Warning: Permanently added '44.204.118.81' (ED25519) to the list of known hosts. You can reproduce this build on your computer by running: sudo dnf install copr-rpmbuild /usr/bin/copr-rpmbuild --verbose --drop-resultdir --task-url https://copr.fedorainfracloud.org/backend/get-build-task/8477802-fedora-rawhide-x86_64 --chroot fedora-rawhide-x86_64 Version: 1.2 PID: 49486 Logging PID: 49487 Task: {'allow_user_ssh': False, 'appstream': False, 'background': True, 'build_id': 8477802, 'buildroot_pkgs': [], 'chroot': 'fedora-rawhide-x86_64', 'enable_net': False, 'fedora_review': False, 'git_hash': 'b5a7993fe080586b143c5e464b7d8ea6d924448a', 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/dmalcolm/gcc-15-smoketest-3.failed.checker/bionetgen', 'isolation': 'default', 'memory_reqs': 2048, 'package_name': 'bionetgen', 'package_version': '2.9.0-4', 'project_dirname': 'gcc-15-smoketest-3.failed.checker', 'project_name': 'gcc-15-smoketest-3.failed.checker', 'project_owner': 'dmalcolm', 'repo_priority': None, 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/dmalcolm/gcc-15-smoketest-3.failed.checker/fedora-rawhide-x86_64/', 'id': 'copr_base', 'name': 'Copr repository', 'priority': None}], 'sandbox': 'dmalcolm/gcc-15-smoketest-3.failed.checker--dmalcolm', 'source_json': {}, 'source_type': None, 'ssh_public_keys': None, 'storage': 0, 'submitter': 'dmalcolm', 'tags': [], 'task_id': '8477802-fedora-rawhide-x86_64', 'timeout': 115200, 'uses_devel_repo': False, 'with_opts': [], 'without_opts': []} Running: git clone https://copr-dist-git.fedorainfracloud.org/git/dmalcolm/gcc-15-smoketest-3.failed.checker/bionetgen /var/lib/copr-rpmbuild/workspace/workdir-pr7w55lb/bionetgen --depth 500 --no-single-branch --recursive cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/dmalcolm/gcc-15-smoketest-3.failed.checker/bionetgen', '/var/lib/copr-rpmbuild/workspace/workdir-pr7w55lb/bionetgen', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-pr7w55lb/bionetgen'... Running: git checkout b5a7993fe080586b143c5e464b7d8ea6d924448a -- cmd: ['git', 'checkout', 'b5a7993fe080586b143c5e464b7d8ea6d924448a', '--'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-pr7w55lb/bionetgen rc: 0 stdout: stderr: Note: switching to 'b5a7993fe080586b143c5e464b7d8ea6d924448a'. 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 b5a7993 automatic import of bionetgen Running: dist-git-client sources cmd: ['dist-git-client', 'sources'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-pr7w55lb/bionetgen 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 bionetgen-BioNetGen-2.9.0.tar.gz INFO: Reading stdout from command: curl --help all INFO: Calling: curl -H Pragma: -o bionetgen-BioNetGen-2.9.0.tar.gz --location --connect-timeout 60 --retry 3 --retry-delay 10 --remote-time --show-error --fail --retry-all-errors https://copr-dist-git.fedorainfracloud.org/repo/pkgs/dmalcolm/gcc-15-smoketest-3.failed.checker/bionetgen/bionetgen-BioNetGen-2.9.0.tar.gz/md5/1b9d5df4ac2f34e1d5c187ffcc73df33/bionetgen-BioNetGen-2.9.0.tar.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 40.0M 100 40.0M 0 0 316M 0 --:--:-- --:--:-- --:--:-- 315M INFO: Reading stdout from command: md5sum bionetgen-BioNetGen-2.9.0.tar.gz /usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated Running (timeout=115200): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-pr7w55lb/bionetgen/bionetgen.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-pr7w55lb/bionetgen --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1736203422.274018 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 6.0 starting (python version = 3.13.0, NVR = mock-6.0-1.fc41), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-pr7w55lb/bionetgen/bionetgen.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-pr7w55lb/bionetgen --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1736203422.274018 -r /var/lib/copr-rpmbuild/results/configs/child.cfg Start(bootstrap): init plugins INFO: tmpfs initialized INFO: selinux enabled INFO: chroot_scan: initialized INFO: compress_logs: initialized Finish(bootstrap): init plugins Start: init plugins INFO: tmpfs initialized INFO: selinux enabled INFO: chroot_scan: initialized INFO: compress_logs: initialized Finish: init plugins INFO: Signal handler active Start: run INFO: Start(/var/lib/copr-rpmbuild/workspace/workdir-pr7w55lb/bionetgen/bionetgen.spec) Config(fedora-rawhide-x86_64) Start: clean chroot Finish: clean chroot Mock Version: 6.0 INFO: Mock Version: 6.0 Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1736203422.274018/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata INFO: Guessed host environment type: unknown INFO: Using container image: registry.fedoraproject.org/fedora:rawhide INFO: Pulling image: registry.fedoraproject.org/fedora:rawhide INFO: Tagging container image as mock-bootstrap-a9f4b468-9701-4dd0-83bd-0ae19b0e8a43 INFO: Checking that 3b26c95bbe87cc88f475ce9c0ba4b394bf23541b10bebe9a634c9c8e61f73b10 image matches host's architecture INFO: Copy content of container 3b26c95bbe87cc88f475ce9c0ba4b394bf23541b10bebe9a634c9c8e61f73b10 to /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1736203422.274018/root INFO: mounting 3b26c95bbe87cc88f475ce9c0ba4b394bf23541b10bebe9a634c9c8e61f73b10 with podman image mount INFO: image 3b26c95bbe87cc88f475ce9c0ba4b394bf23541b10bebe9a634c9c8e61f73b10 as /var/lib/containers/storage/overlay/d3212d8beae72a97d426f4f4cbc9926037985c9d492b381ad2608549e5b9deb3/merged INFO: umounting image 3b26c95bbe87cc88f475ce9c0ba4b394bf23541b10bebe9a634c9c8e61f73b10 (/var/lib/containers/storage/overlay/d3212d8beae72a97d426f4f4cbc9926037985c9d492b381ad2608549e5b9deb3/merged) with podman image umount INFO: Removing image mock-bootstrap-a9f4b468-9701-4dd0-83bd-0ae19b0e8a43 INFO: Package manager dnf5 detected and used (fallback) INFO: Not updating bootstrap chroot, bootstrap_image_ready=True Start(bootstrap): creating root cache Finish(bootstrap): creating root cache Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-1736203422.274018/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin INFO: Package manager dnf5 detected and used (direct choice) INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-4.20.0-1.fc42.x86_64 rpm-sequoia-1.7.0-3.fc42.x86_64 dnf5-5.2.8.1-2.fc42.x86_64 dnf5-plugins-5.2.8.1-2.fc42.x86_64 Start: installing minimal buildroot with dnf5 Updating and loading repositories: fedora 100% | 88.8 KiB/s | 24.3 KiB | 00m00s Copr repository 100% | 84.9 KiB/s | 1.5 KiB | 00m00s Copr repository 100% | 4.1 MiB/s | 134.8 KiB | 00m00s Repositories loaded. Package Arch Version Repository Size Installing group/module packages: bash x86_64 5.2.37-1.fc42 fedora 8.2 MiB bzip2 x86_64 1.0.8-19.fc41 fedora 95.7 KiB coreutils x86_64 9.5-11.fc42 fedora 5.4 MiB cpio x86_64 2.15-2.fc41 fedora 1.1 MiB diffutils x86_64 3.10-8.fc41 fedora 1.6 MiB fedora-release-common noarch 42-0.11 fedora 19.8 KiB findutils x86_64 1:4.10.0-4.fc41 fedora 1.8 MiB gawk x86_64 5.3.0-4.fc41 fedora 1.7 MiB glibc-minimal-langpack x86_64 2.40.9000-26.fc42 fedora 0.0 B grep x86_64 3.11-9.fc41 fedora 1.0 MiB gzip x86_64 1.13-2.fc41 fedora 389.0 KiB info x86_64 7.1.1-2.fc42 fedora 361.8 KiB patch x86_64 2.7.6-25.fc41 fedora 266.7 KiB redhat-rpm-config noarch 296-1.fc42 fedora 186.6 KiB rpm-build x86_64 4.20.0-1.fc42 fedora 194.3 KiB sed x86_64 4.9-3.fc41 fedora 861.5 KiB shadow-utils x86_64 2:4.17.0-2.fc42 fedora 4.0 MiB tar x86_64 2:1.35-4.fc41 fedora 2.9 MiB unzip x86_64 6.0-65.fc42 fedora 398.2 KiB util-linux x86_64 2.40.2-8.fc42 fedora 3.7 MiB which x86_64 2.21-42.fc41 fedora 80.2 KiB xz x86_64 1:5.6.3-2.fc42 fedora 1.2 MiB Installing dependencies: add-determinism x86_64 0.5.0-1.fc42 fedora 2.4 MiB alternatives x86_64 1.31-1.fc42 fedora 64.8 KiB ansible-srpm-macros noarch 1-16.fc41 fedora 35.7 KiB audit-libs x86_64 4.0.2-1.fc41 fedora 331.3 KiB authselect x86_64 1.5.0-8.fc42 fedora 157.5 KiB authselect-libs x86_64 1.5.0-8.fc42 fedora 822.2 KiB basesystem noarch 11-21.fc41 fedora 0.0 B binutils x86_64 2.43.50-9.fc42 fedora 25.8 MiB build-reproducibility-srpm-macros noarch 0.5.0-1.fc42 fedora 735.0 B bzip2-libs x86_64 1.0.8-19.fc41 fedora 80.7 KiB ca-certificates noarch 2024.2.69_v8.0.401-4.fc42 fedora 2.6 MiB coreutils-common x86_64 9.5-11.fc42 fedora 11.2 MiB cracklib x86_64 2.9.11-6.fc41 fedora 238.9 KiB crypto-policies noarch 20241128-1.gitbb7b0b0.fc42 fedora 137.3 KiB curl x86_64 8.11.1-2.fc42 fedora 452.0 KiB cyrus-sasl-lib x86_64 2.1.28-27.fc41 fedora 2.3 MiB debugedit x86_64 5.1-2.fc42 fedora 200.3 KiB dwz x86_64 0.15-8.fc42 fedora 299.2 KiB ed x86_64 1.20.2-2.fc41 fedora 146.9 KiB efi-srpm-macros noarch 5-13.fc42 fedora 40.2 KiB elfutils x86_64 0.192-7.fc42 fedora 2.6 MiB elfutils-debuginfod-client x86_64 0.192-7.fc42 fedora 81.4 KiB elfutils-default-yama-scope noarch 0.192-7.fc42 fedora 1.8 KiB elfutils-libelf x86_64 0.192-7.fc42 fedora 1.2 MiB elfutils-libs x86_64 0.192-7.fc42 fedora 662.9 KiB fedora-gpg-keys noarch 42-0.3 fedora 126.4 KiB fedora-release noarch 42-0.11 fedora 0.0 B fedora-release-identity-basic noarch 42-0.11 fedora 719.0 B fedora-repos noarch 42-0.3 fedora 4.9 KiB fedora-repos-rawhide noarch 42-0.3 fedora 2.2 KiB file x86_64 5.45-8.fc42 fedora 103.7 KiB file-libs x86_64 5.45-8.fc42 fedora 9.9 MiB filesystem x86_64 3.18-29.fc42 fedora 106.0 B fonts-srpm-macros noarch 1:2.0.5-17.fc41 fedora 55.8 KiB forge-srpm-macros noarch 0.4.0-1.fc42 fedora 38.9 KiB fpc-srpm-macros noarch 1.3-13.fc41 fedora 144.0 B gdb-minimal x86_64 15.2-4.fc42 fedora 12.7 MiB gdbm x86_64 1:1.23-7.fc41 fedora 460.9 KiB gdbm-libs x86_64 1:1.23-7.fc41 fedora 121.9 KiB ghc-srpm-macros noarch 1.9.2-1.fc42 fedora 779.0 B glibc x86_64 2.40.9000-26.fc42 fedora 6.7 MiB glibc-common x86_64 2.40.9000-26.fc42 fedora 1.0 MiB glibc-gconv-extra x86_64 2.40.9000-26.fc42 fedora 8.0 MiB gmp x86_64 1:6.3.0-2.fc41 fedora 811.4 KiB gnat-srpm-macros noarch 6-6.fc41 fedora 1.0 KiB go-srpm-macros noarch 3.6.0-5.fc42 fedora 60.8 KiB jansson x86_64 2.14-1.fc42 fedora 93.1 KiB json-c x86_64 0.18-1.fc42 fedora 83.3 KiB kernel-srpm-macros noarch 1.0-24.fc41 fedora 1.9 KiB keyutils-libs x86_64 1.6.3-4.fc41 fedora 54.4 KiB krb5-libs x86_64 1.21.3-3.fc42 fedora 2.3 MiB libacl x86_64 2.3.2-2.fc41 fedora 40.0 KiB libarchive x86_64 3.7.7-1.fc42 fedora 932.3 KiB libattr x86_64 2.5.2-4.fc41 fedora 28.5 KiB libblkid x86_64 2.40.2-8.fc42 fedora 262.5 KiB libbrotli x86_64 1.1.0-5.fc41 fedora 837.6 KiB libcap x86_64 2.71-1.fc42 fedora 210.8 KiB libcap-ng x86_64 0.8.5-3.fc41 fedora 69.2 KiB libcom_err x86_64 1.47.1-6.fc42 fedora 67.2 KiB libcurl x86_64 8.11.1-2.fc42 fedora 817.3 KiB libeconf x86_64 0.7.5-1.fc42 fedora 66.7 KiB libevent x86_64 2.1.12-14.fc41 fedora 895.7 KiB libfdisk x86_64 2.40.2-8.fc42 fedora 362.9 KiB libffi x86_64 3.4.6-3.fc42 fedora 86.4 KiB libgcc x86_64 14.2.1-6.fc42 fedora 270.6 KiB libgomp x86_64 14.2.1-6.fc42 fedora 519.8 KiB libidn2 x86_64 2.3.7-2.fc41 fedora 329.1 KiB libmount x86_64 2.40.2-8.fc42 fedora 355.8 KiB libnghttp2 x86_64 1.64.0-1.fc42 fedora 174.5 KiB libnsl2 x86_64 2.0.1-2.fc41 fedora 57.9 KiB libpkgconf x86_64 2.3.0-1.fc42 fedora 78.2 KiB libpsl x86_64 0.21.5-4.fc41 fedora 80.5 KiB libpwquality x86_64 1.4.5-11.fc41 fedora 417.8 KiB libselinux x86_64 3.8-0.rc3.1.fc42 fedora 191.6 KiB libsemanage x86_64 3.8-0.rc3.1.fc42 fedora 305.3 KiB libsepol x86_64 3.8-0.rc3.1.fc42 fedora 812.3 KiB libsmartcols x86_64 2.40.2-8.fc42 fedora 180.4 KiB libssh x86_64 0.11.1-1.fc42 fedora 569.6 KiB libssh-config noarch 0.11.1-1.fc42 fedora 277.0 B libstdc++ x86_64 14.2.1-6.fc42 fedora 2.8 MiB libtasn1 x86_64 4.19.0-9.fc41 fedora 175.7 KiB libtirpc x86_64 1.3.6-1.rc3.fc42 fedora 197.6 KiB libtool-ltdl x86_64 2.5.4-1.fc42 fedora 68.1 KiB libunistring x86_64 1.1-8.fc41 fedora 1.7 MiB libuuid x86_64 2.40.2-8.fc42 fedora 41.4 KiB libverto x86_64 0.3.2-9.fc41 fedora 29.5 KiB libxcrypt x86_64 4.4.37-4.fc42 fedora 269.6 KiB libxml2 x86_64 2.12.9-1.fc42 fedora 1.7 MiB libzstd x86_64 1.5.6-2.fc41 fedora 795.9 KiB lua-libs x86_64 5.4.7-1.fc42 fedora 285.0 KiB lua-srpm-macros noarch 1-14.fc41 fedora 1.3 KiB lz4-libs x86_64 1.10.0-1.fc41 fedora 145.5 KiB mpfr x86_64 4.2.1-5.fc41 fedora 832.1 KiB ncurses-base noarch 6.5-2.20240629.fc41 fedora 326.3 KiB ncurses-libs x86_64 6.5-2.20240629.fc41 fedora 975.2 KiB ocaml-srpm-macros noarch 10-3.fc41 fedora 1.9 KiB openblas-srpm-macros noarch 2-18.fc41 fedora 112.0 B openldap x86_64 2.6.8-6.fc42 fedora 647.4 KiB openssl-libs x86_64 1:3.2.2-10.fc42 fedora 7.7 MiB p11-kit x86_64 0.25.5-4.fc42 fedora 2.2 MiB p11-kit-trust x86_64 0.25.5-4.fc42 fedora 403.8 KiB package-notes-srpm-macros noarch 0.5-12.fc41 fedora 1.6 KiB pam x86_64 1.7.0-3.fc42 fedora 1.8 MiB pam-libs x86_64 1.7.0-3.fc42 fedora 139.4 KiB pcre2 x86_64 10.44-1.fc41.1 fedora 653.5 KiB pcre2-syntax noarch 10.44-1.fc41.1 fedora 251.6 KiB perl-srpm-macros noarch 1-56.fc41 fedora 861.0 B pkgconf x86_64 2.3.0-1.fc42 fedora 88.6 KiB pkgconf-m4 noarch 2.3.0-1.fc42 fedora 14.4 KiB pkgconf-pkg-config x86_64 2.3.0-1.fc42 fedora 989.0 B popt x86_64 1.19-7.fc41 fedora 136.9 KiB publicsuffix-list-dafsa noarch 20240107-4.fc41 fedora 67.5 KiB pyproject-srpm-macros noarch 1.16.3-1.fc42 fedora 1.9 KiB python-srpm-macros noarch 3.13-3.fc41 fedora 51.0 KiB qt5-srpm-macros noarch 5.15.15-1.fc42 fedora 500.0 B qt6-srpm-macros noarch 6.8.1-4.fc42 fedora 456.0 B readline x86_64 8.2-11.fc42 fedora 493.1 KiB rpm x86_64 4.20.0-1.fc42 fedora 3.1 MiB rpm-build-libs x86_64 4.20.0-1.fc42 fedora 206.7 KiB rpm-libs x86_64 4.20.0-1.fc42 fedora 726.1 KiB rpm-sequoia x86_64 1.7.0-3.fc42 fedora 2.3 MiB rust-srpm-macros noarch 26.3-3.fc42 fedora 4.8 KiB setup noarch 2.15.0-9.fc42 fedora 720.7 KiB sqlite-libs x86_64 3.47.2-1.fc42 fedora 1.4 MiB systemd-libs x86_64 257.1-1.fc42 fedora 2.2 MiB util-linux-core x86_64 2.40.2-8.fc42 fedora 1.5 MiB xxhash-libs x86_64 0.8.3-1.fc42 fedora 88.5 KiB xz-libs x86_64 1:5.6.3-2.fc42 fedora 218.4 KiB zig-srpm-macros noarch 1-3.fc41 fedora 1.1 KiB zip x86_64 3.0-42.fc42 fedora 695.9 KiB zlib-ng-compat x86_64 2.2.2-1.fc42 fedora 134.0 KiB zstd x86_64 1.5.6-2.fc41 fedora 1.7 MiB Installing groups: Buildsystem building group Transaction Summary: Installing: 154 packages Total size of inbound packages is 52 MiB. Need to download 0 B. After this operation, 178 MiB extra will be used (install 178 MiB, remove 0 B). [1/1] tar-2:1.35-4.fc41.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [1/1] Total 100% | 0.0 B/s | 0.0 B | 00m00s [1/2] bzip2-0:1.0.8-19.fc41.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [2/2] Total 100% | 0.0 B/s | 0.0 B | 00m00s [1/3] redhat-rpm-config-0:296-1.fc42.no 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [3/3] Total 100% | 0.0 B/s | 0.0 B | 00m00s [1/4] rpm-build-0:4.20.0-1.fc42.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [4/4] Total 100% | 0.0 B/s | 0.0 B | 00m00s [1/5] unzip-0:6.0-65.fc42.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded 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downloaded -------------------------------------------------------------------------------- [153/153] Total 100% | 0.0 B/s | 0.0 B | 00m00s [ 1/154] libtool-ltdl-0:2.5.4-1.fc42.x 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [154/154] Total 100% | 0.0 B/s | 0.0 B | 00m00s Running transaction Importing OpenPGP key 0x105EF944: UserID : "Fedora (42) " Fingerprint: B0F4950458F69E1150C6C5EDC8AC4916105EF944 From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-42-primary The key was successfully imported. Importing OpenPGP key 0x105EF944: UserID : "Fedora (42) " Fingerprint: B0F4950458F69E1150C6C5EDC8AC4916105EF944 From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-42-primary The key was successfully imported. Importing OpenPGP key 0xE99D6AD1: UserID : "Fedora (41) " Fingerprint: 466CF2D8B60BC3057AA9453ED0622462E99D6AD1 From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-41-primary The key was successfully imported. Importing OpenPGP key 0x31645531: UserID : "Fedora (43) " Fingerprint: C6E7F081CF80E13146676E88829B606631645531 From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-43-primary The key was successfully imported. 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171.5 MiB/s | 175.6 KiB | 00m00s [103/156] Installing libtool-ltdl-0:2.5 100% | 67.6 MiB/s | 69.2 KiB | 00m00s [104/156] Installing coreutils-common-0 100% | 361.0 MiB/s | 11.2 MiB | 00m00s [105/156] Installing openssl-libs-1:3.2 100% | 349.5 MiB/s | 7.7 MiB | 00m00s [106/156] Installing coreutils-0:9.5-11 100% | 234.8 MiB/s | 5.4 MiB | 00m00s [107/156] Installing ca-certificates-0: 100% | 1.8 MiB/s | 2.4 MiB | 00m01s [108/156] Installing krb5-libs-0:1.21.3 100% | 256.1 MiB/s | 2.3 MiB | 00m00s [109/156] Installing libarchive-0:3.7.7 100% | 304.1 MiB/s | 934.2 KiB | 00m00s [110/156] Installing libtirpc-0:1.3.6-1 100% | 194.7 MiB/s | 199.4 KiB | 00m00s [111/156] Installing gzip-0:1.13-2.fc41 100% | 192.7 MiB/s | 394.6 KiB | 00m00s [112/156] Installing authselect-libs-0: 100% | 163.5 MiB/s | 837.2 KiB | 00m00s [113/156] Installing cracklib-0:2.9.11- 100% | 81.5 MiB/s | 250.3 KiB | 00m00s [114/156] Installing libpwquality-0:1.4 100% | 105.0 MiB/s | 430.1 KiB | 00m00s [115/156] Installing libnsl2-0:2.0.1-2. 100% | 57.7 MiB/s | 59.1 KiB | 00m00s [116/156] Installing pam-0:1.7.0-3.fc42 100% | 157.8 MiB/s | 1.9 MiB | 00m00s [117/156] Installing libssh-0:0.11.1-1. 100% | 279.2 MiB/s | 571.7 KiB | 00m00s [118/156] Installing rpm-sequoia-0:1.7. 100% | 332.0 MiB/s | 2.3 MiB | 00m00s [119/156] Installing rpm-libs-0:4.20.0- 100% | 236.9 MiB/s | 727.7 KiB | 00m00s [120/156] Installing rpm-build-libs-0:4 100% | 202.6 MiB/s | 207.5 KiB | 00m00s [121/156] Installing libevent-0:2.1.12- 100% | 292.8 MiB/s | 899.5 KiB | 00m00s [122/156] Installing openldap-0:2.6.8-6 100% | 212.0 MiB/s | 651.2 KiB | 00m00s [123/156] Installing libcurl-0:8.11.1-2 100% | 266.4 MiB/s | 818.4 KiB | 00m00s [124/156] Installing elfutils-debuginfo 100% | 81.8 MiB/s | 83.8 KiB | 00m00s [125/156] Installing elfutils-0:0.192-7 100% | 330.6 MiB/s | 2.6 MiB | 00m00s [126/156] Installing binutils-0:2.43.50 100% | 358.4 MiB/s | 25.8 MiB | 00m00s [127/156] Installing gdb-minimal-0:15.2 100% | 334.9 MiB/s | 12.7 MiB | 00m00s [128/156] Installing debugedit-0:5.1-2. 100% | 198.3 MiB/s | 203.0 KiB | 00m00s [129/156] Installing curl-0:8.11.1-2.fc 100% | 44.4 MiB/s | 454.5 KiB | 00m00s [130/156] Installing rpm-0:4.20.0-1.fc4 100% | 167.1 MiB/s | 2.5 MiB | 00m00s [131/156] Installing efi-srpm-macros-0: 100% | 40.2 MiB/s | 41.2 KiB | 00m00s [132/156] Installing lua-srpm-macros-0: 100% | 0.0 B/s | 1.9 KiB | 00m00s [133/156] Installing zig-srpm-macros-0: 100% | 0.0 B/s | 1.7 KiB | 00m00s [134/156] Installing rust-srpm-macros-0 100% | 0.0 B/s | 5.6 KiB | 00m00s [135/156] Installing qt6-srpm-macros-0: 100% | 0.0 B/s | 732.0 B | 00m00s [136/156] Installing qt5-srpm-macros-0: 100% | 0.0 B/s | 776.0 B | 00m00s [137/156] Installing perl-srpm-macros-0 100% | 0.0 B/s | 1.1 KiB | 00m00s [138/156] Installing package-notes-srpm 100% | 0.0 B/s | 2.0 KiB | 00m00s [139/156] Installing openblas-srpm-macr 100% | 0.0 B/s | 392.0 B | 00m00s [140/156] Installing ocaml-srpm-macros- 100% | 0.0 B/s | 2.2 KiB | 00m00s [141/156] Installing kernel-srpm-macros 100% | 0.0 B/s | 2.3 KiB | 00m00s [142/156] Installing gnat-srpm-macros-0 100% | 0.0 B/s | 1.3 KiB | 00m00s [143/156] Installing ghc-srpm-macros-0: 100% | 0.0 B/s | 1.0 KiB | 00m00s [144/156] Installing fpc-srpm-macros-0: 100% | 0.0 B/s | 420.0 B | 00m00s [145/156] Installing ansible-srpm-macro 100% | 0.0 B/s | 36.2 KiB | 00m00s [146/156] Installing fonts-srpm-macros- 100% | 55.7 MiB/s | 57.0 KiB | 00m00s [147/156] Installing forge-srpm-macros- 100% | 0.0 B/s | 40.3 KiB | 00m00s [148/156] Installing go-srpm-macros-0:3 100% | 60.5 MiB/s | 62.0 KiB | 00m00s [149/156] Installing python-srpm-macros 100% | 50.9 MiB/s | 52.2 KiB | 00m00s [150/156] Installing redhat-rpm-config- 100% | 94.4 MiB/s | 193.2 KiB | 00m00s [151/156] Installing rpm-build-0:4.20.0 100% | 99.1 MiB/s | 202.9 KiB | 00m00s [152/156] Installing pyproject-srpm-mac 100% | 1.2 MiB/s | 2.5 KiB | 00m00s [153/156] Installing util-linux-0:2.40. 100% | 161.5 MiB/s | 3.7 MiB | 00m00s [154/156] Installing authselect-0:1.5.0 100% | 79.1 MiB/s | 161.9 KiB | 00m00s [155/156] Installing which-0:2.21-42.fc 100% | 80.5 MiB/s | 82.4 KiB | 00m00s [156/156] Installing info-0:7.1.1-2.fc4 100% | 208.8 KiB/s | 362.2 KiB | 00m02s Complete! Finish: installing minimal buildroot with dnf5 Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: add-determinism-0.5.0-1.fc42.x86_64 alternatives-1.31-1.fc42.x86_64 ansible-srpm-macros-1-16.fc41.noarch audit-libs-4.0.2-1.fc41.x86_64 authselect-1.5.0-8.fc42.x86_64 authselect-libs-1.5.0-8.fc42.x86_64 basesystem-11-21.fc41.noarch bash-5.2.37-1.fc42.x86_64 binutils-2.43.50-9.fc42.x86_64 build-reproducibility-srpm-macros-0.5.0-1.fc42.noarch bzip2-1.0.8-19.fc41.x86_64 bzip2-libs-1.0.8-19.fc41.x86_64 ca-certificates-2024.2.69_v8.0.401-4.fc42.noarch coreutils-9.5-11.fc42.x86_64 coreutils-common-9.5-11.fc42.x86_64 cpio-2.15-2.fc41.x86_64 cracklib-2.9.11-6.fc41.x86_64 crypto-policies-20241128-1.gitbb7b0b0.fc42.noarch curl-8.11.1-2.fc42.x86_64 cyrus-sasl-lib-2.1.28-27.fc41.x86_64 debugedit-5.1-2.fc42.x86_64 diffutils-3.10-8.fc41.x86_64 dwz-0.15-8.fc42.x86_64 ed-1.20.2-2.fc41.x86_64 efi-srpm-macros-5-13.fc42.noarch elfutils-0.192-7.fc42.x86_64 elfutils-debuginfod-client-0.192-7.fc42.x86_64 elfutils-default-yama-scope-0.192-7.fc42.noarch elfutils-libelf-0.192-7.fc42.x86_64 elfutils-libs-0.192-7.fc42.x86_64 fedora-gpg-keys-42-0.3.noarch fedora-release-42-0.11.noarch fedora-release-common-42-0.11.noarch fedora-release-identity-basic-42-0.11.noarch fedora-repos-42-0.3.noarch fedora-repos-rawhide-42-0.3.noarch file-5.45-8.fc42.x86_64 file-libs-5.45-8.fc42.x86_64 filesystem-3.18-29.fc42.x86_64 findutils-4.10.0-4.fc41.x86_64 fonts-srpm-macros-2.0.5-17.fc41.noarch forge-srpm-macros-0.4.0-1.fc42.noarch fpc-srpm-macros-1.3-13.fc41.noarch gawk-5.3.0-4.fc41.x86_64 gdb-minimal-15.2-4.fc42.x86_64 gdbm-1.23-7.fc41.x86_64 gdbm-libs-1.23-7.fc41.x86_64 ghc-srpm-macros-1.9.2-1.fc42.noarch glibc-2.40.9000-26.fc42.x86_64 glibc-common-2.40.9000-26.fc42.x86_64 glibc-gconv-extra-2.40.9000-26.fc42.x86_64 glibc-minimal-langpack-2.40.9000-26.fc42.x86_64 gmp-6.3.0-2.fc41.x86_64 gnat-srpm-macros-6-6.fc41.noarch go-srpm-macros-3.6.0-5.fc42.noarch gpg-pubkey-105ef944-65ca83d1 gpg-pubkey-31645531-66b6dccf gpg-pubkey-e99d6ad1-64d2612c grep-3.11-9.fc41.x86_64 gzip-1.13-2.fc41.x86_64 info-7.1.1-2.fc42.x86_64 jansson-2.14-1.fc42.x86_64 json-c-0.18-1.fc42.x86_64 kernel-srpm-macros-1.0-24.fc41.noarch keyutils-libs-1.6.3-4.fc41.x86_64 krb5-libs-1.21.3-3.fc42.x86_64 libacl-2.3.2-2.fc41.x86_64 libarchive-3.7.7-1.fc42.x86_64 libattr-2.5.2-4.fc41.x86_64 libblkid-2.40.2-8.fc42.x86_64 libbrotli-1.1.0-5.fc41.x86_64 libcap-2.71-1.fc42.x86_64 libcap-ng-0.8.5-3.fc41.x86_64 libcom_err-1.47.1-6.fc42.x86_64 libcurl-8.11.1-2.fc42.x86_64 libeconf-0.7.5-1.fc42.x86_64 libevent-2.1.12-14.fc41.x86_64 libfdisk-2.40.2-8.fc42.x86_64 libffi-3.4.6-3.fc42.x86_64 libgcc-14.2.1-6.fc42.x86_64 libgomp-14.2.1-6.fc42.x86_64 libidn2-2.3.7-2.fc41.x86_64 libmount-2.40.2-8.fc42.x86_64 libnghttp2-1.64.0-1.fc42.x86_64 libnsl2-2.0.1-2.fc41.x86_64 libpkgconf-2.3.0-1.fc42.x86_64 libpsl-0.21.5-4.fc41.x86_64 libpwquality-1.4.5-11.fc41.x86_64 libselinux-3.8-0.rc3.1.fc42.x86_64 libsemanage-3.8-0.rc3.1.fc42.x86_64 libsepol-3.8-0.rc3.1.fc42.x86_64 libsmartcols-2.40.2-8.fc42.x86_64 libssh-0.11.1-1.fc42.x86_64 libssh-config-0.11.1-1.fc42.noarch libstdc++-14.2.1-6.fc42.x86_64 libtasn1-4.19.0-9.fc41.x86_64 libtirpc-1.3.6-1.rc3.fc42.x86_64 libtool-ltdl-2.5.4-1.fc42.x86_64 libunistring-1.1-8.fc41.x86_64 libuuid-2.40.2-8.fc42.x86_64 libverto-0.3.2-9.fc41.x86_64 libxcrypt-4.4.37-4.fc42.x86_64 libxml2-2.12.9-1.fc42.x86_64 libzstd-1.5.6-2.fc41.x86_64 lua-libs-5.4.7-1.fc42.x86_64 lua-srpm-macros-1-14.fc41.noarch lz4-libs-1.10.0-1.fc41.x86_64 mpfr-4.2.1-5.fc41.x86_64 ncurses-base-6.5-2.20240629.fc41.noarch ncurses-libs-6.5-2.20240629.fc41.x86_64 ocaml-srpm-macros-10-3.fc41.noarch openblas-srpm-macros-2-18.fc41.noarch openldap-2.6.8-6.fc42.x86_64 openssl-libs-3.2.2-10.fc42.x86_64 p11-kit-0.25.5-4.fc42.x86_64 p11-kit-trust-0.25.5-4.fc42.x86_64 package-notes-srpm-macros-0.5-12.fc41.noarch pam-1.7.0-3.fc42.x86_64 pam-libs-1.7.0-3.fc42.x86_64 patch-2.7.6-25.fc41.x86_64 pcre2-10.44-1.fc41.1.x86_64 pcre2-syntax-10.44-1.fc41.1.noarch perl-srpm-macros-1-56.fc41.noarch pkgconf-2.3.0-1.fc42.x86_64 pkgconf-m4-2.3.0-1.fc42.noarch pkgconf-pkg-config-2.3.0-1.fc42.x86_64 popt-1.19-7.fc41.x86_64 publicsuffix-list-dafsa-20240107-4.fc41.noarch pyproject-srpm-macros-1.16.3-1.fc42.noarch python-srpm-macros-3.13-3.fc41.noarch qt5-srpm-macros-5.15.15-1.fc42.noarch qt6-srpm-macros-6.8.1-4.fc42.noarch readline-8.2-11.fc42.x86_64 redhat-rpm-config-296-1.fc42.noarch rpm-4.20.0-1.fc42.x86_64 rpm-build-4.20.0-1.fc42.x86_64 rpm-build-libs-4.20.0-1.fc42.x86_64 rpm-libs-4.20.0-1.fc42.x86_64 rpm-sequoia-1.7.0-3.fc42.x86_64 rust-srpm-macros-26.3-3.fc42.noarch sed-4.9-3.fc41.x86_64 setup-2.15.0-9.fc42.noarch shadow-utils-4.17.0-2.fc42.x86_64 sqlite-libs-3.47.2-1.fc42.x86_64 systemd-libs-257.1-1.fc42.x86_64 tar-1.35-4.fc41.x86_64 unzip-6.0-65.fc42.x86_64 util-linux-2.40.2-8.fc42.x86_64 util-linux-core-2.40.2-8.fc42.x86_64 which-2.21-42.fc41.x86_64 xxhash-libs-0.8.3-1.fc42.x86_64 xz-5.6.3-2.fc42.x86_64 xz-libs-5.6.3-2.fc42.x86_64 zig-srpm-macros-1-3.fc41.noarch zip-3.0-42.fc42.x86_64 zlib-ng-compat-2.2.2-1.fc42.x86_64 zstd-1.5.6-2.fc41.x86_64 Start: buildsrpm Start: rpmbuild -bs Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1721174400 Wrote: /builddir/build/SRPMS/bionetgen-2.9.0-4.fc42.src.rpm Finish: rpmbuild -bs INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-x86_64-1736203422.274018/root/var/log/dnf5.log INFO: chroot_scan: creating tarball /var/lib/copr-rpmbuild/results/chroot_scan.tar.gz /bin/tar: Removing leading `/' from member names Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-pr7w55lb/bionetgen/bionetgen.spec) Config(child) 0 minutes 11 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot INFO: Start(/var/lib/copr-rpmbuild/results/bionetgen-2.9.0-4.fc42.src.rpm) Config(fedora-rawhide-x86_64) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1736203422.274018/root. INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1736203422.274018/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-1736203422.274018/root. INFO: calling preinit hooks INFO: enabled root cache Start: unpacking root cache Finish: unpacking root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-4.20.0-1.fc42.x86_64 rpm-sequoia-1.7.0-3.fc42.x86_64 dnf5-5.2.8.1-2.fc42.x86_64 dnf5-plugins-5.2.8.1-2.fc42.x86_64 Finish: chroot init Start: build phase for bionetgen-2.9.0-4.fc42.src.rpm Start: build setup for bionetgen-2.9.0-4.fc42.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1721174400 Wrote: /builddir/build/SRPMS/bionetgen-2.9.0-4.fc42.src.rpm Updating and loading repositories: fedora 100% | 93.9 KiB/s | 24.3 KiB | 00m00s Copr repository 100% | 127.3 KiB/s | 1.5 KiB | 00m00s Copr repository 100% | 4.1 MiB/s | 135.5 KiB | 00m00s Repositories loaded. Package Arch Version Repository Size Installing: cmake x86_64 3.31.3-1.fc42 fedora 32.9 MiB gcc x86_64 14.2.1-6.fc42 fedora 104.3 MiB gcc-c++ x86_64 14.2.1-6.fc42 fedora 38.1 MiB gcc-gfortran x86_64 14.2.1-6.fc42 fedora 37.2 MiB make x86_64 1:4.4.1-9.fc42 fedora 1.8 MiB perl-Carp noarch 1.54-511.fc41 fedora 46.6 KiB perl-Class-Struct noarch 0.68-512.fc42 fedora 25.4 KiB perl-Data-Dumper x86_64 2.189-512.fc41 fedora 111.7 KiB perl-Exporter noarch 5.78-511.fc41 fedora 54.3 KiB perl-File-Basename noarch 2.86-512.fc42 fedora 14.0 KiB perl-FindBin noarch 1.54-512.fc42 fedora 6.7 KiB perl-Getopt-Long noarch 1:2.58-2.fc41 fedora 144.5 KiB perl-IO x86_64 1.55-512.fc42 fedora 151.1 KiB perl-IPC-Open3 noarch 1.22-512.fc42 fedora 22.5 KiB perl-Math-Complex noarch 1.62-512.fc42 fedora 85.0 KiB perl-POSIX x86_64 2.20-512.fc42 fedora 235.1 KiB perl-PathTools x86_64 3.91-511.fc41 fedora 180.0 KiB perl-Scalar-List-Utils x86_64 5:1.68-1.fc42 fedora 148.9 KiB perl-Symbol noarch 1.09-512.fc42 fedora 6.8 KiB perl-constant noarch 1.33-512.fc41 fedora 26.2 KiB perl-generators noarch 1.16-6.fc41 fedora 21.8 KiB perl-interpreter x86_64 4:5.40.0-512.fc42 fedora 122.3 KiB perl-lib x86_64 0.65-512.fc42 fedora 8.5 KiB perl-libs x86_64 4:5.40.0-512.fc42 fedora 9.9 MiB perl-vars noarch 1.05-512.fc42 fedora 3.9 KiB Installing dependencies: annobin-docs noarch 12.80-1.fc42 fedora 98.6 KiB annobin-plugin-gcc x86_64 12.80-1.fc42 fedora 992.8 KiB cmake-data noarch 3.31.3-1.fc42 fedora 8.5 MiB cmake-filesystem x86_64 3.31.3-1.fc42 fedora 0.0 B cmake-rpm-macros noarch 3.31.3-1.fc42 fedora 7.5 KiB cpp x86_64 14.2.1-6.fc42 fedora 35.0 MiB emacs-filesystem noarch 1:30.0-3.fc41 fedora 0.0 B expat x86_64 2.6.4-1.fc42 fedora 285.5 KiB gcc-plugin-annobin x86_64 14.2.1-6.fc42 fedora 57.6 KiB glibc-devel x86_64 2.40.9000-26.fc42 fedora 2.3 MiB groff-base x86_64 1.23.0-7.fc41 fedora 3.8 MiB jsoncpp x86_64 1.9.5-8.fc41 fedora 253.4 KiB kernel-headers x86_64 6.13.0-0.rc5.42.fc42 fedora 6.5 MiB libb2 x86_64 0.98.1-12.fc41 fedora 42.2 KiB libgfortran x86_64 14.2.1-6.fc42 fedora 3.0 MiB libmpc x86_64 1.3.1-6.fc41 fedora 164.7 KiB libquadmath x86_64 14.2.1-6.fc42 fedora 325.9 KiB libquadmath-devel x86_64 14.2.1-6.fc42 fedora 21.9 KiB libstdc++-devel x86_64 14.2.1-6.fc42 fedora 15.4 MiB libuv x86_64 1:1.49.2-1.fc42 fedora 569.4 KiB libxcrypt-devel x86_64 4.4.37-4.fc42 fedora 30.5 KiB mpdecimal x86_64 2.5.1-16.fc41 fedora 204.9 KiB ncurses x86_64 6.5-2.20240629.fc41 fedora 627.3 KiB perl-AutoLoader noarch 5.74-512.fc42 fedora 20.5 KiB perl-B x86_64 1.89-512.fc42 fedora 498.0 KiB perl-Digest noarch 1.20-511.fc41 fedora 35.3 KiB perl-Digest-MD5 x86_64 2.59-5.fc41 fedora 59.8 KiB perl-DynaLoader x86_64 1.56-512.fc42 fedora 32.1 KiB perl-Encode x86_64 4:3.21-511.fc41 fedora 4.7 MiB perl-Errno x86_64 1.38-512.fc42 fedora 8.4 KiB perl-Fcntl x86_64 1.18-512.fc42 fedora 49.0 KiB perl-Fedora-VSP noarch 0.001-35.fc41 fedora 39.7 KiB perl-File-Path noarch 2.18-511.fc41 fedora 63.5 KiB perl-File-Temp noarch 1:0.231.100-511.fc41 fedora 162.3 KiB perl-File-stat noarch 1.14-512.fc42 fedora 12.5 KiB perl-FileHandle noarch 2.05-512.fc42 fedora 9.3 KiB perl-Getopt-Std noarch 1.14-512.fc42 fedora 11.2 KiB perl-HTTP-Tiny noarch 0.090-1.fc42 fedora 154.4 KiB perl-IO-Socket-IP noarch 0.43-1.fc42 fedora 100.3 KiB perl-IO-Socket-SSL noarch 2.089-1.fc42 fedora 703.3 KiB perl-MIME-Base32 noarch 1.303-21.fc41 fedora 30.7 KiB perl-MIME-Base64 x86_64 3.16-511.fc41 fedora 46.1 KiB perl-Net-SSLeay x86_64 1.94-7.fc41 fedora 1.3 MiB perl-Pod-Escapes noarch 1:1.07-511.fc41 fedora 24.9 KiB perl-Pod-Perldoc noarch 3.28.01-512.fc41 fedora 163.7 KiB perl-Pod-Simple noarch 1:3.45-511.fc41 fedora 560.9 KiB perl-Pod-Usage noarch 4:2.03-511.fc41 fedora 84.8 KiB perl-SelectSaver noarch 1.02-512.fc42 fedora 2.2 KiB perl-Socket x86_64 4:2.038-511.fc41 fedora 124.0 KiB perl-Storable x86_64 1:3.32-511.fc41 fedora 232.4 KiB perl-Term-ANSIColor noarch 5.01-512.fc41 fedora 97.5 KiB perl-Term-Cap noarch 1.18-511.fc41 fedora 29.3 KiB perl-Text-ParseWords noarch 3.31-511.fc41 fedora 13.6 KiB perl-Text-Tabs+Wrap noarch 2024.001-511.fc41 fedora 22.6 KiB perl-Time-Local noarch 2:1.350-511.fc41 fedora 69.0 KiB perl-URI noarch 5.31-1.fc42 fedora 257.0 KiB perl-base noarch 2.27-512.fc42 fedora 12.5 KiB perl-if noarch 0.61.000-512.fc42 fedora 5.8 KiB perl-libnet noarch 3.15-512.fc41 fedora 289.4 KiB perl-locale noarch 1.12-512.fc42 fedora 6.5 KiB perl-macros noarch 4:5.40.0-512.fc42 fedora 5.5 KiB perl-mro x86_64 1.29-512.fc42 fedora 45.6 KiB perl-overload noarch 1.37-512.fc42 fedora 71.5 KiB perl-overloading noarch 0.02-512.fc42 fedora 4.8 KiB perl-parent noarch 1:0.244-1.fc42 fedora 10.3 KiB perl-podlators noarch 1:6.0.2-2.fc41 fedora 317.5 KiB python-pip-wheel noarch 24.3.1-1.fc42 fedora 1.2 MiB python3 x86_64 3.13.1-2.fc42 fedora 30.6 KiB python3-libs x86_64 3.13.1-2.fc42 fedora 39.8 MiB rhash x86_64 1.4.5-1.fc42 fedora 359.3 KiB tzdata noarch 2024b-1.fc42 fedora 1.6 MiB vim-filesystem noarch 2:9.1.984-1.fc42 fedora 40.0 B Transaction Summary: Installing: 97 packages Total size of inbound packages is 117 MiB. Need to download 13 MiB. After this operation, 357 MiB extra will be used (install 357 MiB, remove 0 B). [1/1] gcc-0:14.2.1-6.fc42.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [1/1] Total 100% | 0.0 B/s | 0.0 B | 00m00s [1/2] make-1:4.4.1-9.fc42.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [2/2] Total 100% | 0.0 B/s | 0.0 B | 00m00s [1/3] perl-Carp-0:1.54-511.fc41.noarch 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [3/3] Total 100% | 0.0 B/s | 0.0 B | 00m00s [1/4] perl-Class-Struct-0:0.68-512.fc42 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [4/4] Total 100% | 0.0 B/s | 0.0 B | 00m00s [1/5] perl-PathTools-0:3.91-511.fc41.x8 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded 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Finish: build setup for bionetgen-2.9.0-4.fc42.src.rpm Start: rpmbuild bionetgen-2.9.0-4.fc42.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1721174400 Executing(%mkbuilddir): /bin/sh -e /var/tmp/rpm-tmp.sJyLRF + umask 022 + cd /builddir/build/BUILD/bionetgen-2.9.0-build + test -d /builddir/build/BUILD/bionetgen-2.9.0-build + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w /builddir/build/BUILD/bionetgen-2.9.0-build + /usr/bin/rm -rf /builddir/build/BUILD/bionetgen-2.9.0-build + /usr/bin/mkdir -p /builddir/build/BUILD/bionetgen-2.9.0-build + /usr/bin/mkdir -p /builddir/build/BUILD/bionetgen-2.9.0-build/SPECPARTS + RPM_EC=0 ++ jobs -p + exit 0 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.NZhuRl + umask 022 + cd /builddir/build/BUILD/bionetgen-2.9.0-build + cd /builddir/build/BUILD/bionetgen-2.9.0-build + rm -rf bionetgen-2.9.0 + /usr/bin/mkdir -p bionetgen-2.9.0 + cd bionetgen-2.9.0 + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/bionetgen-BioNetGen-2.9.0.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + pushd bionetgen-BioNetGen-2.9.0 ~/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0 ~/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0 + rm -f bng2/libsource/gsl-1.9.tar.gz bng2/libsource/Mathutils.tar.gz bng2/libsource/muparser_v2_2_4.zip + tar -xvf bng2/libsource/cvode-2.6.0.tar.gz -C bng2/Network3 cvode-2.6.0/README cvode-2.6.0/INSTALL_NOTES cvode-2.6.0/LICENSE cvode-2.6.0/Makefile.in cvode-2.6.0/configure.ac cvode-2.6.0/acinclude.m4 cvode-2.6.0/config.hin cvode-2.6.0/configure cvode-2.6.0/CMakeLists.txt cvode-2.6.0/config/config.guess cvode-2.6.0/config/config.sub cvode-2.6.0/config/install-sh cvode-2.6.0/config/mkinstalldirs cvode-2.6.0/config/rminstalldirs cvode-2.6.0/config/ltmain.sh cvode-2.6.0/config/mod_c.m4 cvode-2.6.0/config/mod_fortran.m4 cvode-2.6.0/config/cust_general.m4 cvode-2.6.0/config/CheckFortranFunctionExists.cmake cvode-2.6.0/config/SundialsFortran.cmake cvode-2.6.0/config/SundialsLapack.cmake cvode-2.6.0/config/SundialsMPIC.cmake cvode-2.6.0/config/SundialsMPIF.cmake cvode-2.6.0/config/FindLAPACK.cmake cvode-2.6.0/config/FindBLAS.cmake cvode-2.6.0/config/FindMPI.cmake cvode-2.6.0/bin/sundials-config.in cvode-2.6.0/bin/fortran-update.in cvode-2.6.0/bin/makefile-update.in cvode-2.6.0/include/sundials/sundials_config.in cvode-2.6.0/include/sundials/sundials_types.h cvode-2.6.0/include/sundials/sundials_math.h cvode-2.6.0/include/sundials/sundials_nvector.h cvode-2.6.0/include/sundials/sundials_fnvector.h cvode-2.6.0/include/sundials/sundials_dense.h cvode-2.6.0/include/sundials/sundials_direct.h cvode-2.6.0/include/sundials/sundials_band.h cvode-2.6.0/include/sundials/sundials_lapack.h cvode-2.6.0/include/sundials/sundials_spgmr.h cvode-2.6.0/include/sundials/sundials_spbcgs.h cvode-2.6.0/include/sundials/sundials_sptfqmr.h cvode-2.6.0/include/sundials/sundials_iterative.h cvode-2.6.0/include/nvector/nvector_serial.h cvode-2.6.0/include/nvector/nvector_parallel.h cvode-2.6.0/src/sundials/README cvode-2.6.0/src/sundials/Makefile.in cvode-2.6.0/src/sundials/CMakeLists.txt cvode-2.6.0/src/sundials/sundials_math.c cvode-2.6.0/src/sundials/sundials_nvector.c cvode-2.6.0/src/sundials/sundials_dense.c cvode-2.6.0/src/sundials/sundials_direct.c cvode-2.6.0/src/sundials/sundials_band.c cvode-2.6.0/src/sundials/sundials_spgmr.c cvode-2.6.0/src/sundials/sundials_spbcgs.c cvode-2.6.0/src/sundials/sundials_sptfqmr.c cvode-2.6.0/src/sundials/sundials_iterative.c cvode-2.6.0/src/nvec_ser/README cvode-2.6.0/src/nvec_ser/Makefile.in cvode-2.6.0/src/nvec_ser/CMakeLists.txt cvode-2.6.0/src/nvec_ser/fnvector_serial.h cvode-2.6.0/src/nvec_ser/nvector_serial.c cvode-2.6.0/src/nvec_ser/fnvector_serial.c cvode-2.6.0/src/nvec_par/README cvode-2.6.0/src/nvec_par/Makefile.in cvode-2.6.0/src/nvec_par/CMakeLists.txt cvode-2.6.0/src/nvec_par/fnvector_parallel.h cvode-2.6.0/src/nvec_par/nvector_parallel.c cvode-2.6.0/src/nvec_par/fnvector_parallel.c cvode-2.6.0/examples/templates/cmakelists_parallel_C_ex.in cvode-2.6.0/examples/templates/cmakelists_parallel_F77_ex.in cvode-2.6.0/examples/templates/cmakelists_serial_C_ex.in cvode-2.6.0/examples/templates/cmakelists_serial_F77_ex.in cvode-2.6.0/examples/templates/makefile_parallel_C_ex.in cvode-2.6.0/examples/templates/makefile_parallel_F77_ex.in cvode-2.6.0/examples/templates/makefile_serial_C_ex.in cvode-2.6.0/examples/templates/makefile_serial_F77_ex.in cvode-2.6.0/doc/cvode/cv_guide.pdf cvode-2.6.0/doc/cvode/cv_examples.pdf cvode-2.6.0/include/cvode/cvode.h cvode-2.6.0/include/cvode/cvode_direct.h cvode-2.6.0/include/cvode/cvode_dense.h cvode-2.6.0/include/cvode/cvode_band.h cvode-2.6.0/include/cvode/cvode_lapack.h cvode-2.6.0/include/cvode/cvode_diag.h cvode-2.6.0/include/cvode/cvode_spgmr.h cvode-2.6.0/include/cvode/cvode_spbcgs.h cvode-2.6.0/include/cvode/cvode_sptfqmr.h cvode-2.6.0/include/cvode/cvode_spils.h cvode-2.6.0/include/cvode/cvode_bandpre.h cvode-2.6.0/include/cvode/cvode_bbdpre.h cvode-2.6.0/src/cvode/LICENSE cvode-2.6.0/src/cvode/README cvode-2.6.0/src/cvode/Makefile.in cvode-2.6.0/src/cvode/CMakeLists.txt cvode-2.6.0/src/cvode/cvode.c cvode-2.6.0/src/cvode/cvode_io.c cvode-2.6.0/src/cvode/cvode_direct.c cvode-2.6.0/src/cvode/cvode_dense.c cvode-2.6.0/src/cvode/cvode_band.c cvode-2.6.0/src/cvode/cvode_lapack.c cvode-2.6.0/src/cvode/cvode_diag.c cvode-2.6.0/src/cvode/cvode_spils.c cvode-2.6.0/src/cvode/cvode_spgmr.c cvode-2.6.0/src/cvode/cvode_spbcgs.c cvode-2.6.0/src/cvode/cvode_sptfqmr.c cvode-2.6.0/src/cvode/cvode_bandpre.c cvode-2.6.0/src/cvode/cvode_bbdpre.c cvode-2.6.0/src/cvode/cvode_impl.h cvode-2.6.0/src/cvode/cvode_direct_impl.h cvode-2.6.0/src/cvode/cvode_diag_impl.h cvode-2.6.0/src/cvode/cvode_spils_impl.h cvode-2.6.0/src/cvode/cvode_bandpre_impl.h cvode-2.6.0/src/cvode/cvode_bbdpre_impl.h cvode-2.6.0/src/cvode/fcmix/Makefile.in cvode-2.6.0/src/cvode/fcmix/CMakeLists.txt cvode-2.6.0/src/cvode/fcmix/fcvode.c cvode-2.6.0/src/cvode/fcmix/fcvewt.c cvode-2.6.0/src/cvode/fcmix/fcvpreco.c cvode-2.6.0/src/cvode/fcmix/fcvjtimes.c cvode-2.6.0/src/cvode/fcmix/fcvband.c cvode-2.6.0/src/cvode/fcmix/fcvdense.c cvode-2.6.0/src/cvode/fcmix/fcvlapack.c cvode-2.6.0/src/cvode/fcmix/fcvlapband.c cvode-2.6.0/src/cvode/fcmix/fcvlapdense.c cvode-2.6.0/src/cvode/fcmix/fcvbp.c cvode-2.6.0/src/cvode/fcmix/fcvbbd.c cvode-2.6.0/src/cvode/fcmix/fcvroot.c cvode-2.6.0/src/cvode/fcmix/fcvode.h cvode-2.6.0/src/cvode/fcmix/fcvbp.h cvode-2.6.0/src/cvode/fcmix/fcvbbd.h cvode-2.6.0/src/cvode/fcmix/fcvroot.h cvode-2.6.0/examples/cvode/serial/README cvode-2.6.0/examples/cvode/serial/Makefile.in cvode-2.6.0/examples/cvode/serial/CMakeLists.txt cvode-2.6.0/examples/cvode/serial/cvAdvDiff_bnd.c cvode-2.6.0/examples/cvode/serial/cvAdvDiff_bndL.c cvode-2.6.0/examples/cvode/serial/cvAdvDiff_bndL.out cvode-2.6.0/examples/cvode/serial/cvAdvDiff_bnd.out cvode-2.6.0/examples/cvode/serial/cvDirectDemo_ls.c cvode-2.6.0/examples/cvode/serial/cvDirectDemo_ls.out cvode-2.6.0/examples/cvode/serial/cvDiurnal_kry_bp.c cvode-2.6.0/examples/cvode/serial/cvDiurnal_kry_bp.out cvode-2.6.0/examples/cvode/serial/cvDiurnal_kry.c cvode-2.6.0/examples/cvode/serial/cvDiurnal_kry.out cvode-2.6.0/examples/cvode/serial/cvKrylovDemo_ls.c cvode-2.6.0/examples/cvode/serial/cvKrylovDemo_ls.out cvode-2.6.0/examples/cvode/serial/cvKrylovDemo_prec.c cvode-2.6.0/examples/cvode/serial/cvKrylovDemo_prec.out cvode-2.6.0/examples/cvode/serial/cvRoberts_dns.c cvode-2.6.0/examples/cvode/serial/cvRoberts_dnsL.c cvode-2.6.0/examples/cvode/serial/cvRoberts_dnsL.out cvode-2.6.0/examples/cvode/serial/cvRoberts_dns.out cvode-2.6.0/examples/cvode/serial/cvRoberts_dns_uw.c cvode-2.6.0/examples/cvode/serial/cvRoberts_dns_uw.out cvode-2.6.0/examples/cvode/fcmix_serial/README cvode-2.6.0/examples/cvode/fcmix_serial/Makefile.in cvode-2.6.0/examples/cvode/fcmix_serial/CMakeLists.txt cvode-2.6.0/examples/cvode/fcmix_serial/fcvAdvDiff_bnd.f cvode-2.6.0/examples/cvode/fcmix_serial/fcvAdvDiff_bnd.out cvode-2.6.0/examples/cvode/fcmix_serial/fcvDiurnal_kry_bp.f cvode-2.6.0/examples/cvode/fcmix_serial/fcvDiurnal_kry_bp.out cvode-2.6.0/examples/cvode/fcmix_serial/fcvDiurnal_kry.f cvode-2.6.0/examples/cvode/fcmix_serial/fcvDiurnal_kry.out cvode-2.6.0/examples/cvode/fcmix_serial/fcvRoberts_dns.f cvode-2.6.0/examples/cvode/fcmix_serial/fcvRoberts_dnsL.f cvode-2.6.0/examples/cvode/fcmix_serial/fcvRoberts_dnsL.out cvode-2.6.0/examples/cvode/fcmix_serial/fcvRoberts_dns.out cvode-2.6.0/examples/cvode/parallel/README cvode-2.6.0/examples/cvode/parallel/Makefile.in cvode-2.6.0/examples/cvode/parallel/CMakeLists.txt cvode-2.6.0/examples/cvode/parallel/cvAdvDiff_non_p.c cvode-2.6.0/examples/cvode/parallel/cvAdvDiff_non_p.out cvode-2.6.0/examples/cvode/parallel/cvDiurnal_kry_bbd_p.c cvode-2.6.0/examples/cvode/parallel/cvDiurnal_kry_bbd_p.out cvode-2.6.0/examples/cvode/parallel/cvDiurnal_kry_p.c cvode-2.6.0/examples/cvode/parallel/cvDiurnal_kry_p.out cvode-2.6.0/examples/cvode/fcmix_parallel/README cvode-2.6.0/examples/cvode/fcmix_parallel/Makefile.in cvode-2.6.0/examples/cvode/fcmix_parallel/CMakeLists.txt cvode-2.6.0/examples/cvode/fcmix_parallel/fcvDiag_non_p.f cvode-2.6.0/examples/cvode/fcmix_parallel/fcvDiag_non_p.out cvode-2.6.0/examples/cvode/fcmix_parallel/fcvDiag_kry_bbd_p.f cvode-2.6.0/examples/cvode/fcmix_parallel/fcvDiag_kry_bbd_p.out cvode-2.6.0/examples/cvode/fcmix_parallel/fcvDiag_kry_p.f cvode-2.6.0/examples/cvode/fcmix_parallel/fcvDiag_kry_p.out + tar -xvf bng2/libsource/muparser_v2_2_4.tar.gz -C bng2/Network3 muparser_v2_2_4/._Changes.txt muparser_v2_2_4/Changes.txt muparser_v2_2_4/._Install.txt muparser_v2_2_4/Install.txt muparser_v2_2_4/._License.txt muparser_v2_2_4/License.txt muparser_v2_2_4/._Makefile.in muparser_v2_2_4/Makefile.in muparser_v2_2_4/._build muparser_v2_2_4/build/ muparser_v2_2_4/build/._autoconf muparser_v2_2_4/build/autoconf/ muparser_v2_2_4/build/._bakefiles muparser_v2_2_4/build/bakefiles/ muparser_v2_2_4/build/._makefile.mingw muparser_v2_2_4/build/makefile.mingw muparser_v2_2_4/build/._makefile.vc muparser_v2_2_4/build/makefile.vc muparser_v2_2_4/build/._msvc2013 muparser_v2_2_4/build/msvc2013/ muparser_v2_2_4/build/._obj muparser_v2_2_4/build/obj/ muparser_v2_2_4/build/msvc2013/._muparser.sln muparser_v2_2_4/build/msvc2013/muparser.sln muparser_v2_2_4/build/msvc2013/._muparser_example1.vcxproj muparser_v2_2_4/build/msvc2013/muparser_example1.vcxproj muparser_v2_2_4/build/msvc2013/._muparser_example1.vcxproj.filters muparser_v2_2_4/build/msvc2013/muparser_example1.vcxproj.filters muparser_v2_2_4/build/msvc2013/._muparser_example2.vcxproj muparser_v2_2_4/build/msvc2013/muparser_example2.vcxproj muparser_v2_2_4/build/msvc2013/._muparser_example2.vcxproj.filters muparser_v2_2_4/build/msvc2013/muparser_example2.vcxproj.filters muparser_v2_2_4/build/msvc2013/._muparser_muParser.vcxproj muparser_v2_2_4/build/msvc2013/muparser_muParser.vcxproj muparser_v2_2_4/build/msvc2013/._muparser_muParser.vcxproj.filters muparser_v2_2_4/build/msvc2013/muparser_muParser.vcxproj.filters muparser_v2_2_4/build/bakefiles/._Bakefiles.bkgen muparser_v2_2_4/build/bakefiles/Bakefiles.bkgen muparser_v2_2_4/build/bakefiles/._howto.txt muparser_v2_2_4/build/bakefiles/howto.txt muparser_v2_2_4/build/bakefiles/._muparser.bkl muparser_v2_2_4/build/bakefiles/muparser.bkl muparser_v2_2_4/build/bakefiles/._presets muparser_v2_2_4/build/bakefiles/presets/ muparser_v2_2_4/build/bakefiles/presets/._debugopt.bkl muparser_v2_2_4/build/bakefiles/presets/debugopt.bkl muparser_v2_2_4/build/bakefiles/presets/._setbuilddir.bkl muparser_v2_2_4/build/bakefiles/presets/setbuilddir.bkl muparser_v2_2_4/build/bakefiles/presets/._sharedopt.bkl muparser_v2_2_4/build/bakefiles/presets/sharedopt.bkl muparser_v2_2_4/build/bakefiles/presets/._unicodeopt.bkl muparser_v2_2_4/build/bakefiles/presets/unicodeopt.bkl muparser_v2_2_4/build/autoconf/._aclocal.m4 muparser_v2_2_4/build/autoconf/aclocal.m4 muparser_v2_2_4/build/autoconf/._acregen.sh muparser_v2_2_4/build/autoconf/acregen.sh muparser_v2_2_4/build/autoconf/._autoconf_inc.m4 muparser_v2_2_4/build/autoconf/autoconf_inc.m4 muparser_v2_2_4/build/autoconf/._bakefile-presets.m4 muparser_v2_2_4/build/autoconf/bakefile-presets.m4 muparser_v2_2_4/build/autoconf/._config.guess muparser_v2_2_4/build/autoconf/config.guess muparser_v2_2_4/build/autoconf/._config.sub muparser_v2_2_4/build/autoconf/config.sub muparser_v2_2_4/build/autoconf/._configure.ac muparser_v2_2_4/build/autoconf/configure.ac muparser_v2_2_4/build/autoconf/._install-sh muparser_v2_2_4/build/autoconf/install-sh muparser_v2_2_4/build/autoconf/._muparser.pc.in muparser_v2_2_4/build/autoconf/muparser.pc.in muparser_v2_2_4/._configure muparser_v2_2_4/configure muparser_v2_2_4/._docs muparser_v2_2_4/docs/ muparser_v2_2_4/docs/._Doxyfile muparser_v2_2_4/docs/Doxyfile muparser_v2_2_4/docs/._muparser_doc.html muparser_v2_2_4/docs/muparser_doc.html muparser_v2_2_4/._include muparser_v2_2_4/include/ muparser_v2_2_4/include/._muParser.h muparser_v2_2_4/include/muParser.h muparser_v2_2_4/include/._muParserBase.h muparser_v2_2_4/include/muParserBase.h muparser_v2_2_4/include/._muParserBytecode.h muparser_v2_2_4/include/muParserBytecode.h muparser_v2_2_4/include/._muParserCallback.h muparser_v2_2_4/include/muParserCallback.h muparser_v2_2_4/include/._muParserDef.h muparser_v2_2_4/include/muParserDef.h muparser_v2_2_4/include/._muParserDLL.h muparser_v2_2_4/include/muParserDLL.h muparser_v2_2_4/include/._muParserError.h muparser_v2_2_4/include/muParserError.h muparser_v2_2_4/include/._muParserFixes.h muparser_v2_2_4/include/muParserFixes.h muparser_v2_2_4/include/._muParserInt.h muparser_v2_2_4/include/muParserInt.h muparser_v2_2_4/include/._muParserStack.h muparser_v2_2_4/include/muParserStack.h muparser_v2_2_4/include/._muParserTemplateMagic.h muparser_v2_2_4/include/muParserTemplateMagic.h muparser_v2_2_4/include/._muParserTest.h muparser_v2_2_4/include/muParserTest.h muparser_v2_2_4/include/._muParserToken.h muparser_v2_2_4/include/muParserToken.h muparser_v2_2_4/include/._muParserTokenReader.h muparser_v2_2_4/include/muParserTokenReader.h muparser_v2_2_4/._lib muparser_v2_2_4/lib/ muparser_v2_2_4/lib/._Readme.txt muparser_v2_2_4/lib/Readme.txt muparser_v2_2_4/._samples muparser_v2_2_4/samples/ muparser_v2_2_4/samples/._example1 muparser_v2_2_4/samples/example1/ muparser_v2_2_4/samples/._example2 muparser_v2_2_4/samples/example2/ muparser_v2_2_4/samples/example2/._example2.c muparser_v2_2_4/samples/example2/example2.c muparser_v2_2_4/samples/example2/._muparser32.dll muparser_v2_2_4/samples/example2/muparser32.dll muparser_v2_2_4/samples/example2/._muparser32.lib muparser_v2_2_4/samples/example2/muparser32.lib muparser_v2_2_4/samples/example2/._muparser64.dll muparser_v2_2_4/samples/example2/muparser64.dll muparser_v2_2_4/samples/example2/._muparser64.lib muparser_v2_2_4/samples/example2/muparser64.lib muparser_v2_2_4/samples/example2/._muparserd32.dll muparser_v2_2_4/samples/example2/muparserd32.dll muparser_v2_2_4/samples/example2/._muparserd32.lib muparser_v2_2_4/samples/example2/muparserd32.lib muparser_v2_2_4/samples/example2/._muparserd64.dll muparser_v2_2_4/samples/example2/muparserd64.dll muparser_v2_2_4/samples/example2/._muparserd64.lib muparser_v2_2_4/samples/example2/muparserd64.lib muparser_v2_2_4/samples/example2/._Readme.txt muparser_v2_2_4/samples/example2/Readme.txt muparser_v2_2_4/samples/example1/._example1.cpp muparser_v2_2_4/samples/example1/example1.cpp muparser_v2_2_4/._src muparser_v2_2_4/src/ muparser_v2_2_4/src/._muParser.cpp muparser_v2_2_4/src/muParser.cpp muparser_v2_2_4/src/._muParserBase.cpp muparser_v2_2_4/src/muParserBase.cpp muparser_v2_2_4/src/._muParserBytecode.cpp muparser_v2_2_4/src/muParserBytecode.cpp muparser_v2_2_4/src/._muParserCallback.cpp muparser_v2_2_4/src/muParserCallback.cpp muparser_v2_2_4/src/._muParserDLL.cpp muparser_v2_2_4/src/muParserDLL.cpp muparser_v2_2_4/src/._muParserError.cpp muparser_v2_2_4/src/muParserError.cpp muparser_v2_2_4/src/._muParserInt.cpp muparser_v2_2_4/src/muParserInt.cpp muparser_v2_2_4/src/._muParserTest.cpp muparser_v2_2_4/src/muParserTest.cpp muparser_v2_2_4/src/._muParserTokenReader.cpp muparser_v2_2_4/src/muParserTokenReader.cpp Patch #0 (bionetgen-fix_linker.patch): + echo 'Patch #0 (bionetgen-fix_linker.patch):' + /usr/bin/patch --no-backup-if-mismatch -f -p1 -b --suffix .backup --fuzz=0 patching file bng2/Network3/CMakeLists.txt Patch #1 (bionetgen-fix_cmake_minimum.patch): + echo 'Patch #1 (bionetgen-fix_cmake_minimum.patch):' + /usr/bin/patch --no-backup-if-mismatch -f -p1 -b --suffix .backup --fuzz=0 patching file bng2/Network3/CMakeLists.txt patching file bng2/Network3/cvode-2.6.0/CMakeLists.txt Patch #2 (bionetgen-cmake-c99.patch): + echo 'Patch #2 (bionetgen-cmake-c99.patch):' + /usr/bin/patch --no-backup-if-mismatch -f -p1 -b --suffix .c99 --fuzz=0 patching file bng2/Network3/cvode-2.6.0/config/SundialsFortran.cmake + rm -f bng2/libsource/cvode-2.6.0.tar.gz bng2/libsource/muparser_v2_2_4.tar.gz + popd ~/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0 + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.Q1Qmjn + umask 022 + cd /builddir/build/BUILD/bionetgen-2.9.0-build + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd bionetgen-2.9.0 + pushd bionetgen-BioNetGen-2.9.0/bng2/Network3 ~/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3 ~/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0 + cd muparser_v2_2_4 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + '[' '-flto=auto -ffat-lto-objectsx' '!=' x ']' ++ find . -type f -name configure -print + for file in $(find . -type f -name configure -print) + /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\) = /__attribute__ ((used)) char (*f) () = /g' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\);/__attribute__ ((used)) char (*f) ();/g' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed -r --in-place=.backup 's/^char \$2 \(\);/__attribute__ ((used)) char \$2 ();/g' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed --in-place=.backup '1{$!N;$!N};$!N;s/int x = 1;\nint y = 0;\nint z;\nint nan;/volatile int x = 1; volatile int y = 0; volatile int z, nan;/;P;D' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed --in-place=.backup 's#^lt_cv_sys_global_symbol_to_cdecl=.*#lt_cv_sys_global_symbol_to_cdecl="sed -n -e '\''s/^T .* \\(.*\\)$/extern int \\1();/p'\'' -e '\''s/^$symcode* .* \\(.*\\)$/extern char \\1;/p'\''"#' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + '[' 1 = 1 ']' +++ dirname ./configure ++ find . -name config.guess -o -name config.sub + for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub) ++ basename ./build/autoconf/config.guess + '[' -f /usr/lib/rpm/redhat/config.guess ']' + /usr/bin/rm -f ./build/autoconf/config.guess ++ basename ./build/autoconf/config.guess + /usr/bin/cp -fv /usr/lib/rpm/redhat/config.guess ./build/autoconf/config.guess '/usr/lib/rpm/redhat/config.guess' -> './build/autoconf/config.guess' + for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub) ++ basename ./build/autoconf/config.sub + '[' -f /usr/lib/rpm/redhat/config.sub ']' + /usr/bin/rm -f ./build/autoconf/config.sub ++ basename ./build/autoconf/config.sub + /usr/bin/cp -fv /usr/lib/rpm/redhat/config.sub ./build/autoconf/config.sub '/usr/lib/rpm/redhat/config.sub' -> './build/autoconf/config.sub' + '[' 1 = 1 ']' + '[' x '!=' 'x-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' ']' ++ find . -name ltmain.sh ++ grep -q runstatedir=DIR ./configure + ./configure --build=x86_64-redhat-linux --host=x86_64-redhat-linux --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/libexec --localstatedir=/var --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared=no --enable-static=yes --enable-samples=no configure: WARNING: unrecognized options: --enable-static checking build system type... x86_64-redhat-linux-gnu checking host system type... x86_64-redhat-linux-gnu checking target system type... x86_64-redhat-linux-gnu checking for gawk... gawk checking for a BSD-compatible install... /usr/bin/install -c checking whether ln -s works... yes checking for x86_64-redhat-linux-ranlib... no checking for ranlib... ranlib checking for x86_64-redhat-linux-gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking how to run the C++ preprocessor... g++ -E checking for the --enable-debug option... no checking for the --enable-shared option... no checking for the --enable-samples option... no checking whether we are using the Intel C compiler... no checking whether we are using the Intel C++ compiler... no checking whether we are using the Sun C++ compiler... no checking for x86_64-redhat-linux-ranlib... ranlib checking whether ln -s works... yes checking whether make sets $(MAKE)... yes checking for x86_64-redhat-linux-ar... no checking for ar... ar checking for x86_64-redhat-linux-strip... no checking for strip... strip checking for x86_64-redhat-linux-nm... no checking for nm... nm checking for command to install directories... /usr/bin/install -c -d checking if make is GNU make... egrep: warning: egrep is obsolescent; using grep -E yes checking for dependency tracking method... disabled configure: creating ./config.status config.status: creating Makefile config.status: creating build/autoconf/muparser.pc ---------------------------------------------------------------- Configuration for muparser 2.2.4 successfully completed. Summary of main configuration settings for muparser: - STATIC mode - RELEASE build configure: WARNING: unrecognized options: --enable-static - SAMPLES disabled Now, just run make. ---------------------------------------------------------------- + /usr/bin/make -O -j4 V=1 VERBOSE=1 g++ -c -o muParser_lib_muParserCallback.o -DNDEBUG -I./include -O2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ./src/muParserCallback.cpp g++ -c -o muParser_lib_muParserDLL.o -DNDEBUG -I./include -O2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ./src/muParserDLL.cpp g++ -c -o muParser_lib_muParser.o -DNDEBUG -I./include -O2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ./src/muParser.cpp In file included from ./include/muParserStack.h:35, from ./include/muParserBase.h:39, from ./include/muParser.h:32, from ./src/muParser.cpp:26: ./include/muParserToken.h:72:12: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 72 | std::auto_ptr m_pCallback; | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from ./include/muParserBase.h:33: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./include/muParserBase.h:291:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 291 | std::auto_ptr m_pTokenReader; ///< Managed pointer to the token reader object. | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ g++ -c -o muParser_lib_muParserBytecode.o -DNDEBUG -I./include -O2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ./src/muParserBytecode.cpp In file included from ./include/muParserBytecode.h:35, from ./src/muParserBytecode.cpp:26: ./include/muParserToken.h:72:12: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 72 | std::auto_ptr m_pCallback; | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from ./include/muParserError.h:34, from ./include/muParserBytecode.h:34: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./src/muParserBytecode.cpp: In member function ‘void mu::ParserByteCode::AddOp(mu::ECmdCode)’: ./src/muParserBytecode.cpp:213:15: warning: enumeration value ‘cmLE’ not handled in switch [-Wswitch] 213 | switch(a_Oprt) | ^ ./src/muParserBytecode.cpp:213:15: warning: enumeration value ‘cmGE’ not handled in switch [-Wswitch] ./src/muParserBytecode.cpp:213:15: warning: enumeration value ‘cmNEQ’ not handled in switch [-Wswitch] ./src/muParserBytecode.cpp:213:15: warning: enumeration value ‘cmEQ’ not handled in switch [-Wswitch] ./src/muParserBytecode.cpp:213:15: warning: enumeration value ‘cmLT’ not handled in switch [-Wswitch] ./src/muParserBytecode.cpp:213:15: warning: enumeration value ‘cmGT’ not handled in switch [-Wswitch] ./src/muParserBytecode.cpp:213:15: warning: enumeration value ‘cmLAND’ not handled in switch [-Wswitch] ./src/muParserBytecode.cpp:213:15: warning: enumeration value ‘cmLOR’ not handled in switch [-Wswitch] ./src/muParserBytecode.cpp:213:15: warning: enumeration value ‘cmASSIGN’ not handled in switch [-Wswitch] ./src/muParserBytecode.cpp:213:15: warning: enumeration value ‘cmBO’ not handled in switch [-Wswitch] ./src/muParserBytecode.cpp:213:15: warning: enumeration value ‘cmBC’ not handled in switch [-Wswitch] ./src/muParserBytecode.cpp:213:15: warning: enumeration value ‘cmIF’ not handled in switch [-Wswitch] ./src/muParserBytecode.cpp:213:15: warning: enumeration value ‘cmELSE’ not handled in switch [-Wswitch] ./src/muParserBytecode.cpp:213:15: warning: enumeration value ‘cmENDIF’ not handled in switch [-Wswitch] ./src/muParserBytecode.cpp:213:15: warning: enumeration value ‘cmARG_SEP’ not handled in switch [-Wswitch] ./src/muParserBytecode.cpp:213:15: warning: enumeration value ‘cmVAR’ not handled in switch [-Wswitch] ./src/muParserBytecode.cpp:213:15: warning: enumeration value ‘cmVAL’ not handled in switch [-Wswitch] ./src/muParserBytecode.cpp:213:15: warning: enumeration value ‘cmVARPOW2’ not handled in switch [-Wswitch] ./src/muParserBytecode.cpp:213:15: warning: enumeration value ‘cmVARPOW3’ not handled in switch [-Wswitch] ./src/muParserBytecode.cpp:213:15: warning: enumeration value ‘cmVARPOW4’ not handled in switch [-Wswitch] ./src/muParserBytecode.cpp:213:15: warning: enumeration value ‘cmVARMUL’ not handled in switch [-Wswitch] ./src/muParserBytecode.cpp:213:15: warning: enumeration value ‘cmPOW2’ not handled in switch [-Wswitch] ./src/muParserBytecode.cpp:213:15: warning: enumeration value ‘cmFUNC’ not handled in switch [-Wswitch] ./src/muParserBytecode.cpp:213:15: warning: enumeration value ‘cmFUNC_STR’ not handled in switch [-Wswitch] ./src/muParserBytecode.cpp:213:15: warning: enumeration value ‘cmFUNC_BULK’ not handled in switch [-Wswitch] ./src/muParserBytecode.cpp:213:15: warning: enumeration value ‘cmSTRING’ not handled in switch [-Wswitch] ./src/muParserBytecode.cpp:213:15: warning: enumeration value ‘cmOPRT_BIN’ not handled in switch [-Wswitch] ./src/muParserBytecode.cpp:213:15: warning: enumeration value ‘cmOPRT_POSTFIX’ not handled in switch [-Wswitch] ./src/muParserBytecode.cpp:213:15: warning: enumeration value ‘cmOPRT_INFIX’ not handled in switch [-Wswitch] ./src/muParserBytecode.cpp:213:15: warning: enumeration value ‘cmEND’ not handled in switch [-Wswitch] ./src/muParserBytecode.cpp:213:15: warning: enumeration value ‘cmUNKNOWN’ not handled in switch [-Wswitch] g++ -c -o muParser_lib_muParserError.o -DNDEBUG -I./include -O2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ./src/muParserError.cpp g++ -c -o muParser_lib_muParserInt.o -DNDEBUG -I./include -O2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ./src/muParserInt.cpp In file included from ./include/muParserStack.h:35, from ./include/muParserBase.h:39, from ./include/muParserInt.h:29, from ./src/muParserInt.cpp:26: ./include/muParserToken.h:72:12: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 72 | std::auto_ptr m_pCallback; | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from ./include/muParserBase.h:33: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./include/muParserBase.h:291:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 291 | std::auto_ptr m_pTokenReader; ///< Managed pointer to the token reader object. | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ g++ -c -o muParser_lib_muParserTokenReader.o -DNDEBUG -I./include -O2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ./src/muParserTokenReader.cpp In file included from ./include/muParserTokenReader.h:39, from ./src/muParserTokenReader.cpp:32: ./include/muParserToken.h:72:12: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 72 | std::auto_ptr m_pCallback; | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from ./include/muParserTokenReader.h:34: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from ./src/muParserTokenReader.cpp:33: ./include/muParserBase.h:291:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 291 | std::auto_ptr m_pTokenReader; ///< Managed pointer to the token reader object. | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./src/muParserTokenReader.cpp: In member function ‘mu::ParserTokenReader* mu::ParserTokenReader::Clone(mu::ParserBase*) const’: ./src/muParserTokenReader.cpp:150:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 150 | std::auto_ptr ptr(new ParserTokenReader(*this)); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ g++ -c -o muParser_lib_muParserBase.o -DNDEBUG -I./include -O2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ./src/muParserBase.cpp In file included from ./include/muParserStack.h:35, from ./include/muParserBase.h:39, from ./src/muParserBase.cpp:26: ./include/muParserToken.h:72:12: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 72 | std::auto_ptr m_pCallback; | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from ./include/muParserBase.h:33: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./include/muParserBase.h:291:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 291 | std::auto_ptr m_pTokenReader; ///< Managed pointer to the token reader object. | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./src/muParserBase.cpp: In member function ‘void mu::ParserBase::ApplyFunc(mu::ParserStack > >&, mu::ParserStack > >&, int) const’: ./src/muParserBase.cpp:838:11: warning: enumeration value ‘cmLE’ not handled in switch [-Wswitch] 838 | switch(funTok.GetCode()) | ^ ./src/muParserBase.cpp:838:11: warning: enumeration value ‘cmGE’ not handled in switch [-Wswitch] ./src/muParserBase.cpp:838:11: warning: enumeration value ‘cmNEQ’ not handled in switch [-Wswitch] ./src/muParserBase.cpp:838:11: warning: enumeration value ‘cmEQ’ not handled in switch [-Wswitch] ./src/muParserBase.cpp:838:11: warning: enumeration value ‘cmLT’ not handled in switch [-Wswitch] ./src/muParserBase.cpp:838:11: warning: enumeration value ‘cmGT’ not handled in switch [-Wswitch] ./src/muParserBase.cpp:838:11: warning: enumeration value ‘cmADD’ not handled in switch [-Wswitch] ./src/muParserBase.cpp:838:11: warning: enumeration value ‘cmSUB’ not handled in switch [-Wswitch] ./src/muParserBase.cpp:838:11: warning: enumeration value ‘cmMUL’ not handled in switch [-Wswitch] ./src/muParserBase.cpp:838:11: warning: enumeration value ‘cmDIV’ not handled in switch [-Wswitch] ./src/muParserBase.cpp:838:11: warning: enumeration value ‘cmPOW’ not handled in switch [-Wswitch] ./src/muParserBase.cpp:838:11: warning: enumeration value ‘cmLAND’ not handled in switch [-Wswitch] ./src/muParserBase.cpp:838:11: warning: enumeration value ‘cmLOR’ not handled in switch [-Wswitch] ./src/muParserBase.cpp:838:11: warning: enumeration value ‘cmASSIGN’ not handled in switch [-Wswitch] ./src/muParserBase.cpp:838:11: warning: enumeration value ‘cmBO’ not handled in switch [-Wswitch] ./src/muParserBase.cpp:838:11: warning: enumeration value ‘cmBC’ not handled in switch [-Wswitch] ./src/muParserBase.cpp:838:11: warning: enumeration value ‘cmIF’ not handled in switch [-Wswitch] ./src/muParserBase.cpp:838:11: warning: enumeration value ‘cmELSE’ not handled in switch [-Wswitch] ./src/muParserBase.cpp:838:11: warning: enumeration value ‘cmENDIF’ not handled in switch [-Wswitch] ./src/muParserBase.cpp:838:11: warning: enumeration value ‘cmARG_SEP’ not handled in switch [-Wswitch] ./src/muParserBase.cpp:838:11: warning: enumeration value ‘cmVAR’ not handled in switch [-Wswitch] ./src/muParserBase.cpp:838:11: warning: enumeration value ‘cmVAL’ not handled in switch [-Wswitch] ./src/muParserBase.cpp:838:11: warning: enumeration value ‘cmVARPOW2’ not handled in switch [-Wswitch] ./src/muParserBase.cpp:838:11: warning: enumeration value ‘cmVARPOW3’ not handled in switch [-Wswitch] ./src/muParserBase.cpp:838:11: warning: enumeration value ‘cmVARPOW4’ not handled in switch [-Wswitch] ./src/muParserBase.cpp:838:11: warning: enumeration value ‘cmVARMUL’ not handled in switch [-Wswitch] ./src/muParserBase.cpp:838:11: warning: enumeration value ‘cmPOW2’ not handled in switch [-Wswitch] ./src/muParserBase.cpp:838:11: warning: enumeration value ‘cmSTRING’ not handled in switch [-Wswitch] ./src/muParserBase.cpp:838:11: warning: enumeration value ‘cmEND’ not handled in switch [-Wswitch] ./src/muParserBase.cpp:838:11: warning: enumeration value ‘cmUNKNOWN’ not handled in switch [-Wswitch] g++ -c -o muParser_lib_muParserTest.o -DNDEBUG -I./include -O2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ./src/muParserTest.cpp ./src/muParserTest.cpp:1387: warning: ignoring ‘#pragma warning ’ [-Wunknown-pragmas] 1387 | #pragma warning(push) ./src/muParserTest.cpp:1388: warning: ignoring ‘#pragma warning ’ [-Wunknown-pragmas] 1388 | #pragma warning(disable:4127) ./src/muParserTest.cpp:1390: warning: ignoring ‘#pragma warning ’ [-Wunknown-pragmas] 1390 | #pragma warning(pop) In file included from ./include/muParserStack.h:35, from ./include/muParserBase.h:39, from ./include/muParser.h:32, from ./include/muParserTest.h:32, from ./src/muParserTest.cpp:26: ./include/muParserToken.h:72:12: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 72 | std::auto_ptr m_pCallback; | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from ./include/muParserBase.h:33: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./include/muParserBase.h:291:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 291 | std::auto_ptr m_pTokenReader; ///< Managed pointer to the token reader object. | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ./src/muParserTest.cpp: In member function ‘int mu::Test::ParserTester::EqnTest(const mu::string_type&, double, bool)’: ./src/muParserTest.cpp:1261:14: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1261 | std::auto_ptr p1; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ rm -f lib/libmuparser.a ar rcu lib/libmuparser.a muParser_lib_muParser.o muParser_lib_muParserBase.o muParser_lib_muParserBytecode.o muParser_lib_muParserCallback.o muParser_lib_muParserDLL.o muParser_lib_muParserError.o muParser_lib_muParserInt.o muParser_lib_muParserTest.o muParser_lib_muParserTokenReader.o ranlib lib/libmuparser.a + cd ../ + make -j1 -C src/util/mathutils make: Entering directory '/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util/mathutils' gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o allocate.o allocate.c allocate.c: In function ‘ALLOC_MATRIX’: allocate.c:9:20: warning: unused variable ‘j’ [-Wunused-variable] 9 | register int i,j; | ^ allocate.c: In function ‘IALLOC_MATRIX’: allocate.c:100:20: warning: unused variable ‘j’ [-Wunused-variable] 100 | register int i,j; | ^ allocate.c: In function ‘ZALLOC_MATRIX’: allocate.c:191:20: warning: unused variable ‘j’ [-Wunused-variable] 191 | register int i,j; | ^ In file included from allocate.c:1: mathutils.h: At top level: mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: ‘marg2’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: ‘marg1’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar -rv libmathutils.a allocate.o ar: creating libmathutils.a a - allocate.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o cabs.o cabs.c In file included from cabs.c:1: mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: ‘marg2’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: ‘marg1’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar -rv libmathutils.a cabs.o a - cabs.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o cadd.o cadd.c In file included from cadd.c:1: mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: ‘marg2’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: ‘marg1’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar -rv libmathutils.a cadd.o a - cadd.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o cconj.o cconj.c In file included from cconj.c:1: mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: ‘marg2’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: ‘marg1’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar -rv libmathutils.a cconj.o a - cconj.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o cmult.o cmult.c In file included from cmult.c:1: mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: ‘marg2’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: ‘marg1’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar -rv libmathutils.a cmult.o a - cmult.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o complex_zero.o complex_zero.c In file included from complex_zero.c:2: mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: ‘marg2’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: ‘marg1’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar -rv libmathutils.a complex_zero.o a - complex_zero.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o copy_vector.o copy_vector.c In file included from copy_vector.c:1: mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: ‘marg2’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: ‘marg1’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar -rv libmathutils.a copy_vector.o a - copy_vector.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o cprob.o cprob.c In file included from cprob.c:1: mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: ‘marg2’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: ‘marg1’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar -rv libmathutils.a cprob.o a - cprob.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o csub.o csub.c In file included from csub.c:1: mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: ‘marg2’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: ‘marg1’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar -rv libmathutils.a csub.o a - csub.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o dotp.o dotp.c In file included from dotp.c:1: mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: ‘marg2’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: ‘marg1’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar -rv libmathutils.a dotp.o a - dotp.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o eigensystem.o eigensystem.c In file included from eigensystem.c:1: mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: ‘marg2’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: ‘marg1’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar -rv libmathutils.a eigensystem.o a - eigensystem.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o expi.o expi.c In file included from expi.c:1: mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: ‘marg2’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: ‘marg1’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar -rv libmathutils.a expi.o a - expi.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o gram_schmidt.o gram_schmidt.c In file included from gram_schmidt.c:1: mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: ‘marg2’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: ‘marg1’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar -rv libmathutils.a gram_schmidt.o a - gram_schmidt.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o herm_matrix_mult.o herm_matrix_mult.c In file included from herm_matrix_mult.c:1: mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: ‘marg2’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: ‘marg1’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar -rv libmathutils.a herm_matrix_mult.o a - herm_matrix_mult.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o herm_matrix_vector_mult.o herm_matrix_vector_mult.c In file included from herm_matrix_vector_mult.c:1: mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: ‘marg2’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: ‘marg1’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar -rv libmathutils.a herm_matrix_vector_mult.o a - herm_matrix_vector_mult.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o icmult.o icmult.c In file included from icmult.c:1: mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: ‘marg2’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: ‘marg1’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar -rv libmathutils.a icmult.o a - icmult.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o init.o init.c In file included from init.c:1: mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: ‘marg2’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: ‘marg1’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar -rv libmathutils.a init.o a - init.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o integration.o integration.c In file included from integration.c:1: mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: ‘marg2’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: ‘marg1’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar -rv libmathutils.a integration.o a - integration.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o linsolve.o linsolve.c linsolve.c: In function ‘LINSOLVE’: linsolve.c:16:20: warning: unused variable ‘j’ [-Wunused-variable] 16 | register int i,j; | ^ linsolve.c:16:18: warning: unused variable ‘i’ [-Wunused-variable] 16 | register int i,j; | ^ In file included from linsolve.c:1: mathutils.h: At top level: mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: ‘marg2’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: ‘marg1’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar -rv libmathutils.a linsolve.o a - linsolve.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o matherr.o matherr.c In file included from matherr.c:1: mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: ‘marg2’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: ‘marg1’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar -rv libmathutils.a matherr.o a - matherr.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o matrix_add.o matrix_add.c In file included from matrix_add.c:1: mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: ‘marg2’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: ‘marg1’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar -rv libmathutils.a matrix_add.o a - matrix_add.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o matrix_elt.o matrix_elt.c In file included from matrix_elt.c:1: mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: ‘marg2’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: ‘marg1’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar -rv libmathutils.a matrix_elt.o a - matrix_elt.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o matrix_mult.o matrix_mult.c In file included from matrix_mult.c:1: mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: ‘marg2’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: ‘marg1’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar -rv libmathutils.a matrix_mult.o a - matrix_mult.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o matrix_sub.o matrix_sub.c In file included from matrix_sub.c:1: mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: ‘marg2’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: ‘marg1’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar -rv libmathutils.a matrix_sub.o a - matrix_sub.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o matrix_transpose.o matrix_transpose.c In file included from matrix_transpose.c:1: mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: ‘marg2’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: ‘marg1’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar -rv libmathutils.a matrix_transpose.o a - matrix_transpose.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o matrix_vector_mult.o matrix_vector_mult.c In file included from matrix_vector_mult.c:1: mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: ‘marg2’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: ‘marg1’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar -rv libmathutils.a matrix_vector_mult.o a - matrix_vector_mult.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o matrixexp.o matrixexp.c In file included from matrixexp.c:5: mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: ‘marg2’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: ‘marg1’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar -rv libmathutils.a matrixexp.o a - matrixexp.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o minimum.o minimum.c minimum.c: In function ‘MIN_BRACKET’: minimum.c:17:26: warning: unused variable ‘dum’ [-Wunused-variable] 17 | double ulim,u,r,q,fu,dum; | ^~~ In file included from minimum.c:3: mathutils.h: At top level: mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar -rv libmathutils.a minimum.o a - minimum.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o norm.o norm.c norm.c: In function ‘NORM’: norm.c:14:12: warning: unused variable ‘norm’ [-Wunused-variable] 14 | double norm; | ^~~~ In file included from norm.c:1: mathutils.h: At top level: mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: ‘marg2’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: ‘marg1’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar -rv libmathutils.a norm.o a - norm.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o normsq.o normsq.c normsq.c: In function ‘NORMSQ’: normsq.c:13:12: warning: unused variable ‘norm’ [-Wunused-variable] 13 | double norm; | ^~~~ In file included from normsq.c:1: mathutils.h: At top level: mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: ‘marg2’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: ‘marg1’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar -rv libmathutils.a normsq.o a - normsq.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o project.o project.c In file included from project.c:1: mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: ‘marg2’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: ‘marg1’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar -rv libmathutils.a project.o a - project.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o random.o random.c In file included from random.c:1: mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: ‘marg2’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: ‘marg1’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar -rv libmathutils.a random.o a - random.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o rcmult.o rcmult.c In file included from rcmult.c:1: mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: ‘marg2’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: ‘marg1’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar -rv libmathutils.a rcmult.o a - rcmult.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o rect_transpose.o rect_transpose.c rect_transpose.c: In function ‘RECT_TRANSPOSE’: rect_transpose.c:5:26: warning: unused variable ‘Atptr’ [-Wunused-variable] 5 | double **At, *Aptr, *Atptr; | ^~~~~ rect_transpose.c:5:19: warning: unused variable ‘Aptr’ [-Wunused-variable] 5 | double **At, *Aptr, *Atptr; | ^~~~ In file included from rect_transpose.c:1: mathutils.h: At top level: mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: ‘marg2’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: ‘marg1’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar -rv libmathutils.a rect_transpose.o a - rect_transpose.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o roots.o roots.c In file included from roots.c:1: mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: ‘marg2’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: ‘marg1’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ roots.c: In function ‘ROOT_FIND’: roots.c:55:13: warning: ‘e’ may be used uninitialized [-Wmaybe-uninitialized] 55 | if (fabs(e) >= tol1 && fabs(fa) > fabs(fb)) { | ^~~~~~~ roots.c:32:29: note: ‘e’ was declared here 32 | double a=x1,b=x2,c=x2,d,e,min1,min2; | ^ ar -rv libmathutils.a roots.o a - roots.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o runge-kutta.o runge-kutta.c In file included from runge-kutta.c:1: mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar -rv libmathutils.a runge-kutta.o a - runge-kutta.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o scale_vector.o scale_vector.c In file included from scale_vector.c:1: mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: ‘marg2’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: ‘marg1’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar -rv libmathutils.a scale_vector.o a - scale_vector.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o splines.o splines.c In file included from splines.c:1: mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: ‘marg2’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: ‘marg1’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar -rv libmathutils.a splines.o a - splines.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o sum_vector.o sum_vector.c In file included from sum_vector.c:1: mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: ‘marg2’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: ‘marg1’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar -rv libmathutils.a sum_vector.o a - sum_vector.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o svd.o svd.c In file included from svd.c:2: mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ ar -rv libmathutils.a svd.o a - svd.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o sym_linsolve.o sym_linsolve.c In file included from sym_linsolve.c:1: mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: ‘marg2’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: ‘marg1’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar -rv libmathutils.a sym_linsolve.o a - sym_linsolve.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o sym_matrix_mult.o sym_matrix_mult.c In file included from sym_matrix_mult.c:1: mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: ‘marg2’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: ‘marg1’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar -rv libmathutils.a sym_matrix_mult.o a - sym_matrix_mult.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o sym_matrix_vector_mult.o sym_matrix_vector_mult.c In file included from sym_matrix_vector_mult.c:1: mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: ‘marg2’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: ‘marg1’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar -rv libmathutils.a sym_matrix_vector_mult.o a - sym_matrix_vector_mult.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o sympos_linsolve.o sympos_linsolve.c In file included from sympos_linsolve.c:1: mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: ‘marg2’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: ‘marg1’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar -rv libmathutils.a sympos_linsolve.o a - sympos_linsolve.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o vector_add.o vector_add.c In file included from vector_add.c:1: mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: ‘marg2’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: ‘marg1’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar -rv libmathutils.a vector_add.o a - vector_add.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o vector_dist.o vector_dist.c In file included from vector_dist.c:1: mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: ‘marg2’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: ‘marg1’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar -rv libmathutils.a vector_dist.o a - vector_dist.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o zcopy_vector.o zcopy_vector.c In file included from zcopy_vector.c:1: mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: ‘marg2’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: ‘marg1’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar -rv libmathutils.a zcopy_vector.o a - zcopy_vector.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o zdotc.o zdotc.c In file included from zdotc.c:1: mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: ‘marg2’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: ‘marg1’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar -rv libmathutils.a zdotc.o a - zdotc.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o zdotu.o zdotu.c In file included from zdotu.c:1: mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: ‘marg2’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: ‘marg1’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar -rv libmathutils.a zdotu.o a - zdotu.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o zmatrix_mult.o zmatrix_mult.c In file included from zmatrix_mult.c:1: mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: ‘marg2’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: ‘marg1’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar -rv libmathutils.a zmatrix_mult.o a - zmatrix_mult.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o zmatrix_transpose.o zmatrix_transpose.c In file included from zmatrix_transpose.c:1: mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: ‘marg2’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: ‘marg1’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar -rv libmathutils.a zmatrix_transpose.o a - zmatrix_transpose.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o zmatrix_vector_mult.o zmatrix_vector_mult.c In file included from zmatrix_vector_mult.c:1: mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: ‘marg2’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: ‘marg1’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar -rv libmathutils.a zmatrix_vector_mult.o a - zmatrix_vector_mult.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o znorm.o znorm.c In file included from znorm.c:1: mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: ‘marg2’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: ‘marg1’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar -rv libmathutils.a znorm.o a - znorm.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o znormsq.o znormsq.c In file included from znormsq.c:1: mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: ‘marg2’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: ‘marg1’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar -rv libmathutils.a znormsq.o a - znormsq.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o zrscale_vector.o zrscale_vector.c In file included from zrscale_vector.c:1: mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: ‘marg2’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: ‘marg1’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar -rv libmathutils.a zrscale_vector.o a - zrscale_vector.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o zscale_vector.o zscale_vector.c In file included from zscale_vector.c:1: mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: ‘marg2’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: ‘marg1’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar -rv libmathutils.a zscale_vector.o a - zscale_vector.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o zsum_vector.o zsum_vector.c In file included from zsum_vector.c:1: mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: ‘marg2’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: ‘marg1’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar -rv libmathutils.a zsum_vector.o a - zsum_vector.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o zsym_linsolve.o zsym_linsolve.c In file included from zsym_linsolve.c:1: mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: ‘marg2’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: ‘marg1’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar -rv libmathutils.a zsym_linsolve.o a - zsym_linsolve.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o zmatrix_add.o zmatrix_add.c In file included from zmatrix_add.c:1: mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: ‘marg2’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: ‘marg1’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar -rv libmathutils.a zmatrix_add.o a - zmatrix_add.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c -o zmatrix_sub.o zmatrix_sub.c In file included from zmatrix_sub.c:1: mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: ‘marg2’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: ‘marg1’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar -rv libmathutils.a zmatrix_sub.o a - zmatrix_sub.o ranlib ./libmathutils.a make: Leaving directory '/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util/mathutils' ++ echo '-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer' ++ sed -e s/-Werror=format-security/-Wno-error=format-security/g + SETOPT_FLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer' + export 'CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer' + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer' + mkdir -p cvode-2.6.0/build + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + /usr/bin/cmake -S . -B cvode-2.6.0/build -DCMAKE_C_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_Fortran_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_INSTALL_DO_STRIP:BOOL=OFF -DCMAKE_INSTALL_PREFIX:PATH=/usr -DINCLUDE_INSTALL_DIR:PATH=/usr/include -DLIB_INSTALL_DIR:PATH=/usr/lib64 -DSYSCONF_INSTALL_DIR:PATH=/etc -DSHARE_INSTALL_PREFIX:PATH=/usr/share -DLIB_SUFFIX=64 -DBUILD_SHARED_LIBS:BOOL=ON -S cvode-2.6.0 -B cvode-2.6.0/build '-DCMAKE_MODULE_LINKER_FLAGS:STRING=-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' -DCMAKE_INSTALL_PREFIX=/usr -DEXAMPLES_ENABLE=OFF -DEXAMPLES_INSTALL=OFF -DBUILD_SHARED_LIBS:BOOL=OFF -DBUILD_STATIC_LIBS:BOOL=ON -DMPI_ENABLE:BOOL=OFF -DFCMIX_ENABLE:BOOL=ON CMake Warning: Ignoring extra path from command line: "/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3" -- The C compiler identification is GNU 14.2.1 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- The Fortran compiler identification is GNU 14.2.1 -- Searching for a Fortran compiler... /usr/bin/gfortran CMake Warning (dev) at /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/FortranTest/CMakeLists.txt:1 (PROJECT): cmake_minimum_required() should be called prior to this top-level project() call. Please see the cmake-commands(7) manual for usage documentation of both commands. This warning is for project developers. Use -Wno-dev to suppress it. -- Trying to compile and link a simple Fortran program... OK CMake Warning (dev) at /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/FortranTest/CMakeLists.txt:1 (PROJECT): cmake_minimum_required() should be called prior to this top-level project() call. Please see the cmake-commands(7) manual for usage documentation of both commands. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) in /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/FortranTest/CMakeLists.txt: No cmake_minimum_required command is present. A line of code such as cmake_minimum_required(VERSION 3.31) should be added at the top of the file. The version specified may be lower if you wish to support older CMake versions for this project. For more information run "cmake --help-policy CMP0000". This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/FortranTest/CMakeLists.txt:1 (PROJECT): cmake_minimum_required() should be called prior to this top-level project() call. Please see the cmake-commands(7) manual for usage documentation of both commands. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) in /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/FortranTest/CMakeLists.txt: No cmake_minimum_required command is present. A line of code such as cmake_minimum_required(VERSION 3.31) should be added at the top of the file. The version specified may be lower if you wish to support older CMake versions for this project. For more information run "cmake --help-policy CMP0000". This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/FortranTest/CMakeLists.txt:1 (PROJECT): cmake_minimum_required() should be called prior to this top-level project() call. Please see the cmake-commands(7) manual for usage documentation of both commands. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) in /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/FortranTest/CMakeLists.txt: No cmake_minimum_required command is present. A line of code such as cmake_minimum_required(VERSION 3.31) should be added at the top of the file. The version specified may be lower if you wish to support older CMake versions for this project. For more information run "cmake --help-policy CMP0000". This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/FortranTest/CMakeLists.txt:1 (PROJECT): cmake_minimum_required() should be called prior to this top-level project() call. Please see the cmake-commands(7) manual for usage documentation of both commands. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) in /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/FortranTest/CMakeLists.txt: No cmake_minimum_required command is present. A line of code such as cmake_minimum_required(VERSION 3.31) should be added at the top of the file. The version specified may be lower if you wish to support older CMake versions for this project. For more information run "cmake --help-policy CMP0000". This warning is for project developers. Use -Wno-dev to suppress it. -- Determining Fortran name-mangling scheme... OK -- Added NVECTOR_SERIAL module -- Added CVODE module -- Added CVODE FCMIX module -- Configuring done (1.1s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_CXX_FLAGS_RELEASE CMAKE_INSTALL_DO_STRIP CMAKE_MODULE_LINKER_FLAGS INCLUDE_INSTALL_DIR LIB_INSTALL_DIR LIB_SUFFIX SHARE_INSTALL_PREFIX SYSCONF_INSTALL_DIR -- Build files have been written to: /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build + /usr/bin/cmake --build cvode-2.6.0/build -j4 --verbose Change Dir: '/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build' Run Build Command(s): /usr/bin/cmake -E env VERBOSE=1 /usr/bin/gmake -f Makefile -j4 /usr/bin/cmake -S/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0 -B/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/CMakeFiles /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build//CMakeFiles/progress.marks /usr/bin/gmake -f CMakeFiles/Makefile2 all gmake[1]: Entering directory '/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build' /usr/bin/gmake -f src/nvec_ser/CMakeFiles/sundials_nvecserial_static.dir/build.make src/nvec_ser/CMakeFiles/sundials_nvecserial_static.dir/depend /usr/bin/gmake -f src/nvec_ser/CMakeFiles/sundials_fnvecserial_static.dir/build.make src/nvec_ser/CMakeFiles/sundials_fnvecserial_static.dir/depend gmake[2]: Entering directory '/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build' cd /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0 /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/nvec_ser /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/src/nvec_ser /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/src/nvec_ser/CMakeFiles/sundials_fnvecserial_static.dir/DependInfo.cmake "--color=" /usr/bin/gmake -f src/cvode/CMakeFiles/sundials_cvode_static.dir/build.make src/cvode/CMakeFiles/sundials_cvode_static.dir/depend gmake[2]: Entering directory '/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build' cd /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0 /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/nvec_ser /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/src/nvec_ser /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/src/nvec_ser/CMakeFiles/sundials_nvecserial_static.dir/DependInfo.cmake "--color=" /usr/bin/gmake -f src/cvode/fcmix/CMakeFiles/sundials_fcvode_static.dir/build.make src/cvode/fcmix/CMakeFiles/sundials_fcvode_static.dir/depend gmake[2]: Entering directory '/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build' cd /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0 /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/src/cvode/fcmix /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/src/cvode/fcmix/CMakeFiles/sundials_fcvode_static.dir/DependInfo.cmake "--color=" gmake[2]: Entering directory '/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build' cd /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0 /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/src/cvode /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/src/cvode/CMakeFiles/sundials_cvode_static.dir/DependInfo.cmake "--color=" gmake[2]: Leaving directory '/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build' gmake[2]: Leaving directory '/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build' gmake[2]: Leaving directory '/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build' /usr/bin/gmake -f src/nvec_ser/CMakeFiles/sundials_nvecserial_static.dir/build.make src/nvec_ser/CMakeFiles/sundials_nvecserial_static.dir/build gmake[2]: Leaving directory '/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build' /usr/bin/gmake -f src/nvec_ser/CMakeFiles/sundials_fnvecserial_static.dir/build.make src/nvec_ser/CMakeFiles/sundials_fnvecserial_static.dir/build /usr/bin/gmake -f src/cvode/CMakeFiles/sundials_cvode_static.dir/build.make src/cvode/CMakeFiles/sundials_cvode_static.dir/build gmake[2]: Entering directory '/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build' gmake[2]: Entering directory '/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build' /usr/bin/gmake -f src/cvode/fcmix/CMakeFiles/sundials_fcvode_static.dir/build.make src/cvode/fcmix/CMakeFiles/sundials_fcvode_static.dir/build gmake[2]: Entering directory '/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build' gmake[2]: Entering directory '/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build' [ 5%] Building C object src/nvec_ser/CMakeFiles/sundials_nvecserial_static.dir/nvector_serial.c.o [ 2%] Building C object src/nvec_ser/CMakeFiles/sundials_fnvecserial_static.dir/fnvector_serial.c.o [ 8%] Building C object src/cvode/CMakeFiles/sundials_cvode_static.dir/cvode.c.o cd /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/src/cvode && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/. -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/../sundials -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer 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-Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -MD -MT src/nvec_ser/CMakeFiles/sundials_fnvecserial_static.dir/fnvector_serial.c.o -MF CMakeFiles/sundials_fnvecserial_static.dir/fnvector_serial.c.o.d -o CMakeFiles/sundials_fnvecserial_static.dir/fnvector_serial.c.o -c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/nvec_ser/fnvector_serial.c cd /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/src/nvec_ser && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/nvec_ser/. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -MD -MT src/nvec_ser/CMakeFiles/sundials_nvecserial_static.dir/nvector_serial.c.o -MF CMakeFiles/sundials_nvecserial_static.dir/nvector_serial.c.o.d -o CMakeFiles/sundials_nvecserial_static.dir/nvector_serial.c.o -c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/nvec_ser/nvector_serial.c [ 10%] Building C object src/cvode/fcmix/CMakeFiles/sundials_fcvode_static.dir/fcvband.c.o cd /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/src/cvode/fcmix && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/. -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -MD -MT src/cvode/fcmix/CMakeFiles/sundials_fcvode_static.dir/fcvband.c.o -MF CMakeFiles/sundials_fcvode_static.dir/fcvband.c.o.d -o CMakeFiles/sundials_fcvode_static.dir/fcvband.c.o -c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/fcvband.c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/fcvband.c: In function ‘fcvbandsetjac_’: /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/fcvband.c:48:12: warning: variable ‘cv_mem’ set but not used [-Wunused-but-set-variable] 48 | CVodeMem cv_mem; | ^~~~~~ [ 13%] Building C object src/cvode/fcmix/CMakeFiles/sundials_fcvode_static.dir/fcvbbd.c.o cd /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/src/cvode/fcmix && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/. -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -MD -MT src/cvode/fcmix/CMakeFiles/sundials_fcvode_static.dir/fcvbbd.c.o -MF CMakeFiles/sundials_fcvode_static.dir/fcvbbd.c.o.d -o CMakeFiles/sundials_fcvode_static.dir/fcvbbd.c.o -c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/fcvbbd.c [ 16%] Linking C static library libsundials_fnvecserial.a cd /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/src/nvec_ser && /usr/bin/cmake -P CMakeFiles/sundials_fnvecserial_static.dir/cmake_clean_target.cmake cd /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/src/nvec_ser && /usr/bin/cmake -E cmake_link_script CMakeFiles/sundials_fnvecserial_static.dir/link.txt --verbose=1 /usr/bin/ar qc libsundials_fnvecserial.a CMakeFiles/sundials_fnvecserial_static.dir/fnvector_serial.c.o /usr/bin/ranlib libsundials_fnvecserial.a gmake[2]: Leaving directory '/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build' [ 16%] Built target sundials_fnvecserial_static [ 18%] Building C object src/nvec_ser/CMakeFiles/sundials_nvecserial_static.dir/__/sundials/sundials_math.c.o cd /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/src/nvec_ser && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/nvec_ser/. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -MD -MT src/nvec_ser/CMakeFiles/sundials_nvecserial_static.dir/__/sundials/sundials_math.c.o -MF CMakeFiles/sundials_nvecserial_static.dir/__/sundials/sundials_math.c.o.d -o CMakeFiles/sundials_nvecserial_static.dir/__/sundials/sundials_math.c.o -c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/sundials/sundials_math.c [ 21%] Building C object src/cvode/fcmix/CMakeFiles/sundials_fcvode_static.dir/fcvbp.c.o cd /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/src/cvode/fcmix && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/. -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -MD -MT src/cvode/fcmix/CMakeFiles/sundials_fcvode_static.dir/fcvbp.c.o -MF CMakeFiles/sundials_fcvode_static.dir/fcvbp.c.o.d -o CMakeFiles/sundials_fcvode_static.dir/fcvbp.c.o -c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/fcvbp.c [ 24%] Building C object src/cvode/fcmix/CMakeFiles/sundials_fcvode_static.dir/fcvdense.c.o cd /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/src/cvode/fcmix && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/. -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -MD -MT src/cvode/fcmix/CMakeFiles/sundials_fcvode_static.dir/fcvdense.c.o -MF CMakeFiles/sundials_fcvode_static.dir/fcvdense.c.o.d -o CMakeFiles/sundials_fcvode_static.dir/fcvdense.c.o -c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/fcvdense.c [ 27%] Building C object src/cvode/CMakeFiles/sundials_cvode_static.dir/cvode_io.c.o cd /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/src/cvode && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/. -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/../sundials -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -MD -MT src/cvode/CMakeFiles/sundials_cvode_static.dir/cvode_io.c.o -MF CMakeFiles/sundials_cvode_static.dir/cvode_io.c.o.d -o CMakeFiles/sundials_cvode_static.dir/cvode_io.c.o -c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/cvode_io.c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/fcvdense.c: In function ‘fcvdensesetjac_’: /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/fcvdense.c:48:12: warning: variable ‘cv_mem’ set but not used [-Wunused-but-set-variable] 48 | CVodeMem cv_mem; | ^~~~~~ [ 29%] Building C object src/cvode/fcmix/CMakeFiles/sundials_fcvode_static.dir/fcvewt.c.o cd /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/src/cvode/fcmix && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/. -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -MD -MT src/cvode/fcmix/CMakeFiles/sundials_fcvode_static.dir/fcvewt.c.o -MF CMakeFiles/sundials_fcvode_static.dir/fcvewt.c.o.d -o CMakeFiles/sundials_fcvode_static.dir/fcvewt.c.o -c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/fcvewt.c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/fcvewt.c: In function ‘fcvewtset_’: /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/fcvewt.c:46:12: warning: variable ‘cv_mem’ set but not used [-Wunused-but-set-variable] 46 | CVodeMem cv_mem; | ^~~~~~ [ 32%] Building C object src/cvode/fcmix/CMakeFiles/sundials_fcvode_static.dir/fcvjtimes.c.o cd /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/src/cvode/fcmix && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/. -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -MD -MT src/cvode/fcmix/CMakeFiles/sundials_fcvode_static.dir/fcvjtimes.c.o -MF CMakeFiles/sundials_fcvode_static.dir/fcvjtimes.c.o.d -o CMakeFiles/sundials_fcvode_static.dir/fcvjtimes.c.o -c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/fcvjtimes.c [ 35%] Linking C static library libsundials_nvecserial.a cd /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/src/nvec_ser && /usr/bin/cmake -P CMakeFiles/sundials_nvecserial_static.dir/cmake_clean_target.cmake cd /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/src/nvec_ser && /usr/bin/cmake -E cmake_link_script CMakeFiles/sundials_nvecserial_static.dir/link.txt --verbose=1 /usr/bin/ar qc libsundials_nvecserial.a CMakeFiles/sundials_nvecserial_static.dir/nvector_serial.c.o CMakeFiles/sundials_nvecserial_static.dir/__/sundials/sundials_math.c.o /usr/bin/ranlib libsundials_nvecserial.a gmake[2]: Leaving directory '/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build' /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/fcvjtimes.c: In function ‘fcvspilssetjac_’: /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/fcvjtimes.c:52:12: warning: variable ‘cv_mem’ set but not used [-Wunused-but-set-variable] 52 | CVodeMem cv_mem; | ^~~~~~ [ 35%] Built target sundials_nvecserial_static [ 37%] Building C object src/cvode/CMakeFiles/sundials_cvode_static.dir/cvode_direct.c.o cd /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/src/cvode && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/. -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/../sundials -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -MD -MT src/cvode/CMakeFiles/sundials_cvode_static.dir/cvode_direct.c.o -MF CMakeFiles/sundials_cvode_static.dir/cvode_direct.c.o.d -o CMakeFiles/sundials_cvode_static.dir/cvode_direct.c.o -c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/cvode_direct.c [ 40%] Building C object src/cvode/fcmix/CMakeFiles/sundials_fcvode_static.dir/fcvode.c.o cd /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/src/cvode/fcmix && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/. -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -MD -MT src/cvode/fcmix/CMakeFiles/sundials_fcvode_static.dir/fcvode.c.o -MF CMakeFiles/sundials_fcvode_static.dir/fcvode.c.o.d -o CMakeFiles/sundials_fcvode_static.dir/fcvode.c.o -c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/fcvode.c [ 43%] Building C object src/cvode/fcmix/CMakeFiles/sundials_fcvode_static.dir/fcvpreco.c.o cd /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/src/cvode/fcmix && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/. -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -MD -MT src/cvode/fcmix/CMakeFiles/sundials_fcvode_static.dir/fcvpreco.c.o -MF CMakeFiles/sundials_fcvode_static.dir/fcvpreco.c.o.d -o CMakeFiles/sundials_fcvode_static.dir/fcvpreco.c.o -c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/fcvpreco.c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/fcvpreco.c: In function ‘fcvspilssetprec_’: /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/fcvpreco.c:59:12: warning: variable ‘cv_mem’ set but not used [-Wunused-but-set-variable] 59 | CVodeMem cv_mem; | ^~~~~~ [ 45%] Building C object src/cvode/CMakeFiles/sundials_cvode_static.dir/cvode_band.c.o cd /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/src/cvode && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/. -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/../sundials -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -MD -MT src/cvode/CMakeFiles/sundials_cvode_static.dir/cvode_band.c.o -MF CMakeFiles/sundials_cvode_static.dir/cvode_band.c.o.d -o CMakeFiles/sundials_cvode_static.dir/cvode_band.c.o -c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/cvode_band.c [ 48%] Building C object src/cvode/fcmix/CMakeFiles/sundials_fcvode_static.dir/fcvroot.c.o cd /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/src/cvode/fcmix && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/. -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -MD -MT src/cvode/fcmix/CMakeFiles/sundials_fcvode_static.dir/fcvroot.c.o -MF CMakeFiles/sundials_fcvode_static.dir/fcvroot.c.o.d -o CMakeFiles/sundials_fcvode_static.dir/fcvroot.c.o -c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/fcvroot.c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/fcvroot.c: In function ‘fcvrootinit_’: /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/fcvroot.c:44:12: warning: variable ‘cv_mem’ set but not used [-Wunused-but-set-variable] 44 | CVodeMem cv_mem; | ^~~~~~ [ 51%] Building C object src/cvode/CMakeFiles/sundials_cvode_static.dir/cvode_dense.c.o cd /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/src/cvode && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/. -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/../sundials -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -MD -MT src/cvode/CMakeFiles/sundials_cvode_static.dir/cvode_dense.c.o -MF CMakeFiles/sundials_cvode_static.dir/cvode_dense.c.o.d -o CMakeFiles/sundials_cvode_static.dir/cvode_dense.c.o -c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/cvode_dense.c [ 54%] Linking C static library libsundials_fcvode.a cd /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/src/cvode/fcmix && /usr/bin/cmake -P CMakeFiles/sundials_fcvode_static.dir/cmake_clean_target.cmake [ 56%] Building C object src/cvode/CMakeFiles/sundials_cvode_static.dir/cvode_diag.c.o cd /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/src/cvode && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/. -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/../sundials -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -MD -MT src/cvode/CMakeFiles/sundials_cvode_static.dir/cvode_diag.c.o -MF CMakeFiles/sundials_cvode_static.dir/cvode_diag.c.o.d -o CMakeFiles/sundials_cvode_static.dir/cvode_diag.c.o -c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/cvode_diag.c cd /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/src/cvode/fcmix && /usr/bin/cmake -E cmake_link_script CMakeFiles/sundials_fcvode_static.dir/link.txt --verbose=1 /usr/bin/ar qc libsundials_fcvode.a CMakeFiles/sundials_fcvode_static.dir/fcvband.c.o CMakeFiles/sundials_fcvode_static.dir/fcvbbd.c.o CMakeFiles/sundials_fcvode_static.dir/fcvbp.c.o CMakeFiles/sundials_fcvode_static.dir/fcvdense.c.o CMakeFiles/sundials_fcvode_static.dir/fcvewt.c.o CMakeFiles/sundials_fcvode_static.dir/fcvjtimes.c.o CMakeFiles/sundials_fcvode_static.dir/fcvode.c.o CMakeFiles/sundials_fcvode_static.dir/fcvpreco.c.o CMakeFiles/sundials_fcvode_static.dir/fcvroot.c.o /usr/bin/ranlib libsundials_fcvode.a gmake[2]: Leaving directory '/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build' [ 56%] Built target sundials_fcvode_static [ 59%] Building C object src/cvode/CMakeFiles/sundials_cvode_static.dir/cvode_spils.c.o cd /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/src/cvode && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/. -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/../sundials -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -MD -MT src/cvode/CMakeFiles/sundials_cvode_static.dir/cvode_spils.c.o -MF CMakeFiles/sundials_cvode_static.dir/cvode_spils.c.o.d -o CMakeFiles/sundials_cvode_static.dir/cvode_spils.c.o -c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/cvode_spils.c [ 62%] Building C object src/cvode/CMakeFiles/sundials_cvode_static.dir/cvode_spbcgs.c.o cd /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/src/cvode && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/. -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/../sundials -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -MD -MT src/cvode/CMakeFiles/sundials_cvode_static.dir/cvode_spbcgs.c.o -MF CMakeFiles/sundials_cvode_static.dir/cvode_spbcgs.c.o.d -o CMakeFiles/sundials_cvode_static.dir/cvode_spbcgs.c.o -c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/cvode_spbcgs.c [ 64%] Building C object src/cvode/CMakeFiles/sundials_cvode_static.dir/cvode_spgmr.c.o cd /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/src/cvode && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/. -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/../sundials -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -MD -MT src/cvode/CMakeFiles/sundials_cvode_static.dir/cvode_spgmr.c.o -MF CMakeFiles/sundials_cvode_static.dir/cvode_spgmr.c.o.d -o CMakeFiles/sundials_cvode_static.dir/cvode_spgmr.c.o -c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/cvode_spgmr.c [ 67%] Building C object src/cvode/CMakeFiles/sundials_cvode_static.dir/cvode_sptfqmr.c.o cd /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/src/cvode && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/. -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/../sundials -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -MD -MT src/cvode/CMakeFiles/sundials_cvode_static.dir/cvode_sptfqmr.c.o -MF CMakeFiles/sundials_cvode_static.dir/cvode_sptfqmr.c.o.d -o CMakeFiles/sundials_cvode_static.dir/cvode_sptfqmr.c.o -c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/cvode_sptfqmr.c [ 70%] Building C object src/cvode/CMakeFiles/sundials_cvode_static.dir/cvode_bandpre.c.o cd /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/src/cvode && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/. -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/../sundials -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -MD -MT src/cvode/CMakeFiles/sundials_cvode_static.dir/cvode_bandpre.c.o -MF CMakeFiles/sundials_cvode_static.dir/cvode_bandpre.c.o.d -o CMakeFiles/sundials_cvode_static.dir/cvode_bandpre.c.o -c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/cvode_bandpre.c [ 72%] Building C object src/cvode/CMakeFiles/sundials_cvode_static.dir/cvode_bbdpre.c.o cd /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/src/cvode && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/. -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/../sundials -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -MD -MT src/cvode/CMakeFiles/sundials_cvode_static.dir/cvode_bbdpre.c.o -MF CMakeFiles/sundials_cvode_static.dir/cvode_bbdpre.c.o.d -o CMakeFiles/sundials_cvode_static.dir/cvode_bbdpre.c.o -c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/cvode_bbdpre.c [ 75%] Building C object src/cvode/CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_nvector.c.o cd /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/src/cvode && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/. -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/../sundials -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -MD -MT src/cvode/CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_nvector.c.o -MF CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_nvector.c.o.d -o CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_nvector.c.o -c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/sundials/sundials_nvector.c [ 78%] Building C object src/cvode/CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_math.c.o cd /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/src/cvode && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/. -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/../sundials -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -MD -MT src/cvode/CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_math.c.o -MF CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_math.c.o.d -o CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_math.c.o -c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/sundials/sundials_math.c [ 81%] Building C object src/cvode/CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_direct.c.o cd /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/src/cvode && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/. -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/../sundials -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -MD -MT src/cvode/CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_direct.c.o -MF CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_direct.c.o.d -o CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_direct.c.o -c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/sundials/sundials_direct.c [ 83%] Building C object src/cvode/CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_band.c.o cd /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/src/cvode && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/. -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/../sundials -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -MD -MT src/cvode/CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_band.c.o -MF CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_band.c.o.d -o CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_band.c.o -c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/sundials/sundials_band.c [ 86%] Building C object src/cvode/CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_dense.c.o cd /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/src/cvode && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/. -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/../sundials -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -MD -MT src/cvode/CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_dense.c.o -MF CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_dense.c.o.d -o CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_dense.c.o -c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/sundials/sundials_dense.c [ 89%] Building C object src/cvode/CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_iterative.c.o cd /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/src/cvode && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/. -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/../sundials -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -MD -MT src/cvode/CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_iterative.c.o -MF CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_iterative.c.o.d -o CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_iterative.c.o -c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/sundials/sundials_iterative.c [ 91%] Building C object src/cvode/CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_spbcgs.c.o cd /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/src/cvode && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/. -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/../sundials -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -MD -MT src/cvode/CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_spbcgs.c.o -MF CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_spbcgs.c.o.d -o CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_spbcgs.c.o -c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/sundials/sundials_spbcgs.c [ 94%] Building C object src/cvode/CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_spgmr.c.o cd /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/src/cvode && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/. -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/../sundials -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -MD -MT src/cvode/CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_spgmr.c.o -MF CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_spgmr.c.o.d -o CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_spgmr.c.o -c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/sundials/sundials_spgmr.c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/sundials/sundials_spgmr.c: In function ‘SpgmrFree’: /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/sundials/sundials_spgmr.c:439:29: warning: variable ‘yg’ set but not used [-Wunused-but-set-variable] 439 | realtype **Hes, *givens, *yg; | ^~ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/sundials/sundials_spgmr.c:439:20: warning: variable ‘givens’ set but not used [-Wunused-but-set-variable] 439 | realtype **Hes, *givens, *yg; | ^~~~~~ [ 97%] Building C object src/cvode/CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_sptfqmr.c.o cd /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/src/cvode && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/. -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/cvode/../sundials -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -MD -MT src/cvode/CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_sptfqmr.c.o -MF CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_sptfqmr.c.o.d -o CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_sptfqmr.c.o -c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/src/sundials/sundials_sptfqmr.c [100%] Linking C static library libsundials_cvode.a cd /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/src/cvode && /usr/bin/cmake -P CMakeFiles/sundials_cvode_static.dir/cmake_clean_target.cmake cd /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/src/cvode && /usr/bin/cmake -E cmake_link_script CMakeFiles/sundials_cvode_static.dir/link.txt --verbose=1 /usr/bin/ar qc libsundials_cvode.a CMakeFiles/sundials_cvode_static.dir/cvode.c.o CMakeFiles/sundials_cvode_static.dir/cvode_io.c.o CMakeFiles/sundials_cvode_static.dir/cvode_direct.c.o CMakeFiles/sundials_cvode_static.dir/cvode_band.c.o CMakeFiles/sundials_cvode_static.dir/cvode_dense.c.o CMakeFiles/sundials_cvode_static.dir/cvode_diag.c.o CMakeFiles/sundials_cvode_static.dir/cvode_spils.c.o CMakeFiles/sundials_cvode_static.dir/cvode_spbcgs.c.o CMakeFiles/sundials_cvode_static.dir/cvode_spgmr.c.o CMakeFiles/sundials_cvode_static.dir/cvode_sptfqmr.c.o CMakeFiles/sundials_cvode_static.dir/cvode_bandpre.c.o CMakeFiles/sundials_cvode_static.dir/cvode_bbdpre.c.o CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_nvector.c.o CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_math.c.o CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_direct.c.o CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_band.c.o CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_dense.c.o CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_iterative.c.o CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_spbcgs.c.o CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_spgmr.c.o CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_sptfqmr.c.o /usr/bin/ranlib libsundials_cvode.a gmake[2]: Leaving directory '/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build' [100%] Built target sundials_cvode_static gmake[1]: Leaving directory '/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build' /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/cvode-2.6.0/build/CMakeFiles 0 ++ echo '-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer' ++ sed -e s/-Werror=format-security/-Wno-error=format-security/g + SETOPT_FLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer' + export 'CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I../src/util/mathutils -I../cvode-2.6.0/include -I../muparser_v2_2_4/include' + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I../src/util/mathutils -I../cvode-2.6.0/include -I../muparser_v2_2_4/include' + export 'CXXFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I../src/util/mathutils -I../cvode-2.6.0/include -I../cvode-2.6.0/include/cvode -I../cvode-2.6.0/build/include -I../cvode-2.6.0/src/cvode/fcmix -L../src/util/mathutils -I../muparser_v2_2_4/include -L../muparser_v2_2_4/lib -L../cvode-2.6.0/build/src/cvode/fcmix -L../cvode-2.6.0/build/src/sundials -L../cvode-2.6.0/build/src/cvode -L../cvode-2.6.0/build/src/nvec_ser' + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I../src/util/mathutils -I../cvode-2.6.0/include -I../cvode-2.6.0/include/cvode -I../cvode-2.6.0/build/include -I../cvode-2.6.0/src/cvode/fcmix -L../src/util/mathutils -I../muparser_v2_2_4/include -L../muparser_v2_2_4/lib -L../cvode-2.6.0/build/src/cvode/fcmix -L../cvode-2.6.0/build/src/sundials -L../cvode-2.6.0/build/src/cvode -L../cvode-2.6.0/build/src/nvec_ser' + mkdir -p build + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I../src/util/mathutils -I../cvode-2.6.0/include -I../muparser_v2_2_4/include' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I../src/util/mathutils -I../cvode-2.6.0/include -I../cvode-2.6.0/include/cvode -I../cvode-2.6.0/build/include -I../cvode-2.6.0/src/cvode/fcmix -L../src/util/mathutils -I../muparser_v2_2_4/include -L../muparser_v2_2_4/lib -L../cvode-2.6.0/build/src/cvode/fcmix -L../cvode-2.6.0/build/src/sundials -L../cvode-2.6.0/build/src/cvode -L../cvode-2.6.0/build/src/nvec_ser' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + /usr/bin/cmake -S . -B build -DCMAKE_C_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_Fortran_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_INSTALL_DO_STRIP:BOOL=OFF -DCMAKE_INSTALL_PREFIX:PATH=/usr -DINCLUDE_INSTALL_DIR:PATH=/usr/include -DLIB_INSTALL_DIR:PATH=/usr/lib64 -DSYSCONF_INSTALL_DIR:PATH=/etc -DSHARE_INSTALL_PREFIX:PATH=/usr/share -DLIB_SUFFIX=64 -DBUILD_SHARED_LIBS:BOOL=ON -DCMAKE_SKIP_RPATH:BOOL=YES -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES -DBUILD_SHARED_LIBS:BOOL=OFF -DBUILD_STATIC_LIBS:BOOL=ON -- The C compiler identification is GNU 14.2.1 -- The CXX compiler identification is GNU 14.2.1 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Configuring done (0.5s) -- Generating done (0.0s) -- Build files have been written to: /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/build CMake Warning: Manually-specified variables were not used by the project: BUILD_SHARED_LIBS BUILD_STATIC_LIBS CMAKE_CXX_FLAGS_RELEASE CMAKE_C_FLAGS_RELEASE CMAKE_Fortran_FLAGS_RELEASE CMAKE_INSTALL_DO_STRIP CMAKE_SKIP_INSTALL_RPATH INCLUDE_INSTALL_DIR LIB_INSTALL_DIR LIB_SUFFIX SHARE_INSTALL_PREFIX SYSCONF_INSTALL_DIR + /usr/bin/cmake --build build -j4 --verbose Change Dir: '/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/build' Run Build Command(s): /usr/bin/cmake -E env VERBOSE=1 /usr/bin/gmake -f Makefile -j4 /usr/bin/cmake -S/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3 -B/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/build/CMakeFiles /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/build//CMakeFiles/progress.marks /usr/bin/gmake -f CMakeFiles/Makefile2 all gmake[1]: Entering directory '/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/build' /usr/bin/gmake -f CMakeFiles/run_network.dir/build.make CMakeFiles/run_network.dir/depend gmake[2]: Entering directory '/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/build' cd /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3 /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3 /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/build /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/build /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/build/CMakeFiles/run_network.dir/DependInfo.cmake "--color=" gmake[2]: Leaving directory '/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/build' /usr/bin/gmake -f CMakeFiles/run_network.dir/build.make CMakeFiles/run_network.dir/build gmake[2]: Entering directory '/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/build' [ 3%] Building CXX object CMakeFiles/run_network.dir/src/network.cpp.o [ 3%] Building CXX object CMakeFiles/run_network.dir/src/model/function.cpp.o [ 5%] Building CXX object CMakeFiles/run_network.dir/src/run_network.cpp.o [ 7%] Building CXX object CMakeFiles/run_network.dir/src/network3.cpp.o /usr/bin/g++ -DRUN_NETWORK_VERSION=\"3.0\" -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3 -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/cvode -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/nvector -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/sundials -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/ssa -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/rateExpressions -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/reactions -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/base -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/eRungeKutta -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/fEuler -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/util -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/eRungeKutta/base -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/eRungeKutta/util -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util/MTrand -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util/rand2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I../src/util/mathutils -I../cvode-2.6.0/include -I../cvode-2.6.0/include/cvode -I../cvode-2.6.0/build/include -I../cvode-2.6.0/src/cvode/fcmix -L../src/util/mathutils -I../muparser_v2_2_4/include -L../muparser_v2_2_4/lib -L../cvode-2.6.0/build/src/cvode/fcmix -L../cvode-2.6.0/build/src/sundials -L../cvode-2.6.0/build/src/cvode -L../cvode-2.6.0/build/src/nvec_ser -MD -MT CMakeFiles/run_network.dir/src/network.cpp.o -MF CMakeFiles/run_network.dir/src/network.cpp.o.d -o CMakeFiles/run_network.dir/src/network.cpp.o -c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp /usr/bin/g++ -DRUN_NETWORK_VERSION=\"3.0\" -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3 -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/cvode -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/nvector -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/sundials -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/ssa -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/rateExpressions -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/reactions -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/base -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/eRungeKutta -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/fEuler -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/util -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/eRungeKutta/base -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/eRungeKutta/util -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util/MTrand -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util/rand2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I../src/util/mathutils -I../cvode-2.6.0/include -I../cvode-2.6.0/include/cvode -I../cvode-2.6.0/build/include -I../cvode-2.6.0/src/cvode/fcmix -L../src/util/mathutils -I../muparser_v2_2_4/include -L../muparser_v2_2_4/lib -L../cvode-2.6.0/build/src/cvode/fcmix -L../cvode-2.6.0/build/src/sundials -L../cvode-2.6.0/build/src/cvode -L../cvode-2.6.0/build/src/nvec_ser -MD -MT CMakeFiles/run_network.dir/src/network3.cpp.o -MF CMakeFiles/run_network.dir/src/network3.cpp.o.d -o CMakeFiles/run_network.dir/src/network3.cpp.o -c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network3.cpp /usr/bin/g++ -DRUN_NETWORK_VERSION=\"3.0\" -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3 -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/cvode -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/nvector -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/sundials -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/ssa -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/rateExpressions -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/reactions -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/base -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/eRungeKutta -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/fEuler -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/util -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/eRungeKutta/base -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/eRungeKutta/util -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util/MTrand -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util/rand2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I../src/util/mathutils -I../cvode-2.6.0/include -I../cvode-2.6.0/include/cvode -I../cvode-2.6.0/build/include -I../cvode-2.6.0/src/cvode/fcmix -L../src/util/mathutils -I../muparser_v2_2_4/include -L../muparser_v2_2_4/lib -L../cvode-2.6.0/build/src/cvode/fcmix -L../cvode-2.6.0/build/src/sundials -L../cvode-2.6.0/build/src/cvode -L../cvode-2.6.0/build/src/nvec_ser -MD -MT CMakeFiles/run_network.dir/src/run_network.cpp.o -MF CMakeFiles/run_network.dir/src/run_network.cpp.o.d -o CMakeFiles/run_network.dir/src/run_network.cpp.o -c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/run_network.cpp /usr/bin/g++ -DRUN_NETWORK_VERSION=\"3.0\" -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3 -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/cvode -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/nvector -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/sundials -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/ssa -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/rateExpressions -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/reactions -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/base -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/eRungeKutta -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/fEuler -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/util -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/eRungeKutta/base -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/eRungeKutta/util -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util/MTrand -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util/rand2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I../src/util/mathutils -I../cvode-2.6.0/include -I../cvode-2.6.0/include/cvode -I../cvode-2.6.0/build/include -I../cvode-2.6.0/src/cvode/fcmix -L../src/util/mathutils -I../muparser_v2_2_4/include -L../muparser_v2_2_4/lib -L../cvode-2.6.0/build/src/cvode/fcmix -L../cvode-2.6.0/build/src/sundials -L../cvode-2.6.0/build/src/cvode -L../cvode-2.6.0/build/src/nvec_ser -MD -MT CMakeFiles/run_network.dir/src/model/function.cpp.o -MF CMakeFiles/run_network.dir/src/model/function.cpp.o.d -o CMakeFiles/run_network.dir/src/model/function.cpp.o -c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/function.cpp In file included from ../muparser_v2_2_4/include/muParserStack.h:35, from ../muparser_v2_2_4/include/muParserBase.h:39, from ../muparser_v2_2_4/include/muParser.h:32, from /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/function.hh:12, from /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/function.cpp:8: ../muparser_v2_2_4/include/muParserToken.h:72:12: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 72 | std::auto_ptr m_pCallback; | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from ../muparser_v2_2_4/include/muParserBase.h:33: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ../muparser_v2_2_4/include/muParserBase.h:291:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 291 | std::auto_ptr m_pTokenReader; ///< Managed pointer to the token reader object. | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from ../muparser_v2_2_4/include/muParserStack.h:35, from ../muparser_v2_2_4/include/muParserBase.h:39, from ../muparser_v2_2_4/include/muParser.h:32, from /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.h:36, from /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network3.hh:12, from /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network3.cpp:8: ../muparser_v2_2_4/include/muParserToken.h:72:12: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 72 | std::auto_ptr m_pCallback; | ^~~~~~~~ In file included from ../muparser_v2_2_4/include/muParserStack.h:35, from ../muparser_v2_2_4/include/muParserBase.h:39, from ../muparser_v2_2_4/include/muParser.h:32, from /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.h:36, from /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:54: ../muparser_v2_2_4/include/muParserToken.h:72:12: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 72 | std::auto_ptr m_pCallback; | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from ../muparser_v2_2_4/include/muParserBase.h:33: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from ../muparser_v2_2_4/include/muParserBase.h:33: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from ../muparser_v2_2_4/include/muParserStack.h:35, from ../muparser_v2_2_4/include/muParserBase.h:39, from ../muparser_v2_2_4/include/muParser.h:32, from /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.h:36, from /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network3.hh:12, from /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/run_network.cpp:46: ../muparser_v2_2_4/include/muParserToken.h:72:12: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 72 | std::auto_ptr m_pCallback; | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from ../muparser_v2_2_4/include/muParserBase.h:33: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ../muparser_v2_2_4/include/muParserBase.h:291:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 291 | std::auto_ptr m_pTokenReader; ///< Managed pointer to the token reader object. | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ../muparser_v2_2_4/include/muParserBase.h:291:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 291 | std::auto_ptr m_pTokenReader; ///< Managed pointer to the token reader object. | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ../muparser_v2_2_4/include/muParserBase.h:291:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 291 | std::auto_ptr m_pTokenReader; ///< Managed pointer to the token reader object. | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp: In function ‘void read_functions_array(const char*, Elt_array*&, std::map, double*>&, std::map, int>, std::map, int>, double*)’: /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:440:13: warning: variable ‘index’ set but not used [-Wunused-but-set-variable] 440 | int index; | ^~~~~ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp: In function ‘Rxn* new_Rxn(int, int, int, int*, int*, int, int, int*, double, Elt_array*)’: /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:1132:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 1132 | register int i; | ^ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp: In function ‘int* read_indices_Rxn(char*, int*, Elt_array*, int)’: /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:1543:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 1543 | register int i; | ^ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp: In function ‘void print_Rxn_array(FILE*, Rxn_array*, Elt_array*, Elt_array*)’: /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:1925:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 1925 | register int i; | ^ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:1927:15: warning: variable ‘sarr’ set but not used [-Wunused-but-set-variable] 1927 | Elt **sarr, **rarr; | ^~~~ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/run_network.cpp: In function ‘int main(int, char**)’: /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/run_network.cpp:95:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 95 | register int i/*, j*/; | ^ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp: In function ‘int n_species_active()’: /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:2068:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 2068 | register int i; | ^ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp: In function ‘int get_conc_network(double*)’: /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:2088:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 2088 | register int i; | ^ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp: In function ‘int set_conc_network(double*)’: /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:2110:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 2110 | register int i, n_species; | ^ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:2110:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 2110 | register int i, n_species; | ^~~~~~~~~ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp: In function ‘int rxn_rates_network(double*, int)’: /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:2729:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 2729 | register int i; | ^ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp: In function ‘void derivs_network(double, double*, double*)’: /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:2782:15: warning: unused variable ‘rarray’ [-Wunused-variable] 2782 | Rxn **rarray, *rxn; | ^~~~~~ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:2783:15: warning: variable ‘rates’ set but not used [-Wunused-but-set-variable] 2783 | Elt** rates; | ^~~~~ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp: In function ‘int print_derivs_network(FILE*)’: /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:2957:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 2957 | register int i/*,j*/; | ^ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp: In function ‘int print_derivs_species_network(FILE*)’: /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:2990:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 2990 | register int i/*,j*/; | ^ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp: In function ‘int print_rates_network(FILE*, int)’: /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:3019:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 3019 | register int i; | ^ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp: In function ‘void sparse_jac_matlab(FILE*)’: /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:3198:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 3198 | register int i, j, r, n; | ^ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:3198:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 3198 | register int i, j, r, n; | ^ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:3198:28: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 3198 | register int i, j, r, n; | ^ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:3198:31: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 3198 | register int i, j, r, n; | ^ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:3204:15: warning: variable ‘rates’ set but not used [-Wunused-but-set-variable] 3204 | Elt** rates; | ^~~~~ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp: In function ‘void CVjac_network(long int, DlsMat, realtype, N_Vector, N_Vector, void*, N_Vector, N_Vector, N_Vector)’: /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:3272:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 3272 | register int i, j, r, n; | ^ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:3272:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 3272 | register int i, j, r, n; | ^ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:3272:28: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 3272 | register int i, j, r, n; | ^ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:3272:31: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 3272 | register int i, j, r, n; | ^ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:3277:15: warning: variable ‘rates’ set but not used [-Wunused-but-set-variable] 3277 | Elt** rates; | ^~~~~ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp: In function ‘int CVjtimes(N_Vector, N_Vector, realtype, N_Vector, N_Vector, void*, N_Vector)’: /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:3333:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 3333 | register int i, j, r, n; | ^ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:3333:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 3333 | register int i, j, r, n; | ^ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:3333:28: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 3333 | register int i, j, r, n; | ^ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:3333:31: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 3333 | register int i, j, r, n; | ^ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:3338:15: warning: variable ‘rates’ set but not used [-Wunused-but-set-variable] 3338 | Elt** rates; | ^~~~~ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp: In function ‘int print_flux_network(FILE*, double, int)’: /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:4037:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 4037 | register int i; | ^ [ 9%] Building CXX object CMakeFiles/run_network.dir/src/model/observable.cpp.o /usr/bin/g++ -DRUN_NETWORK_VERSION=\"3.0\" -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3 -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/cvode -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/nvector -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/sundials -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/ssa -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/rateExpressions -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/reactions -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/base -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/eRungeKutta -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/fEuler -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/util -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/eRungeKutta/base -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/eRungeKutta/util -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util/MTrand -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util/rand2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I../src/util/mathutils -I../cvode-2.6.0/include -I../cvode-2.6.0/include/cvode -I../cvode-2.6.0/build/include -I../cvode-2.6.0/src/cvode/fcmix -L../src/util/mathutils -I../muparser_v2_2_4/include -L../muparser_v2_2_4/lib -L../cvode-2.6.0/build/src/cvode/fcmix -L../cvode-2.6.0/build/src/sundials -L../cvode-2.6.0/build/src/cvode -L../cvode-2.6.0/build/src/nvec_ser -MD -MT CMakeFiles/run_network.dir/src/model/observable.cpp.o -MF CMakeFiles/run_network.dir/src/model/observable.cpp.o.d -o CMakeFiles/run_network.dir/src/model/observable.cpp.o -c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/observable.cpp /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp: In function ‘void print_rxn_update_list(FILE*)’: /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:4376:29: warning: variable ‘rxn’ set but not used [-Wunused-but-set-variable] 4376 | Rxn /* **rarray,*/ *rxn; | ^~~ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp: In function ‘void print_as_reactant_list(FILE*)’: /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:4410:13: warning: variable ‘offset’ set but not used [-Wunused-but-set-variable] 4410 | int offset; | ^~~~~~ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp: In function ‘int create_update_lists()’: /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:4757:37: warning: unused variable ‘pp’ [-Wunused-variable] 4757 | int pp = GSP.func_param_affect.at(ff)-1; | ^~ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp: In function ‘int init_gillespie_direct_network(int, int)’: /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:4837:15: warning: unused variable ‘rarray’ [-Wunused-variable] 4837 | Rxn** rarray; | ^~~~~~ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp: In function ‘int init_adaptive_scaling_network(int, int, double, bool)’: /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:4905:15: warning: unused variable ‘rarray’ [-Wunused-variable] 4905 | Rxn** rarray; | ^~~~~~ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp: In function ‘int update_gillespie_direct_network(int, int)’: /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:4978:13: warning: unused variable ‘ip’ [-Wunused-variable] 4978 | int ip, ir, is, irxn; | ^~ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:4978:17: warning: unused variable ‘ir’ [-Wunused-variable] 4978 | int ip, ir, is, irxn; | ^~ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:4978:21: warning: unused variable ‘is’ [-Wunused-variable] 4978 | int ip, ir, is, irxn; | ^~ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:4978:25: warning: unused variable ‘irxn’ [-Wunused-variable] 4978 | int ip, ir, is, irxn; | ^~~~ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:4980:14: warning: unused variable ‘rxn_dep’ [-Wunused-variable] 4980 | int *rxn_dep/*, *rxn_dep2, *rxn_dep3*/; /* boolean arrays to keep track of dependent | ^~~~~~~ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:4983:17: warning: unused variable ‘arl’ [-Wunused-variable] 4983 | iarray *arl, *apl, *rul; /* species and reaction update lists */ | ^~~ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:4983:23: warning: unused variable ‘apl’ [-Wunused-variable] 4983 | iarray *arl, *apl, *rul; /* species and reaction update lists */ | ^~~ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:4983:29: warning: unused variable ‘rul’ [-Wunused-variable] 4983 | iarray *arl, *apl, *rul; /* species and reaction update lists */ | ^~~ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:4984:13: warning: unused variable ‘offset’ [-Wunused-variable] 4984 | int offset, r_index, p_index; | ^~~~~~ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:4984:21: warning: unused variable ‘r_index’ [-Wunused-variable] 4984 | int offset, r_index, p_index; | ^~~~~~~ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:4984:30: warning: unused variable ‘p_index’ [-Wunused-variable] 4984 | int offset, r_index, p_index; | ^~~~~~~ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:4985:15: warning: unused variable ‘rarray’ [-Wunused-variable] 4985 | Rxn **rarray, *rxn; | ^~~~~~ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:4985:24: warning: unused variable ‘rxn’ [-Wunused-variable] 4985 | Rxn **rarray, *rxn; | ^~~ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp: In function ‘int update_adaptive_scaling_network(int, int)’: /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:5160:13: warning: unused variable ‘ip’ [-Wunused-variable] 5160 | int ip, ir, is, irxn; | ^~ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:5160:17: warning: unused variable ‘ir’ [-Wunused-variable] 5160 | int ip, ir, is, irxn; | ^~ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:5160:21: warning: unused variable ‘is’ [-Wunused-variable] 5160 | int ip, ir, is, irxn; | ^~ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:5160:25: warning: unused variable ‘irxn’ [-Wunused-variable] 5160 | int ip, ir, is, irxn; | ^~~~ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:5162:14: warning: unused variable ‘rxn_dep’ [-Wunused-variable] 5162 | int *rxn_dep/*, *rxn_dep2, *rxn_dep3*/; /* boolean arrays to keep track of dependent | ^~~~~~~ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:5165:17: warning: unused variable ‘arl’ [-Wunused-variable] 5165 | iarray *arl, *apl, *rul; /* species and reaction update lists */ | ^~~ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:5165:23: warning: unused variable ‘apl’ [-Wunused-variable] 5165 | iarray *arl, *apl, *rul; /* species and reaction update lists */ | ^~~ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:5165:29: warning: unused variable ‘rul’ [-Wunused-variable] 5165 | iarray *arl, *apl, *rul; /* species and reaction update lists */ | ^~~ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:5166:13: warning: unused variable ‘offset’ [-Wunused-variable] 5166 | int offset, r_index, p_index; | ^~~~~~ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:5166:21: warning: unused variable ‘r_index’ [-Wunused-variable] 5166 | int offset, r_index, p_index; | ^~~~~~~ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:5166:30: warning: unused variable ‘p_index’ [-Wunused-variable] 5166 | int offset, r_index, p_index; | ^~~~~~~ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:5167:15: warning: unused variable ‘rarray’ [-Wunused-variable] 5167 | Rxn **rarray, *rxn; | ^~~~~~ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:5167:24: warning: unused variable ‘rxn’ [-Wunused-variable] 5167 | Rxn **rarray, *rxn; | ^~~ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp: In function ‘void update_rxn_rates(int)’: /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:5683:27: warning: variable ‘c’ set but not used [-Wunused-but-set-variable] 5683 | double *a, anew, *c; | ^ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp: In function ‘void update_rxn_rates_has(int, double, bool)’: /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:5747:27: warning: variable ‘c’ set but not used [-Wunused-but-set-variable] 5747 | double *a, anew, *c; | ^ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/run_network.cpp:735:84: warning: variable ‘n_deriv_calls_last’ set but not used [-Wunused-but-set-variable] 735 | long int /*n_steps = 0, n_steps_last = 0,*/ n_rate_calls_last = 0, n_deriv_calls_last = 0; | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.h: At global scope: /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.h:262:23: warning: ‘mu::value_type Mratio(mu::value_type, mu::value_type, mu::value_type)’ defined but not used [-Wunused-function] 262 | static mu::value_type Mratio(mu::value_type a, mu::value_type b, mu::value_type z){ | ^~~~~~ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.h:258:23: warning: ‘mu::value_type If(mu::value_type, mu::value_type, mu::value_type)’ defined but not used [-Wunused-function] 258 | static mu::value_type If(mu::value_type v1, mu::value_type v2, mu::value_type v3){ | ^~ In file included from /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/run_network.cpp:39: ../src/util/mathutils/mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ ../src/util/mathutils/mathutils.h:359:20: warning: ‘imarg2’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ ../src/util/mathutils/mathutils.h:359:12: warning: ‘imarg1’ defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ ../src/util/mathutils/mathutils.h:356:22: warning: ‘marg2’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ ../src/util/mathutils/mathutils.h:356:15: warning: ‘marg1’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ ../src/util/mathutils/mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ ../src/util/mathutils/mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp: At global scope: /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:3332:12: warning: ‘int CVjtimes(N_Vector, N_Vector, realtype, N_Vector, N_Vector, void*, N_Vector)’ defined but not used [-Wunused-function] 3332 | static int CVjtimes(N_Vector v, N_Vector Jv, realtype t, N_Vector y, N_Vector fy, void* jac_data, N_Vector tmp) { | ^~~~~~~~ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:3270:13: warning: ‘void CVjac_network(long int, DlsMat, realtype, N_Vector, N_Vector, void*, N_Vector, N_Vector, N_Vector)’ defined but not used [-Wunused-function] 3270 | static void CVjac_network(long int N, DlsMat J, realtype t, N_Vector y, N_Vector fy, void* jac_data, N_Vector tmp1, N_Vector tmp2, | ^~~~~~~~~~~~~ In file included from /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:38: ../src/util/mathutils/mathutils.h:364:15: warning: ‘dswap’ defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ ../src/util/mathutils/mathutils.h:356:22: warning: ‘marg2’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ ../src/util/mathutils/mathutils.h:356:15: warning: ‘marg1’ defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ ../src/util/mathutils/mathutils.h:354:12: warning: ‘isqrarg’ defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ ../src/util/mathutils/mathutils.h:352:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.h:262:23: warning: ‘mu::value_type Mratio(mu::value_type, mu::value_type, mu::value_type)’ defined but not used [-Wunused-function] 262 | static mu::value_type Mratio(mu::value_type a, mu::value_type b, mu::value_type z){ | ^~~~~~ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.h:258:23: warning: ‘mu::value_type If(mu::value_type, mu::value_type, mu::value_type)’ defined but not used [-Wunused-function] 258 | static mu::value_type If(mu::value_type v1, mu::value_type v2, mu::value_type v3){ | ^~ [ 10%] Building CXX object CMakeFiles/run_network.dir/src/model/rateExpression.cpp.o /usr/bin/g++ -DRUN_NETWORK_VERSION=\"3.0\" -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3 -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/cvode -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/nvector -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/sundials -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/ssa -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/rateExpressions -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/reactions -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/base -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/eRungeKutta -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/fEuler -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/util -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/eRungeKutta/base -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/eRungeKutta/util -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util/MTrand -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util/rand2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I../src/util/mathutils -I../cvode-2.6.0/include -I../cvode-2.6.0/include/cvode -I../cvode-2.6.0/build/include -I../cvode-2.6.0/src/cvode/fcmix -L../src/util/mathutils -I../muparser_v2_2_4/include -L../muparser_v2_2_4/lib -L../cvode-2.6.0/build/src/cvode/fcmix -L../cvode-2.6.0/build/src/sundials -L../cvode-2.6.0/build/src/cvode -L../cvode-2.6.0/build/src/nvec_ser -MD -MT CMakeFiles/run_network.dir/src/model/rateExpression.cpp.o -MF CMakeFiles/run_network.dir/src/model/rateExpression.cpp.o.d -o CMakeFiles/run_network.dir/src/model/rateExpression.cpp.o -c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/rateExpression.cpp /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/run_network.cpp: In function ‘main’: /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/run_network.cpp:588:48: warning: ‘sample_time’ may be used uninitialized [-Wmaybe-uninitialized] 588 | else t_end = t_start + (double)n_sample*sample_time; | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/run_network.cpp:106:12: note: ‘sample_time’ was declared here 106 | double sample_time, *sample_times = 0x0/*, *st, t1*/; | ^~~~~~~~~~~ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/run_network.cpp:1014:47: warning: ‘derivs’ may be used uninitialized [-Wmaybe-uninitialized] 1014 | derivs_network(t, conc, derivs); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/run_network.cpp:117:32: note: ‘derivs’ was declared here 117 | double *conc, *conc_last, *derivs; | ^~~~~~ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/run_network.cpp:1009:49: warning: ‘conc’ may be used uninitialized [-Wmaybe-uninitialized] 1009 | get_conc_network(conc); | ~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/run_network.cpp:117:13: note: ‘conc’ was declared here 117 | double *conc, *conc_last, *derivs; | ^~~~ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/run_network.cpp:1010:45: warning: ‘conc_last’ may be used uninitialized [-Wmaybe-uninitialized] 1010 | delta = sqrt(VECTOR_DIST(conc, conc_last, n_species_network())) / n_species_network(); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/run_network.cpp:117:20: note: ‘conc_last’ was declared here 117 | double *conc, *conc_last, *derivs; | ^~~~~~~~~ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp: In function ‘rxn_rate_scaled(RXN*, double*, int, double&, double, bool) [clone .constprop.0]’: /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:2703:22: warning: ‘rate’ may be used uninitialized [-Wmaybe-uninitialized] 2703 | if (discrete && rate < 0.0){ | ~~~~~~~~~^~~~~~~~~~~~~ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:2328:16: note: ‘rate’ was declared here 2328 | double rate; | ^~~~ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp: In function ‘rxn_rate(RXN*, double*, int)’: /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:2303:22: warning: ‘rate’ may be used uninitialized [-Wmaybe-uninitialized] 2303 | if (discrete && rate < 0.0){ | ~~~~~~~~~^~~~~~~~~~~~~ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:2126:16: note: ‘rate’ was declared here 2126 | double rate; | ^~~~ [ 12%] Building CXX object CMakeFiles/run_network.dir/src/model/reaction.cpp.o /usr/bin/g++ -DRUN_NETWORK_VERSION=\"3.0\" -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3 -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/cvode -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/nvector -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/sundials -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/ssa -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/rateExpressions -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/reactions -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/base -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/eRungeKutta -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/fEuler -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/util -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/eRungeKutta/base -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/eRungeKutta/util -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util/MTrand -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util/rand2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I../src/util/mathutils -I../cvode-2.6.0/include -I../cvode-2.6.0/include/cvode -I../cvode-2.6.0/build/include -I../cvode-2.6.0/src/cvode/fcmix -L../src/util/mathutils -I../muparser_v2_2_4/include -L../muparser_v2_2_4/lib -L../cvode-2.6.0/build/src/cvode/fcmix -L../cvode-2.6.0/build/src/sundials -L../cvode-2.6.0/build/src/cvode -L../cvode-2.6.0/build/src/nvec_ser -MD -MT CMakeFiles/run_network.dir/src/model/reaction.cpp.o -MF CMakeFiles/run_network.dir/src/model/reaction.cpp.o.d -o CMakeFiles/run_network.dir/src/model/reaction.cpp.o -c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/reaction.cpp [ 14%] Building CXX object CMakeFiles/run_network.dir/src/model/simpleSpecies.cpp.o /usr/bin/g++ -DRUN_NETWORK_VERSION=\"3.0\" -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3 -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/cvode -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/nvector -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/sundials -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/ssa -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/rateExpressions -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/reactions -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/base -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/eRungeKutta -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/fEuler -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/util -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/eRungeKutta/base -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/eRungeKutta/util -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util/MTrand -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util/rand2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I../src/util/mathutils -I../cvode-2.6.0/include -I../cvode-2.6.0/include/cvode -I../cvode-2.6.0/build/include -I../cvode-2.6.0/src/cvode/fcmix -L../src/util/mathutils -I../muparser_v2_2_4/include -L../muparser_v2_2_4/lib -L../cvode-2.6.0/build/src/cvode/fcmix -L../cvode-2.6.0/build/src/sundials -L../cvode-2.6.0/build/src/cvode -L../cvode-2.6.0/build/src/nvec_ser -MD -MT CMakeFiles/run_network.dir/src/model/simpleSpecies.cpp.o -MF CMakeFiles/run_network.dir/src/model/simpleSpecies.cpp.o.d -o CMakeFiles/run_network.dir/src/model/simpleSpecies.cpp.o -c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/simpleSpecies.cpp [ 16%] Building CXX object CMakeFiles/run_network.dir/src/pla/PLA.cpp.o /usr/bin/g++ -DRUN_NETWORK_VERSION=\"3.0\" -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3 -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/cvode -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/nvector -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/sundials -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/ssa -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/rateExpressions -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/reactions -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/base -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/eRungeKutta -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/fEuler -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/util -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/eRungeKutta/base -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/eRungeKutta/util -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util/MTrand -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util/rand2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I../src/util/mathutils -I../cvode-2.6.0/include -I../cvode-2.6.0/include/cvode -I../cvode-2.6.0/build/include -I../cvode-2.6.0/src/cvode/fcmix -L../src/util/mathutils -I../muparser_v2_2_4/include -L../muparser_v2_2_4/lib -L../cvode-2.6.0/build/src/cvode/fcmix -L../cvode-2.6.0/build/src/sundials -L../cvode-2.6.0/build/src/cvode -L../cvode-2.6.0/build/src/nvec_ser -MD -MT CMakeFiles/run_network.dir/src/pla/PLA.cpp.o -MF CMakeFiles/run_network.dir/src/pla/PLA.cpp.o.d -o CMakeFiles/run_network.dir/src/pla/PLA.cpp.o -c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/PLA.cpp [ 18%] Building CXX object CMakeFiles/run_network.dir/src/util/conversion.cpp.o /usr/bin/g++ -DRUN_NETWORK_VERSION=\"3.0\" -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3 -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/cvode -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/nvector -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/sundials -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/ssa -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/rateExpressions -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/reactions -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/base -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/eRungeKutta -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/fEuler -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/util -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/eRungeKutta/base -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/eRungeKutta/util -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util/MTrand -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util/rand2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I../src/util/mathutils -I../cvode-2.6.0/include -I../cvode-2.6.0/include/cvode -I../cvode-2.6.0/build/include -I../cvode-2.6.0/src/cvode/fcmix -L../src/util/mathutils -I../muparser_v2_2_4/include -L../muparser_v2_2_4/lib -L../cvode-2.6.0/build/src/cvode/fcmix -L../cvode-2.6.0/build/src/sundials -L../cvode-2.6.0/build/src/cvode -L../cvode-2.6.0/build/src/nvec_ser -MD -MT CMakeFiles/run_network.dir/src/util/conversion.cpp.o -MF CMakeFiles/run_network.dir/src/util/conversion.cpp.o.d -o CMakeFiles/run_network.dir/src/util/conversion.cpp.o -c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util/conversion.cpp /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp: In function ‘create_update_lists()’: /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:4474:27: warning: ‘rarray’ may be used uninitialized [-Wmaybe-uninitialized] 4474 | if (!(rxn = rarray[i])) | ~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/network.cpp:4459:15: note: ‘rarray’ was declared here 4459 | Rxn **rarray, *rxn; | ^~~~~~ [ 20%] Building CXX object CMakeFiles/run_network.dir/src/util/misc.cpp.o /usr/bin/g++ -DRUN_NETWORK_VERSION=\"3.0\" -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3 -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/cvode -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/nvector -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/sundials 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-I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/eRungeKutta -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/fEuler -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/util -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/eRungeKutta/base -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/eRungeKutta/util -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util/MTrand -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util/rand2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I../src/util/mathutils -I../cvode-2.6.0/include -I../cvode-2.6.0/include/cvode -I../cvode-2.6.0/build/include -I../cvode-2.6.0/src/cvode/fcmix -L../src/util/mathutils -I../muparser_v2_2_4/include -L../muparser_v2_2_4/lib -L../cvode-2.6.0/build/src/cvode/fcmix -L../cvode-2.6.0/build/src/sundials -L../cvode-2.6.0/build/src/cvode -L../cvode-2.6.0/build/src/nvec_ser -MD -MT CMakeFiles/run_network.dir/src/model/reactions/bioNetGenRxn.cpp.o -MF CMakeFiles/run_network.dir/src/model/reactions/bioNetGenRxn.cpp.o.d -o CMakeFiles/run_network.dir/src/model/reactions/bioNetGenRxn.cpp.o -c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/reactions/bioNetGenRxn.cpp In file included from ../muparser_v2_2_4/include/../include/muParserStack.h:35, from ../muparser_v2_2_4/include/../include/muParserBase.h:39, from ../muparser_v2_2_4/include/../include/muParser.h:32, from /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/rateExpressions/rateMuParser.hh:12, from /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/rateExpressions/rateMuParser.cpp:8: ../muparser_v2_2_4/include/../include/muParserToken.h:72:12: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 72 | std::auto_ptr m_pCallback; | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from ../muparser_v2_2_4/include/../include/muParserBase.h:33: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ../muparser_v2_2_4/include/../include/muParserBase.h:291:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 291 | std::auto_ptr m_pTokenReader; ///< Managed pointer to the token reader object. | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ [ 34%] Building CXX object CMakeFiles/run_network.dir/src/model/reactions/elementaryRxn.cpp.o /usr/bin/g++ -DRUN_NETWORK_VERSION=\"3.0\" -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3 -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/cvode -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/nvector -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/sundials -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/ssa -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/rateExpressions -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/reactions -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/base -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/eRungeKutta -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/fEuler -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/util -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/eRungeKutta/base -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/eRungeKutta/util -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util/MTrand -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util/rand2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I../src/util/mathutils -I../cvode-2.6.0/include -I../cvode-2.6.0/include/cvode -I../cvode-2.6.0/build/include -I../cvode-2.6.0/src/cvode/fcmix -L../src/util/mathutils -I../muparser_v2_2_4/include -L../muparser_v2_2_4/lib -L../cvode-2.6.0/build/src/cvode/fcmix -L../cvode-2.6.0/build/src/sundials -L../cvode-2.6.0/build/src/cvode -L../cvode-2.6.0/build/src/nvec_ser -MD -MT CMakeFiles/run_network.dir/src/model/reactions/elementaryRxn.cpp.o -MF CMakeFiles/run_network.dir/src/model/reactions/elementaryRxn.cpp.o.d -o CMakeFiles/run_network.dir/src/model/reactions/elementaryRxn.cpp.o -c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/reactions/elementaryRxn.cpp In file included from ../muparser_v2_2_4/include/muParserStack.h:35, from ../muparser_v2_2_4/include/muParserBase.h:39, from ../muparser_v2_2_4/include/muParser.h:32, from /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/reactions/../function.hh:12, from /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/reactions/bioNetGenRxn.hh:12, from /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/reactions/bioNetGenRxn.cpp:8: ../muparser_v2_2_4/include/muParserToken.h:72:12: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 72 | std::auto_ptr m_pCallback; | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from ../muparser_v2_2_4/include/muParserBase.h:33: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ [ 36%] Building CXX object CMakeFiles/run_network.dir/src/model/reactions/functionalRxn.cpp.o /usr/bin/g++ -DRUN_NETWORK_VERSION=\"3.0\" -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3 -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/cvode -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/nvector -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/sundials -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/ssa -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/rateExpressions -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/reactions -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/base -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/eRungeKutta -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/fEuler -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/util -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/eRungeKutta/base -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/eRungeKutta/util -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util/MTrand -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util/rand2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I../src/util/mathutils -I../cvode-2.6.0/include -I../cvode-2.6.0/include/cvode -I../cvode-2.6.0/build/include -I../cvode-2.6.0/src/cvode/fcmix -L../src/util/mathutils -I../muparser_v2_2_4/include -L../muparser_v2_2_4/lib -L../cvode-2.6.0/build/src/cvode/fcmix -L../cvode-2.6.0/build/src/sundials -L../cvode-2.6.0/build/src/cvode -L../cvode-2.6.0/build/src/nvec_ser -MD -MT CMakeFiles/run_network.dir/src/model/reactions/functionalRxn.cpp.o -MF CMakeFiles/run_network.dir/src/model/reactions/functionalRxn.cpp.o.d -o CMakeFiles/run_network.dir/src/model/reactions/functionalRxn.cpp.o -c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/reactions/functionalRxn.cpp ../muparser_v2_2_4/include/muParserBase.h:291:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 291 | std::auto_ptr m_pTokenReader; ///< Managed pointer to the token reader object. | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ [ 38%] Building CXX object CMakeFiles/run_network.dir/src/model/reactions/hillRxn.cpp.o /usr/bin/g++ -DRUN_NETWORK_VERSION=\"3.0\" -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3 -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/cvode -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/nvector -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/sundials -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/ssa -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/rateExpressions -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/reactions -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/base -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/eRungeKutta -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/fEuler -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/util -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/eRungeKutta/base -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/eRungeKutta/util -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util/MTrand -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util/rand2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I../src/util/mathutils -I../cvode-2.6.0/include -I../cvode-2.6.0/include/cvode -I../cvode-2.6.0/build/include -I../cvode-2.6.0/src/cvode/fcmix -L../src/util/mathutils -I../muparser_v2_2_4/include -L../muparser_v2_2_4/lib -L../cvode-2.6.0/build/src/cvode/fcmix -L../cvode-2.6.0/build/src/sundials -L../cvode-2.6.0/build/src/cvode -L../cvode-2.6.0/build/src/nvec_ser -MD -MT CMakeFiles/run_network.dir/src/model/reactions/hillRxn.cpp.o -MF CMakeFiles/run_network.dir/src/model/reactions/hillRxn.cpp.o.d -o CMakeFiles/run_network.dir/src/model/reactions/hillRxn.cpp.o -c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/reactions/hillRxn.cpp In file included from ../muparser_v2_2_4/include/muParserStack.h:35, from ../muparser_v2_2_4/include/muParserBase.h:39, from ../muparser_v2_2_4/include/muParser.h:32, from /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/reactions/../function.hh:12, from /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/reactions/bioNetGenRxn.hh:12, from /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/reactions/elementaryRxn.cpp:8: ../muparser_v2_2_4/include/muParserToken.h:72:12: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 72 | std::auto_ptr m_pCallback; | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from ../muparser_v2_2_4/include/muParserBase.h:33: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ../muparser_v2_2_4/include/muParserBase.h:291:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 291 | std::auto_ptr m_pTokenReader; ///< Managed pointer to the token reader object. | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from ../muparser_v2_2_4/include/muParserStack.h:35, from ../muparser_v2_2_4/include/muParserBase.h:39, from ../muparser_v2_2_4/include/muParser.h:32, from /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/reactions/../function.hh:12, from /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/reactions/bioNetGenRxn.hh:12, from /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/reactions/functionalRxn.cpp:8: ../muparser_v2_2_4/include/muParserToken.h:72:12: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 72 | std::auto_ptr m_pCallback; | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from ../muparser_v2_2_4/include/muParserBase.h:33: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ../muparser_v2_2_4/include/muParserBase.h:291:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 291 | std::auto_ptr m_pTokenReader; ///< Managed pointer to the token reader object. | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from ../muparser_v2_2_4/include/muParserStack.h:35, from ../muparser_v2_2_4/include/muParserBase.h:39, from ../muparser_v2_2_4/include/muParser.h:32, from /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/reactions/../function.hh:12, from /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/reactions/bioNetGenRxn.hh:12, from /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/reactions/hillRxn.cpp:8: ../muparser_v2_2_4/include/muParserToken.h:72:12: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 72 | std::auto_ptr m_pCallback; | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from ../muparser_v2_2_4/include/muParserBase.h:33: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ [ 40%] Building CXX object CMakeFiles/run_network.dir/src/model/reactions/michaelisMentenRxn.cpp.o /usr/bin/g++ -DRUN_NETWORK_VERSION=\"3.0\" -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3 -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/cvode -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/nvector -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/sundials -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/ssa -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/rateExpressions -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/reactions -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/base -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/eRungeKutta -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/fEuler -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/util -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/eRungeKutta/base -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/eRungeKutta/util -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util/MTrand -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util/rand2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I../src/util/mathutils -I../cvode-2.6.0/include -I../cvode-2.6.0/include/cvode -I../cvode-2.6.0/build/include -I../cvode-2.6.0/src/cvode/fcmix -L../src/util/mathutils -I../muparser_v2_2_4/include -L../muparser_v2_2_4/lib -L../cvode-2.6.0/build/src/cvode/fcmix -L../cvode-2.6.0/build/src/sundials -L../cvode-2.6.0/build/src/cvode -L../cvode-2.6.0/build/src/nvec_ser -MD -MT CMakeFiles/run_network.dir/src/model/reactions/michaelisMentenRxn.cpp.o -MF CMakeFiles/run_network.dir/src/model/reactions/michaelisMentenRxn.cpp.o.d -o CMakeFiles/run_network.dir/src/model/reactions/michaelisMentenRxn.cpp.o -c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/reactions/michaelisMentenRxn.cpp ../muparser_v2_2_4/include/muParserBase.h:291:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 291 | std::auto_ptr m_pTokenReader; ///< Managed pointer to the token reader object. | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ [ 41%] Building CXX object CMakeFiles/run_network.dir/src/model/reactions/saturationRxn.cpp.o /usr/bin/g++ -DRUN_NETWORK_VERSION=\"3.0\" -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3 -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/cvode -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/nvector -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/sundials -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/ssa -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/rateExpressions -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/reactions -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/base -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/eRungeKutta -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/fEuler -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/util -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/eRungeKutta/base -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/eRungeKutta/util -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util/MTrand -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util/rand2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I../src/util/mathutils -I../cvode-2.6.0/include -I../cvode-2.6.0/include/cvode -I../cvode-2.6.0/build/include -I../cvode-2.6.0/src/cvode/fcmix -L../src/util/mathutils -I../muparser_v2_2_4/include -L../muparser_v2_2_4/lib -L../cvode-2.6.0/build/src/cvode/fcmix -L../cvode-2.6.0/build/src/sundials -L../cvode-2.6.0/build/src/cvode -L../cvode-2.6.0/build/src/nvec_ser -MD -MT CMakeFiles/run_network.dir/src/model/reactions/saturationRxn.cpp.o -MF CMakeFiles/run_network.dir/src/model/reactions/saturationRxn.cpp.o.d -o CMakeFiles/run_network.dir/src/model/reactions/saturationRxn.cpp.o -c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/reactions/saturationRxn.cpp [ 43%] Building CXX object CMakeFiles/run_network.dir/src/pla/base/firingGenerator.cpp.o /usr/bin/g++ -DRUN_NETWORK_VERSION=\"3.0\" -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3 -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/cvode -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/nvector -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/sundials -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/ssa -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/rateExpressions -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/reactions -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/base -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/eRungeKutta -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/fEuler -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/util -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/eRungeKutta/base -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/eRungeKutta/util -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util/MTrand -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util/rand2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I../src/util/mathutils -I../cvode-2.6.0/include -I../cvode-2.6.0/include/cvode -I../cvode-2.6.0/build/include -I../cvode-2.6.0/src/cvode/fcmix -L../src/util/mathutils -I../muparser_v2_2_4/include -L../muparser_v2_2_4/lib -L../cvode-2.6.0/build/src/cvode/fcmix -L../cvode-2.6.0/build/src/sundials -L../cvode-2.6.0/build/src/cvode -L../cvode-2.6.0/build/src/nvec_ser -MD -MT CMakeFiles/run_network.dir/src/pla/base/firingGenerator.cpp.o -MF CMakeFiles/run_network.dir/src/pla/base/firingGenerator.cpp.o.d -o CMakeFiles/run_network.dir/src/pla/base/firingGenerator.cpp.o -c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/base/firingGenerator.cpp In file included from ../muparser_v2_2_4/include/muParserStack.h:35, from ../muparser_v2_2_4/include/muParserBase.h:39, from ../muparser_v2_2_4/include/muParser.h:32, from /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/reactions/../function.hh:12, from /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/reactions/bioNetGenRxn.hh:12, from /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/reactions/michaelisMentenRxn.cpp:8: ../muparser_v2_2_4/include/muParserToken.h:72:12: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 72 | std::auto_ptr m_pCallback; | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from ../muparser_v2_2_4/include/muParserBase.h:33: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ [ 45%] Building CXX object CMakeFiles/run_network.dir/src/pla/base/postleapChecker.cpp.o /usr/bin/g++ -DRUN_NETWORK_VERSION=\"3.0\" -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3 -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/cvode -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/nvector -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/sundials -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/ssa -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/rateExpressions -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/reactions -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/base -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/eRungeKutta -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/fEuler -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/util -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/eRungeKutta/base -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/eRungeKutta/util -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util/MTrand -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util/rand2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I../src/util/mathutils -I../cvode-2.6.0/include -I../cvode-2.6.0/include/cvode -I../cvode-2.6.0/build/include -I../cvode-2.6.0/src/cvode/fcmix -L../src/util/mathutils -I../muparser_v2_2_4/include -L../muparser_v2_2_4/lib -L../cvode-2.6.0/build/src/cvode/fcmix -L../cvode-2.6.0/build/src/sundials -L../cvode-2.6.0/build/src/cvode -L../cvode-2.6.0/build/src/nvec_ser -MD -MT CMakeFiles/run_network.dir/src/pla/base/postleapChecker.cpp.o -MF CMakeFiles/run_network.dir/src/pla/base/postleapChecker.cpp.o.d -o CMakeFiles/run_network.dir/src/pla/base/postleapChecker.cpp.o -c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/base/postleapChecker.cpp ../muparser_v2_2_4/include/muParserBase.h:291:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 291 | std::auto_ptr m_pTokenReader; ///< Managed pointer to the token reader object. | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from ../muparser_v2_2_4/include/muParserStack.h:35, from ../muparser_v2_2_4/include/muParserBase.h:39, from ../muparser_v2_2_4/include/muParser.h:32, from /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/reactions/../function.hh:12, from /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/reactions/bioNetGenRxn.hh:12, from /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/reactions/saturationRxn.cpp:8: ../muparser_v2_2_4/include/muParserToken.h:72:12: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 72 | std::auto_ptr m_pCallback; | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from ../muparser_v2_2_4/include/muParserBase.h:33: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ../muparser_v2_2_4/include/muParserBase.h:291:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 291 | std::auto_ptr m_pTokenReader; ///< Managed pointer to the token reader object. | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ [ 47%] Building CXX object CMakeFiles/run_network.dir/src/pla/base/rxnClassifier.cpp.o /usr/bin/g++ -DRUN_NETWORK_VERSION=\"3.0\" -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3 -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/cvode -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/nvector -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/sundials -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/ssa -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/rateExpressions -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/reactions -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/base -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/eRungeKutta 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-specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I../src/util/mathutils -I../cvode-2.6.0/include -I../cvode-2.6.0/include/cvode -I../cvode-2.6.0/build/include -I../cvode-2.6.0/src/cvode/fcmix -L../src/util/mathutils -I../muparser_v2_2_4/include -L../muparser_v2_2_4/lib -L../cvode-2.6.0/build/src/cvode/fcmix -L../cvode-2.6.0/build/src/sundials -L../cvode-2.6.0/build/src/cvode -L../cvode-2.6.0/build/src/nvec_ser -MD -MT CMakeFiles/run_network.dir/src/pla/base/rxnClassifier.cpp.o -MF CMakeFiles/run_network.dir/src/pla/base/rxnClassifier.cpp.o.d -o CMakeFiles/run_network.dir/src/pla/base/rxnClassifier.cpp.o -c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/base/rxnClassifier.cpp [ 49%] Building CXX object CMakeFiles/run_network.dir/src/pla/base/tauCalculator.cpp.o /usr/bin/g++ -DRUN_NETWORK_VERSION=\"3.0\" -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3 -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/cvode -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/nvector -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/sundials -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/ssa -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/rateExpressions -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/reactions -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/base -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/eRungeKutta -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/fEuler -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/util 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-I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/cvode -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/nvector -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/include/sundials -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/ssa -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/rateExpressions -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/reactions -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/base -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/eRungeKutta -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/fEuler -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/util -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/eRungeKutta/base -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/pla/eRungeKutta/util -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util/MTrand -I/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util/rand2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I../src/util/mathutils -I../cvode-2.6.0/include -I../cvode-2.6.0/include/cvode -I../cvode-2.6.0/build/include -I../cvode-2.6.0/src/cvode/fcmix -L../src/util/mathutils -I../muparser_v2_2_4/include -L../muparser_v2_2_4/lib -L../cvode-2.6.0/build/src/cvode/fcmix -L../cvode-2.6.0/build/src/sundials -L../cvode-2.6.0/build/src/cvode -L../cvode-2.6.0/build/src/nvec_ser -MD -MT CMakeFiles/run_network.dir/src/util/rand2/rand2.cpp.o -MF CMakeFiles/run_network.dir/src/util/rand2/rand2.cpp.o.d -o CMakeFiles/run_network.dir/src/util/rand2/rand2.cpp.o -c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util/rand2/rand2.cpp [100%] Linking CXX executable run_network /usr/bin/cmake -E cmake_link_script CMakeFiles/run_network.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Wno-error=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I../src/util/mathutils -I../cvode-2.6.0/include -I../cvode-2.6.0/include/cvode -I../cvode-2.6.0/build/include -I../cvode-2.6.0/src/cvode/fcmix -L../src/util/mathutils -I../muparser_v2_2_4/include -L../muparser_v2_2_4/lib -L../cvode-2.6.0/build/src/cvode/fcmix -L../cvode-2.6.0/build/src/sundials -L../cvode-2.6.0/build/src/cvode -L../cvode-2.6.0/build/src/nvec_ser -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--dependency-file=CMakeFiles/run_network.dir/link.d CMakeFiles/run_network.dir/src/network.cpp.o CMakeFiles/run_network.dir/src/network3.cpp.o CMakeFiles/run_network.dir/src/run_network.cpp.o CMakeFiles/run_network.dir/src/model/function.cpp.o CMakeFiles/run_network.dir/src/model/observable.cpp.o CMakeFiles/run_network.dir/src/model/rateExpression.cpp.o CMakeFiles/run_network.dir/src/model/reaction.cpp.o CMakeFiles/run_network.dir/src/model/simpleSpecies.cpp.o CMakeFiles/run_network.dir/src/pla/PLA.cpp.o CMakeFiles/run_network.dir/src/util/conversion.cpp.o CMakeFiles/run_network.dir/src/util/misc.cpp.o CMakeFiles/run_network.dir/src/util/rand.cpp.o CMakeFiles/run_network.dir/src/model/rateExpressions/rateElementary.cpp.o CMakeFiles/run_network.dir/src/model/rateExpressions/rateHill.cpp.o CMakeFiles/run_network.dir/src/model/rateExpressions/rateMM.cpp.o CMakeFiles/run_network.dir/src/model/rateExpressions/rateMuParser.cpp.o CMakeFiles/run_network.dir/src/model/rateExpressions/rateSaturation.cpp.o CMakeFiles/run_network.dir/src/model/reactions/bioNetGenRxn.cpp.o CMakeFiles/run_network.dir/src/model/reactions/elementaryRxn.cpp.o CMakeFiles/run_network.dir/src/model/reactions/functionalRxn.cpp.o CMakeFiles/run_network.dir/src/model/reactions/hillRxn.cpp.o CMakeFiles/run_network.dir/src/model/reactions/michaelisMentenRxn.cpp.o CMakeFiles/run_network.dir/src/model/reactions/saturationRxn.cpp.o CMakeFiles/run_network.dir/src/pla/base/firingGenerator.cpp.o CMakeFiles/run_network.dir/src/pla/base/postleapChecker.cpp.o CMakeFiles/run_network.dir/src/pla/base/rxnClassifier.cpp.o CMakeFiles/run_network.dir/src/pla/base/tauCalculator.cpp.o CMakeFiles/run_network.dir/src/pla/eRungeKutta/eRungeKutta_postTC_RC_FG_rbPL.cpp.o CMakeFiles/run_network.dir/src/pla/eRungeKutta/eRungeKutta_postTC_RC_FG_sbPL.cpp.o CMakeFiles/run_network.dir/src/pla/eRungeKutta/eRungeKutta_preTC_RC_FG_negPL.cpp.o CMakeFiles/run_network.dir/src/pla/eRungeKutta/eRungeKutta_preTC_RC_FG_rbPL.cpp.o CMakeFiles/run_network.dir/src/pla/eRungeKutta/eRungeKutta_preTC_RC_FG_sbPL.cpp.o CMakeFiles/run_network.dir/src/pla/fEuler/fEulerPreleapRB_TC.cpp.o CMakeFiles/run_network.dir/src/pla/fEuler/fEulerPreleapSB_TC.cpp.o CMakeFiles/run_network.dir/src/pla/fEuler/fEulerRB_PL.cpp.o CMakeFiles/run_network.dir/src/pla/fEuler/fEulerRB_TC_PL.cpp.o CMakeFiles/run_network.dir/src/pla/fEuler/fEulerSB_PL.cpp.o CMakeFiles/run_network.dir/src/pla/fEuler/fEulerSB_TC_PL.cpp.o CMakeFiles/run_network.dir/src/pla/fEuler/fEuler_FG.cpp.o CMakeFiles/run_network.dir/src/pla/fEuler/fEuler_RC.cpp.o CMakeFiles/run_network.dir/src/pla/util/fixed_TC.cpp.o CMakeFiles/run_network.dir/src/pla/util/g_Getter.cpp.o CMakeFiles/run_network.dir/src/pla/util/negPopChecker.cpp.o CMakeFiles/run_network.dir/src/pla/util/preleap_TC.cpp.o CMakeFiles/run_network.dir/src/pla/util/rbChecker.cpp.o CMakeFiles/run_network.dir/src/pla/util/sbChecker.cpp.o CMakeFiles/run_network.dir/src/pla/eRungeKutta/base/eRungeKutta_TC_RC_FG_PL.cpp.o CMakeFiles/run_network.dir/src/pla/eRungeKutta/base/eRungeKutta_TC_RC_FG_rbPL.cpp.o CMakeFiles/run_network.dir/src/pla/eRungeKutta/base/eRungeKutta_TC_RC_FG_sbPL.cpp.o CMakeFiles/run_network.dir/src/pla/eRungeKutta/util/aEff_Calculator.cpp.o CMakeFiles/run_network.dir/src/pla/eRungeKutta/util/binomialCorrector_RK.cpp.o CMakeFiles/run_network.dir/src/pla/eRungeKutta/util/butcherTableau.cpp.o CMakeFiles/run_network.dir/src/util/MTrand/mtrand.cpp.o CMakeFiles/run_network.dir/src/util/rand2/rand2.cpp.o -o run_network -L/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/lib -Wl,-Bstatic -lmathutils -lmuparser -lsundials_cvode -lsundials_fcvode -lsundials_nvecserial -Wl,-Bdynamic gmake[2]: Leaving directory '/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/build' [100%] Built target run_network gmake[1]: Leaving directory '/builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/build' /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/build/CMakeFiles 0 + popd ~/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0 + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.H2Nfqu + umask 022 + cd /builddir/build/BUILD/bionetgen-2.9.0-build + '[' /builddir/build/BUILD/bionetgen-2.9.0-build/BUILDROOT '!=' / ']' + rm -rf /builddir/build/BUILD/bionetgen-2.9.0-build/BUILDROOT ++ dirname /builddir/build/BUILD/bionetgen-2.9.0-build/BUILDROOT + mkdir -p /builddir/build/BUILD/bionetgen-2.9.0-build + mkdir /builddir/build/BUILD/bionetgen-2.9.0-build/BUILDROOT + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd bionetgen-2.9.0 + pushd bionetgen-BioNetGen-2.9.0/bng2/Network3/build ~/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/build ~/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0 + mkdir -vp /builddir/build/BUILD/bionetgen-2.9.0-build/BUILDROOT/usr/bin mkdir: created directory '/builddir/build/BUILD/bionetgen-2.9.0-build/BUILDROOT/usr' mkdir: created directory '/builddir/build/BUILD/bionetgen-2.9.0-build/BUILDROOT/usr/bin' + install -pm 755 run_network /builddir/build/BUILD/bionetgen-2.9.0-build/BUILDROOT/usr/bin/ + popd ~/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0 + mkdir -vp /builddir/build/BUILD/bionetgen-2.9.0-build/BUILDROOT/usr/share/perl5/vendor_perl/BioNetGen mkdir: created directory '/builddir/build/BUILD/bionetgen-2.9.0-build/BUILDROOT/usr/share' mkdir: created directory '/builddir/build/BUILD/bionetgen-2.9.0-build/BUILDROOT/usr/share/perl5' mkdir: created directory '/builddir/build/BUILD/bionetgen-2.9.0-build/BUILDROOT/usr/share/perl5/vendor_perl' mkdir: created directory '/builddir/build/BUILD/bionetgen-2.9.0-build/BUILDROOT/usr/share/perl5/vendor_perl/BioNetGen' + cp -r bionetgen-BioNetGen-2.9.0/bng2/Perl2 /builddir/build/BUILD/bionetgen-2.9.0-build/BUILDROOT/usr/share/perl5/vendor_perl/BioNetGen/ + cp -r bionetgen-BioNetGen-2.9.0/bng2/BNG2.pl /builddir/build/BUILD/bionetgen-2.9.0-build/BUILDROOT/usr/share/perl5/vendor_perl/BioNetGen/ + cp -a bionetgen-BioNetGen-2.9.0/bng2/Models2 /builddir/build/BUILD/bionetgen-2.9.0-build/BUILDROOT/usr/share/perl5/vendor_perl/BioNetGen/ + rm -f /builddir/build/BUILD/bionetgen-2.9.0-build/BUILDROOT/usr/share/perl5/vendor_perl/BioNetGen/Models2/bin/run_network_x86_64-linux + rm -f /builddir/build/BUILD/bionetgen-2.9.0-build/BUILDROOT/usr/share/perl5/vendor_perl/BioNetGen/Models2/run_network + /usr/bin/find-debuginfo -j4 --strict-build-id -m -i --build-id-seed 2.9.0-4.fc42 --unique-debug-suffix -2.9.0-4.fc42.x86_64 --unique-debug-src-base bionetgen-2.9.0-4.fc42.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0 find-debuginfo: starting Extracting debug info from 1 files DWARF-compressing 1 files sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match. Creating .debug symlinks for symlinks to ELF files Copying sources found by 'debugedit -l' to /usr/src/debug/bionetgen-2.9.0-4.fc42.x86_64 find-debuginfo: done + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + /usr/lib/rpm/brp-compress + /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/check-rpaths + /usr/lib/rpm/redhat/brp-mangle-shebangs + /usr/lib/rpm/brp-remove-la-files + env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j4 + /usr/lib/rpm/redhat/brp-python-hardlink + /usr/bin/add-determinism --brp -j4 /builddir/build/BUILD/bionetgen-2.9.0-build/BUILDROOT Scanned 59 directories and 289 files, processed 0 inodes, 0 modified (0 replaced + 0 rewritten), 0 unsupported format, 0 errors Reading /builddir/build/BUILD/bionetgen-2.9.0-build/SPECPARTS/rpm-debuginfo.specpart Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.cK9BGH + umask 022 + cd /builddir/build/BUILD/bionetgen-2.9.0-build + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS ~/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Models2 ~/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0 + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd bionetgen-2.9.0 + pushd bionetgen-BioNetGen-2.9.0/bng2/Models2 + install -pm 755 ../Network3/build/run_network -D ./bin/run_network_x86_64-linux + install -pm 755 ../Network3/build/run_network -D ../bin/run_network_x86_64-linux Running some tests ... + echo 'Running some tests ...' + ../BNG2.pl CaOscillate_Func.bngl CaOscillate_Sat.bngl catalysis.bngl egfr_net.bngl egfr_net_red.bngl egfr_path.bngl energy_example1.bngl fceri_ji.bngl test_continue.bngl BioNetGen version 2.9.0 Reading from file CaOscillate_Func.bngl (level 0) Read 17 parameters. Read 4 molecule types. Read 4 species. Read 4 observable(s). Read 8 reaction rule(s). ACTION: generate_network( CaOscillate_Func ) Iteration 0: 4 species 0 rxns 0.00e+00 CPU s Iteration 1: 4 species 8 rxns 0.00e+00 CPU s Cumulative CPU time for each rule Rule 1: 1 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 2: 1 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 3: 1 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 4: 1 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 5: 1 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 6: 1 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 7: 1 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 8: 1 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Total : 8 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Wrote network in net format to ./CaOscillate_Func.net. CPU TIME: generate_network 0.01 s. ACTION: simulate( method=>"cvode" ) Network simulation using cvode WARNING: writeFile(): Overwriting existing file ./CaOscillate_Func.net. Wrote network in net format to ./CaOscillate_Func.net. Can't exec "hostname": No such file or directory at /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Perl2/BNGAction.pm line 548. Running run_network on full command: /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/bin/run_network_x86_64-linux -o ./CaOscillate_Func -p cvode -a 1e-12 -r 1e-12 --cdat 1 --fdat 0 -v -g ./CaOscillate_Func.net ./CaOscillate_Func.net 0.1 200 [simulation PID is: 3091] run_network 3.0 Read 17 parameters from ./CaOscillate_Func.net Read 4 species from ./CaOscillate_Func.net Read 4 group(s) from ./CaOscillate_Func.net Read 4 function(s) from ./CaOscillate_Func.net Read 8 reaction(s) from ./CaOscillate_Func.net 8 reaction(s) have nonzero rate Initialization took 0.00 CPU seconds Propagating with cvode using dense LU time n_steps n_deriv_calls 0.00 0 0 0.10 717 850 0.20 741 879 0.30 765 904 0.40 790 930 0.50 814 960 0.60 838 985 0.70 863 1015 0.80 887 1040 0.90 912 1067 1.00 936 1099 1.10 961 1129 1.20 993 1171 1.30 1025 1207 1.40 1063 1260 1.50 1105 1310 1.60 1152 1368 1.70 1208 1436 1.80 1281 1523 1.90 1354 1611 2.00 1434 1704 2.10 1509 1792 2.20 1584 1871 2.30 1638 1932 2.40 1688 1984 2.50 1741 2047 2.60 1880 2222 2.70 2351 2772 2.80 2453 2892 2.90 2501 2946 3.00 2552 3007 3.10 2616 3078 3.20 2672 3143 3.30 2730 3208 3.40 2789 3271 3.50 2847 3333 3.60 2903 3395 3.70 2956 3464 3.80 3084 3620 3.90 3240 3799 4.00 3350 3920 4.10 3415 3990 4.20 3465 4046 4.30 3516 4103 4.40 3563 4151 4.50 3599 4196 4.60 3644 4249 4.70 3690 4304 4.80 3746 4371 4.90 3802 4441 5.00 3856 4498 5.10 3895 4545 5.20 3929 4585 5.30 3961 4618 5.40 3984 4642 5.50 4007 4671 5.60 4031 4697 5.70 4054 4722 5.80 4075 4750 5.90 4095 4773 6.00 4115 4795 6.10 4136 4821 6.20 4155 4841 6.30 4168 4854 6.40 4181 4872 6.50 4194 4885 6.60 4207 4898 6.70 4220 4911 6.80 4231 4927 6.90 4239 4935 7.00 4248 4945 7.10 4257 4954 7.20 4265 4963 7.30 4274 4972 7.40 4283 4982 7.50 4292 4996 7.60 4300 5004 7.70 4309 5015 7.80 4318 5024 7.90 4329 5044 8.00 4341 5059 8.10 4352 5077 8.20 4364 5090 8.30 4377 5108 8.40 4396 5135 8.50 4423 5174 8.60 4453 5207 8.70 4492 5256 8.80 4549 5327 8.90 4658 5465 9.00 4979 5847 9.10 5283 6181 9.20 5392 6300 9.30 5431 6345 9.40 5447 6363 9.50 5460 6376 9.60 5473 6389 9.70 5485 6405 9.80 5498 6418 9.90 5511 6431 10.00 5524 6445 10.10 5537 6458 10.20 5549 6475 10.30 5562 6489 10.40 5575 6502 10.50 5588 6516 10.60 5601 6534 10.70 5613 6547 10.80 5626 6562 10.90 5639 6575 11.00 5652 6590 11.10 5664 6608 11.20 5677 6621 11.30 5690 6638 11.40 5708 6656 11.50 5725 6674 11.60 5742 6696 11.70 5759 6714 11.80 5777 6733 11.90 5794 6755 12.00 5811 6773 12.10 5829 6791 12.20 5846 6809 12.30 5863 6832 12.40 5880 6851 12.50 5898 6871 12.60 5915 6894 12.70 5934 6915 12.80 5958 6940 12.90 5981 6969 13.00 6004 6994 13.10 6031 7026 13.20 6063 7065 13.30 6095 7100 13.40 6129 7145 13.50 6172 7196 13.60 6218 7252 13.70 6272 7316 13.80 6345 7398 13.90 6417 7485 14.00 6498 7583 14.10 6573 7669 14.20 6648 7748 14.30 6704 7810 14.40 6754 7867 14.50 6806 7929 14.60 6933 8086 14.70 7392 8627 14.80 7505 8764 14.90 7557 8822 15.00 7606 8884 15.10 7667 8954 15.20 7727 9021 15.30 7788 9088 15.40 7849 9153 15.50 7910 9218 15.60 7968 9281 15.70 8020 9346 15.80 8144 9498 15.90 8284 9667 16.00 8401 9791 16.10 8469 9868 16.20 8525 9928 16.30 8581 9988 16.40 8629 10037 16.50 8666 10082 16.60 8711 10136 16.70 8761 10188 16.80 8819 10257 16.90 8879 10326 17.00 8937 10391 17.10 8976 10441 17.20 9012 10480 17.30 9045 10518 17.40 9069 10542 17.50 9092 10572 17.60 9115 10597 17.70 9139 10623 17.80 9160 10651 17.90 9180 10674 18.00 9200 10696 18.10 9221 10722 18.20 9240 10742 18.30 9251 10758 18.40 9262 10769 18.50 9273 10785 18.60 9284 10796 18.70 9295 10807 18.80 9306 10818 18.90 9316 10828 19.00 9327 10839 19.10 9338 10854 19.20 9349 10865 19.30 9360 10876 19.40 9371 10887 19.50 9382 10898 19.60 9393 10913 19.70 9404 10924 19.80 9415 10935 19.90 9426 10946 20.00 9437 10959 Time course of concentrations written to file ./CaOscillate_Func.cdat. Time course of groups written to file ./CaOscillate_Func.gdat. Propagation took 0.00e+00 CPU seconds Program times: 0.00 CPU s 0.00 clock s Updating species concentrations from ./CaOscillate_Func.cdat CPU TIME: simulate 0.00 s. Finished processing file CaOscillate_Func.bngl. CPU TIME: total 0.02 s. BioNetGen version 2.9.0 Reading from file CaOscillate_Sat.bngl (level 0) Read 17 parameters. Read 4 molecule types. Read 4 species. Read 4 observable(s). Read 8 reaction rule(s). ACTION: generate_network( CaOscillate_Sat ) Iteration 0: 4 species 0 rxns 0.00e+00 CPU s Iteration 1: 4 species 8 rxns 1.00e-02 CPU s Cumulative CPU time for each rule Rule 1: 1 reactions 1.00e-02 CPU s 1.00e-02 CPU s/rxn Rule 2: 1 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 3: 1 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 4: 1 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 5: 1 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 6: 1 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 7: 1 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 8: 1 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Total : 8 reactions 1.00e-02 CPU s 1.25e-03 CPU s/rxn Wrote network in net format to ./CaOscillate_Sat.net. CPU TIME: generate_network 0.01 s. ACTION: simulate( method=>"cvode" ) Network simulation using cvode WARNING: writeFile(): Overwriting existing file ./CaOscillate_Sat.net. Wrote network in net format to ./CaOscillate_Sat.net. Can't exec "hostname": No such file or directory at /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Perl2/BNGAction.pm line 548. Running run_network on full command: /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/bin/run_network_x86_64-linux -o ./CaOscillate_Sat -p cvode -a 1e-12 -r 1e-12 --cdat 1 --fdat 0 -v -g ./CaOscillate_Sat.net ./CaOscillate_Sat.net 0.1 200 [simulation PID is: 3093] run_network 3.0 Read 17 parameters from ./CaOscillate_Sat.net Read 4 species from ./CaOscillate_Sat.net Read 4 group(s) from ./CaOscillate_Sat.net Read 0 function(s) from ./CaOscillate_Sat.net Read 8 reaction(s) from ./CaOscillate_Sat.net 8 reaction(s) have nonzero rate Initialization took 0.00 CPU seconds Propagating with cvode using dense LU time n_steps n_deriv_calls 0.00 0 0 0.10 719 851 0.20 753 889 0.30 788 924 0.40 819 960 0.50 842 984 0.60 865 1008 0.70 888 1036 0.80 911 1060 0.90 934 1091 1.00 957 1116 1.10 983 1146 1.20 1014 1184 1.30 1046 1218 1.40 1079 1259 1.50 1122 1310 1.60 1169 1362 1.70 1226 1428 1.80 1296 1512 1.90 1370 1605 2.00 1450 1698 2.10 1526 1787 2.20 1601 1866 2.30 1655 1927 2.40 1705 1979 2.50 1759 2043 2.60 1897 2217 2.70 2371 2794 2.80 2470 2900 2.90 2528 2962 3.00 2575 3020 3.10 2628 3083 3.20 2680 3143 3.30 2732 3204 3.40 2784 3261 3.50 2836 3315 3.60 2888 3373 3.70 2941 3438 3.80 3067 3595 3.90 3224 3777 4.00 3337 3901 4.10 3402 3971 4.20 3456 4029 4.30 3510 4087 4.40 3558 4140 4.50 3594 4180 4.60 3640 4236 4.70 3688 4292 4.80 3746 4359 4.90 3805 4430 5.00 3862 4493 5.10 3903 4540 5.20 3941 4580 5.30 3975 4619 5.40 4000 4645 5.50 4025 4675 5.60 4051 4705 5.70 4076 4735 5.80 4099 4760 5.90 4119 4782 6.00 4140 4808 6.10 4162 4831 6.20 4181 4855 6.30 4192 4871 6.40 4204 4883 6.50 4216 4896 6.60 4228 4908 6.70 4240 4920 6.80 4252 4936 6.90 4264 4948 7.00 4276 4960 7.10 4288 4972 7.20 4299 4983 7.30 4311 4999 7.40 4323 5011 7.50 4335 5023 7.60 4347 5035 7.70 4359 5047 7.80 4371 5063 7.90 4383 5075 8.00 4395 5087 8.10 4407 5099 8.20 4419 5113 8.30 4434 5143 8.40 4450 5161 8.50 4471 5189 8.60 4498 5230 8.70 4533 5272 8.80 4592 5345 8.90 4696 5473 9.00 5025 5862 9.10 5314 6183 9.20 5422 6298 9.30 5462 6344 9.40 5475 6364 9.50 5485 6378 9.60 5494 6387 9.70 5503 6402 9.80 5513 6412 9.90 5522 6423 10.00 5532 6433 10.10 5541 6444 10.20 5551 6454 10.30 5562 6471 10.40 5575 6485 10.50 5588 6498 10.60 5600 6511 10.70 5613 6525 10.80 5626 6544 10.90 5638 6558 11.00 5651 6571 11.10 5664 6586 11.20 5677 6605 11.30 5691 6621 11.40 5708 6639 11.50 5725 6661 11.60 5742 6678 11.70 5760 6697 11.80 5777 6715 11.90 5794 6737 12.00 5811 6755 12.10 5828 6773 12.20 5845 6795 12.30 5862 6813 12.40 5880 6833 12.50 5897 6852 12.60 5914 6875 12.70 5934 6897 12.80 5957 6921 12.90 5980 6950 13.00 6003 6975 13.10 6031 7008 13.20 6063 7047 13.30 6094 7086 13.40 6128 7126 13.50 6171 7177 13.60 6218 7234 13.70 6273 7301 13.80 6345 7381 13.90 6417 7472 14.00 6501 7568 14.10 6578 7655 14.20 6655 7740 14.30 6708 7800 14.40 6759 7858 14.50 6813 7917 14.60 6940 8079 14.70 7388 8611 14.80 7506 8741 14.90 7559 8800 15.00 7608 8861 15.10 7668 8930 15.20 7728 8997 15.30 7788 9063 15.40 7848 9127 15.50 7908 9191 15.60 7965 9253 15.70 8017 9318 15.80 8141 9471 15.90 8281 9636 16.00 8398 9764 16.10 8466 9837 16.20 8522 9897 16.30 8578 9957 16.40 8626 10010 16.50 8664 10052 16.60 8708 10105 16.70 8758 10161 16.80 8816 10230 16.90 8876 10295 17.00 8934 10360 17.10 8976 10408 17.20 9014 10452 17.30 9048 10487 17.40 9073 10516 17.50 9099 10543 17.60 9124 10576 17.70 9149 10602 17.80 9172 10627 17.90 9192 10653 18.00 9213 10675 18.10 9234 10697 18.20 9253 10721 18.30 9265 10738 18.40 9275 10748 18.50 9285 10759 18.60 9295 10769 18.70 9305 10783 18.80 9315 10793 18.90 9325 10803 19.00 9335 10813 19.10 9345 10823 19.20 9354 10832 19.30 9364 10846 19.40 9374 10856 19.50 9384 10868 19.60 9394 10878 19.70 9404 10889 19.80 9414 10901 19.90 9424 10919 20.00 9434 10929 Time course of concentrations written to file ./CaOscillate_Sat.cdat. Time course of groups written to file ./CaOscillate_Sat.gdat. Propagation took 0.00e+00 CPU seconds Program times: 0.00 CPU s 0.00 clock s Updating species concentrations from ./CaOscillate_Sat.cdat CPU TIME: simulate 0.02 s. Finished processing file CaOscillate_Sat.bngl. CPU TIME: total 0.03 s. BioNetGen version 2.9.0 Reading from file catalysis.bngl (level 0) CPU TIME: version 0.00 s. Warning: Parameter Gf_S_kinase is set to a negative value: -41.5 Warning: Parameter Gf_S_pptase is set to a negative value: -41.5 Warning: Parameter Ea0_S_kinase is set to a negative value: -7.7 Warning: Parameter Ea0_S_pptase is set to a negative value: -7.7 Warning: Parameter Ea0_cat_kinase is set to a negative value: -11.9 Read 17 parameters. Read 1 compartments. Read 5 molecule types. Read 5 species. Read 4 reaction rule(s). Read 4 energy patterns(s). Read 6 observable(s). ACTION: generate_network( catalysis ) Iteration 0: 5 species 0 rxns 0.00e+00 CPU s Iteration 1: 7 species 2 rxns 0.00e+00 CPU s Iteration 2: 9 species 6 rxns 0.00e+00 CPU s Iteration 3: 10 species 10 rxns 1.00e-02 CPU s Iteration 4: 10 species 12 rxns 0.00e+00 CPU s Cumulative CPU time for each rule Rule 1: 4 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 2: 4 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 3: 2 reactions 1.00e-02 CPU s 5.00e-03 CPU s/rxn Rule 4: 2 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Total : 12 reactions 1.00e-02 CPU s 8.33e-04 CPU s/rxn Wrote network in net format to ./catalysis.net. CPU TIME: generate_network 0.01 s. ACTION: simulate( method=>"cvode" ) Network simulation using cvode WARNING: writeFile(): Overwriting existing file ./catalysis.net. Wrote network in net format to ./catalysis.net. Can't exec "hostname": No such file or directory at /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Perl2/BNGAction.pm line 548. Running run_network on full command: /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/bin/run_network_x86_64-linux -o ./catalysis -p cvode -a 0.001 -r 1e-07 --cdat 1 --fdat 0 -g ./catalysis.net ./catalysis.net 30 120 [simulation PID is: 3095] run_network 3.0 Read 30 parameters from ./catalysis.net @C::$ATP() is a fixed (boundaryCondition) variable @C::$ADP() is a fixed (boundaryCondition) variable Read 10 species from ./catalysis.net Read 6 group(s) from ./catalysis.net Read 0 function(s) from ./catalysis.net Read 12 reaction(s) from ./catalysis.net 12 reaction(s) have nonzero rate Initialization took 0.00 CPU seconds Propagating with cvode using dense LU Time course of concentrations written to file ./catalysis.cdat. Time course of groups written to file ./catalysis.gdat. Propagation took 0.00e+00 CPU seconds Program times: 0.00 CPU s 0.00 clock s Updating species concentrations from ./catalysis.cdat CPU TIME: simulate 0.01 s. Finished processing file catalysis.bngl. CPU TIME: total 0.03 s. BioNetGen version 2.9.0 Reading from file egfr_net.bngl (level 0) Read 48 parameters. Read 5 molecule types. Read 6 species. Read 23 reaction rule(s). Read 15 observable(s). ACTION: generate_network( egfr_net ) Iteration 0: 6 species 0 rxns 0.00e+00 CPU s Iteration 1: 7 species 3 rxns 0.00e+00 CPU s Iteration 2: 8 species 5 rxns 1.00e-02 CPU s Iteration 3: 10 species 8 rxns 0.00e+00 CPU s Iteration 4: 19 species 21 rxns 1.00e-02 CPU s Iteration 5: 37 species 76 rxns 5.00e-02 CPU s Iteration 6: 69 species 213 rxns 1.20e-01 CPU s Iteration 7: 131 species 494 rxns 2.60e-01 CPU s Iteration 8: 295 species 1260 rxns 8.30e-01 CPU s Iteration 9: 356 species 3088 rxns 2.19e+00 CPU s Iteration 10: 356 species 3749 rxns 1.00e+00 CPU s Cumulative CPU time for each rule Rule 1: 48 reactions 7.00e-02 CPU s 1.46e-03 CPU s/rxn Rule 2: 600 reactions 1.05e+00 CPU s 1.75e-03 CPU s/rxn Rule 3: 144 reactions 1.30e-01 CPU s 9.03e-04 CPU s/rxn Rule 4: 96 reactions 9.00e-02 CPU s 9.38e-04 CPU s/rxn Rule 5: 156 reactions 1.10e-01 CPU s 7.05e-04 CPU s/rxn Rule 6: 104 reactions 7.00e-02 CPU s 6.73e-04 CPU s/rxn Rule 7: 96 reactions 1.10e-01 CPU s 1.15e-03 CPU s/rxn Rule 8: 104 reactions 8.00e-02 CPU s 7.69e-04 CPU s/rxn Rule 9: 312 reactions 2.90e-01 CPU s 9.29e-04 CPU s/rxn Rule 10: 312 reactions 3.40e-01 CPU s 1.09e-03 CPU s/rxn Rule 11: 312 reactions 3.30e-01 CPU s 1.06e-03 CPU s/rxn Rule 12: 208 reactions 2.10e-01 CPU s 1.01e-03 CPU s/rxn Rule 13: 208 reactions 1.90e-01 CPU s 9.13e-04 CPU s/rxn Rule 14: 208 reactions 2.70e-01 CPU s 1.30e-03 CPU s/rxn Rule 15: 208 reactions 2.80e-01 CPU s 1.35e-03 CPU s/rxn Rule 16: 208 reactions 2.40e-01 CPU s 1.15e-03 CPU s/rxn Rule 17: 208 reactions 2.80e-01 CPU s 1.35e-03 CPU s/rxn Rule 18: 208 reactions 2.40e-01 CPU s 1.15e-03 CPU s/rxn Rule 19: 2 reactions 4.00e-02 CPU s 2.00e-02 CPU s/rxn Rule 20: 2 reactions 1.00e-02 CPU s 5.00e-03 CPU s/rxn Rule 21: 1 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 22: 2 reactions 2.00e-02 CPU s 1.00e-02 CPU s/rxn Rule 23: 2 reactions 2.00e-02 CPU s 1.00e-02 CPU s/rxn Total : 3749 reactions 4.47e+00 CPU s 1.19e-03 CPU s/rxn Wrote network in net format to ./egfr_net.net. CPU TIME: generate_network 4.55 s. ACTION: simulate( method=>"cvode" ) Network simulation using cvode WARNING: writeFile(): Overwriting existing file ./egfr_net.net. Wrote network in net format to ./egfr_net.net. Can't exec "hostname": No such file or directory at /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Perl2/BNGAction.pm line 548. Running run_network on full command: /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/bin/run_network_x86_64-linux -o ./egfr_net -p cvode -a 1e-08 -r 1e-08 -b --cdat 1 --fdat 0 -g ./egfr_net.net ./egfr_net.net 0.8 50 [simulation PID is: 3097] run_network 3.0 Read 48 parameters from ./egfr_net.net Read 356 species from ./egfr_net.net Read 15 group(s) from ./egfr_net.net Read 0 function(s) from ./egfr_net.net Read 3749 reaction(s) from ./egfr_net.net 3749 reaction(s) have nonzero rate Initialization took 0.01 CPU seconds Propagating with cvode using GMRES Time course of concentrations written to file ./egfr_net.cdat. Time course of groups written to file ./egfr_net.gdat. Propagation took 5.00e-02 CPU seconds Program times: 0.06 CPU s 0.00 clock s Updating species concentrations from ./egfr_net.cdat CPU TIME: simulate 0.13 s. Finished processing file egfr_net.bngl. CPU TIME: total 4.72 s. BioNetGen version 2.9.0 Reading from file egfr_net_red.bngl (level 0) Read 48 parameters. Read 7 molecule types. Read 7 species. Read 14 observable(s). Read 26 reaction rule(s). ACTION: generate_network( egfr_net_red ) Iteration 0: 7 species 0 rxns 0.00e+00 CPU s Iteration 1: 11 species 4 rxns 1.00e-02 CPU s Iteration 2: 13 species 10 rxns 1.00e-02 CPU s Iteration 3: 15 species 14 rxns 0.00e+00 CPU s Iteration 4: 20 species 21 rxns 1.00e-02 CPU s Iteration 5: 26 species 39 rxns 1.00e-02 CPU s Iteration 6: 33 species 62 rxns 2.00e-02 CPU s Iteration 7: 38 species 90 rxns 2.00e-02 CPU s Iteration 8: 40 species 115 rxns 2.00e-02 CPU s Iteration 9: 40 species 123 rxns 0.00e+00 CPU s Cumulative CPU time for each rule Rule 1: 2 reactions 1.00e-02 CPU s 5.00e-03 CPU s/rxn Rule 2: 8 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 3: 12 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 4: 8 reactions 1.00e-02 CPU s 1.25e-03 CPU s/rxn Rule 5: 12 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 6: 1 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 7: 1 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 8: 3 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 9: 3 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 10: 1 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 11: 3 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 12: 6 reactions 2.00e-02 CPU s 3.33e-03 CPU s/rxn Rule 13: 6 reactions 1.00e-02 CPU s 1.67e-03 CPU s/rxn Rule 14: 6 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 15: 6 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 16: 6 reactions 1.00e-02 CPU s 1.67e-03 CPU s/rxn Rule 17: 6 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 18: 6 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 19: 6 reactions 1.00e-02 CPU s 1.67e-03 CPU s/rxn Rule 20: 6 reactions 1.00e-02 CPU s 1.67e-03 CPU s/rxn Rule 21: 6 reactions 1.00e-02 CPU s 1.67e-03 CPU s/rxn Rule 22: 2 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 23: 2 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 24: 1 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 25: 2 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 26: 2 reactions 1.00e-02 CPU s 5.00e-03 CPU s/rxn Total : 123 reactions 1.00e-01 CPU s 8.13e-04 CPU s/rxn Wrote network in net format to ./egfr_net_red.net. CPU TIME: generate_network 0.11 s. Set concentration of species egf(r) to value 0 CPU TIME: setConcentration 0.00 s. ACTION: simulate( method=>"cvode" ) Network simulation using cvode WARNING: writeFile(): Overwriting existing file ./egfr_net_red.net. Wrote network in net format to ./egfr_net_red.net. Can't exec "hostname": No such file or directory at /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Perl2/BNGAction.pm line 548. Running run_network on full command: /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/bin/run_network_x86_64-linux -o ./egfr_net_red -p cvode -a 1e-08 -r 1e-08 -b -c --cdat 1 --fdat 0 -g ./egfr_net_red.net ./egfr_net_red.net 10000 10 [simulation PID is: 3099] run_network 3.0 Read 48 parameters from ./egfr_net_red.net Read 40 species from ./egfr_net_red.net Read 14 group(s) from ./egfr_net_red.net Read 3 function(s) from ./egfr_net_red.net Read 123 reaction(s) from ./egfr_net_red.net 123 reaction(s) have nonzero rate Initialization took 0.00 CPU seconds Propagating with cvode using GMRES Time course of concentrations written to file ./egfr_net_red.cdat. Time course of groups written to file ./egfr_net_red.gdat. Propagation took 0.00e+00 CPU seconds Program times: 0.00 CPU s 0.00 clock s Simulation reached steady state by t_end=100000 Updating species concentrations from ./egfr_net_red.cdat CPU TIME: simulate 0.02 s. Set concentration of species egf(r) to value egf_tot CPU TIME: setConcentration 0.00 s. ACTION: simulate( method=>"cvode" ) Network simulation using cvode WARNING: writeFile(): Overwriting existing file ./egfr_net_red.net. Wrote network in net format to ./egfr_net_red.net. Can't exec "hostname": No such file or directory at /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Perl2/BNGAction.pm line 548. Running run_network on full command: /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/bin/run_network_x86_64-linux -o ./egfr_net_red -p cvode -a 1e-08 -r 1e-08 -b --cdat 1 --fdat 0 -g ./egfr_net_red.net ./egfr_net_red.net 1 120 [simulation PID is: 3101] run_network 3.0 Read 48 parameters from ./egfr_net_red.net Read 40 species from ./egfr_net_red.net Read 14 group(s) from ./egfr_net_red.net Read 3 function(s) from ./egfr_net_red.net Read 123 reaction(s) from ./egfr_net_red.net 123 reaction(s) have nonzero rate Initialization took 0.00 CPU seconds Propagating with cvode using GMRES Time course of concentrations written to file ./egfr_net_red.cdat. Time course of groups written to file ./egfr_net_red.gdat. Propagation took 0.00e+00 CPU seconds Program times: 0.00 CPU s 0.00 clock s Updating species concentrations from ./egfr_net_red.cdat CPU TIME: simulate 0.01 s. Finished processing file egfr_net_red.bngl. CPU TIME: total 0.18 s. BioNetGen version 2.9.0 Reading from file egfr_path.bngl (level 0) Read 48 parameters. Read 18 species. Read 19 reaction rule(s). Read 11 observable(s). ACTION: generate_network( egfr_path ) Iteration 0: 18 species 0 rxns 0.00e+00 CPU s Iteration 1: 18 species 37 rxns 1.00e-02 CPU s Cumulative CPU time for each rule Rule 1: 2 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 2: 2 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 3: 2 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 4: 2 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 5: 2 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 6: 2 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 7: 2 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 8: 2 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 9: 2 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 10: 2 reactions 1.00e-02 CPU s 5.00e-03 CPU s/rxn Rule 11: 2 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 12: 2 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 13: 2 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 14: 2 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 15: 2 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 16: 2 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 17: 1 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 18: 2 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 19: 2 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Total : 37 reactions 1.00e-02 CPU s 2.70e-04 CPU s/rxn Wrote network in net format to ./egfr_path.net. CPU TIME: generate_network 0.02 s. Set concentration of species EGF() to value 0 CPU TIME: setConcentration 0.00 s. ACTION: simulate( method=>"cvode" ) Network simulation using cvode WARNING: writeFile(): Overwriting existing file ./egfr_path.net. Wrote network in net format to ./egfr_path.net. Can't exec "hostname": No such file or directory at /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Perl2/BNGAction.pm line 548. Running run_network on full command: /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/bin/run_network_x86_64-linux -o ./egfr_path -p cvode -a 1e-08 -r 1e-08 -c --cdat 1 --fdat 0 -g ./egfr_path.net ./egfr_path.net 10000 10 [simulation PID is: 3103] run_network 3.0 Read 48 parameters from ./egfr_path.net Read 18 species from ./egfr_path.net Read 11 group(s) from ./egfr_path.net Read 0 function(s) from ./egfr_path.net Read 37 reaction(s) from ./egfr_path.net 37 reaction(s) have nonzero rate Initialization took 0.00 CPU seconds Propagating with cvode using dense LU Time course of concentrations written to file ./egfr_path.cdat. Time course of groups written to file ./egfr_path.gdat. Propagation took 0.00e+00 CPU seconds Program times: 0.00 CPU s 0.00 clock s Simulation reached steady state by t_end=100000 Updating species concentrations from ./egfr_path.cdat CPU TIME: simulate 0.02 s. Set concentration of species EGF() to value EGF_tot CPU TIME: setConcentration 0.00 s. ACTION: simulate( method=>"cvode" ) Network simulation using cvode WARNING: writeFile(): Overwriting existing file ./egfr_path.net. Wrote network in net format to ./egfr_path.net. Can't exec "hostname": No such file or directory at /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Perl2/BNGAction.pm line 548. Running run_network on full command: /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/bin/run_network_x86_64-linux -o ./egfr_path -p cvode -a 1e-08 -r 1e-08 --cdat 1 --fdat 0 -g ./egfr_path.net ./egfr_path.net 1 120 [simulation PID is: 3105] run_network 3.0 Read 48 parameters from ./egfr_path.net Read 18 species from ./egfr_path.net Read 11 group(s) from ./egfr_path.net Read 0 function(s) from ./egfr_path.net Read 37 reaction(s) from ./egfr_path.net 37 reaction(s) have nonzero rate Initialization took 0.00 CPU seconds Propagating with cvode using dense LU Time course of concentrations written to file ./egfr_path.cdat. Time course of groups written to file ./egfr_path.gdat. Propagation took 0.00e+00 CPU seconds Program times: 0.00 CPU s 0.00 clock s Updating species concentrations from ./egfr_path.cdat CPU TIME: simulate 0.00 s. Finished processing file egfr_path.bngl. CPU TIME: total 0.06 s. BioNetGen version 2.9.0 Reading from file energy_example1.bngl (level 0) CPU TIME: version 0.00 s. Warning: Parameter Gf_SA is set to a negative value: -47.5 Warning: Parameter Gf_SB is set to a negative value: -47.5 Warning: Parameter Gf_SC is set to a negative value: -47.5 Warning: Parameter Gf_SBC is set to a negative value: -5.9 Warning: Parameter Gf_SABC is set to a negative value: -1.8 Warning: Parameter Ea0_SA is set to a negative value: -17.8 Warning: Parameter Ea0_SB is set to a negative value: -17.8 Warning: Parameter Ea0_SC is set to a negative value: -17.8 Read 19 parameters. Read 1 compartments. Read 4 molecule types. Read 4 species. Read 6 energy patterns(s). Read 11 observable(s). Read 3 reaction rule(s). ACTION: generate_network( energy_example1 ) Iteration 0: 4 species 0 rxns 0.00e+00 CPU s Iteration 1: 7 species 3 rxns 0.00e+00 CPU s Iteration 2: 10 species 12 rxns 1.00e-02 CPU s Iteration 3: 11 species 21 rxns 1.00e-02 CPU s Iteration 4: 11 species 24 rxns 1.00e-02 CPU s Cumulative CPU time for each rule Rule 1: 8 reactions 2.00e-02 CPU s 2.50e-03 CPU s/rxn Rule 2: 8 reactions 1.00e-02 CPU s 1.25e-03 CPU s/rxn Rule 3: 8 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Total : 24 reactions 3.00e-02 CPU s 1.25e-03 CPU s/rxn Wrote network in net format to ./energy_example1.net. CPU TIME: generate_network 0.03 s. Wrote SBML to ./energy_example1_sbml.xml. CPU TIME: writeSBML 0.01 s. Finished processing file energy_example1.bngl. CPU TIME: total 0.05 s. BioNetGen version 2.9.0 Reading from file fceri_ji.bngl (level 0) Read 26 parameters. Read 4 species. Adding pY as allowed state of component b of molecule Rec Adding pY as allowed state of component g of molecule Rec Adding pY as allowed state of component l of molecule Syk Adding pY as allowed state of component a of molecule Syk Read 19 reaction rule(s). Read 10 observable(s). ACTION: generate_network( fceri_ji ) Iteration 0: 4 species 0 rxns 0.00e+00 CPU s Iteration 1: 6 species 2 rxns 1.00e-02 CPU s Iteration 2: 9 species 8 rxns 0.00e+00 CPU s Iteration 3: 12 species 20 rxns 1.00e-02 CPU s Iteration 4: 22 species 36 rxns 2.00e-02 CPU s Iteration 5: 43 species 100 rxns 4.00e-02 CPU s Iteration 6: 78 species 255 rxns 1.00e-01 CPU s Iteration 7: 139 species 586 rxns 2.40e-01 CPU s Iteration 8: 199 species 1190 rxns 4.60e-01 CPU s Iteration 9: 303 species 1841 rxns 5.70e-01 CPU s Iteration 10: 354 species 3143 rxns 9.80e-01 CPU s Iteration 11: 354 species 3680 rxns 4.20e-01 CPU s Cumulative CPU time for each rule Rule 1: 48 reactions 5.00e-02 CPU s 1.04e-03 CPU s/rxn Rule 2: 1152 reactions 8.00e-01 CPU s 6.94e-04 CPU s/rxn Rule 3: 312 reactions 2.60e-01 CPU s 8.33e-04 CPU s/rxn Rule 4: 36 reactions 4.00e-02 CPU s 1.11e-03 CPU s/rxn Rule 5: 24 reactions 4.00e-02 CPU s 1.67e-03 CPU s/rxn Rule 6: 312 reactions 2.60e-01 CPU s 8.33e-04 CPU s/rxn Rule 7: 36 reactions 4.00e-02 CPU s 1.11e-03 CPU s/rxn Rule 8: 24 reactions 3.00e-02 CPU s 1.25e-03 CPU s/rxn Rule 9: 832 reactions 5.90e-01 CPU s 7.09e-04 CPU s/rxn Rule 10: 48 reactions 7.00e-02 CPU s 1.46e-03 CPU s/rxn Rule 11: 48 reactions 6.00e-02 CPU s 1.25e-03 CPU s/rxn Rule 12: 64 reactions 9.00e-02 CPU s 1.41e-03 CPU s/rxn Rule 13: 64 reactions 9.00e-02 CPU s 1.41e-03 CPU s/rxn Rule 14: 156 reactions 1.10e-01 CPU s 7.05e-04 CPU s/rxn Rule 15: 104 reactions 5.00e-02 CPU s 4.81e-04 CPU s/rxn Rule 16: 208 reactions 1.30e-01 CPU s 6.25e-04 CPU s/rxn Rule 17: 208 reactions 1.40e-01 CPU s 6.73e-04 CPU s/rxn Rule 18: 2 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 19: 2 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Total : 3680 reactions 2.85e+00 CPU s 7.74e-04 CPU s/rxn Wrote network in net format to ./fceri_ji.net. CPU TIME: generate_network 2.94 s. ACTION: simulate( method=>"cvode" ) Network simulation using cvode WARNING: writeFile(): Overwriting existing file ./fceri_ji.net. Wrote network in net format to ./fceri_ji.net. Can't exec "hostname": No such file or directory at /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Perl2/BNGAction.pm line 548. Running run_network on full command: /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/bin/run_network_x86_64-linux -o ./fceri_ji -p cvode -a 1e-08 -r 1e-08 --cdat 1 --fdat 0 -g ./fceri_ji.net ./fceri_ji.net 60 10 [simulation PID is: 3107] run_network 3.0 Read 26 parameters from ./fceri_ji.net Read 354 species from ./fceri_ji.net Read 10 group(s) from ./fceri_ji.net Read 0 function(s) from ./fceri_ji.net Read 3680 reaction(s) from ./fceri_ji.net Removed 600 reactions with zero rate 3080 reaction(s) have nonzero rate Initialization took 0.01 CPU seconds Propagating with cvode using dense LU Time course of concentrations written to file ./fceri_ji.cdat. Time course of groups written to file ./fceri_ji.gdat. Propagation took 4.50e-01 CPU seconds Program times: 0.46 CPU s 1.00 clock s Updating species concentrations from ./fceri_ji.cdat CPU TIME: simulate 0.54 s. Finished processing file fceri_ji.bngl. CPU TIME: total 3.50 s. BioNetGen version 2.9.0 Reading from file test_continue.bngl (level 0) Read 19 parameters. Read 5 molecule types. Read 4 species. Read 6 observable(s). Read 6 reaction rule(s). ACTION: generate_network( test_continue ) Iteration 0: 4 species 0 rxns 0.00e+00 CPU s Iteration 1: 6 species 2 rxns 1.00e-02 CPU s Iteration 2: 7 species 5 rxns 0.00e+00 CPU s Iteration 3: 8 species 7 rxns 0.00e+00 CPU s Iteration 4: 12 species 12 rxns 0.00e+00 CPU s Iteration 5: 17 species 30 rxns 2.00e-02 CPU s Iteration 6: 22 species 59 rxns 2.00e-02 CPU s Iteration 7: 22 species 76 rxns 2.00e-02 CPU s Cumulative CPU time for each rule Rule 1: 8 reactions 2.00e-02 CPU s 2.50e-03 CPU s/rxn Rule 2: 20 reactions 2.00e-02 CPU s 1.00e-03 CPU s/rxn Rule 3: 4 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 4: 6 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 5: 24 reactions 2.00e-02 CPU s 8.33e-04 CPU s/rxn Rule 6: 14 reactions 1.00e-02 CPU s 7.14e-04 CPU s/rxn Total : 76 reactions 7.00e-02 CPU s 9.21e-04 CPU s/rxn Wrote network in net format to ./test_continue.net. CPU TIME: generate_network 0.07 s. Set concentration of species EGF(R) to value EGF_init CPU TIME: setConcentration 0.00 s. ACTION: simulate( method=>"cvode" ) Network simulation using cvode WARNING: writeFile(): Overwriting existing file ./test_continue.net. Wrote network in net format to ./test_continue.net. Can't exec "hostname": No such file or directory at /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Perl2/BNGAction.pm line 548. Running run_network on full command: /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/bin/run_network_x86_64-linux -o ./test_continue -p cvode -a 1e-08 -r 1e-08 --cdat 1 --fdat 0 -g ./test_continue.net ./test_continue.net 2.5 40 [simulation PID is: 3109] run_network 3.0 Read 19 parameters from ./test_continue.net Read 22 species from ./test_continue.net Read 6 group(s) from ./test_continue.net Read 0 function(s) from ./test_continue.net Read 76 reaction(s) from ./test_continue.net 76 reaction(s) have nonzero rate Initialization took 0.00 CPU seconds Propagating with cvode using dense LU Time course of concentrations written to file ./test_continue.cdat. Time course of groups written to file ./test_continue.gdat. Propagation took 0.00e+00 CPU seconds Program times: 0.00 CPU s 0.00 clock s Updating species concentrations from ./test_continue.cdat CPU TIME: simulate 0.01 s. Set concentration of species EGF(R) to value 10*EGF_init CPU TIME: setConcentration 0.01 s. ACTION: simulate( method=>"cvode" ) Network simulation using cvode WARNING: writeFile(): Overwriting existing file ./test_continue.net. Wrote network in net format to ./test_continue.net. Can't exec "hostname": No such file or directory at /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Perl2/BNGAction.pm line 548. Running run_network on full command: /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/bin/run_network_x86_64-linux -o ./test_continue -p cvode -a 1e-08 -r 1e-08 --cdat 1 --fdat 0 -x -i 1.000000000000e+02 -g ./test_continue.net ./test_continue.net 2.5 40 [simulation PID is: 3111] run_network 3.0 Read 20 parameters from ./test_continue.net Read 22 species from ./test_continue.net Read 6 group(s) from ./test_continue.net Read 0 function(s) from ./test_continue.net Read 76 reaction(s) from ./test_continue.net 76 reaction(s) have nonzero rate Initialization took 0.00 CPU seconds Propagating with cvode using dense LU Time course of concentrations written to file ./test_continue.cdat. Time course of groups written to file ./test_continue.gdat. Propagation took 0.00e+00 CPU seconds Program times: 0.00 CPU s 0.00 clock s Updating species concentrations from ./test_continue.cdat CPU TIME: simulate 0.01 s. Set concentration of species EGF(R) to value 0.1*EGF_init CPU TIME: setConcentration 0.00 s. ACTION: simulate( method=>"cvode" ) Network simulation using cvode WARNING: writeFile(): Overwriting existing file ./test_continue.net. Wrote network in net format to ./test_continue.net. Can't exec "hostname": No such file or directory at /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Perl2/BNGAction.pm line 548. Running run_network on full command: /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/bin/run_network_x86_64-linux -o ./test_continue -p cvode -a 1e-08 -r 1e-08 --cdat 1 --fdat 0 -x -i 2.000000000000e+02 -g ./test_continue.net ./test_continue.net 2.5 40 [simulation PID is: 3113] run_network 3.0 Read 21 parameters from ./test_continue.net Read 22 species from ./test_continue.net Read 6 group(s) from ./test_continue.net Read 0 function(s) from ./test_continue.net Read 76 reaction(s) from ./test_continue.net 76 reaction(s) have nonzero rate Initialization took 0.00 CPU seconds Propagating with cvode using dense LU Time course of concentrations written to file ./test_continue.cdat. Time course of groups written to file ./test_continue.gdat. Propagation took 0.00e+00 CPU seconds Program times: 0.00 CPU s 0.00 clock s Updating species concentrations from ./test_continue.cdat CPU TIME: simulate 0.01 s. Reset species concentrations to "DEFAULT" saved values. CPU TIME: resetConcentrations 0.00 s. Set concentration of species EGF(R) to value EGF_init CPU TIME: setConcentration 0.00 s. ACTION: simulate( method=>"ssa" ) Network simulation using ssa Wrote network in net format to ./test_continue_ssa.net. Can't exec "hostname": No such file or directory at /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Perl2/BNGAction.pm line 548. Running run_network on full command: /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/bin/run_network_x86_64-linux -o ./test_continue_ssa -p ssa -h 812941321 --cdat 1 --fdat 0 -g ./test_continue_ssa.net ./test_continue_ssa.net 2.5 40 [simulation PID is: 3115] run_network 3.0 Read 21 parameters from ./test_continue_ssa.net Read 22 species from ./test_continue_ssa.net Read 6 group(s) from ./test_continue_ssa.net Read 0 function(s) from ./test_continue_ssa.net Read 76 reaction(s) from ./test_continue_ssa.net 76 reaction(s) have nonzero rate rxn_rate_update_interval=1 Average number of update rxns is 14.17 Initialization took 0.00 CPU seconds Stochastic simulation using direct Gillespie algorithm TOTAL STEPS: 72380 Time course of concentrations written to file ./test_continue_ssa.cdat. Time course of groups written to file ./test_continue_ssa.gdat. Propagation took 1.00e-02 CPU seconds Program times: 0.01 CPU s 0.00 clock s Updating species concentrations from ./test_continue_ssa.cdat CPU TIME: simulate 0.02 s. Set concentration of species EGF(R) to value 10*EGF_init CPU TIME: setConcentration 0.00 s. ACTION: simulate( method=>"ssa" ) Network simulation using ssa WARNING: writeFile(): Overwriting existing file ./test_continue_ssa.net. Wrote network in net format to ./test_continue_ssa.net. Can't exec "hostname": No such file or directory at /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Perl2/BNGAction.pm line 548. Running run_network on full command: /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/bin/run_network_x86_64-linux -o ./test_continue_ssa -p ssa -h 1933214594 --cdat 1 --fdat 0 -x -i 1.000000000000e+02 -g ./test_continue_ssa.net ./test_continue_ssa.net 2.5 40 [simulation PID is: 3117] run_network 3.0 Read 22 parameters from ./test_continue_ssa.net Read 22 species from ./test_continue_ssa.net Read 6 group(s) from ./test_continue_ssa.net Read 0 function(s) from ./test_continue_ssa.net Read 76 reaction(s) from ./test_continue_ssa.net 76 reaction(s) have nonzero rate rxn_rate_update_interval=1 Average number of update rxns is 14.17 Initialization took 0.00 CPU seconds Stochastic simulation using direct Gillespie algorithm TOTAL STEPS: 129695 Time course of concentrations written to file ./test_continue_ssa.cdat. Time course of groups written to file ./test_continue_ssa.gdat. Propagation took 1.00e-02 CPU seconds Program times: 0.01 CPU s 0.00 clock s Updating species concentrations from ./test_continue_ssa.cdat CPU TIME: simulate 0.02 s. Set concentration of species EGF(R) to value 0.1*EGF_init CPU TIME: setConcentration 0.00 s. ACTION: simulate( method=>"ssa" ) Network simulation using ssa WARNING: writeFile(): Overwriting existing file ./test_continue_ssa.net. Wrote network in net format to ./test_continue_ssa.net. Can't exec "hostname": No such file or directory at /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Perl2/BNGAction.pm line 548. Running run_network on full command: /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/bin/run_network_x86_64-linux -o ./test_continue_ssa -p ssa -h 560484120 --cdat 1 --fdat 0 -x -i 2.000000000000e+02 -g ./test_continue_ssa.net ./test_continue_ssa.net 2.5 40 [simulation PID is: 3119] run_network 3.0 Read 23 parameters from ./test_continue_ssa.net Read 22 species from ./test_continue_ssa.net Read 6 group(s) from ./test_continue_ssa.net Read 0 function(s) from ./test_continue_ssa.net Read 76 reaction(s) from ./test_continue_ssa.net 76 reaction(s) have nonzero rate rxn_rate_update_interval=1 Average number of update rxns is 14.17 Initialization took 0.00 CPU seconds Stochastic simulation using direct Gillespie algorithm TOTAL STEPS: 107662 Time course of concentrations written to file ./test_continue_ssa.cdat. Time course of groups written to file ./test_continue_ssa.gdat. Propagation took 1.00e-02 CPU seconds Program times: 0.01 CPU s 0.00 clock s Updating species concentrations from ./test_continue_ssa.cdat CPU TIME: simulate 0.04 s. Finished processing file test_continue.bngl. CPU TIME: total 0.20 s. Tests finished. + echo 'Tests finished.' + RPM_EC=0 ++ jobs -p + exit 0 Processing files: bionetgen-2.9.0-4.fc42.x86_64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.36GRve + umask 022 + cd /builddir/build/BUILD/bionetgen-2.9.0-build + cd bionetgen-2.9.0 + DOCDIR=/builddir/build/BUILD/bionetgen-2.9.0-build/BUILDROOT/usr/share/doc/bionetgen + export LC_ALL=C.UTF-8 + LC_ALL=C.UTF-8 + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILD/bionetgen-2.9.0-build/BUILDROOT/usr/share/doc/bionetgen + cp -pr /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/README.md /builddir/build/BUILD/bionetgen-2.9.0-build/BUILDROOT/usr/share/doc/bionetgen + cp -pr /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/CREDITS.txt /builddir/build/BUILD/bionetgen-2.9.0-build/BUILDROOT/usr/share/doc/bionetgen + cp -pr /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/CHANGES.txt /builddir/build/BUILD/bionetgen-2.9.0-build/BUILDROOT/usr/share/doc/bionetgen + cp -pr /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/VERSION /builddir/build/BUILD/bionetgen-2.9.0-build/BUILDROOT/usr/share/doc/bionetgen + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.lud5J1 + umask 022 + cd /builddir/build/BUILD/bionetgen-2.9.0-build + cd bionetgen-2.9.0 + LICENSEDIR=/builddir/build/BUILD/bionetgen-2.9.0-build/BUILDROOT/usr/share/licenses/bionetgen + export LC_ALL=C.UTF-8 + LC_ALL=C.UTF-8 + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILD/bionetgen-2.9.0-build/BUILDROOT/usr/share/licenses/bionetgen + cp -pr /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/LICENSE /builddir/build/BUILD/bionetgen-2.9.0-build/BUILDROOT/usr/share/licenses/bionetgen + RPM_EC=0 ++ jobs -p + exit 0 Provides: bionetgen = 2.9.0-4.fc42 bionetgen(x86-64) = 2.9.0-4.fc42 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.32)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.38)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_ABI_DT_RELR)(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgcc_s.so.1(GCC_3.3.1)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.29)(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.8)(64bit) libstdc++.so.6(CXXABI_1.3.9)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.11)(64bit) libstdc++.so.6(GLIBCXX_3.4.15)(64bit) libstdc++.so.6(GLIBCXX_3.4.20)(64bit) libstdc++.so.6(GLIBCXX_3.4.21)(64bit) libstdc++.so.6(GLIBCXX_3.4.26)(64bit) libstdc++.so.6(GLIBCXX_3.4.29)(64bit) libstdc++.so.6(GLIBCXX_3.4.30)(64bit) libstdc++.so.6(GLIBCXX_3.4.32)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) rtld(GNU_HASH) Processing files: bionetgen-perl-2.9.0-4.fc42.noarch Provides: bionetgen-perl = 2.9.0-4.fc42 bundled(XML-TreePP) = 0.41 perl(Viz) Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: /usr/bin/perl perl(Carp) perl(Class::Struct) perl(Config) perl(Cwd) perl(Data::Dumper) perl(Exporter) perl(File::Basename) perl(File::Path) perl(File::Spec) perl(File::Spec::Win32) perl(FindBin) perl(Getopt::Long) perl(IO::Handle) perl(IO::Select) perl(IPC::Open3) perl(List::Util) perl(Math::Trig) perl(POSIX) perl(Scalar::Util) perl(Storable) perl(Symbol) perl(constant) perl(lib) perl(strict) perl(vars) perl(warnings) perl-libs Processing files: bionetgen-debugsource-2.9.0-4.fc42.x86_64 Provides: bionetgen-debugsource = 2.9.0-4.fc42 bionetgen-debugsource(x86-64) = 2.9.0-4.fc42 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: bionetgen-debuginfo-2.9.0-4.fc42.x86_64 Provides: bionetgen-debuginfo = 2.9.0-4.fc42 bionetgen-debuginfo(x86-64) = 2.9.0-4.fc42 debuginfo(build-id) = 8a22bf20b5c0f70c58cde52e9d73d80c643c7f65 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: bionetgen-debugsource(x86-64) = 2.9.0-4.fc42 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILD/bionetgen-2.9.0-build/BUILDROOT Wrote: /builddir/build/RPMS/bionetgen-2.9.0-4.fc42.x86_64.rpm Wrote: /builddir/build/RPMS/bionetgen-debugsource-2.9.0-4.fc42.x86_64.rpm Wrote: /builddir/build/RPMS/bionetgen-perl-2.9.0-4.fc42.noarch.rpm Wrote: /builddir/build/RPMS/bionetgen-debuginfo-2.9.0-4.fc42.x86_64.rpm Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.4n6MfS + umask 022 + cd /builddir/build/BUILD/bionetgen-2.9.0-build + test -d /builddir/build/BUILD/bionetgen-2.9.0-build + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w /builddir/build/BUILD/bionetgen-2.9.0-build + rm -rf /builddir/build/BUILD/bionetgen-2.9.0-build + RPM_EC=0 ++ jobs -p + exit 0 Finish: rpmbuild bionetgen-2.9.0-4.fc42.src.rpm Finish: build phase for bionetgen-2.9.0-4.fc42.src.rpm INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-x86_64-1736203422.274018/root/var/log/dnf5.log INFO: chroot_scan: creating tarball /var/lib/copr-rpmbuild/results/chroot_scan.tar.gz /bin/tar: Removing leading `/' from member names INFO: Done(/var/lib/copr-rpmbuild/results/bionetgen-2.9.0-4.fc42.src.rpm) Config(child) 0 minutes 59 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot Finish: run Running RPMResults tool Package info: { "packages": [ { "name": "bionetgen-perl", "epoch": null, "version": "2.9.0", "release": "4.fc42", "arch": "noarch" }, { "name": "bionetgen-debugsource", "epoch": null, "version": "2.9.0", "release": "4.fc42", "arch": "x86_64" }, { "name": "bionetgen", "epoch": null, "version": "2.9.0", "release": "4.fc42", "arch": "x86_64" }, { "name": "bionetgen", "epoch": null, "version": "2.9.0", "release": "4.fc42", "arch": "src" }, { "name": "bionetgen-debuginfo", "epoch": null, "version": "2.9.0", "release": "4.fc42", "arch": "x86_64" } ] } RPMResults finished