Warning: Permanently added '2620:52:3:1:dead:beef:cafe:c1d8' (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/7994924-fedora-rawhide-x86_64 --chroot fedora-rawhide-x86_64 Version: 0.73 PID: 8905 Logging PID: 8906 Task: {'allow_user_ssh': False, 'appstream': False, 'background': True, 'bootstrap': 'off', 'build_id': 7994924, 'buildroot_pkgs': [], 'chroot': 'fedora-rawhide-x86_64', 'enable_net': False, 'fedora_review': False, 'git_hash': 'c15c29e6b7f39331cdd806c56b7aaa62f00a84d8', 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/@python/python3.13/smoldyn', 'isolation': 'default', 'memory_reqs': 2048, 'package_name': 'smoldyn', 'package_version': '2.72-6', 'project_dirname': 'python3.13', 'project_name': 'python3.13', 'project_owner': '@python', 'repo_priority': 9, 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/@python/python3.13/fedora-rawhide-x86_64/', 'id': 'copr_base', 'name': 'Copr repository', 'priority': 9}, {'baseurl': 'http://kojipkgs.fedoraproject.org/repos/f41-build/latest/$basearch/', 'id': 'http_kojipkgs_fedoraproject_org_repos_f41_build_latest_basearch', 'name': 'Additional repo http_kojipkgs_fedoraproject_org_repos_f41_build_latest_basearch'}], 'sandbox': '@python/python3.13--ksurma', 'source_json': {}, 'source_type': None, 'ssh_public_keys': None, 'submitter': 'ksurma', 'tags': [], 'task_id': '7994924-fedora-rawhide-x86_64', 'timeout': None, 'uses_devel_repo': False, 'with_opts': [], 'without_opts': []} Running: git clone https://copr-dist-git.fedorainfracloud.org/git/@python/python3.13/smoldyn /var/lib/copr-rpmbuild/workspace/workdir-4eigp91z/smoldyn --depth 500 --no-single-branch --recursive cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/@python/python3.13/smoldyn', '/var/lib/copr-rpmbuild/workspace/workdir-4eigp91z/smoldyn', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-4eigp91z/smoldyn'... Running: git checkout c15c29e6b7f39331cdd806c56b7aaa62f00a84d8 -- cmd: ['git', 'checkout', 'c15c29e6b7f39331cdd806c56b7aaa62f00a84d8', '--'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-4eigp91z/smoldyn rc: 0 stdout: stderr: Note: switching to 'c15c29e6b7f39331cdd806c56b7aaa62f00a84d8'. 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 c15c29e automatic import of smoldyn Running: copr-distgit-client sources /usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated INFO: Calling: curl -H Pragma: -o Smoldyn-2.72.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/@python/python3.13/smoldyn/Smoldyn-2.72.tar.gz/md5/55177f82859a034ac5418e6894089192/Smoldyn-2.72.tar.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 96.4M 100 96.4M 0 0 26.6M 0 0:00:03 0:00:03 --:--:-- 26.6M INFO: Reading stdout from command: md5sum Smoldyn-2.72.tar.gz Running (timeout=None): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-4eigp91z/smoldyn/smoldyn.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-4eigp91z/smoldyn --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1725755594.437893 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 5.6 starting (python version = 3.12.1, NVR = mock-5.6-1.fc39), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-4eigp91z/smoldyn/smoldyn.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-4eigp91z/smoldyn --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1725755594.437893 -r /var/lib/copr-rpmbuild/results/configs/child.cfg 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-4eigp91z/smoldyn/smoldyn.spec) Config(fedora-rawhide-x86_64) Start: clean chroot Finish: clean chroot Mock Version: 5.6 INFO: Mock Version: 5.6 Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-1725755594.437893/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 (fallback) INFO: Buildroot is handled by package management from host and used with --installroot: rpm-4.19.1.1-1.fc39.x86_64 rpm-sequoia-1.6.0-1.fc39.x86_64 python3-dnf-4.21.1-1.fc39.noarch python3-dnf-plugins-core-4.9.0-1.fc39.noarch yum-4.21.1-1.fc39.noarch dnf5-5.1.17-2.fc39.x86_64 dnf5-plugins-5.1.17-2.fc39.x86_64 Start: installing minimal buildroot with dnf5 Updating and loading repositories: fedora 100% | 923.9 KiB/s | 26.8 KiB | 00m00s Copr repository 100% | 46.6 KiB/s | 1.5 KiB | 00m00s Additional repo http_kojipkgs_fedorapr 100% | 63.9 KiB/s | 3.8 KiB | 00m00s Copr repository 100% | 49.4 MiB/s | 12.6 MiB | 00m00s Repositories loaded. Package Arch Version Repository Size Installing group/module packages: bash x86_64 5.2.32-2.fc42 fedora 8.2 MiB bzip2 x86_64 1.0.8-19.fc41 http_kojipkgs_fedoraproject_org_repos_f41_build_latest_basearch 95.7 KiB coreutils x86_64 9.5-9.fc42 fedora 5.7 MiB cpio x86_64 2.15-2.fc41 http_kojipkgs_fedoraproject_org_repos_f41_build_latest_basearch 1.1 MiB diffutils x86_64 3.10-8.fc41 http_kojipkgs_fedoraproject_org_repos_f41_build_latest_basearch 1.6 MiB fedora-release-common noarch 42-0.3 fedora 19.4 KiB findutils x86_64 1:4.10.0-4.fc41 http_kojipkgs_fedoraproject_org_repos_f41_build_latest_basearch 1.8 MiB gawk x86_64 5.3.0-4.fc41 http_kojipkgs_fedoraproject_org_repos_f41_build_latest_basearch 1.7 MiB glibc-minimal-langpack x86_64 2.40-3.fc41 http_kojipkgs_fedoraproject_org_repos_f41_build_latest_basearch 0.0 B grep x86_64 3.11-9.fc41 http_kojipkgs_fedoraproject_org_repos_f41_build_latest_basearch 1.0 MiB gzip x86_64 1.13-2.fc41 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1.6.1-6.fc42 fedora 139.0 KiB pcre2 x86_64 10.44-1.fc41.1 http_kojipkgs_fedoraproject_org_repos_f41_build_latest_basearch 653.5 KiB pcre2-syntax noarch 10.44-1.fc41.1 http_kojipkgs_fedoraproject_org_repos_f41_build_latest_basearch 251.6 KiB perl-srpm-macros noarch 1-56.fc41 http_kojipkgs_fedoraproject_org_repos_f41_build_latest_basearch 861.0 B pkgconf x86_64 2.3.0-1.fc42 fedora 88.6 KiB pkgconf-m4 noarch 2.3.0-1.fc42 fedora 14.4 KiB pkgconf-pkg-config x86_64 2.3.0-1.fc42 fedora 989.0 B popt x86_64 1.19-7.fc41 http_kojipkgs_fedoraproject_org_repos_f41_build_latest_basearch 136.9 KiB publicsuffix-list-dafsa noarch 20240107-4.fc41 http_kojipkgs_fedoraproject_org_repos_f41_build_latest_basearch 67.5 KiB pyproject-srpm-macros noarch 1.14.0-1.fc41 http_kojipkgs_fedoraproject_org_repos_f41_build_latest_basearch 1.9 KiB python-srpm-macros noarch 3.13-3.fc41 http_kojipkgs_fedoraproject_org_repos_f41_build_latest_basearch 51.0 KiB qt5-srpm-macros noarch 5.15.15-1.fc42 fedora 500.0 B qt6-srpm-macros noarch 6.7.2-3.fc41 http_kojipkgs_fedoraproject_org_repos_f41_build_latest_basearch 456.0 B readline x86_64 8.2-11.fc42 fedora 493.1 KiB rpm x86_64 4.19.93-1.fc42 copr_base 3.1 MiB rpm-build-libs x86_64 4.19.93-1.fc42 copr_base 206.7 KiB rpm-libs x86_64 4.19.93-1.fc42 copr_base 721.9 KiB rpm-sequoia x86_64 1.7.0-2.fc41 http_kojipkgs_fedoraproject_org_repos_f41_build_latest_basearch 2.4 MiB rust-srpm-macros noarch 26.3-3.fc42 fedora 4.8 KiB setup noarch 2.15.0-5.fc41 http_kojipkgs_fedoraproject_org_repos_f41_build_latest_basearch 720.7 KiB sqlite-libs x86_64 3.46.1-1.fc41 http_kojipkgs_fedoraproject_org_repos_f41_build_latest_basearch 1.4 MiB systemd-libs x86_64 256.5-1.fc42 fedora 2.0 MiB util-linux-core x86_64 2.40.2-8.fc42 copr_base 1.5 MiB xxhash-libs x86_64 0.8.2-3.fc41 http_kojipkgs_fedoraproject_org_repos_f41_build_latest_basearch 88.5 KiB xz-libs x86_64 1:5.6.2-2.fc41 http_kojipkgs_fedoraproject_org_repos_f41_build_latest_basearch 214.4 KiB zig-srpm-macros noarch 1-3.fc41 http_kojipkgs_fedoraproject_org_repos_f41_build_latest_basearch 1.1 KiB zip x86_64 3.0-41.fc41 http_kojipkgs_fedoraproject_org_repos_f41_build_latest_basearch 703.2 KiB zlib-ng-compat x86_64 2.1.7-2.fc41 http_kojipkgs_fedoraproject_org_repos_f41_build_latest_basearch 134.0 KiB zstd x86_64 1.5.6-2.fc41 http_kojipkgs_fedoraproject_org_repos_f41_build_latest_basearch 1.7 MiB Installing groups: Buildsystem building group Transaction Summary: Installing: 153 packages Total size of inbound packages is 53 MiB. Need to download 0 B. After this operation 180 MiB will be used (install 180 MiB, remove 0 B). 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B | 00m00s >>> Already downloaded [149/153] cyrus-sasl-lib-0:2.1.28-27.fc 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [150/153] libevent-0:2.1.12-14.fc41.x86 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [151/153] libtool-ltdl-0:2.4.7-12.fc41. 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [152/153] libunistring-0:1.1-8.fc41.x86 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [153/153] publicsuffix-list-dafsa-0:202 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [153/153] Total 100% | 0.0 B/s | 0.0 B | 00m00s Running transaction Importing PGP 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 PGP 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 PGP key 0xE99D6AD1: Userid : "Fedora (41) " Fingerprint: 466CF2D8B60BC3057AA9453ED0622462E99D6AD1 From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-41-primary The key was successfully imported. Importing PGP 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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[130/155] Installing libevent-0:2.1.12- 100% | 175.7 MiB/s | 899.5 KiB | 00m00s [131/155] Installing openldap-0:2.6.8-5 100% | 126.6 MiB/s | 648.0 KiB | 00m00s [132/155] Installing libcurl-0:8.9.1-3. 100% | 200.0 MiB/s | 819.2 KiB | 00m00s [133/155] Installing elfutils-libs-0:0. 100% | 158.2 MiB/s | 648.0 KiB | 00m00s [134/155] Installing elfutils-debuginfo 100% | 21.8 MiB/s | 66.9 KiB | 00m00s [135/155] Installing binutils-0:2.43.1- 100% | 220.3 MiB/s | 27.5 MiB | 00m00s >>> Running post-install scriptlet: binutils-0:2.43.1-1.fc42.x86_64 >>> Stop post-install scriptlet: binutils-0:2.43.1-1.fc42.x86_64 [136/155] Installing elfutils-0:0.191-8 100% | 196.9 MiB/s | 2.6 MiB | 00m00s [137/155] Installing gdb-minimal-0:15.1 100% | 270.6 MiB/s | 13.0 MiB | 00m00s [138/155] Installing debugedit-0:5.0-17 100% | 65.8 MiB/s | 202.0 KiB | 00m00s [139/155] Installing rpm-build-libs-0:4 100% | 67.5 MiB/s | 207.5 KiB | 00m00s [140/155] Installing curl-0:8.9.1-3.fc4 100% | 26.9 MiB/s | 798.6 KiB | 00m00s >>> Running pre-install scriptlet: rpm-0:4.19.93-1.fc42.x86_64 >>> Stop pre-install scriptlet: rpm-0:4.19.93-1.fc42.x86_64 [141/155] Installing rpm-0:4.19.93-1.fc 100% | 80.7 MiB/s | 2.5 MiB | 00m00s [142/155] Installing efi-srpm-macros-0: 100% | 40.2 MiB/s | 41.2 KiB | 00m00s [143/155] Installing lua-srpm-macros-0: 100% | 0.0 B/s | 1.9 KiB | 00m00s [144/155] Installing zig-srpm-macros-0: 100% | 1.6 MiB/s | 1.7 KiB | 00m00s [145/155] Installing fonts-srpm-macros- 100% | 55.7 MiB/s | 57.0 KiB | 00m00s [146/155] Installing forge-srpm-macros- 100% | 39.4 MiB/s | 40.4 KiB | 00m00s [147/155] Installing go-srpm-macros-0:3 100% | 60.5 MiB/s | 62.0 KiB | 00m00s [148/155] Installing python-srpm-macros 100% | 50.9 MiB/s | 52.2 KiB | 00m00s [149/155] Installing redhat-rpm-config- 100% | 62.8 MiB/s | 192.9 KiB | 00m00s [150/155] Installing rpm-build-0:4.19.9 100% | 39.6 MiB/s | 202.8 KiB | 00m00s [151/155] Installing pyproject-srpm-mac 100% | 2.4 MiB/s | 2.5 KiB | 00m00s [152/155] Installing util-linux-0:2.40. 100% | 71.4 MiB/s | 3.7 MiB | 00m00s >>> Running post-install scriptlet: util-linux-0:2.40.2-8.fc42.x86_64 >>> Stop post-install scriptlet: util-linux-0:2.40.2-8.fc42.x86_64 [153/155] Installing authselect-0:1.5.0 100% | 30.8 MiB/s | 157.9 KiB | 00m00s [154/155] Installing which-0:2.21-42.fc 100% | 40.2 MiB/s | 82.4 KiB | 00m00s [155/155] Installing info-0:7.1-3.fc41. 100% | 246.1 KiB/s | 362.2 KiB | 00m01s >>> Running post-transaction scriptlet: filesystem-0:3.18-23.fc41.x86_64 >>> Stop post-transaction scriptlet: filesystem-0:3.18-23.fc41.x86_64 >>> Running post-transaction scriptlet: ca-certificates-0:2024.2.68_v8.0.302-3.f >>> Stop post-transaction scriptlet: ca-certificates-0:2024.2.68_v8.0.302-3.fc41 >>> Running post-transaction scriptlet: authselect-libs-0:1.5.0-7.fc41.x86_64 >>> Stop post-transaction scriptlet: authselect-libs-0:1.5.0-7.fc41.x86_64 >>> Running post-transaction scriptlet: rpm-0:4.19.93-1.fc42.x86_64 >>> Stop post-transaction scriptlet: rpm-0:4.19.93-1.fc42.x86_64 >>> Running trigger-install scriptlet: glibc-common-0:2.40-3.fc41.x86_64 >>> Stop trigger-install scriptlet: glibc-common-0:2.40-3.fc41.x86_64 >>> Running trigger-install scriptlet: info-0:7.1-3.fc41.x86_64 >>> Stop trigger-install scriptlet: info-0:7.1-3.fc41.x86_64 Warning: skipped PGP checks for 122 package(s). Finish: installing minimal buildroot with dnf5 Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: add-determinism-0.3.6-1.fc41.x86_64 alternatives-1.30-1.fc41.x86_64 ansible-srpm-macros-1-16.fc41.noarch audit-libs-4.0.2-1.fc42.x86_64 authselect-1.5.0-7.fc41.x86_64 authselect-libs-1.5.0-7.fc41.x86_64 basesystem-11-21.fc41.noarch bash-5.2.32-2.fc42.x86_64 binutils-2.43.1-1.fc42.x86_64 build-reproducibility-srpm-macros-0.3.6-1.fc41.noarch bzip2-1.0.8-19.fc41.x86_64 bzip2-libs-1.0.8-19.fc41.x86_64 ca-certificates-2024.2.68_v8.0.302-3.fc41.noarch coreutils-9.5-9.fc42.x86_64 coreutils-common-9.5-9.fc42.x86_64 cpio-2.15-2.fc41.x86_64 cracklib-2.9.11-6.fc41.x86_64 crypto-policies-20240828-1.git5f66e81.fc42.noarch curl-8.9.1-3.fc42.x86_64 cyrus-sasl-lib-2.1.28-27.fc41.x86_64 debugedit-5.0-17.fc41.x86_64 diffutils-3.10-8.fc41.x86_64 dwz-0.15-7.fc41.x86_64 ed-1.20.2-2.fc41.x86_64 efi-srpm-macros-5-12.fc41.noarch elfutils-0.191-8.fc41.x86_64 elfutils-debuginfod-client-0.191-8.fc41.x86_64 elfutils-default-yama-scope-0.191-8.fc41.noarch elfutils-libelf-0.191-8.fc41.x86_64 elfutils-libs-0.191-8.fc41.x86_64 fedora-gpg-keys-42-0.1.noarch fedora-release-42-0.3.noarch fedora-release-common-42-0.3.noarch fedora-release-identity-basic-42-0.3.noarch fedora-repos-42-0.1.noarch fedora-repos-rawhide-42-0.1.noarch file-5.45-7.fc42.x86_64 file-libs-5.45-7.fc42.x86_64 filesystem-3.18-23.fc41.x86_64 findutils-4.10.0-4.fc41.x86_64 fonts-srpm-macros-2.0.5-17.fc41.noarch forge-srpm-macros-0.3.2-1.fc41.noarch fpc-srpm-macros-1.3-13.fc41.noarch gawk-5.3.0-4.fc41.x86_64 gdb-minimal-15.1-1.fc42.x86_64 gdbm-1.23-7.fc41.x86_64 gdbm-libs-1.23-7.fc41.x86_64 ghc-srpm-macros-1.9.1-2.fc41.noarch glibc-2.40-3.fc41.x86_64 glibc-common-2.40-3.fc41.x86_64 glibc-gconv-extra-2.40-3.fc41.x86_64 glibc-minimal-langpack-2.40-3.fc41.x86_64 gmp-6.3.0-2.fc41.x86_64 gnat-srpm-macros-6-6.fc41.noarch go-srpm-macros-3.6.0-3.fc41.noarch gpg-pubkey-105ef944-65ca83d1 gpg-pubkey-31645531-66b6dccf gpg-pubkey-e99d6ad1-64d2612c grep-3.11-9.fc41.x86_64 gzip-1.13-2.fc41.x86_64 info-7.1-3.fc41.x86_64 jansson-2.13.1-10.fc41.x86_64 kernel-srpm-macros-1.0-24.fc41.noarch keyutils-libs-1.6.3-4.fc41.x86_64 krb5-libs-1.21.3-2.fc41.x86_64 libacl-2.3.2-2.fc41.x86_64 libarchive-3.7.4-3.fc41.x86_64 libattr-2.5.2-4.fc41.x86_64 libblkid-2.40.2-8.fc42.x86_64 libbrotli-1.1.0-5.fc42.x86_64 libcap-2.70-4.fc41.x86_64 libcap-ng-0.8.5-3.fc42.x86_64 libcom_err-1.47.1-3.fc41.x86_64 libcurl-8.9.1-3.fc42.x86_64 libeconf-0.6.2-3.fc41.x86_64 libevent-2.1.12-14.fc41.x86_64 libfdisk-2.40.2-8.fc42.x86_64 libffi-3.4.6-3.fc42.x86_64 libgcc-14.2.1-1.fc42.x86_64 libgomp-14.2.1-1.fc42.x86_64 libidn2-2.3.7-2.fc41.x86_64 libmount-2.40.2-8.fc42.x86_64 libnghttp2-1.63.0-1.fc42.x86_64 libnsl2-2.0.1-2.fc41.x86_64 libpkgconf-2.3.0-1.fc42.x86_64 libpsl-0.21.5-4.fc41.x86_64 libpwquality-1.4.5-11.fc42.x86_64 libselinux-3.7-5.fc42.x86_64 libsemanage-3.7-2.fc42.x86_64 libsepol-3.7-2.fc41.x86_64 libsmartcols-2.40.2-8.fc42.x86_64 libssh-0.11.1-1.fc42.x86_64 libssh-config-0.11.1-1.fc42.noarch libstdc++-14.2.1-1.fc42.x86_64 libtasn1-4.19.0-9.fc41.x86_64 libtirpc-1.3.5-0.fc41.x86_64 libtool-ltdl-2.4.7-12.fc41.x86_64 libunistring-1.1-8.fc41.x86_64 libuuid-2.40.2-8.fc42.x86_64 libverto-0.3.2-9.fc41.x86_64 libxcrypt-4.4.36-7.fc41.x86_64 libxml2-2.12.8-2.fc42.x86_64 libzstd-1.5.6-2.fc41.x86_64 lua-libs-5.4.6-6.fc41.x86_64 lua-srpm-macros-1-14.fc41.noarch lz4-libs-1.10.0-1.fc41.x86_64 mpfr-4.2.1-5.fc41.x86_64 ncurses-base-6.5-2.20240629.fc41.noarch ncurses-libs-6.5-2.20240629.fc41.x86_64 ocaml-srpm-macros-10-3.fc41.noarch openblas-srpm-macros-2-18.fc41.noarch openldap-2.6.8-5.fc41.x86_64 openssl-libs-3.2.2-5.fc41.x86_64 p11-kit-0.25.5-3.fc41.x86_64 p11-kit-trust-0.25.5-3.fc41.x86_64 package-notes-srpm-macros-0.5-12.fc41.noarch pam-1.6.1-6.fc42.x86_64 pam-libs-1.6.1-6.fc42.x86_64 patch-2.7.6-25.fc41.x86_64 pcre2-10.44-1.fc41.1.x86_64 pcre2-syntax-10.44-1.fc41.1.noarch perl-srpm-macros-1-56.fc41.noarch pkgconf-2.3.0-1.fc42.x86_64 pkgconf-m4-2.3.0-1.fc42.noarch pkgconf-pkg-config-2.3.0-1.fc42.x86_64 popt-1.19-7.fc41.x86_64 publicsuffix-list-dafsa-20240107-4.fc41.noarch pyproject-srpm-macros-1.14.0-1.fc41.noarch python-srpm-macros-3.13-3.fc41.noarch qt5-srpm-macros-5.15.15-1.fc42.noarch qt6-srpm-macros-6.7.2-3.fc41.noarch readline-8.2-11.fc42.x86_64 redhat-rpm-config-294-1.fc42.noarch rpm-4.19.93-1.fc42.x86_64 rpm-build-4.19.93-1.fc42.x86_64 rpm-build-libs-4.19.93-1.fc42.x86_64 rpm-libs-4.19.93-1.fc42.x86_64 rpm-sequoia-1.7.0-2.fc41.x86_64 rust-srpm-macros-26.3-3.fc42.noarch sed-4.9-3.fc41.x86_64 setup-2.15.0-5.fc41.noarch shadow-utils-4.15.1-9.fc41.x86_64 sqlite-libs-3.46.1-1.fc41.x86_64 systemd-libs-256.5-1.fc42.x86_64 tar-1.35-4.fc41.x86_64 unzip-6.0-64.fc41.x86_64 util-linux-2.40.2-8.fc42.x86_64 util-linux-core-2.40.2-8.fc42.x86_64 which-2.21-42.fc41.x86_64 xxhash-libs-0.8.2-3.fc41.x86_64 xz-5.6.2-2.fc41.x86_64 xz-libs-5.6.2-2.fc41.x86_64 zig-srpm-macros-1-3.fc41.noarch zip-3.0-41.fc41.x86_64 zlib-ng-compat-2.1.7-2.fc41.x86_64 zstd-1.5.6-2.fc41.x86_64 Start: buildsrpm Start: rpmbuild -bs Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1725408000 Wrote: /builddir/build/SRPMS/smoldyn-2.72-6.fc42.src.rpm Finish: rpmbuild -bs cp: preserving permissions for ‘/var/lib/copr-rpmbuild/results/chroot_scan/var/lib/mock/fedora-rawhide-x86_64-1725755594.437893/root/var/log’: No such file or directory INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-x86_64-1725755594.437893/root/var/log/dnf5.log Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-4eigp91z/smoldyn/smoldyn.spec) Config(child) 0 minutes 19 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/smoldyn-2.72-6.fc42.src.rpm) Config(fedora-rawhide-x86_64) Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-1725755594.437893/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 from host and used with --installroot: rpm-4.19.1.1-1.fc39.x86_64 rpm-sequoia-1.6.0-1.fc39.x86_64 python3-dnf-4.21.1-1.fc39.noarch python3-dnf-plugins-core-4.9.0-1.fc39.noarch yum-4.21.1-1.fc39.noarch dnf5-5.1.17-2.fc39.x86_64 dnf5-plugins-5.1.17-2.fc39.x86_64 Finish: chroot init Start: build phase for smoldyn-2.72-6.fc42.src.rpm Start: build setup for smoldyn-2.72-6.fc42.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1725408000 Wrote: /builddir/build/SRPMS/smoldyn-2.72-6.fc42.src.rpm Updating and loading repositories: fedora 100% | 956.8 KiB/s | 26.8 KiB | 00m00s Additional repo http_kojipkgs_fedorapr 100% | 69.7 KiB/s | 3.8 KiB | 00m00s Copr repository 100% | 45.3 KiB/s | 1.5 KiB | 00m00s Repositories loaded. Package Arch Version Repository Size Installing: boost-devel x86_64 1.83.0-8.fc42 copr_base 143.0 MiB cmake x86_64 3.28.3-7.fc41 copr_base 31.6 MiB freeglut-devel x86_64 3.6.0-2.fc41 http_kojipkgs_fedoraproject_org_repos_f41_build_latest_basearch 2.3 MiB gcc x86_64 14.2.1-1.fc42 fedora 104.1 MiB gcc-c++ x86_64 14.2.1-1.fc42 fedora 38.2 MiB libXi-devel x86_64 1.8.2-1.fc42 fedora 132.5 KiB libXmu-devel x86_64 1.2.1-2.fc41 http_kojipkgs_fedoraproject_org_repos_f41_build_latest_basearch 66.2 KiB libglvnd-devel x86_64 1:1.7.0-5.fc41 http_kojipkgs_fedoraproject_org_repos_f41_build_latest_basearch 2.1 MiB libtiff-devel x86_64 4.6.0-6.fc42 fedora 709.2 KiB make x86_64 1:4.4.1-8.fc41 http_kojipkgs_fedoraproject_org_repos_f41_build_latest_basearch 1.8 MiB perl-macros noarch 4:5.40.0-511.fc41 http_kojipkgs_fedoraproject_org_repos_f41_build_latest_basearch 5.5 KiB pybind11-devel x86_64 2.13.1-3.fc42 copr_base 846.0 KiB python3-devel x86_64 3.13.0~rc2-1.fc42 copr_base 1.8 MiB python3-flaky noarch 3.8.1-4.fc42 copr_base 129.3 KiB python3-matplotlib x86_64 3.9.1-2.fc41 copr_base 21.1 MiB python3-setuptools noarch 69.2.0-8.fc42 copr_base 7.2 MiB python3-wheel noarch 1:0.43.0-4.fc41 copr_base 516.1 KiB xorg-x11-server-Xvfb x86_64 1.20.14-37.fc41 http_kojipkgs_fedoraproject_org_repos_f41_build_latest_basearch 1.9 MiB zlib-ng-compat-devel x86_64 2.1.7-2.fc41 http_kojipkgs_fedoraproject_org_repos_f41_build_latest_basearch 106.8 KiB Installing dependencies: abattis-cantarell-vf-fonts noarch 0.301-13.fc41 http_kojipkgs_fedoraproject_org_repos_f41_build_latest_basearch 192.7 KiB annobin-docs noarch 12.70-1.fc42 fedora 97.7 KiB annobin-plugin-gcc x86_64 12.70-1.fc42 fedora 985.6 KiB boost x86_64 1.83.0-8.fc42 copr_base 1.3 KiB boost-atomic x86_64 1.83.0-8.fc42 copr_base 24.9 KiB boost-chrono x86_64 1.83.0-8.fc42 copr_base 41.6 KiB boost-container x86_64 1.83.0-8.fc42 copr_base 69.5 KiB boost-context x86_64 1.83.0-8.fc42 copr_base 16.5 KiB boost-contract x86_64 1.83.0-8.fc42 copr_base 103.2 KiB boost-coroutine x86_64 1.83.0-8.fc42 copr_base 25.1 KiB boost-date-time x86_64 1.83.0-8.fc42 copr_base 16.3 KiB boost-fiber x86_64 1.83.0-8.fc42 copr_base 82.8 KiB boost-filesystem x86_64 1.83.0-8.fc42 copr_base 147.6 KiB boost-graph x86_64 1.83.0-8.fc42 copr_base 346.3 KiB boost-iostreams x86_64 1.83.0-8.fc42 copr_base 94.7 KiB boost-json x86_64 1.83.0-8.fc42 copr_base 329.1 KiB boost-locale x86_64 1.83.0-8.fc42 copr_base 606.2 KiB boost-log x86_64 1.83.0-8.fc42 copr_base 1.5 MiB boost-math x86_64 1.83.0-8.fc42 copr_base 662.9 KiB boost-nowide x86_64 1.83.0-8.fc42 copr_base 24.9 KiB boost-numpy3 x86_64 1.83.0-8.fc42 copr_base 57.6 KiB boost-program-options x86_64 1.83.0-8.fc42 copr_base 272.7 KiB boost-python3 x86_64 1.83.0-8.fc42 copr_base 254.4 KiB boost-random x86_64 1.83.0-8.fc42 copr_base 33.7 KiB boost-regex x86_64 1.83.0-8.fc42 copr_base 275.0 KiB boost-serialization x86_64 1.83.0-8.fc42 copr_base 441.6 KiB boost-stacktrace x86_64 1.83.0-8.fc42 copr_base 68.1 KiB 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http_kojipkgs_fedoraproject_org_repos_f41_build_latest_basearch 78.4 KiB xorg-x11-proto-devel noarch 2024.1-3.fc41 http_kojipkgs_fedoraproject_org_repos_f41_build_latest_basearch 1.7 MiB xorg-x11-server-common x86_64 1.20.14-37.fc41 http_kojipkgs_fedoraproject_org_repos_f41_build_latest_basearch 127.3 KiB xorg-x11-xauth x86_64 1:1.1.3-2.fc41 http_kojipkgs_fedoraproject_org_repos_f41_build_latest_basearch 56.2 KiB Transaction Summary: Installing: 271 packages Total size of inbound packages is 260 MiB. 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Installing boost-test-0:1.83. 100% | 157.4 MiB/s | 644.5 KiB | 00m00s [252/273] Installing boost-stacktrace-0 100% | 34.2 MiB/s | 70.0 KiB | 00m00s [253/273] Installing boost-serializatio 100% | 144.2 MiB/s | 443.1 KiB | 00m00s [254/273] Installing boost-random-0:1.8 100% | 33.9 MiB/s | 34.7 KiB | 00m00s [255/273] Installing boost-program-opti 100% | 133.7 MiB/s | 273.7 KiB | 00m00s [256/273] Installing boost-nowide-0:1.8 100% | 25.3 MiB/s | 25.9 KiB | 00m00s [257/273] Installing boost-math-0:1.83. 100% | 162.6 MiB/s | 665.9 KiB | 00m00s [258/273] Installing boost-iostreams-0: 100% | 93.5 MiB/s | 95.7 KiB | 00m00s [259/273] Installing boost-contract-0:1 100% | 50.9 MiB/s | 104.2 KiB | 00m00s [260/273] Installing boost-0:1.83.0-8.f 100% | 68.8 KiB/s | 1.7 KiB | 00m00s [261/273] Installing boost-devel-0:1.83 100% | 142.3 MiB/s | 145.8 MiB | 00m01s [262/273] Installing pybind11-devel-0:2 100% | 166.8 MiB/s | 853.9 KiB | 00m00s [263/273] Installing python3-flaky-0:3. 100% | 44.0 MiB/s | 135.2 KiB | 00m00s [264/273] Installing python3-wheel-1:0. 100% | 74.7 MiB/s | 535.1 KiB | 00m00s [265/273] Installing xorg-x11-server-Xv 100% | 241.5 MiB/s | 1.9 MiB | 00m00s [266/273] Installing freeglut-devel-0:3 100% | 122.0 MiB/s | 2.3 MiB | 00m00s [267/273] Installing libXmu-devel-0:1.2 100% | 22.9 MiB/s | 70.2 KiB | 00m00s [268/273] Installing libXi-devel-0:1.8. 100% | 35.3 MiB/s | 144.6 KiB | 00m00s [269/273] Installing libtiff-devel-0:4. 100% | 140.6 MiB/s | 720.0 KiB | 00m00s [270/273] Installing gcc-c++-0:14.2.1-1 100% | 300.5 MiB/s | 38.2 MiB | 00m00s [271/273] Installing annobin-plugin-gcc 100% | 38.6 MiB/s | 987.3 KiB | 00m00s >>> Running trigger-install scriptlet: redhat-rpm-config-0:294-1.fc42.noarch >>> Stop trigger-install scriptlet: redhat-rpm-config-0:294-1.fc42.noarch [272/273] Installing gcc-plugin-annobin 100% | 2.3 MiB/s | 62.7 KiB | 00m00s >>> Running trigger-install scriptlet: redhat-rpm-config-0:294-1.fc42.noarch >>> Stop trigger-install scriptlet: redhat-rpm-config-0:294-1.fc42.noarch [273/273] Installing perl-macros-4:5.40 100% | 15.6 KiB/s | 5.8 KiB | 00m00s >>> Running post-transaction scriptlet: fontconfig-0:2.15.0-8.fc41.x86_64 >>> Stop post-transaction scriptlet: fontconfig-0:2.15.0-8.fc41.x86_64 >>> Running trigger-install scriptlet: glibc-common-0:2.40-3.fc41.x86_64 >>> Stop trigger-install scriptlet: glibc-common-0:2.40-3.fc41.x86_64 >>> Running trigger-install scriptlet: info-0:7.1-3.fc41.x86_64 >>> Stop trigger-install scriptlet: info-0:7.1-3.fc41.x86_64 >>> Running trigger-install scriptlet: glib2-0:2.82.0-1.fc42.x86_64 >>> Stop trigger-install scriptlet: glib2-0:2.82.0-1.fc42.x86_64 >>> Running trigger-install scriptlet: fontconfig-0:2.15.0-8.fc41.x86_64 >>> Stop trigger-install scriptlet: fontconfig-0:2.15.0-8.fc41.x86_64 Warning: skipped PGP checks for 232 package(s). Finish: build setup for smoldyn-2.72-6.fc42.src.rpm Start: rpmbuild smoldyn-2.72-6.fc42.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1725408000 Executing(%mkbuilddir): /bin/sh -e /var/tmp/rpm-tmp.6QMr3o + umask 022 + cd /builddir/build/BUILD/smoldyn-2.72-build + test -d /builddir/build/BUILD/smoldyn-2.72-build + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w /builddir/build/BUILD/smoldyn-2.72-build + /usr/bin/rm -rf /builddir/build/BUILD/smoldyn-2.72-build + /usr/bin/mkdir -p /builddir/build/BUILD/smoldyn-2.72-build + /usr/bin/mkdir -p /builddir/build/BUILD/smoldyn-2.72-build/SPECPARTS + RPM_EC=0 ++ jobs -p + exit 0 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.BaLV2H + umask 022 + cd /builddir/build/BUILD/smoldyn-2.72-build + cd /builddir/build/BUILD/smoldyn-2.72-build + rm -rf Smoldyn-2.72 + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/Smoldyn-2.72.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + cd Smoldyn-2.72 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . Patch #0 (smoldyn-fix_libpaths.patch): + echo 'Patch #0 (smoldyn-fix_libpaths.patch):' + /usr/bin/patch --no-backup-if-mismatch -f -p0 -b --suffix .fix_libpaths --fuzz=0 patching file CMakeLists.txt Patch #1 (smoldyn-freeglut.patch): + echo 'Patch #1 (smoldyn-freeglut.patch):' + /usr/bin/patch --no-backup-if-mismatch -f -p0 -b --suffix .freeglut --fuzz=0 patching file CMakeLists.txt Hunk #1 succeeded at 370 (offset 44 lines). Patch #2 (smoldyn-create_soname.patch): + echo 'Patch #2 (smoldyn-create_soname.patch):' + /usr/bin/patch --no-backup-if-mismatch -f -p0 -b --suffix .create_soname --fuzz=0 patching file CMakeLists.txt Hunk #1 succeeded at 490 (offset 5 lines). Hunk #2 succeeded at 522 (offset 52 lines). Patch #3 (smoldyn-avoid_automatic_wheel.patch): + echo 'Patch #3 (smoldyn-avoid_automatic_wheel.patch):' + /usr/bin/patch --no-backup-if-mismatch -f -p0 -b --suffix .avoid_automatic_wheel --fuzz=0 patching file source/python/CMakeLists.txt Hunk #1 succeeded at 20 (offset -3 lines). + rm -rf source/MSVClibs + rm -rf source/pybind11 + rm -rf source/BioNetGen source/MinGWlibs Toolchain-mingw32.cmake + rm -rf source/vcell/SimpleMesh.cpp source/vcell/SimpleMesh.h source/vcell/SimpleValueProvider.cpp source/vcell/SimpleValueProvider.h source/vcell/zconf.h source/vcell/zlib.h source/vcell/zlib.lib source/NextSubVolume/Eigen + rm -rf source/NextSubVolume/boost_include + rm -f 'source/vtk/*' + find . -type f -name '*.h' -exec chmod 0644 '{}' ';' + find . -type f -name '*.c' -exec chmod 0644 '{}' ';' + find . -type f -name '*.pdf' -exec chmod 0644 '{}' ';' + find . -type f -name '*.txt' -exec chmod 0644 '{}' ';' + find . -type f -name '*.txt' -exec sed -i 's/\r$//' '{}' ';' + sed -e 's|../../../source/BioNetGen/BNG2.pl|/usr/share/perl5/vendor_perl/BioNetGen/BNG2.pl|g' -i examples/S95_regression/lrmsim.txt examples/S12_bionetgen/lrm/lrmsim.txt examples/S12_bionetgen/abba/abbasim.txt examples/S94_archive/Andrews_2016/BioNetGen/lrm/lrmsim.txt examples/S94_archive/Andrews_2016/BioNetGen/abba/abbasim.txt + cp -p source/libSteve/SFMT/LICENSE.txt source/libSteve/SFMT/SFMT-LICENSE.txt + cp -p source/libSteve/SFMT/README.txt source/libSteve/SFMT/SFMT-README.txt + find -name '*.pyc' -delete + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.UYNr30 + umask 022 + cd /builddir/build/BUILD/smoldyn-2.72-build + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd Smoldyn-2.72 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + /usr/bin/cmake -S . -B redhat-linux-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 -Wno-dev -DCPACK_BINARY_STGZ:BOOL=OFF -DCPACK_BINARY_TGZ:BOOL=OFF -DCPACK_BINARY_TZ:BOOL=OFF -DCPACK_SOURCE_TBZ2:BOOL=OFF -DCPACK_SOURCE_TGZ:BOOL=OFF -DCPACK_SOURCE_TXZ:BOOL=OFF -DCPACK_SOURCE_TZ:BOOL=OFF -DOPTION_VCELL:BOOL=OFF -DOPTION_VTK:BOOL=OFF -DBUILD_SHARED_LIBS:BOOL=ON -DSMOLDYN_VERSION:STRING=2.72 -DSMOLDYN_VERSION_MAJOR:STRING=2 -DOPTION_TARGET_LIBSMOLDYN:BOOL=ON -DOPTION_STATIC:BOOL=OFF -DOPTION_PYTHON:BOOL=ON -DPYBIND11_FINDPYTHON:BOOL=ON -Dpybind11_DIR:PATH=/usr/share/cmake/pybind11 -DOPTION_USE_ZLIB:BOOL=ON -DOPTION_PDE:BOOL=ON -DPERL_VENDORLIB:PATH=/usr/share/perl5/vendor_perl -DCMAKE_BUILD_TYPE:STRING=Release -DCMAKE_INSTALL_LIBDIR:PATH=/usr/lib64 -DCMAKE_INSTALL_PREFIX:PATH=/usr -DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE -DCMAKE_COLOR_MAKEFILE:BOOL=ON -DCMAKE_SKIP_RPATH:BOOL=YES -DHAVE_GL_FREEGLUT_H=TRUE -DOPTION_EXAMPLES:BOOL=OFF -DOPTION_DOCS:BOOL=OFF -- The CXX compiler identification is GNU 14.2.1 -- The C compiler identification is GNU 14.2.1 -- 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 -- 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 -- Smoldyn version is set to: '2.72' -- Compiling for Smoldyn: ON -- Compiling for Libsmoldyn: ON -- Option to compile Smoldyn for VCell: OFF -- Option to cross-compile for Windows using MinGW: OFF -- Option to include NextSubvolume: ON -- Option to include VTK: OFF -- Option to compile with static libraries: OFF -- Option to include OpenGL support: ON -- Option to include LibTiff: ON -- Option to include Zlib: ON -- Option to incude Python module: ON -- Option to run Libsmoldyn examples: OFF -- Option to build documentation: OFF -- Performing Test C_FLAG_EXISTS -- Performing Test C_FLAG_EXISTS - Success -- Performing Test CXX_FLAG_EXISTS -- Performing Test CXX_FLAG_EXISTS - Success -- [COMPILER] Adding -Wno-unused-parameter -- Build type: Release -- Compiling on a Linux computer -- CMAKE_CXX_FLAGS variable: '-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer' -- BioNetGen path: '/usr/share/perl5/vendor_perl/BioNetGen/BNG2.pl' -- Found OpenGL: /usr/lib64/libOpenGL.so -- OpenGL found: '/usr/include', '/usr/lib64/libGL.so;/usr/lib64/libGLU.so' -- Found GLUT: /usr/lib64/libglut.so -- Found TIFF: /usr/lib64/libtiff.so (found version "4.6.0") -- Found Libtiff: '/usr/include', '/usr/lib64/libtiff.so' -- Found Zlib: '/usr/include', '/usr/lib64/libz.so' -- Boost headers found: '/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume/boost_include' -- Found Python3: /usr/bin/python3.13 (found version "3.13.0") found components: Interpreter Development Development.Module Development.Embed -- Performing Test HAS_FLTO -- Performing Test HAS_FLTO - Success -- Found pybind11: /usr/include (found version "2.13.1") -- [TEST] Found 15 test scripts -- Configuring done (1.8s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_Fortran_FLAGS_RELEASE CMAKE_INSTALL_DO_STRIP LIB_INSTALL_DIR SHARE_INSTALL_PREFIX SYSCONF_INSTALL_DIR -- Build files have been written to: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build + /usr/bin/cmake --build redhat-linux-build -j2 --verbose Change Dir: '/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build' Run Build Command(s): /usr/bin/cmake -E env VERBOSE=1 /usr/bin/gmake -f Makefile -j2 /usr/bin/cmake -S/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72 -B/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/CMakeFiles /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build//CMakeFiles/progress.marks /usr/bin/gmake -f CMakeFiles/Makefile2 all gmake[1]: Entering directory '/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build' /usr/bin/gmake -f source/libSteve/CMakeFiles/Steve.dir/build.make source/libSteve/CMakeFiles/Steve.dir/depend gmake[2]: Entering directory '/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build' cd /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72 /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/libSteve /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/libSteve/CMakeFiles/Steve.dir/DependInfo.cmake "--color=" /usr/bin/gmake -f source/NextSubVolume/CMakeFiles/nsv.dir/build.make source/NextSubVolume/CMakeFiles/nsv.dir/depend gmake[2]: Entering directory '/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build' cd /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72 /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/NextSubVolume /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/NextSubVolume/CMakeFiles/nsv.dir/DependInfo.cmake "--color=" gmake[2]: Leaving directory '/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build' /usr/bin/gmake -f source/NextSubVolume/CMakeFiles/nsv.dir/build.make source/NextSubVolume/CMakeFiles/nsv.dir/build gmake[2]: Leaving directory '/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build' gmake[2]: Entering directory '/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build' /usr/bin/gmake -f source/libSteve/CMakeFiles/Steve.dir/build.make source/libSteve/CMakeFiles/Steve.dir/build gmake[2]: Entering directory '/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build' [ 1%] Building CXX object source/NextSubVolume/CMakeFiles/nsv.dir/StructuredGrid.cpp.o [ 2%] Building C object source/libSteve/CMakeFiles/Steve.dir/Geometry.c.o cd /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/NextSubVolume && /usr/bin/g++ -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -isystem /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume/boost_include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu++14 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT source/NextSubVolume/CMakeFiles/nsv.dir/StructuredGrid.cpp.o -MF CMakeFiles/nsv.dir/StructuredGrid.cpp.o.d -o CMakeFiles/nsv.dir/StructuredGrid.cpp.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume/StructuredGrid.cpp cd /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/libSteve && /usr/bin/gcc -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve/../Smoldyn -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT source/libSteve/CMakeFiles/Steve.dir/Geometry.c.o -MF CMakeFiles/Steve.dir/Geometry.c.o.d -o CMakeFiles/Steve.dir/Geometry.c.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve/Geometry.c [ 3%] Building CXX object source/NextSubVolume/CMakeFiles/nsv.dir/Species.cpp.o cd /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/NextSubVolume && /usr/bin/g++ -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -isystem /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume/boost_include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu++14 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT source/NextSubVolume/CMakeFiles/nsv.dir/Species.cpp.o -MF CMakeFiles/nsv.dir/Species.cpp.o.d -o CMakeFiles/nsv.dir/Species.cpp.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume/Species.cpp [ 4%] Building C object source/libSteve/CMakeFiles/Steve.dir/List.c.o cd /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/libSteve && /usr/bin/gcc -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve/../Smoldyn -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT source/libSteve/CMakeFiles/Steve.dir/List.c.o -MF CMakeFiles/Steve.dir/List.c.o.d -o CMakeFiles/Steve.dir/List.c.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve/List.c [ 6%] Building C object source/libSteve/CMakeFiles/Steve.dir/math2.c.o cd /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/libSteve && /usr/bin/gcc -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve/../Smoldyn -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT source/libSteve/CMakeFiles/Steve.dir/math2.c.o -MF CMakeFiles/Steve.dir/math2.c.o.d -o CMakeFiles/Steve.dir/math2.c.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve/math2.c [ 7%] Building CXX object source/NextSubVolume/CMakeFiles/nsv.dir/ReactionEquation.cpp.o cd /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/NextSubVolume && /usr/bin/g++ -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -isystem /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume/boost_include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu++14 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT source/NextSubVolume/CMakeFiles/nsv.dir/ReactionEquation.cpp.o -MF CMakeFiles/nsv.dir/ReactionEquation.cpp.o.d -o CMakeFiles/nsv.dir/ReactionEquation.cpp.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume/ReactionEquation.cpp [ 8%] Building C object source/libSteve/CMakeFiles/Steve.dir/opengl2.c.o cd /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/libSteve && /usr/bin/gcc -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve/../Smoldyn -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT source/libSteve/CMakeFiles/Steve.dir/opengl2.c.o -MF CMakeFiles/Steve.dir/opengl2.c.o.d -o CMakeFiles/Steve.dir/opengl2.c.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve/opengl2.c [ 9%] Building CXX object source/NextSubVolume/CMakeFiles/nsv.dir/NextSubvolumeMethod.cpp.o cd /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/NextSubVolume && /usr/bin/g++ -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -isystem /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume/boost_include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu++14 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT source/NextSubVolume/CMakeFiles/nsv.dir/NextSubvolumeMethod.cpp.o -MF CMakeFiles/nsv.dir/NextSubvolumeMethod.cpp.o.d -o CMakeFiles/nsv.dir/NextSubvolumeMethod.cpp.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume/NextSubvolumeMethod.cpp [ 11%] Building C object source/libSteve/CMakeFiles/Steve.dir/parse.c.o cd /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/libSteve && /usr/bin/gcc -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve/../Smoldyn -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT source/libSteve/CMakeFiles/Steve.dir/parse.c.o -MF CMakeFiles/Steve.dir/parse.c.o.d -o CMakeFiles/Steve.dir/parse.c.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve/parse.c [ 12%] Building C object source/libSteve/CMakeFiles/Steve.dir/queue.c.o cd /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/libSteve && /usr/bin/gcc -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve/../Smoldyn -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT source/libSteve/CMakeFiles/Steve.dir/queue.c.o -MF CMakeFiles/Steve.dir/queue.c.o.d -o CMakeFiles/Steve.dir/queue.c.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve/queue.c [ 13%] Building C object source/libSteve/CMakeFiles/Steve.dir/random2.c.o cd /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/libSteve && 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CMakeFiles/Steve.dir/random2.c.o.d -o CMakeFiles/Steve.dir/random2.c.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve/random2.c [ 14%] Building C object source/libSteve/CMakeFiles/Steve.dir/Rn.c.o cd /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/libSteve && /usr/bin/gcc -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve/../Smoldyn -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT source/libSteve/CMakeFiles/Steve.dir/Rn.c.o -MF CMakeFiles/Steve.dir/Rn.c.o.d -o CMakeFiles/Steve.dir/Rn.c.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve/Rn.c [ 16%] Building C object source/libSteve/CMakeFiles/Steve.dir/RnSort.c.o cd /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/libSteve && /usr/bin/gcc -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve/../Smoldyn -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT source/libSteve/CMakeFiles/Steve.dir/RnSort.c.o -MF CMakeFiles/Steve.dir/RnSort.c.o.d -o CMakeFiles/Steve.dir/RnSort.c.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve/RnSort.c [ 17%] Building C object source/libSteve/CMakeFiles/Steve.dir/rxnparam.c.o cd /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/libSteve && /usr/bin/gcc -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve/../Smoldyn -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT source/libSteve/CMakeFiles/Steve.dir/rxnparam.c.o -MF CMakeFiles/Steve.dir/rxnparam.c.o.d -o CMakeFiles/Steve.dir/rxnparam.c.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve/rxnparam.c [ 18%] Building CXX object source/NextSubVolume/CMakeFiles/nsv.dir/Kairos.cpp.o cd /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/NextSubVolume && /usr/bin/g++ -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -isystem /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume/boost_include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu++14 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT source/NextSubVolume/CMakeFiles/nsv.dir/Kairos.cpp.o -MF CMakeFiles/nsv.dir/Kairos.cpp.o.d -o CMakeFiles/nsv.dir/Kairos.cpp.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume/Kairos.cpp [ 19%] Building C object source/libSteve/CMakeFiles/Steve.dir/SimCommand.c.o cd /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/libSteve && /usr/bin/gcc -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve/../Smoldyn -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT source/libSteve/CMakeFiles/Steve.dir/SimCommand.c.o -MF CMakeFiles/Steve.dir/SimCommand.c.o.d -o CMakeFiles/Steve.dir/SimCommand.c.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve/SimCommand.c [ 20%] Building C object source/libSteve/CMakeFiles/Steve.dir/Sphere.c.o cd 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-specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT source/libSteve/CMakeFiles/Steve.dir/string2.c.o -MF CMakeFiles/Steve.dir/string2.c.o.d -o CMakeFiles/Steve.dir/string2.c.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve/string2.c [ 23%] Building CXX object source/NextSubVolume/CMakeFiles/nsv.dir/Io.cpp.o cd /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/NextSubVolume && /usr/bin/g++ -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -isystem /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume/boost_include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu++14 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT source/NextSubVolume/CMakeFiles/nsv.dir/Io.cpp.o -MF CMakeFiles/nsv.dir/Io.cpp.o.d -o CMakeFiles/nsv.dir/Io.cpp.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume/Io.cpp [ 24%] Building CXX object source/NextSubVolume/CMakeFiles/nsv.dir/Geometry.cpp.o cd /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/NextSubVolume && /usr/bin/g++ -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -isystem /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume/boost_include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu++14 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT source/NextSubVolume/CMakeFiles/nsv.dir/Geometry.cpp.o -MF CMakeFiles/nsv.dir/Geometry.cpp.o.d -o CMakeFiles/nsv.dir/Geometry.cpp.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume/Geometry.cpp [ 25%] Building CXX object source/NextSubVolume/CMakeFiles/nsv.dir/nsvc.cpp.o cd /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/NextSubVolume && /usr/bin/g++ -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -isystem /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume/boost_include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu++14 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT source/NextSubVolume/CMakeFiles/nsv.dir/nsvc.cpp.o -MF CMakeFiles/nsv.dir/nsvc.cpp.o.d -o CMakeFiles/nsv.dir/nsvc.cpp.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume/nsvc.cpp /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve/string2.c: In function ‘strmatheval’: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve/string2.c:1415:9: warning: ‘strncpy’ specified bound 512 equals destination size [-Wstringop-truncation] 1415 | strncpy(expr,expression,STRCHAR); | ^ [ 27%] Building C object source/libSteve/CMakeFiles/Steve.dir/SurfaceParam.c.o cd /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/libSteve && /usr/bin/gcc -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve/../Smoldyn -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT source/libSteve/CMakeFiles/Steve.dir/SurfaceParam.c.o -MF CMakeFiles/Steve.dir/SurfaceParam.c.o.d -o CMakeFiles/Steve.dir/SurfaceParam.c.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve/SurfaceParam.c [ 28%] Building C object source/libSteve/CMakeFiles/Steve.dir/Zn.c.o cd /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/libSteve && /usr/bin/gcc -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve/../Smoldyn -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT source/libSteve/CMakeFiles/Steve.dir/Zn.c.o -MF CMakeFiles/Steve.dir/Zn.c.o.d -o CMakeFiles/Steve.dir/Zn.c.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve/Zn.c [ 29%] Building C object source/libSteve/CMakeFiles/Steve.dir/SFMT/SFMT.c.o cd /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/libSteve && /usr/bin/gcc -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve/../Smoldyn -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT source/libSteve/CMakeFiles/Steve.dir/SFMT/SFMT.c.o -MF CMakeFiles/Steve.dir/SFMT/SFMT.c.o.d -o CMakeFiles/Steve.dir/SFMT/SFMT.c.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve/SFMT/SFMT.c gmake[2]: Leaving directory '/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build' [ 29%] Built target Steve gmake[2]: Leaving directory '/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build' [ 29%] Built target nsv /usr/bin/gmake -f CMakeFiles/smoldyn_static.dir/build.make CMakeFiles/smoldyn_static.dir/depend /usr/bin/gmake -f CMakeFiles/smoldyn_shared.dir/build.make CMakeFiles/smoldyn_shared.dir/depend gmake[2]: Entering directory '/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build' cd /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72 /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72 /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/CMakeFiles/smoldyn_static.dir/DependInfo.cmake "--color=" gmake[2]: Entering directory '/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build' cd /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72 /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72 /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/CMakeFiles/smoldyn_shared.dir/DependInfo.cmake "--color=" gmake[2]: Leaving directory '/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build' /usr/bin/gmake -f CMakeFiles/smoldyn_static.dir/build.make CMakeFiles/smoldyn_static.dir/build gmake[2]: Entering directory '/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build' gmake[2]: Leaving directory '/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build' /usr/bin/gmake -f CMakeFiles/smoldyn_shared.dir/build.make CMakeFiles/smoldyn_shared.dir/build gmake[2]: Entering directory '/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build' [ 30%] Building C object CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolbng.c.o [ 32%] Building C object CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolbng.c.o /usr/bin/gcc -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolbng.c.o -MF CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolbng.c.o.d -o CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolbng.c.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c /usr/bin/gcc -Dsmoldyn_shared_EXPORTS -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolbng.c.o -MF CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolbng.c.o.d -o CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolbng.c.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c In file included from /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:14: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c: In function ‘bngreadstring’: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:1496:30: warning: ‘%s’ directive output may be truncated writing up to 4095 bytes into a region of size 4066 [-Wformat-truncation=] 1496 | CHECKS(er!=3,"Error reading BioNetGen file '%s'. Try again with '-v' flag for more information.",str1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:1496:61: note: format string is defined here 1496 | CHECKS(er!=3,"Error reading BioNetGen file '%s'. Try again with '-v' flag for more information.",str1); | ^~ In file included from /usr/include/stdio.h:970, from /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:8: In function ‘snprintf’, inlined from ‘bngreadstring’ at /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:1496:3: /usr/include/bits/stdio2.h:68:10: note: ‘__snprintf_chk’ output between 80 and 4175 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c: In function ‘bngreadstring’: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:1495:30: warning: ‘%s’ directive output may be truncated writing up to 4095 bytes into a region of size 4080 [-Wformat-truncation=] 1495 | CHECKS(er!=2,"BioNetGen file '%s' not found",str1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:1495:47: note: format string is defined here 1495 | CHECKS(er!=2,"BioNetGen file '%s' not found",str1); | ^~ In function ‘snprintf’, inlined from ‘bngreadstring’ at /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:1495:3: /usr/include/bits/stdio2.h:68:10: note: ‘__snprintf_chk’ output between 28 and 4123 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c: In function ‘bngreadstring’: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:1450:31: warning: ‘%s’ directive output may be truncated writing up to 4095 bytes into a region of size 4087 [-Wformat-truncation=] 1450 | CHECKS(er!=-2,"invalid '%s' monomer name",str1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:1450:41: note: format string is defined here 1450 | CHECKS(er!=-2,"invalid '%s' monomer name",str1); | ^~ In function ‘snprintf’, inlined from ‘bngreadstring’ at /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:1450:3: /usr/include/bits/stdio2.h:68:10: note: ‘__snprintf_chk’ output between 24 and 4119 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c: In function ‘bngreadstring’: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:1442:36: warning: ‘%s’ directive output may be truncated writing up to 4095 bytes into a region of size 4075 [-Wformat-truncation=] 1442 | CHECKS(!er,"error adding monomer %s",str1); }} | ^~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:1442:58: note: format string is defined here 1442 | CHECKS(!er,"error adding monomer %s",str1); }} | ^~ In function ‘snprintf’, inlined from ‘bngreadstring’ at /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:1442:4: /usr/include/bits/stdio2.h:68:10: note: ‘__snprintf_chk’ output between 22 and 4117 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c: In function ‘bngreadstring’: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:1441:39: warning: ‘%s’ directive output may be truncated writing up to 4095 bytes into a region of size 4082 [-Wformat-truncation=] 1441 | CHECKS(er!=-2,"monomer name '%s' is not permitted",str1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:1441:54: note: format string is defined here 1441 | CHECKS(er!=-2,"monomer name '%s' is not permitted",str1); | ^~ In function ‘snprintf’, inlined from ‘bngreadstring’ at /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:1441:4: /usr/include/bits/stdio2.h:68:10: note: ‘__snprintf_chk’ output between 33 and 4128 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c: In function ‘bngreadstring’: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:1440:39: warning: ‘%s’ directive output may be truncated writing up to 4095 bytes into a region of size 4067 [-Wformat-truncation=] 1440 | CHECKS(er!=-1,"out of memory adding monomer %s",str1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:1440:69: note: format string is defined here 1440 | CHECKS(er!=-1,"out of memory adding monomer %s",str1); | ^~ In function ‘snprintf’, inlined from ‘bngreadstring’ at /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:1440:4: /usr/include/bits/stdio2.h:68:10: note: ‘__snprintf_chk’ output between 30 and 4125 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:14: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c: In function ‘bngreadstring’: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:1496:30: warning: ‘%s’ directive output may be truncated writing up to 4095 bytes into a region of size 4066 [-Wformat-truncation=] 1496 | CHECKS(er!=3,"Error reading BioNetGen file '%s'. Try again with '-v' flag for more information.",str1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:1496:61: note: format string is defined here 1496 | CHECKS(er!=3,"Error reading BioNetGen file '%s'. Try again with '-v' flag for more information.",str1); | ^~ In file included from /usr/include/stdio.h:970, from /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:8: In function ‘snprintf’, inlined from ‘bngreadstring’ at /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:1496:3: /usr/include/bits/stdio2.h:68:10: note: ‘__snprintf_chk’ output between 80 and 4175 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c: In function ‘bngreadstring’: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:1495:30: warning: ‘%s’ directive output may be truncated writing up to 4095 bytes into a region of size 4080 [-Wformat-truncation=] 1495 | CHECKS(er!=2,"BioNetGen file '%s' not found",str1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:1495:47: note: format string is defined here 1495 | CHECKS(er!=2,"BioNetGen file '%s' not found",str1); | ^~ In function ‘snprintf’, inlined from ‘bngreadstring’ at /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:1495:3: /usr/include/bits/stdio2.h:68:10: note: ‘__snprintf_chk’ output between 28 and 4123 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c: In function ‘bngreadstring’: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:1450:31: warning: ‘%s’ directive output may be truncated writing up to 4095 bytes into a region of size 4087 [-Wformat-truncation=] 1450 | CHECKS(er!=-2,"invalid '%s' monomer name",str1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:1450:41: note: format string is defined here 1450 | CHECKS(er!=-2,"invalid '%s' monomer name",str1); | ^~ In function ‘snprintf’, inlined from ‘bngreadstring’ at /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:1450:3: /usr/include/bits/stdio2.h:68:10: note: ‘__snprintf_chk’ output between 24 and 4119 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c: In function ‘bngreadstring’: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:1442:36: warning: ‘%s’ directive output may be truncated writing up to 4095 bytes into a region of size 4075 [-Wformat-truncation=] 1442 | CHECKS(!er,"error adding monomer %s",str1); }} | ^~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:1442:58: note: format string is defined here 1442 | CHECKS(!er,"error adding monomer %s",str1); }} | ^~ In function ‘snprintf’, inlined from ‘bngreadstring’ at /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:1442:4: /usr/include/bits/stdio2.h:68:10: note: ‘__snprintf_chk’ output between 22 and 4117 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c: In function ‘bngreadstring’: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:1441:39: warning: ‘%s’ directive output may be truncated writing up to 4095 bytes into a region of size 4082 [-Wformat-truncation=] 1441 | CHECKS(er!=-2,"monomer name '%s' is not permitted",str1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:1441:54: note: format string is defined here 1441 | CHECKS(er!=-2,"monomer name '%s' is not permitted",str1); | ^~ In function ‘snprintf’, inlined from ‘bngreadstring’ at /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:1441:4: /usr/include/bits/stdio2.h:68:10: note: ‘__snprintf_chk’ output between 33 and 4128 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c: In function ‘bngreadstring’: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:1440:39: warning: ‘%s’ directive output may be truncated writing up to 4095 bytes into a region of size 4067 [-Wformat-truncation=] 1440 | CHECKS(er!=-1,"out of memory adding monomer %s",str1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:1440:69: note: format string is defined here 1440 | CHECKS(er!=-1,"out of memory adding monomer %s",str1); | ^~ In function ‘snprintf’, inlined from ‘bngreadstring’ at /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:1440:4: /usr/include/bits/stdio2.h:68:10: note: ‘__snprintf_chk’ output between 30 and 4125 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 33%] Building C object CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolboxes.c.o /usr/bin/gcc -Dsmoldyn_shared_EXPORTS -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolboxes.c.o -MF CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolboxes.c.o.d -o CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolboxes.c.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolboxes.c [ 34%] Building C object CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolboxes.c.o /usr/bin/gcc -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolboxes.c.o -MF CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolboxes.c.o.d -o CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolboxes.c.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolboxes.c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolboxes.c: In function ‘boxesupdatelists’: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolboxes.c:783:55: warning: argument 1 range [18446744071562067968, 18446744073709551614] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 783 | bptr->neigh=(boxptr*) calloc(nneigh,sizeof(boxptr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve/random2.h:17, from /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolboxes.c:13: /usr/include/stdlib.h:675:14: note: in a call to allocation function ‘calloc’ declared here 675 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolboxes.c: In function ‘boxesupdatelists’: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolboxes.c:783:55: warning: argument 1 range [18446744071562067968, 18446744073709551614] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 783 | bptr->neigh=(boxptr*) calloc(nneigh,sizeof(boxptr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve/random2.h:17, from /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolboxes.c:13: /usr/include/stdlib.h:675:14: note: in a call to allocation function ‘calloc’ declared here 675 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ [ 35%] Building C object CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolcmd.c.o /usr/bin/gcc -Dsmoldyn_shared_EXPORTS -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolcmd.c.o -MF CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolcmd.c.o.d -o CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolcmd.c.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolcmd.c [ 37%] Building C object CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolcmd.c.o /usr/bin/gcc -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolcmd.c.o -MF CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolcmd.c.o.d -o CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolcmd.c.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolcmd.c [ 38%] Building C object CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolcomparts.c.o /usr/bin/gcc -Dsmoldyn_shared_EXPORTS -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolcomparts.c.o -MF CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolcomparts.c.o.d -o CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolcomparts.c.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolcomparts.c [ 39%] Building C object CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolcomparts.c.o /usr/bin/gcc -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolcomparts.c.o -MF CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolcomparts.c.o.d -o CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolcomparts.c.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolcomparts.c In file included from /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolcomparts.c:18: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolcomparts.c: In function ‘compartreadstring’: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolcomparts.c:894:29: warning: ‘%s’ directive output may be truncated writing up to 4095 bytes into a region of size 4082 [-Wformat-truncation=] 894 | CHECKS(s>=0,"surface name '%s' not recognized",nm); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~ /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolcomparts.c:894:44: note: format string is defined here 894 | CHECKS(s>=0,"surface name '%s' not recognized",nm); | ^~ In file included from /usr/include/stdio.h:970, from /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolcomparts.c:9: In function ‘snprintf’, inlined from ‘compartreadstring’ at /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolcomparts.c:894:3: /usr/include/bits/stdio2.h:68:10: note: ‘__snprintf_chk’ output between 31 and 4126 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 40%] Building C object CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolfilament.c.o /usr/bin/gcc -Dsmoldyn_shared_EXPORTS -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolfilament.c.o -MF CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolfilament.c.o.d -o CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolfilament.c.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolfilament.c In file included from /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolcomparts.c:18: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolcomparts.c: In function ‘compartreadstring’: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolcomparts.c:894:29: warning: ‘%s’ directive output may be truncated writing up to 4095 bytes into a region of size 4082 [-Wformat-truncation=] 894 | CHECKS(s>=0,"surface name '%s' not recognized",nm); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~ /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolcomparts.c:894:44: note: format string is defined here 894 | CHECKS(s>=0,"surface name '%s' not recognized",nm); | ^~ In file included from /usr/include/stdio.h:970, from /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolcomparts.c:9: In function ‘snprintf’, inlined from ‘compartreadstring’ at /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolcomparts.c:894:3: /usr/include/bits/stdio2.h:68:10: note: ‘__snprintf_chk’ output between 31 and 4126 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 41%] Building C object CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolfilament.c.o /usr/bin/gcc -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolfilament.c.o -MF CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolfilament.c.o.d -o CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolfilament.c.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolfilament.c [ 43%] Building C object CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolgraphics.c.o /usr/bin/gcc -Dsmoldyn_shared_EXPORTS -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolgraphics.c.o -MF CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolgraphics.c.o.d -o CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolgraphics.c.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolgraphics.c [ 44%] Building C object CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolgraphics.c.o /usr/bin/gcc -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolgraphics.c.o -MF CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolgraphics.c.o.d -o CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolgraphics.c.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolgraphics.c [ 45%] Building C object CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolmolec.c.o /usr/bin/gcc -Dsmoldyn_shared_EXPORTS -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolmolec.c.o -MF CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolmolec.c.o.d -o CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolmolec.c.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolmolec.c [ 46%] Building C object CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolmolec.c.o /usr/bin/gcc -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolmolec.c.o -MF CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolmolec.c.o.d -o CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolmolec.c.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolmolec.c [ 48%] Building C object CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolport.c.o /usr/bin/gcc -Dsmoldyn_shared_EXPORTS -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolport.c.o -MF CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolport.c.o.d -o CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolport.c.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolport.c [ 49%] Building C object CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolport.c.o /usr/bin/gcc -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolport.c.o -MF CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolport.c.o.d -o CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolport.c.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolport.c [ 50%] Building C object CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smollattice.c.o /usr/bin/gcc -Dsmoldyn_shared_EXPORTS -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smollattice.c.o -MF CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smollattice.c.o.d -o CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smollattice.c.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smollattice.c [ 51%] Building C object CMakeFiles/smoldyn_static.dir/source/Smoldyn/smollattice.c.o /usr/bin/gcc -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT CMakeFiles/smoldyn_static.dir/source/Smoldyn/smollattice.c.o -MF CMakeFiles/smoldyn_static.dir/source/Smoldyn/smollattice.c.o.d -o CMakeFiles/smoldyn_static.dir/source/Smoldyn/smollattice.c.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smollattice.c [ 53%] Building C object CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolreact.c.o /usr/bin/gcc -Dsmoldyn_shared_EXPORTS -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolreact.c.o -MF CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolreact.c.o.d -o CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolreact.c.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolreact.c [ 54%] Building C object CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolreact.c.o /usr/bin/gcc -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolreact.c.o -MF CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolreact.c.o.d -o CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolreact.c.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolreact.c [ 55%] Building C object CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolrule.c.o /usr/bin/gcc -Dsmoldyn_shared_EXPORTS -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolrule.c.o -MF CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolrule.c.o.d -o CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolrule.c.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolrule.c [ 56%] Building C object CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolrule.c.o /usr/bin/gcc -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolrule.c.o -MF CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolrule.c.o.d -o CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolrule.c.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolrule.c [ 58%] Building CXX object CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolsim.cpp.o /usr/bin/g++ -Dsmoldyn_shared_EXPORTS -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu++14 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolsim.cpp.o -MF CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolsim.cpp.o.d -o CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolsim.cpp.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolsim.cpp [ 59%] Building CXX object CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolsim.cpp.o /usr/bin/g++ -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu++14 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolsim.cpp.o -MF CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolsim.cpp.o.d -o CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolsim.cpp.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolsim.cpp /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolsim.cpp: In function ‘simParseError’: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolsim.cpp:166:58: warning: ‘%s’ directive writing up to 4095 bytes into a region of size between 603 and 4698 [-Wformat-overflow=] 166 | sprintf(ErrorLineAndString,"%s\nMessage: %s",parseerrstr,ErrorString); | ^~ ~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolsim.cpp:12: In function ‘sprintf’, inlined from ‘simParseError’ at /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolsim.cpp:166:10: /usr/include/bits/stdio2.h:30:34: note: ‘__sprintf_chk’ output between 11 and 8201 bytes into a destination of size 4708 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolsim.cpp: In function ‘simParseError’: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolsim.cpp:166:58: warning: ‘%s’ directive writing up to 4095 bytes into a region of size between 603 and 4698 [-Wformat-overflow=] 166 | sprintf(ErrorLineAndString,"%s\nMessage: %s",parseerrstr,ErrorString); | ^~ ~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolsim.cpp:12: In function ‘sprintf’, inlined from ‘simParseError’ at /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolsim.cpp:166:10: /usr/include/bits/stdio2.h:30:34: note: ‘__sprintf_chk’ output between 11 and 8201 bytes into a destination of size 4708 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 60%] Building C object CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolsurface.c.o /usr/bin/gcc -Dsmoldyn_shared_EXPORTS -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolsurface.c.o -MF CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolsurface.c.o.d -o CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolsurface.c.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolsurface.c [ 61%] Building C object CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolsurface.c.o /usr/bin/gcc -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolsurface.c.o -MF CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolsurface.c.o.d -o CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolsurface.c.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolsurface.c [ 62%] Building C object CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolwall.c.o /usr/bin/gcc -Dsmoldyn_shared_EXPORTS -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolwall.c.o -MF CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolwall.c.o.d -o CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolwall.c.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolwall.c [ 64%] Building C object CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolwall.c.o /usr/bin/gcc -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolwall.c.o -MF CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolwall.c.o.d -o CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolwall.c.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolwall.c [ 65%] Building CXX object CMakeFiles/smoldyn_shared.dir/source/Smoldyn/libsmoldyn.cpp.o /usr/bin/g++ -Dsmoldyn_shared_EXPORTS -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu++14 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT CMakeFiles/smoldyn_shared.dir/source/Smoldyn/libsmoldyn.cpp.o -MF CMakeFiles/smoldyn_shared.dir/source/Smoldyn/libsmoldyn.cpp.o.d -o CMakeFiles/smoldyn_shared.dir/source/Smoldyn/libsmoldyn.cpp.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/libsmoldyn.cpp [ 66%] Building CXX object CMakeFiles/smoldyn_static.dir/source/Smoldyn/libsmoldyn.cpp.o /usr/bin/g++ -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu++14 -fPIC 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-fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -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 -shared -Wl,-soname,libsmoldyn_shared.so.2 -o libsmoldyn_shared.so.2.72 CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolbng.c.o CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolboxes.c.o CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolcmd.c.o CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolcomparts.c.o CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolfilament.c.o CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolgraphics.c.o CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolmolec.c.o CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolport.c.o CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smollattice.c.o CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolreact.c.o CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolrule.c.o CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolsim.cpp.o CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolsurface.c.o CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolwall.c.o CMakeFiles/smoldyn_shared.dir/source/Smoldyn/libsmoldyn.cpp.o source/libSteve/CMakeFiles/Steve.dir/Geometry.c.o source/libSteve/CMakeFiles/Steve.dir/List.c.o source/libSteve/CMakeFiles/Steve.dir/math2.c.o source/libSteve/CMakeFiles/Steve.dir/opengl2.c.o source/libSteve/CMakeFiles/Steve.dir/parse.c.o source/libSteve/CMakeFiles/Steve.dir/queue.c.o source/libSteve/CMakeFiles/Steve.dir/random2.c.o source/libSteve/CMakeFiles/Steve.dir/Rn.c.o source/libSteve/CMakeFiles/Steve.dir/RnSort.c.o source/libSteve/CMakeFiles/Steve.dir/rxnparam.c.o source/libSteve/CMakeFiles/Steve.dir/SimCommand.c.o source/libSteve/CMakeFiles/Steve.dir/Sphere.c.o source/libSteve/CMakeFiles/Steve.dir/string2.c.o source/libSteve/CMakeFiles/Steve.dir/SurfaceParam.c.o source/libSteve/CMakeFiles/Steve.dir/Zn.c.o source/libSteve/CMakeFiles/Steve.dir/SFMT/SFMT.c.o source/NextSubVolume/CMakeFiles/nsv.dir/StructuredGrid.cpp.o source/NextSubVolume/CMakeFiles/nsv.dir/Species.cpp.o source/NextSubVolume/CMakeFiles/nsv.dir/ReactionEquation.cpp.o source/NextSubVolume/CMakeFiles/nsv.dir/NextSubvolumeMethod.cpp.o source/NextSubVolume/CMakeFiles/nsv.dir/Kairos.cpp.o source/NextSubVolume/CMakeFiles/nsv.dir/Io.cpp.o source/NextSubVolume/CMakeFiles/nsv.dir/Geometry.cpp.o source/NextSubVolume/CMakeFiles/nsv.dir/nsvc.cpp.o /usr/lib64/libGL.so /usr/lib64/libGLU.so -lglut /usr/lib64/libtiff.so /usr/lib64/libz.so /usr/bin/cmake -E cmake_link_script CMakeFiles/smoldyn_static.dir/link.txt --verbose=1 /usr/bin/ar qc libsmoldyn_static.a CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolbng.c.o CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolboxes.c.o CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolcmd.c.o CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolcomparts.c.o CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolfilament.c.o CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolgraphics.c.o CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolmolec.c.o CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolport.c.o CMakeFiles/smoldyn_static.dir/source/Smoldyn/smollattice.c.o CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolreact.c.o CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolrule.c.o CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolsim.cpp.o CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolsurface.c.o CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolwall.c.o CMakeFiles/smoldyn_static.dir/source/Smoldyn/libsmoldyn.cpp.o source/libSteve/CMakeFiles/Steve.dir/Geometry.c.o source/libSteve/CMakeFiles/Steve.dir/List.c.o source/libSteve/CMakeFiles/Steve.dir/math2.c.o source/libSteve/CMakeFiles/Steve.dir/opengl2.c.o source/libSteve/CMakeFiles/Steve.dir/parse.c.o source/libSteve/CMakeFiles/Steve.dir/queue.c.o source/libSteve/CMakeFiles/Steve.dir/random2.c.o source/libSteve/CMakeFiles/Steve.dir/Rn.c.o source/libSteve/CMakeFiles/Steve.dir/RnSort.c.o source/libSteve/CMakeFiles/Steve.dir/rxnparam.c.o source/libSteve/CMakeFiles/Steve.dir/SimCommand.c.o source/libSteve/CMakeFiles/Steve.dir/Sphere.c.o source/libSteve/CMakeFiles/Steve.dir/string2.c.o source/libSteve/CMakeFiles/Steve.dir/SurfaceParam.c.o source/libSteve/CMakeFiles/Steve.dir/Zn.c.o source/libSteve/CMakeFiles/Steve.dir/SFMT/SFMT.c.o source/NextSubVolume/CMakeFiles/nsv.dir/StructuredGrid.cpp.o source/NextSubVolume/CMakeFiles/nsv.dir/Species.cpp.o source/NextSubVolume/CMakeFiles/nsv.dir/ReactionEquation.cpp.o source/NextSubVolume/CMakeFiles/nsv.dir/NextSubvolumeMethod.cpp.o source/NextSubVolume/CMakeFiles/nsv.dir/Kairos.cpp.o source/NextSubVolume/CMakeFiles/nsv.dir/Io.cpp.o source/NextSubVolume/CMakeFiles/nsv.dir/Geometry.cpp.o source/NextSubVolume/CMakeFiles/nsv.dir/nsvc.cpp.o /usr/bin/ranlib libsmoldyn_static.a /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smoldyn.h:714:16: warning: type ‘struct latticestruct’ violates the C++ One Definition Rule [-Wodr] 714 | typedef struct latticestruct | ^ /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smoldyn.h:714:16: note: a different type is defined in another translation unit 714 | typedef struct latticestruct | ^ /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smoldyn.h:739:26: note: the first difference of corresponding definitions is field ‘nsv’ 739 | NextSubvolumeMethod* nsv; // nsv class | ^ /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smoldyn.h:739:26: note: a field of same name but different type is defined in another translation unit 739 | NextSubvolumeMethod* nsv; // nsv class | ^ /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smoldyn.h:714:16: note: type name ‘NextSubvolumeMethod’ should match type name ‘Kairos::NextSubvolumeMethod’ 714 | typedef struct latticestruct | ^ /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume/NextSubvolumeMethod.h:137:7: note: the incompatible type is defined here 137 | class NextSubvolumeMethod | ^ gmake[2]: Leaving directory '/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build' [ 69%] Built target smoldyn_static /usr/bin/gmake -f source/python/CMakeFiles/_pysmoldyn.dir/build.make source/python/CMakeFiles/_pysmoldyn.dir/depend gmake[2]: Entering directory '/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build' cd /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72 /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/python /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/python /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/python/CMakeFiles/_pysmoldyn.dir/DependInfo.cmake "--color=" gmake[2]: Leaving directory '/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build' /usr/bin/gmake -f source/python/CMakeFiles/_pysmoldyn.dir/build.make source/python/CMakeFiles/_pysmoldyn.dir/build gmake[2]: Entering directory '/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build' [ 70%] Building C object source/python/CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolbng.c.o cd /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/python && /usr/bin/gcc -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -I/usr/include/python3.13 -I/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -DENABLE_PYTHON_CALLBACK -DCOMPILE_AS_PY_MODULE -MD -MT source/python/CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolbng.c.o -MF CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolbng.c.o.d -o CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolbng.c.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c In file included from /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:14: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c: In function ‘bngreadstring’: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:1496:30: warning: ‘%s’ directive output may be truncated writing up to 4095 bytes into a region of size 4066 [-Wformat-truncation=] 1496 | CHECKS(er!=3,"Error reading BioNetGen file '%s'. Try again with '-v' flag for more information.",str1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:1496:61: note: format string is defined here 1496 | CHECKS(er!=3,"Error reading BioNetGen file '%s'. Try again with '-v' flag for more information.",str1); | ^~ In file included from /usr/include/stdio.h:970, from /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:8: In function ‘snprintf’, inlined from ‘bngreadstring’ at /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:1496:3: /usr/include/bits/stdio2.h:68:10: note: ‘__snprintf_chk’ output between 80 and 4175 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c: In function ‘bngreadstring’: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:1495:30: warning: ‘%s’ directive output may be truncated writing up to 4095 bytes into a region of size 4080 [-Wformat-truncation=] 1495 | CHECKS(er!=2,"BioNetGen file '%s' not found",str1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:1495:47: note: format string is defined here 1495 | CHECKS(er!=2,"BioNetGen file '%s' not found",str1); | ^~ In function ‘snprintf’, inlined from ‘bngreadstring’ at /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:1495:3: /usr/include/bits/stdio2.h:68:10: note: ‘__snprintf_chk’ output between 28 and 4123 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c: In function ‘bngreadstring’: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:1450:31: warning: ‘%s’ directive output may be truncated writing up to 4095 bytes into a region of size 4087 [-Wformat-truncation=] 1450 | CHECKS(er!=-2,"invalid '%s' monomer name",str1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:1450:41: note: format string is defined here 1450 | CHECKS(er!=-2,"invalid '%s' monomer name",str1); | ^~ In function ‘snprintf’, inlined from ‘bngreadstring’ at /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:1450:3: /usr/include/bits/stdio2.h:68:10: note: ‘__snprintf_chk’ output between 24 and 4119 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c: In function ‘bngreadstring’: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:1442:36: warning: ‘%s’ directive output may be truncated writing up to 4095 bytes into a region of size 4075 [-Wformat-truncation=] 1442 | CHECKS(!er,"error adding monomer %s",str1); }} | ^~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:1442:58: note: format string is defined here 1442 | CHECKS(!er,"error adding monomer %s",str1); }} | ^~ In function ‘snprintf’, inlined from ‘bngreadstring’ at /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:1442:4: /usr/include/bits/stdio2.h:68:10: note: ‘__snprintf_chk’ output between 22 and 4117 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c: In function ‘bngreadstring’: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:1441:39: warning: ‘%s’ directive output may be truncated writing up to 4095 bytes into a region of size 4082 [-Wformat-truncation=] 1441 | CHECKS(er!=-2,"monomer name '%s' is not permitted",str1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:1441:54: note: format string is defined here 1441 | CHECKS(er!=-2,"monomer name '%s' is not permitted",str1); | ^~ In function ‘snprintf’, inlined from ‘bngreadstring’ at /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:1441:4: /usr/include/bits/stdio2.h:68:10: note: ‘__snprintf_chk’ output between 33 and 4128 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c: In function ‘bngreadstring’: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:1440:39: warning: ‘%s’ directive output may be truncated writing up to 4095 bytes into a region of size 4067 [-Wformat-truncation=] 1440 | CHECKS(er!=-1,"out of memory adding monomer %s",str1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:1440:69: note: format string is defined here 1440 | CHECKS(er!=-1,"out of memory adding monomer %s",str1); | ^~ In function ‘snprintf’, inlined from ‘bngreadstring’ at /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolbng.c:1440:4: /usr/include/bits/stdio2.h:68:10: note: ‘__snprintf_chk’ output between 30 and 4125 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 71%] Building C object source/python/CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolboxes.c.o cd /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/python && /usr/bin/gcc -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -I/usr/include/python3.13 -I/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -DENABLE_PYTHON_CALLBACK -DCOMPILE_AS_PY_MODULE -MD -MT source/python/CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolboxes.c.o -MF CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolboxes.c.o.d -o CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolboxes.c.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolboxes.c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolboxes.c: In function ‘boxesupdatelists’: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolboxes.c:783:55: warning: argument 1 range [18446744071562067968, 18446744073709551614] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 783 | bptr->neigh=(boxptr*) calloc(nneigh,sizeof(boxptr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve/random2.h:17, from /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolboxes.c:13: /usr/include/stdlib.h:675:14: note: in a call to allocation function ‘calloc’ declared here 675 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ [ 72%] Building C object source/python/CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolcmd.c.o cd /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/python && /usr/bin/gcc -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -I/usr/include/python3.13 -I/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -DENABLE_PYTHON_CALLBACK -DCOMPILE_AS_PY_MODULE -MD -MT source/python/CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolcmd.c.o -MF CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolcmd.c.o.d -o CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolcmd.c.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolcmd.c [ 74%] Building C object source/python/CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolcomparts.c.o cd /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/python && /usr/bin/gcc -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -I/usr/include/python3.13 -I/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -DENABLE_PYTHON_CALLBACK -DCOMPILE_AS_PY_MODULE -MD -MT source/python/CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolcomparts.c.o -MF CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolcomparts.c.o.d -o CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolcomparts.c.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolcomparts.c In file included from /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolcomparts.c:18: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolcomparts.c: In function ‘compartreadstring’: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolcomparts.c:894:29: warning: ‘%s’ directive output may be truncated writing up to 4095 bytes into a region of size 4082 [-Wformat-truncation=] 894 | CHECKS(s>=0,"surface name '%s' not recognized",nm); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~ /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolcomparts.c:894:44: note: format string is defined here 894 | CHECKS(s>=0,"surface name '%s' not recognized",nm); | ^~ In file included from /usr/include/stdio.h:970, from /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolcomparts.c:9: In function ‘snprintf’, inlined from ‘compartreadstring’ at /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolcomparts.c:894:3: /usr/include/bits/stdio2.h:68:10: note: ‘__snprintf_chk’ output between 31 and 4126 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 75%] Building C object source/python/CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolfilament.c.o cd /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/python && /usr/bin/gcc -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -I/usr/include/python3.13 -I/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -DENABLE_PYTHON_CALLBACK -DCOMPILE_AS_PY_MODULE -MD -MT source/python/CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolfilament.c.o -MF CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolfilament.c.o.d -o CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolfilament.c.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolfilament.c [ 76%] Building C object source/python/CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolgraphics.c.o cd /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/python && /usr/bin/gcc -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -I/usr/include/python3.13 -I/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -DENABLE_PYTHON_CALLBACK -DCOMPILE_AS_PY_MODULE -MD -MT source/python/CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolgraphics.c.o -MF CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolgraphics.c.o.d -o CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolgraphics.c.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolgraphics.c [ 77%] Building C object source/python/CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolmolec.c.o cd /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/python && /usr/bin/gcc -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -I/usr/include/python3.13 -I/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -DENABLE_PYTHON_CALLBACK -DCOMPILE_AS_PY_MODULE -MD -MT source/python/CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolmolec.c.o -MF CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolmolec.c.o.d -o CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolmolec.c.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolmolec.c [ 79%] Building C object source/python/CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolport.c.o cd /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/python && /usr/bin/gcc -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -I/usr/include/python3.13 -I/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -DENABLE_PYTHON_CALLBACK -DCOMPILE_AS_PY_MODULE -MD -MT source/python/CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolport.c.o -MF CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolport.c.o.d -o CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolport.c.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolport.c [ 80%] Building C object source/python/CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smollattice.c.o cd /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/python && /usr/bin/gcc -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -I/usr/include/python3.13 -I/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -DENABLE_PYTHON_CALLBACK -DCOMPILE_AS_PY_MODULE -MD -MT source/python/CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smollattice.c.o -MF CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smollattice.c.o.d -o CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smollattice.c.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smollattice.c [ 81%] Building C object source/python/CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolreact.c.o cd /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/python && /usr/bin/gcc -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -I/usr/include/python3.13 -I/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -DENABLE_PYTHON_CALLBACK -DCOMPILE_AS_PY_MODULE -MD -MT source/python/CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolreact.c.o -MF CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolreact.c.o.d -o CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolreact.c.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolreact.c [ 82%] Building C object source/python/CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolrule.c.o cd /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/python && /usr/bin/gcc -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -I/usr/include/python3.13 -I/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -DENABLE_PYTHON_CALLBACK -DCOMPILE_AS_PY_MODULE -MD -MT source/python/CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolrule.c.o -MF CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolrule.c.o.d -o CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolrule.c.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolrule.c [ 83%] Building CXX object source/python/CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolsim.cpp.o cd /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/python && /usr/bin/g++ -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -I/usr/include/python3.13 -I/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu++14 -fPIC -Wno-unused-parameter -Wall -Wextra -DENABLE_PYTHON_CALLBACK -DCOMPILE_AS_PY_MODULE -MD -MT source/python/CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolsim.cpp.o -MF CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolsim.cpp.o.d -o CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolsim.cpp.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolsim.cpp In file included from /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smoldyn.h:15, from /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolsim.cpp:27: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/../python/CallbackFunc.h:20:7: warning: ‘CallbackFunc’ declared with greater visibility than the type of its field ‘CallbackFunc::func_’ [-Wattributes] 20 | class CallbackFunc | ^~~~~~~~~~~~ /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/../python/CallbackFunc.h:20:7: warning: ‘CallbackFunc’ declared with greater visibility than the type of its field ‘CallbackFunc::target_’ [-Wattributes] /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/../python/CallbackFunc.h:20:7: warning: ‘CallbackFunc’ declared with greater visibility than the type of its field ‘CallbackFunc::args_’ [-Wattributes] /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolsim.cpp: In function ‘simParseError’: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolsim.cpp:166:58: warning: ‘%s’ directive writing up to 4095 bytes into a region of size between 603 and 4698 [-Wformat-overflow=] 166 | sprintf(ErrorLineAndString,"%s\nMessage: %s",parseerrstr,ErrorString); | ^~ ~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolsim.cpp:12: In function ‘sprintf’, inlined from ‘simParseError’ at /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolsim.cpp:166:10: /usr/include/bits/stdio2.h:30:34: note: ‘__sprintf_chk’ output between 11 and 8201 bytes into a destination of size 4708 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 85%] Building C object source/python/CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolsurface.c.o cd /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/python && /usr/bin/gcc -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -I/usr/include/python3.13 -I/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -DENABLE_PYTHON_CALLBACK -DCOMPILE_AS_PY_MODULE -MD -MT source/python/CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolsurface.c.o -MF CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolsurface.c.o.d -o CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolsurface.c.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolsurface.c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolboxes.c: In function ‘boxesupdatelists’: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolboxes.c:783:55: warning: argument 1 range [18446744071562067968, 18446744073709551614] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 783 | bptr->neigh=(boxptr*) calloc(nneigh,sizeof(boxptr)); | ^ /usr/include/stdlib.h:675:14: note: in a call to allocation function ‘calloc’ declared here 675 | extern void *calloc (size_t __nmemb, size_t __size) | ^ [ 86%] Building C object source/python/CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolwall.c.o cd /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/python && /usr/bin/gcc -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -I/usr/include/python3.13 -I/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -DENABLE_PYTHON_CALLBACK -DCOMPILE_AS_PY_MODULE -MD -MT source/python/CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolwall.c.o -MF CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolwall.c.o.d -o CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolwall.c.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolwall.c [ 87%] Building CXX object source/python/CMakeFiles/_pysmoldyn.dir/__/Smoldyn/libsmoldyn.cpp.o cd /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/python && /usr/bin/g++ -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -I/usr/include/python3.13 -I/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu++14 -fPIC -Wno-unused-parameter -Wall -Wextra -DENABLE_PYTHON_CALLBACK -DCOMPILE_AS_PY_MODULE -MD -MT source/python/CMakeFiles/_pysmoldyn.dir/__/Smoldyn/libsmoldyn.cpp.o -MF CMakeFiles/_pysmoldyn.dir/__/Smoldyn/libsmoldyn.cpp.o.d -o CMakeFiles/_pysmoldyn.dir/__/Smoldyn/libsmoldyn.cpp.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/libsmoldyn.cpp /usr/bin/cmake -E cmake_symlink_library libsmoldyn_shared.so.2.72 libsmoldyn_shared.so.2 libsmoldyn_shared.so gmake[2]: Leaving directory '/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build' [ 87%] Built target smoldyn_shared /usr/bin/gmake -f CMakeFiles/smoldyn.dir/build.make CMakeFiles/smoldyn.dir/depend gmake[2]: Entering directory '/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build' cd /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72 /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72 /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/CMakeFiles/smoldyn.dir/DependInfo.cmake "--color=" gmake[2]: Leaving directory '/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build' /usr/bin/gmake -f CMakeFiles/smoldyn.dir/build.make CMakeFiles/smoldyn.dir/build gmake[2]: Entering directory '/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build' [ 88%] Building CXX object CMakeFiles/smoldyn.dir/source/Smoldyn/smoldyn.cpp.o /usr/bin/g++ -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu++14 -Wno-unused-parameter -Wall -Wextra -MD -MT CMakeFiles/smoldyn.dir/source/Smoldyn/smoldyn.cpp.o -MF CMakeFiles/smoldyn.dir/source/Smoldyn/smoldyn.cpp.o.d -o CMakeFiles/smoldyn.dir/source/Smoldyn/smoldyn.cpp.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smoldyn.cpp [ 90%] Linking CXX executable smoldyn /usr/bin/cmake -E cmake_link_script CMakeFiles/smoldyn.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -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 CMakeFiles/smoldyn.dir/source/Smoldyn/smoldyn.cpp.o -o smoldyn libsmoldyn_shared.so.2.72 /usr/lib64/libGL.so /usr/lib64/libGLU.so -lglut /usr/lib64/libtiff.so /usr/lib64/libz.so gmake[2]: Leaving directory '/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build' [ 90%] Built target smoldyn In file included from /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smoldyn.h:15, from /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/libsmoldyn.cpp:15: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/../python/CallbackFunc.h:20:7: warning: ‘CallbackFunc’ declared with greater visibility than the type of its field ‘CallbackFunc::func_’ [-Wattributes] 20 | class CallbackFunc | ^~~~~~~~~~~~ /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/../python/CallbackFunc.h:20:7: warning: ‘CallbackFunc’ declared with greater visibility than the type of its field ‘CallbackFunc::target_’ [-Wattributes] /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/../python/CallbackFunc.h:20:7: warning: ‘CallbackFunc’ declared with greater visibility than the type of its field ‘CallbackFunc::args_’ [-Wattributes] [ 91%] Linking CXX static library lib_pysmoldyn.a cd /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/python && /usr/bin/cmake -P CMakeFiles/_pysmoldyn.dir/cmake_clean_target.cmake cd /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/python && /usr/bin/cmake -E cmake_link_script CMakeFiles/_pysmoldyn.dir/link.txt --verbose=1 /usr/bin/ar qc lib_pysmoldyn.a CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolbng.c.o CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolboxes.c.o CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolcmd.c.o CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolcomparts.c.o CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolfilament.c.o CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolgraphics.c.o CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolmolec.c.o CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolport.c.o CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smollattice.c.o CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolreact.c.o CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolrule.c.o CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolsim.cpp.o CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolsurface.c.o CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolwall.c.o CMakeFiles/_pysmoldyn.dir/__/Smoldyn/libsmoldyn.cpp.o ../libSteve/CMakeFiles/Steve.dir/Geometry.c.o ../libSteve/CMakeFiles/Steve.dir/List.c.o ../libSteve/CMakeFiles/Steve.dir/math2.c.o ../libSteve/CMakeFiles/Steve.dir/opengl2.c.o ../libSteve/CMakeFiles/Steve.dir/parse.c.o ../libSteve/CMakeFiles/Steve.dir/queue.c.o ../libSteve/CMakeFiles/Steve.dir/random2.c.o ../libSteve/CMakeFiles/Steve.dir/Rn.c.o ../libSteve/CMakeFiles/Steve.dir/RnSort.c.o ../libSteve/CMakeFiles/Steve.dir/rxnparam.c.o ../libSteve/CMakeFiles/Steve.dir/SimCommand.c.o ../libSteve/CMakeFiles/Steve.dir/Sphere.c.o ../libSteve/CMakeFiles/Steve.dir/string2.c.o ../libSteve/CMakeFiles/Steve.dir/SurfaceParam.c.o ../libSteve/CMakeFiles/Steve.dir/Zn.c.o ../libSteve/CMakeFiles/Steve.dir/SFMT/SFMT.c.o ../NextSubVolume/CMakeFiles/nsv.dir/StructuredGrid.cpp.o ../NextSubVolume/CMakeFiles/nsv.dir/Species.cpp.o ../NextSubVolume/CMakeFiles/nsv.dir/ReactionEquation.cpp.o ../NextSubVolume/CMakeFiles/nsv.dir/NextSubvolumeMethod.cpp.o ../NextSubVolume/CMakeFiles/nsv.dir/Kairos.cpp.o ../NextSubVolume/CMakeFiles/nsv.dir/Io.cpp.o ../NextSubVolume/CMakeFiles/nsv.dir/Geometry.cpp.o ../NextSubVolume/CMakeFiles/nsv.dir/nsvc.cpp.o /usr/bin/ranlib lib_pysmoldyn.a gmake[2]: Leaving directory '/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build' [ 91%] Built target _pysmoldyn /usr/bin/gmake -f source/python/CMakeFiles/_smoldyn.dir/build.make source/python/CMakeFiles/_smoldyn.dir/depend gmake[2]: Entering directory '/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build' cd /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72 /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/python /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/python /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/python/CMakeFiles/_smoldyn.dir/DependInfo.cmake "--color=" gmake[2]: Leaving directory '/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build' /usr/bin/gmake -f source/python/CMakeFiles/_smoldyn.dir/build.make source/python/CMakeFiles/_smoldyn.dir/build gmake[2]: Entering directory '/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build' [ 92%] Building CXX object source/python/CMakeFiles/_smoldyn.dir/CallbackFunc.cpp.o [ 93%] Building CXX object source/python/CMakeFiles/_smoldyn.dir/Command.cpp.o cd /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/python && /usr/bin/g++ -D_smoldyn_EXPORTS -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/external/pybind11/include -isystem /usr/include/python3.13 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu++14 -fPIC -fvisibility=hidden -Wno-unused-parameter -Wall -Wextra -DSMOLDYN_VERSION=2.72 -DENABLE_PYTHON_CALLBACK -fvisibility=hidden -flto 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-Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu++14 -fPIC -fvisibility=hidden -Wno-unused-parameter -Wall -Wextra -DSMOLDYN_VERSION=2.72 -DENABLE_PYTHON_CALLBACK -fvisibility=hidden -flto -fno-fat-lto-objects -MD -MT source/python/CMakeFiles/_smoldyn.dir/Command.cpp.o -MF CMakeFiles/_smoldyn.dir/Command.cpp.o.d -o CMakeFiles/_smoldyn.dir/Command.cpp.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/python/Command.cpp [ 95%] Building CXX object source/python/CMakeFiles/_smoldyn.dir/Simulation.cpp.o cd /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/python && /usr/bin/g++ -D_smoldyn_EXPORTS -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/external/pybind11/include -isystem /usr/include/python3.13 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu++14 -fPIC -fvisibility=hidden -Wno-unused-parameter -Wall -Wextra -DSMOLDYN_VERSION=2.72 -DENABLE_PYTHON_CALLBACK -fvisibility=hidden -flto -fno-fat-lto-objects -MD -MT source/python/CMakeFiles/_smoldyn.dir/Simulation.cpp.o -MF CMakeFiles/_smoldyn.dir/Simulation.cpp.o.d -o CMakeFiles/_smoldyn.dir/Simulation.cpp.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/python/Simulation.cpp [ 96%] Building CXX object source/python/CMakeFiles/_smoldyn.dir/module.cpp.o cd /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/python && /usr/bin/g++ -D_smoldyn_EXPORTS -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume -I/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/external/pybind11/include -isystem /usr/include/python3.13 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu++14 -fPIC -fvisibility=hidden -Wno-unused-parameter -Wall -Wextra -DSMOLDYN_VERSION=2.72 -DENABLE_PYTHON_CALLBACK -fvisibility=hidden -flto -fno-fat-lto-objects -MD -MT source/python/CMakeFiles/_smoldyn.dir/module.cpp.o -MF CMakeFiles/_smoldyn.dir/module.cpp.o.d -o CMakeFiles/_smoldyn.dir/module.cpp.o -c /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/python/module.cpp [ 97%] Linking CXX shared module /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/python/smoldyn/_smoldyn.cpython-313-x86_64-linux-gnu.so cd /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/python && /usr/bin/cmake -E cmake_link_script CMakeFiles/_smoldyn.dir/link.txt --verbose=1 /usr/bin/g++ -fPIC -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -flto -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 -shared -o /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/python/smoldyn/_smoldyn.cpython-313-x86_64-linux-gnu.so CMakeFiles/_smoldyn.dir/CallbackFunc.cpp.o CMakeFiles/_smoldyn.dir/Command.cpp.o CMakeFiles/_smoldyn.dir/Simulation.cpp.o CMakeFiles/_smoldyn.dir/module.cpp.o lib_pysmoldyn.a /usr/lib64/libGL.so /usr/lib64/libGLU.so -lglut /usr/lib64/libtiff.so /usr/lib64/libz.so /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/python/../Smoldyn/smoldyn.h:1045:16: warning: type ‘struct simstruct’ violates the C++ One Definition Rule [-Wodr] 1045 | typedef struct simstruct | ^ /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smoldyn.h:1045:16: note: a different type is defined in another translation unit 1045 | typedef struct simstruct | ^ /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/python/../Smoldyn/smoldyn.h:1106:19: note: the first difference of corresponding definitions is field ‘callbacks’ 1106 | CallbackFunc* callbacks[MAX_PY_CALLBACK]; // Python callback. | ^ /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smoldyn.h:1045:16: note: a type with different number of fields is defined in another translation unit 1045 | typedef struct simstruct | ^ /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smoldyn.h:714:16: warning: type ‘struct latticestruct’ violates the C++ One Definition Rule [-Wodr] 714 | typedef struct latticestruct | ^ /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smoldyn.h:714:16: note: a different type is defined in another translation unit 714 | typedef struct latticestruct | ^ /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smoldyn.h:739:26: note: the first difference of corresponding definitions is field ‘nsv’ 739 | NextSubvolumeMethod* nsv; // nsv class | ^ /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smoldyn.h:739:26: note: a field of same name but different type is defined in another translation unit 739 | NextSubvolumeMethod* nsv; // nsv class | ^ /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smoldyn.h:714:16: note: type name ‘NextSubvolumeMethod’ should match type name ‘Kairos::NextSubvolumeMethod’ 714 | typedef struct latticestruct | ^ /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/NextSubVolume/NextSubvolumeMethod.h:137:7: note: the incompatible type is defined here 137 | class NextSubvolumeMethod | ^ /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolboxes.c: In function ‘boxesupdatelists’: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/Smoldyn/smolboxes.c:783:55: warning: argument 1 range [18446744071562067968, 18446744073709551614] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 783 | bptr->neigh=(boxptr*) calloc(nneigh,sizeof(boxptr)); | ^ /usr/include/stdlib.h:675:14: note: in a call to allocation function ‘calloc’ declared here 675 | extern void *calloc (size_t __nmemb, size_t __size) | ^ cd /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/python && /usr/bin/strip /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/python/smoldyn/_smoldyn.cpython-313-x86_64-linux-gnu.so gmake[2]: Leaving directory '/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build' [ 97%] Built target _smoldyn /usr/bin/gmake -f source/python/CMakeFiles/copy_python_tree.dir/build.make source/python/CMakeFiles/copy_python_tree.dir/depend /usr/bin/gmake -f source/python/CMakeFiles/wheel.dir/build.make source/python/CMakeFiles/wheel.dir/depend gmake[2]: Entering directory '/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build' cd /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72 /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/python /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/python /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/python/CMakeFiles/copy_python_tree.dir/DependInfo.cmake "--color=" gmake[2]: Entering directory '/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build' cd /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72 /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/python /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/python /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/python/CMakeFiles/wheel.dir/DependInfo.cmake "--color=" gmake[2]: Leaving directory '/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build' /usr/bin/gmake -f source/python/CMakeFiles/copy_python_tree.dir/build.make source/python/CMakeFiles/copy_python_tree.dir/build gmake[2]: Entering directory '/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build' gmake[2]: Leaving directory '/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build' /usr/bin/gmake -f source/python/CMakeFiles/wheel.dir/build.make source/python/CMakeFiles/wheel.dir/build gmake[2]: Entering directory '/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build' [ 98%] Copying python source tree to binary directory cd /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/python && /usr/bin/cmake -E copy_directory /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/python/smoldyn /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/py/smoldyn [100%] Generating wheel in /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build cd /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/py && /usr/bin/python3.13 setup.py bdist_wheel -d /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build gmake[2]: Leaving directory '/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build' [100%] Built target copy_python_tree running bdist_wheel running build running build_py creating build creating build/lib.linux-x86_64-cpython-313 creating build/lib.linux-x86_64-cpython-313/smoldyn copying smoldyn/__init__.py -> build/lib.linux-x86_64-cpython-313/smoldyn copying smoldyn/__main__.py -> build/lib.linux-x86_64-cpython-313/smoldyn copying smoldyn/smoldyn.py -> build/lib.linux-x86_64-cpython-313/smoldyn copying smoldyn/types.py -> build/lib.linux-x86_64-cpython-313/smoldyn copying smoldyn/utils.py -> build/lib.linux-x86_64-cpython-313/smoldyn creating build/lib.linux-x86_64-cpython-313/smoldyn/biosimulators copying smoldyn/biosimulators/__init__.py -> build/lib.linux-x86_64-cpython-313/smoldyn/biosimulators copying smoldyn/biosimulators/__main__.py -> build/lib.linux-x86_64-cpython-313/smoldyn/biosimulators copying smoldyn/biosimulators/_version.py -> build/lib.linux-x86_64-cpython-313/smoldyn/biosimulators copying smoldyn/biosimulators/combine.py -> build/lib.linux-x86_64-cpython-313/smoldyn/biosimulators copying smoldyn/biosimulators/data_model.py -> build/lib.linux-x86_64-cpython-313/smoldyn/biosimulators copying smoldyn/biosimulators/utils.py -> build/lib.linux-x86_64-cpython-313/smoldyn/biosimulators copying smoldyn/_smoldyn.cpython-313-x86_64-linux-gnu.so -> build/lib.linux-x86_64-cpython-313/smoldyn running build_ext /usr/lib/python3.13/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. Follow the current Python packaging guidelines when building Python RPM packages. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html and https://docs.fedoraproject.org/en-US/packaging-guidelines/Python/ for details. ******************************************************************************** !! self.initialize_options() installing to build/bdist.linux-x86_64/wheel running install running install_lib creating build/bdist.linux-x86_64 creating build/bdist.linux-x86_64/wheel creating build/bdist.linux-x86_64/wheel/smoldyn copying build/lib.linux-x86_64-cpython-313/smoldyn/__init__.py -> build/bdist.linux-x86_64/wheel/smoldyn copying build/lib.linux-x86_64-cpython-313/smoldyn/__main__.py -> build/bdist.linux-x86_64/wheel/smoldyn copying build/lib.linux-x86_64-cpython-313/smoldyn/smoldyn.py -> build/bdist.linux-x86_64/wheel/smoldyn copying build/lib.linux-x86_64-cpython-313/smoldyn/types.py -> build/bdist.linux-x86_64/wheel/smoldyn copying build/lib.linux-x86_64-cpython-313/smoldyn/utils.py -> build/bdist.linux-x86_64/wheel/smoldyn creating build/bdist.linux-x86_64/wheel/smoldyn/biosimulators copying build/lib.linux-x86_64-cpython-313/smoldyn/biosimulators/__init__.py -> build/bdist.linux-x86_64/wheel/smoldyn/biosimulators copying build/lib.linux-x86_64-cpython-313/smoldyn/biosimulators/__main__.py -> build/bdist.linux-x86_64/wheel/smoldyn/biosimulators copying build/lib.linux-x86_64-cpython-313/smoldyn/biosimulators/_version.py -> build/bdist.linux-x86_64/wheel/smoldyn/biosimulators copying build/lib.linux-x86_64-cpython-313/smoldyn/biosimulators/combine.py -> build/bdist.linux-x86_64/wheel/smoldyn/biosimulators copying build/lib.linux-x86_64-cpython-313/smoldyn/biosimulators/data_model.py -> build/bdist.linux-x86_64/wheel/smoldyn/biosimulators copying build/lib.linux-x86_64-cpython-313/smoldyn/biosimulators/utils.py -> build/bdist.linux-x86_64/wheel/smoldyn/biosimulators copying build/lib.linux-x86_64-cpython-313/smoldyn/_smoldyn.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/smoldyn running install_egg_info running egg_info creating smoldyn.egg-info writing smoldyn.egg-info/PKG-INFO writing dependency_links to smoldyn.egg-info/dependency_links.txt writing requirements to smoldyn.egg-info/requires.txt writing top-level names to smoldyn.egg-info/top_level.txt writing manifest file 'smoldyn.egg-info/SOURCES.txt' reading manifest file 'smoldyn.egg-info/SOURCES.txt' writing manifest file 'smoldyn.egg-info/SOURCES.txt' Copying smoldyn.egg-info to build/bdist.linux-x86_64/wheel/smoldyn-2.72-py3.13.egg-info running install_scripts creating build/bdist.linux-x86_64/wheel/smoldyn-2.72.dist-info/WHEEL creating '/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/smoldyn-2.72-cp313-cp313-linux_x86_64.whl' and adding 'build/bdist.linux-x86_64/wheel' to it adding 'smoldyn/__init__.py' adding 'smoldyn/__main__.py' adding 'smoldyn/_smoldyn.cpython-313-x86_64-linux-gnu.so' adding 'smoldyn/smoldyn.py' adding 'smoldyn/types.py' adding 'smoldyn/utils.py' adding 'smoldyn/biosimulators/__init__.py' adding 'smoldyn/biosimulators/__main__.py' adding 'smoldyn/biosimulators/_version.py' adding 'smoldyn/biosimulators/combine.py' adding 'smoldyn/biosimulators/data_model.py' adding 'smoldyn/biosimulators/utils.py' adding 'smoldyn-2.72.dist-info/METADATA' adding 'smoldyn-2.72.dist-info/WHEEL' adding 'smoldyn-2.72.dist-info/top_level.txt' adding 'smoldyn-2.72.dist-info/RECORD' removing build/bdist.linux-x86_64/wheel gmake[2]: Leaving directory '/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build' [100%] Built target wheel gmake[1]: Leaving directory '/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build' /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/CMakeFiles 0 + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.izFysr + umask 022 + cd /builddir/build/BUILD/smoldyn-2.72-build + '[' /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT '!=' / ']' + rm -rf /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT ++ dirname /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT + mkdir -p /builddir/build/BUILD/smoldyn-2.72-build + mkdir /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd Smoldyn-2.72 + DESTDIR=/builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT + /usr/bin/cmake --install redhat-linux-build -- Install configuration: "Release" -- Installing: /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/bin/smoldyn -- Installing: /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/lib64/libsmoldyn_shared.so.2.72 -- Installing: /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/lib64/libsmoldyn_shared.so.2 -- Installing: /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/lib64/libsmoldyn_shared.so -- Installing: /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/lib64/libsmoldyn_static.a -- Installing: /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/include/smoldyn/libsmoldyn.h -- Installing: /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/include/smoldyn/smoldyn.h -- Installing: /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/include/smoldyn/smoldynconfigure.h + pushd redhat-linux-build/py ~/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/py ~/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72 + mkdir -p /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/lib64/python3.13/site-packages + cp -a smoldyn smoldyn.egg-info /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/lib64/python3.13/site-packages/ + popd ~/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72 + /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 2.72-6.fc42 --unique-debug-suffix -2.72-6.fc42.x86_64 --unique-debug-src-base smoldyn-2.72-6.fc42.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72 find-debuginfo: starting Extracting debug info from 2 files DWARF-compressing 2 files sepdebugcrcfix: Updated 2 CRC32s, 0 CRC32s did match. Creating .debug symlinks for symlinks to ELF files Copying sources found by 'debugedit -l' to /usr/src/debug/smoldyn-2.72-6.fc42.x86_64 3558 blocks find-debuginfo: done + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + /usr/lib/rpm/brp-compress + /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/check-rpaths + /usr/lib/rpm/redhat/brp-mangle-shebangs + /usr/lib/rpm/brp-remove-la-files + env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j2 Bytecompiling .py files below /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/lib64/python3.13 using python3.13 + /usr/lib/rpm/redhat/brp-python-hardlink + /usr/bin/add-determinism --brp -j2 /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/lib64/python3.13/site-packages/smoldyn/biosimulators/__pycache__/__init__.cpython-313.pyc: rewriting with normalized contents /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/lib64/python3.13/site-packages/smoldyn/biosimulators/__pycache__/__main__.cpython-313.pyc: rewriting with normalized contents /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/lib64/python3.13/site-packages/smoldyn/biosimulators/__pycache__/_version.cpython-313.pyc: rewriting with normalized contents /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/lib64/python3.13/site-packages/smoldyn/biosimulators/__pycache__/utils.cpython-313.pyc: rewriting with normalized contents /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/lib64/python3.13/site-packages/smoldyn/biosimulators/__pycache__/combine.cpython-313.pyc: rewriting with normalized contents /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/lib64/python3.13/site-packages/smoldyn/biosimulators/__pycache__/data_model.cpython-313.pyc: rewriting with normalized contents /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/lib64/python3.13/site-packages/smoldyn/__pycache__/__init__.cpython-313.pyc: rewriting with normalized contents /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/lib64/libsmoldyn_static.a: replacing with normalized version /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/lib64/python3.13/site-packages/smoldyn/__pycache__/__main__.cpython-313.pyc: rewriting with normalized contents /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/lib64/python3.13/site-packages/smoldyn/__pycache__/smoldyn.cpython-313.pyc: replacing with normalized version /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/lib64/python3.13/site-packages/smoldyn/__pycache__/types.cpython-313.pyc: replacing with normalized version /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/lib64/python3.13/site-packages/smoldyn/__pycache__/types.cpython-313.opt-1.pyc: replacing with normalized version /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/lib64/python3.13/site-packages/smoldyn/__pycache__/utils.cpython-313.pyc: rewriting with normalized contents /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/lib64/python3.13/site-packages/smoldyn/__pycache__/smoldyn.cpython-313.opt-1.pyc: replacing with normalized version Scanned 31 directories and 119 files, processed 14 inodes, 14 modified (5 replaced + 9 rewritten), 0 unsupported format, 0 errors Reading /builddir/build/BUILD/smoldyn-2.72-build/SPECPARTS/rpm-debuginfo.specpart Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.ywRq6A ~/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build ~/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72 + umask 022 + cd /builddir/build/BUILD/smoldyn-2.72-build + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd Smoldyn-2.72 + pushd redhat-linux-build + export LD_LIBRARY_PATH=/builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/lib64 + LD_LIBRARY_PATH=/builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/lib64 + export PYTHONPATH=/builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/lib64/python3.13/site-packages + PYTHONPATH=/builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/lib64/python3.13/site-packages + xvfb-run ctest -j1 -VV -R 'test_api|test_sanity|test_biosimulator' --output-on-failure --debug /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/cmCTest.cxx:425 Here: 425 /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/cmCTest.cxx:710 UpdateCTestConfiguration from :/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/DartConfiguration.tcl /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/cmCTest.cxx:437 Here: 437 /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/cmCTest.cxx:3036 * Read custom CTest configuration directory: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/cmCTest.cxx:3041 * Check for file: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/CTestCustom.cmake /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/cmCTest.cxx:3061 * Check for file: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/CTestCustom.ctest /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/cmCTest.cxx:710 UpdateCTestConfiguration from :/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/DartConfiguration.tcl /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:407 Test project /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:1770 Constructing a list of tests /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2431 Add test: test_actions /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2474 Set test directory: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/python /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2431 Add test: test_api /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2474 Set test directory: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/python /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2431 Add test: test_biosimulators /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2474 Set test directory: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/python /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2431 Add test: test_concurrent_simulation /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2474 Set test directory: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/python /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2431 Add test: test_connect_func /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2474 Set test directory: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/python /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2431 Add test: test_connect_var /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2474 Set test directory: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/python /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2431 Add test: test_data_in_array /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2474 Set test directory: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/python /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2431 Add test: test_data_outputfile /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2474 Set test directory: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/python /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2431 Add test: test_getters /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2474 Set test directory: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/python /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2431 Add test: test_issue_118 /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2474 Set test directory: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/python /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2431 Add test: test_libsmoldyn /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2474 Set test directory: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/python /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2431 Add test: test_multiple_iterations /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2474 Set test directory: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/python /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2431 Add test: test_prd_placement /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2474 Set test directory: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/python /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2431 Add test: test_sanity /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2474 Set test directory: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/python /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2431 Add test: test_sim_from_file /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2474 Set test directory: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/source/python /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:1821 Done constructing a list of tests /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:984 Updating test list for fixtures /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:1207 Added 0 tests to meet fixture requirements /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/cmCTest.cxx:310 Current_Time: Sep 08 00:35 UTC /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/cmCTest.cxx:310 Current_Time: Sep 08 00:35 UTC /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestMultiProcessHandler.cxx:1418 Checking test dependency graph... /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestMultiProcessHandler.cxx:1447 Checking test dependency graph end /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestMultiProcessHandler.cxx:172 test 2 /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:549 Start 2: test_api /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:710 2: Test command: /usr/bin/python3.13 "/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/tests/test_api.py" /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:718 2: Working Directory: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/tests /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:726 2: Environment variables: /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:731 2: PYTHONPATH=/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/py /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:731 2: SMOLDYN_NO_PROMPT=1 /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/cmCTest.cxx:310 Current_Time: Sep 08 00:35 UTC /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:830 2: Test timeout computed to be: 10000000 /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:1009 1/3 Test #2: test_api ......................... /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:1012 Testing test_api ... /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:268 Passed 0.27 sec /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/cmCTest.cxx:310 Current_Time: Sep 08 00:35 UTC /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestMultiProcessHandler.cxx:172 test 3 /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:549 Start 3: test_biosimulators /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:710 3: Test command: /usr/bin/python3.13 "/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/tests/test_biosimulators.py" /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:718 3: Working Directory: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/tests /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:726 3: Environment variables: /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:731 3: PYTHONPATH=/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/py /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:731 3: SMOLDYN_NO_PROMPT=1 /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/cmCTest.cxx:310 Current_Time: Sep 08 00:35 UTC /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:830 3: Test timeout computed to be: 10000000 /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:39 3: ssssssssssssssssssssssss /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:39 3: ---------------------------------------------------------------------- /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:39 3: Ran 24 tests in 0.001s /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:39 3: /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:39 3: OK (skipped=24) /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:1009 2/3 Test #3: test_biosimulators ............... /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:1012 Testing test_biosimulators ... /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:268 Passed 0.32 sec /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/cmCTest.cxx:310 Current_Time: Sep 08 00:35 UTC /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestMultiProcessHandler.cxx:172 test 14 /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:549 Start 14: test_sanity /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:710 14: Test command: /usr/bin/python3.13 "/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/tests/test_sanity.py" /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:718 14: Working Directory: /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/tests /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:726 14: Environment variables: /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:731 14: PYTHONPATH=/builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/py /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:731 14: SMOLDYN_NO_PROMPT=1 /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/cmCTest.cxx:310 Current_Time: Sep 08 00:35 UTC /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:830 14: Test timeout computed to be: 10000000 /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:39 14: Using smoldyn from /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/redhat-linux-build/py/smoldyn/__init__.py /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:39 14: test_newcursim /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:39 14: /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:39 14: Testing test_get_err /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:39 14: (, '') /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:1009 3/3 Test #14: test_sanity ...................... /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:1012 Testing test_sanity ... /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:268 Passed 0.26 sec /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/cmCTest.cxx:310 Current_Time: Sep 08 00:35 UTC /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/cmCTest.cxx:310 Current_Time: Sep 08 00:35 UTC /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/cmCTest.cxx:310 Current_Time: Sep 08 00:35 UTC /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:446 The following tests passed: /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:451 test_api /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:451 test_biosimulators /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:451 test_sanity /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:612 100% tests passed, 0 tests failed out of 3 /builddir/build/BUILD/cmake-3.28.3-build/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:628 Total Test time (real) = 0.86 sec + popd + RPM_EC=0 ~/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72 ++ jobs -p + exit 0 Processing files: smoldyn-2.72-6.fc42.x86_64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.X4Re73 + umask 022 + cd /builddir/build/BUILD/smoldyn-2.72-build + cd Smoldyn-2.72 + DOCDIR=/builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/share/doc/smoldyn + export LC_ALL=C.UTF-8 + LC_ALL=C.UTF-8 + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/share/doc/smoldyn + cp -pr /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/Using-Smoldyn-with-SED-ML-COMBINE-BioSimulators.md /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/share/doc/smoldyn + cp -pr /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/README.md /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/share/doc/smoldyn + RPM_EC=0 ++ jobs -p + exit 0 Provides: bundled(SFMT) = 1.3.3 smoldyn = 2.72-6.fc42 smoldyn(x86-64) = 2.72-6.fc42 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: libc.so.6()(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_ABI_DT_RELR)(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libsmoldyn_shared.so.2()(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) rtld(GNU_HASH) Processing files: smoldyn-doc-2.72-6.fc42.noarch Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.zawTCf + umask 022 + cd /builddir/build/BUILD/smoldyn-2.72-build + cd Smoldyn-2.72 + DOCDIR=/builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/share/doc/smoldyn-doc + export LC_ALL=C.UTF-8 + LC_ALL=C.UTF-8 + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/share/doc/smoldyn-doc + cp -pr /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/docs/BioNetGen /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/share/doc/smoldyn-doc + cp -pr /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/docs/CMakeLists.txt /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/share/doc/smoldyn-doc + cp -pr /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/docs/Doxyfile.in /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/share/doc/smoldyn-doc + cp -pr /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/docs/README.md /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/share/doc/smoldyn-doc + cp -pr /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/docs/SmolCrowd /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/share/doc/smoldyn-doc + cp -pr /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/docs/SmolEmulate /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/share/doc/smoldyn-doc + cp -pr /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/docs/Smoldyn /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/share/doc/smoldyn-doc + cp -pr /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/docs/_static /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/share/doc/smoldyn-doc + cp -pr /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/docs/build_doxygen /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/share/doc/smoldyn-doc + cp -pr /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/docs/conf.py /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/share/doc/smoldyn-doc + cp -pr /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/docs/doxygen /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/share/doc/smoldyn-doc + cp -pr /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/docs/examples /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/share/doc/smoldyn-doc + cp -pr /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/docs/index.rst /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/share/doc/smoldyn-doc + cp -pr /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/docs/libSteve /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/share/doc/smoldyn-doc + cp -pr /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/docs/python /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/share/doc/smoldyn-doc + cp -pr /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/docs/requirements.txt /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/share/doc/smoldyn-doc + cp -pr /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/docs/tikz /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/share/doc/smoldyn-doc + cp -pr /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/docs/user /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/share/doc/smoldyn-doc + cp -pr /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/docs/wrl2smol /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/share/doc/smoldyn-doc + RPM_EC=0 ++ jobs -p + exit 0 Provides: smoldyn-doc = 2.72-6.fc42 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: smoldyn-libs-2.72-6.fc42.x86_64 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.wSHSZE + umask 022 + cd /builddir/build/BUILD/smoldyn-2.72-build + cd Smoldyn-2.72 + LICENSEDIR=/builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/share/licenses/smoldyn-libs + export LC_ALL=C.UTF-8 + LC_ALL=C.UTF-8 + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/share/licenses/smoldyn-libs + cp -pr /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/License.txt /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/share/licenses/smoldyn-libs + cp -pr /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve/SFMT/SFMT-LICENSE.txt /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/share/licenses/smoldyn-libs + cp -pr /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/LICENSE /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/share/licenses/smoldyn-libs + RPM_EC=0 ++ jobs -p + exit 0 Provides: libsmoldyn_shared.so.2()(64bit) smoldyn-libs = 2.72-6.fc42 smoldyn-libs(x86-64) = 2.72-6.fc42 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: libGL.so.1()(64bit) libGLU.so.1()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.38)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.7)(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) libglut.so.3()(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.29)(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.8)(64bit) libstdc++.so.6(CXXABI_1.3.9)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.11)(64bit) libstdc++.so.6(GLIBCXX_3.4.21)(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) libtiff.so.6()(64bit) libtiff.so.6(LIBTIFF_4.0)(64bit) rtld(GNU_HASH) Processing files: smoldyn-libs-devel-2.72-6.fc42.x86_64 Provides: smoldyn-libs-devel = 2.72-6.fc42 smoldyn-libs-devel(x86-64) = 2.72-6.fc42 smoldyn-libs-static = 0:2.72-6.fc42 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: libsmoldyn_shared.so.2()(64bit) Processing files: python3-smoldyn-2.72-6.fc42.x86_64 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.qwQL41 + umask 022 + cd /builddir/build/BUILD/smoldyn-2.72-build + cd Smoldyn-2.72 + LICENSEDIR=/builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/share/licenses/python3-smoldyn + export LC_ALL=C.UTF-8 + LC_ALL=C.UTF-8 + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/share/licenses/python3-smoldyn + cp -pr /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/License.txt /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/share/licenses/python3-smoldyn + cp -pr /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/source/libSteve/SFMT/SFMT-LICENSE.txt /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/share/licenses/python3-smoldyn + cp -pr /builddir/build/BUILD/smoldyn-2.72-build/Smoldyn-2.72/LICENSE /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT/usr/share/licenses/python3-smoldyn + RPM_EC=0 ++ jobs -p + exit 0 Provides: python-smoldyn = 2.72-6.fc42 python3-smoldyn = 2.72-6.fc42 python3-smoldyn(x86-64) = 2.72-6.fc42 python3.13-smoldyn = 2.72-6.fc42 python3.13dist(smoldyn) = 2.72 python3dist(smoldyn) = 2.72 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PartialHardlinkSets) <= 4.0.4-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: libGL.so.1()(64bit) libGLU.so.1()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.32)(64bit) libc.so.6(GLIBC_2.38)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.7)(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) libglut.so.3()(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.29)(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.13)(64bit) libstdc++.so.6(CXXABI_1.3.15)(64bit) libstdc++.so.6(CXXABI_1.3.2)(64bit) libstdc++.so.6(CXXABI_1.3.3)(64bit) libstdc++.so.6(CXXABI_1.3.5)(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_3.4.18)(64bit) libstdc++.so.6(GLIBCXX_3.4.20)(64bit) libstdc++.so.6(GLIBCXX_3.4.21)(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) libtiff.so.6()(64bit) libtiff.so.6(LIBTIFF_4.0)(64bit) python(abi) = 3.13 rtld(GNU_HASH) Obsoletes: python-smoldyn < 2.72-6.fc42 Processing files: smoldyn-debugsource-2.72-6.fc42.x86_64 Provides: smoldyn-debugsource = 2.72-6.fc42 smoldyn-debugsource(x86-64) = 2.72-6.fc42 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: smoldyn-debuginfo-2.72-6.fc42.x86_64 Provides: debuginfo(build-id) = f1b99bf3299115177774b977affe2342210e2670 smoldyn-debuginfo = 2.72-6.fc42 smoldyn-debuginfo(x86-64) = 2.72-6.fc42 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: smoldyn-debugsource(x86-64) = 2.72-6.fc42 Processing files: smoldyn-libs-debuginfo-2.72-6.fc42.x86_64 Provides: debuginfo(build-id) = 37a731d1f4a203287ddb1ae1b98f0b59a5c9fa7b libsmoldyn_shared.so.2.72-2.72-6.fc42.x86_64.debug()(64bit) smoldyn-libs-debuginfo = 2.72-6.fc42 smoldyn-libs-debuginfo(x86-64) = 2.72-6.fc42 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: smoldyn-debugsource(x86-64) = 2.72-6.fc42 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILD/smoldyn-2.72-build/BUILDROOT Wrote: /builddir/build/RPMS/smoldyn-libs-debuginfo-2.72-6.fc42.x86_64.rpm Wrote: /builddir/build/RPMS/python3-smoldyn-2.72-6.fc42.x86_64.rpm Wrote: /builddir/build/RPMS/smoldyn-libs-devel-2.72-6.fc42.x86_64.rpm Wrote: /builddir/build/RPMS/smoldyn-debugsource-2.72-6.fc42.x86_64.rpm Wrote: /builddir/build/RPMS/smoldyn-libs-2.72-6.fc42.x86_64.rpm Wrote: /builddir/build/RPMS/smoldyn-debuginfo-2.72-6.fc42.x86_64.rpm Wrote: /builddir/build/RPMS/smoldyn-2.72-6.fc42.x86_64.rpm Wrote: /builddir/build/RPMS/smoldyn-doc-2.72-6.fc42.noarch.rpm Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.CEMiMF + umask 022 + cd /builddir/build/BUILD/smoldyn-2.72-build + test -d /builddir/build/BUILD/smoldyn-2.72-build + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w /builddir/build/BUILD/smoldyn-2.72-build + rm -rf /builddir/build/BUILD/smoldyn-2.72-build + RPM_EC=0 ++ jobs -p + exit 0 Finish: rpmbuild smoldyn-2.72-6.fc42.src.rpm Finish: build phase for smoldyn-2.72-6.fc42.src.rpm INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-x86_64-1725755594.437893/root/var/log/dnf5.log INFO: Done(/var/lib/copr-rpmbuild/results/smoldyn-2.72-6.fc42.src.rpm) Config(child) 2 minutes 25 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": "smoldyn-doc", "epoch": null, "version": "2.72", "release": "6.fc42", "arch": "noarch" }, { "name": "python3-smoldyn", "epoch": null, "version": "2.72", "release": "6.fc42", "arch": "x86_64" }, { "name": "smoldyn-debuginfo", "epoch": null, "version": "2.72", "release": "6.fc42", "arch": "x86_64" }, { "name": "smoldyn-libs-debuginfo", "epoch": null, "version": "2.72", "release": "6.fc42", "arch": "x86_64" }, { "name": "smoldyn", "epoch": null, "version": "2.72", "release": "6.fc42", "arch": "src" }, { "name": "smoldyn-libs", "epoch": null, "version": "2.72", "release": "6.fc42", "arch": "x86_64" }, { "name": "smoldyn", "epoch": null, "version": "2.72", "release": "6.fc42", "arch": "x86_64" }, { "name": "smoldyn-debugsource", "epoch": null, "version": "2.72", "release": "6.fc42", "arch": "x86_64" }, { "name": "smoldyn-libs-devel", "epoch": null, "version": "2.72", "release": "6.fc42", "arch": "x86_64" } ] } RPMResults finished