise estwisedb genewise genewisedb promoterwise scanwise scanwise_server psw pswdb + install -pm 755 pswdb /builddir/build/BUILDROOT/wise2-2.4.1-16.fc38.i386/usr/bin + popd ~/build/BUILD/wise2.4.1 + mkdir -p /builddir/build/BUILDROOT/wise2-2.4.1-16.fc38.i386/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/wise2-2.4.1-16.fc38.i386/usr/share/wise2 + popd ~/build/BUILD/wise2.4.1 + mkdir -p /builddir/build/BUILDROOT/wise2-2.4.1-16.fc38.i386/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/wise2-2.4.1-16.fc38.i386/usr/share/wise2/examples ~/build/BUILD/wise2.4.1 + popd + mkdir -p /builddir/build/BUILDROOT/wise2-2.4.1-16.fc38.i386/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 2.4.1-16.fc38 --unique-debug-suffix -2.4.1-16.fc38.i386 --unique-debug-src-base wise2-2.4.1-16.fc38.i386 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/wise2.4.1 extracting debug info from /builddir/build/BUILDROOT/wise2-2.4.1-16.fc38.i386/usr/bin/dba extracting debug info from /builddir/build/BUILDROOT/wise2-2.4.1-16.fc38.i386/usr/bin/dnal extracting debug info from /builddir/build/BUILDROOT/wise2-2.4.1-16.fc38.i386/usr/bin/estwise extracting debug info from /builddir/build/BUILDROOT/wise2-2.4.1-16.fc38.i386/usr/bin/estwisedb extracting debug info from /builddir/build/BUILDROOT/wise2-2.4.1-16.fc38.i386/usr/bin/genewise extracting debug info from /builddir/build/BUILDROOT/wise2-2.4.1-16.fc38.i386/usr/bin/genewisedb extracting debug info from /builddir/build/BUILDROOT/wise2-2.4.1-16.fc38.i386/usr/bin/promoterwise extracting debug info from /builddir/build/BUILDROOT/wise2-2.4.1-16.fc38.i386/usr/bin/psw extracting debug info from /builddir/build/BUILDROOT/wise2-2.4.1-16.fc38.i386/usr/bin/pswdb extracting debug info from /builddir/build/BUILDROOT/wise2-2.4.1-16.fc38.i386/usr/bin/scanwise extracting debug info from /builddir/build/BUILDROOT/wise2-2.4.1-16.fc38.i386/usr/bin/scanwise_server original debug info size: 13776kB, size after compression: 10324kB /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/wise2-2.4.1-16.fc38.i386/src/base/wisetime.dy is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/wise2-2.4.1-16.fc38.i386/src/base/wiseoverlay.dy is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/wise2-2.4.1-16.fc38.i386/src/base/wisememman.dy is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/wise2-2.4.1-16.fc38.i386/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.RMEyIp + 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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/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/lib: + 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] >>> hmm-binary-cdna ... Passed >>> 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: wise2-2.4.1-16.fc38.i686 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.qyWWga + umask 022 + cd /builddir/build/BUILD + cd wise2.4.1 + DOCDIR=/builddir/build/BUILDROOT/wise2-2.4.1-16.fc38.i386/usr/share/doc/wise2 + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/wise2-2.4.1-16.fc38.i386/usr/share/doc/wise2 + cp -pr README /builddir/build/BUILDROOT/wise2-2.4.1-16.fc38.i386/usr/share/doc/wise2 + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.rFUp09 + umask 022 + cd /builddir/build/BUILD + cd wise2.4.1 + LICENSEDIR=/builddir/build/BUILDROOT/wise2-2.4.1-16.fc38.i386/usr/share/licenses/wise2 + export LC_ALL=C + LC_ALL=C + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/wise2-2.4.1-16.fc38.i386/usr/share/licenses/wise2 + cp -pr LICENSE /builddir/build/BUILDROOT/wise2-2.4.1-16.fc38.i386/usr/share/licenses/wise2 + cp -pr LICENSE.base /builddir/build/BUILDROOT/wise2-2.4.1-16.fc38.i386/usr/share/licenses/wise2 + cp -pr LICENSE.dynlibsrc /builddir/build/BUILDROOT/wise2-2.4.1-16.fc38.i386/usr/share/licenses/wise2 + cp -pr LICENSE.dyc /builddir/build/BUILDROOT/wise2-2.4.1-16.fc38.i386/usr/share/licenses/wise2 + cp -pr LICENSE.GPL /builddir/build/BUILDROOT/wise2-2.4.1-16.fc38.i386/usr/share/licenses/wise2 + RPM_EC=0 ++ jobs -p + exit 0 Provides: config(wise2) = 2.4.1-16.fc38 wise2 = 2.4.1-16.fc38 wise2(x86-32) = 2.4.1-16.fc38 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: libc.so.6 libc.so.6(GLIBC_2.0) libc.so.6(GLIBC_2.1) libc.so.6(GLIBC_2.1.3) libc.so.6(GLIBC_2.3) libc.so.6(GLIBC_2.3.4) libc.so.6(GLIBC_2.34) libc.so.6(GLIBC_2.4) libc.so.6(GLIBC_2.7) libglib-2.0.so.0 libm.so.6 libm.so.6(GLIBC_2.0) libm.so.6(GLIBC_2.29) rtld(GNU_HASH) Processing files: wise2-doc-2.4.1-16.fc38.noarch Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.5PYCh9 + umask 022 + cd /builddir/build/BUILD + cd wise2.4.1 + DOCDIR=/builddir/build/BUILDROOT/wise2-2.4.1-16.fc38.i386/usr/share/doc/wise2-doc + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/wise2-2.4.1-16.fc38.i386/usr/share/doc/wise2-doc + cp -pr docs /builddir/build/BUILDROOT/wise2-2.4.1-16.fc38.i386/usr/share/doc/wise2-doc + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.tkFzC3 + umask 022 + cd /builddir/build/BUILD + cd wise2.4.1 + LICENSEDIR=/builddir/build/BUILDROOT/wise2-2.4.1-16.fc38.i386/usr/share/licenses/wise2-doc + export LC_ALL=C + LC_ALL=C + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/wise2-2.4.1-16.fc38.i386/usr/share/licenses/wise2-doc + cp -pr LICENSE /builddir/build/BUILDROOT/wise2-2.4.1-16.fc38.i386/usr/share/licenses/wise2-doc + RPM_EC=0 ++ jobs -p + exit 0 Provides: wise2-doc = 2.4.1-16.fc38 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: wise2-examples-2.4.1-16.fc38.i686 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.C8B43D + umask 022 + cd /builddir/build/BUILD + cd wise2.4.1 + DOCDIR=/builddir/build/BUILDROOT/wise2-2.4.1-16.fc38.i386/usr/share/doc/wise2-examples + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/wise2-2.4.1-16.fc38.i386/usr/share/doc/wise2-examples + cp -pr test_data/README /builddir/build/BUILDROOT/wise2-2.4.1-16.fc38.i386/usr/share/doc/wise2-examples + RPM_EC=0 ++ jobs -p + exit 0 Provides: wise2-examples = 2.4.1-16.fc38 wise2-examples(x86-32) = 2.4.1-16.fc38 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: wise2-debugsource-2.4.1-16.fc38.i686 Provides: wise2-debugsource = 2.4.1-16.fc38 wise2-debugsource(x86-32) = 2.4.1-16.fc38 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: wise2-debuginfo-2.4.1-16.fc38.i686 Provides: debuginfo(build-id) = 0d7d00832261a897d48b47154b766c2494ea7a12 debuginfo(build-id) = 0e6ebb2654c7d5021bb656824b6212e93804fa3d debuginfo(build-id) = 16714e407e0acc778d34359aed7e1680907554d3 debuginfo(build-id) = 454de33cf0509469e5730e47b17b28abf98d69cf debuginfo(build-id) = 5d6737d2ba44b98b409e8b7fd2417b2608a92f9a debuginfo(build-id) = 68723ebc4424e54f9ff81e83a53eb5e02e18f867 debuginfo(build-id) = 9deb2c18e674d5591a7140433d1e34597318810f debuginfo(build-id) = cfc3664cfdf429966b10be797372429082a5e273 debuginfo(build-id) = f217e5dc256b26acc787d24e7a3a0627810ef1a9 debuginfo(build-id) = f3d100348df080473932bd30fe57bf7ddabaac33 debuginfo(build-id) = fe5ac52c6d6bca84e695558473ad63a1e2551a16 wise2-debuginfo = 2.4.1-16.fc38 wise2-debuginfo(x86-32) = 2.4.1-16.fc38 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: wise2-debugsource(x86-32) = 2.4.1-16.fc38 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/wise2-2.4.1-16.fc38.i386 Wrote: /builddir/build/RPMS/wise2-debuginfo-2.4.1-16.fc38.i686.rpm Wrote: /builddir/build/RPMS/wise2-2.4.1-16.fc38.i686.rpm Wrote: /builddir/build/RPMS/wise2-examples-2.4.1-16.fc38.i686.rpm Wrote: /builddir/build/RPMS/wise2-doc-2.4.1-16.fc38.noarch.rpm Wrote: /builddir/build/RPMS/wise2-debugsource-2.4.1-16.fc38.i686.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.0iKf1R + umask 022 + cd /builddir/build/BUILD + cd wise2.4.1 + /usr/bin/rm -rf /builddir/build/BUILDROOT/wise2-2.4.1-16.fc38.i386 + RPM_EC=0 ++ jobs -p + exit 0 Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.vGUQka + umask 022 + cd /builddir/build/BUILD + rm -rf wise2.4.1 wise2.4.1.gemspec + RPM_EC=0 ++ jobs -p + exit 0 Finish: rpmbuild wise2-2.4.1-16.fc38.src.rpm Finish: build phase for wise2-2.4.1-16.fc38.src.rpm INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-i686-1672387198.750766/root/var/log/dnf.rpm.log /var/lib/mock/fedora-rawhide-i686-1672387198.750766/root/var/log/dnf.librepo.log /var/lib/mock/fedora-rawhide-i686-1672387198.750766/root/var/log/dnf.log INFO: Done(/var/lib/copr-rpmbuild/results/wise2-2.4.1-16.fc38.src.rpm) Config(child) 3 minutes 31 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