Warning: Permanently added '34.235.131.21' (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-aarch64 --chroot fedora-rawhide-aarch64 Version: 1.2 PID: 52143 Logging PID: 52144 Task: {'allow_user_ssh': False, 'appstream': False, 'background': True, 'build_id': 8477802, 'buildroot_pkgs': [], 'chroot': 'fedora-rawhide-aarch64', '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-aarch64/', '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-aarch64', '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-voh3lkt2/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-voh3lkt2/bionetgen', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-voh3lkt2/bionetgen'... Running: git checkout b5a7993fe080586b143c5e464b7d8ea6d924448a -- cmd: ['git', 'checkout', 'b5a7993fe080586b143c5e464b7d8ea6d924448a', '--'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-voh3lkt2/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-voh3lkt2/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 255M 0 --:--:-- --:--:-- --:--:-- 257M 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-voh3lkt2/bionetgen/bionetgen.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-voh3lkt2/bionetgen --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1736203564.750723 -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-voh3lkt2/bionetgen/bionetgen.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-voh3lkt2/bionetgen --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1736203564.750723 -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-voh3lkt2/bionetgen/bionetgen.spec) Config(fedora-rawhide-aarch64) 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-aarch64-bootstrap-1736203564.750723/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-4b1340af-2c3c-44d5-9751-aeedfe46332a INFO: Checking that 8bdf9579651bb717d3b8362a9dd4aaa791939300192b4b01a4ae900ef40d7294 image matches host's architecture INFO: Copy content of container 8bdf9579651bb717d3b8362a9dd4aaa791939300192b4b01a4ae900ef40d7294 to /var/lib/mock/fedora-rawhide-aarch64-bootstrap-1736203564.750723/root INFO: mounting 8bdf9579651bb717d3b8362a9dd4aaa791939300192b4b01a4ae900ef40d7294 with podman image mount INFO: image 8bdf9579651bb717d3b8362a9dd4aaa791939300192b4b01a4ae900ef40d7294 as /var/lib/containers/storage/overlay/e77e12a870edb150bee8cd159dba0ac31236bc8f639cc8a5f1c425ab3febda81/merged INFO: umounting image 8bdf9579651bb717d3b8362a9dd4aaa791939300192b4b01a4ae900ef40d7294 (/var/lib/containers/storage/overlay/e77e12a870edb150bee8cd159dba0ac31236bc8f639cc8a5f1c425ab3febda81/merged) with podman image umount INFO: Removing image mock-bootstrap-4b1340af-2c3c-44d5-9751-aeedfe46332a 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-aarch64-1736203564.750723/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.aarch64 rpm-sequoia-1.7.0-3.fc42.aarch64 dnf5-5.2.8.1-2.fc42.aarch64 dnf5-plugins-5.2.8.1-2.fc42.aarch64 Start: installing minimal buildroot with dnf5 Updating and loading repositories: fedora 100% | 96.0 KiB/s | 10.3 KiB | 00m00s Copr repository 100% | 80.4 KiB/s | 1.5 KiB | 00m00s Copr repository 100% | 4.1 MiB/s | 130.9 KiB | 00m00s Repositories loaded. Package Arch Version Repository Size Installing group/module packages: bash aarch64 5.2.37-1.fc42 fedora 8.2 MiB bzip2 aarch64 1.0.8-19.fc41 fedora 427.6 KiB coreutils aarch64 9.5-11.fc42 fedora 8.1 MiB cpio aarch64 2.15-2.fc41 fedora 1.2 MiB diffutils aarch64 3.10-8.fc41 fedora 2.1 MiB fedora-release-common noarch 42-0.11 fedora 19.8 KiB findutils aarch64 1:4.10.0-4.fc41 fedora 2.1 MiB gawk aarch64 5.3.0-4.fc41 fedora 4.2 MiB glibc-minimal-langpack aarch64 2.40.9000-26.fc42 fedora 0.0 B grep aarch64 3.11-9.fc41 fedora 1.1 MiB gzip aarch64 1.13-2.fc41 fedora 488.9 KiB info aarch64 7.1.1-2.fc42 fedora 613.6 KiB patch aarch64 2.7.6-25.fc41 fedora 390.6 KiB redhat-rpm-config noarch 296-1.fc42 fedora 186.6 KiB rpm-build aarch64 4.20.0-1.fc42 fedora 1.4 MiB sed aarch64 4.9-3.fc41 fedora 1.0 MiB shadow-utils aarch64 2:4.17.0-2.fc42 fedora 4.4 MiB tar aarch64 2:1.35-4.fc41 fedora 3.1 MiB unzip aarch64 6.0-65.fc42 fedora 2.3 MiB util-linux aarch64 2.40.2-8.fc42 fedora 16.9 MiB which aarch64 2.21-42.fc41 fedora 248.2 KiB xz aarch64 1:5.6.3-2.fc42 fedora 1.5 MiB Installing dependencies: add-determinism aarch64 0.5.0-1.fc42 fedora 2.0 MiB alternatives aarch64 1.31-1.fc42 fedora 88.7 KiB ansible-srpm-macros noarch 1-16.fc41 fedora 35.7 KiB audit-libs aarch64 4.0.2-1.fc41 fedora 547.4 KiB authselect aarch64 1.5.0-8.fc42 fedora 309.5 KiB authselect-libs aarch64 1.5.0-8.fc42 fedora 931.9 KiB basesystem noarch 11-21.fc41 fedora 0.0 B binutils aarch64 2.43.50-9.fc42 fedora 29.4 MiB build-reproducibility-srpm-macros noarch 0.5.0-1.fc42 fedora 735.0 B bzip2-libs aarch64 1.0.8-19.fc41 fedora 200.7 KiB ca-certificates noarch 2024.2.69_v8.0.401-4.fc42 fedora 2.6 MiB coreutils-common aarch64 9.5-11.fc42 fedora 11.2 MiB cracklib aarch64 2.9.11-6.fc41 fedora 935.0 KiB crypto-policies noarch 20241128-1.gitbb7b0b0.fc42 fedora 137.3 KiB curl aarch64 8.11.1-2.fc42 fedora 452.0 KiB cyrus-sasl-lib aarch64 2.1.28-27.fc41 fedora 3.1 MiB debugedit aarch64 5.1-2.fc42 fedora 244.2 KiB dwz aarch64 0.15-8.fc42 fedora 386.8 KiB ed aarch64 1.20.2-2.fc41 fedora 282.8 KiB efi-srpm-macros noarch 5-13.fc42 fedora 40.2 KiB elfutils aarch64 0.192-7.fc42 fedora 3.1 MiB elfutils-debuginfod-client aarch64 0.192-7.fc42 fedora 141.3 KiB elfutils-default-yama-scope noarch 0.192-7.fc42 fedora 1.8 KiB elfutils-libelf aarch64 0.192-7.fc42 fedora 1.2 MiB elfutils-libs aarch64 0.192-7.fc42 fedora 734.9 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 aarch64 5.45-8.fc42 fedora 139.5 KiB file-libs aarch64 5.45-8.fc42 fedora 10.0 MiB filesystem aarch64 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 aarch64 15.2-4.fc42 fedora 12.7 MiB gdbm aarch64 1:1.23-7.fc41 fedora 928.5 KiB gdbm-libs aarch64 1:1.23-7.fc41 fedora 426.0 KiB ghc-srpm-macros noarch 1.9.2-1.fc42 fedora 779.0 B glibc aarch64 2.40.9000-26.fc42 fedora 6.1 MiB glibc-common aarch64 2.40.9000-26.fc42 fedora 1.3 MiB glibc-gconv-extra aarch64 2.40.9000-26.fc42 fedora 18.3 MiB gmp aarch64 1:6.3.0-2.fc41 fedora 722.0 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 aarch64 2.14-1.fc42 fedora 221.3 KiB json-c aarch64 0.18-1.fc42 fedora 139.2 KiB kernel-srpm-macros noarch 1.0-24.fc41 fedora 1.9 KiB keyutils-libs aarch64 1.6.3-4.fc41 fedora 226.4 KiB krb5-libs aarch64 1.21.3-3.fc42 fedora 2.6 MiB libacl aarch64 2.3.2-2.fc41 fedora 196.1 KiB libarchive aarch64 3.7.7-1.fc42 fedora 912.2 KiB libattr aarch64 2.5.2-4.fc41 fedora 196.6 KiB libblkid aarch64 2.40.2-8.fc42 fedora 418.6 KiB libbrotli aarch64 1.1.0-5.fc41 fedora 1.1 MiB libcap aarch64 2.71-1.fc42 fedora 509.8 KiB libcap-ng aarch64 0.8.5-3.fc41 fedora 417.2 KiB libcom_err aarch64 1.47.1-6.fc42 fedora 239.3 KiB libcurl aarch64 8.11.1-2.fc42 fedora 845.2 KiB libeconf aarch64 0.7.5-1.fc42 fedora 78.7 KiB libevent aarch64 2.1.12-14.fc41 fedora 1.5 MiB libfdisk aarch64 2.40.2-8.fc42 fedora 482.9 KiB libffi aarch64 3.4.6-3.fc42 fedora 282.4 KiB libgcc aarch64 14.2.1-6.fc42 fedora 222.2 KiB libgomp aarch64 14.2.1-6.fc42 fedora 503.2 KiB libidn2 aarch64 2.3.7-2.fc41 fedora 457.2 KiB libmount aarch64 2.40.2-8.fc42 fedora 483.9 KiB libnghttp2 aarch64 1.64.0-1.fc42 fedora 262.2 KiB libnsl2 aarch64 2.0.1-2.fc41 fedora 222.0 KiB libpkgconf aarch64 2.3.0-1.fc42 fedora 198.1 KiB libpsl aarch64 0.21.5-4.fc41 fedora 196.6 KiB libpwquality aarch64 1.4.5-11.fc41 fedora 1.1 MiB libselinux aarch64 3.8-0.rc3.1.fc42 fedora 195.6 KiB libsemanage aarch64 3.8-0.rc3.1.fc42 fedora 353.3 KiB libsepol aarch64 3.8-0.rc3.1.fc42 fedora 796.3 KiB libsmartcols aarch64 2.40.2-8.fc42 fedora 288.5 KiB libssh aarch64 0.11.1-1.fc42 fedora 649.6 KiB libssh-config noarch 0.11.1-1.fc42 fedora 277.0 B libstdc++ aarch64 14.2.1-6.fc42 fedora 2.8 MiB libtasn1 aarch64 4.19.0-9.fc41 fedora 283.8 KiB libtirpc aarch64 1.3.6-1.rc3.fc42 fedora 205.5 KiB libtool-ltdl aarch64 2.5.4-1.fc42 fedora 92.1 KiB libunistring aarch64 1.1-8.fc41 fedora 1.8 MiB libuuid aarch64 2.40.2-8.fc42 fedora 197.5 KiB libverto aarch64 0.3.2-9.fc41 fedora 197.5 KiB libxcrypt aarch64 4.4.37-4.fc42 fedora 269.6 KiB libxml2 aarch64 2.12.9-1.fc42 fedora 1.9 MiB libzstd aarch64 1.5.6-2.fc41 fedora 796.0 KiB lua-libs aarch64 5.4.7-1.fc42 fedora 393.1 KiB lua-srpm-macros noarch 1-14.fc41 fedora 1.3 KiB lz4-libs aarch64 1.10.0-1.fc41 fedora 261.6 KiB mpfr aarch64 4.2.1-5.fc41 fedora 818.9 KiB ncurses-base noarch 6.5-2.20240629.fc41 fedora 326.3 KiB ncurses-libs aarch64 6.5-2.20240629.fc41 fedora 2.2 MiB ocaml-srpm-macros noarch 10-3.fc41 fedora 1.9 KiB openblas-srpm-macros noarch 2-18.fc41 fedora 112.0 B openldap aarch64 2.6.8-6.fc42 fedora 747.0 KiB openssl-libs aarch64 1:3.2.2-10.fc42 fedora 6.3 MiB p11-kit aarch64 0.25.5-4.fc42 fedora 2.6 MiB p11-kit-trust aarch64 0.25.5-4.fc42 fedora 655.7 KiB package-notes-srpm-macros noarch 0.5-12.fc41 fedora 1.6 KiB pam aarch64 1.7.0-3.fc42 fedora 4.3 MiB pam-libs aarch64 1.7.0-3.fc42 fedora 223.4 KiB pcre2 aarch64 10.44-1.fc41.1 fedora 905.5 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 aarch64 2.3.0-1.fc42 fedora 240.6 KiB pkgconf-m4 noarch 2.3.0-1.fc42 fedora 14.4 KiB pkgconf-pkg-config aarch64 2.3.0-1.fc42 fedora 990.0 B popt aarch64 1.19-7.fc41 fedora 272.9 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 aarch64 8.2-11.fc42 fedora 753.3 KiB rpm aarch64 4.20.0-1.fc42 fedora 3.9 MiB rpm-build-libs aarch64 4.20.0-1.fc42 fedora 262.7 KiB rpm-libs aarch64 4.20.0-1.fc42 fedora 797.9 KiB rpm-sequoia aarch64 1.7.0-3.fc42 fedora 2.2 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 aarch64 3.47.2-1.fc42 fedora 1.4 MiB systemd-libs aarch64 257.1-1.fc42 fedora 2.4 MiB util-linux-core aarch64 2.40.2-8.fc42 fedora 6.2 MiB xxhash-libs aarch64 0.8.3-1.fc42 fedora 84.5 KiB xz-libs aarch64 1:5.6.3-2.fc42 fedora 266.4 KiB zig-srpm-macros noarch 1-3.fc41 fedora 1.1 KiB zip aarch64 3.0-42.fc42 fedora 755.7 KiB zlib-ng-compat aarch64 2.2.2-1.fc42 fedora 133.8 KiB zstd aarch64 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 51 MiB. Need to download 0 B. After this operation, 235 MiB extra will be used (install 235 MiB, remove 0 B). [1/1] tar-2:1.35-4.fc41.aarch64 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.aarch64 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.aarch64 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.aarch64 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.a 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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100% | 301.6 MiB/s | 12.7 MiB | 00m00s [128/156] Installing debugedit-0:5.1-2. 100% | 120.6 MiB/s | 246.9 KiB | 00m00s [129/156] Installing curl-0:8.11.1-2.fc 100% | 34.1 MiB/s | 454.4 KiB | 00m00s [130/156] Installing rpm-0:4.20.0-1.fc4 100% | 146.0 MiB/s | 3.4 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% | 39.3 MiB/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% | 62.9 MiB/s | 193.2 KiB | 00m00s [151/156] Installing rpm-build-0:4.20.0 100% | 349.3 MiB/s | 1.4 MiB | 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% | 346.0 MiB/s | 17.0 MiB | 00m00s [154/156] Installing authselect-0:1.5.0 100% | 102.2 MiB/s | 313.9 KiB | 00m00s [155/156] Installing which-0:2.21-42.fc 100% | 122.2 MiB/s | 250.4 KiB | 00m00s [156/156] Installing info-0:7.1.1-2.fc4 100% | 279.2 KiB/s | 614.0 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.aarch64 alternatives-1.31-1.fc42.aarch64 ansible-srpm-macros-1-16.fc41.noarch audit-libs-4.0.2-1.fc41.aarch64 authselect-1.5.0-8.fc42.aarch64 authselect-libs-1.5.0-8.fc42.aarch64 basesystem-11-21.fc41.noarch bash-5.2.37-1.fc42.aarch64 binutils-2.43.50-9.fc42.aarch64 build-reproducibility-srpm-macros-0.5.0-1.fc42.noarch bzip2-1.0.8-19.fc41.aarch64 bzip2-libs-1.0.8-19.fc41.aarch64 ca-certificates-2024.2.69_v8.0.401-4.fc42.noarch coreutils-9.5-11.fc42.aarch64 coreutils-common-9.5-11.fc42.aarch64 cpio-2.15-2.fc41.aarch64 cracklib-2.9.11-6.fc41.aarch64 crypto-policies-20241128-1.gitbb7b0b0.fc42.noarch curl-8.11.1-2.fc42.aarch64 cyrus-sasl-lib-2.1.28-27.fc41.aarch64 debugedit-5.1-2.fc42.aarch64 diffutils-3.10-8.fc41.aarch64 dwz-0.15-8.fc42.aarch64 ed-1.20.2-2.fc41.aarch64 efi-srpm-macros-5-13.fc42.noarch elfutils-0.192-7.fc42.aarch64 elfutils-debuginfod-client-0.192-7.fc42.aarch64 elfutils-default-yama-scope-0.192-7.fc42.noarch elfutils-libelf-0.192-7.fc42.aarch64 elfutils-libs-0.192-7.fc42.aarch64 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.aarch64 file-libs-5.45-8.fc42.aarch64 filesystem-3.18-29.fc42.aarch64 findutils-4.10.0-4.fc41.aarch64 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.aarch64 gdb-minimal-15.2-4.fc42.aarch64 gdbm-1.23-7.fc41.aarch64 gdbm-libs-1.23-7.fc41.aarch64 ghc-srpm-macros-1.9.2-1.fc42.noarch glibc-2.40.9000-26.fc42.aarch64 glibc-common-2.40.9000-26.fc42.aarch64 glibc-gconv-extra-2.40.9000-26.fc42.aarch64 glibc-minimal-langpack-2.40.9000-26.fc42.aarch64 gmp-6.3.0-2.fc41.aarch64 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.aarch64 gzip-1.13-2.fc41.aarch64 info-7.1.1-2.fc42.aarch64 jansson-2.14-1.fc42.aarch64 json-c-0.18-1.fc42.aarch64 kernel-srpm-macros-1.0-24.fc41.noarch keyutils-libs-1.6.3-4.fc41.aarch64 krb5-libs-1.21.3-3.fc42.aarch64 libacl-2.3.2-2.fc41.aarch64 libarchive-3.7.7-1.fc42.aarch64 libattr-2.5.2-4.fc41.aarch64 libblkid-2.40.2-8.fc42.aarch64 libbrotli-1.1.0-5.fc41.aarch64 libcap-2.71-1.fc42.aarch64 libcap-ng-0.8.5-3.fc41.aarch64 libcom_err-1.47.1-6.fc42.aarch64 libcurl-8.11.1-2.fc42.aarch64 libeconf-0.7.5-1.fc42.aarch64 libevent-2.1.12-14.fc41.aarch64 libfdisk-2.40.2-8.fc42.aarch64 libffi-3.4.6-3.fc42.aarch64 libgcc-14.2.1-6.fc42.aarch64 libgomp-14.2.1-6.fc42.aarch64 libidn2-2.3.7-2.fc41.aarch64 libmount-2.40.2-8.fc42.aarch64 libnghttp2-1.64.0-1.fc42.aarch64 libnsl2-2.0.1-2.fc41.aarch64 libpkgconf-2.3.0-1.fc42.aarch64 libpsl-0.21.5-4.fc41.aarch64 libpwquality-1.4.5-11.fc41.aarch64 libselinux-3.8-0.rc3.1.fc42.aarch64 libsemanage-3.8-0.rc3.1.fc42.aarch64 libsepol-3.8-0.rc3.1.fc42.aarch64 libsmartcols-2.40.2-8.fc42.aarch64 libssh-0.11.1-1.fc42.aarch64 libssh-config-0.11.1-1.fc42.noarch libstdc++-14.2.1-6.fc42.aarch64 libtasn1-4.19.0-9.fc41.aarch64 libtirpc-1.3.6-1.rc3.fc42.aarch64 libtool-ltdl-2.5.4-1.fc42.aarch64 libunistring-1.1-8.fc41.aarch64 libuuid-2.40.2-8.fc42.aarch64 libverto-0.3.2-9.fc41.aarch64 libxcrypt-4.4.37-4.fc42.aarch64 libxml2-2.12.9-1.fc42.aarch64 libzstd-1.5.6-2.fc41.aarch64 lua-libs-5.4.7-1.fc42.aarch64 lua-srpm-macros-1-14.fc41.noarch lz4-libs-1.10.0-1.fc41.aarch64 mpfr-4.2.1-5.fc41.aarch64 ncurses-base-6.5-2.20240629.fc41.noarch ncurses-libs-6.5-2.20240629.fc41.aarch64 ocaml-srpm-macros-10-3.fc41.noarch openblas-srpm-macros-2-18.fc41.noarch openldap-2.6.8-6.fc42.aarch64 openssl-libs-3.2.2-10.fc42.aarch64 p11-kit-0.25.5-4.fc42.aarch64 p11-kit-trust-0.25.5-4.fc42.aarch64 package-notes-srpm-macros-0.5-12.fc41.noarch pam-1.7.0-3.fc42.aarch64 pam-libs-1.7.0-3.fc42.aarch64 patch-2.7.6-25.fc41.aarch64 pcre2-10.44-1.fc41.1.aarch64 pcre2-syntax-10.44-1.fc41.1.noarch perl-srpm-macros-1-56.fc41.noarch pkgconf-2.3.0-1.fc42.aarch64 pkgconf-m4-2.3.0-1.fc42.noarch pkgconf-pkg-config-2.3.0-1.fc42.aarch64 popt-1.19-7.fc41.aarch64 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.aarch64 redhat-rpm-config-296-1.fc42.noarch rpm-4.20.0-1.fc42.aarch64 rpm-build-4.20.0-1.fc42.aarch64 rpm-build-libs-4.20.0-1.fc42.aarch64 rpm-libs-4.20.0-1.fc42.aarch64 rpm-sequoia-1.7.0-3.fc42.aarch64 rust-srpm-macros-26.3-3.fc42.noarch sed-4.9-3.fc41.aarch64 setup-2.15.0-9.fc42.noarch shadow-utils-4.17.0-2.fc42.aarch64 sqlite-libs-3.47.2-1.fc42.aarch64 systemd-libs-257.1-1.fc42.aarch64 tar-1.35-4.fc41.aarch64 unzip-6.0-65.fc42.aarch64 util-linux-2.40.2-8.fc42.aarch64 util-linux-core-2.40.2-8.fc42.aarch64 which-2.21-42.fc41.aarch64 xxhash-libs-0.8.3-1.fc42.aarch64 xz-5.6.3-2.fc42.aarch64 xz-libs-5.6.3-2.fc42.aarch64 zig-srpm-macros-1-3.fc41.noarch zip-3.0-42.fc42.aarch64 zlib-ng-compat-2.2.2-1.fc42.aarch64 zstd-1.5.6-2.fc41.aarch64 Start: buildsrpm Start: rpmbuild -bs Building target platforms: aarch64 Building for target aarch64 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-aarch64-1736203564.750723/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-voh3lkt2/bionetgen/bionetgen.spec) Config(child) 0 minutes 13 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-aarch64) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-aarch64-bootstrap-1736203564.750723/root. INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-aarch64-bootstrap-1736203564.750723/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-aarch64-1736203564.750723/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.aarch64 rpm-sequoia-1.7.0-3.fc42.aarch64 dnf5-5.2.8.1-2.fc42.aarch64 dnf5-plugins-5.2.8.1-2.fc42.aarch64 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: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1721174400 Wrote: /builddir/build/SRPMS/bionetgen-2.9.0-4.fc42.src.rpm Updating and loading repositories: fedora 100% | 218.6 KiB/s | 10.3 KiB | 00m00s Copr repository 100% | 109.1 KiB/s | 1.5 KiB | 00m00s Repositories loaded. Package Arch Version Repository Size Installing: cmake aarch64 3.31.3-1.fc42 fedora 28.8 MiB gcc aarch64 14.2.1-6.fc42 fedora 96.6 MiB gcc-c++ aarch64 14.2.1-6.fc42 fedora 36.8 MiB gcc-gfortran aarch64 14.2.1-6.fc42 fedora 35.7 MiB make aarch64 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 aarch64 2.189-512.fc41 fedora 263.8 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 aarch64 1.55-512.fc42 fedora 319.2 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 aarch64 2.20-512.fc42 fedora 327.3 KiB perl-PathTools aarch64 3.91-511.fc41 fedora 352.1 KiB perl-Scalar-List-Utils aarch64 5:1.68-1.fc42 fedora 281.0 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 aarch64 4:5.40.0-512.fc42 fedora 302.3 KiB perl-lib aarch64 0.65-512.fc42 fedora 8.5 KiB perl-libs aarch64 4:5.40.0-512.fc42 fedora 10.9 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 aarch64 12.80-1.fc42 fedora 1.0 MiB cmake-data noarch 3.31.3-1.fc42 fedora 8.5 MiB cmake-filesystem aarch64 3.31.3-1.fc42 fedora 0.0 B cmake-rpm-macros noarch 3.31.3-1.fc42 fedora 7.5 KiB cpp aarch64 14.2.1-6.fc42 fedora 33.7 MiB emacs-filesystem noarch 1:30.0-3.fc41 fedora 0.0 B expat aarch64 2.6.4-1.fc42 fedora 349.3 KiB gcc-plugin-annobin aarch64 14.2.1-6.fc42 fedora 73.5 KiB glibc-devel aarch64 2.40.9000-26.fc42 fedora 2.2 MiB groff-base aarch64 1.23.0-7.fc41 fedora 5.2 MiB jsoncpp aarch64 1.9.5-8.fc41 fedora 335.7 KiB kernel-headers aarch64 6.13.0-0.rc5.42.fc42 fedora 6.4 MiB libasan aarch64 14.2.1-6.fc42 fedora 1.5 MiB libatomic aarch64 14.2.1-6.fc42 fedora 69.0 KiB libb2 aarch64 0.98.1-12.fc41 fedora 202.2 KiB libgfortran aarch64 14.2.1-6.fc42 fedora 1.5 MiB libmpc aarch64 1.3.1-6.fc41 fedora 280.8 KiB libstdc++-devel aarch64 14.2.1-6.fc42 fedora 15.1 MiB libubsan aarch64 14.2.1-6.fc42 fedora 475.2 KiB libuv aarch64 1:1.49.2-1.fc42 fedora 664.8 KiB libxcrypt-devel aarch64 4.4.37-4.fc42 fedora 30.5 KiB mpdecimal aarch64 2.5.1-16.fc41 fedora 328.9 KiB ncurses aarch64 6.5-2.20240629.fc41 fedora 1.7 MiB perl-AutoLoader noarch 5.74-512.fc42 fedora 20.5 KiB perl-B aarch64 1.89-512.fc42 fedora 606.1 KiB perl-Digest noarch 1.20-511.fc41 fedora 35.3 KiB perl-Digest-MD5 aarch64 2.59-5.fc41 fedora 231.9 KiB perl-DynaLoader aarch64 1.56-512.fc42 fedora 32.1 KiB perl-Encode aarch64 4:3.21-511.fc41 fedora 5.9 MiB perl-Errno aarch64 1.38-512.fc42 fedora 8.4 KiB perl-Fcntl aarch64 1.18-512.fc42 fedora 221.1 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 aarch64 3.16-511.fc41 fedora 222.2 KiB perl-Net-SSLeay aarch64 1.94-7.fc41 fedora 1.4 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 aarch64 4:2.038-511.fc41 fedora 272.1 KiB perl-Storable aarch64 1:3.32-511.fc41 fedora 372.5 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 aarch64 1.29-512.fc42 fedora 209.7 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 aarch64 3.13.1-2.fc42 fedora 82.5 KiB python3-libs aarch64 3.13.1-2.fc42 fedora 41.7 MiB rhash aarch64 1.4.5-1.fc42 fedora 587.1 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: 98 packages Total size of inbound packages is 107 MiB. Need to download 12 MiB. After this operation, 351 MiB extra will be used (install 351 MiB, remove 0 B). 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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: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1721174400 Executing(%mkbuilddir): /bin/sh -e /var/tmp/rpm-tmp.RVEZRn + 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.c9brIP + 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 + echo 'Patch #0 (bionetgen-fix_linker.patch):' 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.G1RQxv + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 ~/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 + 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 + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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=aarch64-redhat-linux --host=aarch64-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... aarch64-redhat-linux-gnu checking host system type... aarch64-redhat-linux-gnu checking target system type... aarch64-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 aarch64-redhat-linux-ranlib... no checking for ranlib... ranlib checking for aarch64-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 aarch64-redhat-linux-ranlib... ranlib checking whether ln -s works... yes checking whether make sets $(MAKE)... yes checking for aarch64-redhat-linux-ar... no checking for ar... ar checking for aarch64-redhat-linux-strip... no checking for strip... strip checking for aarch64-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 configure: WARNING: unrecognized options: --enable-static - RELEASE build - 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 (1.6s) -- 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 /usr/bin/gmake -f src/cvode/CMakeFiles/sundials_cvode_static.dir/build.make src/cvode/CMakeFiles/sundials_cvode_static.dir/depend /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/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=" 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=" 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' 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=" 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]: 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 /usr/bin/gmake -f src/nvec_ser/CMakeFiles/sundials_fnvecserial_static.dir/build.make src/nvec_ser/CMakeFiles/sundials_fnvecserial_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' /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]: 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]: 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' [ 2%] Building C object src/nvec_ser/CMakeFiles/sundials_nvecserial_static.dir/nvector_serial.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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 [ 5%] 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/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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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/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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -MD -MT src/cvode/CMakeFiles/sundials_cvode_static.dir/cvode.c.o -MF CMakeFiles/sundials_cvode_static.dir/cvode.c.o.d -o CMakeFiles/sundials_cvode_static.dir/cvode.c.o -c 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-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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer 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-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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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/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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 [ 27%] 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 /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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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%] 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 [ 35%] 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/nvec_ser && /usr/bin/cmake -E cmake_link_script CMakeFiles/sundials_nvecserial_static.dir/link.txt --verbose=1 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 /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' [ 35%] Built target sundials_nvecserial_static /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; | ^~~~~~ [ 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 [ 48%] 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 [ 51%] 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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; | ^~~~~~ [ 54%] 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 [ 56%] 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 [ 59%] 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 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' [ 59%] Built target sundials_fcvode_static [ 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 [ 86%] Building C object src/cvode/CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_band.c.o [ 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 [ 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 (0.7s) -- Generating done (0.0s) 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 -- 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 + /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' [ 5%] Building CXX object CMakeFiles/run_network.dir/src/model/function.cpp.o [ 3%] Building CXX object CMakeFiles/run_network.dir/src/network3.cpp.o [ 5%] Building CXX object CMakeFiles/run_network.dir/src/network.cpp.o [ 7%] Building CXX object CMakeFiles/run_network.dir/src/run_network.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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 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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 -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 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-Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 /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/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 ../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/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* 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/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; | ^~~~~~~~~ [ 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 ‘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; | ^ /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/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.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/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.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){ | ^~ /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; | ^~~~~~ [ 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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:588:20: 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 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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/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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 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-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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 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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/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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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/rateExpressions/rateSaturation.cpp.o -MF CMakeFiles/run_network.dir/src/model/rateExpressions/rateSaturation.cpp.o.d -o CMakeFiles/run_network.dir/src/model/rateExpressions/rateSaturation.cpp.o -c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/model/rateExpressions/rateSaturation.cpp [ 32%] Building CXX object CMakeFiles/run_network.dir/src/model/reactions/bioNetGenRxn.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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 [ 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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/../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; | ^~~~~~~~ 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; | ^~~~~~~~ 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; | ^~~~~~~~ [ 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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; | ^~~~~~~~ ../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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 [ 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 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; | ^~~~~~~~ [ 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 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; | ^~~~~~~~ ../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/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; | ^~~~~~~~ ../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; | ^~~~~~~~ [ 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 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-specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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/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; | ^~~~~~~~ [ 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 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-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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 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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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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/MTrand/mtrand.cpp.o -MF CMakeFiles/run_network.dir/src/util/MTrand/mtrand.cpp.o.d -o CMakeFiles/run_network.dir/src/util/MTrand/mtrand.cpp.o -c /builddir/build/BUILD/bionetgen-2.9.0-build/bionetgen-2.9.0/bionetgen-BioNetGen-2.9.0/bng2/Network3/src/util/MTrand/mtrand.cpp [ 98%] Building CXX object CMakeFiles/run_network.dir/src/util/rand2/rand2.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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 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-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 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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.gICaHt + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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/Network3/build ~/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/Network3/build + 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_aarch64-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.aarch64 --unique-debug-src-base bionetgen-2.9.0-4.fc42.aarch64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -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.aarch64 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.Ao4YRu + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 ~/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 + pushd bionetgen-BioNetGen-2.9.0/bng2/Models2 + install -pm 755 ../Network3/build/run_network -D ./bin/run_network_aarch64-linux + install -pm 755 ../Network3/build/run_network -D ../bin/run_network_aarch64-linux + echo 'Running some tests ...' 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 1.00e-02 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 1.00e-02 CPU s 1.00e-02 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_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_aarch64-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 0.10 719 851 0.20 753 889 0.30 788 924 0.40 822 962 0.50 857 997 0.60 891 1035 0.70 926 1070 0.80 960 1108 0.90 995 1147 1.00 1029 1181 1.10 1064 1221 1.20 1098 1257 1.30 1133 1299 1.40 1167 1335 1.50 1215 1393 1.60 1263 1449 1.70 1324 1520 1.80 1389 1596 1.90 1460 1680 2.00 1544 1781 2.10 1620 1865 2.20 1697 1946 2.30 1749 2005 2.40 1800 2063 2.50 1854 2128 2.60 1993 2299 2.70 2464 2852 2.80 2562 2973 2.90 2607 3025 3.00 2657 3086 3.10 2718 3156 3.20 2779 3224 3.30 2839 3290 3.40 2900 3355 3.50 2961 3420 3.60 3018 3482 3.70 3071 3550 3.80 3200 3708 3.90 3345 3881 4.00 3456 4003 4.10 3521 4073 4.20 3572 4129 4.30 3624 4186 4.40 3671 4234 4.50 3707 4279 4.60 3753 4333 4.70 3799 4383 4.80 3856 4451 4.90 3913 4526 5.00 3969 4585 5.10 4010 4632 5.20 4047 4675 5.30 4080 4709 5.40 4105 4739 5.50 4129 4764 5.60 4154 4797 5.70 4178 4823 5.80 4201 4848 5.90 4221 4871 6.00 4241 4897 6.10 4261 4918 6.20 4281 4943 6.30 4294 4956 6.40 4307 4970 6.50 4321 4984 6.60 4334 4997 6.70 4347 5014 6.80 4356 5024 6.90 4365 5033 7.00 4374 5042 7.10 4383 5052 7.20 4392 5062 7.30 4401 5071 7.40 4410 5086 7.50 4419 5095 7.60 4427 5103 7.70 4436 5113 7.80 4445 5123 7.90 4457 5142 8.00 4469 5165 8.10 4481 5179 8.20 4491 5192 8.30 4504 5211 8.40 4522 5240 8.50 4543 5268 8.60 4568 5298 8.70 4607 5350 8.80 4663 5420 8.90 4772 5555 9.00 5104 5945 9.10 5399 6270 9.20 5507 6389 9.30 5546 6435 9.40 5561 6451 9.50 5573 6463 9.60 5585 6475 9.70 5597 6492 9.80 5608 6503 9.90 5620 6516 10.00 5632 6528 10.10 5644 6541 10.20 5656 6558 10.30 5668 6570 10.40 5680 6584 10.50 5692 6596 10.60 5703 6609 10.70 5715 6626 10.80 5727 6639 10.90 5739 6653 11.00 5751 6665 11.10 5767 6683 11.20 5783 6704 11.30 5799 6721 11.40 5815 6738 11.50 5831 6754 11.60 5847 6776 11.70 5863 6794 11.80 5879 6812 11.90 5895 6834 12.00 5911 6850 12.10 5927 6868 12.20 5943 6886 12.30 5959 6908 12.40 5975 6926 12.50 5991 6942 12.60 6012 6967 12.70 6034 6994 12.80 6056 7020 12.90 6078 7048 13.00 6100 7072 13.10 6128 7108 13.20 6158 7140 13.30 6188 7177 13.40 6223 7216 13.50 6263 7264 13.60 6311 7322 13.70 6366 7387 13.80 6435 7464 13.90 6507 7550 14.00 6594 7646 14.10 6673 7738 14.20 6750 7820 14.30 6803 7880 14.40 6856 7939 14.50 6911 8005 14.60 7038 8162 14.70 7513 8728 14.80 7634 8876 14.90 7681 8925 15.00 7731 8985 15.10 7793 9054 15.20 7848 9121 15.30 7904 9185 15.40 7960 9246 15.50 8016 9306 15.60 8072 9366 15.70 8129 9434 15.80 8253 9587 15.90 8393 9752 16.00 8510 9880 16.10 8578 9953 16.20 8634 10013 16.30 8690 10073 16.40 8738 10126 16.50 8776 10172 16.60 8820 10221 16.70 8870 10277 16.80 8928 10346 16.90 8988 10415 17.00 9046 10480 17.10 9088 10524 17.20 9126 10568 17.30 9160 10607 17.40 9185 10632 17.50 9211 10659 17.60 9236 10692 17.70 9261 10718 17.80 9284 10747 17.90 9304 10769 18.00 9325 10791 18.10 9346 10817 18.20 9365 10837 18.30 9376 10850 18.40 9385 10859 18.50 9394 10874 18.60 9404 10884 18.70 9413 10894 18.80 9422 10903 18.90 9431 10912 19.00 9440 10921 19.10 9449 10930 19.20 9459 10945 19.30 9468 10954 19.40 9477 10964 19.50 9486 10973 19.60 9495 10984 19.70 9505 10994 19.80 9514 11012 19.90 9523 11021 20.00 9532 11031 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 0.01 s. Finished processing file CaOscillate_Func.bngl. CPU TIME: total 0.03 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 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_Sat.net. CPU TIME: generate_network 0.00 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_aarch64-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 0.10 717 850 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 0.90 911 1066 1.00 936 1099 1.10 961 1129 1.20 993 1171 1.30 1025 1207 1.40 1064 1257 1.50 1108 1309 1.60 1155 1366 1.70 1210 1431 1.80 1284 1514 1.90 1358 1601 2.00 1442 1703 2.10 1521 1789 2.20 1596 1869 2.30 1649 1928 2.40 1701 1987 2.50 1757 2053 2.60 1896 2222 2.70 2360 2768 2.80 2463 2900 2.90 2511 2957 3.00 2560 3015 3.10 2618 3082 3.20 2677 3148 3.30 2735 3213 3.40 2793 3275 3.50 2852 3338 3.60 2910 3400 3.70 2969 3470 3.80 3099 3626 3.90 3243 3798 4.00 3343 3906 4.10 3413 3985 4.20 3479 4055 4.30 3546 4126 4.40 3590 4175 4.50 3634 4222 4.60 3679 4275 4.70 3723 4327 4.80 3778 4394 4.90 3835 4465 5.00 3890 4527 5.10 3930 4571 5.20 3966 4613 5.30 3999 4651 5.40 4023 4676 5.50 4047 4702 5.60 4071 4732 5.70 4095 4759 5.80 4117 4787 5.90 4138 4811 6.00 4158 4833 6.10 4178 4854 6.20 4198 4879 6.30 4211 4892 6.40 4225 4907 6.50 4238 4924 6.60 4252 4938 6.70 4265 4951 6.80 4274 4961 6.90 4283 4970 7.00 4292 4979 7.10 4301 4989 7.20 4310 5003 7.30 4319 5012 7.40 4328 5022 7.50 4337 5031 7.60 4345 5040 7.70 4354 5050 7.80 4363 5064 7.90 4372 5079 8.00 4381 5088 8.10 4390 5099 8.20 4400 5115 8.30 4412 5134 8.40 4431 5179 8.50 4456 5205 8.60 4483 5240 8.70 4519 5286 8.80 4575 5356 8.90 4682 5482 9.00 5014 5875 9.10 5309 6200 9.20 5417 6315 9.30 5456 6361 9.40 5471 6377 9.50 5482 6388 9.60 5493 6404 9.70 5505 6417 9.80 5516 6428 9.90 5527 6440 10.00 5539 6452 10.10 5550 6468 10.20 5561 6479 10.30 5573 6493 10.40 5584 6504 10.50 5595 6517 10.60 5607 6535 10.70 5618 6546 10.80 5630 6560 10.90 5643 6575 11.00 5658 6595 11.10 5673 6610 11.20 5689 6627 11.30 5704 6644 11.40 5719 6665 11.50 5735 6681 11.60 5750 6698 11.70 5765 6715 11.80 5781 6737 11.90 5796 6753 12.00 5811 6769 12.10 5827 6787 12.20 5842 6808 12.30 5857 6825 12.40 5873 6841 12.50 5892 6863 12.60 5913 6889 12.70 5934 6912 12.80 5955 6935 12.90 5975 6961 13.00 6001 6992 13.10 6029 7028 13.20 6057 7058 13.30 6095 7112 13.40 6133 7157 13.50 6171 7203 13.60 6220 7263 13.70 6275 7328 13.80 6345 7407 13.90 6415 7492 14.00 6497 7592 14.10 6572 7678 14.20 6647 7757 14.30 6703 7819 14.40 6753 7876 14.50 6805 7938 14.60 6932 8095 14.70 7381 8618 14.80 7498 8747 14.90 7552 8807 15.00 7599 8867 15.10 7663 8938 15.20 7718 9002 15.30 7774 9065 15.40 7831 9127 15.50 7887 9187 15.60 7944 9244 15.70 8001 9317 15.80 8126 9469 15.90 8281 9649 16.00 8392 9771 16.10 8457 9841 16.20 8507 9898 16.30 8557 9954 16.40 8604 10006 16.50 8640 10047 16.60 8685 10100 16.70 8730 10154 16.80 8785 10215 16.90 8841 10289 17.00 8895 10347 17.10 8935 10395 17.20 8971 10437 17.30 9004 10471 17.40 9028 10499 17.50 9051 10525 17.60 9075 10551 17.70 9098 10580 17.80 9120 10605 17.90 9140 10629 18.00 9160 10655 18.10 9181 10677 18.20 9200 10701 18.30 9210 10716 18.40 9221 10728 18.50 9232 10740 18.60 9243 10751 18.70 9254 10762 18.80 9265 10773 18.90 9276 10788 19.00 9287 10799 19.10 9298 10810 19.20 9309 10821 19.30 9320 10832 19.40 9331 10847 19.50 9342 10858 19.60 9353 10869 19.70 9364 10880 19.80 9375 10891 19.90 9386 10903 20.00 9397 10919 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 1.00e-02 CPU s Iteration 2: 9 species 6 rxns 0.00e+00 CPU s Iteration 3: 10 species 10 rxns 0.00e+00 CPU s Iteration 4: 10 species 12 rxns 1.00e-02 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 1.00e-02 CPU s 2.50e-03 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 2.00e-02 CPU s 1.67e-03 CPU s/rxn Wrote network in net format to ./catalysis.net. CPU TIME: generate_network 0.02 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_aarch64-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 0.04 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 0.00e+00 CPU s Iteration 3: 10 species 8 rxns 1.00e-02 CPU s Iteration 4: 19 species 21 rxns 2.00e-02 CPU s Iteration 5: 37 species 76 rxns 7.00e-02 CPU s Iteration 6: 69 species 213 rxns 1.70e-01 CPU s Iteration 7: 131 species 494 rxns 3.70e-01 CPU s Iteration 8: 295 species 1260 rxns 1.16e+00 CPU s Iteration 9: 356 species 3088 rxns 3.04e+00 CPU s Iteration 10: 356 species 3749 rxns 1.41e+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 1.53e+00 CPU s 2.55e-03 CPU s/rxn Rule 3: 144 reactions 1.70e-01 CPU s 1.18e-03 CPU s/rxn Rule 4: 96 reactions 1.30e-01 CPU s 1.35e-03 CPU s/rxn Rule 5: 156 reactions 1.50e-01 CPU s 9.62e-04 CPU s/rxn Rule 6: 104 reactions 1.20e-01 CPU s 1.15e-03 CPU s/rxn Rule 7: 96 reactions 1.20e-01 CPU s 1.25e-03 CPU s/rxn Rule 8: 104 reactions 1.20e-01 CPU s 1.15e-03 CPU s/rxn Rule 9: 312 reactions 4.30e-01 CPU s 1.38e-03 CPU s/rxn Rule 10: 312 reactions 4.80e-01 CPU s 1.54e-03 CPU s/rxn Rule 11: 312 reactions 4.70e-01 CPU s 1.51e-03 CPU s/rxn Rule 12: 208 reactions 2.50e-01 CPU s 1.20e-03 CPU s/rxn Rule 13: 208 reactions 3.00e-01 CPU s 1.44e-03 CPU s/rxn Rule 14: 208 reactions 3.60e-01 CPU s 1.73e-03 CPU s/rxn Rule 15: 208 reactions 3.80e-01 CPU s 1.83e-03 CPU s/rxn Rule 16: 208 reactions 3.30e-01 CPU s 1.59e-03 CPU s/rxn Rule 17: 208 reactions 3.90e-01 CPU s 1.88e-03 CPU s/rxn Rule 18: 208 reactions 3.30e-01 CPU s 1.59e-03 CPU s/rxn Rule 19: 2 reactions 4.00e-02 CPU s 2.00e-02 CPU s/rxn Rule 20: 2 reactions 3.00e-02 CPU s 1.50e-02 CPU s/rxn Rule 21: 1 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 22: 2 reactions 4.00e-02 CPU s 2.00e-02 CPU s/rxn Rule 23: 2 reactions 1.00e-02 CPU s 5.00e-03 CPU s/rxn Total : 3749 reactions 6.25e+00 CPU s 1.67e-03 CPU s/rxn Wrote network in net format to ./egfr_net.net. CPU TIME: generate_network 6.36 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_aarch64-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 7.00e-02 CPU seconds Program times: 0.08 CPU s 0.00 clock s Updating species concentrations from ./egfr_net.cdat CPU TIME: simulate 0.18 s. Finished processing file egfr_net.bngl. CPU TIME: total 6.58 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 2.00e-02 CPU s Iteration 6: 33 species 62 rxns 2.00e-02 CPU s Iteration 7: 38 species 90 rxns 3.00e-02 CPU s Iteration 8: 40 species 115 rxns 3.00e-02 CPU s Iteration 9: 40 species 123 rxns 1.00e-02 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 2.00e-02 CPU s 1.67e-03 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 1.00e-02 CPU s 3.33e-03 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 1.00e-02 CPU s 1.67e-03 CPU s/rxn Rule 13: 6 reactions 1.00e-02 CPU s 1.67e-03 CPU s/rxn Rule 14: 6 reactions 1.00e-02 CPU s 1.67e-03 CPU s/rxn Rule 15: 6 reactions 1.00e-02 CPU s 1.67e-03 CPU s/rxn Rule 16: 6 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 17: 6 reactions 1.00e-02 CPU s 1.67e-03 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 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 22: 2 reactions 1.00e-02 CPU s 5.00e-03 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 1.00e-02 CPU s 5.00e-03 CPU s/rxn Rule 26: 2 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Total : 123 reactions 1.40e-01 CPU s 1.14e-03 CPU s/rxn Wrote network in net format to ./egfr_net_red.net. CPU TIME: generate_network 0.14 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_aarch64-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_aarch64-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 0.02 s. Finished processing file egfr_net_red.bngl. CPU TIME: total 0.24 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 3.00e-02 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: 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 1.00e-02 CPU s 5.00e-03 CPU s/rxn Rule 10: 2 reactions 0.00e+00 CPU s 0.00e+00 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 1.00e-02 CPU s 5.00e-03 CPU s/rxn Total : 37 reactions 3.00e-02 CPU s 8.11e-04 CPU s/rxn Wrote network in net format to ./egfr_path.net. CPU TIME: generate_network 0.04 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_aarch64-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 0.01 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_aarch64-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 0.02 s. Finished processing file egfr_path.bngl. CPU TIME: total 0.10 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 1.00e-02 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 0.00e+00 CPU s Cumulative CPU time for each rule Rule 1: 8 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 2: 8 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 3: 8 reactions 3.00e-02 CPU s 3.75e-03 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 0.04 s. Wrote SBML to ./energy_example1_sbml.xml. CPU TIME: writeSBML 0.01 s. Finished processing file energy_example1.bngl. CPU TIME: total 0.07 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 0.00e+00 CPU s Iteration 2: 9 species 8 rxns 1.00e-02 CPU s Iteration 3: 12 species 20 rxns 1.00e-02 CPU s Iteration 4: 22 species 36 rxns 3.00e-02 CPU s Iteration 5: 43 species 100 rxns 5.00e-02 CPU s Iteration 6: 78 species 255 rxns 1.50e-01 CPU s Iteration 7: 139 species 586 rxns 3.40e-01 CPU s Iteration 8: 199 species 1190 rxns 6.50e-01 CPU s Iteration 9: 303 species 1841 rxns 8.20e-01 CPU s Iteration 10: 354 species 3143 rxns 1.41e+00 CPU s Iteration 11: 354 species 3680 rxns 6.20e-01 CPU s Cumulative CPU time for each rule Rule 1: 48 reactions 9.00e-02 CPU s 1.87e-03 CPU s/rxn Rule 2: 1152 reactions 1.14e+00 CPU s 9.90e-04 CPU s/rxn Rule 3: 312 reactions 3.50e-01 CPU s 1.12e-03 CPU s/rxn Rule 4: 36 reactions 6.00e-02 CPU s 1.67e-03 CPU s/rxn Rule 5: 24 reactions 7.00e-02 CPU s 2.92e-03 CPU s/rxn Rule 6: 312 reactions 3.40e-01 CPU s 1.09e-03 CPU s/rxn Rule 7: 36 reactions 6.00e-02 CPU s 1.67e-03 CPU s/rxn Rule 8: 24 reactions 6.00e-02 CPU s 2.50e-03 CPU s/rxn Rule 9: 832 reactions 8.40e-01 CPU s 1.01e-03 CPU s/rxn Rule 10: 48 reactions 1.00e-01 CPU s 2.08e-03 CPU s/rxn Rule 11: 48 reactions 7.00e-02 CPU s 1.46e-03 CPU s/rxn Rule 12: 64 reactions 1.50e-01 CPU s 2.34e-03 CPU s/rxn Rule 13: 64 reactions 1.10e-01 CPU s 1.72e-03 CPU s/rxn Rule 14: 156 reactions 1.40e-01 CPU s 8.97e-04 CPU s/rxn Rule 15: 104 reactions 9.00e-02 CPU s 8.65e-04 CPU s/rxn Rule 16: 208 reactions 2.00e-01 CPU s 9.62e-04 CPU s/rxn Rule 17: 208 reactions 1.90e-01 CPU s 9.13e-04 CPU s/rxn Rule 18: 2 reactions 1.00e-02 CPU s 5.00e-03 CPU s/rxn Rule 19: 2 reactions 2.00e-02 CPU s 1.00e-02 CPU s/rxn Total : 3680 reactions 4.09e+00 CPU s 1.11e-03 CPU s/rxn Wrote network in net format to ./fceri_ji.net. CPU TIME: generate_network 4.18 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_aarch64-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 5.30e-01 CPU seconds Program times: 0.54 CPU s 1.00 clock s Updating species concentrations from ./fceri_ji.cdat CPU TIME: simulate 0.65 s. Finished processing file fceri_ji.bngl. CPU TIME: total 4.86 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 1.00e-02 CPU s Iteration 5: 17 species 30 rxns 2.00e-02 CPU s Iteration 6: 22 species 59 rxns 3.00e-02 CPU s Iteration 7: 22 species 76 rxns 2.00e-02 CPU s Cumulative CPU time for each rule Rule 1: 8 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 2: 20 reactions 4.00e-02 CPU s 2.00e-03 CPU s/rxn Rule 3: 4 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 4: 6 reactions 1.00e-02 CPU s 1.67e-03 CPU s/rxn Rule 5: 24 reactions 3.00e-02 CPU s 1.25e-03 CPU s/rxn Rule 6: 14 reactions 1.00e-02 CPU s 7.14e-04 CPU s/rxn Total : 76 reactions 9.00e-02 CPU s 1.18e-03 CPU s/rxn Wrote network in net format to ./test_continue.net. CPU TIME: generate_network 0.10 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_aarch64-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 0.00 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_aarch64-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 0.02 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_aarch64-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 0.01 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_aarch64-linux -o ./test_continue_ssa -p ssa -h 1980621709 --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: 71192 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_aarch64-linux -o ./test_continue_ssa -p ssa -h 724305791 --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: 130235 Time course of concentrations written to file ./test_continue_ssa.cdat. Time course of groups written to file ./test_continue_ssa.gdat. Propagation took 2.00e-02 CPU seconds Program times: 0.02 CPU s 0.00 clock s Updating species concentrations from ./test_continue_ssa.cdat CPU TIME: simulate 0.05 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_aarch64-linux -o ./test_continue_ssa -p ssa -h 1921336071 --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: 107048 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 0.03 s. Finished processing file test_continue.bngl. CPU TIME: total 0.26 s. + echo 'Tests finished.' + RPM_EC=0 Tests finished. ++ jobs -p + exit 0 Processing files: bionetgen-2.9.0-4.fc42.aarch64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.uTSjVn + 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.pnxPoq + 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(aarch-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: ld-linux-aarch64.so.1()(64bit) ld-linux-aarch64.so.1(GLIBC_2.17)(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.17)(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_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_2.17)(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.aarch64 Provides: bionetgen-debugsource = 2.9.0-4.fc42 bionetgen-debugsource(aarch-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.aarch64 Provides: bionetgen-debuginfo = 2.9.0-4.fc42 bionetgen-debuginfo(aarch-64) = 2.9.0-4.fc42 debuginfo(build-id) = 0f6fcf71273012d8fbad121c63ec87fb064bc72b Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: bionetgen-debugsource(aarch-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.aarch64.rpm Wrote: /builddir/build/RPMS/bionetgen-debugsource-2.9.0-4.fc42.aarch64.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.aarch64.rpm Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.GRiPBg + 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-aarch64-1736203564.750723/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) 1 minutes 1 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot Finish: run Running RPMResults tool Package info: { "packages": [ { "name": "bionetgen-debugsource", "epoch": null, "version": "2.9.0", "release": "4.fc42", "arch": "aarch64" }, { "name": "bionetgen-debuginfo", "epoch": null, "version": "2.9.0", "release": "4.fc42", "arch": "aarch64" }, { "name": "bionetgen", "epoch": null, "version": "2.9.0", "release": "4.fc42", "arch": "aarch64" }, { "name": "bionetgen-perl", "epoch": null, "version": "2.9.0", "release": "4.fc42", "arch": "noarch" }, { "name": "bionetgen", "epoch": null, "version": "2.9.0", "release": "4.fc42", "arch": "src" } ] } RPMResults finished